+
`
+ },
+ select : (modalID, selectID, title, label, options) => {
+ return `
+
+
+
+
+
+ ${label}
+
+ ${options}
+
+
+
+
+
+
`
}
}
@@ -102,6 +181,18 @@ module.exports = {
return templates.confirmation(modalID, title)
},
+ moveToTrashConfirmHtml : (fileType) => {
+ let modalID = "moveToTrashConfirmModal"
+ let title = `Move this ${fileType} to trash?`
+
+ return templates.confirmation(modalID, title)
+ },
+ emptyTrashConfirmHtml : () => {
+ let modalID = "emptyTrashConfirmModal"
+ let title = "Are you sure you want to permanently erase the items in the Trash?"
+
+ return templates.confirmation(modalID, title)
+ },
operationInfoModalHtml : (page) => {
let modalID = "operationInfoModal"
let title = "Help"
@@ -109,10 +200,85 @@ module.exports = {
return templates.message(modalID, title, message)
},
+ newProjectModalHtml : () => {
+ let modalID = "newProjectModal"
+ let inputID = "projectNameInput"
+ let title = "New Project"
+ let label = "Project Name"
+ let value = ""
+
+ return templates.input(modalID, inputID, title, label, value)
+ },
+ newWorkflowGroupModalHtml : () => {
+ let modalID = "newWorkflowGroupModal"
+ let inputID = "workflowGroupNameInput"
+ let title = "New Workflow Group"
+ let label = "Workflow Group Name"
+ let value = ""
+
+ return templates.input(modalID, inputID, title, label, value)
+ },
+ newProjectModelHtml : () => {
+ let modalID = "newProjectModelModal"
+ let inputID = "modelPathInput"
+ let title = "Add Existing Model to Project"
+ let label = "Path to the Model"
+ let value = ""
+
+ return templates.input(modalID, inputID, title, label, value)
+ },
+ addExistingWorkflowToProjectHtml : () => {
+ let modalID = "newProjectWorkflowModal"
+ let inputID = "workflowPathInput"
+ let title = "Add Existing Workflow to Workflow Group"
+ let label = "Path to the workflow"
+ let value = ""
+
+ return templates.input(modalID, inputID, title, label, value)
+ },
+ addExistingWorkflowToProjectSuccessHtml : (message) => {
+ let modalID = "newProjectModelSuccessModal"
+ let title = "Success!"
+
+ return templates.message(modalID, title, message)
+ },
+ addExistingWorkflowToProjectErrorHtml : (title, message) => {
+ let modalID = "newProjectModelErrorModal"
+
+ return templates.message(modalID, title, message)
+ },
+ newProjectModelSuccessHtml : (message) => {
+ let modalID = "newProjectModelSuccessModal"
+ let title = "Success!"
+
+ return templates.message(modalID, title, message)
+ },
+ newProjectModelErrorHtml : (title, message) => {
+ let modalID = "newProjectModelErrorModal"
+
+ return templates.message(modalID, title, message)
+ },
+ newProjectOrWorkflowGroupErrorHtml : (title, error) => {
+ let modalID = "newProjectOrWorkflowGroupModal"
+
+ return templates.message(modalID, title, error)
+ },
+ newWorkflowGroupSuccessHtml: (message) => {
+ let modalID = "newWorkflowGroupSuccessModal"
+ let title = "Success!"
+
+ return templates.message(modalID, title, message)
+ },
+ newProjectModelWarningHtml : (message) => {
+ let modalID = "newProjectModelWarningModal"
+ let title = "Warnings"
+
+ return templates.confirmation_with_message(modalID, title, message)
+ },
renderCreateModalHtml : (isModel, isSpatial) => {
var title = 'Directory';
if(isModel){
- title = isSpatial ? 'Spatial Model' : 'Non-Spatial Model';
+ title = isSpatial ? 'Spatial Model' : 'Model';
}
title = "New " + title
let modalID = "newModalModel"
@@ -137,7 +303,13 @@ module.exports = {
},
uploadFileErrorsHtml : (file, type, statusMessage, errors) => {
let modalID = "sbmlToModelModal"
- let title = `Errors uploading ${file} as a ${type} file`
+ let types = {"mdl":"model file", "sbml":"sbml file", "smdl":"spatial model file", "zip":"zip archive"}
+ if(type === "file") {
+ type = types[file.split('.').pop()]
+ }else{
+ type += " file"
+ }
+ let title = `Errors uploading ${file} as a ${type}`
for(var i = 0; i < errors.length; i++) {
errors[i] = "
Error : " + errors[i]
}
@@ -163,13 +335,23 @@ module.exports = {
return templates.message(modalID, title, message)
},
+ wkflModelPathErrorHtml : () => {
+ let modalID = "wkflModelPathErrorModal"
+ let title = "Premission Denied"
+ let message = "Models for workflow in a project must also be in the same project."
+
+ return templates.message(modalID, title, message)
+ },
annotationModalHtml : (type, name, annotation) => {
let modalID = `${type}AnnotationModal`
let inputID = `${type}AnnotationInput`
let title = `Annotation for ${name}`
let label = "Annotation:"
+ if(!annotation) {
+ annotation = ""
+ }
- return templates.input(modalID, inputID, title, label, annotation)
+ return templates.input_long(modalID, inputID, title, label, annotation)
},
modelSaveErrorHtml : (title, error) => {
let modalID = "modelSaveErrorModal"
@@ -181,6 +363,48 @@ module.exports = {
return templates.message(modalID, title, error)
},
+ newProjectWorkflowHtml : (label, options) => {
+ let modalID = "newProjectWorkflowModal"
+ let selectID = "select"
+ let title = "New Workflow"
+ options = options.map(function (name) {
+ return `
${name} `
+ })
+ options = options.join(" ")
+
+ return templates.select(modalID, selectID, title, label, options)
+ },
+ projectExportSuccessHtml : (fileType, message) => {
+ let modalID = "projectExportSuccessModal"
+ let title = `Successfully Exported the ${fileType}`
+
+ return templates.message(modalID, title, message)
+ },
+ projectExportErrorHtml : (title, message) => {
+ let modalID = "projectExportErrorModal"
+
+ return templates.message(modalID, title, message)
+ },
+ existingCreatorConfirmationHtml : (title) => {
+ let modalID = "existingCreatorConfirmationModal"
+
+ return templates.confirmation(modalID, title)
+ },
+ addMetaDataHtml: (title) => {
+ let modalID = "addMetaDataModal"
+
+ return templates.confirmation(modalID, title)
+ },
+ noModelsMessageHtml: (title, message) => {
+ let modalID = "noModelsMessageModal"
+
+ return templates.message(modalID, title, message)
+ },
+ noWorkflowGroupMessageHtml: (title, message) => {
+ let modalID = "noWorkflowGroupMessageModal"
+
+ return templates.message(modalID, title, message)
+ },
renderDefaultModeModalHtml : () => {
let concentrationDesciption = `Species will only be represented using continuous (floating point) values.`;
let populationDescription = `Population - Species will only be represented using discrete (integer count) values.`;
diff --git a/client/models/creator.js b/client/models/creator.js
new file mode 100644
index 0000000000..48b899cf16
--- /dev/null
+++ b/client/models/creator.js
@@ -0,0 +1,14 @@
+//models
+var State = require('ampersand-state');
+
+module.exports = State.extend({
+ props: {
+ fname: 'string',
+ lname: 'string',
+ email: 'string',
+ organization: 'string'
+ },
+ initialize: function(attrs, options) {
+ State.prototype.initialize.apply(this, arguments)
+ }
+});
\ No newline at end of file
diff --git a/client/models/model.js b/client/models/model.js
index e3d47d3a6b..afa1640508 100644
--- a/client/models/model.js
+++ b/client/models/model.js
@@ -21,7 +21,8 @@ module.exports = Model.extend({
props: {
is_spatial: 'boolean',
defaultID: 'number',
- defaultMode: 'string'
+ defaultMode: 'string',
+ annotation: 'string'
},
collections: {
species: Species,
@@ -58,14 +59,11 @@ module.exports = Model.extend({
saveModel: function () {
var self = this;
this.species.map(function (specie) {
- self.species.trigger('update-species', specie.compID, specie, false);
+ self.species.trigger('update-species', specie.compID, specie, false, false);
});
this.parameters.map(function (parameter) {
self.parameters.trigger('update-parameters', parameter.compID, parameter);
});
- if(!isPreview){
- this.simulationSettings.letUsChooseForUse()
- }
this.save();
},
});
diff --git a/client/models/models.js b/client/models/models.js
index e067014705..2fe24c9801 100644
--- a/client/models/models.js
+++ b/client/models/models.js
@@ -4,12 +4,5 @@ var Model = require('./model');
var path = require('path');
module.exports = RestCollection.extend({
- model: Model,
- url: function () {
- return path.join(
- app.getApiPath(),
- 'models',
- String(app.me.name)
- )
- }
+ model: Model
});
diff --git a/client/models/parameter.js b/client/models/parameter.js
index 2a008962bd..1db4e83019 100644
--- a/client/models/parameter.js
+++ b/client/models/parameter.js
@@ -6,7 +6,7 @@ module.exports = State.extend({
props: {
compID: 'number',
name: 'string',
- expression: 'string',
+ expression: 'any',
annotation: 'string'
},
session: {
diff --git a/client/models/parameters.js b/client/models/parameters.js
index ba2655bc58..c8e48ac625 100644
--- a/client/models/parameters.js
+++ b/client/models/parameters.js
@@ -12,7 +12,7 @@ module.exports = Collection.extend({
var parameter = this.add({
compID: id,
name: name,
- expression: '0.0',
+ expression: 0.0,
annotation: "",
});
},
diff --git a/client/models/plots.js b/client/models/plots.js
new file mode 100644
index 0000000000..3f7e990f71
--- /dev/null
+++ b/client/models/plots.js
@@ -0,0 +1,13 @@
+//models
+var State = require('ampersand-state');
+
+module.exports = State.extend({
+ props: {
+ key: 'string',
+ title: 'string',
+ xaxis: 'string',
+ yaxis: 'string',
+ stamp: 'number',
+ species: 'object'
+ }
+});
\ No newline at end of file
diff --git a/client/models/project.js b/client/models/project.js
new file mode 100644
index 0000000000..329adc2757
--- /dev/null
+++ b/client/models/project.js
@@ -0,0 +1,24 @@
+var path = require('path');
+//Support Files
+var app = require('../app.js');
+//Collections
+var ModelsCollection = require('./models');
+var WorkflowGroupsCollection = require('./workflow-groups');
+//Models
+var Model = require('ampersand-model');
+
+module.exports = Model.extend({
+ url: function () {
+ return path.join(app.getApiPath(), "project/load-project")+"?path="+this.directory;
+ },
+ collections: {
+ models: ModelsCollection,
+ workflowGroups: WorkflowGroupsCollection
+ },
+ session: {
+ directory: 'string',
+ parentDir: 'string',
+ plot: 'object',
+ annotation: 'string'
+ }
+})
\ No newline at end of file
diff --git a/client/models/workflow-group.js b/client/models/workflow-group.js
new file mode 100644
index 0000000000..ce59a2cf68
--- /dev/null
+++ b/client/models/workflow-group.js
@@ -0,0 +1,13 @@
+//collections
+var WorkflowCollection = require('./workflows');
+//models
+var State = require('ampersand-state');
+
+module.exports = State.extend({
+ collections: {
+ workflows: WorkflowCollection
+ },
+ session: {
+ name: 'string'
+ }
+});
\ No newline at end of file
diff --git a/client/models/workflow-groups.js b/client/models/workflow-groups.js
new file mode 100644
index 0000000000..134e8e561c
--- /dev/null
+++ b/client/models/workflow-groups.js
@@ -0,0 +1,8 @@
+//collections
+var Collection = require('ampersand-collection');
+//models
+var WorkflowGroup = require('./workflow-group');
+
+module.exports = Collection.extend({
+ model: WorkflowGroup
+});
\ No newline at end of file
diff --git a/client/models/workflow.js b/client/models/workflow.js
new file mode 100644
index 0000000000..b3c8749d06
--- /dev/null
+++ b/client/models/workflow.js
@@ -0,0 +1,16 @@
+//collections
+//models
+var State = require('ampersand-state');
+
+module.exports = State.extend({
+ props: {
+ path: 'string',
+ annotation: 'string',
+ outputs: 'object',
+ type: 'string'
+ },
+ session: {
+ name: 'string',
+ status: 'string'
+ }
+});
\ No newline at end of file
diff --git a/client/models/workflows.js b/client/models/workflows.js
new file mode 100644
index 0000000000..d6aa302d5d
--- /dev/null
+++ b/client/models/workflows.js
@@ -0,0 +1,8 @@
+//collections
+var Collection = require('ampersand-collection');
+//models
+var Workflow = require('./workflow');
+
+module.exports = Collection.extend({
+ model: Workflow
+});
\ No newline at end of file
diff --git a/client/pages/file-browser.js b/client/pages/file-browser.js
index 881e53ce7b..965bac54cf 100644
--- a/client/pages/file-browser.js
+++ b/client/pages/file-browser.js
@@ -13,116 +13,6 @@ let template = require('../templates/pages/fileBrowser.pug');
import initPage from './page.js';
-let ajaxData = {
- "url" : function (node) {
- if(node.parent === null){
- return path.join(app.getApiPath(), "file/browser-list")+"?path=none"
- }
- return path.join(app.getApiPath(), "file/browser-list")+"?path="+ node.original._path
- },
- "dataType" : "json",
- "data" : function (node) {
- return { 'id' : node.id}
- },
-}
-
-let treeSettings = {
- 'plugins': [
- 'types',
- 'wholerow',
- 'changed',
- 'contextmenu',
- 'dnd',
- ],
- 'core': {
- 'multiple' : false,
- 'animation': 0,
- 'check_callback': function (op, node, par, pos, more) {
- if(op === 'move_node' && node && node.type && node.type === "workflow" && node.original && node.original._status && node.original._status === "running"){
- return false
- }
- if(op === 'move_node' && more && more.ref && more.ref.type && !(more.ref.type == 'folder' || more.ref.type == 'root')){
- return false
- }
- if(op === 'move_node' && more && more.ref && more.ref.type && more.ref.type === 'folder'){
- if(!more.ref.state.loaded){
- return false
- }
- var exists = false
- var BreakException = {}
- try{
- more.ref.children.forEach(function (child) {
- var child_node = $('#models-jstree').jstree().get_node(child)
- exists = child_node.text === node.text
- if(exists){
- throw BreakException;
- }
- })
- }catch{
- return false;
- }
- }
- if(op === 'move_node' && more && (pos != 0 || more.pos !== "i") && !more.core){
- return false
- }
- if(op === 'move_node' && more && more.core) {
- var newDir = par.type !== "root" ? par.original._path : ""
- var file = node.original._path.split('/').pop()
- var oldPath = node.original._path
- let queryStr = "?srcPath="+oldPath+"&dstPath="+path.join(newDir, file)
- var endpoint = path.join(app.getApiPath(), "file/move")+queryStr
- xhr({uri: endpoint}, function(err, response, body) {
- if(response.statusCode < 400) {
- node.original._path = path.join(newDir, file)
- }else{
- body = JSON.parse(body)
- if(par.type === 'root'){
- $('#models-jstree').jstree().refresh()
- }else{
- $('#models-jstree').jstree().refresh_node(par);
- }
- }
- });
- }
- return true
- },
- 'themes': {
- 'stripes': true,
- 'variant': 'large'
- },
- 'data': ajaxData,
- },
- 'types' : {
- 'root' : {
- "icon": "jstree-icon jstree-folder"
- },
- 'folder' : {
- "icon": "jstree-icon jstree-folder"
- },
- 'spatial' : {
- "icon": "jstree-icon jstree-file"
- },
- 'nonspatial' : {
- "icon": "jstree-icon jstree-file"
- },
- 'workflow' : {
- "icon": "jstree-icon jstree-file"
- },
- 'notebook' : {
- "icon": "jstree-icon jstree-file"
- },
- 'mesh' : {
- "icon": "jstree-icon jstree-file"
- },
- 'sbml-model' : {
- "icon": "jstree-icon jstree-file"
- },
- 'other' : {
- "icon": "jstree-icon jstree-file"
- },
- },
-}
-
let FileBrowser = PageView.extend({
pageTitle: 'StochSS | File Browser',
template: template,
@@ -130,12 +20,105 @@ let FileBrowser = PageView.extend({
'click [data-hook=refresh-jstree]' : 'refreshJSTree',
'click [data-hook=options-for-node]' : 'showContextMenuForNode',
'click [data-hook=new-directory]' : 'handleCreateDirectoryClick',
+ 'click [data-hook=new-project]' : 'handleCreateProjectClick',
'click [data-hook=new-model]' : 'handleCreateModelClick',
'click [data-hook=upload-file-btn]' : 'handleUploadFileClick',
'click [data-hook=file-browser-help]' : function () {
let modal = $(modals.operationInfoModalHtml('file-browser')).modal();
},
},
+ initialize: function (attrs, options) {
+ PageView.prototype.initialize.apply(this, arguments)
+ var self = this
+ this.root = "none"
+ this.ajaxData = {
+ "url" : function (node) {
+ if(node.parent === null){
+ return path.join(app.getApiPath(), "file/browser-list")+"?path="+self.root
+ }
+ return path.join(app.getApiPath(), "file/browser-list")+"?path="+ node.original._path
+ },
+ "dataType" : "json",
+ "data" : function (node) {
+ return { 'id' : node.id}
+ },
+ }
+ this.treeSettings = {
+ 'plugins': ['types', 'wholerow', 'changed', 'contextmenu', 'dnd'],
+ 'core': {'multiple' : false, 'animation': 0,
+ 'check_callback': function (op, node, par, pos, more) {
+ if(op === "rename_node" && self.validateName(pos, true) !== ""){
+ document.querySelector("#renameSpecialCharError").style.display = "block"
+ setTimeout(function () {
+ document.querySelector("#renameSpecialCharError").style.display = "none"
+ }, 5000)
+ return false
+ }
+ if(op === 'move_node' && node && node.type && node.type === "workflow" && node.original && node.original._status && node.original._status === "running"){
+ return false
+ }
+ if(op === 'move_node' && more && more.ref && more.ref.type && !(more.ref.type == 'folder' || more.ref.type == 'root')){
+ return false
+ }
+ if(op === 'move_node' && more && more.ref && more.ref.type && more.ref.type === 'folder'){
+ if(!more.ref.state.loaded){
+ return false
+ }
+ var exists = false
+ var BreakException = {}
+ try{
+ more.ref.children.forEach(function (child) {
+ var child_node = $('#models-jstree').jstree().get_node(child)
+ exists = child_node.text === node.text
+ if(exists){
+ throw BreakException;
+ }
+ })
+ }catch{
+ return false;
+ }
+ }
+ if(op === 'move_node' && more && (pos != 0 || more.pos !== "i") && !more.core){
+ return false
+ }
+ if(op === 'move_node' && more && more.core) {
+ var newDir = par.type !== "root" ? par.original._path : ""
+ var file = node.original._path.split('/').pop()
+ var oldPath = node.original._path
+ let queryStr = "?srcPath="+oldPath+"&dstPath="+path.join(newDir, file)
+ var endpoint = path.join(app.getApiPath(), "file/move")+queryStr
+ xhr({uri: endpoint}, function(err, response, body) {
+ if(response.statusCode < 400) {
+ node.original._path = path.join(newDir, file)
+ if(node.type === "folder") {
+ $('#models-jstree').jstree().refresh_node(node);
+ }
+ }else{
+ body = JSON.parse(body)
+ $('#models-jstree').jstree().refresh()
+ }
+ });
+ }
+ return true
+ },
+ 'themes': {'stripes': true, 'variant': 'large'},
+ 'data': this.ajaxData,
+ },
+ 'types' : {
+ 'root' : {"icon": "jstree-icon jstree-folder"},
+ 'folder' : {"icon": "jstree-icon jstree-folder"},
+ 'spatial' : {"icon": "jstree-icon jstree-file"},
+ 'nonspatial' : {"icon": "jstree-icon jstree-file"},
+ 'project' : {"icon": "jstree-icon jstree-file"},
+ 'workflow-group' : {"icon": "jstree-icon jstree-file"},
+ 'workflow' : {"icon": "jstree-icon jstree-file"},
+ 'notebook' : {"icon": "jstree-icon jstree-file"},
+ 'mesh' : {"icon": "jstree-icon jstree-file"},
+ 'sbml-model' : {"icon": "jstree-icon jstree-file"},
+ 'other' : {"icon": "jstree-icon jstree-file"},
+ },
+ }
+ },
render: function () {
var self = this;
this.nodeForContextMenu = "";
@@ -147,10 +130,14 @@ let FileBrowser = PageView.extend({
window.location.reload()
}
});
- this.setupJstree();
- setTimeout(function () {
- self.refreshInitialJSTree();
- }, 3000);
+ this.setupJstree(function () {
+ setTimeout(function () {
+ self.refreshInitialJSTree();
+ }, 3000);
+ });
+ $(document).on('hide.bs.modal', '.modal', function (e) {
+ e.target.remove()
+ });
},
refreshJSTree: function () {
this.jstreeIsLoaded = false
@@ -202,21 +189,49 @@ let FileBrowser = PageView.extend({
let uploadBtn = document.querySelector('#uploadFileModal .upload-modal-btn');
let fileInput = document.querySelector('#uploadFileModal #fileForUpload');
let input = document.querySelector('#uploadFileModal #fileNameInput');
+ let fileCharErrMsg = document.querySelector('#uploadFileModal #fileSpecCharError')
+ let nameEndErrMsg = document.querySelector('#uploadFileModal #fileNameInputEndCharError')
+ let nameCharErrMsg = document.querySelector('#uploadFileModal #fileNameInputSpecCharError')
+ let nameUsageMsg = document.querySelector('#uploadFileModal #fileNameUsageMessage')
fileInput.addEventListener('change', function (e) {
- if(fileInput.files.length){
+ let fileErr = !fileInput.files.length ? "" : self.validateName(fileInput.files[0].name)
+ let nameErr = self.validateName(input.value)
+ if(!fileInput.files.length) {
+ uploadBtn.disabled = true
+ fileCharErrMsg.style.display = 'none'
+ }else if(fileErr === "" || (Boolean(input.value) && nameErr === "")){
uploadBtn.disabled = false
+ fileCharErrMsg.style.display = 'none'
}else{
uploadBtn.disabled = true
+ fileCharErrMsg.style.display = 'block'
}
})
+ input.addEventListener("input", function (e) {
+ let fileErr = !fileInput.files.length ? "" : self.validateName(fileInput.files[0].name)
+ let nameErr = self.validateName(input.value)
+ if(!fileInput.files.length) {
+ uploadBtn.disabled = true
+ fileCharErrMsg.style.display = 'none'
+ }else if(fileErr === "" || (Boolean(input.value) && nameErr === "")){
+ uploadBtn.disabled = false
+ fileCharErrMsg.style.display = 'none'
+ }else{
+ uploadBtn.disabled = true
+ fileCharErrMsg.style.display = 'block'
+ }
+ nameCharErrMsg.style.display = nameErr === "both" || nameErr === "special" ? "block" : "none"
+ nameEndErrMsg.style.display = nameErr === "both" || nameErr === "forward" ? "block" : "none"
+ nameUsageMsg.style.display = nameErr !== "" ? "block" : "none"
+ });
uploadBtn.addEventListener('click', function (e) {
let file = fileInput.files[0]
var fileinfo = {"type":type,"name":"","path":"/"}
if(o && o.original){
fileinfo.path = o.original._path
}
- if(Boolean(input.value)){
- fileinfo.name = input.value
+ if(Boolean(input.value) && self.validateName(input.value) === ""){
+ fileinfo.name = input.value.trim()
}
let formData = new FormData()
formData.append("datafile", file)
@@ -240,6 +255,8 @@ let FileBrowser = PageView.extend({
if(resp.errors.length > 0){
let errorModal = $(modals.uploadFileErrorsHtml(file.name, type, resp.message, resp.errors)).modal();
}
+ }else{
+ let zipErrorModal = $(modals.projectExportErrorHtml(resp.Reason, resp.Message)).modal()
}
}
req.send(formData)
@@ -254,6 +271,8 @@ let FileBrowser = PageView.extend({
fileType = "spatial model"
else if(fileType === "sbml-model")
fileType = "sbml model"
+ else if(fileType === "other")
+ fileType = "file"
var self = this
if(document.querySelector('#deleteFileModal')) {
document.querySelector('#deleteFileModal').remove()
@@ -267,6 +286,12 @@ let FileBrowser = PageView.extend({
var node = $('#models-jstree').jstree().get_node(o.parent);
if(node.type === "root"){
self.refreshJSTree();
+ let actionsBtn = $(self.queryByHook("options-for-node"))
+ if(actionsBtn.text().endsWith(o.text)) {
+ actionsBtn.text("Actions")
+ actionsBtn.prop("disabled", true)
+ self.nodeForContextMenu = ""
+ }
}else{
$('#models-jstree').jstree().refresh_node(node);
}
@@ -532,7 +557,141 @@ let FileBrowser = PageView.extend({
targetPath = o.original._path
}
var endpoint = path.join(app.getBasePath(), "/files", targetPath);
- window.location.href = endpoint
+ window.open(endpoint)
+ },
+ validateName(input, rename = false) {
+ var error = ""
+ if(input.endsWith('/')) {
+ error = 'forward'
+ }
+ var invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\"
+ if(rename) {
+ invalidChars += "/"
+ }
+ for(var i = 0; i < input.length; i++) {
+ if(invalidChars.includes(input.charAt(i))) {
+ error = error === "" || error === "special" ? "special" : "both"
+ }
+ }
+ return error
+ },
+ newProjectOrWorkflowGroup: function (o, isProject) {
+ var self = this
+ if(document.querySelector("#newProjectModal")) {
+ document.querySelector("#newProjectModal").remove()
+ }
+ if(document.querySelector("#newWorkflowGroupModal")) {
+ document.querySelector("#newWorkflowGroupModal").remove()
+ }
+ var modal = ""
+ var okBtn = ""
+ var input = ""
+ if(isProject) {
+ modal = $(modals.newProjectModalHtml()).modal();
+ okBtn = document.querySelector('#newProjectModal .ok-model-btn');
+ input = document.querySelector('#newProjectModal #projectNameInput');
+ }else{
+ modal = $(modals.newWorkflowGroupModalHtml()).modal();
+ okBtn = document.querySelector('#newWorkflowGroupModal .ok-model-btn');
+ input = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInput');
+ }
+ input.addEventListener("keyup", function (event) {
+ if(event.keyCode === 13){
+ event.preventDefault();
+ okBtn.click();
+ }
+ });
+ input.addEventListener("input", function (e) {
+ var endErrMsg = ""
+ var charErrMsg = ""
+ if(isProject){
+ endErrMsg = document.querySelector('#newProjectModal #projectNameInputEndCharError')
+ charErrMsg = document.querySelector('#newProjectModal #projectNameInputSpecCharError')
+ }else{
+ endErrMsg = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInputEndCharError')
+ charErrMsg = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInputSpecCharError')
+ }
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== "" || input.value.trim() === ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ okBtn.addEventListener("click", function (e) {
+ if(Boolean(input.value)) {
+ var parentPath = ""
+ if(o && o.original && o.original.type !== "root") {
+ parentPath = o.original._path
+ }
+ var endpoint = ""
+ if(isProject){
+ var projectName = input.value.trim() + ".proj"
+ var projectPath = path.join(parentPath, projectName)
+ endpoint = path.join(app.getApiPath(), "project/new-project")+"?path="+projectPath
+ }else{
+ var workflowGroupName = input.value.trim() + ".wkgp"
+ var workflowGroupPath = path.join(parentPath, workflowGroupName)
+ endpoint = path.join(app.getApiPath(), "project/new-workflow-group")+"?path="+workflowGroupPath
+ }
+ xhr({uri: endpoint,json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ if(isProject) {
+ if(o){//directory was created with context menu option
+ var node = $('#models-jstree').jstree().get_node(o);
+ if(node.type === "root"){
+ self.refreshJSTree()
+ }else{
+ $('#models-jstree').jstree().refresh_node(node);
+ }
+ }else{//directory was created with create directory button
+ self.refreshJSTree()
+ }
+ }else{
+ let successModal = $(modals.newWorkflowGroupSuccessHtml(body.message)).modal()
+ }
+ }else{
+ let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal()
+ }
+ modal.modal('hide')
+ })
+ }
+ })
+ },
+ addExistingModel: function (o) {
+ var self = this
+ if(document.querySelector('#newProjectModelModal')){
+ document.querySelector('#newProjectModelModal').remove()
+ }
+ let modal = $(modals.newProjectModelHtml()).modal()
+ let okBtn = document.querySelector('#newProjectModelModal .ok-model-btn')
+ let input = document.querySelector('#newProjectModelModal #modelPathInput')
+ input.addEventListener("keyup", function (event) {
+ if(event.keyCode === 13){
+ event.preventDefault();
+ okBtn.click();
+ }
+ });
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#newProjectModelModal #modelPathInputEndCharError')
+ var charErrMsg = document.querySelector('#newProjectModelModal #modelPathInputSpecCharError')
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ okBtn.addEventListener("click", function (e) {
+ if(Boolean(input.value)) {
+ let queryString = "?path="+o.original._path+"&mdlPath="+input.value.trim()
+ let endpoint = path.join(app.getApiPath(), 'project/add-existing-model') + queryString
+ xhr({uri:endpoint, json:true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ let successModal = $(modals.newProjectModelSuccessHtml(body.message)).modal()
+ }else{
+ let errorModal = $(modals.newProjectModelErrorHtml(body.Reason, body.Message)).modal()
+ }
+ });
+ modal.modal('hide')
+ }
+ });
},
newModelOrDirectory: function (o, isModel, isSpatial) {
var self = this
@@ -548,19 +707,46 @@ let FileBrowser = PageView.extend({
okBtn.click();
}
});
- let modelName;
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#newModalModel #modelNameInputEndCharError')
+ var charErrMsg = document.querySelector('#newModalModel #modelNameInputSpecCharError')
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== "" || input.value.trim() === ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
okBtn.addEventListener('click', function (e) {
if (Boolean(input.value)) {
+ modal.modal('hide')
var parentPath = ""
if(o && o.original && o.original.type !== "root"){
parentPath = o.original._path
}
if(isModel) {
- let modelName = input.value + '.mdl';
- var modelPath = path.join(app.getBasePath(), app.routePrefix, 'models/edit')+"?path="+path.join(parentPath, modelName);
- window.location.href = modelPath;
+ let modelName = o && o.type === "project" ? input.value.trim().split("/").pop() + '.mdl' : input.value.trim() + '.mdl';
+ let message = modelName.split(".")[0] !== input.value.trim() ?
+ "Warning: Models are saved directly in StochSS Projects and cannot be saved to the "+input.value.trim().split("/")[0]+" directory in the project.
Your model will be saved directly in your project.
" : ""
+ let modelPath = path.join(parentPath, modelName)
+ if(message){
+ let warningModal = $(modals.newProjectModelWarningHtml(message)).modal()
+ let yesBtn = document.querySelector('#newProjectModelWarningModal .yes-modal-btn');
+ yesBtn.addEventListener('click', function (e) {window.location.href = endpoint;})
+ }else{
+ let queryString = "?path="+modelPath+"&message="+message;
+ let existEP = path.join(app.getApiPath(), "model/exists")+queryString
+ xhr({uri: existEP, json: true}, function (err, response, body) {
+ if(body.exists) {
+ let title = "Model Already Exists"
+ let message = "A model already exists with that name"
+ let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal()
+ }else{
+ let endpoint = path.join(app.getBasePath(), "stochss/models/edit")+queryString
+ window.location.href = endpoint
+ }
+ })
+ }
}else{
- let dirName = input.value;
+ let dirName = input.value.trim();
let endpoint = path.join(app.getApiPath(), "directory/create")+"?path="+path.join(parentPath, dirName);
xhr({uri:endpoint}, function (err, response, body) {
if(response.statusCode < 400){
@@ -579,7 +765,6 @@ let FileBrowser = PageView.extend({
let errorModal = $(modals.newDirectoryErrorHtml(body.Reason, body.Message)).modal()
}
});
- modal.modal('hide')
}
}
});
@@ -587,6 +772,9 @@ let FileBrowser = PageView.extend({
handleCreateDirectoryClick: function (e) {
this.newModelOrDirectory(undefined, false, false);
},
+ handleCreateProjectClick: function (e) {
+ this.newProjectOrWorkflowGroup(undefined, true)
+ },
handleCreateModelClick: function (e) {
let isSpatial = false
this.newModelOrDirectory(undefined, true, isSpatial);
@@ -611,8 +799,15 @@ let FileBrowser = PageView.extend({
setupJstree: function () {
var self = this;
$.jstree.defaults.contextmenu.items = (o, cb) => {
+ let optionsButton = $(self.queryByHook("options-for-node"))
+ if(!self.nodeForContextMenu){
+ optionsButton.prop('disabled', false)
+ }
+ optionsButton.text("Actions for " + o.original.text)
+ self.nodeForContextMenu = o;
let nodeType = o.original.type
- let asZip = (nodeType === "workflow" || nodeType === "folder" || nodeType === "other" || nodeType === "mesh")
+ let zipTypes = ["workflow", "folder", "other", "mesh", "project", "workflow-group"]
+ let asZip = zipTypes.includes(nodeType)
// common to all type except root
let common = {
"Download" : {
@@ -639,7 +834,7 @@ let FileBrowser = PageView.extend({
},
"Duplicate" : {
"label" : (nodeType === "workflow") ? "Duplicate as new" : "Duplicate",
- "_disabled" : false,
+ "_disabled" : (nodeType === "project"),
"separator_before" : false,
"separator_after" : false,
"action" : function (data) {
@@ -681,6 +876,15 @@ let FileBrowser = PageView.extend({
self.newModelOrDirectory(o, false, false);
}
},
+ "New Project" : {
+ "label" : "New Project",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.newProjectOrWorkflowGroup(o, true)
+ }
+ },
"New_model" : {
"label" : "New Model",
"_disabled" : false,
@@ -842,6 +1046,8 @@ let FileBrowser = PageView.extend({
"action" : function (data) {
if(nodeType === "workflow"){
window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+o.original._path+"&type=none";
+ }else if(nodeType === "project"){
+ window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+o.original._path
}else{
if(nodeType === "notebook") {
var identifier = "notebooks"
@@ -855,6 +1061,26 @@ let FileBrowser = PageView.extend({
}
}
}
+ let project = {
+ "Add Model" : {
+ "label" : "Add Model",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "submenu" : {
+ "New Model" : folder.New_model,
+ "Existing Model" : {
+ "label" : "Existing Model",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.addExistingModel(o)
+ }
+ }
+ }
+ }
+ }
// specific to workflows
let workflow = {
"Convert to Notebook" : {
@@ -943,6 +1169,9 @@ let FileBrowser = PageView.extend({
if (o.type === 'nonspatial') {
return $.extend(model, modelConvert, common)
}
+ if (o.type === 'project'){
+ return $.extend(open, project, common)
+ }
if (o.type === 'workflow') {
return $.extend(open, workflow, common)
}
@@ -959,7 +1188,7 @@ let FileBrowser = PageView.extend({
$(document).on('dnd_start.vakata', function (data, element, helper, event) {
$('#models-jstree').jstree().load_all()
});
- $('#models-jstree').jstree(treeSettings).bind("loaded.jstree", function (event, data) {
+ $('#models-jstree').jstree(this.treeSettings).bind("loaded.jstree", function (event, data) {
self.jstreeIsLoaded = true
}).bind("refresh.jstree", function (event, data) {
self.jstreeIsLoaded = true
@@ -991,6 +1220,8 @@ let FileBrowser = PageView.extend({
}else if(file.endsWith('.sbml')){
var openPath = path.join(app.getBasePath(), "edit", _path)
window.open(openPath, '_blank')
+ }else if(file.endsWith('.proj')){
+ window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+_path;
}else if(file.endsWith('.wkfl')){
window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+_path+"&type=none";
}else if(node.type === "folder" && $('#models-jstree').jstree().is_open(node) && $('#models-jstree').jstree().is_loaded(node)){
diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js
index acd60e5dd5..28e018607b 100644
--- a/client/pages/model-editor.js
+++ b/client/pages/model-editor.js
@@ -1,5 +1,6 @@
var _ = require('underscore');
var $ = require('jquery');
+let path = require('path');
//support files
var app = require('../app');
var modals = require('../modals')
@@ -28,23 +29,33 @@ let ModelEditor = PageView.extend({
'click [data-hook=edit-model-help]' : function () {
let modal = $(modals.operationInfoModalHtml('model-editor')).modal();
},
+ 'click [data-hook=project-breadcrumb-link]' : 'handleProjectBreadcrumbClick'
},
initialize: function (attrs, options) {
PageView.prototype.initialize.apply(this, arguments);
var self = this;
- var directory = (new URLSearchParams(window.location.search)).get('path');
+ let urlParams = new URLSearchParams(window.location.search)
+ var directory = urlParams.get('path');
var modelFile = directory.split('/').pop();
- var name = decodeURI(modelFile.split('.')[0]);
+ var name = this.getFileName(decodeURI(modelFile));
var isSpatial = modelFile.split('.').pop().startsWith('s');
this.model = new Model({
name: name,
directory: directory,
is_spatial: isSpatial,
isPreview: true,
- for: 'edit',
+ for: "edit",
});
+ if(directory.includes('.proj')) {
+ this.projectPath = path.dirname(directory)
+ this.projectName = this.projectPath.split('/').pop().split('.')[0]
+ }
this.model.fetch({
success: function (model, response, options) {
+ if(directory.includes('.proj')) {
+ self.queryByHook("project-breadcrumb-links").style.display = "block"
+ self.queryByHook("model-name-header").style.display = "none"
+ }
self.renderSubviews();
if(!self.model.is_spatial){
self.queryByHook('mesh-editor-container').style.display = "none";
@@ -72,6 +83,24 @@ let ModelEditor = PageView.extend({
},
updateValid: function () {
},
+ getFileName: function (file) {
+ if(file.endsWith('/')) {
+ file.slice(0, -1)
+ }
+ if(file.includes('/')) {
+ file = file.split('/').pop()
+ }
+ if(!file.includes('.')) {
+ return file
+ }
+ return file.split('.').slice(0, -1).join('.')
+ },
+ handleProjectBreadcrumbClick: function () {
+ this.modelStateButtons.saveModel(_.bind(function (e) {
+ let endpoint = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+this.projectPath
+ window.location.href = endpoint
+ }, this))
+ },
updateSpeciesInUse: function () {
var species = this.model.species;
var reactions = this.model.reactions;
@@ -116,7 +145,9 @@ let ModelEditor = PageView.extend({
});
}
reactions.forEach(function (reaction) {
- updateInUse(reaction.rate);
+ if(reaction.reactionType !== "custom-propensity"){
+ updateInUse(reaction.rate);
+ }
});
events.forEach(function (event) {
event.eventAssignments.forEach(function (assignment) {
@@ -152,7 +183,7 @@ let ModelEditor = PageView.extend({
parent: this,
model: this.model.modelSettings,
});
- var modelStateButtons = new ModelStateButtonsView({
+ this.modelStateButtons = new ModelStateButtonsView({
model: this.model
});
this.registerRenderSubview(meshEditor, 'mesh-editor-container');
@@ -162,7 +193,7 @@ let ModelEditor = PageView.extend({
this.registerRenderSubview(reactionsEditor, 'reactions-editor-container');
this.registerRenderSubview(sbmlComponentView, 'sbml-component-container');
this.registerRenderSubview(modelSettings, 'model-settings-container');
- this.registerRenderSubview(modelStateButtons, 'model-state-buttons-container');
+ this.registerRenderSubview(this.modelStateButtons, 'model-state-buttons-container');
$(document).ready(function () {
$('[data-toggle="tooltip"]').tooltip();
$('[data-toggle="tooltip"]').click(function () {
@@ -170,6 +201,9 @@ let ModelEditor = PageView.extend({
});
});
+ $(document).on('hide.bs.modal', '.modal', function (e) {
+ e.target.remove()
+ });
},
registerRenderSubview: function (view, hook) {
this.registerSubview(view);
diff --git a/client/pages/project-browser.js b/client/pages/project-browser.js
new file mode 100644
index 0000000000..4178d8578b
--- /dev/null
+++ b/client/pages/project-browser.js
@@ -0,0 +1,101 @@
+let $ = require('jquery');
+let path = require('path');
+let xhr = require('xhr');
+//support files
+let app = require('../app');
+let modals = require('../modals');
+//models
+let Project = require('../models/project');
+//collections
+let Collection = require('ampersand-collection');
+//views
+var PageView = require('./base');
+let EditProjectView = require('../views/edit-project');
+//templates
+var template = require('../templates/pages/projectBrowser.pug');
+
+import initPage from './page.js';
+
+let projectBrowser = PageView.extend({
+ template: template,
+ events: {
+ 'click [data-hook=new-project-btn]' : 'handleNewProjectClick'
+ },
+ initialize: function (attrs, options) {
+ PageView.prototype.initialize.apply(this, arguments)
+ let self = this
+ let endpoint = path.join(app.getApiPath(), "project/load-browser")
+ xhr({uri:endpoint, json:true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ self.projects = body.projects
+ self.renderProjectsView()
+ }
+ });
+ },
+ render: function (attrs, options) {
+ PageView.prototype.render.apply(this, arguments)
+ $(document).on('hide.bs.modal', '.modal', function (e) {
+ e.target.remove()
+ });
+ },
+ renderProjectsView: function () {
+ if(this.projectsView) {
+ this.projectsView.remove()
+ }
+ let projects = new Collection(this.projects, {model: Project, comparator: 'parentDir'})
+ this.projectsView = this.renderCollection(projects, EditProjectView, this.queryByHook("projects-view-container"))
+ },
+ validateName(input) {
+ var error = ""
+ if(input.endsWith('/')) {
+ error = 'forward'
+ }
+ let invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\"
+ for(var i = 0; i < input.length; i++) {
+ if(invalidChars.includes(input.charAt(i))) {
+ error = error === "" || error === "special" ? "special" : "both"
+ }
+ }
+ return error
+ },
+ handleNewProjectClick: function (e) {
+ let self = this
+ if(document.querySelector("#newProjectModal")) {
+ document.querySelector("#newProjectModal").remove()
+ }
+ let modal = $(modals.newProjectModalHtml()).modal()
+ let input = document.querySelector("#newProjectModal #projectNameInput")
+ input.focus()
+ let okBtn = document.querySelector("#newProjectModal .ok-model-btn")
+ input.addEventListener("keyup", function (event) {
+ if(event.keyCode === 13){
+ event.preventDefault();
+ okBtn.click();
+ }
+ });
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#newProjectModal #projectNameInputEndCharError')
+ var charErrMsg = document.querySelector('#newProjectModal #projectNameInputSpecCharError')
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ okBtn.addEventListener("click", function (e) {
+ if(Boolean(input.value)) {
+ modal.modal('hide')
+ let projectPath = input.value.trim() + ".proj"
+ let endpoint = path.join(app.getApiPath(), "project/new-project")+"?path="+projectPath
+ xhr({uri:endpoint, json:true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+body.path
+ }else{
+ let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal()
+ }
+ })
+ }
+ });
+ }
+});
+
+initPage(projectBrowser);
\ No newline at end of file
diff --git a/client/pages/project-manager.js b/client/pages/project-manager.js
new file mode 100644
index 0000000000..e7c3a2da1a
--- /dev/null
+++ b/client/pages/project-manager.js
@@ -0,0 +1,481 @@
+var $ = require('jquery');
+var xhr = require('xhr');
+var path = require('path');
+//support files
+var app = require('../app');
+var modals = require('../modals');
+//views
+var PageView = require('./base');
+var PlotsView = require('../views/plots-view');
+var EditModelsView = require('../views/edit-models-view');
+var EditWorkflowGroupsView = require('../views/edit-workflow-groups-view');
+var ProjectViewer = require('../views/project-viewer');
+var FileBrowser = require('../views/file-browser-view');
+var MetaDataView = require('../views/meta-data');
+//models
+var Project = require('../models/project');
+var Plot = require('../models/plots');
+//templates
+var template = require('../templates/pages/projectManager.pug');
+
+import initPage from './page.js'
+
+let ProjectManager = PageView.extend({
+ template: template,
+ events: {
+ 'click [data-hook=new-model]' : 'handleNewModelClick',
+ 'click [data-hook=new-workflow-group]' : 'handleNewWorkflowGroupClick',
+ 'click [data-hook=existing-model]' : 'handleExistingModelClick',
+ 'click [data-hook=export-project-as-zip]' : 'handleExportZipClick',
+ 'click [data-hook=export-project-as-combine]' : 'handleExportCombineClick',
+ 'click [data-hook=empty-project-trash]' : 'handleEmptyTrashClick',
+ 'click [data-hook=collapse-most-recent-plot-btn]' : 'changeCollapseButtonText',
+ 'click [data-hook=project-manager-advanced-btn]' : 'changeCollapseButtonText',
+ 'click [data-hook=collapse-annotation-container]' : 'changeCollapseButtonText',
+ 'change [data-hook=annotation-text-container]' : 'updateAnnotation',
+ 'click [data-hook=upload-file-btn]' : 'handleUploadModelClick',
+ 'click [data-hook=edit-annotation-btn]' : 'handleEditAnnotationClick'
+ },
+ initialize: function (attrs, options) {
+ PageView.prototype.initialize.apply(this, arguments)
+ let self = this
+ this.url = decodeURI(document.URL)
+ let urlParams = new URLSearchParams(window.location.search)
+ this.projectPath = urlParams.get('path')
+ this.projectName = this.getFileName(this.projectPath)
+ this.model = new Project({
+ directory: self.projectPath
+ });
+ this.model.fetch({
+ success: function (model, response, options) {
+ if(response.trash_empty) {
+ $(self.queryByHook('empty-project-trash')).prop('disabled', true)
+ }
+ self.renderSubviews()
+ }
+ });
+ },
+ update: function (target) {
+ let self = this
+ this.model.fetch({
+ success: function (model, response, options) {
+ self.renderProjectViewer()
+ $(self.queryByHook('empty-project-trash')).prop('disabled', response.trash_empty)
+ if(target === "model-editor" || target === "workflows-editor" || target === "trash") {
+ self.projectFileBrowser.refreshJSTree()
+ }else if(target === "workflow-group-editor"){
+ self.projectFileBrowser.refreshJSTree()
+ self.renderEditModelsView()
+ }else if(target === "file-browser") {
+ self.renderEditModelsView()
+ self.renderEditWorkflowGroupsView()
+ }else{
+ self.renderEditModelsView()
+ self.renderEditWorkflowGroupsView()
+ self.projectFileBrowser.refreshJSTree()
+ }
+ }
+ });
+ },
+ getFileName: function (file) {
+ if(file.endsWith('/')) {
+ file.slice(0, -1)
+ }
+ if(file.includes('/')) {
+ file = file.split('/').pop()
+ }
+ if(!file.includes('.')) {
+ return file
+ }
+ return file.split('.').slice(0, -1).join('.')
+ },
+ renderSubviews: function () {
+ this.renderProjectViewer();
+ this.renderProjectFileBrowser();
+ this.renderRecentPlotView();
+ this.renderEditModelsView();
+ this.renderEditWorkflowGroupsView();
+ if(this.model.annotation){
+ $(this.queryByHook('annotation-text-container')).text(this.model.annotation)
+ $(this.queryByHook("collapse-annotation-container")).collapse('show')
+ }else{
+ $(this.queryByHook('edit-annotation-btn')).text('Add Notes')
+ }
+ $(document).on('hide.bs.modal', '.modal', function (e) {
+ e.target.remove()
+ });
+ },
+ renderRecentPlotView: function () {
+ if(this.recentPlotView) {
+ this.recentPlotView.remove()
+ }
+ if(this.model.plot) {
+ var plot = new Plot(this.model.plot.output)
+ var expName = path.dirname(this.model.plot.path).split('/').pop().split('.')[0]
+ var wkflName = this.model.plot.path.split('/').pop().split('.')[0]
+ this.recentPlotView = new PlotsView({
+ model: plot,
+ path: this.model.plot.path,
+ heading: expName + " - " + wkflName
+ });
+ this.registerRenderSubview(this.recentPlotView, "project-most-recent-plot");
+ }else{
+ let message = "Their are no saved plots in the workflows of this project"
+ $(this.queryByHook("project-most-recent-plot")).text(message)
+ }
+ },
+ renderEditModelsView: function () {
+ if(this.editModelsView) {
+ this.editModelsView.remove()
+ }
+ this.editModelsView = new EditModelsView({
+ collection: this.model.models
+ });
+ this.registerRenderSubview(this.editModelsView, "edit-models-container")
+ },
+ renderEditWorkflowGroupsView: function () {
+ if(this.editWorkflowGroupsView) {
+ this.editWorkflowGroupsView.remove()
+ }
+ this.editWorkflowGroupsView = new EditWorkflowGroupsView({
+ collection: this.model.workflowGroups
+ });
+ this.registerRenderSubview(this.editWorkflowGroupsView, "edit-workflow-groups-container")
+ },
+ renderProjectViewer: function () {
+ if(this.projectViewer) {
+ this.projectViewer.remove()
+ }
+ this.projectViewer = new ProjectViewer({
+ model: this.model,
+ name: this.projectName
+ });
+ this.registerRenderSubview(this.projectViewer, "project-viewer")
+ },
+ renderProjectFileBrowser: function () {
+ let self = this
+ if(this.projectFileBrowser) {
+ this.projectFileBrowser.remove()
+ }
+ this.projectFileBrowser = new FileBrowser({
+ root: self.projectPath
+ })
+ this.registerRenderSubview(this.projectFileBrowser, "file-browser")
+ },
+ renderMetaDataView: function (target, files, download) {
+ if(this.metaDataView) {
+ this.metaDataView.remove()
+ }
+ this.metaDataView = new MetaDataView({
+ parent: this,
+ projectName: this.model.directory,
+ files: files,
+ path: target,
+ download: download
+ });
+ this.registerRenderSubview(this.metaDataView, "project-meta-data-container")
+ $(this.queryByHook("project-meta-data-container")).collapse("show")
+ },
+ registerRenderSubview: function (view, hook) {
+ this.registerSubview(view);
+ this.renderSubview(view, this.queryByHook(hook));
+ },
+ handleEditAnnotationClick: function (e) {
+ let buttonTxt = e.target.innerText;
+ if(buttonTxt.startsWith("Add")){
+ $(this.queryByHook('collapse-annotation-container')).collapse('show')
+ $(this.queryByHook('edit-annotation-btn')).text('Edit Notes')
+ }else if(!$("#annotation-text").attr('class').includes('show')){
+ $("#annotation-text").collapse('show')
+ $(this.queryByHook("collapse-annotation-text")).text('-')
+ }
+ document.querySelector("#annotation").focus()
+ },
+ updateAnnotation: function (e) {
+ this.model.annotation = e.target.value.trim();
+ if(this.model.annotation === ""){
+ $(this.queryByHook('edit-annotation-btn')).text('Add Notes')
+ $(this.queryByHook("collapse-annotation-container")).collapse('hide')
+ }
+ let endpoint = path.join(app.getApiPath(), "project/save-annotation")+"?path="+this.model.directory
+ xhr({uri: endpoint, json: true, method: "post", data: {'annotation': this.model.annotation}}, function (err, response, body) {
+ console.log("Saved project notes")
+ })
+ },
+ handleNewModelClick: function () {
+ this.addNewModel(false)
+ },
+ handleNewWorkflowGroupClick: function () {
+ this.addNewWorkflowGroup()
+ },
+ handleExistingModelClick: function () {
+ this.addExistingModel()
+ },
+ handleExportZipClick: function () {
+ let self = this
+ let queryStr = "?path="+this.projectPath+"&action=generate"
+ let endpoint = path.join(app.getApiPath(), "file/download-zip")+queryStr
+ xhr({uri:endpoint, json:true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ var downloadEP = path.join(app.getBasePath(), "/files", body.Path);
+ window.open(downloadEP)
+ }
+ })
+ },
+ handleExportCombineClick: function () {
+ this.exportAsCombine(this.projectPath, true)
+ },
+ handleEmptyTrashClick: function () {
+ let self = this;
+ if(document.querySelector("#emptyTrashConfirmModal")) {
+ document.querySelector("#emptyTrashConfirmModal").remove()
+ }
+ let modal = $(modals.emptyTrashConfirmHtml()).modal();
+ let yesBtn = document.querySelector('#emptyTrashConfirmModal .yes-modal-btn');
+ yesBtn.addEventListener('click', function (e) {
+ modal.modal('hide')
+ let endpoint = path.join(app.getApiPath(), "project/empty-trash")+"?path="+path.join(self.projectPath, "trash")
+ xhr({uri: endpoint, json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ $(self.queryByHook('empty-project-trash')).prop('disabled', true)
+ self.update("trash")
+ console.log(body)
+ }else{
+ console.log(body)
+ }
+ });
+ });
+ },
+ handleUploadModelClick: function (e) {
+ let self = this
+ let type = e.target.dataset.type
+ if(document.querySelector('#uploadFileModal')) {
+ document.querySelector('#uploadFileModal').remove()
+ }
+ let modal = $(modals.uploadFileHtml(type)).modal();
+ let uploadBtn = document.querySelector('#uploadFileModal .upload-modal-btn');
+ let fileInput = document.querySelector('#uploadFileModal #fileForUpload');
+ let input = document.querySelector('#uploadFileModal #fileNameInput');
+ fileInput.addEventListener('change', function (e) {
+ if(fileInput.files.length){
+ uploadBtn.disabled = false
+ }else{
+ uploadBtn.disabled = true
+ }
+ })
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#uploadFileModal #fileNameInputEndCharError')
+ var charErrMsg = document.querySelector('#uploadFileModal #fileNameInputSpecCharError')
+ let error = self.validateName(input.value)
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ uploadBtn.addEventListener('click', function (e) {
+ let file = fileInput.files[0]
+ var fileinfo = {"type":type,"name":"","path":self.projectPath}
+ if(Boolean(input.value) && self.validateName(input.value) === ""){
+ fileinfo.name = input.value
+ }
+ let formData = new FormData()
+ formData.append("datafile", file)
+ formData.append("fileinfo", JSON.stringify(fileinfo))
+ let endpoint = path.join(app.getApiPath(), 'file/upload');
+ let req = new XMLHttpRequest();
+ req.open("POST", endpoint)
+ req.onload = function (e) {
+ var resp = JSON.parse(req.response)
+ if(req.status < 400) {
+ if(resp.errors.length > 0){
+ let errorModal = $(modals.uploadFileErrorsHtml(file.name, type, resp.message, resp.errors)).modal();
+ }else{
+ self.update("model-editor")
+ }
+ }
+ }
+ req.send(formData)
+ modal.modal('hide')
+ })
+ },
+ addNewModel: function (isSpatial) {
+ let self = this
+ let isModel = true
+ if(document.querySelector('#newModalModel')) {
+ document.querySelector('#newModalModel').remove()
+ }
+ let modal = $(modals.renderCreateModalHtml(isModel, isSpatial)).modal();
+ let okBtn = document.querySelector('#newModalModel .ok-model-btn');
+ let input = document.querySelector('#newModalModel #modelNameInput');
+ okBtn.addEventListener('click', function (e) {
+ if (Boolean(input.value)) {
+ let modelName = input.value.split("/").pop() + '.mdl';
+ let message = modelName.split(".")[0] !== input.value ?
+ "Warning: Models are saved directly in StochSS Projects and cannot be saved to the "+input.value.split("/")[0]+" directory in the project.
Your model will be saved directly in your project.
" : ""
+ let modelPath = path.join(self.projectPath, modelName)
+ let endpoint = path.join(app.getBasePath(), app.routePrefix, 'models/edit')+"?path="+modelPath+"&message="+message
+ if(message){
+ modal.modal('hide')
+ let warningModal = $(modals.newProjectModelWarningHtml(message)).modal()
+ let yesBtn = document.querySelector('#newProjectModelWarningModal .yes-modal-btn');
+ yesBtn.addEventListener('click', function (e) {window.location.href = endpoint;})
+ }else{
+ window.location.href = endpoint;
+ }
+ }
+ });
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#newModalModel #modelNameInputEndCharError')
+ var charErrMsg = document.querySelector('#newModalModel #modelNameInputSpecCharError')
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ input.addEventListener("keyup", function (event) {
+ if(event.keyCode === 13){
+ event.preventDefault();
+ okBtn.click();
+ }
+ });
+ },
+ validateName(input) {
+ var error = ""
+ if(input.endsWith('/')) {
+ error = 'forward'
+ }
+ let invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\"
+ for(var i = 0; i < input.length; i++) {
+ if(invalidChars.includes(input.charAt(i))) {
+ error = error === "" || error === "special" ? "special" : "both"
+ }
+ }
+ return error
+ },
+ addNewWorkflowGroup: function (cb) {
+ let self = this
+ if(document.querySelector("#newWorkflowGroupModal")) {
+ document.querySelector("#newWorkflowGroupModal").remove()
+ }
+ let modal = $(modals.newWorkflowGroupModalHtml()).modal();
+ let okBtn = document.querySelector('#newWorkflowGroupModal .ok-model-btn');
+ let input = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInput');
+ input.addEventListener("keyup", function (event) {
+ if(event.keyCode === 13){
+ event.preventDefault();
+ okBtn.click();
+ }
+ });
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInputEndCharError')
+ var charErrMsg = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInputSpecCharError')
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ okBtn.addEventListener("click", function (e) {
+ if(Boolean(input.value)) {
+ let workflowGroupName = input.value + ".wkgp"
+ let workflowGroupPath = path.join(self.projectPath, workflowGroupName)
+ let endpoint = path.join(app.getApiPath(), "project/new-workflow-group")+"?path="+workflowGroupPath
+ xhr({uri: endpoint,json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ if(cb) {
+ cb(workflowGroupName)
+ }else{
+ self.update("workflow-group")
+ }
+ }else{
+ let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal()
+ }
+ modal.modal('hide')
+ });
+ }
+ });
+ },
+ addExistingModel: function () {
+ let self = this
+ if(document.querySelector('#newProjectModelModal')){
+ document.querySelector('#newProjectModelModal').remove()
+ }
+ let modal = $(modals.newProjectModelHtml()).modal()
+ let okBtn = document.querySelector('#newProjectModelModal .ok-model-btn')
+ let input = document.querySelector('#newProjectModelModal #modelPathInput')
+ input.addEventListener("keyup", function (event) {
+ if(event.keyCode === 13){
+ event.preventDefault();
+ okBtn.click();
+ }
+ });
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#newProjectModelModal #modelPathInputEndCharError')
+ var charErrMsg = document.querySelector('#newProjectModelModal #modelPathInputSpecCharError')
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ okBtn.addEventListener("click", function (e) {
+ if(Boolean(input.value)) {
+ let queryString = "?path="+self.projectPath+"&mdlPath="+input.value
+ let endpoint = path.join(app.getApiPath(), 'project/add-existing-model') + queryString
+ xhr({uri:endpoint, json:true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ let successModal = $(modals.newProjectModelSuccessHtml(body.message)).modal()
+ }else{
+ let errorModal = $(modals.newProjectModelErrorHtml(body.Reason, body.Message)).modal()
+ }
+ });
+ modal.modal('hide')
+ self.update("existing-model")
+ }
+ });
+ },
+ exportAsCombine: function(target, download) {
+ let self = this
+ if(document.querySelector("#addMetaDataModal")) {
+ document.querySelector("#addMetaDataModal").remove()
+ }
+ let modal = $(modals.addMetaDataHtml("Do you wish to add/update the meta-data for this archive?")).modal()
+ let yesBtn = document.querySelector("#addMetaDataModal .yes-modal-btn")
+ let noBtn = document.querySelector("#addMetaDataModal .no-modal-btn")
+ yesBtn.addEventListener('click', function (e) {
+ modal.modal('hide')
+ var files = []
+ if(target === self.projectPath){
+ files = self.model.workflowGroups.map(function (workflowGroup) {return workflowGroup.name+".wkgp"})
+ files.unshift(self.model.directory)
+ }else{
+ files = [self.model.directory, target.split('/').pop()]
+ }
+ self.renderMetaDataView(target, files, download)
+ });
+ noBtn.addEventListener('click', function (e) {
+ let queryString = "?path="+target+"&projectPath="+self.projectPath
+ let endpoint = path.join(app.getApiPath(), "project/export-combine")+queryString
+ xhr({uri:endpoint, json:true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ if(download) {
+ let downloadEP = path.join(app.getBasePath(), "/files", body.file_path);
+ window.open(downloadEP)
+ }else{
+ let modal = $(modals.projectExportSuccessHtml(body.file_type, body.message)).modal()
+ }
+ }else{
+ let modal = $(modals.projectExportErrorHtml(body.Reason, body.Message))
+ }
+ });
+ });
+ },
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let isBtn = $(this.queryByHook(source)).attr("class").includes("btn")
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(isBtn && !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
+ }
+});
+
+initPage(ProjectManager)
\ No newline at end of file
diff --git a/client/pages/users-home.js b/client/pages/users-home.js
new file mode 100644
index 0000000000..1d4747bddc
--- /dev/null
+++ b/client/pages/users-home.js
@@ -0,0 +1,174 @@
+let $ = require('jquery');
+let xhr = require('xhr');
+let path = require('path');
+//support files
+let app = require('../app');
+let modals = require('../modals');
+//views
+let PageView = require('./base');
+//templates
+let template = require('../templates/pages/usersHome.pug');
+
+import initPage from './page.js';
+
+let usersHomePage = PageView.extend({
+ template: template,
+ events: {
+ 'click [data-hook=new-model-btn]' : 'handleNewModelClick',
+ 'click [data-hook=new-project-btn]' : 'handleNewProjectClick',
+ 'click [data-hook=browse-projects-btn]' : 'handleBrowseProjectsClick',
+ 'click [data-hook=browse-files-btn]' : 'handleBrowseFilesClick',
+ 'click [data-hook=quickstart-btn]' : 'handleQuickstartClick'
+ },
+ initialize: function (attrs, options) {
+ PageView.prototype.initialize.apply(this, arguments)
+ let urlParams = new URLSearchParams(window.location.search)
+ if(urlParams.has("open")){
+ let uploadPath = urlParams.get("open")
+ let endpoint = path.join(app.getApiPath(), 'file/upload-from-link')+"?path="+uploadPath
+ let self = this
+ xhr({uri:endpoint, json:true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ self.responsePath = body.responsePath
+ self.getUploadResponse()
+ }
+ })
+ }
+ },
+ render: function (attrs, options) {
+ PageView.prototype.render.apply(this, arguments);
+ $(document).on('hide.bs.modal', '.modal', function (e) {
+ e.target.remove()
+ });
+ },
+ getUploadResponse: function () {
+ let self = this
+ setTimeout(function () {
+ let endpoint = path.join(app.getApiPath(), 'file/upload-from-link')+"?path="+self.responsePath+"&cmd=read"
+ xhr({uri: endpoint, json: true}, function (err, response, body) {
+ if(response.statusCode >= 400 || Object.keys(body).includes("reason")) {
+ let model = $(modals.projectExportErrorHtml(body.reason, body.message)).modal()
+ }else if(body.done) {
+ if(body.file_path.endsWith(".proj")){
+ window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+body.file_path
+ }
+ }else{
+ self.getUploadResponse()
+ }
+ })
+ }, 1000)
+ },
+ validateName(input) {
+ var error = ""
+ if(input.endsWith('/')) {
+ error = 'forward'
+ }
+ let invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\"
+ for(var i = 0; i < input.length; i++) {
+ if(invalidChars.includes(input.charAt(i))) {
+ error = error === "" || error === "special" ? "special" : "both"
+ }
+ }
+ return error
+ },
+ handleNewModelClick: function (e) {
+ let self = this
+ if(document.querySelector("#newModalModel")) {
+ document.querySelector("#newModalModel").remove()
+ }
+ let modal = $(modals.renderCreateModalHtml(true, false)).modal()
+ let okBtn = document.querySelector("#newModalModel .ok-model-btn")
+ let input = document.querySelector("#newModalModel #modelNameInput")
+ input.focus()
+ input.addEventListener("keyup", function (event) {
+ if(event.keyCode === 13){
+ event.preventDefault();
+ okBtn.click();
+ }
+ });
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#newModalModel #modelNameInputEndCharError')
+ var charErrMsg = document.querySelector('#newModalModel #modelNameInputSpecCharError')
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== "" || input.value.trim() === ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ okBtn.addEventListener("click", function (e) {
+ if(Boolean(input.value)){
+ modal.modal('hide')
+ let modelPath = input.value + '.mdl'
+ let queryString = "?path="+modelPath
+ let existEP = path.join(app.getApiPath(), "model/exists")+queryString
+ xhr({uri: existEP, json: true}, function (err, response, body) {
+ if(body.exists) {
+ let title = "Model Already Exists"
+ let message = "A model already exists with that name"
+ let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal()
+ }else{
+ let endpoint = path.join(app.getBasePath(), "stochss/models/edit")+queryString
+ self.navToPage(endpoint)
+ }
+ })
+ }
+ });
+ },
+ handleNewProjectClick: function (e) {
+ let self = this
+ if(document.querySelector("#newProjectModal")) {
+ document.querySelector("#newProjectModal").remove()
+ }
+ let modal = $(modals.newProjectModalHtml()).modal()
+ let okBtn = document.querySelector("#newProjectModal .ok-model-btn")
+ let input = document.querySelector("#newProjectModal #projectNameInput")
+ input.focus()
+ input.addEventListener("keyup", function (event) {
+ if(event.keyCode === 13){
+ event.preventDefault();
+ okBtn.click();
+ }
+ });
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#newProjectModal #projectNameInputEndCharError')
+ var charErrMsg = document.querySelector('#newProjectModal #projectNameInputSpecCharError')
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== "" || input.value.trim() === ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ okBtn.addEventListener("click", function (e) {
+ if(Boolean(input.value)) {
+ modal.modal('hide')
+ let projectPath = input.value + ".proj"
+ let queryString = "?path="+projectPath
+ let endpoint = path.join(app.getApiPath(), "project/new-project")+queryString
+ xhr({uri:endpoint, json:true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ let projectQS = "?path="+body.path
+ let projectEP = path.join(app.getBasePath(), "stochss/project/manager")+projectQS
+ self.navToPage(projectEP)
+ }else{
+ let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal()
+ }
+ });
+ }
+ });
+ },
+ handleBrowseProjectsClick: function (e) {
+ let endpoint = path.join(app.getBasePath(), "stochss/project/browser")
+ this.navToPage(endpoint)
+ },
+ handleBrowseFilesClick: function (e) {
+ let endpoint = path.join(app.getBasePath(), "stochss/files")
+ this.navToPage(endpoint)
+ },
+ handleQuickstartClick: function (e) {
+ let endpoint = path.join(app.getBasePath(), "stochss/quickstart")
+ this.navToPage(endpoint)
+ },
+ navToPage: function (endpoint) {
+ window.location.href = endpoint
+ }
+});
+
+initPage(usersHomePage);
\ No newline at end of file
diff --git a/client/pages/workflow-manager.js b/client/pages/workflow-manager.js
index b73f321dd7..facee01c89 100644
--- a/client/pages/workflow-manager.js
+++ b/client/pages/workflow-manager.js
@@ -14,6 +14,7 @@ var WorkflowResultsView = require('../views/workflow-results');
var ModelViewer = require('../views/model-viewer');
var InfoView = require('../views/workflow-info');
var InputView = require('../views/input');
+var SelectView = require('ampersand-select-view');
//models
var Model = require('../models/model')
//templates
@@ -25,10 +26,14 @@ let WorkflowManager = PageView.extend({
template: template,
events: {
'change [data-hook=workflow-name]' : 'setWorkflowName',
+ 'input [data-hook=workflow-name' : 'validateWorkflowName',
'change [data-hook=model-path]' : 'updateWkflModel',
+ 'input [data-hook=model-path]' : 'validateModelPath',
'click [data-hook=edit-workflow-help]' : function () {
let modal = $(modals.operationInfoModalHtml('wkfl-manager')).modal();
},
+ 'click [data-hook=project-breadcrumb]' : 'handleReturnToProjectClick',
+ 'click [data-hook=return-to-project-btn]' : 'handleReturnToProjectClick'
},
initialize: function (attrs, options) {
PageView.prototype.initialize.apply(this, arguments);
@@ -40,9 +45,12 @@ let WorkflowManager = PageView.extend({
this.url = decodeURI(document.URL)
let urlParams = new URLSearchParams(window.location.search)
let type = urlParams.get('type');
- let wkflPath = urlParams.get('path');
+ this.urlPathParam = urlParams.get('path');
var stamp = this.getCurrentDate();
- let queryStr = "?stamp="+stamp+"&type="+type+"&path="+wkflPath
+ var queryStr = "?stamp="+stamp+"&type="+type+"&path="+this.urlPathParam
+ if(urlParams.has('parentPath')) {
+ queryStr += ("&parentPath=" + urlParams.get('parentPath'))
+ }
var endpoint = path.join(app.getApiPath(), "workflow/load-workflow")+queryStr
xhr({uri: endpoint, json: true}, function (err, resp, body) {
if(resp.statusCode < 400) {
@@ -59,6 +67,13 @@ let WorkflowManager = PageView.extend({
self.wkflPath = path.join(self.wkflParPath, self.wkflDirectory)
self.buildWkflModel(body)
self.renderSubviews();
+ if(self.wkflPath.includes('.proj')) {
+ self.projectPath = path.dirname(self.wkflParPath)
+ $(self.queryByHook('project-breadcrumb')).text(self.projectPath.split('/').pop().split('.')[0])
+ $(self.queryByHook('workflow-breadcrumb')).text(self.workflowName)
+ self.queryByHook("project-breadcrumb-links").style.display = "block"
+ self.queryByHook("return-to-project-btn").style.display = "inline-block"
+ }
}
});
},
@@ -70,8 +85,12 @@ let WorkflowManager = PageView.extend({
this.model.is_spatial = this.modelDirectory.endsWith(".smdl")
this.model.isPreview = false
this.model.for = "wkfl"
- if(!model)
+ if(!model) {
+ this.modelLoadError = true
this.wkflModelNotFound(data.error)
+ }else{
+ this.modelLoadError = false
+ }
},
wkflModelNotFound: function (error) {
let modal = $(modals.modelNotFoundHtml(error.Reason, error.Message)).modal()
@@ -110,13 +129,20 @@ let WorkflowManager = PageView.extend({
this.renderWkflNameInputView();
this.renderMdlPathInputView();
this.renderWorkflowEditor();
- this.renderWorkflowStatusView();
- this.renderResultsView();
- this.renderInfoView();
- this.renderModelViewer();
+ if(this.status !== "new" && this.status !== "ready") {
+ this.renderWorkflowStatusView();
+ this.renderModelViewer();
+ }
+ if(this.status === "error" || this.status === "complete") {
+ this.renderResultsView();
+ this.renderInfoView();
+ }
if(this.status === 'running'){
this.getWorkflowStatus();
}
+ $(document).on('hide.bs.modal', '.modal', function (e) {
+ e.target.remove()
+ });
},
registerRenderSubview: function (view, hook) {
this.registerSubview(view);
@@ -181,6 +207,7 @@ let WorkflowManager = PageView.extend({
this.workflowResultsView.remove();
}
var resultsView = new WorkflowResultsView({
+ parent: this,
trajectories: this.settings.simulationSettings.realizations,
status: this.status,
species: this.model.species,
@@ -229,36 +256,112 @@ let WorkflowManager = PageView.extend({
}
});
},
+ validateName(input, rename = false) {
+ var error = ""
+ if(input.endsWith('/')) {
+ error = 'forward'
+ }
+ var invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\"
+ if(rename) {
+ invalidChars += "/"
+ }
+ for(var i = 0; i < input.length; i++) {
+ if(invalidChars.includes(input.charAt(i))) {
+ error = error === "" || error === "special" ? "special" : "both"
+ }
+ }
+ return error
+ },
+ validateWorkflowName: function (e) {
+ if(this.validateName(e.target.value, true) !== ""){
+ document.querySelector("#workflowNameSpecialCharError").style.display = "block"
+ }else{
+ document.querySelector("#workflowNameSpecialCharError").style.display = "none"
+ }
+ },
+ validateModelPath: function (e) {
+ if(this.validateName(e.target.value) !== ""){
+ document.querySelector("#modelPathSpecialCharError").style.display = "block"
+ }else{
+ document.querySelector("#modelPathSpecialCharError").style.display = "none"
+ }
+ },
setWorkflowName: function(e) {
var newWorkflowName = e.target.value.trim();
- if(newWorkflowName.endsWith(this.workflowDate)){
- this.workflowName = newWorkflowName
+ if(this.validateName(newWorkflowName) === "") {
+ if(newWorkflowName.endsWith(this.workflowDate)){
+ this.workflowName = newWorkflowName
+ }else{
+ this.workflowName = newWorkflowName + this.workflowDate
+ e.target.value = this.workflowName
+ }
+ $(this.queryByHook('workflow-breadcrumb')).text(this.workflowName)
+ this.wkflDirectory = this.workflowName + ".wkfl"
+ this.wkflPath = path.join(this.wkflParPath, this.wkflDirectory)
}else{
- this.workflowName = newWorkflowName + this.workflowDate
e.target.value = this.workflowName
+ setTimeout(function (e) {
+ document.querySelector("#workflowNameSpecialCharError").style.display = "none"
+ }, 5000)
}
- this.wkflDirectory = this.workflowName + ".wkfl"
- this.wkflPath = path.join(this.wkflParPath, this.wkflDirectory)
},
updateWkflModel: function (e) {
- let self = this;
- this.model.fetch({
- json: true,
- success: function (model, response, options) {
- self.renderWorkflowEditor()
- },
- error: function (model, response, options) {
- self.wkflModelNotFound(response.body)
+ if(this.validateName(e.target.value) === "") {
+ let self = this;
+ let parPath = path.dirname(self.modelDirectory)
+ if(parPath.endsWith(".proj") && parPath !== path.dirname(e.target.value)) {
+ self.model.directory = self.modelDirectory
+ $(self.queryByHook("model-path")).find('input').val(self.modelDirectory)
+ let mdlPathErr = $(modals.wkflModelPathErrorHtml()).modal()
+ }else{
+ self.modelDirectory = e.target.value
+ this.model.directory = e.target.value
+ this.model.fetch({
+ json: true,
+ success: function (model, response, options) {
+ self.modelLoadError = false
+ self.renderWorkflowEditor()
+ },
+ error: function (model, response, options) {
+ self.modelLoadError = true
+ self.renderWorkflowEditor()
+ self.wkflModelNotFound(response.body)
+ }
+ });
}
- });
+ }else{
+ e.target.value = this.modelDirectory
+ setTimeout(function (e) {
+ document.querySelector("#modelPathSpecialCharError").style.display = "none"
+ }, 5000)
+ }
},
reloadWkfl: function () {
let self = this;
- if(self.status === 'new')
- window.location.href = self.url.replace(self.modelDirectory.split('/').pop(), self.wkflDirectory)
+ if(self.status === 'new') {
+ // Need to refactor this
+ let mdlParPath = path.dirname(this.modelDirectory)
+ if(mdlParPath !== "."){
+ let replaceText = this.wkflPath.split(mdlParPath+'/').slice(1).join(mdlParPath)
+ this.url = this.url.replace(this.modelDirectory.split('/').pop(), replaceText)
+ }else{
+ this.url = this.url.replace(this.modelDirectory, this.wkflPath)
+ }
+ window.location.href = this.url
+ }
else
window.location.reload()
},
+ handleReturnToProjectClick: function(e) {
+ let self = this
+ if((this.status === 'ready' || this.status === 'new') && !this.modelLoadError){
+ this.workflowEditorView.workflowStateButtons.clickSaveHandler(e, function (e) {
+ window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+self.projectPath
+ })
+ }else{
+ window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+self.projectPath
+ }
+ }
});
initPage(WorkflowManager);
diff --git a/client/pages/workflow-selection.js b/client/pages/workflow-selection.js
index 528cae2a74..014e88840e 100644
--- a/client/pages/workflow-selection.js
+++ b/client/pages/workflow-selection.js
@@ -21,11 +21,24 @@ let workflowSelection = PageView.extend({
"click [data-hook=twod-parameter-sweep]" : "notebookWorkflow",
"click [data-hook=sciope-model-exploration]" : "notebookWorkflow",
"click [data-hook=model-inference]" : "notebookWorkflow",
+ "click [data-hook=stochss-es]" : "handleEnsembleSimulationClick",
+ "click [data-hook=stochss-ps]" : "handleParameterSweepClick"
},
initialize: function (attrs, options) {
PageView.prototype.initialize.apply(this, arguments);
var self = this
- this.modelDir = (new URLSearchParams(window.location.search)).get('path');
+ let urlParams = new URLSearchParams(window.location.search)
+ this.modelDir = urlParams.get('path');
+ if(urlParams.has('parentPath')){
+ this.parentPath = urlParams.get('parentPath')
+ }else{
+ this.parentPath = path.dirname(this.modelDir)
+ }
+ if(this.modelDir.includes(".proj")) {
+ this.projectPath = path.dirname(this.modelDir)
+ this.projectName = this.projectPath.split('/').pop().split('.')[0]
+ this.workflowGroupName = this.parentPath.split('/').pop().split('.')[0]
+ }
this.tooltips = Tooltips.workflowSelection
$(document).ready(function () {
$('[data-toggle="tooltip"]').tooltip();
@@ -34,7 +47,7 @@ let workflowSelection = PageView.extend({
});
});
- this.modelFile = this.modelDir.split('/').pop().split('.').shift();
+ this.modelFile = this.getFileName(this.modelDir)
var isSpatial = this.modelDir.endsWith('.smdl');
this.model = new Model({
name: this.modelFile,
@@ -45,26 +58,64 @@ let workflowSelection = PageView.extend({
});
this.model.fetch({
success: function (model, response, options) {
+ if(self.modelDir.includes(".proj")) {
+ self.queryByHook("workflow-selection-breadcrumb-links").style.display = "block"
+ }
self.validateWorkflows()
}
});
},
+ getFileName: function (file) {
+ if(file.endsWith('/')) {
+ file.slice(0, -1)
+ }
+ if(file.includes('/')) {
+ file = file.split('/').pop()
+ }
+ if(!file.includes('.')) {
+ return file
+ }
+ return file.split('.').slice(0, -1).join('.')
+ },
validateWorkflows: function () {
- if(this.model.parameters.length < 1 || this.model.species.length < 1){
- $(this.queryByHook('oned-parameter-sweep')).addClass('disabled')
- $(this.queryByHook('twod-parameter-sweep')).addClass('disabled')
- $(this.queryByHook('sciope-model-exploration')).addClass('disabled')
+ let modelInvalid = this.checkForErrors()
+ if(this.model.species.length < 1 || (this.model.reactions.length < 1 && this.model.eventsCollection.length < 1 && this.model.rules.length < 1) || modelInvalid){
+ $(this.queryByHook('stochss-es')).prop('disabled', true)
+ $(this.queryByHook('stochss-ps')).prop('disabled', true)
+ $(this.queryByHook('ensemble-simulation')).prop('disabled', true)
+ $(this.queryByHook('model-inference')).prop('disabled', true)
+ $(this.queryByHook('oned-parameter-sweep')).prop('disabled', true)
+ $(this.queryByHook('twod-parameter-sweep')).prop('disabled', true)
+ $(this.queryByHook('sciope-model-exploration')).prop('disabled', true)
+ if(modelInvalid) {
+ let endpoint = path.join(app.getBasePath(), "stochss/models/edit")+'?path='+this.model.directory
+ $(this.queryByHook('invalid-model-message')).html('Errors were detected in you model
click here to fix your model ')
+ }
+ $(this.queryByHook('invalid-model-message')).css('display', 'block')
+ }else if(this.model.parameters.length < 1){
+ $(this.queryByHook('oned-parameter-sweep')).prop('disabled', true)
+ $(this.queryByHook('twod-parameter-sweep')).prop('disabled', true)
+ $(this.queryByHook('stochss-ps')).prop('disabled', true)
+ $(this.queryByHook('psweep-workflow-message')).css('display', 'block')
}else if(this.model.parameters.length < 2){
- $(this.queryByHook('twod-parameter-sweep')).addClass('disabled')
+ $(this.queryByHook('twod-parameter-sweep')).prop('disabled', true)
+ $(this.queryByHook('psweep-workflow-message')).text('2D Parameter Sweep workflows require at least two parameters')
+ $(this.queryByHook('psweep-workflow-message')).css('display', 'block')
}
},
+ checkForErrors: function (e) {
+ let invalidParams = this.model.parameters.filter(function (parameter) {
+ if(typeof parameter.expression === "string") return true
+ })
+ if(invalidParams.length) {return true}
+ },
notebookWorkflow: function (e) {
var type = e.target.dataset.type;
- console.log(type)
this.toNotebook(type);
},
toNotebook: function (type) {
- var endpoint = path.join(app.getApiPath(), "/workflow/notebook")+"?type="+type+"&path="+this.modelDir
+ let queryString = "?type="+type+"&path="+this.modelDir+"&parentPath="+this.parentPath
+ var endpoint = path.join(app.getApiPath(), "/workflow/notebook")+queryString
xhr({uri:endpoint, json:true}, function (err, response, body) {
if(response.statusCode < 400){
var notebookPath = path.join(app.getBasePath(), "notebooks", body.FilePath)
@@ -72,6 +123,17 @@ let workflowSelection = PageView.extend({
}
});
},
+ handleEnsembleSimulationClick: function (e) {
+ this.launchStochssWorkflow("gillespy")
+ },
+ handleParameterSweepClick: function (e) {
+ this.launchStochssWorkflow("parameterSweep")
+ },
+ launchStochssWorkflow: function (type) {
+ let queryString = "?type=" + type + "&path=" + this.modelDir + "&parentPath=" + this.parentPath
+ let endpoint = path.join(app.getBasePath(), "stochss/workflow/edit")+queryString
+ window.location.href = endpoint
+ }
});
initPage(workflowSelection);
diff --git a/client/styles/styles.css b/client/styles/styles.css
index 45cfc54c13..0177c3797d 100644
--- a/client/styles/styles.css
+++ b/client/styles/styles.css
@@ -1,5 +1,5 @@
body {
-
+ min-width: 650px
}
img.quickstart {
@@ -26,7 +26,11 @@ img.quickstart {
}
.inline{
- display: inline-block !important;
+ display: inline-block;
+}
+
+.table {
+ table-layout: fixed;
}
span {
@@ -35,6 +39,8 @@ span {
select {
margin-left: 10px;
+ width: auto;
+ max-width: 100%;
}
label {
@@ -51,6 +57,26 @@ button.custom {
margin: 0.25rem;
}
+div.head {
+ border-bottom: 2px solid #dee2e6;
+}
+
+a.active-link:not([href]):not([tabindex]) {
+ color: #007bff;
+ text-decoration: none;
+ background-color: transparent;
+}
+
+a.active-link:not([href]):not([tabindex]):hover {
+ color: #0056b3;
+ text-decoration: underline;
+ cursor: pointer;
+}
+
+a.active-link:not([href]):not([tabindex]):focus {
+ color: rgba(0, 0, 0, 0.9);
+}
+
a.disabled {
pointer-events: none;
cursor: default;
@@ -64,6 +90,10 @@ a.disabled {
padding: 0.5rem 0.25rem 0.5rem 1rem;
}
+.dropdown-toggle {
+ white-space: normal;
+}
+
.dropdown-menu li:hover {
cursor: pointer;
}
@@ -72,6 +102,26 @@ a.disabled {
width: 8rem;
}
+.invalid-feedback.wkfl-name {
+ margin-top: 0;
+ margin-left: 8rem;
+ margin-bottom: 1rem;
+}
+
+.invalid-feedback.mdl-path {
+ margin-top: 0;
+ margin-left: 6rem;
+ margin-bottom: 1rem;
+}
+
+.invalid-feedback.warning {
+ color: #ffc107 !important;
+}
+
+button.name {
+ width: 75%;
+}
+
.form-input {
width: 100%;
}
@@ -244,8 +294,21 @@ input[type="file"]::-ms-browse {
font-size: 12px;
}
-.modal-content.info {
- width: 150%;
+.modal-title {
+ width: 95%;
+ word-break: break-word !important;
+ overflow-wrap: break-word !important;
+}
+
+.modal-dialog {
+ width: 75%;
+ min-width: 487.5px;
+ max-width: 750px;
+}
+
+.modal-content {
+ min-width: 487.5px;
+ max-width: 750px;
}
.modal-content.default-species {
@@ -263,6 +326,23 @@ input[type="file"]::-ms-browse {
border-right-color: #007bff;
}
+.spinner-border.workflow-plot {
+ /*display: inline-block;*/
+ margin-bottom: 45px;
+}
+
+.spinner-border.status {
+ vertical-align: middle;
+ position: relative;
+ display: inline-block;
+ margin: 5px;
+ left: 0;
+ width: 30px;
+ height: 30px;
+ border: 4px solid rgba(0, 0, 0, 0.125);
+ border-right-color: #007bff;
+}
+
.errors {
display: none;
}
@@ -348,6 +428,14 @@ span.checkbox {
padding-bottom: 10px;
}
+.verticle-space-2 {
+ padding-bottom: 20px
+}
+
+.verticle-space-3 {
+ padding-bottom: 30px
+}
+
.horizontal-space {
padding-left: 5px;
padding-right: 5px;
@@ -370,8 +458,10 @@ span.checkbox {
}
.logo img {
- width: 40em;
- margin-left: -8em;
+ width: 95%;
+ max-height: 176px;
+ max-width: 40em;
+ margin-left: -13.5%;
}
.try-stochss-btn {
@@ -381,6 +471,14 @@ span.checkbox {
border-radius: 1.5rem;
}
+.user-home-btn {
+ padding: 1rem 1rem;
+ font-size: 1.5rem;
+ line-height: 1;
+ border-radius: 1.5rem;
+ width: 100%
+}
+
.home-list {
line-height: 2;
}
@@ -404,3 +502,50 @@ span.checkbox {
/*h-offset v-offset blur spread color*/
box-shadow: 6px 6px 10px 1px rgba(0, 0, 0, .2), 2.25px 2.25px 14px 2px rgba(0, 0, 0, .1), 3.75px 3.75px 5px -3px rgba(0, 0, 0, .4)
}
+
+.no-gutters-padding {
+ padding-right: 0px;
+ padding-left: 0px;
+}
+
+.dropbtn {
+ border: none;
+ background-color: inherit;
+}
+
+.dropdown {
+ background-color: inherit;
+}
+
+.dropdown-content {
+ display: none;
+ position: absolute;
+ background-color: rgb(248, 249, 250);
+ min-width: 160px;
+ box-shadow: 0px 8px 16px 0px rgba(0,0,0,0.2);
+ z-index: 1;
+}
+
+.dropdown:hover .dropdown-content {
+ display: block;
+}
+
+#models-jstree-view .jstree-anchor {
+ white-space: normal;
+ word-break: break-word;
+ height: auto;
+}
+
+#models-jstree-view .jstree-default .jstree-anchor {
+ height: auto;
+}
+
+#models-jstree .jstree-anchor {
+ white-space: normal;
+ word-break: break-word;
+ height: auto;
+}
+
+#models-jstree .jstree-default .jstree-anchor {
+ height: auto;
+}
diff --git a/client/templates/body.pug b/client/templates/body.pug
index 7c3de43fa6..206fa084af 100644
--- a/client/templates/body.pug
+++ b/client/templates/body.pug
@@ -1,9 +1,12 @@
body
- nav.navbar.navbar-expand-lg.p-1.navbar-light.bg-light.fixed-top
+ nav.navbar.navbar-expand-md.p-1.navbar-light.bg-light.fixed-top
a.navbar-brand(href="/hub/spawn")
img(style="height: 38px;margin-left: -1.2em;" src="static/stochss-logo.png")
- div#navbar.collapse.navbar-collapse.justify-content-end
+ button.navbar-toggler(type="button" data-toggle="collapse" data-target="#navbar" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation")
+ span.navbar-toggler-icon
+
+ div#navbar.collapse.navbar-collapse.justify-content-end(role="navigation")
ul.navbar-nav.float-right
li.nav-item: a.nav-link(href="http://www.stochss.org", target="_blank")
| About
@@ -11,14 +14,18 @@ body
li.nav-item: a.nav-link(href="https://docs.google.com/forms/d/12tAH4f8CJ-3F-lK44Q9uQHFio_mGoK0oY829q5lD7i4/viewform?embedded=true", target="_blank")
| Register
- li.nav-item: a.nav-link(href="http://www.stochss.org/?page_id=476", target="_blank")
+ li.nav-item: a.nav-link(href="http://www.stochss.org/documentation", target="_blank")
| Documentation
- li.nav-item: a.nav-link(href="mailto:stochss-users@googlegroups.com")
- | Contact
+ li.nav-item: a.nav-link(href="https://forms.gle/hpGJ1ruxR7wTT43h8" target="_blank")
+ | Submit Feedback
- li.nav-item: a.nav-link(href="https://github.com/StochSS/stochss/issues/new", target="_blank")
- | Report Issue
+ li.nav-item
+ div.dropdown
+ button.dropdown-toggle.nav-item.nav-link.dropbtn Contact
+ div.dropdown-content
+ a.nav-link(href="https://gitter.im/StochSS/community#", target="_blank") Community Chat
+ a.nav-link(href="https://github.com/StochSS/stochss/issues/new", target="_blank") Report Issue
li.nav-item: a.nav-link(href="/logout")
| Sign Out
@@ -29,15 +36,19 @@ body
nav.sidebar.d-md-block
div.sidebar-sticky.tools
ul.nav.flex-column
- li.nav-item: h5.icon-flask Tools
+ li.nav-item: a.nav-link(href="stochss/home", title="Users Home Page")
+ | Home
+
+ li.nav-item: a.nav-link(href="stochss/project/browser", title="Explore your StochSS projects")
+ | Projects
- li.nav-item: a.nav-link(href="stochss/models", title="Explore your StochSS models")
- | Browser
+ li.nav-item: a.nav-link(href="stochss/files", title="Explore your StochSS files")
+ | Files
li.nav-item: a.nav-link(target="_blank", href="tree", title="Browse your files in a Jupyter interface")
| Jupyter
li.nav-item: a.nav-link(href="stochss/quickstart", title="Quickstart")
- | Quickstart
+ | Tutorial
main.col-md-10.body(role="main"): div.container-fluid(data-hook="page-container")
diff --git a/client/templates/head.pug b/client/templates/head.pug
index df74956cc0..1c592483bd 100644
--- a/client/templates/head.pug
+++ b/client/templates/head.pug
@@ -1,6 +1,6 @@
head
meta(charset="utf-8")
- title StochSS: Stochastic Simlation Service
+ title StochSS: Stochastic Simulation Service
meta(name="viewport", content="width=device-width, initial-scale=1.0")
meta(name="description", content="")
meta(name="author", content="")
diff --git a/client/templates/includes/creatorList.pug b/client/templates/includes/creatorList.pug
new file mode 100644
index 0000000000..fcf0f2119e
--- /dev/null
+++ b/client/templates/includes/creatorList.pug
@@ -0,0 +1,11 @@
+tr
+
+ td: div(data-hook="given-name-container")=this.model.fname
+
+ td: div(data-hook="family-name-container")=this.model.lname
+
+ td: div(data-hook="email-container")=this.model.email
+
+ td: div(data-hook="organization-container")=this.model.organization
+
+ td: button.btn.btn-outline-secondary.box-shadow(data-hook="remove-creator-btn") X
\ No newline at end of file
diff --git a/client/templates/includes/editCustomStoichSpecie.pug b/client/templates/includes/editCustomStoichSpecie.pug
index 96b2305592..5f0d1a6d7f 100644
--- a/client/templates/includes/editCustomStoichSpecie.pug
+++ b/client/templates/includes/editCustomStoichSpecie.pug
@@ -1,9 +1,10 @@
div
- label.select
- button.btn.btn-outline-secondary(class='btn-sm', data-hook='increment') +
- span.custom(data-hook="ratio")
+ div.inline
button.btn.btn-outline-secondary(class='btn-sm', data-hook='decrement') -
- select(data-hook="select-stoich-specie")
- span.message.message-below.message-error(data-hook="message-container")
- p(data-hook="message-text")
- button.btn.btn-outline-secondary.custom(class='btn-sm', data-hook='remove') X
\ No newline at end of file
+ span.custom(data-hook="ratio")
+ div.inline
+ button.btn.btn-outline-secondary(class='btn-sm', data-hook='increment') +
+ select(data-hook="select-stoich-specie")
+ span.message.message-below.message-error(data-hook="message-container")
+ p(data-hook="message-text")
+ button.btn.btn-outline-secondary.custom(class='btn-sm', data-hook='remove') X
\ No newline at end of file
diff --git a/client/templates/includes/editModelView.pug b/client/templates/includes/editModelView.pug
new file mode 100644
index 0000000000..fc9ab3e849
--- /dev/null
+++ b/client/templates/includes/editModelView.pug
@@ -0,0 +1,36 @@
+- var workflowGroups = this.workflowGroupOptions;
+div
+
+ div.ml-1.row
+
+ div.col-md-5: button.btn.btn-outline-secondary.box-shadow.text-break(data-hook="project-model-edit" style="width: 100%;")=this.model.name
+
+ div.col-md-4
+
+ button.btn.btn-outline-secondary.inline.box-shadow(
+ id="new-workflow-btn",
+ data-hook="new-workflow-btn",
+ type="button",
+ ) New Workflow Using Model
+
+ div.col-md-2
+
+ button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook="edit-model-annotation-btn") Edit Notes
+
+ div.col-md-1: button.btn.btn-outline-secondary.box-shadow(data-hook="project-model-remove")
+
+ div.mx-5.mt-4.collapse(data-hook="collapse-annotation-container"+this.model.name.replace(/ /g,""))
+
+ div.col-md-1.inline.align-top
+
+ div.row
+
+ div: h5="Notes: "
+
+ div: button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#annotation-text"+this.model.name.replace(/ /g,"") data-hook="collapse-annotation-text") -
+
+ div.collapse.show.col-md-11.inline(id="annotation-text"+this.model.name.replace(/ /g,""))
+
+ div: textarea(id="annotation"+this.model.name.replace(/ /g,"") data-hook="annotation" rows="7" style="width: 100%;")=this.model.annotation
+
+ hr
\ No newline at end of file
diff --git a/client/templates/includes/editModelsView.pug b/client/templates/includes/editModelsView.pug
new file mode 100644
index 0000000000..c96de731c0
--- /dev/null
+++ b/client/templates/includes/editModelsView.pug
@@ -0,0 +1,9 @@
+div#edit-project-models
+
+ div
+
+ h3.inline Models
+
+ div.mx-1.row.head
+
+ div.mt-3(id="project-models-list" data-hook="project-models-list")
\ No newline at end of file
diff --git a/client/templates/includes/editProject.pug b/client/templates/includes/editProject.pug
new file mode 100644
index 0000000000..de5a7934bc
--- /dev/null
+++ b/client/templates/includes/editProject.pug
@@ -0,0 +1,7 @@
+tr
+
+ td: button.btn.btn-outline-secondary.box-shadow.name(id="open-project-btn" data-hook="open-project-btn")=this.projectName
+
+ td: div=this.location
+
+ td: button.btn.btn-outline-secondary.box-shadow(id="remove-project-btn" data-hook="remove-project-btn")
\ No newline at end of file
diff --git a/client/templates/includes/editWorkflowGroupView.pug b/client/templates/includes/editWorkflowGroupView.pug
new file mode 100644
index 0000000000..a968850cca
--- /dev/null
+++ b/client/templates/includes/editWorkflowGroupView.pug
@@ -0,0 +1,20 @@
+div
+
+ div.ml-1.row.verticle-space(style="display: none;")
+
+ div.col-md-11
+
+ h4.inline=this.model.name
+
+ button.btn.btn-outline-collapse(data-hook="project-workflow-group-view") +
+
+ div.col-md-1: button.btn.btn-outline-secondary.box-shadow(data-hook="project-workflow-group-remove")
+
+ div
+
+ if(this.model.name === "WorkflowGroup1")
+ div.verticle-space(data-hook="project-workflows-container")
+ else
+ div.verticle-space(data-hook="project-workflows-container" style="display: none;")
+
+ hr(style="display: none;")
\ No newline at end of file
diff --git a/client/templates/includes/editWorkflowGroupsView.pug b/client/templates/includes/editWorkflowGroupsView.pug
new file mode 100644
index 0000000000..b77400e518
--- /dev/null
+++ b/client/templates/includes/editWorkflowGroupsView.pug
@@ -0,0 +1,9 @@
+div#edit-project-workflow-groups
+
+ div
+
+ h3.inline Workflows
+
+ div.mx-1.row
+
+ div(id="project-workflow-groups-list" data-hook="project-workflow-groups-list")
\ No newline at end of file
diff --git a/client/templates/includes/editWorkflowView.pug b/client/templates/includes/editWorkflowView.pug
new file mode 100644
index 0000000000..7bc36e88d2
--- /dev/null
+++ b/client/templates/includes/editWorkflowView.pug
@@ -0,0 +1,35 @@
+div
+
+ div.ml-1.row
+
+ div.col-md-5: button.btn.btn-outline-secondary.box-shadow.text-break(data-hook="project-workflow-open" style="width: 100%")=this.model.name
+
+ div.col-md-4
+
+ div(data-hook="project-workflow-type")="Type: "+this.model.type
+
+ div(data-hook="project-workflow-status")="Status: "+this.model.status
+
+ div.col-md-2
+
+ div(data-hook="annotation-container")
+
+ button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook="edit-workflow-annotation-btn") Edit Notes
+
+ div.col-md-1: button.btn.btn-outline-secondary.box-shadow(data-hook="project-workflow-remove")
+
+ div.mx-5.mt-2.collapse(data-hook="collapse-annotation-container"+this.model.name.replace(/ /g,""))
+
+ div.col-md-1.inline.align-top
+
+ div.row
+
+ div: h5="Notes: "
+
+ div: button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#annotation-text"+this.model.name.replace(/ /g,"") data-hook="collapse-annotation-text") -
+
+ div.collapse.show.col-md-11.inline(id="annotation-text"+this.model.name.replace(/ /g,""))
+
+ div: textarea(id="annotation"+this.model.name.replace(/ /g,"") data-hook="annotation" rows="7" style="width: 100%;")=this.model.annotation
+
+ hr
\ No newline at end of file
diff --git a/client/templates/includes/editWorkflowsView.pug b/client/templates/includes/editWorkflowsView.pug
new file mode 100644
index 0000000000..a7cd96aa58
--- /dev/null
+++ b/client/templates/includes/editWorkflowsView.pug
@@ -0,0 +1,23 @@
+div#edit-project-workflows
+
+ div.mx-1.row.head
+
+ div.mt-3(id="project-workflows-list" data-hook="project-workflows-list")
+
+ div
+
+ button.btn.btn-outline-primary.dropdown-toggle.box-shadow(
+ id="add-workflow-btn",
+ data-hook="add-workflow-btn",
+ data-toggle="dropdown",
+ aria-haspopup="true",
+ aria-expanded="false",
+ type="button"
+ ) Add Workflow
+
+ ul.dropdown-menu(aria-labelledby="add-workflow-btn")
+ li.dropdown-item(id="project-workflow-group-new-workflow" data-hook="project-workflow-group-new-workflow") New Workflow
+ li.dropdown-divider
+ li.dropdown-item(id="project-workflow-group-add-workflow" data-hook="project-workflow-group-add-workflow") Existing Workflow
+
+
\ No newline at end of file
diff --git a/client/templates/includes/fileBrowserView.pug b/client/templates/includes/fileBrowserView.pug
new file mode 100644
index 0000000000..a0dbad0555
--- /dev/null
+++ b/client/templates/includes/fileBrowserView.pug
@@ -0,0 +1,43 @@
+div#browse-files.card.card-body
+
+ div
+
+ h3.inline Browse Files
+ div.inline
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-browse-files", id="collapse-browse-files-btn" data-hook="collapse-browse-files") +
+
+ div.collapse(id="collapse-browse-files")
+
+ div.alert-warning(class="collapse", id="extension-warning" data-hook="extension-warning") You should avoid changing the file extension unless you know what you are doing!
+
+ div.alert-warning(class="collapse", id="rename-warning" data-hook="rename-warning") MESSAGE
+
+ div.alert-danger(id="renameSpecialCharError" style="display: none;") Names can only include the following characters: (0-9), (a-z), (A-Z) and (., -, _, (, or ))
+
+ div#models-jstree-view
+
+ div
+
+ button.btn.btn-primary.inline.box-shadow(
+ id="project-browse-files-add-btn"
+ data-hook="new-file-directory",
+ data-toggle="dropdown",
+ aria-haspopup="true",
+ aria-expanded="false",
+ type="button"
+ )
+
+
+ ul.dropdown-menu(aria-labelledby="project-browse-files-add-btn")
+ li.dropdown-item(id="new-directory" data-hook="new-directory") Create Directory
+ li.dropdown-item(id="browser-new-workflow-group" data-hook="browser-new-workflow-group") Create Workflow Group
+ li.dropdown-item(id="browser-new-model" data-hook="browser-new-model") Create Model
+ li.dropdown-divider
+ li.dropdown-item(id="browser-existing-model" data-hook="browser-existing-model") Add Existing Model
+ li.dropdown-divider
+ li.dropdown-item(id="upload-file-btn" data-hook="upload-file-btn", data-type="model") Upload StochSS Model
+ li.dropdown-item(id="upload-file-btn" data-hook="upload-file-btn", data-type="sbml") Upload SBML Model
+ li.dropdown-item(id="upload-file-btn" data-hook="upload-file-btn", data-type="file") Upload File
+
+ button.btn.btn-primary.box-shadow(id="options-for-node" data-hook="options-for-node" disabled) Actions
+
+ button.btn.btn-primary.inline.box-shadow(id="refresh-jstree" data-hook="refresh-jstree") Refresh
\ No newline at end of file
diff --git a/client/templates/includes/gillespyResults.pug b/client/templates/includes/gillespyResults.pug
index 4de69b6b4f..18798bfb5c 100644
--- a/client/templates/includes/gillespyResults.pug
+++ b/client/templates/includes/gillespyResults.pug
@@ -3,11 +3,11 @@ div#workflow-results.card.card-body
div
h3.inline Results
- button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-results", data-hook="collapse", disabled) +
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-results", id="collapse" data-hook="collapse", disabled) +
div.collapse(id="collapse-results", data-hook="workflow-results")
- div.collapse(data-hook="edit-plot-args")
+ div.collapse(id="edit-plot-args" data-hook="edit-plot-args")
table.table
thead
@@ -18,21 +18,23 @@ div#workflow-results.card.card-body
tbody
tr
- td: div(data-hook="title")
- td: div(data-hook="xaxis")
- td: div(data-hook="yaxis")
+ td: div(id="title" data-hook="title")
+ td: div(id="xaxis" data-hook="xaxis")
+ td: div(id="yaxis" data-hook="yaxis")
div.card.card-body
div
h5.inline Plot Trajectories
- button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-trajectories", data-hook="collapse-trajectories") -
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-trajectories", id="collapse-trajectories-btn" data-hook="collapse-trajectories") -
div.collapse(class="show", id="collapse-trajectories")
- div(data-hook="trajectories")
+ div(id="trajectories" data-hook="trajectories")
+ div.spinner-border.workflow-plot(id="trajectories" data-hook="plot-spinner")
button.btn.btn-primary.box-shadow(id="trajectories" data-hook="plot") Edit Plot
+ button.btn.btn-primary.box-shadow(id="trajectories" data-hook="save-plot" disabled) Save Plot to Project Viewer
button.btn.btn-primary.box-shadow(id="trajectories" data-hook="download-png-custom" disabled) Download PNG
button.btn.btn-primary.box-shadow(id="trajectories" data-hook="download-json" disabled) Download JSON
- button.btn.btn-primary.box-shadow(data-hook="download-results-csv") Download Results as .csv
+ button.btn.btn-primary.box-shadow(id="download-results-csv" data-hook="download-results-csv") Download Results as .csv
\ No newline at end of file
diff --git a/client/templates/includes/gillespyResultsEnsemble.pug b/client/templates/includes/gillespyResultsEnsemble.pug
index 870c2c59e1..0ef1e9fe04 100644
--- a/client/templates/includes/gillespyResultsEnsemble.pug
+++ b/client/templates/includes/gillespyResultsEnsemble.pug
@@ -3,11 +3,11 @@ div#workflow-results-ensemble.card.card-body
div
h3.inline Results
- button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-results", data-hook="collapse", disabled) +
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-results", id="collapse" data-hook="collapse", disabled) +
div.collapse(id="collapse-results", data-hook="workflow-results")
- div.collapse(data-hook="edit-plot-args")
+ div.collapse(id="edit-plot-args" data-hook="edit-plot-args")
table.table
thead
@@ -18,20 +18,22 @@ div#workflow-results-ensemble.card.card-body
tbody
tr
- td: div(data-hook="title")
- td: div(data-hook="xaxis")
- td: div(data-hook="yaxis")
+ td: div(id="title" data-hook="title")
+ td: div(id="xaxis" data-hook="xaxis")
+ td: div(id="yaxis" data-hook="yaxis")
div.card.card-body
div
h5.inline Plot Standard Deviation Range
- button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-stddevrange", data-hook="collapse-stddevrange") -
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-stddevrange", id="collapse-stddevrange-btn" data-hook="collapse-stddevrange") -
div.collapse(class="show", id="collapse-stddevrange")
- div(data-hook="stddevran")
+ div(id="stddevran" data-hook="stddevran")
+ div.spinner-border.workflow-plot(id="stddevran" data-hook="plot-spinner")
button.btn.btn-primary.box-shadow(id="stddevran" data-hook="plot") Edit Plot
+ button.btn.btn-primary.box-shadow(id="stddevran" data-hook="save-plot") Save Plot to Project Viewer
button.btn.btn-primary.box-shadow(id="stddevran" data-hook="download-png-custom" disabled) Download PNG
button.btn.btn-primary.box-shadow(id="stddevran" data-hook="download-json" disabled) Download JSON
@@ -39,13 +41,15 @@ div#workflow-results-ensemble.card.card-body
div
h5.inline Plot Trajectories
- button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-trajectories", data-hook="collapse-trajectories") +
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-trajectories", id="collapse-trajectories-btn" data-hook="collapse-trajectories") +
div.collapse(id="collapse-trajectories")
- div(data-hook="trajectories")
- button.btn.btn-primary.box-shadow(id="trajectories" data-hook="plot") Plot
- button.btn.btn-primary.box-shadow(data-hook="plot-multiple", disabled) Multiple Plots
+ div(id="trajectories" data-hook="trajectories")
+ div.spinner-border.workflow-plot(id="trajectories" data-hook="plot-spinner")
+ button.btn.btn-primary.box-shadow(id="trajectories" data-hook="plot") Edit Plot
+ button.btn.btn-primary.box-shadow(id="trajectories" data-hook="save-plot" disabled) Save Plot to Project Viewer
+ button.btn.btn-primary.box-shadow(id="plot-multiple" data-hook="plot-multiple", disabled) Multiple Plots
button.btn.btn-primary.box-shadow(id="trajectories" data-hook="download-png-custom" disabled) Download PNG
button.btn.btn-primary.box-shadow(id="trajectories" data-hook="download-json" disabled) Download JSON
@@ -53,12 +57,14 @@ div#workflow-results-ensemble.card.card-body
div
h5.inline Plot Standard Deviation
- button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-stddev", data-hook="collapse-stddev") +
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-stddev", id="collapse-stddev-btn" data-hook="collapse-stddev") +
div.collapse(id="collapse-stddev")
- div(data-hook="stddev")
- button.btn.btn-primary.box-shadow(id="stddev" data-hook="plot") Plot
+ div(id="stddev" data-hook="stddev")
+ div.spinner-border.workflow-plot(id="stddev" data-hook="plot-spinner")
+ button.btn.btn-primary.box-shadow(id="stddev" data-hook="plot") Edit Plot
+ button.btn.btn-primary.box-shadow(id="stddev" data-hook="save-plot" disabled) Save Plot to Project Viewer
button.btn.btn-primary.box-shadow(id="stddev" data-hook="download-png-custom" disabled) Download PNG
button.btn.btn-primary.box-shadow(id="stddev" data-hook="download-json" disabled) Download JSON
@@ -66,13 +72,15 @@ div#workflow-results-ensemble.card.card-body
div
h5.inline Plot Trajectory Mean
- button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-trajmean", data-hook="collapse-trajmean") +
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-trajmean", id="collapse-trajmean-btn" data-hook="collapse-trajmean") +
div.collapse(id="collapse-trajmean")
- div(data-hook="avg")
- button.btn.btn-primary.box-shadow(id="avg" data-hook="plot") Plot
+ div(id="avg" data-hook="avg")
+ div.spinner-border.workflow-plot(id="avg" data-hook="plot-spinner")
+ button.btn.btn-primary.box-shadow(id="avg" data-hook="plot") Edit Plot
+ button.btn.btn-primary.box-shadow(id="avg" data-hook="save-plot" disabled) Save Plot to Project Viewer
button.btn.btn-primary.box-shadow(id="avg" data-hook="download-png-custom" disabled) Download PNG
button.btn.btn-primary.box-shadow(id="avg" data-hook="download-json" disabled) Download JSON
- button.btn.btn-primary.box-shadow(data-hook="download-results-csv") Download Results as .csv
\ No newline at end of file
+ button.btn.btn-primary.box-shadow(id="download-results-csv" data-hook="download-results-csv") Download Results as .csv
\ No newline at end of file
diff --git a/client/templates/includes/metaData.pug b/client/templates/includes/metaData.pug
new file mode 100644
index 0000000000..ce6f62be4f
--- /dev/null
+++ b/client/templates/includes/metaData.pug
@@ -0,0 +1,57 @@
+div#project-meta-data.card.card-body
+
+ h3 Metadata
+
+ div(id="file-select-view" data-hook="file-select-view")
+
+ div
+
+ span(for="description-input-view") Description:
+
+ textarea(id="description-input-view" data-hook="description-input-view" rows="5" style="width: 100%;")
+
+ table.table
+
+ thead
+
+ tr
+
+ th(scope="col") Given Name
+
+ th(scope="col") Family Name
+
+ th(scope="col") E-Mail
+
+ th(scope="col") Organization
+
+ th(scpoe="col") Remove
+
+ tbody(id="list-of-creators" data-hook="list-of-creators")
+
+ hr
+
+ p Add a new creator or update an existing creators information by selecting the appropriate 'creator' option and entering their information below.
+
+ div(id="creator-select-view" data-hook="creator-select-view")
+
+ div.inline
+
+ div.inline(id="given-name-input-view" data-hook="given-name-input-view")
+
+ div.inline(id="family-name-input-view" data-hook="family-name-input-view")
+
+ div.inline(id="email-input-view" data-hook="email-input-view")
+
+ div.inline(id="organization-input-view" data-hook="organization-input-view")
+
+ div
+
+ button.btn.btn-outline-secondary.box-shadow(id="add-creator-btn" data-hook="add-creator-btn" disabled) Add
+
+ hr
+
+ div.inline
+
+ button.btn.btn-primary.box-shadow(id="save-meta-data-button" data-hook="save-meta-data-button") Save
+
+ button.btn.btn-primary.box-shadow(id="submit-meta-data-button" data-hook="submit-meta-data-button") Submit
\ No newline at end of file
diff --git a/client/templates/includes/modelSettings.pug b/client/templates/includes/modelSettings.pug
index bcae80b64d..5c731e94b1 100644
--- a/client/templates/includes/modelSettings.pug
+++ b/client/templates/includes/modelSettings.pug
@@ -2,7 +2,7 @@ div#preview-settings.card.card-body
div
- h3.inline Preview Settings
+ h3.inline Model Settings
div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.previewSettings)
@@ -20,7 +20,7 @@ div#preview-settings.card.card-body
th(scope="col")
div
- div.inline Time Units
+ div.inline Sample Frequency
div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.timeUnits)
diff --git a/client/templates/includes/modelSettingsViewer.pug b/client/templates/includes/modelSettingsViewer.pug
index d2a8a5ecc4..4e7a260a05 100644
--- a/client/templates/includes/modelSettingsViewer.pug
+++ b/client/templates/includes/modelSettingsViewer.pug
@@ -15,7 +15,7 @@ div#model-settings-viewer.card.card-body
th(scope="col") End Simulation
- th(scope="col") Time Steps
+ th(scope="col") Sample Frequency
th(scope="col") Volume
diff --git a/client/templates/includes/modelStateButtons.pug b/client/templates/includes/modelStateButtons.pug
index 6f418866dd..f3d5c9ebc7 100644
--- a/client/templates/includes/modelStateButtons.pug
+++ b/client/templates/includes/modelStateButtons.pug
@@ -13,7 +13,9 @@ div.mdl-edit-btn
span Saved
button.btn.btn-primary.box-shadow(data-hook="run") Run Preview
+
+ button.btn.btn-primary.box-shadow(data-hook="new-workflow") New Workflow Using Model
- button.btn.btn-primary.box-shadow(data-hook="start-workflow") New Workflow
+ button.btn.btn-primary.box-shadow(data-hook="return-to-project-btn" style="display: none;") Return to Project
diff --git a/client/templates/includes/modelViewer.pug b/client/templates/includes/modelViewer.pug
index b6186121da..a40e0504e7 100644
--- a/client/templates/includes/modelViewer.pug
+++ b/client/templates/includes/modelViewer.pug
@@ -1,13 +1,11 @@
-div#model-viewer.card.card-body
+div.card.card-body
- div
+ div(id="model-viewer-header")
- h3.inline Model
- button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-model", data-hook="collapse-model" disabled) +
+ h3.inline="Review Model: "+this.model.name
+ button.btn.btn-outline-collapse(id=this.model.name, data-toggle="collapse", data-target="#collapse-model"+this.model.name.replace(/ /g, ''), data-hook="collapse-model") +
- div.collapse(id="collapse-model")
-
- div: h5=this.model.name
+ div.collapse(id="collapse-model"+this.model.name.replace(/ /g, ''))
div(data-hook="species-viewer-container")
diff --git a/client/templates/includes/modelsViewer.pug b/client/templates/includes/modelsViewer.pug
new file mode 100644
index 0000000000..3946f4979b
--- /dev/null
+++ b/client/templates/includes/modelsViewer.pug
@@ -0,0 +1,10 @@
+div#models-viewer.card.card-body
+
+ div
+
+ h3.inline Models
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-models", id="collapse-models-btn" data-hook="collapse-models") +
+
+ div.collapse(id="collapse-models")
+
+ div(id="model-container" data-hook="model-container")
\ No newline at end of file
diff --git a/client/templates/includes/parameterSweepResults.pug b/client/templates/includes/parameterSweepResults.pug
index 5ea02e5901..880ab203d7 100644
--- a/client/templates/includes/parameterSweepResults.pug
+++ b/client/templates/includes/parameterSweepResults.pug
@@ -3,11 +3,11 @@ div#workflow-results.card.card-body
div
h3.inline Results
- button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-results", data-hook="collapse", disabled) +
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-results", id="collapse" data-hook="collapse", disabled) +
div.collapse(id="collapse-results", data-hook="workflow-results")
- div.collapse(data-hook="edit-plot-args")
+ div.collapse(id="edit-plot-args" data-hook="edit-plot-args")
table.table
thead
@@ -18,9 +18,9 @@ div#workflow-results.card.card-body
tbody
tr
- td: div(data-hook="title")
- td: div(data-hook="xaxis")
- td: div(data-hook="yaxis")
+ td: div(id="title" data-hook="title")
+ td: div(id="xaxis" data-hook="xaxis")
+ td: div(id="yaxis" data-hook="yaxis")
div
@@ -40,7 +40,7 @@ div#workflow-results.card.card-body
div.inline(id="feature-extractor" data-hook="feature-extraction-list")
- div.horizontal-space.collapse(class="show" data-hook="ensemble-aggragator-container")
+ div.horizontal-space.collapse(class="show" id="ensemble-aggragator-container" data-hook="ensemble-aggragator-container")
span.inline(for="ensemble-aggragator") Ensemble Aggragator:
@@ -52,13 +52,15 @@ div#workflow-results.card.card-body
div
h5.inline Parameter Sweep
- button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-psweep", data-hook="collapse-psweep") -
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-psweep", id="collapse-psweep-btn" data-hook="collapse-psweep") -
div.collapse(class="show", id="collapse-psweep")
- div(data-hook="psweep")
+ div(id="psweep" data-hook="psweep")
+ div.spinner-border.workflow-plot(id="psweep" data-hook="plot-spinner")
button.btn.btn-primary.box-shadow(id="psweep" data-hook="plot") Edit Plot
+ button.btn.btn-primary.box-shadow(id="psweep" data-hook="save-plot" disabled) Save Plot to Project Viewer
button.btn.btn-primary.box-shadow(id="psweep" data-hook="download-png-custom" disabled) Download PNG
button.btn.btn-primary.box-shadow(id="psweep" data-hook="download-json" disabled) Download JSON
- button.btn.btn-primary.box-shadow(data-hook="download-results-csv") Download Results as .csv
\ No newline at end of file
+ button.btn.btn-primary.box-shadow(id="download-results-csv" data-hook="download-results-csv") Download Results as .csv
\ No newline at end of file
diff --git a/client/templates/includes/plotsView.pug b/client/templates/includes/plotsView.pug
new file mode 100644
index 0000000000..0d72e785bc
--- /dev/null
+++ b/client/templates/includes/plotsView.pug
@@ -0,0 +1,10 @@
+div.card.card-body
+
+ div
+
+ h5.inline=this.heading
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse"+this.model.key+this.model.stamp data-hook="collapse-plot")
+
+ div.collapse(class="show", id="collapse"+this.model.key+this.model.stamp)
+
+ div(data-hook=this.model.key+this.model.stamp)
\ No newline at end of file
diff --git a/client/templates/includes/projectViewer.pug b/client/templates/includes/projectViewer.pug
new file mode 100644
index 0000000000..4ae225f576
--- /dev/null
+++ b/client/templates/includes/projectViewer.pug
@@ -0,0 +1,12 @@
+div#project-viewer.card.card-body
+
+ div
+
+ h3.inline Project Viewer
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-project", data-hook="collapse-project") +
+
+ div.collapse(id="collapse-project")
+
+ div(id="models-collection-container" data-hook="models-collection-container")
+
+ div(id="workflow-groups-collection-container" data-hook="workflow-groups-collection-container")
\ No newline at end of file
diff --git a/client/templates/includes/reactionsEditor.pug b/client/templates/includes/reactionsEditor.pug
index e52fe3b257..6c2c9c0eff 100644
--- a/client/templates/includes/reactionsEditor.pug
+++ b/client/templates/includes/reactionsEditor.pug
@@ -16,7 +16,7 @@ div#reactions-editor.card.card-body
p
| For a species that is NOT consumed in the reaction but is part of a massaction reaction, add it as both a reactant and a product. Mass-action reactions
- | must also have a rate term added. Note that the inputrate represents the mass-action constant rate independent of volume.
+ | must also have a rate term added. Note that the input rate represents the mass-action constant rate independent of volume.
div.row
div.col-md-7.container-part: table.table
diff --git a/client/templates/includes/ruleEditor.pug b/client/templates/includes/ruleEditor.pug
index 268f9af8a6..c864f84192 100644
--- a/client/templates/includes/ruleEditor.pug
+++ b/client/templates/includes/ruleEditor.pug
@@ -34,7 +34,7 @@ div#rules-editor.card.card-body
th(scope="col")
div
- div.inline Expression
+ div.inline Formula
div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.expression)
diff --git a/client/templates/includes/rulesViewer.pug b/client/templates/includes/rulesViewer.pug
index a99ec5a373..9624792313 100644
--- a/client/templates/includes/rulesViewer.pug
+++ b/client/templates/includes/rulesViewer.pug
@@ -13,6 +13,6 @@ div#rules-viewer.card.card-body
th.col-md-3-view(scope="col") Name
th.col-md-3-view(scope="col") Type
th.col-md-3-view(scope="col") Variable
- th.col-md-3-view(scope="col") Expression
+ th.col-md-3-view(scope="col") Formula
tbody(data-hook="rules-list")
\ No newline at end of file
diff --git a/client/templates/includes/workflowGroupViewer.pug b/client/templates/includes/workflowGroupViewer.pug
new file mode 100644
index 0000000000..cd0cdc6a0b
--- /dev/null
+++ b/client/templates/includes/workflowGroupViewer.pug
@@ -0,0 +1,10 @@
+div.card.card-body
+
+ div
+
+ h3.inline=this.model.name
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-workflow-group"+this.model.name data-hook="collapse-workflow-group") +
+
+ div.collapse(id="collapse-workflow-group"+this.model.name)
+
+ div(data-hook="workflows-viewer-container")
\ No newline at end of file
diff --git a/client/templates/includes/workflowGroupsViewer.pug b/client/templates/includes/workflowGroupsViewer.pug
new file mode 100644
index 0000000000..cd3f50d613
--- /dev/null
+++ b/client/templates/includes/workflowGroupsViewer.pug
@@ -0,0 +1,10 @@
+div#workflow-groups-viewer.card.card-body
+
+ div
+
+ h3.inline Workflow Groups
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-workflow-groups", id="collapse-workflow-groups-btn" data-hook="collapse-workflow-groups") +
+
+ div.collapse(id="collapse-workflow-groups")
+
+ div(id="workflow-group-container" data-hook="workflow-group-container")
\ No newline at end of file
diff --git a/client/templates/includes/workflowStatus.pug b/client/templates/includes/workflowStatus.pug
index 6907219e0b..4e0de7bf3b 100644
--- a/client/templates/includes/workflowStatus.pug
+++ b/client/templates/includes/workflowStatus.pug
@@ -18,8 +18,11 @@ div#workflow-status.card.card-body
tbody
tr
- td=this.startTime
- td=this.status
+ td: div=this.startTime
+ td
+ div
+ div.inline=this.status
+ div.inline.spinner-border.status(data-hook="running-spinner")
div(style="display: none;")
diff --git a/client/templates/includes/workflowViewer.pug b/client/templates/includes/workflowViewer.pug
new file mode 100644
index 0000000000..ca65d5d864
--- /dev/null
+++ b/client/templates/includes/workflowViewer.pug
@@ -0,0 +1,10 @@
+div.card.card-body
+
+ div
+
+ h3.inline=this.model.name
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-workflow"+this.model.name data-hook="collapse-workflow") +
+
+ div.collapse(id="collapse-workflow"+this.model.name)
+
+ div(data-hook="workflow-plots")
\ No newline at end of file
diff --git a/client/templates/includes/workflowsViewer.pug b/client/templates/includes/workflowsViewer.pug
new file mode 100644
index 0000000000..336994a46b
--- /dev/null
+++ b/client/templates/includes/workflowsViewer.pug
@@ -0,0 +1,10 @@
+div.card.card-body
+
+ div
+
+ h3.inline Workflows
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-workflows"+this.collection.parent.name data-hook="collapse-workflows") +
+
+ div.collapse(id="collapse-workflows"+this.collection.parent.name)
+
+ div(data-hook="workflow-container")
\ No newline at end of file
diff --git a/client/templates/pages/fileBrowser.pug b/client/templates/pages/fileBrowser.pug
index 9451fc80fd..500f7a3465 100644
--- a/client/templates/pages/fileBrowser.pug
+++ b/client/templates/pages/fileBrowser.pug
@@ -3,15 +3,18 @@ section.page
div
h2.inline File Browser
- button.big-tip.btn.information-btn.help(data-hook="file-browser-help")
+ button.big-tip.btn.information-btn.help(id="file-browser-help" data-hook="file-browser-help")
- div.alert-warning(class="collapse", data-hook="extension-warning") You should avoid changing the file extension unless you know what you are doing!
+ div.alert-warning(class="collapse", id="extension-warning" data-hook="extension-warning") You should avoid changing the file extension unless you know what you are doing!
- div.alert-warning(class="collapse", data-hook="rename-warning") MESSAGE
+ div.alert-warning(class="collapse", id="rename-warning" data-hook="rename-warning") MESSAGE
+
+ div.alert-danger(id="renameSpecialCharError" style="display: none;") Names can only include the following characters: (0-9), (a-z), (A-Z) and (., -, _, (, or ))
div#models-jstree
button.btn.btn-primary.inline.box-shadow(
+ id="new-file-directory",
data-hook="new-file-directory",
data-toggle="dropdown",
aria-haspopup="true",
@@ -19,14 +22,15 @@ section.page
type="button"
)
+
- ul.dropdown-menu(aria-labelledby="addReactionBtn")
- li.dropdown-item(data-hook="new-directory") Create Directory
- li.dropdown-item(data-hook="new-model") Create Model
+ ul.dropdown-menu(aria-labelledby="new-file-directory")
+ li.dropdown-item(id="new-directory" data-hook="new-directory") Create Directory
+ li.dropdown-item(id="new-project" data-hook="new-project") Create Project
+ li.dropdown-item(id="new-model" data-hook="new-model") Create Model
li.dropdown-divider
- li.dropdown-item(data-hook="upload-file-btn", data-type="model") Upload StochSS Model
- li.dropdown-item(data-hook="upload-file-btn", data-type="sbml") Upload SBML Model
- li.dropdown-item(data-hook="upload-file-btn", data-type="file") Upload File
+ li.dropdown-item(id="upload-file-btn" data-hook="upload-file-btn", data-type="model") Upload StochSS Model
+ li.dropdown-item(id="upload-file-btn" data-hook="upload-file-btn", data-type="sbml") Upload SBML Model
+ li.dropdown-item(id="upload-file-btn" data-hook="upload-file-btn", data-type="file") Upload File
- button.btn.btn-primary.box-shadow(data-hook="options-for-node" disabled) Actions
+ button.btn.btn-primary.box-shadow(id="options-for-node" data-hook="options-for-node" disabled) Actions
- button.btn.btn-primary.inline.box-shadow(data-hook="refresh-jstree") Refresh
\ No newline at end of file
+ button.btn.btn-primary.inline.box-shadow(id="refresh-jstree" data-hook="refresh-jstree") Refresh
\ No newline at end of file
diff --git a/client/templates/pages/home.pug b/client/templates/pages/home.pug
index 6a1c83228d..36f584d211 100644
--- a/client/templates/pages/home.pug
+++ b/client/templates/pages/home.pug
@@ -2,7 +2,7 @@ html
head
meta(charset="utf-8")
- title StochSS: Stochastic Simlation Service
+ title StochSS: Stochastic Simulation Service
meta(name="viewport", content="width=device-width, initial-scale=1.0")
meta(name="description", content="")
meta(name="author", content="")
@@ -14,10 +14,10 @@ html
img(src="/hub/static/stochss-logo.png")
div.centered
- h1.display-5 Welcome to the Stochastic Simulation Service!
+ h1.display-5 Welcome to StochSS Live!
p.home-p
- | StochSS 2.0 is an accessible platform for modeling biochemical systems.
+ | An accessible platform for modeling mathematical, biological, and biochemical systems.
div.row.home-highlights
div.col-md-2
@@ -55,4 +55,4 @@ html
div.collapse.show(data-hook="registration-form" id="registration-form")
- iframe(src="https://docs.google.com/forms/d/12tAH4f8CJ-3F-lK44Q9uQHFio_mGoK0oY829q5lD7i4/viewform?embedded=true" width="100%" height="800" frameborder="0")
\ No newline at end of file
+ iframe(src="https://docs.google.com/forms/d/12tAH4f8CJ-3F-lK44Q9uQHFio_mGoK0oY829q5lD7i4/viewform?embedded=true" width="100%" height="800" frameborder="0")
diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug
index eb8e586226..b3a540bd22 100644
--- a/client/templates/pages/modelEditor.pug
+++ b/client/templates/pages/modelEditor.pug
@@ -5,7 +5,19 @@ section.page
button.big-tip.btn.information-btn.help(data-hook="edit-model-help")
- div: h5=this.model.name
+ div(data-hook="project-breadcrumb-links" style="display: none")
+ h5
+ nav(aria-label="breadcrumb")
+ ol.breadcrumb
+ li.breadcrumb-item
+ a.active-link(data-hook="project-breadcrumb-link")=this.projectName
+ li.breadcrumb-item.active(aria-current="page")=this.model.name
+
+ div(data-hook="model-name-header")
+ h5
+ nav(aria-label="breadcrumb")
+ ol.breadcrumb
+ li.breadcrumb-item.active(aria-current="page")=this.model.name
div(data-hook="mesh-editor-container")
diff --git a/client/templates/pages/projectBrowser.pug b/client/templates/pages/projectBrowser.pug
new file mode 100644
index 0000000000..fda8ef1435
--- /dev/null
+++ b/client/templates/pages/projectBrowser.pug
@@ -0,0 +1,9 @@
+section.page.col-md-10
+
+ h2 Project Browser
+
+ table.table
+
+ tbody(id="projects-view-container" data-hook="projects-view-container")
+
+ button.btn.btn-outline-primary.box-shadow(id="new-project-btn" data-hook="new-project-btn") New
\ No newline at end of file
diff --git a/client/templates/pages/projectManager.pug b/client/templates/pages/projectManager.pug
new file mode 100644
index 0000000000..fa945e6aef
--- /dev/null
+++ b/client/templates/pages/projectManager.pug
@@ -0,0 +1,99 @@
+section.page
+
+ div.verticle-space
+
+ h2.inline(id="page-title" data-hook="page-title")= "Project: "+this.projectName
+
+ div.col-md-12.col-lg-10.no-gutters-padding
+
+ if !this.annotation
+ div.verticle-space-2
+ button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook="edit-annotation-btn") Edit Notes
+ else
+ div
+ button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook="edit-annotation-btn") Edit Notes
+
+ div.mx-3.mt-2.collapse.verticle-space-2(data-hook="collapse-annotation-container")
+
+ div.col-md-1.inline.align-top
+
+ div.row
+
+ div: h5="Notes: "
+
+ div: button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#annotation-text" data-hook="collapse-annotation-text") -
+
+ div.collapse.show.col-md-11.inline(id="annotation-text")
+
+ div: textarea(id="annotation" data-hook="annotation-text-container" rows="7" style="width: 100%;")
+
+ div(id="edit-models-container" data-hook="edit-models-container")
+
+ div.verticle-space-3
+
+ button.btn.btn-outline-primary.inline.dropdown-toggle.box-shadow(
+ id="project-manager-add-model-btn",
+ data-hook="add-element-btn",
+ data-toggle="dropdown",
+ aria-haspopup="true",
+ aria-expanded="false",
+ type="button"
+ ) Add Model
+
+ ul.dropdown-menu(aria-labelledby="project-manager-add-model-btn")
+ li.dropdown-item(id="new-model" data-hook="new-model") New Model
+ li.dropdown-divider
+ li.dropdown-item(id="existing-model" data-hook="existing-model") Existing Model
+ li.dropdown-divider
+ li.dropdown-item(id="upload-file-btn" data-hook="upload-file-btn", data-type="model") Upload StochSS Model (.mdl)
+
+ div.verticle-space(id="edit-workflow-groups-container" data-hook="edit-workflow-groups-container")
+
+ div.verticle-space-3(style="display: none;")
+
+ button.btn.btn-outline-primary.inline.box-shadow(id="new-workflow-group-btn" data-hook="new-workflow-group") Add New Workflow Group
+
+ div(style="display: none;")
+
+ div
+
+ h3.inline Most Recent Plot
+
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#project-most-recent-plot-container", data-hook="collapse-most-recent-plot-btn") -
+
+ div.collapse.show(id="project-most-recent-plot-container")
+
+ div(id="project-most-recent-plot" data-hook="project-most-recent-plot")
+
+ div(id="project-viewer" data-hook="project-viewer" style="display: none;")
+
+ div.card.card-body
+
+ div
+
+ h3.inline Advanced
+ button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#project-manager-advanced", data-hook="project-manager-advanced-btn") +
+
+ div.collapse(id="project-manager-advanced" data-hook="project-manager-advanced")
+
+ div(id="project-manager-file-browser" data-hook="file-browser")
+
+ div
+
+ button.btn.btn-primary.inline.dropdown-toggle.box-shadow(
+ id="download-project-btn",
+ data-hook="download-project-btn",
+ data-toggle="dropdown",
+ aria-haspopup="true",
+ aria-expanded="false",
+ type="button"
+ ) Download
+
+ ul.dropdown-menu(aria-labelledby="download-project-btn")
+ li.dropdown-item(id="export-project-as-zip" data-hook="export-project-as-zip") as .zip
+ li.dropdown-item(id="export-project-as-combine" data-hook="export-project-as-combine") as COMBINE
+
+ button.btn.btn-primary.inline.box-shadow(id="empty-project-trash" data-hook="empty-project-trash") Empty Trash
+
+ div.collapse(id="project-meta-data-container" data-hook="project-meta-data-container")
+
\ No newline at end of file
diff --git a/client/templates/pages/quickstart.pug b/client/templates/pages/quickstart.pug
index 79c9eaaff1..d4099cfb51 100644
--- a/client/templates/pages/quickstart.pug
+++ b/client/templates/pages/quickstart.pug
@@ -5,30 +5,25 @@ section.page
div.col-md-10
- h2 Quickstart
+ h2 Tutorial
- p Welcome to the Stochastic Simulation Service! In this tutorial we'll take you through the process of creating, simulating, and analyzing a model of a biochemical system.
+ p Welcome to StochSS Live! In this tutorial we'll take you through the process of creating, simulating, and analyzing a model of a biochemical system.
h4 Help and Information
p As we move through the different parts of StochSS, watch for the blue
button by the top of each page, and the smaller blue
i tooltips in superscript throughout each page. Because StochSS supports a wide variety of features, it includes numerous “tooltips” providing helpful information. Click on the large
button at the top of the page for an overview of the page contents. Hovering over the blue
i icons will provide more info on an item.
- h4 Creating a Model
+ h4 Create a Project
- p We start our journey on the
file browser . To start, let's make a new project folder where we can keep files. You can access the root directory in two ways: either right-click on the root folder (named '/'), or click the blue + button below the file browser. To create the project folder, right-click on the root folder and click 'New Directory', or click on the blue + button and select 'Create Directory'. Let’s name the directory Quickstart. Click on the new directory so it’s selected, then click the 'Actions for Quickstart' button at the bottom of the browser.
+ p We start our journey on the
Project Browser . To start, let's make a new project where we can create models and run simulations. Click New and give your project a name. From here you’re taken to the Project Viewer.
- p Actions for a directory include renaming or duplicating the directory, as well as creating, uploading, or downloading files to the selected directory. As you've seen, you can access these options by right-clicking on a directory in the StochSS file browser, or by left-clicking the directory to select it and then clicking the 'Actions for (Name)' button below the browser.
+ h4 Create a Model
- p For now, choose the 'New Model' option, then 'Non-Spatial'.
-
- img.quickstart(style="width: 80%;", src="static/file-browser-new-model-dropdown.png")
-
- h4 Editing a Model
- p From here you’re taken to the model editor. Since you're creating a new model, you'll need to choose the default species "mode" for your model. StochSS supports deterministic ODE-based simulations (concentration) as well as discrete stochastic simulations (population). An exciting feature of StochSS is the ability to run "hybrid" simulations that utilize both deterministic and probabilistic algorithms during a simulation, thanks to the powerful
GillesPy2 library. If you’re unsure of which to choose, go ahead and select “Population.”
+ p Let’s create a new model by pressing the “Add Model” button and selecting “New Model” and give it a name. Since you're creating a new model you'll need to choose the default species "mode" for your model. StochSS supports deterministic ODE-based simulations (concentration) as well as discrete stochastic simulations (population). One exciting feature of StochSS is the ability to run "hybrid" simulations that utilize both deterministic and probabilistic algorithms during a simulation, thanks to the powerful
GillesPy2 library. If you’re unsure of which to choose, go ahead and select “Population.”
img.quickstart(style="width: 60%;", src="static/model-editor-select-default-species-mode.png")
- p Proceeding with the model editor, let’s recreate the Degradation model that’s in the Examples folder. This model contains one species, one parameter, and one reaction to represent protein decay. To start, add a new species called “protein” with an initial condition of 50, and make a parameter called “decayrate” with a value of 0.05. At this point we’re ready to create a reaction to apply the “decayrate” parameter to our “protein” species. Since we are modeling decay we’ll select the A → ∅ reaction type.
+ p Now we are ready to begin defining the model. Our model contains one species, one parameter, and one reaction to represent protein decay. To start, add a new species called “protein” with an initial condition of 50, and make a parameter called “decayrate” with a value of 0.05. At this point we’re ready to create a reaction to apply the “decayrate” parameter to our “protein” species. Since we are modeling decay we’ll select the A → ∅ reaction type.
img.quickstart(style="width: 100%;", src="static/model-editor-reaction-editor.png")
@@ -40,13 +35,13 @@ section.page
h4 Workflows
- p To run a full simulation and explore the results more thoroughly, you’ll need to create a StochSS Workflow. Click New Workflow at the bottom of the page to head to the Workflow Selection page. You can also create a new workflow from the browser window by right-clicking a Model (.mdl file) or selecting it and pressing the Actions for (Name) button. From here you’ll see several different options for exploring your model, but at the moment we’re interested in the Ensemble Simulation workflow.
+ p To run a full simulation and explore the results more fully, we’ll need to create a StochSS Workflow. Click the "Return to Project" button at the bottom of the page. Now click “Add Workflow” and select “New Workflow to head to the Workflow Selection page. From here you’ll see several different options for exploring your model, but at the moment we’re interested in the Ensemble Simulation workflow.
img.quickstart(style="width: 90%;", src="static/workflow-editor-ensemble-simulation.png")
- p From here you’ll choose a simulation algorithm and set configuration for your workflow. By default StochSS will choose a simulation style for you, but for this example let’s go with SSA (Stochastic Simulation Algorithm). In the “Stochastic Settings” section set trajectories to 10. This will create an “ensemble” of 10 different stochastic time series. Click the “Start Workflow” button when you’re ready. Your results should appear momentarily.
+ p At this point you’ll choose a simulation algorithm and set configuration for your workflow. By default StochSS will choose a simulation style for you, but for this example let’s go with SSA (Stochastic Simulation Algorithm). In the “Stochastic Settings” section set trajectories to 10. This will create an “ensemble” of 10 different stochastic time series. Click the “Start Workflow” button when you’re ready. Your results should appear momentarily.
img.quickstart(style="width: 90%;", src="static/workflow-results-std-deviation-plot.png")
- p Once your workflow is complete you can explore various graphs describing the simulation results, download the raw data, and download JSON files describing each graph that you can use with the
Plotly graphing library. You can also come back to your results later by accessing the .wkfl file in your quickstart project folder.
+ p Once your workflow is complete you can explore various graphs describing the simulation results, download the raw data, and download JSON files describing each graph that you can use with the
Plotly graphing library.
diff --git a/client/templates/pages/usersHome.pug b/client/templates/pages/usersHome.pug
new file mode 100644
index 0000000000..249b37f645
--- /dev/null
+++ b/client/templates/pages/usersHome.pug
@@ -0,0 +1,55 @@
+selction.page
+
+ div#home-wrapper.card.card-body.col-md-10
+
+ div.logo(id="stochss-logo" data-hook="stochss-logo")
+
+ img(src="/static/stochss-logo.png")
+
+ div.centered.verticle-space-2
+
+ h1.display-5 Welcome to the Stochastic Simulation Service!
+
+ div.row.verticle-space
+
+ div.col-md-0.col-lg-1.col-xl-2
+
+ div.col-md-6.col-lg-5.col-xl-4.inline.text-right
+ button.btn.btn-primary.box-shadow.user-home-btn(id="new-project-btn" data-hook="new-project-btn")
+ | Create a new project
+
+ div.col-md-6.col-lg-5.col-xl-4.inline.text-right
+ button.btn.btn-primary.box-shadow.user-home-btn(id="browse-projects-btn" data-hook="browse-projects-btn")
+ | Browse your projects
+
+ div.col-md-0.col-lg-1.col-xl-2
+
+ div.row.verticle-space-3(style="display: none;")
+
+ div.col-md-0.col-lg-1.col-xl-2
+
+ div.col-md-6.col-lg-5.col-xl-4.inline
+ button.btn.btn-primary.box-shadow.user-home-btn(id="new-model-btn" data-hook="new-model-btn")
+ | Create a new model
+
+ div.col-md-6.col-lg-5.col-xl-4.inline
+ button.btn.btn-primary.box-shadow.user-home-btn(id="browse-files-btn" data-hook="browse-files-btn")
+ | Browse all your files
+
+ div.col-md-0.col-lg-1.col-xl-2
+
+ div.head
+
+ div.verticle-space-3
+
+ div.centered.verticle-space-2
+ h5 Are you new to StochSS? Do you need some help? Learn more about StochSS with our tutorial.
+
+ div.row
+ div.col-md-2.col-lg-3.col-xl-4
+
+ div.col-md-8.col-lg-6.col-xl-4
+ button.btn.btn-primary.box-shadow.user-home-btn(id="quickstart-btn" data-hook="quickstart-btn")
+ | Click here for a tutorial
+
+ div.col-md-2.col-lg-3.col-xl-4
\ No newline at end of file
diff --git a/client/templates/pages/workflowManager.pug b/client/templates/pages/workflowManager.pug
index 15780ce145..6309d6c279 100644
--- a/client/templates/pages/workflowManager.pug
+++ b/client/templates/pages/workflowManager.pug
@@ -6,10 +6,22 @@ section.page
button.big-tip.btn.information-btn.help(data-hook="edit-workflow-help")
+ div(data-hook="project-breadcrumb-links" style="display: none")
+ h5
+ nav(aria-label="breadcrumb")
+ ol.breadcrumb
+ li.breadcrumb-item
+ a.active-link(data-hook="project-breadcrumb")
+ li.breadcrumb-item.active(aria-current="page" data-hook="workflow-breadcrumb")
+
div(data-hook="workflow-name")
+ div.invalid-feedback.wkfl-name(id="workflowNameSpecialCharError") Names can only include the following characters: (0-9), (a-z), (A-Z) and (., -, _, (, or ))
+
div(data-hook="model-path")
+ div.invalid-feedback.mdl-path(id="modelPathSpecialCharError") Names can only include the following characters: (0-9), (a-z), (A-Z) and (., -, _, (, or ))
+
div(data-hook="workflow-editor-container")
div(data-hook="workflow-status-container")
@@ -21,3 +33,5 @@ section.page
div(data-hook="model-viewer-container")
div(data-hook="computational-resources-container")
+
+ button.btn.btn-primary.box-shadow(data-hook="return-to-project-btn" style="display: none;") Return to Project
diff --git a/client/templates/pages/workflowSelection.pug b/client/templates/pages/workflowSelection.pug
index 37e788d3d4..c4de55d0b6 100644
--- a/client/templates/pages/workflowSelection.pug
+++ b/client/templates/pages/workflowSelection.pug
@@ -2,6 +2,19 @@ section.page.col-md-10
h3="Workflow Selection for " + this.modelFile
+ div(data-hook="workflow-selection-breadcrumb-links" style="display: none")
+ h5
+ nav(aria-label="breadcrumb")
+ ol.breadcrumb
+ li.breadcrumb-item
+ a(href="stochss/project/manager?path="+this.projectPath data-hook="project-breadcrumb")=this.projectName
+
+ div.alert-danger(data-hook="invalid-model-message" style="display: none;")
+ | You cannot create a workflow if your model does not have at least one Species and one Reaction, Event, or Rule
+
+ div.alert-info(data-hook="psweep-workflow-message" style="display: none;")
+ | Parameter Sweep workflows require at least one parameter
+
table.table
thead
tr
@@ -9,18 +22,14 @@ section.page.col-md-10
tbody
tr
td
- div
- li.nav-item: a.nav-link(href="stochss/workflow/edit?type=gillespy&path=" + this.modelDir)
- | Ensemble Simulation
-
- div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.ensembleSimulation)
+ button.btn.btn-outline-primary.box-shadow.inline(id="stochss-es" data-hook="stochss-es") Ensemble Simulation
+ div.tooltip-icon.horizontal-space(data-html="true" data-toggle="tooltip" title=this.tooltips.ensembleSimulation)
+
td
- div
- li.nav-item: a.nav-link(href="stochss/workflow/edit?type=parameterSweep&path=" + this.modelDir)
- | Parameter Sweep
-
- div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.parameterSweep)
+ button.btn.btn-outline-primary.box-shadow.inline(id="stochss-ps" data-hook="stochss-ps") Parameter Sweep
+
+ div.tooltip-icon.horizontal-space(data-html="true" data-toggle="tooltip" title=this.tooltips.parameterSweep)
table.table
thead
@@ -28,15 +37,16 @@ section.page.col-md-10
th(scope="col" colspan="4") Jupyter Notebook Workflows
tbody
tr
- td: li.nav-item: button.btn.information-btn.nav-link(data-hook="ensemble-simulation" data-type="gillespy")
+ td: button.btn.btn-outline-primary.box-shadow(id="ensemble-simulation" data-hook="ensemble-simulation" data-type="gillespy")
| Ensemble Simulation
- td: li.nav-item: button.btn.information-btn.nav-link(data-hook="oned-parameter-sweep" data-type="1d_parameter_sweep")
+ td: button.btn.btn-outline-primary.box-shadow(id="oned-parameter-sweep" data-hook="oned-parameter-sweep" data-type="1d_parameter_sweep")
| 1D Parameter Sweep
- td: li.nav-item: button.btn.information-btn.nav-link(data-hook="twod-parameter-sweep" data-type="2d_parameter_sweep")
+ td: button.btn.btn-outline-primary.box-shadow(id="twod-parameter-sweep" data-hook="twod-parameter-sweep" data-type="2d_parameter_sweep")
| 2D Parameter Sweep
tr
- td: li.nav-item: button.btn.information-btn.nav-link(data-hook="sciope-model-exploration" data-type="sciope_model_exploration")
+ td: button.btn.btn-outline-primary.box-shadow(id="sciope-model-exploration" data-hook="sciope-model-exploration" data-type="sciope_model_exploration")
| Sciope Model Exploration
- td: li.nav-item: button.btn.information-btn.nav-link(data-hook="model-inference" data-type="model_inference")
+ td: button.btn.btn-outline-primary.box-shadow(id="model-inference" data-hook="model-inference" data-type="model_inference")
| Sciope Model Inference
+ td: div
diff --git a/client/views/creator-listing.js b/client/views/creator-listing.js
new file mode 100644
index 0000000000..720102e158
--- /dev/null
+++ b/client/views/creator-listing.js
@@ -0,0 +1,20 @@
+//views
+var View = require('ampersand-view');
+//templates
+var template = require('../templates/includes/creatorList.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=remove-creator-btn]' : 'removeCreator'
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments);
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments);
+ },
+ removeCreator: function (e) {
+ this.model.collection.remove(this.model)
+ }
+});
\ No newline at end of file
diff --git a/client/views/edit-advanced-specie.js b/client/views/edit-advanced-specie.js
index df186b9595..6fcefbcbb4 100644
--- a/client/views/edit-advanced-specie.js
+++ b/client/views/edit-advanced-specie.js
@@ -48,7 +48,7 @@ module.exports = View.extend({
var value = e.target.selectedOptions.item(0).text
var modeDict = {"Concentration":"continuous","Population":"discrete","Hybrid Concentration/Population":"dynamic"}
this.model.mode = modeDict[value]
- this.model.collection.trigger('update-species', this.model.compID, this.model, false);
+ this.model.collection.trigger('update-species', this.model.compID, this.model, false, false);
this.toggleSwitchingSettings();
},
setSwitchingType: function (e) {
diff --git a/client/views/edit-event-assignment.js b/client/views/edit-event-assignment.js
index 5099b8234e..0540c8eef8 100644
--- a/client/views/edit-event-assignment.js
+++ b/client/views/edit-event-assignment.js
@@ -37,6 +37,7 @@ module.exports = View.extend({
removeAssignment: function () {
this.remove();
this.collection.removeEventAssignment(this.model)
+ this.collection.parent.collection.trigger('change')
},
getOptions: function () {
var species = this.model.collection.parent.collection.parent.species;
diff --git a/client/views/edit-function-definition.js b/client/views/edit-function-definition.js
index 24e98004ce..484a0e9570 100644
--- a/client/views/edit-function-definition.js
+++ b/client/views/edit-function-definition.js
@@ -17,6 +17,9 @@ module.exports = View.extend({
},
render: function () {
View.prototype.render.apply(this, arguments);
+ $(document).on('hide.bs.modal', '.modal', function (e) {
+ e.target.remove()
+ });
},
editAnnotation: function () {
var self = this;
@@ -35,7 +38,7 @@ module.exports = View.extend({
}
});
okBtn.addEventListener('click', function (e) {
- self.model.annotation = input.value;
+ self.model.annotation = input.value.trim();
self.parent.renderEdirFunctionDefinitionView();
modal.modal('hide');
});
diff --git a/client/views/edit-model-view.js b/client/views/edit-model-view.js
new file mode 100644
index 0000000000..cdcca8ec82
--- /dev/null
+++ b/client/views/edit-model-view.js
@@ -0,0 +1,122 @@
+var $ = require('jquery');
+var _ = require('underscore');
+var xhr = require('xhr');
+var path = require('path');
+//support files
+var app = require('../app');
+var modals = require('../modals');
+//views
+var View = require('ampersand-view');
+//templates
+var template = require('../templates/includes/editModelView.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=project-model-edit]' : 'handleEditModelClick',
+ 'click [data-hook=new-workflow-btn]' : 'handleNewWorkflowClick',
+ 'click [data-hook=edit-model-annotation-btn]' : 'handleEditAnnotationClick',
+ 'click [data-hook=project-model-remove]' : 'handleRemoveModelClick',
+ 'click [data-hook=collapse-annotation-text]' : 'changeCollapseButtonText',
+ 'change [data-hook=annotation]' : 'updateAnnotation'
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments);
+ this.workflowGroupOptions = this.model.collection.parent.workflowGroups.map(function (wg) {
+ return wg.name
+ })
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments);
+ if(!this.model.annotation){
+ $(this.queryByHook('edit-model-annotation-btn')).text('Add Notes')
+ }else{
+ $(this.queryByHook('collapse-annotation-container'+this.model.name.replace(/ /g,""))).collapse('show')
+ }
+ },
+ handleEditModelClick: function (e) {
+ let queryString = "?path="+this.model.directory
+ window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+queryString
+ },
+ handleNewWorkflowClick: function (e) {
+ let wkgpNames = this.model.collection.parent.workflowGroups.map(function (model) {
+ return model.name
+ })
+ if(this.model.collection.parent.workflowGroups.length <= 0 || !wkgpNames.includes("WorkflowGroup1")) {
+ this.addNewWorkflowGroup(_.bind(this.openWorkflowManager, this))
+ }else{
+ let wkgpFile = "WorkflowGroup1.wkgp"
+ this.openWorkflowManager(wkgpFile)
+ }
+ },
+ addNewWorkflowGroup: function (cb) {
+ let self = this
+ let workflowGroupName = "WorkflowGroup1.wkgp"
+ let workflowGroupPath = path.join(this.parent.parent.projectPath, workflowGroupName)
+ let endpoint = path.join(app.getApiPath(), "project/new-workflow-group")+"?path="+workflowGroupPath
+ xhr({uri: endpoint,json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ if(cb) {
+ cb(workflowGroupName)
+ }else{
+ self.update("workflow-group")
+ }
+ }else{
+ let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal()
+ }
+ });
+ },
+ openWorkflowManager: function (wkgpFile) {
+ let parentPath = path.join(path.dirname(this.model.directory), wkgpFile)
+ let queryString = "?path="+this.model.directory+"&parentPath="+parentPath
+ let endpoint = path.join(app.getBasePath(), 'stochss/workflow/selection')+queryString
+ window.location.href = endpoint
+ },
+ handleRemoveModelClick: function (e) {
+ let self = this
+ if(document.querySelector('#moveToTrashConfirmModal')) {
+ document.querySelector('#moveToTrashConfirmModal').remove();
+ }
+ let modal = $(modals.moveToTrashConfirmHtml("model")).modal();
+ let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn');
+ yesBtn.addEventListener('click', function (e) {
+ let trashPath = path.join(path.dirname(self.model.directory), "trash", self.model.directory.split('/').pop())
+ let queryString = "?srcPath="+self.model.directory+"&dstPath="+trashPath
+ let endpoint = path.join(app.getApiPath(), 'file/move')+queryString
+ xhr({uri: endpoint, json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ self.parent.parent.update("model-editor")
+ }
+ });
+ modal.modal('hide')
+ });
+ },
+ handleEditAnnotationClick: function (e) {
+ let buttonTxt = e.target.innerText;
+ if(buttonTxt.startsWith("Add")){
+ $(this.queryByHook('collapse-annotation-container'+this.model.name.replace(/ /g,""))).collapse('show')
+ $(this.queryByHook('edit-model-annotation-btn')).text('Edit Notes')
+ }else if(!$("#annotation-text"+this.model.name.replace(/ /g,"")).attr('class').includes('show')){
+ $("#annotation-text"+this.model.name.replace(/ /g,"")).collapse('show')
+ $(this.queryByHook("collapse-annotation-text")).text('-')
+ }
+ document.querySelector("#annotation"+this.model.name.replace(/ /g,"")).focus()
+ },
+ updateAnnotation: function (e) {
+ this.model.annotation = e.target.value.trim();
+ if(this.model.annotation === "") {
+ $(this.queryByHook('collapse-annotation-container'+this.model.name.replace(/ /g,""))).collapse('hide')
+ $(this.queryByHook('edit-model-annotation-btn')).text('Add Notes')
+ }
+ this.model.saveModel()
+ },
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
+ }
+});
\ No newline at end of file
diff --git a/client/views/edit-models-view.js b/client/views/edit-models-view.js
new file mode 100644
index 0000000000..f7e43e941a
--- /dev/null
+++ b/client/views/edit-models-view.js
@@ -0,0 +1,30 @@
+let $ = require('jquery');
+//views
+var View = require('ampersand-view');
+var EditModelView = require('./edit-model-view');
+//templates
+var template = require('../templates/includes/editModelsView.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {},
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments)
+ },
+ render: function (attrs, arguments) {
+ View.prototype.render.apply(this, arguments)
+ this.renderEditModelview()
+ },
+ renderEditModelview: function () {
+ if(this.editModelView) {
+ this.editModelView.remove()
+ }
+ this.editModelView = this.renderCollection(this.collection, EditModelView, this.queryByHook("project-models-list"))
+ $(document).ready(function () {
+ $('[data-toggle="tooltip"]').tooltip();
+ $('[data-toggle="tooltip"]').click(function () {
+ $('[data-toggle="tooltip"]').tooltip("hide");
+ });
+ });
+ }
+});
\ No newline at end of file
diff --git a/client/views/edit-parameter.js b/client/views/edit-parameter.js
index f496514668..5775acebd0 100644
--- a/client/views/edit-parameter.js
+++ b/client/views/edit-parameter.js
@@ -30,6 +30,9 @@ module.exports = View.extend({
$(document).on('shown.bs.modal', function (e) {
$('[autofocus]', e.target).focus();
});
+ $(document).on('hide.bs.modal', '.modal', function (e) {
+ e.target.remove()
+ });
if(!this.model.annotation){
$(this.queryByHook('edit-annotation-btn')).text('Add')
}
@@ -49,7 +52,7 @@ module.exports = View.extend({
if(document.querySelector('#parameterAnnotationModal')) {
document.querySelector('#parameterAnnotationModal').remove();
}
- let modal = $(annotationModalHtml("parameter", name, annotation)).modal();
+ let modal = $(modals.annotationModalHtml("parameter", name, annotation)).modal();
let okBtn = document.querySelector('#parameterAnnotationModal .ok-model-btn');
let input = document.querySelector('#parameterAnnotationModal #parameterAnnotationInput');
input.addEventListener("keyup", function (event) {
@@ -59,13 +62,13 @@ module.exports = View.extend({
}
});
okBtn.addEventListener('click', function (e) {
- self.model.annotation = input.value;
+ self.model.annotation = input.value.trim();
self.parent.renderEditParameter();
modal.modal('hide');
});
},
setParameterName: function (e) {
- this.model.name = e.target.value;
+ this.model.name = e.target.value.trim();
this.model.collection.trigger('update-parameters', this.model.compID, this.model);
this.model.collection.trigger('remove')
},
@@ -93,9 +96,9 @@ module.exports = View.extend({
required: true,
name: 'expression',
label: '',
- tests: '',
+ tests: tests.valueTests,
modelKey: 'expression',
- valueType: 'string',
+ valueType: 'number',
value: this.model.expression,
});
},
diff --git a/client/views/edit-project.js b/client/views/edit-project.js
new file mode 100644
index 0000000000..beae9ec95e
--- /dev/null
+++ b/client/views/edit-project.js
@@ -0,0 +1,57 @@
+let $ = require('jquery');
+let xhr = require('xhr');
+let path = require('path');
+//support files
+let app = require('../app');
+let modals = require('../modals')
+//views
+let View = require('ampersand-view');
+//templates
+let template = require('../templates/includes/editProject.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=open-project-btn]' : 'handleOpenProjectClick',
+ 'click [data-hook=remove-project-btn]' : 'handleRemoveProjectClick'
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments);
+ this.projectName = this.model.directory.split('/').pop().split('.')[0]
+ this.location = this.getLocationString(this.model.directory)
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments);
+ },
+ getLocationString: function (projectPath) {
+ let parent = path.dirname(projectPath)
+ if(parent === '.') {
+ return ''
+ }
+ return 'Location: '+parent
+ },
+ handleOpenProjectClick: function (e) {
+ window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+this.model.directory
+ },
+ handleRemoveProjectClick: function (e) {
+ console.log("deleting the project")
+ let endpoint = path.join(app.getApiPath(), "file/delete")+"?path="+this.model.directory
+ var self = this
+ if(document.querySelector('#deleteFileModal')) {
+ document.querySelector('#deleteFileModal').remove()
+ }
+ let modal = $(modals.deleteFileHtml("project")).modal();
+ let yesBtn = document.querySelector('#deleteFileModal .yes-modal-btn');
+ yesBtn.addEventListener('click', function (e) {
+ xhr({uri: endpoint}, function(err, response, body) {
+ if(response.statusCode < 400) {
+ self.model.collection.remove(self.model)
+ console.log(body)
+ }else{
+ body = JSON.parse(body)
+ }
+ })
+ modal.modal('hide')
+ });
+ }
+});
\ No newline at end of file
diff --git a/client/views/edit-rule.js b/client/views/edit-rule.js
index f61d786f55..d6f4aa1b9a 100644
--- a/client/views/edit-rule.js
+++ b/client/views/edit-rule.js
@@ -47,6 +47,9 @@ module.exports = View.extend({
$(document).on('shown.bs.modal', function (e) {
$('[autofocus]', e.target).focus();
});
+ $(document).on('hide.bs.modal', '.modal', function (e) {
+ e.target.remove()
+ });
if(!this.model.annotation){
$(this.queryByHook('edit-annotation-btn')).text('Add')
}
@@ -72,7 +75,7 @@ module.exports = View.extend({
}
});
okBtn.addEventListener('click', function (e) {
- self.model.annotation = input.value;
+ self.model.annotation = input.value.trim();
self.parent.renderRules();
modal.modal('hide');
});
diff --git a/client/views/edit-specie.js b/client/views/edit-specie.js
index 17b3c0ba22..d641c56d09 100644
--- a/client/views/edit-specie.js
+++ b/client/views/edit-specie.js
@@ -30,6 +30,9 @@ module.exports = View.extend({
$(document).on('shown.bs.modal', function (e) {
$('[autofocus]', e.target).focus();
});
+ $(document).on('hide.bs.modal', '.modal', function (e) {
+ e.target.remove()
+ });
if(!this.model.annotation){
$(this.queryByHook('edit-annotation-btn')).text('Add')
}
@@ -43,8 +46,8 @@ module.exports = View.extend({
this.collection.removeSpecie(this.model);
},
setSpeciesName: function (e) {
- this.model.name = e.target.value;
- this.model.collection.trigger('update-species', this.model.compID, this.model, true);
+ this.model.name = e.target.value.trim();
+ this.model.collection.trigger('update-species', this.model.compID, this.model, true, false);
this.model.collection.trigger('remove');
},
editAnnotation: function () {
@@ -64,7 +67,7 @@ module.exports = View.extend({
}
});
okBtn.addEventListener('click', function (e) {
- self.model.annotation = input.value;
+ self.model.annotation = input.value.trim();
self.parent.renderEditSpeciesView();
modal.modal('hide');
});
diff --git a/client/views/edit-workflow-group-view.js b/client/views/edit-workflow-group-view.js
new file mode 100644
index 0000000000..a9545e50d8
--- /dev/null
+++ b/client/views/edit-workflow-group-view.js
@@ -0,0 +1,73 @@
+var $ = require('jquery');
+var xhr = require('xhr');
+var path = require('path');
+//support files
+var app = require('../app');
+var modals = require('../modals');
+//views
+var View = require('ampersand-view');
+var EditWorkflowsView = require('./edit-workflows-view');
+//templates
+var template = require('../templates/includes/editWorkflowGroupView.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=project-workflow-group-view]' : 'handleViewWorkflowsClick',
+ 'click [data-hook=project-workflow-group-remove]' : 'handleRemoveWorkflowGroupClick'
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments);
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments);
+ this.renderEditWorkflowsView();
+ if(this.model.collection.length === 1) {
+ this.handleViewWorkflowsClick(undefined)
+ $(this.queryByHook("project-workflow-group-remove")).prop('disabled', true)
+ }
+ },
+ renderEditWorkflowsView: function () {
+ if(this.editWorkflowsView){
+ this.editWorkflowsView.remove()
+ }
+ this.editWorkflowsView = new EditWorkflowsView({
+ collection: this.model.workflows
+ });
+ this.registerRenderSubview(this.editWorkflowsView, "project-workflows-container")
+ },
+ registerRenderSubview: function (view, hook) {
+ this.registerSubview(view);
+ this.renderSubview(view, this.queryByHook(hook));
+ },
+ handleViewWorkflowsClick: function (e) {
+ let options = {"+":"show", "-":"hide"}
+ let newText = {"+":"-", "-":"+"}
+ let text = $(this.queryByHook("project-workflow-group-view")).text()
+ $(this.queryByHook("project-workflows-container")).collapse(options[text])
+ $(this.queryByHook("project-workflow-group-view")).text(newText[text])
+ },
+ handleRemoveWorkflowGroupClick: function (e) {
+ if(this.model.collection.length > 1) {
+ let self = this
+ if(document.querySelector('#moveToTrashConfirmModal')) {
+ document.querySelector('#moveToTrashConfirmModal').remove();
+ }
+ let title = "workflow group and it workflows"
+ let modal = $(modals.moveToTrashConfirmHtml(title)).modal();
+ let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn');
+ yesBtn.addEventListener('click', function (e) {
+ let expPath = path.join(self.parent.parent.projectPath, self.model.name)+".wkgp"
+ let trashPath = path.join(self.parent.parent.projectPath, "trash", self.model.name + ".wkgp")
+ let queryString = "?srcPath="+expPath+"&dstPath="+trashPath
+ let endpoint = path.join(app.getApiPath(), 'file/move')+queryString
+ xhr({uri: endpoint, json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ self.parent.parent.update("workflow-group-editor")
+ }
+ });
+ modal.modal('hide')
+ });
+ }
+ },
+});
\ No newline at end of file
diff --git a/client/views/edit-workflow-groups-view.js b/client/views/edit-workflow-groups-view.js
new file mode 100644
index 0000000000..89109e2c92
--- /dev/null
+++ b/client/views/edit-workflow-groups-view.js
@@ -0,0 +1,17 @@
+//views
+var View = require('ampersand-view');
+var EditWorkflowGroupView = require('./edit-workflow-group-view');
+//templates
+var template = require('../templates/includes/editWorkflowGroupsView.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {},
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments);
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments);
+ this.renderCollection(this.collection, EditWorkflowGroupView, this.queryByHook("project-workflow-groups-list"))
+ }
+});
\ No newline at end of file
diff --git a/client/views/edit-workflow-view.js b/client/views/edit-workflow-view.js
new file mode 100644
index 0000000000..e4f15df186
--- /dev/null
+++ b/client/views/edit-workflow-view.js
@@ -0,0 +1,111 @@
+var $ = require('jquery');
+var _ = require('underscore');
+var xhr = require('xhr');
+var path = require('path');
+//support files
+var app = require('../app');
+var modals = require('../modals');
+//views
+var View = require('ampersand-view');
+//templates
+var template = require('../templates/includes/editWorkflowView.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=project-workflow-open]' : 'handleOpenWorkflowClick',
+ 'click [data-hook=edit-workflow-annotation-btn]' : 'handleEditAnnotationClick',
+ 'click [data-hook=project-workflow-remove]' : 'handleDeleteWorkflowClick',
+ 'click [data-hook=collapse-annotation-text]' : 'changeCollapseButtonText',
+ 'change [data-hook=annotation]' : 'updateAnnotation'
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments);
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments);
+ if(this.model.status === "running"){
+ this.getStatus()
+ }
+ if(this.model.path.endsWith('.ipynb')) {
+ this.queryByHook('annotation-container').style.display = "none"
+ }
+ if(!this.model.annotation || !this.model.annotation.trim()){
+ $(this.queryByHook('edit-workflow-annotation-btn')).text('Add Notes')
+ }else{
+ $(this.queryByHook('collapse-annotation-container'+this.model.name.replace(/ /g,""))).collapse('show')
+ }
+ },
+ getStatus: function () {
+ var self = this;
+ var endpoint = path.join(app.getApiPath(), "workflow/workflow-status")+"?path="+this.model.path;
+ xhr({uri: endpoint}, function (err, response, body) {
+ if(self.model.status !== body )
+ self.model.status = body;
+ if(self.model.status === 'running')
+ setTimeout(_.bind(self.getStatus, self), 1000);
+ else{
+ $(self.queryByHook("project-workflow-status")).text(self.model.status)
+ }
+ });
+ },
+ handleOpenWorkflowClick: function (e) {
+ if(this.model.path.endsWith('.ipynb')) {
+ window.open(path.join(app.getBasePath(), "notebooks", this.model.path))
+ }else{
+ let endpoint = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+this.model.path+"&type=none";
+ window.location.href = endpoint
+ }
+ },
+ handleDeleteWorkflowClick: function (e) {
+ let self = this
+ if(document.querySelector('#moveToTrashConfirmModal')) {
+ document.querySelector('#moveToTrashConfirmModal').remove();
+ }
+ let modal = $(modals.moveToTrashConfirmHtml("workflow")).modal();
+ let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn');
+ yesBtn.addEventListener('click', function (e) {
+ let file = self.model.path.split('/').pop()
+ let trashPath = path.join(path.dirname(path.dirname(self.model.path)), "trash", file)
+ let queryString = "?srcPath="+self.model.path+"&dstPath="+trashPath
+ let endpoint = path.join(app.getApiPath(), 'file/move')+queryString
+ xhr({uri: endpoint, json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ self.parent.parent.parent.parent.update("workflows-editor")
+ }
+ });
+ modal.modal('hide')
+ });
+ },
+ handleEditAnnotationClick: function (e) {
+ let buttonTxt = e.target.innerText;
+ if(buttonTxt.startsWith("Add")){
+ $(this.queryByHook('collapse-annotation-container'+this.model.name.replace(/ /g,""))).collapse('show')
+ $(this.queryByHook('edit-workflow-annotation-btn')).text('Edit Notes')
+ }else if(!$("#annotation-text"+this.model.name.replace(/ /g,"")).attr('class').includes('show')){
+ $("#annotation-text"+this.model.name.replace(/ /g,"")).collapse('show')
+ $(this.queryByHook("collapse-annotation-text")).text('-')
+ }
+ document.querySelector("#annotation"+this.model.name.replace(/ /g,"")).focus()
+ },
+ updateAnnotation: function (e) {
+ this.model.annotation = e.target.value.trim();
+ if(this.model.annotation === "") {
+ $(this.queryByHook('collapse-annotation-container'+this.model.name.replace(/ /g,""))).collapse('hide')
+ $(this.queryByHook('edit-workflow-annotation-btn')).text('Add Notes')
+ }
+ let queryString = "?path="+path.join(this.model.path, "info.json")
+ let endpoint = path.join(app.getApiPath(), "workflow/save-annotation")+queryString
+ let body = {'annotation':this.model.annotation}
+ xhr({uri:endpoint, json:true, method:'post', body:body}, function (err, response, body) {console.log("Saved Notes")})
+ },
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
+ }
+});
\ No newline at end of file
diff --git a/client/views/edit-workflows-view.js b/client/views/edit-workflows-view.js
new file mode 100644
index 0000000000..a7bae109c4
--- /dev/null
+++ b/client/views/edit-workflows-view.js
@@ -0,0 +1,116 @@
+var $ = require('jquery');
+var xhr = require('xhr');
+var path = require('path');
+//support files
+var app = require('../app');
+var modals = require('../modals');
+//views
+var View = require('ampersand-view');
+var EditWorkflowView = require('./edit-workflow-view');
+//templates
+var template = require('../templates/includes/editWorkflowsView.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=project-workflow-group-new-workflow]' : 'handleNewWorkflowClick',
+ 'click [data-hook=project-workflow-group-add-workflow]' : 'handleAddWorkflowClick',
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments)
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments)
+ this.renderEditWorkflowView()
+ },
+ renderEditWorkflowView: function () {
+ if(this.editWorkflowView) {
+ this.editWorkflowView.remove()
+ }
+ this.editWorkflowView = this.renderCollection(this.collection, EditWorkflowView, this.queryByHook("project-workflows-list"))
+ $(document).ready(function () {
+ $('[data-toggle="tooltip"]').tooltip();
+ $('[data-toggle="tooltip"]').click(function () {
+ $('[data-toggle="tooltip"]').tooltip("hide");
+ });
+ });
+ },
+ validateName(input) {
+ var error = ""
+ if(input.endsWith('/')) {
+ error = 'forward'
+ }
+ let invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\"
+ for(var i = 0; i < input.length; i++) {
+ if(invalidChars.includes(input.charAt(i))) {
+ error = error === "" || error === "special" ? "special" : "both"
+ }
+ }
+ return error
+ },
+ handleNewWorkflowClick: function (e) {
+ let models = this.parent.parent.parent.model.models
+ if(models.length > 0) {
+ let self = this
+ if(document.querySelector("#newProjectWorkflowModal")) {
+ document.querySelector("#newProjectWorkflowModal").remove()
+ }
+ let options = models.map(function (model) { return model.name });
+ let modal = $(modals.newProjectWorkflowHtml("Name of the model: ", options)).modal()
+ let okBtn = document.querySelector("#newProjectWorkflowModal .ok-model-btn")
+ let select = document.querySelector("#newProjectWorkflowModal #select")
+ okBtn.addEventListener('click', function (e) {
+ let mdlFile = select.value.endsWith('.mdl') ? select.value : select.value + ".mdl"
+ let mdlPath = path.join(self.parent.parent.parent.projectPath, mdlFile)
+ let parentPath = path.join(self.parent.parent.parent.projectPath, self.parent.model.name)+".wkgp"
+ let queryString = "?path="+mdlPath+"&parentPath="+parentPath
+ let endpoint = path.join(app.getBasePath(), 'stochss/workflow/selection')+queryString
+ modal.modal('hide')
+ window.location.href = endpoint
+ });
+ }else{
+ let title = "No Models Found"
+ let message = "You need to add a model before you can create a new workflow."
+ let modal = $(modals.noModelsMessageHtml(title, message)).modal()
+ }
+ },
+ handleAddWorkflowClick: function (e) {
+ let self = this
+ if(document.querySelector("#newProjectWorkflowModal")) {
+ document.querySelector("#newProjectWorkflowModal").remove()
+ }
+ let modal = $(modals.addExistingWorkflowToProjectHtml()).modal()
+ let okBtn = document.querySelector("#newProjectWorkflowModal .ok-model-btn")
+ let input = document.querySelector("#newProjectWorkflowModal #workflowPathInput")
+ input.addEventListener("keyup", function (event) {
+ if(event.keyCode === 13){
+ event.preventDefault();
+ okBtn.click();
+ }
+ });
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#newProjectWorkflowModal #workflowPathInputEndCharError')
+ var charErrMsg = document.querySelector('#newProjectWorkflowModal #workflowPathInputSpecCharError')
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ okBtn.addEventListener('click', function (e) {
+ if(Boolean(input.value)) {
+ let expPath = path.join(self.parent.parent.projectPath, self.model.name)+".wkgp"
+ let queryString = "?path="+expPath+"&wkflPath="+input.value
+ let endpoint = path.join(app.getApiPath(), "project/add-existing-workflow")+queryString
+ xhr({uri: endpoint, json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ self.parent.parent.update("workflow-group-editor")
+ let successModal = $(modals.addExistingWorkflowToProjectSuccessHtml(body.message)).modal()
+ }else{
+ let errorModal = $(modals.addExistingWorkflowToProjectErrorHtml(body.Reason, body.Message)).modal()
+ }
+ });
+ modal.modal('hide')
+ }
+ });
+ }
+});
\ No newline at end of file
diff --git a/client/views/event-assignments-editor.js b/client/views/event-assignments-editor.js
index 36b4d4eda5..552566702c 100644
--- a/client/views/event-assignments-editor.js
+++ b/client/views/event-assignments-editor.js
@@ -26,5 +26,6 @@ module.exports = View.extend({
},
addAssignment: function () {
this.collection.addEventAssignment();
+ this.collection.parent.collection.trigger('change')
},
})
\ No newline at end of file
diff --git a/client/views/event-details.js b/client/views/event-details.js
index d93d9a54b8..c435f0017b 100644
--- a/client/views/event-details.js
+++ b/client/views/event-details.js
@@ -78,8 +78,13 @@ module.exports = View.extend({
this.model.useValuesFromTriggerTime = e.target.dataset.name === "trigger";
},
changeCollapseButtonText: function (e) {
- var text = $(this.queryByHook('advanced-event-button')).text();
- text === '+' ? $(this.queryByHook('advanced-event-button')).text('-') : $(this.queryByHook('advanced-event-button')).text('+');
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
subviews: {
inputDelay: {
diff --git a/client/views/event-listings.js b/client/views/event-listings.js
index ef5cfa083e..9bd75fcc1a 100644
--- a/client/views/event-listings.js
+++ b/client/views/event-listings.js
@@ -60,6 +60,9 @@ module.exports = View.extend({
$(document).on('shown.bs.modal', function (e) {
$('[autofocus]', e.target).focus();
});
+ $(document).on('hide.bs.modal', '.modal', function (e) {
+ e.target.remove()
+ });
if(!this.model.annotation){
$(this.queryByHook('edit-annotation-btn')).text('Add')
}
@@ -78,7 +81,7 @@ module.exports = View.extend({
if(document.querySelector('#eventAnnotationModal')) {
document.querySelector('#eventAnnotationModal').remove();
}
- let modal = $(annotationModalHtml("event", name, annotation)).modal();
+ let modal = $(modals.annotationModalHtml("event", name, annotation)).modal();
let okBtn = document.querySelector('#eventAnnotationModal .ok-model-btn');
let input = document.querySelector('#eventAnnotationModal #eventAnnotationInput');
input.addEventListener("keyup", function (event) {
@@ -88,7 +91,7 @@ module.exports = View.extend({
}
});
okBtn.addEventListener('click', function (e) {
- self.model.annotation = input.value;
+ self.model.annotation = input.value.trim();
self.parent.renderEventListingsView();
modal.modal('hide');
});
diff --git a/client/views/events-editor.js b/client/views/events-editor.js
index 63dad858fe..ad1e47c55e 100644
--- a/client/views/events-editor.js
+++ b/client/views/events-editor.js
@@ -107,7 +107,12 @@ module.exports = View.extend({
return detailsView
},
changeCollapseButtonText: function (e) {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+');
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
})
\ No newline at end of file
diff --git a/client/views/file-browser-view.js b/client/views/file-browser-view.js
new file mode 100644
index 0000000000..a3181b61eb
--- /dev/null
+++ b/client/views/file-browser-view.js
@@ -0,0 +1,1394 @@
+let jstree = require('jstree');
+let path = require('path');
+let xhr = require('xhr');
+let $ = require('jquery');
+let _ = require('underscore');
+//support files
+let app = require('../app');
+let modals = require('../modals');
+//views
+let View = require('ampersand-view');
+//templates
+let template = require('../templates/includes/fileBrowserView.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=collapse-browse-files]' : 'changeCollapseButtonText',
+ 'click [data-hook=refresh-jstree]' : 'refreshJSTree',
+ 'click [data-hook=options-for-node]' : 'showContextMenuForNode',
+ 'click [data-hook=new-directory]' : 'handleCreateDirectoryClick',
+ 'click [data-hook=browser-new-workflow-group]' : 'handleCreateWorkflowGroupClick',
+ 'click [data-hook=browser-new-model]' : 'handleCreateModelClick',
+ 'click [data-hook=browser-existing-model]' : 'handleAddExistingModelClick',
+ 'click [data-hook=upload-file-btn]' : 'handleUploadFileClick',
+ 'click [data-hook=file-browser-help]' : function () {
+ let modal = $(modals.operationInfoModalHtml('file-browser')).modal();
+ },
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments)
+ var self = this
+ this.root = "none"
+ if(attrs && attrs.root){
+ this.root = attrs.root
+ }
+ this.ajaxData = {
+ "url" : function (node) {
+ if(node.parent === null){
+ var endpoint = path.join(app.getApiPath(), "file/browser-list")+"?path="+self.root
+ if(self.root !== "none") {
+ endpoint += "&isRoot=True"
+ }
+ return endpoint
+ }
+ return path.join(app.getApiPath(), "file/browser-list")+"?path="+ node.original._path
+ },
+ "dataType" : "json",
+ "data" : function (node) {
+ return { 'id' : node.id}
+ },
+ }
+ this.treeSettings = {
+ 'plugins': ['types', 'wholerow', 'changed', 'contextmenu', 'dnd'],
+ 'core': {'multiple' : false, 'animation': 0,
+ 'check_callback': function (op, node, par, pos, more) {
+ if(op === "rename_node" && self.validateName(pos, true) !== ""){
+ document.querySelector("#renameSpecialCharError").style.display = "block"
+ setTimeout(function () {
+ document.querySelector("#renameSpecialCharError").style.display = "none"
+ }, 5000)
+ return false
+ }
+ if(op === 'move_node' && node && node.type && node.type === "workflow" && node.original && node.original._status && node.original._status === "running"){
+ return false
+ }
+ if(op === 'move_node' && more && more.ref && more.ref.original && node && node.type && (node.type === "nonspatial" || node.type === "spatial") &&
+ !(node.original._path.includes("trash") || more.ref.original.text === "trash")) {
+ return false
+ }
+ if(op === 'move_node' && more && more.ref && more.ref.original && node && node.type && node.type === "workflow-group") {
+ return false
+ }
+ if(op === 'move_node' && more && more.ref && more.ref.original && node && node.type && (node.type === "workflow") &&
+ !(node.original._path.includes("trash") || more.ref.original.text === "trash")) {
+ return false
+ }
+ if(op === 'move_node' && more && more.ref && more.ref.type && node.original._path.includes("trash") &&
+ ((node.type === "workflow" && more.ref.type !== 'workflow-group') ||
+ ((node.type === "nonspatial" || node.type === "spatial" || node.type === "workflow-group") && more.ref.type !== 'root'))){
+ return false
+ }
+ if(op === 'move_node' && more && more.ref && more.ref.type && !(node.type === "workflow" || node.type === "notebook") && !(more.ref.type == 'folder' || more.ref.type == 'root')){
+ return false
+ }
+ if(op === 'move_node' && more && more.ref && more.ref.type && node.type === "notebook" && !(more.ref.type == 'folder' || more.ref.type == 'root' || more.ref.type == 'workflow-group')) {
+ return false
+ }
+ if(op === 'move_node' && more && more.ref && more.ref.type && node.original._path.includes("trash") && more.ref.original.text == 'trash') {
+ return false
+ }
+ if(op === 'move_node' && more && more.ref && more.ref.type && (more.ref.type === 'folder' || more.ref.type === 'root')){
+ if(!more.ref.state.loaded){
+ return false
+ }
+ var exists = false
+ var BreakException = {}
+ var text = node.text
+ if(!isNaN(text.split(' ').pop().split('.').join(""))){
+ text = text.replace(text.split(' ').pop(), '').trim()
+ }
+ if(more.ref.text !== "trash"){
+ try{
+ more.ref.children.forEach(function (child) {
+ var child_node = $('#models-jstree-view').jstree().get_node(child)
+ exists = child_node.text === text
+ if(exists){
+ throw BreakException;
+ }
+ })
+ }catch{
+ return false;
+ }
+ }
+ }
+ if(op === 'move_node' && more && (pos != 0 || more.pos !== "i") && !more.core){
+ return false
+ }
+ if(op === 'move_node' && more && more.core) {
+ var newDir = par.original._path !== "/" ? par.original._path : ""
+ var file = node.original._path.split('/').pop()
+ var oldPath = node.original._path
+ let queryStr = "?srcPath="+oldPath+"&dstPath="+path.join(newDir, file)
+ var endpoint = path.join(app.getApiPath(), "file/move")+queryStr
+ xhr({uri: endpoint}, function(err, response, body) {
+ if(response.statusCode < 400) {
+ node.original._path = path.join(newDir, file)
+ console.log((oldPath.includes('trash/') || newDir.endsWith('trash')))
+ self.updateParent(node.type, (oldPath.includes('trash/') || newDir.endsWith('trash')))
+ }else{
+ body = JSON.parse(body)
+ if(par.type === 'root'){
+ $('#models-jstree-view').jstree().refresh()
+ }else{
+ $('#models-jstree-view').jstree().refresh_node(par);
+ }
+ }
+ });
+ }
+ return true
+ },
+ 'themes': {'stripes': true, 'variant': 'large'},
+ 'data': self.ajaxData,
+ },
+ 'types' : {
+ 'root' : {"icon": "jstree-icon jstree-folder"},
+ 'folder' : {"icon": "jstree-icon jstree-folder"},
+ 'spatial' : {"icon": "jstree-icon jstree-file"},
+ 'nonspatial' : {"icon": "jstree-icon jstree-file"},
+ 'project' : {"icon": "jstree-icon jstree-file"},
+ 'workflow-group' : {"icon": "jstree-icon jstree-folder"},
+ 'workflow' : {"icon": "jstree-icon jstree-file"},
+ 'notebook' : {"icon": "jstree-icon jstree-file"},
+ 'mesh' : {"icon": "jstree-icon jstree-file"},
+ 'sbml-model' : {"icon": "jstree-icon jstree-file"},
+ 'other' : {"icon": "jstree-icon jstree-file"},
+ },
+ }
+ this.setupJstree()
+ },
+ render: function () {
+ View.prototype.render.apply(this, arguments)
+ var self = this;
+ this.nodeForContextMenu = "";
+ this.jstreeIsLoaded = false
+ // Remove all backdrop on close
+ $(document).on('hide.bs.modal', '.modal', function (e) {
+ if($(".modal-backdrop").length > 1) {
+ $(".modal-backdrop").remove();
+ }
+ e.target.remove()
+ });
+ window.addEventListener('pageshow', function (e) {
+ var navType = window.performance.navigation.type
+ if(navType === 2){
+ window.location.reload()
+ }
+ });
+ },
+ updateParent: function (type, trash = false) {
+ if(trash){
+ this.parent.update("all")
+ }else if(type === "nonspatial" || type === "workflow" || type === "workflow-group") {
+ this.parent.update("file-browser")
+ }
+ },
+ refreshJSTree: function () {
+ this.jstreeIsLoaded = false
+ $('#models-jstree-view').jstree().deselect_all(true)
+ $('#models-jstree-view').jstree().refresh()
+ },
+ refreshInitialJSTree: function () {
+ var self = this;
+ var count = $('#models-jstree-view').jstree()._model.data['#'].children.length;
+ if(count == 0) {
+ self.refreshJSTree();
+ setTimeout(function () {
+ self.refreshInitialJSTree();
+ }, 3000);
+ }
+ },
+ selectNode: function (node, fileName) {
+ let self = this
+ if(!this.jstreeIsLoaded || !$('#models-jstree-view').jstree().is_loaded(node) && $('#models-jstree-view').jstree().is_loading(node)) {
+ setTimeout(_.bind(self.selectNode, self, node, fileName), 1000);
+ }else{
+ node = $('#models-jstree-view').jstree().get_node(node)
+ var child = ""
+ for(var i = 0; i < node.children.length; i++) {
+ var child = $('#models-jstree-view').jstree().get_node(node.children[i])
+ if(child.original.text === fileName) {
+ $('#models-jstree-view').jstree().select_node(child)
+ let optionsButton = $(self.queryByHook("options-for-node"))
+ if(!self.nodeForContextMenu){
+ optionsButton.prop('disabled', false)
+ }
+ optionsButton.text("Actions for " + child.original.text)
+ self.nodeForContextMenu = child;
+ break
+ }
+ }
+ }
+ },
+ handleUploadFileClick: function (e) {
+ let type = e.target.dataset.type
+ this.uploadFile(undefined, type)
+ },
+ uploadFile: function (o, type) {
+ var self = this
+ if(document.querySelector('#uploadFileModal')) {
+ document.querySelector('#uploadFileModal').remove()
+ }
+ let modal = $(modals.uploadFileHtml(type)).modal();
+ let uploadBtn = document.querySelector('#uploadFileModal .upload-modal-btn');
+ let fileInput = document.querySelector('#uploadFileModal #fileForUpload');
+ let input = document.querySelector('#uploadFileModal #fileNameInput');
+ fileInput.addEventListener('change', function (e) {
+ if(fileInput.files.length){
+ uploadBtn.disabled = false
+ }else{
+ uploadBtn.disabled = true
+ }
+ })
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#uploadFileModal #fileNameInputEndCharError')
+ var charErrMsg = document.querySelector('#uploadFileModal #fileNameInputSpecCharError')
+ let error = self.validateName(input.value)
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ uploadBtn.addEventListener('click', function (e) {
+ let file = fileInput.files[0]
+ var fileinfo = {"type":type,"name":"","path":"/"}
+ if(o && o.original){
+ fileinfo.path = o.original._path
+ }
+ if(Boolean(input.value) && self.validateName(input.value) === ""){
+ fileinfo.name = input.value.trim()
+ }
+ let formData = new FormData()
+ formData.append("datafile", file)
+ formData.append("fileinfo", JSON.stringify(fileinfo))
+ let endpoint = path.join(app.getApiPath(), 'file/upload');
+ let req = new XMLHttpRequest();
+ req.open("POST", endpoint)
+ req.onload = function (e) {
+ var resp = JSON.parse(req.response)
+ if(req.status < 400) {
+ if(o){
+ var node = $('#models-jstree-view').jstree().get_node(o.parent);
+ if(node.type === "root" || node.type === "#"){
+ self.refreshJSTree();
+ }else{
+ $('#models-jstree-view').jstree().refresh_node(node);
+ }
+ }else{
+ self.refreshJSTree();
+ }
+ if(resp.errors.length > 0){
+ let errorModal = $(modals.uploadFileErrorsHtml(file.name, type, resp.message, resp.errors)).modal();
+ }
+ }
+ }
+ req.send(formData)
+ modal.modal('hide')
+ })
+ },
+ deleteFile: function (o) {
+ var fileType = o.type
+ if(fileType === "nonspatial")
+ fileType = "model";
+ else if(fileType === "spatial")
+ fileType = "spatial model"
+ else if(fileType === "sbml-model")
+ fileType = "sbml model"
+ else if(fileType === "other")
+ fileType = "file"
+ var self = this
+ if(document.querySelector('#deleteFileModal')) {
+ document.querySelector('#deleteFileModal').remove()
+ }
+ let modal = $(modals.deleteFileHtml(fileType)).modal();
+ let yesBtn = document.querySelector('#deleteFileModal .yes-modal-btn');
+ yesBtn.addEventListener('click', function (e) {
+ var endpoint = path.join(app.getApiPath(), "file/delete")+"?path="+o.original._path
+ xhr({uri: endpoint}, function(err, response, body) {
+ if(response.statusCode < 400) {
+ var node = $('#models-jstree-view').jstree().get_node(o.parent);
+ if(node.type === "root"){
+ self.refreshJSTree();
+ }else{
+ $('#models-jstree-view').jstree().refresh_node(node);
+ }
+ }else{
+ body = JSON.parse(body)
+ }
+ })
+ modal.modal('hide')
+ self.updateParent(o.type)
+ });
+ },
+ duplicateFileOrDirectory: function(o, type) {
+ var self = this;
+ var parentID = o.parent;
+ var queryStr = "?path="+o.original._path
+ if(!type && o.original.type === 'folder'){
+ type = "directory"
+ }else if(!type && o.original.type === 'workflow'){
+ type = "workflow"
+ }else if(!type){
+ type = "file"
+ }
+ if(type === "directory"){
+ var identifier = "directory/duplicate"
+ }else if(type === "workflow" || type === "wkfl_model"){
+ var timeStamp = type === "workflow" ? this.getTimeStamp() : "None"
+ var identifier = "workflow/duplicate"
+ queryStr = queryStr.concat("&target="+type+"&stamp="+timeStamp)
+ }else{
+ var identifier = "file/duplicate"
+ }
+ var endpoint = path.join(app.getApiPath(), identifier)+queryStr
+ xhr({uri: endpoint, json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ var node = $('#models-jstree-view').jstree().get_node(parentID);
+ if(node.type === "root" || type === "wkfl_model"){
+ self.refreshJSTree()
+ }else{
+ $('#models-jstree-view').jstree().refresh_node(node);
+ }
+ if(type === "workflow"){
+ var message = ""
+ if(body.error){
+ message = body.error
+ }else{
+ message = "The model for
"+body.File+" is located here:
"+body.mdlPath+" "
+ }
+ let modal = $(modals.duplicateWorkflowHtml(body.File, message)).modal()
+ }
+ self.selectNode(node, body.File)
+ self.updateParent(o.type)
+ }
+ }
+ );
+ },
+ getTimeStamp: function () {
+ var date = new Date();
+ var year = date.getFullYear();
+ var month = date.getMonth() + 1;
+ if(month < 10){
+ month = "0" + month
+ }
+ var day = date.getDate();
+ if(day < 10){
+ day = "0" + day
+ }
+ var hours = date.getHours();
+ if(hours < 10){
+ hours = "0" + hours
+ }
+ var minutes = date.getMinutes();
+ if(minutes < 10){
+ minutes = "0" + minutes
+ }
+ var seconds = date.getSeconds();
+ if(seconds < 10){
+ seconds = "0" + seconds
+ }
+ return "_" + month + day + year + "_" + hours + minutes + seconds;
+ },
+ toSpatial: function (o) {
+ var self = this;
+ var parentID = o.parent;
+ var endpoint = path.join(app.getApiPath(), "model/to-spatial")+"?path="+o.original._path;
+ xhr({uri: endpoint, json: true},
+ function (err, response, body) {
+ if(response.statusCode < 400) {
+ var node = $('#models-jstree-view').jstree().get_node(parentID);
+ if(node.type === "root"){
+ self.refreshJSTree()
+ }else{
+ $('#models-jstree-view').jstree().refresh_node(node);
+ }
+ self.selectNode(node, body.File)
+ }
+ }
+ );
+ },
+ toModel: function (o, from) {
+ var self = this;
+ var parentID = o.parent;
+ if(from === "Spatial"){
+ var identifier = "spatial/to-model"
+ }else{
+ var identifier = "sbml/to-model"
+ }
+ let endpoint = path.join(app.getApiPath(), identifier)+"?path="+o.original._path;
+ xhr({uri: endpoint, json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ var node = $('#models-jstree-view').jstree().get_node(parentID);
+ if(node.type === "root"){
+ self.refreshJSTree()
+ }else{
+ $('#models-jstree-view').jstree().refresh_node(node);
+ }
+ self.selectNode(node, body.File)
+ if(from === "SBML" && body.errors.length > 0){
+ var title = ""
+ var msg = body.message
+ var errors = body.errors
+ let modal = $(modals.sbmlToModelHtml(msg, errors)).modal();
+ }
+ }
+ }
+ );
+ },
+ toNotebook: function (o, type) {
+ let self = this
+ var endpoint = path.join(app.getApiPath(), "workflow/notebook")+"?type=none&path="+o.original._path
+ xhr({ uri: endpoint, json: true}, function (err, response, body) {
+ if(response.statusCode < 400){
+ var node = $('#models-jstree-view').jstree().get_node(o.parent)
+ if(node.type === 'root'){
+ self.refreshJSTree();
+ }else{
+ $('#models-jstree-view').jstree().refresh_node(node);
+ }
+ var notebookPath = path.join(app.getBasePath(), "notebooks", body.FilePath)
+ self.selectNode(node, body.File)
+ window.open(notebookPath, '_blank')
+ }
+ });
+ },
+ toSBML: function (o) {
+ var self = this;
+ var parentID = o.parent;
+ var endpoint = path.join(app.getApiPath(), "model/to-sbml")+"?path="+o.original._path;
+ xhr({uri: endpoint, json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ var node = $('#models-jstree-view').jstree().get_node(parentID);
+ if(node.type === "root"){
+ self.refreshJSTree()
+ }else{
+ $('#models-jstree-view').jstree().refresh_node(node);
+ }
+ self.selectNode(node, body.File)
+ }
+ });
+ },
+ renameNode: function (o) {
+ var self = this
+ var text = o.text;
+ var parent = $('#models-jstree-view').jstree().get_node(o.parent)
+ var extensionWarning = $(this.queryByHook('extension-warning'));
+ var nameWarning = $(this.queryByHook('rename-warning'));
+ extensionWarning.collapse('show')
+ $('#models-jstree-view').jstree().edit(o, null, function(node, status) {
+ if(text != node.text){
+ var endpoint = path.join(app.getApiPath(), "file/rename")+"?path="+ o.original._path+"&name="+node.text
+ xhr({uri: endpoint, json: true}, function (err, response, body){
+ if(response.statusCode < 400) {
+ if(body.changed) {
+ nameWarning.text(body.message)
+ nameWarning.collapse('show');
+ window.scrollTo(0,0)
+ setTimeout(_.bind(self.hideNameWarning, self), 10000);
+ }
+ node.original._path = body._path
+ }
+ if(text.split('.').pop() != node.text.split('.').pop()){
+ if(parent.type === "root"){
+ self.refreshJSTree()
+ }else{
+ $('#models-jstree-view').jstree().refresh_node(parent);
+ }
+ }
+ self.updateParent(o.type)
+ })
+ }
+ extensionWarning.collapse('hide');
+ nameWarning.collapse('hide');
+ });
+ },
+ hideNameWarning: function () {
+ $(this.queryByHook('rename-warning')).collapse('hide')
+ },
+ getExportData: function (o, asZip) {
+ var self = this;
+ let nodeType = o.original.type
+ let isJSON = nodeType === "sbml-model" ? false : true
+ if(nodeType === "sbml-model"){
+ var dataType = "plain-text"
+ var identifier = "file/download"
+ }else if(asZip) {
+ var dataType = "zip"
+ var identifier = "file/download-zip"
+ }else{
+ var dataType = "json"
+ var identifier = "file/json-data"
+ }
+ var queryStr = "?path="+o.original._path
+ if(dataType === "json"){
+ queryStr = queryStr.concat("&for=None")
+ }else if(dataType === "zip"){
+ queryStr = queryStr.concat("&action=generate")
+ }
+ var endpoint = path.join(app.getApiPath(), identifier)+queryStr
+ xhr({uri: endpoint, json: isJSON}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ if(dataType === "json") {
+ self.exportToJsonFile(body, o.original.text);
+ }else if(dataType === "zip") {
+ var node = $('#models-jstree-view').jstree().get_node(o.parent);
+ if(node.type === "root"){
+ self.refreshJSTree();
+ }else{
+ $('#models-jstree-view').jstree().refresh_node(node);
+ }
+ self.exportToZipFile(body.Path)
+ }else{
+ self.exportToFile(body, o.original.text);
+ }
+ }else{
+ if(dataType === "plain-text") {
+ body = JSON.parse(body)
+ }
+ }
+ });
+ },
+ exportToJsonFile: function (fileData, fileName) {
+ let dataStr = JSON.stringify(fileData);
+ let dataURI = 'data:application/json;charset=utf-8,' + encodeURIComponent(dataStr);
+ let exportFileDefaultName = fileName
+
+ let linkElement = document.createElement('a');
+ linkElement.setAttribute('href', dataURI);
+ linkElement.setAttribute('download', exportFileDefaultName);
+ linkElement.click();
+ },
+ exportToFile: function (fileData, fileName) {
+ let dataURI = 'data:text/plain;charset=utf-8,' + encodeURIComponent(fileData);
+
+ let linkElement = document.createElement('a');
+ linkElement.setAttribute('href', dataURI);
+ linkElement.setAttribute('download', fileName);
+ linkElement.click();
+ },
+ exportToZipFile: function (o) {
+ var targetPath = o
+ if(o.original){
+ targetPath = o.original._path
+ }
+ var endpoint = path.join(app.getBasePath(), "/files", targetPath);
+ window.open(endpoint)
+ },
+ validateName(input, rename = false) {
+ var error = ""
+ if(input.endsWith('/')) {
+ error = 'forward'
+ }
+ var invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\"
+ if(rename) {
+ invalidChars += "/"
+ }
+ for(var i = 0; i < input.length; i++) {
+ if(invalidChars.includes(input.charAt(i))) {
+ error = error === "" || error === "special" ? "special" : "both"
+ }
+ }
+ return error
+ },
+ newWorkflowGroup: function (o) {
+ var self = this
+ if(document.querySelector("#newWorkflowGroupModal")) {
+ document.querySelector("#newWorkflowGroupModal").remove()
+ }
+ let modal = $(modals.newWorkflowGroupModalHtml()).modal();
+ let okBtn = document.querySelector('#newWorkflowGroupModal .ok-model-btn');
+ let input = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInput');
+ input.addEventListener("keyup", function (event) {
+ if(event.keyCode === 13){
+ event.preventDefault();
+ okBtn.click();
+ }
+ });
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInputEndCharError')
+ var charErrMsg = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInputSpecCharError')
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ okBtn.addEventListener("click", function (e) {
+ if(Boolean(input.value)) {
+ modal.modal('hide')
+ var parentPath = self.parent.projectPath
+ if(o && o.original && o.original._path !== "/") {
+ parentPath = o.original._path
+ }
+ var workflowGroupName = input.value.trim() + ".wkgp"
+ var workflowGroupPath = path.join(parentPath, workflowGroupName)
+ let endpoint = path.join(app.getApiPath(), "project/new-workflow-group")+"?path="+workflowGroupPath
+ xhr({uri: endpoint,json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ if(o){//directory was created with context menu option
+ var node = $('#models-jstree-view').jstree().get_node(o);
+ if(node.type === "root"){
+ self.refreshJSTree()
+ }else{
+ $('#models-jstree-view').jstree().refresh_node(node);
+ }
+ }else{//directory was created with create directory button
+ self.refreshJSTree()
+ }
+ self.updateParent('workflow-group')
+ }else{
+ let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal()
+ }
+ })
+ }
+ })
+ },
+ handleAddExistingModelClick: function () {
+ this.addExistingModel(undefined)
+ },
+ addExistingModel: function (o) {
+ var self = this
+ if(document.querySelector('#newProjectModelModal')){
+ document.querySelector('#newProjectModelModal').remove()
+ }
+ let modal = $(modals.newProjectModelHtml()).modal()
+ let okBtn = document.querySelector('#newProjectModelModal .ok-model-btn')
+ let input = document.querySelector('#newProjectModelModal #modelPathInput')
+ input.addEventListener("keyup", function (event) {
+ if(event.keyCode === 13){
+ event.preventDefault();
+ okBtn.click();
+ }
+ });
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#newProjectModelModal #modelPathInputEndCharError')
+ var charErrMsg = document.querySelector('#newProjectModelModal #modelPathInputSpecCharError')
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ okBtn.addEventListener("click", function (e) {
+ if(Boolean(input.value)) {
+ let queryString = "?path="+self.parent.projectPath+"&mdlPath="+input.value.trim()
+ let endpoint = path.join(app.getApiPath(), 'project/add-existing-model') + queryString
+ xhr({uri:endpoint, json:true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ self.updateParent("nonspatial")
+ let successModal = $(modals.newProjectModelSuccessHtml(body.message)).modal()
+ self.refreshJSTree()
+ }else{
+ let errorModal = $(modals.newProjectModelErrorHtml(body.Reason, body.Message)).modal()
+ }
+ });
+ modal.modal('hide')
+ }
+ });
+ },
+ addNewWorkflow: function (o) {
+ if(o.type !== "workflow-group" && this.parent.model.workflowGroups.length <= 0) {
+ let title = "No Workflow Groups Found"
+ let message = "You need to create an workflow group before you can create a new workflow."
+ let modal = $(modals.noWorkflowGroupMessageHtml(title, message)).modal()
+ }else if(o.type === "workflow-group" && this.parent.model.models.length <= 0) {
+ let title = "No Models Found"
+ let message = "You need to add a model before you can create a new workflow."
+ let modal = $(modals.noWorkflowGroupMessageHtml(title, message)).modal()
+ }else if(o.type !== "workflow-group" && this.parent.model.workflowGroups.length == 1) {
+ let expName = this.parent.model.workflowGroups.models[0].name
+ let parentPath = path.join(path.dirname(o.original._path), expName + ".wkgp")
+ let modelPath = o.original._path
+ let endpoint = path.join(app.getBasePath(), "stochss/workflow/selection")+"?path="+modelPath+"&parentPath="+parentPath
+ window.location.href = endpoint
+ }else{
+ let self = this
+ if(document.querySelector('#newProjectWorkflowModal')){
+ document.querySelector('#newProjectWorkflowModal').remove()
+ }
+ let options = o.type === "workflow-group" ?
+ this.parent.model.models.map(function (model) {return model.name}) :
+ this.parent.model.workflowGroups.map(function (workflowGroup) {return workflowGroup.name})
+ let label = o.type === "workflow-group" ? "Model file name: " : "Workflow Group file name: "
+ let modal = $(modals.newProjectWorkflowHtml(label, options)).modal()
+ let okBtn = document.querySelector('#newProjectWorkflowModal .ok-model-btn')
+ let select = document.querySelector('#newProjectWorkflowModal #select')
+ okBtn.addEventListener("click", function (e) {
+ let parentPath = o.type === "workflow-group" ? o.original._path : path.join(path.dirname(o.original._path), select.value + ".wkgp")
+ let modelPath = o.type === "workflow-group" ? path.join(path.dirname(o.original._path), select.value + ".mdl") : o.original._path
+ let endpoint = path.join(app.getBasePath(), "stochss/workflow/selection")+"?path="+modelPath+"&parentPath="+parentPath
+ window.location.href = endpoint
+ });
+ }
+ },
+ addExistingWorkflow: function (o) {
+ let self = this;
+ if(document.querySelector('#newProjectWorkflowModal')) {
+ document.querySelector('#newProjectWorkflowModal').remove()
+ }
+ let modal = $(modals.addExistingWorkflowToProjectHtml()).modal()
+ let okBtn = document.querySelector('#newProjectWorkflowModal .ok-model-btn')
+ let input = document.querySelector('#newProjectWorkflowModal #workflowPathInput')
+ input.addEventListener("keyup", function (event) {
+ if(event.keyCode === 13){
+ event.preventDefault();
+ okBtn.click();
+ }
+ });
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#newProjectWorkflowModal #workflowPathInputEndCharError')
+ var charErrMsg = document.querySelector('#newProjectWorkflowModal #workflowPathInputSpecCharError')
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ okBtn.addEventListener("click", function (e) {
+ if(Boolean(input.value)) {
+ let queryString = "?path="+o.original._path+"&wkflPath="+input.value.trim()
+ let endpoint = path.join(app.getApiPath(), "project/add-existing-workflow")+queryString
+ xhr({uri: endpoint, json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ self.updateParent("workflow")
+ let successModal = $(modals.addExistingWorkflowToProjectSuccessHtml(body.message)).modal()
+ }else{
+ let errorModal = $(modals.addExistingWorkflowToProjectErrorHtml(body.Reason, body.Message)).modal()
+ }
+ });
+ modal.modal('hide')
+ }
+ });
+ },
+ newModelOrDirectory: function (o, isModel, isSpatial) {
+ var self = this
+ if(document.querySelector('#newModalModel')) {
+ document.querySelector('#newModalModel').remove()
+ }
+ let modal = $(modals.renderCreateModalHtml(isModel, isSpatial)).modal();
+ let okBtn = document.querySelector('#newModalModel .ok-model-btn');
+ let input = document.querySelector('#newModalModel #modelNameInput');
+ input.addEventListener("keyup", function (event) {
+ if(event.keyCode === 13){
+ event.preventDefault();
+ okBtn.click();
+ }
+ });
+ input.addEventListener("input", function (e) {
+ var endErrMsg = document.querySelector('#newModalModel #modelNameInputEndCharError')
+ var charErrMsg = document.querySelector('#newModalModel #modelNameInputSpecCharError')
+ let error = self.validateName(input.value)
+ okBtn.disabled = error !== ""
+ charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+ endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+ });
+ okBtn.addEventListener('click', function (e) {
+ if (Boolean(input.value)) {
+ var parentPath = self.parent.projectPath
+ if(o && o.original && o.original._path !== "/"){
+ parentPath = o.original._path
+ }
+ if(isModel) {
+ let modelName = o && o.type === "project" ? input.value.trim().split("/").pop() + '.mdl' : input.value.trim() + '.mdl';
+ let message = modelName.split(".")[0] !== input.value.trim() ?
+ "Warning: Models are saved directly in StochSS Projects and cannot be saved to the "+input.value.trim().split("/")[0]+" directory in the project.
Your model will be saved directly in your project.
" : ""
+ let modelPath = path.join(parentPath, modelName)
+ let endpoint = path.join(app.getBasePath(), app.routePrefix, 'models/edit')+"?path="+modelPath+"&message="+message;
+ if(message){
+ modal.modal('hide')
+ let warningModal = $(modals.newProjectModelWarningHtml(message)).modal()
+ let yesBtn = document.querySelector('#newProjectModelWarningModal .yes-modal-btn');
+ yesBtn.addEventListener('click', function (e) {window.location.href = endpoint;})
+ }else{
+ window.location.href = endpoint;
+ }
+ }else{
+ let dirName = input.value.trim();
+ let endpoint = path.join(app.getApiPath(), "directory/create")+"?path="+path.join(parentPath, dirName);
+ xhr({uri:endpoint}, function (err, response, body) {
+ if(response.statusCode < 400){
+ if(o){//directory was created with context menu option
+ var node = $('#models-jstree-view').jstree().get_node(o);
+ if(node.type === "root"){
+ self.refreshJSTree()
+ }else{
+ $('#models-jstree-view').jstree().refresh_node(node);
+ }
+ }else{//directory was created with create directory button
+ self.refreshJSTree()
+ }
+ }else{//new directory not created no need to refresh
+ body = JSON.parse(body)
+ let errorModal = $(modals.newDirectoryErrorHtml(body.Reason, body.Message)).modal()
+ }
+ });
+ modal.modal('hide')
+ }
+ }
+ });
+ },
+ handleCreateDirectoryClick: function (e) {
+ this.newModelOrDirectory(undefined, false, false);
+ },
+ handleCreateWorkflowGroupClick: function (e) {
+ this.newWorkflowGroup(undefined)
+ },
+ handleCreateModelClick: function (e) {
+ let isSpatial = false
+ this.newModelOrDirectory(undefined, true, isSpatial);
+ },
+ handleExtractModelClick: function (o) {
+ let self = this
+ let projectParent = path.dirname(this.parent.projectPath) === '.' ? "" : path.dirname(this.parent.projectPath)
+ let queryString = "?srcPath="+o.original._path+"&dstPath="+path.join(projectParent, o.original._path.split('/').pop())
+ let endpoint = path.join(app.getApiPath(), "project/extract-model")+queryString
+ xhr({uri: endpoint}, function (err, response, body) {
+ if(response.statusCode < 400){
+ let successModel = $(modals.projectExportSuccessHtml("Model", body)).modal()
+ }else{
+ body = JSON.parse(body)
+ let successModel = $(modals.projectExportErrorHtml(body.Reason, body.message)).modal()
+ }
+ });
+ },
+ handleExportWorkflowClick: function (o) {
+ let self = this
+ let projectParent = path.dirname(this.parent.projectPath) === '.' ? "" : path.dirname(this.parent.projectPath)
+ let queryString = "?srcPath="+o.original._path+"&dstPath="+path.join(projectParent, o.original._path.split('/').pop())
+ let endpoint = path.join(app.getApiPath(), "project/extract-workflow")+queryString
+ xhr({uri: endpoint}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ let successModel = $(modals.projectExportSuccessHtml("Workflow", body)).modal()
+ }
+ else {
+ body = JSON.parse(body)
+ let successModel = $(modals.projectExportErrorHtml(body.Reason, body.message)).modal()
+ }
+ })
+ },
+ handleExportCombineClick: function (o, download) {
+ let target = o.original._path
+ this.parent.exportAsCombine(target, download)
+ },
+ showContextMenuForNode: function (e) {
+ $('#models-jstree-view').jstree().show_contextmenu(this.nodeForContextMenu)
+ },
+ editWorkflowModel: function (o) {
+ let endpoint = path.join(app.getApiPath(), "workflow/edit-model")+"?path="+o.original._path
+ xhr({uri: endpoint, json: true}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ if(body.error){
+ let title = o.text + " Not Found"
+ let message = body.error
+ let modal = $(modals.duplicateWorkflowHtml(title, message)).modal()
+ }else{
+ window.location.href = path.join(app.routePrefix, "models/edit")+"?path="+body.file
+ }
+ }
+ });
+ },
+ setupJstree: function () {
+ var self = this;
+ $.jstree.defaults.contextmenu.items = (o, cb) => {
+ let nodeType = o.original.type
+ let zipTypes = ["workflow", "folder", "other", "mesh", "project", "workflow-group"]
+ let asZip = zipTypes.includes(nodeType)
+ // refresh context menu option
+ let refresh = {
+ "Refresh" : {
+ "label" : "Refresh",
+ "_disabled" : false,
+ "_class" : "font-weight-bold",
+ "separator_before" : false,
+ "separator_after" : o.text !== "trash",
+ "action" : function (data) {
+ if(nodeType === "root"){
+ self.refreshJSTree();
+ }else{
+ $('#models-jstree-view').jstree().refresh_node(o);
+ }
+ }
+ }
+ }
+ // For notebooks, workflows, sbml models, and other files
+ let open = {
+ "Open" : {
+ "label" : "Open",
+ "_disabled" : false,
+ "_class" : "font-weight-bolder",
+ "separator_before" : false,
+ "separator_after" : true,
+ "action" : function (data) {
+ if(nodeType === "workflow"){
+ window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+o.original._path+"&type=none";
+ }else if(nodeType === "project"){
+ window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+o.original._path
+ }else{
+ if(nodeType === "notebook") {
+ var identifier = "notebooks"
+ }else if(nodeType === "sbml-model") {
+ var identifier = "edit"
+ }else{
+ var identifier = "view"
+ }
+ window.open(path.join(app.getBasePath(), identifier, o.original._path));
+ }
+ }
+ }
+ }
+ // project contect menu option
+ let project = {
+ "Add_Model" : {
+ "label" : "Add Model",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "submenu" : {
+ "New_model" : {
+ "label" : "New Model",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "submenu" : {
+ "spatial" : {
+ "label" : "Spatial",
+ "_disabled" : true,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ console.log("Spatial Models Coming Soon!")
+ }
+ },
+ "nonspatial" : {
+ "label" : "Non-Spatial",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.newModelOrDirectory(o, true, false);
+ }
+ }
+ }
+ },
+ "Existing Model" : {
+ "label" : "Existing Model",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.addExistingModel(o)
+ }
+ }
+ }
+ }
+ }
+ // option for uploading files
+ let uploadFile = {
+ "Upload": {
+ "label" : o.type === "root" ? "File" : "Upload File",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : o.type !== "root",
+ "action" : function (data) {
+ self.uploadFile(o, "file")
+ }
+ }
+ }
+ // all upload options
+ let uploadAll = {
+ "Upload" : {
+ "label" : "Upload File",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : true,
+ "submenu" : {
+ "Model" : {
+ "label" : "StochSS Model",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.uploadFile(o, "model")
+ }
+ },
+ "SBML" : {
+ "label" : "SBML Model",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.uploadFile(o, "sbml")
+ }
+ },
+ "File" : uploadFile.Upload
+ }
+ }
+ }
+ // common to folder and root
+ let commonFolder = {
+ "New_Directory" : {
+ "label" : "New Directory",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.newModelOrDirectory(o, false, false);
+ }
+ },
+ "Upload": o.type === "root" ? uploadAll.Upload : uploadFile.Upload
+ }
+ if(o.type === "root" || o.type === "workflow-group" || o.type === "workflow")
+ var downloadLabel = "as .zip"
+ else if(asZip)
+ var downloadLabel = "Download as .zip"
+ else
+ var downloadLabel = "Download"
+ let download = {
+ "Download" : {
+ "label" : downloadLabel,
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : !(o.type === "root" || o.type === "workflow-group" || o.type === "workflow"),
+ "action" : function (data) {
+ if(o.original.text.endsWith('.zip')){
+ self.exportToZipFile(o);
+ }else{
+ self.getExportData(o, asZip)
+ }
+ }
+ }
+ }
+ // download options for .zip and COMBINE
+ let downloadWCombine = {
+ "Download" : {
+ "label" : "Download",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : true,
+ "submenu" : {
+ "DownloadAsZip": download.Download,
+ "downloadAsCombine" : {
+ "label" : "as COMBINE",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.handleExportCombineClick(o, true)
+ }
+ }
+ }
+ }
+ }
+ // menu option for creating new workflows
+ let newWorkflow = {
+ "NewWorkflow" : {
+ "label" : "New Workflow",
+ "_disabled" : (nodeType === "spatial") ? true : false,
+ "separator_before" : false,
+ "separator_after" : o.type !== "workflow-group",
+ "action" : function (data) {
+ self.addNewWorkflow(o)
+ }
+ }
+ }
+ // common to all models
+ let commonModel = {
+ "Edit" : {
+ "label" : "Edit",
+ "_disabled" : (nodeType === "spatial") ? true : false,
+ "_class" : "font-weight-bolder",
+ "separator_before" : false,
+ "separator_after" : true,
+ "action" : function (data) {
+ window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+o.original._path;
+ }
+ },
+ "Extract" : {
+ "label" : "Extract",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.handleExtractModelClick(o);
+ }
+ },
+ "New Workflow" : newWorkflow.NewWorkflow
+ }
+ // convert options for non-spatial models
+ let modelConvert = {
+ "Convert" : {
+ "label" : "Convert",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : true,
+ "submenu" : {
+ "Convert to Spatial" : {
+ "label" : "To Spatial Model",
+ "_disabled" : true,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.toSpatial(o)
+ }
+ },
+ "Convert to SBML" : {
+ "label" : "To SBML Model",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.toSBML(o)
+ }
+ }
+ }
+ }
+ }
+ // convert options for spatial models
+ let spatialConvert = {
+ "Convert" : {
+ "label" : "Convert",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : true,
+ "submenu" : {
+ "Convert to Model" : {
+ "label" : "Convert to Non Spatial",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.toModel(o, "Spatial");
+ }
+ },
+ "Convert to Notebook" : {
+ "label" : "Convert to Notebook",
+ "_disabled" : true,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ }
+ }
+ }
+ }
+ }
+ // specific to workflow groups
+ let workflowGroup = {
+ "Add Workflow" : {
+ "label" : "Add Workflow",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : true,
+ "submenu" : {
+ "New Workflow" : newWorkflow.NewWorkflow,
+ "Existing Workflow" : {
+ "label" : "Existing Workflow",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.addExistingWorkflow(o)
+ }
+ }
+ }
+ }
+ }
+ // specific to workflows
+ let workflow = {
+ "Convert to Notebook" : {
+ "label" : "To Notebook",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.toNotebook(o, "workflow")
+ }
+ },
+ "Start/Restart Workflow" : {
+ "label" : (o.original._status === "ready") ? "Start Workflow" : "Restart Workflow",
+ "_disabled" : true,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+
+ }
+ },
+ "Stop Workflow" : {
+ "label" : "Stop Workflow",
+ "_disabled" : true,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+
+ }
+ },
+ "Model" : {
+ "label" : "Model",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "submenu" : {
+ "Edit" : {
+ "label" : " Edit",
+ "_disabled" : !(o.original._status === "ready"),
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.editWorkflowModel(o)
+ }
+ },
+ "Extract" : {
+ "label" : "Extract",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.duplicateFileOrDirectory(o, "wkfl_model")
+ }
+ }
+ }
+ },
+ "Extract" : {
+ "label" : "Extract",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : true,
+ "action" : function (data) {
+ self.handleExportWorkflowClick(o)
+ }
+ },
+ }
+ // Specific to sbml files
+ let sbml = {
+ "Convert" : {
+ "label" : "Convert",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "submenu" : {
+ "Convert to Model" : {
+ "label" : "To Model",
+ "_disabled" : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.toModel(o, "SBML");
+ }
+ }
+ }
+ }
+ }
+ // common to all type except root and trash
+ let common = {
+ "Rename" : {
+ "label" : "Rename",
+ "_disabled" : (o.type === "workflow" && o.original._status === "running"),
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.renameNode(o);
+ }
+ },
+ "Duplicate" : {
+ "label" : (nodeType === "workflow") ? "Duplicate as new" : "Duplicate",
+ "_disabled" : (nodeType === "project" || nodeType === "workflow-group"),
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.duplicateFileOrDirectory(o, null)
+ }
+ },
+ "Delete" : {
+ "label" : "Delete",
+ "_disabled" : o.type === 'workflow-group' && self.parent.model.workflowGroups.length === 1 ? true : false,
+ "separator_before" : false,
+ "separator_after" : false,
+ "action" : function (data) {
+ self.deleteFile(o);
+ }
+ }
+ }
+ if (o.type === 'root'){
+ return $.extend(refresh, project, commonFolder, downloadWCombine, {"Rename": common.Rename})
+ }
+ if (o.type === 'folder' && o.text !== "trash") {
+ return $.extend(refresh, commonFolder, download, common)
+ }
+ if (o.text === "trash"){
+ return refresh
+ }
+ if (o.type === 'spatial') {
+ return $.extend(commonModel, spatialConvert, download, common)
+ }
+ if (o.type === 'nonspatial') {
+ return $.extend(commonModel, modelConvert, download, common)
+ }
+ if (o.type === 'workflow-group') {
+ return $.extend(refresh, workflowGroup, downloadWCombine)
+ }
+ if (o.type === 'workflow') {
+ return $.extend(open, workflow, downloadWCombine, common)
+ }
+ if (o.type === 'notebook' || o.type === "other") {
+ return $.extend(open, common)
+ }
+ if (o.type === 'sbml-model') {
+ return $.extend(open, sbml, common)
+ }
+ }
+ $(document).ready(function () {
+ $(document).on('shown.bs.modal', function (e) {
+ $('[autofocus]', e.target).focus();
+ });
+ $(document).on('dnd_start.vakata', function (data, element, helper, event) {
+ $('#models-jstree-view').jstree().load_all()
+ });
+ $('#models-jstree-view').jstree(self.treeSettings).bind("loaded.jstree", function (event, data) {
+ self.jstreeIsLoaded = true
+ }).bind("refresh.jstree", function (event, data) {
+ self.jstreeIsLoaded = true
+ });
+ $('#models-jstree-view').on('click.jstree', function(e) {
+ var parent = e.target.parentElement
+ var _node = parent.children[parent.children.length - 1]
+ var node = $('#models-jstree-view').jstree().get_node(_node)
+ if(_node.nodeName === "A" && $('#models-jstree-view').jstree().is_loaded(node) && node.type === "folder"){
+ $('#models-jstree-view').jstree().refresh_node(node)
+ }else{
+ let optionsButton = $(self.queryByHook("options-for-node"))
+ if(!self.nodeForContextMenu){
+ optionsButton.prop('disabled', false)
+ }
+ optionsButton.text("Actions for " + node.original.text)
+ self.nodeForContextMenu = node;
+ }
+ });
+ $('#models-jstree-view').on('dblclick.jstree', function(e) {
+ var file = e.target.text
+ var node = $('#models-jstree-view').jstree().get_node(e.target)
+ var _path = node.original._path;
+ if(file.endsWith('.mdl') || file.endsWith('.smdl')){
+ window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+_path;
+ }else if(file.endsWith('.ipynb')){
+ var notebookPath = path.join(app.getBasePath(), "notebooks", _path)
+ window.open(notebookPath, '_blank')
+ }else if(file.endsWith('.sbml')){
+ var openPath = path.join(app.getBasePath(), "edit", _path)
+ window.open(openPath, '_blank')
+ }else if(file.endsWith('.proj')){
+ window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+_path;
+ }else if(file.endsWith('.wkfl')){
+ window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+_path+"&type=none";
+ }else if(node.type === "folder" && $('#models-jstree-view').jstree().is_open(node) && $('#models-jstree-view').jstree().is_loaded(node)){
+ $('#models-jstree-view').jstree().refresh_node(node)
+ }else if(node.type === "other"){
+ var openPath = path.join(app.getBasePath(), "view", _path);
+ window.open(openPath, "_blank");
+ }
+ });
+ })
+ },
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
+ }
+});
\ No newline at end of file
diff --git a/client/views/initial-conditions-editor.js b/client/views/initial-conditions-editor.js
index 78e23f3fb5..f5845d4866 100644
--- a/client/views/initial-conditions-editor.js
+++ b/client/views/initial-conditions-editor.js
@@ -32,8 +32,13 @@ module.exports = View.extend({
var initialConditionType = e.target.textContent;
this.collection.addInitialCondition(initialConditionType);
},
- changeCollapseButtonText: function () {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+');
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
});
\ No newline at end of file
diff --git a/client/views/input.js b/client/views/input.js
index c34fbcf452..e52ea6d14c 100644
--- a/client/views/input.js
+++ b/client/views/input.js
@@ -14,21 +14,32 @@ module.exports = AmpersandInputView.extend({
AmpersandInputView.prototype.initialize.apply(this, arguments);
},
render: function () {
- if(this.label)
+ if(this.label) {
this.template = [
'
',
'',
+ '
',
''
].join('')
+ }else{
+ this.template = [
+ '
',
+ ' '
+ ].join('')
+ }
AmpersandInputView.prototype.render.apply(this, arguments);
+ this.shouldValidate = this.required || this.tests.length > 0
},
changeInputHandler: function (e) {
if(this.modelKey){
- var value = this.valueType === 'number' ? Number(e.target.value) : e.target.value;
+ var value = this.valueType === 'number' ? Number(e.target.value.trim()) : e.target.value.trim();
this.parent.model[this.modelKey] = value;
}
},
diff --git a/client/views/main.js b/client/views/main.js
index 31ee0a1138..77cdebe121 100644
--- a/client/views/main.js
+++ b/client/views/main.js
@@ -100,7 +100,7 @@ module.exports = View.extend({
}
});
- var homePath = window.location.pathname.startsWith("/user") ? "/hub/stochss" : "stochss/models"
+ var homePath = window.location.pathname.startsWith("/user") ? "/hub/stochss" : "stochss/home"
$(this.queryByHook("home-link")).prop('href', homePath);
return this;
diff --git a/client/views/mesh-editor.js b/client/views/mesh-editor.js
index fda6adb95f..426bca1ef2 100644
--- a/client/views/mesh-editor.js
+++ b/client/views/mesh-editor.js
@@ -27,8 +27,13 @@ module.exports = View.extend({
this.model.parent.trigger('mesh-update');
},
changeCollapseButtonText: function (e) {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+')
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
subviews: {
inputSubdomains: {
diff --git a/client/views/meta-data.js b/client/views/meta-data.js
new file mode 100644
index 0000000000..ba9c723e33
--- /dev/null
+++ b/client/views/meta-data.js
@@ -0,0 +1,277 @@
+var $ = require('jquery');
+var path = require('path');
+var xhr = require('xhr');
+//support files
+var app = require('../app');
+var tests = require('./tests');
+var modals = require('../modals');
+//collections
+var Collection = require('ampersand-collection');
+//models
+var Creator = require('../models/creator');
+//views
+var View = require('ampersand-view');
+var SelectView = require('ampersand-select-view');
+var InputView = require('./input');
+var CreatorListingView = require('./creator-listing');
+//templates
+var template = require('../templates/includes/metaData.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'change [data-hook=file-select-view]' : 'updateMetaData',
+ 'change [data-hook=description-input-view]' : 'updateFileDescription',
+ 'change [data-hook=creator-select-view]' : 'updateCreator',
+ 'click [data-hook=add-creator-btn]' : 'handleAddCreatorClick',
+ 'change [data-hook=email-input-view]' : 'toggleAddCreatorBtn',
+ 'click [data-hook=save-meta-data-button]' : 'saveMetaData',
+ 'click [data-hook=submit-meta-data-button]' : 'submitMetaData'
+ },
+ initialize: function(attrs, options) {
+ View.prototype.initialize.apply(this, arguments);
+ this.projectName = attrs.projectName;
+ this.files = attrs.files;
+ this.path = attrs.path;
+ this.download = attrs.download;
+ this.selectedFile = attrs.projectName;
+ this.selectedCreator = "New Creator"
+ let self = this
+ let queryString = "?path="+this.parent.projectPath+"&files="+this.files.join(',')
+ let endpoint = path.join(app.getApiPath(), "project/meta-data")+queryString
+ xhr({uri:endpoint, json:true}, function(err, response, body) {
+ if(response.statusCode < 400) {
+ self.metaData = body.meta_data
+ self.creators = body.creators
+ self.renderSubviews()
+ }
+ })
+ },
+ update: function() {},
+ renderSubviews: function () {
+ this.renderFilesSelectView()
+ this.renderCreatorListingView()
+ this.renderCreatorsSelectView()
+ let fileMetaData = this.metaData[this.selectedFile]
+ $(this.queryByHook("description-input-view")).val(fileMetaData["description"])
+ $(document).ready(function () {
+ $("html, body").animate({
+ scrollTop: $("#project-meta-data-container").offset().top - 50
+ }, false);
+ });
+ },
+ renderFilesSelectView: function() {
+ if(this.filesSelectView) {
+ this.filesSelectView.remove()
+ }
+ this.filesSelectView = new SelectView({
+ label: 'File: ',
+ name: 'file',
+ required: true,
+ idAttribute: 'cid',
+ textAttribute: 'name',
+ eagerValidate: true,
+ options: this.files,
+ value: this.projectName
+ });
+ this.registerRenderSubview(this.filesSelectView, "file-select-view");
+ },
+ renderCreatorListingView: function () {
+ if(this.creatorListingView) {
+ this.creatorListingView.remove()
+ }
+ let self = this
+ let listOfCreators = this.metaData[this.selectedFile].creators.map(function (key) {
+ return self.creators[key]
+ });
+ let creators = new Collection(listOfCreators, {model: Creator})
+ this.creatorListingView = this.renderCollection(creators, CreatorListingView, this.queryByHook("list-of-creators"))
+ },
+ renderCreatorsSelectView: function () {
+ if(this.creatorsSelectView){
+ this.creatorsSelectView.remove()
+ }
+ var options = Object.keys(this.creators)
+ options.unshift("New Creator")
+ this.creatorsSelectView = new SelectView({
+ label: 'Creator: ',
+ name: 'creator',
+ required: false,
+ idAttribute: 'cid',
+ textAttribute: 'name',
+ eagerValidate: true,
+ options: options,
+ value: this.selectedCreator
+ });
+ this.registerRenderSubview(this.creatorsSelectView, "creator-select-view")
+ },
+ registerRenderSubview: function (view, hook) {
+ this.registerSubview(view);
+ this.renderSubview(view, this.queryByHook(hook));
+ },
+ updateMetaData: function (e) {
+ this.selectedFile = e.target.selectedOptions.item(0).text
+ let fileMetaData = this.metaData[this.selectedFile]
+ $(this.queryByHook("description-input-view")).val(fileMetaData["description"])
+ this.renderCreatorListingView()
+ this.selectedCreator = "New Creator"
+ this.renderCreatorsSelectView()
+ this.updateCreator(undefined)
+ },
+ updateFileDescription: function (e) {
+ let description = e.target.value
+ this.metaData[this.selectedFile]["description"] = description
+ },
+ updateCreator: function (e) {
+ if(e){
+ this.selectedCreator = e.target.selectedOptions.item(0).text
+ }
+ var fName = this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator].fname
+ var lName = this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator].lname
+ var email = this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator].email
+ var organization = this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator].organization
+ $(this.queryByHook("given-name-input-view")).find("input").val(fName)
+ $(this.queryByHook("family-name-input-view")).find("input").val(lName)
+ $(this.queryByHook("email-input-view")).find("input").val(email)
+ $(this.queryByHook("organization-input-view")).find("input").val(organization)
+ $(this.queryByHook("add-creator-btn")).prop('disabled', this.selectedCreator === "New Creator")
+ if(this.metaData[this.selectedFile].creators.includes(this.selectedCreator)) {
+ $(this.queryByHook("add-creator-btn")).text("Update")
+ }else{
+ $(this.queryByHook("add-creator-btn")).text("Add")
+ }
+ },
+ handleAddCreatorClick: function (e) {
+ let fName = $(this.queryByHook("given-name-input-view")).find("input").val()
+ let lName = $(this.queryByHook("family-name-input-view")).find("input").val()
+ let email = $(this.queryByHook("email-input-view")).find("input").val()
+ let organization = $(this.queryByHook("organization-input-view")).find("input").val()
+ if(email in this.creators && this.selectedCreator === "New Creator"){
+ if(document.querySelector("#existingCreatorConfirmationModal")) {
+ document.querySelector("#existingCreatorConfirmationModal").remove()
+ }
+ let self = this
+ let message = "A creator already exists with this email. Do you wish to update that creators information?"
+ let modal = $(modals.existingCreatorConfirmationHtml(message)).modal()
+ let yesBtn = document.querySelector("#existingCreatorConfirmationModal .yes-modal-btn")
+ yesBtn.addEventListener('click', function (e) {
+ modal.modal('hide')
+ let creator = {"fname":fName,"lname":lName,"email":email,"organization":organization}
+ self.addCreator(email, creator)
+ })
+ console.log("A creator already exists with this name. Do you wish to update that creators data?")
+ }else if(this.selectedCreator !== "New Creator" && email !== this.selectedCreator){
+ let index = this.metaData[this.selectedFile].creators.indexOf(this.selectedCreator)
+ this.metaData[this.selectedFile].creators.splice(index, 1)
+ let creator = {"fname":fName,"lname":lName,"email":email,"organization":organization}
+ this.addCreator(email, creator)
+ }else{
+ let creator = {"fname":fName,"lname":lName,"email":email,"organization":organization}
+ this.addCreator(email, creator)
+ }
+ },
+ addCreator: function (key, creator) {
+ this.creators[key] = creator
+ if(!this.metaData[this.selectedFile].creators.includes(key)){
+ this.metaData[this.selectedFile].creators.push(key)
+ }
+ this.selectedCreator = key
+ this.renderCreatorsSelectView()
+ $(this.queryByHook("add-creator-btn")).text("Update")
+ this.renderCreatorListingView()
+ },
+ toggleAddCreatorBtn: function (e) {
+ $(this.queryByHook("add-creator-btn")).prop('disabled', !Boolean(e.target.value))
+ },
+ saveMetaData: function (e) {
+ let data = {"meta-data":this.metaData,"creators":this.creators}
+ let endpoint = path.join(app.getApiPath(), "project/meta-data")+"?path="+this.parent.projectPath
+ xhr({uri:endpoint, json:true, method:"post", body:data}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ console.log("Successfully Saved Mete Data")
+ }
+ });
+ },
+ submitMetaData: function (e) {
+ let self = this
+ $(this.parent.queryByHook("project-meta-data-container")).collapse('hide')
+ let data = {"meta-data":this.metaData,"creators":this.creators}
+ let queryString = "?path="+this.path+"&projectPath="+this.parent.projectPath
+ let endpoint = path.join(app.getApiPath(), "project/export-combine")+queryString
+ xhr({uri:endpoint, json:true, method:"post", body:data}, function (err, response, body) {
+ if(response.statusCode < 400) {
+ if(self.download) {
+ let downloadEP = path.join(app.getBasePath(), "/files", body.file_path);
+ window.open(downloadEP)
+ }else{
+ let modal = $(modals.projectExportSuccessHtml(body.file_type, body.message)).modal()
+ }
+ }else{
+ let modal = $(modals.projectExportErrorHtml(body.Reason, body.Message)).modal()
+ }
+ })
+ },
+ subviews: {
+ inputGivenName: {
+ hook: 'given-name-input-view',
+ prepareView: function (el) {
+ return new InputView({
+ parent: this,
+ required: false,
+ name: 'gvien-name',
+ label: 'Given Name: ',
+ tests: null,
+ modelKey: null,
+ valueType: 'string',
+ value: this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator]["fname"],
+ });
+ },
+ },
+ inputFamilyName: {
+ hook: 'family-name-input-view',
+ prepareView: function (el) {
+ return new InputView({
+ parent: this,
+ required: false,
+ name: 'family-name',
+ label: 'Family Name: ',
+ tests: null,
+ modelKey: null,
+ valueType: 'string',
+ value: this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator]["lname"],
+ });
+ },
+ },
+ inputEmailName: {
+ hook: 'email-input-view',
+ prepareView: function (el) {
+ return new InputView({
+ parent: this,
+ required: true,
+ placeholder: 'e-mail required',
+ name: 'email',
+ label: 'e-Mail: ',
+ tests: null,
+ modelKey: null,
+ valueType: 'string',
+ value: this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator]["email"],
+ });
+ },
+ },
+ inputOrganizationName: {
+ hook: 'organization-input-view',
+ prepareView: function (el) {
+ return new InputView({
+ parent: this,
+ required: false,
+ name: 'organization',
+ label: 'Organization: ',
+ tests: null,
+ modelKey: null,
+ valueType: 'string',
+ value: this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator]["organization"],
+ });
+ },
+ },
+ }
+});
\ No newline at end of file
diff --git a/client/views/model-settings.js b/client/views/model-settings.js
index c8c8638c9b..bc4d5e2356 100644
--- a/client/views/model-settings.js
+++ b/client/views/model-settings.js
@@ -27,8 +27,13 @@ module.exports = View.extend({
updateValid: function () {
},
changeCollapseButtonText: function (e) {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+')
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
subviews: {
inputSimEnd: {
diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js
index dea72bbe2d..a79707c4df 100644
--- a/client/views/model-state-buttons.js
+++ b/client/views/model-state-buttons.js
@@ -1,8 +1,10 @@
-var app = require('../app');
var xhr = require('xhr');
var path = require('path');
var Plotly = require('../lib/plotly');
var $ = require('jquery');
+//support file
+var app = require('../app');
+var modals = require('../modals');
//views
var View = require('ampersand-view');
//templates
@@ -13,7 +15,8 @@ module.exports = View.extend({
events: {
'click [data-hook=save]' : 'clickSaveHandler',
'click [data-hook=run]' : 'clickRunHandler',
- 'click [data-hook=start-workflow]' : 'clickStartWorkflowHandler',
+ 'click [data-hook=new-workflow]' : 'clickNewWorkflowHandler',
+ 'click [data-hook=return-to-project-btn]' : 'clickReturnToProjectHandler',
},
initialize: function (attrs, options) {
View.prototype.initialize.apply(this, arguments);
@@ -25,6 +28,9 @@ module.exports = View.extend({
render: function () {
View.prototype.render.apply(this, arguments);
this.togglePreviewWorkflowBtn();
+ if(this.model.directory.includes('.proj')) {
+ this.queryByHook("return-to-project-btn").style.display = "inline-block"
+ }
},
clickSaveHandler: function (e) {
this.saveModel(this.saved.bind(this));
@@ -36,8 +42,26 @@ module.exports = View.extend({
Plotly.purge(el)
this.saveModel(this.runModel.bind(this));
},
- clickStartWorkflowHandler: function (e) {
- window.location.href = path.join(app.getBasePath(), "stochss/workflow/selection")+"?path="+this.model.directory;
+ clickReturnToProjectHandler: function (e) {
+ let self = this
+ this.saveModel(function () {
+ self.saved()
+ var queryString = "?path="+path.dirname(self.model.directory)
+ window.location.href = path.join(app.getBasePath(), "/stochss/project/manager")+queryString;
+ })
+ },
+ clickNewWorkflowHandler: function (e) {
+ let self = this
+ this.saveModel(function () {
+ self.saved()
+ var queryString = "?path="+self.model.directory
+ if(self.model.directory.includes('.proj')) {
+ let parentPath = path.join(path.dirname(self.model.directory), "WorkflowGroup1.wkgp")
+ queryString += "&parentPath="+parentPath
+ }
+ let endpoint = path.join(app.getBasePath(), "stochss/workflow/selection")+queryString
+ window.location.href = endpoint
+ })
},
togglePreviewWorkflowBtn: function () {
var numSpecies = this.model.species.length;
@@ -45,7 +69,6 @@ module.exports = View.extend({
var numEvents = this.model.eventsCollection.length
var numRules = this.model.rules.length
$(this.queryByHook('run')).prop('disabled', (!numSpecies || (!numReactions && !numEvents && !numRules)))
- $(this.queryByHook('start-workflow')).prop('disabled', (!numSpecies || (!numReactions && !numEvents && !numRules)))
},
saveModel: function (cb) {
this.saving();
@@ -114,6 +137,10 @@ module.exports = View.extend({
let queryStr = "?cmd=read&outfile="+self.outfile+"&path="+model.directory
endpoint = path.join(app.getApiPath(), 'model/run')+queryStr;
xhr({ uri: endpoint, json: true}, function (err, response, body) {
+ if(typeof body === "string") {
+ body = body.replace(/NaN/g, null)
+ body = JSON.parse(body)
+ }
var data = body.Results;
if(response.statusCode >= 400){
self.ran(false);
diff --git a/client/views/model-viewer.js b/client/views/model-viewer.js
index 7360c01fc3..81a008ef56 100644
--- a/client/views/model-viewer.js
+++ b/client/views/model-viewer.js
@@ -8,20 +8,21 @@ var ReactionsViewer = require('./reactions-viewer');
var EventsViewer = require('./events-viewer');
var RulesViewer = require('./rules-viewer');
var ModelSettingsViewer = require('./model-settings-viewer');
-//models
-var Model = require('../models/model');
//templates
var template = require('../templates/includes/modelViewer.pug');
module.exports = View.extend({
template: template,
events: {
- 'click [data-hook=collapse-model]' : 'changeCollapseButtonText',
+ 'click [data-hook=collapse-model]' : 'changeCollapseButtonText'
},
initialize: function (attrs, options) {
View.prototype.initialize.apply(this, arguments);
- this.status = attrs.status;
- this.wkflType = attrs.type;
+ if(attrs.status) {
+ this.status = attrs.status;
+ }else{
+ this.status = "complete"
+ }
},
render: function () {
View.prototype.render.apply(this, arguments);
@@ -49,19 +50,18 @@ module.exports = View.extend({
this.registerRenderSubview(eventsViewer, "events-viewer-container");
this.registerRenderSubview(rulesViewer, "rules-viewer-container");
this.registerRenderSubview(modelSettingsViewer, "model-settings-viewer-container");
- if(this.status === 'complete'){
- this.enableCollapseButton();
- }
},
registerRenderSubview: function (view, hook) {
this.registerSubview(view);
this.renderSubview(view, this.queryByHook(hook));
},
- changeCollapseButtonText: function () {
- var text = $(this.queryByHook('collapse-model')).text();
- text === '+' ? $(this.queryByHook('collapse-model')).text('-') : $(this.queryByHook('collapse-model')).text('+');
- },
- enableCollapseButton: function () {
- $(this.queryByHook('collapse-model')).prop('disabled', false);
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
});
\ No newline at end of file
diff --git a/client/views/models-viewer.js b/client/views/models-viewer.js
new file mode 100644
index 0000000000..fcc2c3c7c5
--- /dev/null
+++ b/client/views/models-viewer.js
@@ -0,0 +1,29 @@
+var $ = require('jquery');
+//views
+var View = require('ampersand-view');
+var ModelViewer = require('./model-viewer');
+//templates
+var template = require('../templates/includes/modelsViewer.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=collapse-models]' : 'changeCollapseButtonText'
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments);
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments);
+ this.renderCollection(this.collection, ModelViewer, this.queryByHook('model-container'))
+ },
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
+ }
+})
\ No newline at end of file
diff --git a/client/views/parameter-sweep-settings.js b/client/views/parameter-sweep-settings.js
index 3594911ccd..94bf1e7376 100644
--- a/client/views/parameter-sweep-settings.js
+++ b/client/views/parameter-sweep-settings.js
@@ -126,8 +126,13 @@ module.exports = View.extend({
return parameter;
},
changeCollapseButtonText: function (e) {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+')
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
subviews: {
param1MinValueInput: {
diff --git a/client/views/parameters-editor.js b/client/views/parameters-editor.js
index 327f78e44b..cb4aa760ab 100644
--- a/client/views/parameters-editor.js
+++ b/client/views/parameters-editor.js
@@ -75,7 +75,12 @@ module.exports = View.extend({
});
},
changeCollapseButtonText: function (e) {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+');
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
});
\ No newline at end of file
diff --git a/client/views/parameters-viewer.js b/client/views/parameters-viewer.js
index 5bd1541360..9c09acb76c 100644
--- a/client/views/parameters-viewer.js
+++ b/client/views/parameters-viewer.js
@@ -17,8 +17,13 @@ module.exports = View.extend({
View.prototype.render.apply(this, arguments);
this.renderCollection(this.collection, ViewParameter, this.queryByHook('parameter-list'))
},
- changeCollapseButtonText: function () {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+');
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
});
\ No newline at end of file
diff --git a/client/views/plots-view.js b/client/views/plots-view.js
new file mode 100644
index 0000000000..22c871a093
--- /dev/null
+++ b/client/views/plots-view.js
@@ -0,0 +1,53 @@
+var $ = require('jquery');
+var path = require('path');
+var xhr = require('xhr');
+//support files
+var Plotly = require('../lib/plotly');
+var app = require('../app');
+//views
+var View = require('ampersand-view');
+//templates
+var template = require('../templates/includes/plotsView.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=collapse-plot]' : 'changeCollapseButtonText',
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments)
+ this.path = attrs.path ? attrs.path : this.parent.model.path
+ this.heading = attrs.heading ? attrs.heading + " - " + this.model.key : this.model.key
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments)
+ this.getPlot()
+ },
+ getPlot: function () {
+ var self = this;
+ var plotArgs = {"title":this.model.title,"xaxis":this.model.xaxis,"yaxis":this.model.yaxis}
+ var data = {"plt_key":this.model.key, "plt_data":plotArgs}
+ var endpoint = path.join(app.getApiPath(), 'workflow/plot-results')+"?path="+this.path+"&data="+JSON.stringify(data);
+ xhr({uri: endpoint, json: true}, function (err, response, body) {
+ if(response.statusCode >= 400) {
+ $(self.queryByHook(self.model.key+self.model.stamp)).html(body.Message)
+ }else{
+ self.plotFigure(body)
+ }
+ });
+ },
+ plotFigure: function (figure) {
+ var self = this;
+ var el = this.queryByHook(this.model.key+this.model.stamp);
+ Plotly.newPlot(el, figure);
+ },
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
+ }
+})
\ No newline at end of file
diff --git a/client/views/project-viewer.js b/client/views/project-viewer.js
new file mode 100644
index 0000000000..d9f4d476d0
--- /dev/null
+++ b/client/views/project-viewer.js
@@ -0,0 +1,55 @@
+var path = require('path');
+var $ = require('jquery');
+//Views
+var View = require('ampersand-view');
+var ModelsCollectionView = require('./models-viewer');
+var WorkflowGroupsCollectionView = require('./workflow-groups-viewer');
+//templates
+var template = require('../templates/includes/projectViewer.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=collapse-project]' : 'changeCollapseButtonText'
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments)
+ this.name = attrs.name
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments)
+ this.renderModelsCollection()
+ this.renderWorkflowGroupsCollection()
+ },
+ renderModelsCollection: function () {
+ if(this.modelsCollectionView) {
+ this.modelsCollectionView.remove()
+ }
+ this.modelsCollectionView = new ModelsCollectionView({
+ collection: this.model.models
+ });
+ this.registerRenderSubview(this.modelsCollectionView, "models-collection-container")
+ },
+ renderWorkflowGroupsCollection: function () {
+ if(this.workflowGroupsCollectionView) {
+ this.workflowGroupsCollectionView.remove()
+ }
+ this.workflowGroupsCollectionView = new WorkflowGroupsCollectionView({
+ collection: this.model.workflowGroups
+ });
+ this.registerRenderSubview(this.workflowGroupsCollectionView, "workflow-groups-collection-container")
+ },
+ registerRenderSubview: function (view, hook) {
+ this.registerSubview(view);
+ this.renderSubview(view, this.queryByHook(hook));
+ },
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
+ }
+});
\ No newline at end of file
diff --git a/client/views/reaction-details.js b/client/views/reaction-details.js
index 6f388eda9d..bd26e34b37 100644
--- a/client/views/reaction-details.js
+++ b/client/views/reaction-details.js
@@ -32,9 +32,11 @@ module.exports = View.extend({
},
'model.hasConflict': {
type: function (el, value, previousValue) {
- this.model.hasConflict ?
- $(this.queryByHook('conflicting-modes-message')).collapse('show') :
+ if(value) {
+ $(this.queryByHook('conflicting-modes-message')).collapse('show')
+ }else{
$(this.queryByHook('conflicting-modes-message')).collapse('hide')
+ }
},
hook: 'conflicting-modes-message',
},
@@ -49,26 +51,11 @@ module.exports = View.extend({
this.model.on("change:reaction_type", function (model) {
self.updateStoichSpeciesForReactionType(model.reactionType);
});
- this.model.collection.parent.parameters.on('add remove', this.render, this);
},
render: function () {
View.prototype.render.apply(this, arguments);
- var options = [];
- if(this.model.collection.parent.parameters.length <= 0){
- options = ["Custom propensity"];
- }
- else{
- options = this.getReactionTypeLabels();
- }
var self = this;
- var reactionTypeSelectView = new SelectView({
- label: 'Reaction Type:',
- name: 'reaction-type',
- required: true,
- idAttribute: 'cid',
- options: options,
- value: ReactionTypes[self.model.reactionType].label,
- });
+ this.renderReactionTypesSelectView()
var rateParameterView = new SelectView({
label: '',
name: 'rate',
@@ -109,8 +96,6 @@ module.exports = View.extend({
fieldTitle: 'Products',
isReactants: false
});
- this.registerRenderSubview(reactionTypeSelectView, 'select-reaction-type');
- this.renderReactionTypes();
if(this.model.reactionType === 'custom-propensity'){
this.registerRenderSubview(propensityView, 'select-rate-parameter')
var inputField = this.queryByHook('select-rate-parameter').children[0].children[1];
@@ -140,6 +125,31 @@ module.exports = View.extend({
},
updateValid: function () {
},
+ renderReactionTypesSelectView: function () {
+ if(this.reactionTypesSelectView) {
+ this.reactionTypesSelectView.remove()
+ }
+
+ var options = [];
+ if(this.model.collection.parent.parameters.length <= 0){
+ options = ["Custom propensity"];
+ }
+ else{
+ options = this.getReactionTypeLabels();
+ }
+
+ this.reactionTypesSelectView = new SelectView({
+ label: 'Reaction Type:',
+ name: 'reaction-type',
+ required: true,
+ idAttribute: 'cid',
+ options: options,
+ value: ReactionTypes[this.model.reactionType].label,
+ });
+
+ this.registerRenderSubview(this.reactionTypesSelectView, 'select-reaction-type');
+ this.renderReactionTypes();
+ },
selectRateParam: function (e) {
if(this.model.reactionType !== 'custom-propensity') {
var val = e.target.selectedOptions.item(0).text;
diff --git a/client/views/reaction-listing.js b/client/views/reaction-listing.js
index bd416f5f5d..24f110abc9 100644
--- a/client/views/reaction-listing.js
+++ b/client/views/reaction-listing.js
@@ -46,6 +46,9 @@ module.exports = View.extend({
$(document).on('shown.bs.modal', function (e) {
$('[autofocus]', e.target).focus();
});
+ $(document).on('hide.bs.modal', '.modal', function (e) {
+ e.target.remove()
+ });
if(!this.model.annotation){
$(this.queryByHook('edit-annotation-btn')).text('Add')
}
@@ -78,7 +81,7 @@ module.exports = View.extend({
}
});
okBtn.addEventListener('click', function (e) {
- self.model.annotation = input.value;
+ self.model.annotation = input.value.trim();
self.parent.renderReactionListingView();
modal.modal('hide');
});
diff --git a/client/views/reactions-editor.js b/client/views/reactions-editor.js
index 5707847031..ae53fa0f00 100644
--- a/client/views/reactions-editor.js
+++ b/client/views/reactions-editor.js
@@ -102,6 +102,9 @@ module.exports = View.extend({
$(this.queryByHook('add-reaction-full')).prop('hidden', true);
$(this.queryByHook('add-reaction-partial')).prop('hidden', false);
}
+ if(this.selectedReaction){
+ this.selectedReaction.detailsView.renderReactionTypesSelectView()
+ }
},
setSelectedReaction: function (reaction) {
this.collection.each(function (m) { m.selected = false; });
@@ -109,7 +112,7 @@ module.exports = View.extend({
this.selectedReaction = reaction;
},
setDetailsView: function (reaction) {
- reaction.detailsView = reaction.detailsView || this.newDetailsView(reaction);
+ reaction.detailsView = this.newDetailsView(reaction);
this.detailsViewSwitcher.set(reaction.detailsView);
},
handleAddReactionClick: function (e) {
@@ -137,8 +140,13 @@ module.exports = View.extend({
return detailsView
},
changeCollapseButtonText: function (e) {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+')
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
getDefaultSpecie: function () {
var value = this.collection.parent.species.models[0];
diff --git a/client/views/reactions-viewer.js b/client/views/reactions-viewer.js
index a28993130f..1c9aef5414 100644
--- a/client/views/reactions-viewer.js
+++ b/client/views/reactions-viewer.js
@@ -17,8 +17,13 @@ module.exports = View.extend({
View.prototype.render.apply(this, arguments);
this.renderCollection(this.collection, ViewReactions, this.queryByHook('reaction-list'))
},
- changeCollapseButtonText: function () {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+');
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
});
\ No newline at end of file
diff --git a/client/views/rules-editor.js b/client/views/rules-editor.js
index af5a57f634..22e9400fd0 100644
--- a/client/views/rules-editor.js
+++ b/client/views/rules-editor.js
@@ -64,7 +64,12 @@ module.exports = View.extend({
});
},
changeCollapseButtonText: function (e) {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+');
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
});
\ No newline at end of file
diff --git a/client/views/rules-viewer.js b/client/views/rules-viewer.js
index cc04479c6d..4d980e4db8 100644
--- a/client/views/rules-viewer.js
+++ b/client/views/rules-viewer.js
@@ -17,8 +17,13 @@ module.exports = View.extend({
View.prototype.render.apply(this, arguments);
this.renderCollection(this.collection, ViewRules, this.queryByHook('rules-list'))
},
- changeCollapseButtonText: function () {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+');
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
});
\ No newline at end of file
diff --git a/client/views/sbml-component-editor.js b/client/views/sbml-component-editor.js
index 5a7f593eb0..577a065692 100644
--- a/client/views/sbml-component-editor.js
+++ b/client/views/sbml-component-editor.js
@@ -10,12 +10,8 @@ var template = require('../templates/includes/sbmlComponentEditor.pug');
module.exports = View.extend({
template: template,
events: {
- 'click [data-hook=collapse]' : function () {
- this.changeCollapseButtonText('collapse');
- },
- 'click [data-hook=collapse-function-definitions]' : function () {
- this.changeCollapseButtonText('collapse-function-definitions');
- },
+ 'click [data-hook=collapse]' : 'changeCollapseButtonText',
+ 'click [data-hook=collapse-function-definitions]' : 'changeCollapseButtonText'
},
initialize: function (attrs, options) {
View.prototype.initialize.apply(this, arguments);
@@ -42,8 +38,13 @@ module.exports = View.extend({
});
});
},
- changeCollapseButtonText: function (hook) {
- var text = $(this.queryByHook(hook)).text();
- text === '+' ? $(this.queryByHook(hook)).text('-') : $(this.queryByHook(hook)).text('+');
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
});
\ No newline at end of file
diff --git a/client/views/simulation-settings.js b/client/views/simulation-settings.js
index 186c092efa..6ddff6c62c 100644
--- a/client/views/simulation-settings.js
+++ b/client/views/simulation-settings.js
@@ -50,8 +50,13 @@ module.exports = View.extend({
updateValid: function () {
},
changeCollapseButtonText: function (e) {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+')
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
handleSelectSimulationAlgorithmClick: function (e) {
var value = e.target.dataset.name;
diff --git a/client/views/species-editor.js b/client/views/species-editor.js
index 910741cdd6..989bef7f8f 100644
--- a/client/views/species-editor.js
+++ b/client/views/species-editor.js
@@ -24,7 +24,7 @@ module.exports = View.extend({
View.prototype.initialize.apply(this, arguments);
this.baseModel = this.collection.parent;
this.tooltips = Tooltips.speciesEditor
- this.collection.on('update-species', function (compID, specie, isNameUpdate) {
+ this.collection.on('update-species', function (compID, specie, isNameUpdate, isDefaultMode) {
self.collection.parent.reactions.map(function (reaction) {
reaction.reactants.map(function (reactant) {
if(reactant.specie.compID === compID) {
@@ -38,7 +38,7 @@ module.exports = View.extend({
});
if(isNameUpdate) {
reaction.buildSummary();
- }else{
+ }else if(!isDefaultMode || specie.compID === self.collection.models[self.collection.length-1].compID){
reaction.checkModes();
}
});
@@ -110,14 +110,15 @@ module.exports = View.extend({
},
getDefaultSpeciesMode: function (e) {
var self = this;
- this.setAllSpeciesModes(e.target.dataset.name, function () {
- self.collection.trigger('update-species', specie.compID, specie, false)
+ this.setAllSpeciesModes(e.target.dataset.name, function (specie) {
+ self.collection.trigger('update-species', specie.compID, specie, false, true)
});
},
- setAllSpeciesModes: function (defaultMode) {
+ setAllSpeciesModes: function (defaultMode, cb) {
this.collection.parent.defaultMode = defaultMode;
this.collection.map(function (specie) {
specie.mode = defaultMode
+ cb(specie)
});
if(defaultMode === "dynamic"){
this.renderSpeciesAdvancedView()
@@ -170,8 +171,13 @@ module.exports = View.extend({
});
});
},
- changeCollapseButtonText: function () {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+');
- },
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
+ }
});
\ No newline at end of file
diff --git a/client/views/species-viewer.js b/client/views/species-viewer.js
index 5704033fba..d4a9ae0b9e 100644
--- a/client/views/species-viewer.js
+++ b/client/views/species-viewer.js
@@ -17,8 +17,13 @@ module.exports = View.extend({
View.prototype.render.apply(this, arguments);
this.renderCollection(this.collection, ViewSpecie, this.queryByHook('specie-list'))
},
- changeCollapseButtonText: function () {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+');
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
});
\ No newline at end of file
diff --git a/client/views/tests.js b/client/views/tests.js
index 192ccc38c9..d6d276d138 100644
--- a/client/views/tests.js
+++ b/client/views/tests.js
@@ -10,15 +10,15 @@ module.exports = {
return "Invalid characters. Please only use letters, numbers, or underscores."
}
},
- function (text) {
- if(this.parent.model && this.parent.model.collection){
- var isDuplicate = this.parent.model.collection.some(function (m) { return m.name === text && this.parent.model !== m;
- }, this);
- if (isDuplicate) {
- return "No duplicate entries."
- }
- }
- },
+ // function (text) {
+ // if(this.parent.model && this.parent.model.collection){
+ // var isDuplicate = this.parent.model.collection.some(function (m) { return m.name === text && this.parent.model !== m;
+ // }, this);
+ // if (isDuplicate) {
+ // return "No duplicate entries."
+ // }
+ // }
+ // },
],
valueTests: [
function (value) {
diff --git a/client/views/view-events.js b/client/views/view-events.js
index 0625fd5400..d1b8a53ca6 100644
--- a/client/views/view-events.js
+++ b/client/views/view-events.js
@@ -1,3 +1,4 @@
+var $ = require('jquery');
//views
var View = require('ampersand-view');
var AssignmentsViewer = require('./event-assignments-viewer');
@@ -16,12 +17,7 @@ module.exports = View.extend({
hook: 'event-trigger-persistent',
type: 'booleanAttribute',
name: 'checked',
- },
- 'model.useValuesFromTriggerTime': {
- hook: 'use-values-from-trigger-time',
- type: 'booleanAttribute',
- name: 'checked',
- },
+ }
},
initialize: function (attrs, options) {
View.prototype.initialize.apply(this, arguments);
@@ -33,6 +29,11 @@ module.exports = View.extend({
collection: this.model.eventAssignments
});
this.registerRenderSubview(assignmentsViewer, 'assignment-viewer');
+ if(this.model.useValuesFromTriggerTime) {
+ $(this.queryByHook("trigger-time")).prop('checked', true)
+ }else{
+ $(this.queryByHook("assignment-time")).prop('checked', true)
+ }
},
registerRenderSubview: function (view, hook) {
this.registerSubview(view);
diff --git a/client/views/view-reactions.js b/client/views/view-reactions.js
index 491611d48e..0a24116766 100644
--- a/client/views/view-reactions.js
+++ b/client/views/view-reactions.js
@@ -14,8 +14,9 @@ module.exports = View.extend({
render: function () {
View.prototype.render.apply(this, arguments);
katex.render(this.model.summary, this.queryByHook('summary'), {
- displayMode: true,
- output: 'mathml'
+ displayMode: false,
+ output: 'html',
+ throwOnError: false
});
},
});
\ No newline at end of file
diff --git a/client/views/workflow-editor.js b/client/views/workflow-editor.js
index 392a19a99e..b2f48b6305 100644
--- a/client/views/workflow-editor.js
+++ b/client/views/workflow-editor.js
@@ -39,15 +39,11 @@ module.exports = View.extend({
this.renderWorkflowStateButtons()
}else{
this.collapseContainer()
- $(this.queryByHook('collapse-settings')).prop('disabled', true);
this.renderSimulationSettingViewer()
if(this.type === "parameterSweep"){
this.renderParameterSweepSettingsViewer()
}
}
- if(this.status === "complete"){
- this.enableCollapseButton();
- }
},
registerRenderSubview: function (view, hook) {
this.registerSubview(view);
@@ -84,11 +80,14 @@ module.exports = View.extend({
this.registerRenderSubview(parameterSweepSettingsView, 'param-sweep-settings-container');
},
renderWorkflowStateButtons: function () {
- let workflowStateButtons = new WorkflowStateButtonsView({
+ if(this.workflowStateButtons) {
+ this.workflowStateButtons.remove()
+ }
+ this.workflowStateButtons = new WorkflowStateButtonsView({
model: this.model,
type: this.type,
});
- this.registerRenderSubview(workflowStateButtons, 'workflow-state-buttons-container');
+ this.registerRenderSubview(this.workflowStateButtons, 'workflow-state-buttons-container');
},
validatePsweep: function () {
let species = this.model.species;
@@ -124,15 +123,17 @@ module.exports = View.extend({
}).length) // if true child exits within the model
return exists
},
- changeCollapseButtonText: function () {
- var text = $(this.queryByHook('collapse-settings')).text();
- text === '+' ? $(this.queryByHook('collapse-settings')).text('-') : $(this.queryByHook('collapse-settings')).text('+');
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
collapseContainer: function () {
$(this.queryByHook("workflow-editor-container")).collapse()
- this.changeCollapseButtonText()
- },
- enableCollapseButton: function () {
- $(this.queryByHook('collapse-settings')).prop('disabled', false);
+ $(this.queryByHook("collapse-settings")).click()
},
});
\ No newline at end of file
diff --git a/client/views/workflow-group-viewer.js b/client/views/workflow-group-viewer.js
new file mode 100644
index 0000000000..f9400435dd
--- /dev/null
+++ b/client/views/workflow-group-viewer.js
@@ -0,0 +1,42 @@
+var $ = require('jquery');
+//views
+var View = require('ampersand-view');
+var WorkflowCollectionsViewer = require('./workflows-viewer');
+//templates
+var template = require('../templates/includes/workflowGroupViewer.pug')
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=collapse-workflow-group]' : 'changeCollapseButtonText'
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments)
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments)
+ this.renderWorkflowsCollectionViewer()
+ },
+ renderWorkflowsCollectionViewer: function () {
+ if(this.workflowsCollectionViewer) {
+ this.workflowsCollectionViewer.remove()
+ }
+ this.workflowsCollectionViewer = new WorkflowCollectionsViewer({
+ collection: this.model.workflows
+ });
+ this.registerRenderSubview(this.workflowsCollectionViewer, "workflows-viewer-container")
+ },
+ registerRenderSubview: function (view, hook) {
+ this.registerSubview(view);
+ this.renderSubview(view, this.queryByHook(hook));
+ },
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
+ }
+})
\ No newline at end of file
diff --git a/client/views/workflow-groups-viewer.js b/client/views/workflow-groups-viewer.js
new file mode 100644
index 0000000000..cd7dcd3c05
--- /dev/null
+++ b/client/views/workflow-groups-viewer.js
@@ -0,0 +1,29 @@
+var $ = require('jquery');
+//views
+var View = require('ampersand-view');
+var WorkflowGroupView = require('./workflow-group-viewer');
+//templates
+var template = require('../templates/includes/workflowGroupsViewer.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=collapse-workflow-groups]' : 'changeCollapseButtonText'
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments)
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments)
+ this.renderCollection(this.collection, WorkflowGroupView, this.queryByHook('workflow-group-container'))
+ },
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
+ }
+})
\ No newline at end of file
diff --git a/client/views/workflow-info.js b/client/views/workflow-info.js
index 73f4f28ee6..371be73647 100644
--- a/client/views/workflow-info.js
+++ b/client/views/workflow-info.js
@@ -59,7 +59,7 @@ module.exports = View.extend({
expandInfoContainer: function () {
this.enableCollapseButton();
$(this.queryByHook('workflow-info')).collapse('show');
- this.changeCollapseButtonText("collapse")
+ $(this.queryByHook("collapse")).click()
},
expandLogContainers: function () {
if(this.listOfWarnings.length) {
@@ -78,8 +78,13 @@ module.exports = View.extend({
$(this.queryByHook('list-of-notes')).html(listOfNotes);
}
},
- changeCollapseButtonText: function () {
- var text = $(this.queryByHook("collapse")).text();
- text === '+' ? $(this.queryByHook("collapse")).text('-') : $(this.queryByHook("collapse")).text('+');
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
});
diff --git a/client/views/workflow-results.js b/client/views/workflow-results.js
index 7338b08a4f..510163d19a 100644
--- a/client/views/workflow-results.js
+++ b/client/views/workflow-results.js
@@ -16,24 +16,12 @@ var parameterSweepResultsTemplate = require('../templates/includes/parameterSwee
module.exports = View.extend({
events: {
- 'click [data-hook=collapse-stddevrange]' : function () {
- this.changeCollapseButtonText("collapse-stddevrange");
- },
- 'click [data-hook=collapse-trajectories]' : function () {
- this.changeCollapseButtonText("collapse-trajectories");
- },
- 'click [data-hook=collapse-stddev]' : function () {
- this.changeCollapseButtonText("collapse-stddev");
- },
- 'click [data-hook=collapse-trajmean]' : function () {
- this.changeCollapseButtonText("collapse-trajmean");
- },
- 'click [data-hook=collapse-psweep]' : function () {
- this.changeCollapseButtonText("collapse-psweep");
- },
- 'click [data-hook=collapse]' : function () {
- this.changeCollapseButtonText("collapse");
- },
+ 'click [data-hook=collapse-stddevrange]' : 'handleCollapseStddevrangeClick',
+ 'click [data-hook=collapse-trajectories]' : 'handleCollapseTrajectoriesClick',
+ 'click [data-hook=collapse-stddev]' : 'handleCollapseStddevClick',
+ 'click [data-hook=collapse-trajmean]' : 'handleCollapseTrajmeanClick',
+ 'click [data-hook=collapse-psweep]' : 'handleCollapsePsweepClick',
+ 'click [data-hook=collapse]' : 'changeCollapseButtonText',
'change [data-hook=title]' : 'setTitle',
'change [data-hook=xaxis]' : 'setXAxis',
'change [data-hook=yaxis]' : 'setYAxis',
@@ -41,13 +29,12 @@ module.exports = View.extend({
'change [data-hook=feature-extraction-list]' : 'getPlotForFeatureExtractor',
'change [data-hook=ensemble-aggragator-list]' : 'getPlotForEnsembleAggragator',
'click [data-hook=plot]' : function (e) {
- var type = e.target.id
- if(this.plots[type]) {
- $(this.queryByHook("edit-plot-args")).collapse("show");
- }else{
- this.getPlot(type);
- e.target.innerText = "Edit Plot"
- }
+ $(this.queryByHook("edit-plot-args")).collapse("show");
+ $(document).ready(function () {
+ $("html, body").animate({
+ scrollTop: $("#edit-plot-args").offset().top - 50
+ }, false);
+ });
},
'click [data-hook=download-png-custom]' : function (e) {
var type = e.target.id;
@@ -57,6 +44,12 @@ module.exports = View.extend({
var type = e.target.id;
this.exportToJsonFile(this.plots[type], type)
},
+ 'click [data-hook=save-plot]' : function (e) {
+ var type = e.target.id;
+ e.target.disabled = true
+ $("button[data-hook=save-plot]").filter("#"+type).text('Saved Plot to Project Viewer')
+ this.savePlot(type)
+ },
'click [data-hook=download-results-csv]' : 'handlerDownloadResultsCsvClick',
},
initialize: function (attrs, options) {
@@ -71,6 +64,7 @@ module.exports = View.extend({
this.ensembleAggragator = "avg";
this.plots = {}
this.plotArgs = {}
+ this.savedPlots = this.parent.settings.resultsSettings.outputs
},
render: function () {
if(this.type === "parameterSweep"){
@@ -130,9 +124,14 @@ module.exports = View.extend({
},
updateValid: function () {
},
- changeCollapseButtonText: function (source) {
- var text = $(this.queryByHook(source)).text();
- text === '+' ? $(this.queryByHook(source)).text('-') : $(this.queryByHook(source)).text('+');
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
setTitle: function (e) {
this.plotArgs['title'] = e.target.value
@@ -162,6 +161,7 @@ module.exports = View.extend({
var self = this;
var el = this.queryByHook(type)
Plotly.purge(el)
+ this.queryAll("#"+type).filter(function (el) {return el.dataset.hook === "plot-spinner"})[0].style.display = "block"
var data = {}
if(type === 'psweep'){
let key = this.getPsweepKey()
@@ -181,6 +181,17 @@ module.exports = View.extend({
}else{
self.plots[type] = body
self.plotFigure(body, type);
+ let plotSaved = Boolean(self.savedPlots.filter(function (plot) {
+ if(plot.key === data.plt_key)
+ return true
+ }).length > 0)
+ let saveBtn = $("button[data-hook=save-plot]").filter("#"+type)
+ if(!self.parent.wkflPath.includes('.proj')) {
+ saveBtn.hide()
+ }else if(plotSaved) {
+ saveBtn.prop('disabled', true)
+ saveBtn.text('Plot Saved to Project Viewer')
+ }
}
});
},
@@ -190,13 +201,15 @@ module.exports = View.extend({
var el = this.queryByHook(hook)
Plotly.newPlot(el, figure)
this.queryAll("#" + type).forEach(function (el) {
- if(el.disabled){
+ if(el.dataset.hook === "plot-spinner"){
+ el.style.display = "none"
+ }else if(el.disabled){
el.disabled = false;
}
});
},
clickDownloadPNGButton: function (type) {
- var pngButton = $('div[data-hook*='+type+'] a[data-title*="Download plot as a png"]')[0]
+ var pngButton = $('div[data-hook='+type+'] a[data-title*="Download plot as a png"]')[0]
pngButton.click()
},
exportToJsonFile: function (jsonData, plotType) {
@@ -224,12 +237,13 @@ module.exports = View.extend({
},
exportToZipFile: function (resultsPath) {
var endpoint = path.join("files", resultsPath);
- window.location.href = endpoint
+ window.open(endpoint)
},
expandContainer: function () {
$(this.queryByHook('workflow-results')).collapse('show');
- $(this.queryByHook('collapse')).prop('disabled', false);
- this.changeCollapseButtonText("collapse")
+ let collapseBtn = $(this.queryByHook('collapse'));
+ collapseBtn.prop('disabled', false)
+ collapseBtn.click()
if(this.type === "parameterSweep"){
this.getPlot("psweep")
}else{
@@ -270,6 +284,71 @@ module.exports = View.extend({
}
return key
},
+ savePlot: function (type) {
+ var species = []
+ if(type === "psweep"){
+ type = this.getPsweepKey()
+ species = [this.speciesOfInterest]
+ }else{
+ species = this.species.map(function (specie) { return specie.name; });
+ }
+ let stamp = this.getTimeStamp()
+ var plotInfo = {"key":type, "stamp":stamp, "species":species};
+ plotInfo = Object.assign({}, plotInfo, this.plotArgs)
+ this.savedPlots.push(plotInfo)
+ let queryString = "?path="+path.join(this.parent.wkflPath, "settings.json")
+ let endpoint = path.join(app.getApiPath(), "workflow/save-plot")+queryString
+ xhr({uri: endpoint, method: "post", json: true, body: plotInfo}, function (err, response, body) {
+ if(response.statusCode > 400) {
+ console.log(body.message)
+ }
+ })
+ },
+ getTimeStamp: function () {
+ var date = new Date()
+ let year = date.getFullYear().toString().slice(-2)
+ let month = date.getMonth() >= 10 ? date.getMonth().toString() : "0" + date.getMonth()
+ let day = date.getDate() >= 10 ? date.getDate().toString() : "0" + date.getDate()
+ let hour = date.getHours() >= 10 ? date.getHours().toString() : "0" + date.getHours()
+ let minutes = date.getMinutes() >= 10 ? date.getMinutes().toString() : "0" + date.getMinutes()
+ let seconds = date.getSeconds() >= 10 ? date.getSeconds().toString() : "0" + date.getSeconds()
+ return parseInt(year+month+day+hour+minutes+seconds)
+ },
+ handleCollapseStddevrangeClick: function (e) {
+ this.changeCollapseButtonText(e)
+ let type = "stddevran"
+ if(!this.plots[type]){
+ this.getPlot(type);
+ }
+ },
+ handleCollapseTrajectoriesClick: function (e) {
+ this.changeCollapseButtonText(e)
+ let type = "trajectories"
+ if(!this.plots[type]){
+ this.getPlot(type);
+ }
+ },
+ handleCollapseStddevClick: function (e) {
+ this.changeCollapseButtonText(e)
+ let type = "stddev"
+ if(!this.plots[type]){
+ this.getPlot(type);
+ }
+ },
+ handleCollapseTrajmeanClick: function (e) {
+ this.changeCollapseButtonText(e)
+ let type = "avg"
+ if(!this.plots[type]){
+ this.getPlot(type);
+ }
+ },
+ handleCollapsePsweepClick: function (e) {
+ this.changeCollapseButtonText(e)
+ let type = "psweep"
+ if(!this.plots[type]){
+ this.getPlot(type);
+ }
+ },
subviews: {
inputTitle: {
hook: 'title',
diff --git a/client/views/workflow-state-buttons.js b/client/views/workflow-state-buttons.js
index c7eebad465..2c6e45c38f 100644
--- a/client/views/workflow-state-buttons.js
+++ b/client/views/workflow-state-buttons.js
@@ -22,26 +22,35 @@ module.exports = View.extend({
},
render: function () {
View.prototype.render.apply(this, arguments);
+ $(this.queryByHook("save")).prop('disabled', this.parent.parent.modelLoadError)
+ $(this.queryByHook("start-workflow")).prop('disabled', this.parent.parent.modelLoadError)
+ $(this.queryByHook("edit-model")).prop('disabled', this.parent.parent.modelLoadError)
},
- clickSaveHandler: function (e) {
+ clickSaveHandler: function (e, cb) {
this.saving();
var self = this;
var model = this.model
- var optType = document.URL.endsWith(".mdl") ? "sn" : "se";
+ var optType = this.parent.parent.urlPathParam.endsWith(".mdl") ? "sn" : "se";
this.saveModel(function () {
- let query = JSON.stringify({"type":self.type,
+ self.saveWorkflow(model, optType, cb)
+ });
+ },
+ saveWorkflow: function (model, optType, cb) {
+ let self = this
+ let query = JSON.stringify({"type":self.type,
"optType":optType,
"mdlPath":model.directory,
"wkflPath":self.parent.parent.wkflPath,
"settings":self.parent.settings
})
- var endpoint = path.join(app.getApiPath(), 'workflow/save-workflow') + "?data=" + query;
- xhr({uri: endpoint}, function (err, response, body) {
- self.saved();
- if(document.URL.endsWith('.mdl')){
- self.parent.parent.reloadWkfl();
- }
- });
+ var endpoint = path.join(app.getApiPath(), 'workflow/save-workflow') + "?data=" + query;
+ xhr({uri: endpoint}, function (err, response, body) {
+ self.saved();
+ if(cb){
+ cb()
+ }else if(self.parent.parent.urlPathParam.endsWith('.mdl')){
+ self.parent.parent.reloadWkfl();
+ }
});
},
clickStartWorkflowHandler: function (e) {
@@ -99,7 +108,7 @@ module.exports = View.extend({
runWorkflow: function () {
var self = this;
var model = this.model;
- var optType = document.URL.endsWith(".mdl") ? "rn" : "re";
+ var optType = this.parent.parent.urlPathParam.endsWith(".mdl") ? "rn" : "re";
var query = {"type":this.type,
"optType":"s"+optType,
"mdlPath":model.directory,
diff --git a/client/views/workflow-status.js b/client/views/workflow-status.js
index b9cfbcf52e..6e33fe9ac2 100644
--- a/client/views/workflow-status.js
+++ b/client/views/workflow-status.js
@@ -13,7 +13,9 @@ module.exports = View.extend({
initialize: function (attrs, options) {
View.prototype.initialize.apply(this, arguments);
var localDate = new Date(attrs.startTime)
+ console.log(localDate, typeof localDate)
var localStartTime = this.getFormattedDate(localDate)
+ console.log(localStartTime, typeof localStartTime)
this.startTime = localStartTime;
this.status = attrs.status;
},
@@ -22,15 +24,24 @@ module.exports = View.extend({
if(this.status !== 'ready' && this.status !== 'new'){
this.expandContainer()
}
+ if(this.status !== 'running') {
+ $(this.queryByHook('running-spinner')).css('display', "none")
+ }
},
expandContainer: function () {
$(this.queryByHook('workflow-status')).collapse('show');
- $(this.queryByHook('collapse')).prop('disabled', false);
- this.changeCollapseButtonText()
+ let collapseBtn = $(this.queryByHook('collapse'))
+ collapseBtn.prop('disabled', false);
+ collapseBtn.trigger('click')
},
- changeCollapseButtonText: function () {
- var text = $(this.queryByHook('collapse')).text();
- text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+');
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
},
getFormattedDate: function (date) {
var months = ['Jan.', 'Feb.', 'Mar.', 'Apr.', 'May', 'Jun.', 'Jul.', 'Aug.', 'Sept.', 'Oct.', 'Nov.', 'Dec.'];
@@ -43,8 +54,15 @@ module.exports = View.extend({
hours = hours ? hours : 12; // replace 0 with 12
var minutes = date.getMinutes();
minutes = minutes < 10 ? '0' + minutes : minutes; // format minutes to always have two chars
- var timeZone = date.toString().split(' ').pop() // get the timezone from the date
- timeZone = timeZone.replace('(', '').replace(')', '') // remove the '()' from the timezone
+ var timeZone = date.toString().split('(').pop().split(')').shift() // get the timezone from the date
+ if(timeZone.includes(" ")){
+ tzparts = timeZone.split(" ")
+ tzparts = tzparts.map(function (element) {
+ return element.charAt(0)
+ })
+ timeZone = tzparts.join("")
+ }
+ // timeZone = timeZone.replace('(', '').replace(')', '') // remove the '()' from the timezone
return month + " " + day + ", " + year + " " + hours + ":" + minutes + " " + ampm + " " + timeZone;
},
});
\ No newline at end of file
diff --git a/client/views/workflow-viewer.js b/client/views/workflow-viewer.js
new file mode 100644
index 0000000000..098ab91df8
--- /dev/null
+++ b/client/views/workflow-viewer.js
@@ -0,0 +1,40 @@
+var $ = require('jquery');
+//collection
+var Collection = require('ampersand-collection');
+//models
+var Plot = require('../models/plots');
+//views
+var View = require('ampersand-view');
+var PlotsView = require('./plots-view');
+//templates
+var template = require('../templates/includes/workflowViewer.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=collapse-workflow]' : 'renderPlots'
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments)
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments)
+ },
+ renderPlots: function (e) {
+ this.changeCollapseButtonText(e)
+ if(this.plotsView) {
+ return
+ }
+ var outputs = new Collection(this.model.outputs, {model: Plot})
+ this.plotsView = this.renderCollection(outputs, PlotsView, this.queryByHook("workflow-plots"))
+ },
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
+ }
+})
\ No newline at end of file
diff --git a/client/views/workflows-viewer.js b/client/views/workflows-viewer.js
new file mode 100644
index 0000000000..1c8a10f229
--- /dev/null
+++ b/client/views/workflows-viewer.js
@@ -0,0 +1,29 @@
+var $ = require('jquery');
+//views
+var View = require('ampersand-view');
+var WorkflowViewer = require('./workflow-viewer');
+//templates
+var template = require('../templates/includes/workflowsViewer.pug');
+
+module.exports = View.extend({
+ template: template,
+ events: {
+ 'click [data-hook=collapse-workflows]' : 'changeCollapseButtonText'
+ },
+ initialize: function (attrs, options) {
+ View.prototype.initialize.apply(this, arguments)
+ },
+ render: function (attrs, options) {
+ View.prototype.render.apply(this, arguments)
+ this.renderCollection(this.collection, WorkflowViewer, this.queryByHook('workflow-container'))
+ },
+ changeCollapseButtonText: function (e) {
+ let source = e.target.dataset.hook
+ let collapseContainer = $(this.queryByHook(source).dataset.target)
+ if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) {
+ let collapseBtn = $(this.queryByHook(source))
+ let text = collapseBtn.text();
+ text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+ }
+ }
+})
\ No newline at end of file
diff --git a/jupyter_notebook_config.py b/jupyter_notebook_config.py
index 3b5c45ff19..66b8ea4bad 100644
--- a/jupyter_notebook_config.py
+++ b/jupyter_notebook_config.py
@@ -8,33 +8,12 @@
## This is an application.
-## The date format used by logging formatters for %(asctime)s
-#c.Application.log_datefmt = '%Y-%m-%d %H:%M:%S'
-
-## The Logging format template
-#c.Application.log_format = '[%(name)s]%(highlevel)s %(message)s'
-
-## Set the log level by value or name.
-#c.Application.log_level = 30
-
#------------------------------------------------------------------------------
# JupyterApp(Application) configuration
#------------------------------------------------------------------------------
## Base class for Jupyter applications
-## Answer yes to any prompts.
-#c.JupyterApp.answer_yes = False
-
-## Full path of a config file.
-#c.JupyterApp.config_file = ''
-
-## Specify a config file to load.
-#c.JupyterApp.config_file_name = ''
-
-## Generate default config file.
-#c.JupyterApp.generate_config = False
-
#------------------------------------------------------------------------------
# NotebookApp(JupyterApp) configuration
#------------------------------------------------------------------------------
@@ -47,7 +26,7 @@
}
## Extra paths to search for serving static files.
-#
+#
# This allows adding javascript/css to be available from the notebook server
# machine, or overriding individual files in the IPython
#
@@ -58,480 +37,56 @@
]
## Disable cross-site-request-forgery protection
-#
+#
# Jupyter notebook 4.3.1 introduces protection from cross-site request
# forgeries, requiring API requests to either:
-#
+#
# - originate from pages served by this server (validated with XSRF cookie and
# token), or - authenticate with a token
-#
+#
# Some anonymous compute resources still desire the ability to run code,
# completely without authentication. These services can disable all
# authentication and security checks, with the full knowledge of what that
# implies.
c.NotebookApp.disable_check_xsrf = True
-## The directory to use for notebooks and kernels.
-#c.NotebookApp.notebook_dir = ''
-
-## Extra paths to search for serving jinja templates.
-#
-# Can be used to override templates from notebook.templates.
-#c.NotebookApp.extra_template_paths = []
-
-## Set the Access-Control-Allow-Credentials: true header
-#c.NotebookApp.allow_credentials = False
-
-## Set the Access-Control-Allow-Origin header
-#
-# Use '*' to allow any origin to access your server.
-#
-# Takes precedence over allow_origin_pat.
-#c.NotebookApp.allow_origin = ''
-
-## Use a regular expression for the Access-Control-Allow-Origin header
-#
-# Requests from an origin matching the expression will get replies with:
-#
-# Access-Control-Allow-Origin: origin
-#
-# where `origin` is the origin of the request.
-#
-# Ignored if allow_origin is set.
-#c.NotebookApp.allow_origin_pat = ''
-
-## Allow password to be changed at login for the notebook server.
-#
-# While loggin in with a token, the notebook server UI will give the opportunity
-# to the user to enter a new password at the same time that will replace the
-# token login mechanism.
-#
-# This can be set to false to prevent changing password from the UI/API.
-#c.NotebookApp.allow_password_change = True
-
-## Allow requests where the Host header doesn't point to a local server
-#
-# By default, requests get a 403 forbidden response if the 'Host' header shows
-# that the browser thinks it's on a non-local domain. Setting this option to
-# True disables this check.
-#
-# This protects against 'DNS rebinding' attacks, where a remote web server
-# serves you a page and then changes its DNS to send later requests to a local
-# IP, bypassing same-origin checks.
-#
-# Local IP addresses (such as 127.0.0.1 and ::1) are allowed as local, along
-# with hostnames configured in local_hostnames.
-#c.NotebookApp.allow_remote_access = False
-
-## Whether to allow the user to run the notebook as root.
-#c.NotebookApp.allow_root = False
-
-## DEPRECATED use base_url
-#c.NotebookApp.base_project_url = '/'
-
-## The base URL for the notebook server.
-#
-# Leading and trailing slashes can be omitted, and will automatically be added.
-#c.NotebookApp.base_url = '/'
-
-## Specify what command to use to invoke a web browser when opening the notebook.
-# If not specified, the default browser will be determined by the `webbrowser`
-# standard library module, which allows setting of the BROWSER environment
-# variable to override it.
-#c.NotebookApp.browser = ''
-
-## The full path to an SSL/TLS certificate file.
-#c.NotebookApp.certfile = ''
-
-## The full path to a certificate authority certificate for SSL/TLS client
-# authentication.
-#c.NotebookApp.client_ca = ''
-
-## The config manager class to use
-#c.NotebookApp.config_manager_class = 'notebook.services.config.manager.ConfigManager'
-
-## The notebook manager class to use.
-#c.NotebookApp.contents_manager_class = 'notebook.services.contents.largefilemanager.LargeFileManager'
-
-## Extra keyword arguments to pass to `set_secure_cookie`. See tornado's
-# set_secure_cookie docs for details.
-#c.NotebookApp.cookie_options = {}
-
-## The random bytes used to secure cookies. By default this is a new random
-# number every time you start the Notebook. Set it to a value in a config file
-# to enable logins to persist across server sessions.
-#
-# Note: Cookie secrets should be kept private, do not share config files with
-# cookie_secret stored in plaintext (you can read the value from a file).
-#c.NotebookApp.cookie_secret = b''
-
-## The file where the cookie secret is stored.
-#c.NotebookApp.cookie_secret_file = ''
-
-## Override URL shown to users.
-#
-# Replace actual URL, including protocol, address, port and base URL, with the
-# given value when displaying URL to the users. Do not change the actual
-# connection URL. If authentication token is enabled, the token is added to the
-# custom URL automatically.
-#
-# This option is intended to be used when the URL to display to the user cannot
-# be determined reliably by the Jupyter notebook server (proxified or
-# containerized setups for example).
-#c.NotebookApp.custom_display_url = ''
-
## The default URL to redirect to from `/`
-c.NotebookApp.default_url = '/stochss/models'
-
-
-## Whether to enable MathJax for typesetting math/TeX
-#
-# MathJax is the javascript library Jupyter uses to render math/LaTeX. It is
-# very large, so you may want to disable it if you have a slow internet
-# connection, or for offline use of the notebook.
-#
-# When disabled, equations etc. will appear as their untransformed TeX source.
-#c.NotebookApp.enable_mathjax = True
-
-## extra paths to look for Javascript notebook extensions
-#c.NotebookApp.extra_nbextensions_path = []
-
-## handlers that should be loaded at higher priority than the default services
-#c.NotebookApp.extra_services = []
-
-##
-#c.NotebookApp.file_to_run = ''
-
-## Extra keyword arguments to pass to `get_secure_cookie`. See tornado's
-# get_secure_cookie docs for details.
-#c.NotebookApp.get_secure_cookie_kwargs = {}
-
-## Deprecated: Use minified JS file or not, mainly use during dev to avoid JS
-# recompilation
-#c.NotebookApp.ignore_minified_js = False
-
-## (bytes/sec) Maximum rate at which stream output can be sent on iopub before
-# they are limited.
-#c.NotebookApp.iopub_data_rate_limit = 1000000
-
-## (msgs/sec) Maximum rate at which messages can be sent on iopub before they are
-# limited.
-#c.NotebookApp.iopub_msg_rate_limit = 1000
-
-## The IP address the notebook server will listen on.
-#c.NotebookApp.ip = 'localhost'
-
-## Supply extra arguments that will be passed to Jinja environment.
-#c.NotebookApp.jinja_environment_options = {}
-
-## Extra variables to supply to jinja templates when rendering.
-#c.NotebookApp.jinja_template_vars = {}
-
-## The kernel manager class to use.
-#c.NotebookApp.kernel_manager_class = 'notebook.services.kernels.kernelmanager.MappingKernelManager'
-
-## The kernel spec manager class to use. Should be a subclass of
-# `jupyter_client.kernelspec.KernelSpecManager`.
-#
-# The Api of KernelSpecManager is provisional and might change without warning
-# between this version of Jupyter and the next stable one.
-#c.NotebookApp.kernel_spec_manager_class = 'jupyter_client.kernelspec.KernelSpecManager'
-
-## The full path to a private key file for usage with SSL/TLS.
-#c.NotebookApp.keyfile = ''
-
-## Hostnames to allow as local when allow_remote_access is False.
-#
-# Local IP addresses (such as 127.0.0.1 and ::1) are automatically accepted as
-# local as well.
-#c.NotebookApp.local_hostnames = ['localhost']
-
-## The login handler class to use.
-#c.NotebookApp.login_handler_class = 'notebook.auth.login.LoginHandler'
-
-## The logout handler class to use.
-#c.NotebookApp.logout_handler_class = 'notebook.auth.logout.LogoutHandler'
-
-## The MathJax.js configuration file that is to be used.
-#c.NotebookApp.mathjax_config = 'TeX-AMS-MML_HTMLorMML-full,Safe'
-
-## A custom url for MathJax.js. Should be in the form of a case-sensitive url to
-# MathJax, for example: /static/components/MathJax/MathJax.js
-#c.NotebookApp.mathjax_url = ''
-
-## Sets the maximum allowed size of the client request body, specified in the
-# Content-Length request header field. If the size in a request exceeds the
-# configured value, a malformed HTTP message is returned to the client.
-#
-# Note: max_body_size is applied even in streaming mode.
-#c.NotebookApp.max_body_size = 536870912
-
-## Gets or sets the maximum amount of memory, in bytes, that is allocated for
-# use by the buffer manager.
-#c.NotebookApp.max_buffer_size = 536870912
-
-## Gets or sets a lower bound on the open file handles process resource limit.
-# This may need to be increased if you run into an OSError: [Errno 24] Too many
-# open files. This is not applicable when running on Windows.
-#c.NotebookApp.min_open_files_limit = 0
-
-## Whether to open in a browser after starting. The specific browser used is
-# platform dependent and determined by the python standard library `webbrowser`
-# module, unless it is overridden using the --browser (NotebookApp.browser)
-# configuration option.
-#c.NotebookApp.open_browser = True
-
-## Hashed password to use for web authentication.
-#
-# To generate, type in a python/IPython shell:
-#
-# from notebook.auth import passwd; passwd()
-#
-# The string should be of the form type:salt:hashed-password.
-#c.NotebookApp.password = ''
-
-## Forces users to use a password for the Notebook server. This is useful in a
-# multi user environment, for instance when everybody in the LAN can access each
-# other's machine through ssh.
-#
-# In such a case, server the notebook server on localhost is not secure since
-# any user can connect to the notebook server via ssh.
-#c.NotebookApp.password_required = False
-
-## The port the notebook server will listen on.
-#c.NotebookApp.port = 8888
-
-## The number of additional ports to try if the specified port is not available.
-#c.NotebookApp.port_retries = 50
-
-## DISABLED: use %pylab or %matplotlib in the notebook to enable matplotlib.
-#c.NotebookApp.pylab = 'disabled'
-
-## If True, display a button in the dashboard to quit (shutdown the notebook
-# server).
-#c.NotebookApp.quit_button = True
-
-## (sec) Time window used to check the message and data rate limits.
-#c.NotebookApp.rate_limit_window = 3
-
-## Reraise exceptions encountered loading server extensions?
-#c.NotebookApp.reraise_server_extension_failures = False
-
-## DEPRECATED use the nbserver_extensions dict instead
-#c.NotebookApp.server_extensions = []
-
-## The session manager class to use.
-#c.NotebookApp.session_manager_class = 'notebook.services.sessions.sessionmanager.SessionManager'
-
-## Shut down the server after N seconds with no kernels or terminals running and
-# no activity. This can be used together with culling idle kernels
-# (MappingKernelManager.cull_idle_timeout) to shutdown the notebook server when
-# it's not in use. This is not precisely timed: it may shut down up to a minute
-# later. 0 (the default) disables this automatic shutdown.
-#c.NotebookApp.shutdown_no_activity_timeout = 0
-
-## Supply SSL options for the tornado HTTPServer. See the tornado docs for
-# details.
-#c.NotebookApp.ssl_options = {}
-
-## Supply overrides for terminado. Currently only supports "shell_command".
-#c.NotebookApp.terminado_settings = {}
-
-## Set to False to disable terminals.
-#
-# This does *not* make the notebook server more secure by itself. Anything the
-# user can in a terminal, they can also do in a notebook.
-#
-# Terminals may also be automatically disabled if the terminado package is not
-# available.
-#c.NotebookApp.terminals_enabled = True
-
-## Token used for authenticating first-time connections to the server.
-#
-# When no password is enabled, the default is to generate a new, random token.
-#
-# Setting to an empty string disables authentication altogether, which is NOT
-# RECOMMENDED.
-#c.NotebookApp.token = '
'
-
-## Supply overrides for the tornado.web.Application that the Jupyter notebook
-# uses.
-#c.NotebookApp.tornado_settings = {}
-
-## Whether to trust or not X-Scheme/X-Forwarded-Proto and X-Real-Ip/X-Forwarded-
-# For headerssent by the upstream reverse proxy. Necessary if the proxy handles
-# SSL
-#c.NotebookApp.trust_xheaders = False
-
-## Disable launching browser by redirect file
-#
-# For versions of notebook > 5.7.2, a security feature measure was added that
-# prevented the authentication token used to launch the browser from being
-# visible. This feature makes it difficult for other users on a multi-user
-# system from running code in your Jupyter session as you.
-#
-# However, some environments (like Windows Subsystem for Linux (WSL) and
-# Chromebooks), launching a browser using a redirect file can lead the browser
-# failing to load. This is because of the difference in file structures/paths
-# between the runtime and the browser.
-#
-# Disabling this setting to False will disable this behavior, allowing the
-# browser to launch by using a URL and visible token (as before).
-#c.NotebookApp.use_redirect_file = True
-
-## DEPRECATED, use tornado_settings
-#c.NotebookApp.webapp_settings = {}
-
-## Specify Where to open the notebook on startup. This is the `new` argument
-# passed to the standard library method `webbrowser.open`. The behaviour is not
-# guaranteed, but depends on browser support. Valid values are:
-#
-# - 2 opens a new tab,
-# - 1 opens a new window,
-# - 0 opens in an existing window.
-#
-# See the `webbrowser.open` documentation for details.
-#c.NotebookApp.webbrowser_open_new = 2
-
-## Set the tornado compression options for websocket connections.
-#
-# This value will be returned from
-# :meth:`WebSocketHandler.get_compression_options`. None (default) will disable
-# compression. A dict (even an empty one) will enable compression.
-#
-# See the tornado docs for WebSocketHandler.get_compression_options for details.
-#c.NotebookApp.websocket_compression_options = None
-
-## The base URL for websockets, if it differs from the HTTP server (hint: it
-# almost certainly doesn't).
-#
-# Should be in the form of an HTTP origin: ws[s]://hostname[:port]
-#c.NotebookApp.websocket_url = ''
-
-#------------------------------------------------------------------------------
-# LabApp(NotebookApp) configuration
-#------------------------------------------------------------------------------
-
-## The app directory to launch JupyterLab from.
-#c.LabApp.app_dir = '/Users/mgeiger/.local/share/virtualenvs/stochss-zql4rYfM/share/jupyter/lab'
-
-## Whether to start the app in core mode. In this mode, JupyterLab will run using
-# the JavaScript assets that are within the installed JupyterLab Python package.
-# In core mode, third party extensions are disabled. The `--dev-mode` flag is an
-# alias to this to be used when the Python package itself is installed in
-# development mode (`pip install -e .`).
-#c.LabApp.core_mode = False
-
-## The default URL to redirect to from `/`
-#c.LabApp.default_url = '/lab'
-
-## Whether to start the app in dev mode. Uses the unpublished local JavaScript
-# packages in the `dev_mode` folder. In this case JupyterLab will show a red
-# stripe at the top of the page. It can only be used if JupyterLab is installed
-# as `pip install -e .`.
-#c.LabApp.dev_mode = False
-
-## The override url for static lab assets, typically a CDN.
-#c.LabApp.override_static_url = ''
-
-## The override url for static lab theme assets, typically a CDN.
-#c.LabApp.override_theme_url = ''
-
-## The directory for user settings.
-#c.LabApp.user_settings_dir = '/Users/mgeiger/.jupyter/lab/user-settings'
-
-## Whether to serve the app in watch mode
-#c.LabApp.watch = False
-
-## The directory for workspaces
-#c.LabApp.workspaces_dir = '/Users/mgeiger/.jupyter/lab/workspaces'
-
-#------------------------------------------------------------------------------
-# ConnectionFileMixin(LoggingConfigurable) configuration
-#------------------------------------------------------------------------------
-
-## Mixin for configurable classes that work with connection files
-
-## JSON file in which to store connection info [default: kernel-.json]
-#
-# This file will contain the IP, ports, and authentication key needed to connect
-# clients to this kernel. By default, this file will be created in the security
-# dir of the current profile, but can be specified by absolute path.
-#c.ConnectionFileMixin.connection_file = ''
-
-## set the control (ROUTER) port [default: random]
-#c.ConnectionFileMixin.control_port = 0
-
-## set the heartbeat port [default: random]
-#c.ConnectionFileMixin.hb_port = 0
-
-## set the iopub (PUB) port [default: random]
-#c.ConnectionFileMixin.iopub_port = 0
-
-## Set the kernel's IP address [default localhost]. If the IP address is
-# something other than localhost, then Consoles on other machines will be able
-# to connect to the Kernel, so be careful!
-#c.ConnectionFileMixin.ip = ''
-
-## set the shell (ROUTER) port [default: random]
-#c.ConnectionFileMixin.shell_port = 0
-
-## set the stdin (ROUTER) port [default: random]
-#c.ConnectionFileMixin.stdin_port = 0
-
-##
-#c.ConnectionFileMixin.transport = 'tcp'
+c.NotebookApp.default_url = '/stochss/home'
#------------------------------------------------------------------------------
# KernelManager(ConnectionFileMixin) configuration
#------------------------------------------------------------------------------
## Manages a single kernel in a subprocess on this host.
-#
+#
# This version starts kernels with Popen.
-## Should we autorestart the kernel if it dies.
-#c.KernelManager.autorestart = True
-
-## DEPRECATED: Use kernel_name instead.
-#
-# The Popen Command to launch the kernel. Override this if you have a custom
-# kernel. If kernel_cmd is specified in a configuration file, Jupyter does not
-# pass any arguments to the kernel, because it cannot make any assumptions about
-# the arguments that the kernel understands. In particular, this means that the
-# kernel does not receive the option --debug if it given on the Jupyter command
-# line.
-#c.KernelManager.kernel_cmd = []
-
-## Time to wait for a kernel to terminate before killing it, in seconds.
-#c.KernelManager.shutdown_wait_time = 5.0
-
#------------------------------------------------------------------------------
# Session(Configurable) configuration
#------------------------------------------------------------------------------
## Object for handling serialization and sending of messages.
-#
+#
# The Session object handles building messages and sending them with ZMQ sockets
# or ZMQStream objects. Objects can communicate with each other over the
# network via Session objects, and only need to work with the dict-based IPython
# message spec. The Session will handle serialization/deserialization, security,
# and metadata.
-#
+#
# Sessions support configurable serialization via packer/unpacker traits, and
# signing with HMAC digests via the key/keyfile traits.
-#
+#
# Parameters ----------
-#
+#
# debug : bool
# whether to trigger extra debugging statements
# packer/unpacker : str : 'json', 'pickle' or import_string
# importstrings for methods to serialize message parts. If just
# 'json' or 'pickle', predefined JSON and pickle packers will be used.
# Otherwise, the entire importstring must be used.
-#
+#
# The functions must accept at least valid JSON input, and output *bytes*.
-#
+#
# For example, to use msgpack:
# packer = 'msgpack.packb', unpacker='msgpack.unpackb'
# pack/unpack : callables
@@ -547,296 +102,68 @@
# The file containing a key. If this is set, `key` will be initialized
# to the contents of the file.
-## Threshold (in bytes) beyond which an object's buffer should be extracted to
-# avoid pickling.
-#c.Session.buffer_threshold = 1024
-
-## Whether to check PID to protect against calls after fork.
-#
-# This check can be disabled if fork-safety is handled elsewhere.
-#c.Session.check_pid = True
-
-## Threshold (in bytes) beyond which a buffer should be sent without copying.
-#c.Session.copy_threshold = 65536
-
-## Debug output in the Session
-#c.Session.debug = False
-
-## The maximum number of digests to remember.
-#
-# The digest history will be culled when it exceeds this value.
-#c.Session.digest_history_size = 65536
-
-## The maximum number of items for a container to be introspected for custom
-# serialization. Containers larger than this are pickled outright.
-#c.Session.item_threshold = 64
-
-## execution key, for signing messages.
-#c.Session.key = b''
-
-## path to file containing execution key.
-#c.Session.keyfile = ''
-
-## Metadata dictionary, which serves as the default top-level metadata dict for
-# each message.
-#c.Session.metadata = {}
-
-## The name of the packer for serializing messages. Should be one of 'json',
-# 'pickle', or an import name for a custom callable serializer.
-#c.Session.packer = 'json'
-
-## The UUID identifying this session.
-#c.Session.session = ''
-
-## The digest scheme used to construct the message signatures. Must have the form
-# 'hmac-HASH'.
-#c.Session.signature_scheme = 'hmac-sha256'
-
-## The name of the unpacker for unserializing messages. Only used with custom
-# functions for `packer`.
-#c.Session.unpacker = 'json'
-
-## Username for the Session. Default is your system username.
-#c.Session.username = 'mgeiger'
-
#------------------------------------------------------------------------------
# MultiKernelManager(LoggingConfigurable) configuration
#------------------------------------------------------------------------------
## A class for managing multiple kernels.
-## The name of the default kernel to start
-#c.MultiKernelManager.default_kernel_name = 'python3'
-
-## The kernel manager class. This is configurable to allow subclassing of the
-# KernelManager for customized behavior.
-#c.MultiKernelManager.kernel_manager_class = 'jupyter_client.ioloop.IOLoopKernelManager'
-
#------------------------------------------------------------------------------
# MappingKernelManager(MultiKernelManager) configuration
#------------------------------------------------------------------------------
## A KernelManager that handles notebook mapping and HTTP error handling
-## White list of allowed kernel message types. When the list is empty, all
-# message types are allowed.
-#c.MappingKernelManager.allowed_message_types = []
-
-## Whether messages from kernels whose frontends have disconnected should be
-# buffered in-memory.
-#
-# When True (default), messages are buffered and replayed on reconnect, avoiding
-# lost messages due to interrupted connectivity.
-#
-# Disable if long-running kernels will produce too much output while no
-# frontends are connected.
-#c.MappingKernelManager.buffer_offline_messages = True
-
-## Whether to consider culling kernels which are busy. Only effective if
-# cull_idle_timeout > 0.
-#c.MappingKernelManager.cull_busy = False
-
-## Whether to consider culling kernels which have one or more connections. Only
-# effective if cull_idle_timeout > 0.
-#c.MappingKernelManager.cull_connected = False
-
-## Timeout (in seconds) after which a kernel is considered idle and ready to be
-# culled. Values of 0 or lower disable culling. Very short timeouts may result
-# in kernels being culled for users with poor network connections.
-#c.MappingKernelManager.cull_idle_timeout = 0
-
-## The interval (in seconds) on which to check for idle kernels exceeding the
-# cull timeout value.
-#c.MappingKernelManager.cull_interval = 300
-
-## Timeout for giving up on a kernel (in seconds).
-#
-# On starting and restarting kernels, we check whether the kernel is running and
-# responsive by sending kernel_info_requests. This sets the timeout in seconds
-# for how long the kernel can take before being presumed dead. This affects the
-# MappingKernelManager (which handles kernel restarts) and the
-# ZMQChannelsHandler (which handles the startup).
-#c.MappingKernelManager.kernel_info_timeout = 60
-
-##
-#c.MappingKernelManager.root_dir = ''
-
#------------------------------------------------------------------------------
# KernelSpecManager(LoggingConfigurable) configuration
#------------------------------------------------------------------------------
-## If there is no Python kernelspec registered and the IPython kernel is
-# available, ensure it is added to the spec list.
-#c.KernelSpecManager.ensure_native_kernel = True
-
-## The kernel spec class. This is configurable to allow subclassing of the
-# KernelSpecManager for customized behavior.
-#c.KernelSpecManager.kernel_spec_class = 'jupyter_client.kernelspec.KernelSpec'
-
-## Whitelist of allowed kernel names.
-#
-# By default, all installed kernels are allowed.
-#c.KernelSpecManager.whitelist = set()
-
#------------------------------------------------------------------------------
# ContentsManager(LoggingConfigurable) configuration
#------------------------------------------------------------------------------
## Base class for serving files and directories.
-#
+#
# This serves any text or binary file, as well as directories, with special
# handling for JSON notebook documents.
-#
+#
# Most APIs take a path argument, which is always an API-style unicode path, and
# always refers to a directory.
-#
+#
# - unicode, not url-escaped
# - '/'-separated
# - leading and trailing '/' will be stripped
# - if unspecified, path defaults to '',
# indicating the root path.
-## Allow access to hidden files
-#c.ContentsManager.allow_hidden = False
-
-##
-#c.ContentsManager.checkpoints = None
-
-##
-#c.ContentsManager.checkpoints_class = 'notebook.services.contents.checkpoints.Checkpoints'
-
-##
-#c.ContentsManager.checkpoints_kwargs = {}
-
-## handler class to use when serving raw file requests.
-#
-# Default is a fallback that talks to the ContentsManager API, which may be
-# inefficient, especially for large files.
-#
-# Local files-based ContentsManagers can use a StaticFileHandler subclass, which
-# will be much more efficient.
-#
-# Access to these files should be Authenticated.
-#c.ContentsManager.files_handler_class = 'notebook.files.handlers.FilesHandler'
-
-## Extra parameters to pass to files_handler_class.
-#
-# For example, StaticFileHandlers generally expect a `path` argument specifying
-# the root directory from which to serve files.
-#c.ContentsManager.files_handler_params = {}
-
-## Glob patterns to hide in file and directory listings.
-#c.ContentsManager.hide_globs = ['__pycache__', '*.pyc', '*.pyo', '.DS_Store', '*.so', '*.dylib', '*~']
-
-## Python callable or importstring thereof
-#
-# To be called on a contents model prior to save.
-#
-# This can be used to process the structure, such as removing notebook outputs
-# or other side effects that should not be saved.
-#
-# It will be called as (all arguments passed by keyword)::
-#
-# hook(path=path, model=model, contents_manager=self)
-#
-# - model: the model to be saved. Includes file contents.
-# Modifying this dict will affect the file that is stored.
-# - path: the API path of the save destination
-# - contents_manager: this ContentsManager instance
-#c.ContentsManager.pre_save_hook = None
-
-##
-#c.ContentsManager.root_dir = '/'
-
-## The base name used when creating untitled directories.
-#c.ContentsManager.untitled_directory = 'Untitled Folder'
-
-## The base name used when creating untitled files.
-#c.ContentsManager.untitled_file = 'untitled'
-
-## The base name used when creating untitled notebooks.
-#c.ContentsManager.untitled_notebook = 'Untitled'
-
#------------------------------------------------------------------------------
# FileManagerMixin(Configurable) configuration
#------------------------------------------------------------------------------
## Mixin for ContentsAPI classes that interact with the filesystem.
-#
+#
# Provides facilities for reading, writing, and copying both notebooks and
# generic files.
-#
+#
# Shared by FileContentsManager and FileCheckpoints.
-#
+#
# Note ---- Classes using this mixin must provide the following attributes:
-#
+#
# root_dir : unicode
# A directory against against which API-style paths are to be resolved.
-#
+#
# log : logging.Logger
-## By default notebooks are saved on disk on a temporary file and then if
-# successfully written, it replaces the old ones. This procedure, namely
-# 'atomic_writing', causes some bugs on file system without operation order
-# enforcement (like some networked fs). If set to False, the new notebook is
-# written directly on the old one which could fail (eg: full filesystem or quota
-# )
-#c.FileManagerMixin.use_atomic_writing = True
-
#------------------------------------------------------------------------------
# FileContentsManager(FileManagerMixin,ContentsManager) configuration
#------------------------------------------------------------------------------
-## If True (default), deleting files will send them to the platform's
-# trash/recycle bin, where they can be recovered. If False, deleting files
-# really deletes them.
-#c.FileContentsManager.delete_to_trash = True
-
-## Python callable or importstring thereof
-#
-# to be called on the path of a file just saved.
-#
-# This can be used to process the file on disk, such as converting the notebook
-# to a script or HTML via nbconvert.
-#
-# It will be called as (all arguments passed by keyword)::
-#
-# hook(os_path=os_path, model=model, contents_manager=instance)
-#
-# - path: the filesystem path to the file just written - model: the model
-# representing the file - contents_manager: this ContentsManager instance
-#c.FileContentsManager.post_save_hook = None
-
-##
-#c.FileContentsManager.root_dir = ''
-
-## DEPRECATED, use post_save_hook. Will be removed in Notebook 5.0
-#c.FileContentsManager.save_script = False
-
#------------------------------------------------------------------------------
# NotebookNotary(LoggingConfigurable) configuration
#------------------------------------------------------------------------------
## A class for computing and verifying notebook signatures.
-## The hashing algorithm used to sign notebooks.
-#c.NotebookNotary.algorithm = 'sha256'
-
-## The sqlite file in which to store notebook signatures. By default, this will
-# be in your Jupyter data directory. You can set it to ':memory:' to disable
-# sqlite writing to the filesystem.
-#c.NotebookNotary.db_file = ''
-
-## The secret key with which notebooks are signed.
-#c.NotebookNotary.secret = b''
-
-## The file where the secret key is stored.
-#c.NotebookNotary.secret_file = ''
-
-## A callable returning the storage backend for notebook signatures. The default
-# uses an SQLite database.
-#c.NotebookNotary.store_factory = traitlets.Undefined
-
#------------------------------------------------------------------------------
# GatewayKernelManager(MappingKernelManager) configuration
#------------------------------------------------------------------------------
@@ -856,69 +183,3 @@
# can share these values across all objects. It also contains some helper methods
# to build request arguments out of the various config options.
-## The authorization token used in the HTTP headers. (JUPYTER_GATEWAY_AUTH_TOKEN
-# env var)
-#c.GatewayClient.auth_token = None
-
-## The filename of CA certificates or None to use defaults.
-# (JUPYTER_GATEWAY_CA_CERTS env var)
-#c.GatewayClient.ca_certs = None
-
-## The filename for client SSL certificate, if any. (JUPYTER_GATEWAY_CLIENT_CERT
-# env var)
-#c.GatewayClient.client_cert = None
-
-## The filename for client SSL key, if any. (JUPYTER_GATEWAY_CLIENT_KEY env var)
-#c.GatewayClient.client_key = None
-
-## The time allowed for HTTP connection establishment with the Gateway server.
-# (JUPYTER_GATEWAY_CONNECT_TIMEOUT env var)
-#c.GatewayClient.connect_timeout = 60.0
-
-## A comma-separated list of environment variable names that will be included,
-# along with their values, in the kernel startup request. The corresponding
-# `env_whitelist` configuration value must also be set on the Gateway server -
-# since that configuration value indicates which environmental values to make
-# available to the kernel. (JUPYTER_GATEWAY_ENV_WHITELIST env var)
-#c.GatewayClient.env_whitelist = ''
-
-## Additional HTTP headers to pass on the request. This value will be converted
-# to a dict. (JUPYTER_GATEWAY_HEADERS env var)
-#c.GatewayClient.headers = '{}'
-
-## The password for HTTP authentication. (JUPYTER_GATEWAY_HTTP_PWD env var)
-#c.GatewayClient.http_pwd = None
-
-## The username for HTTP authentication. (JUPYTER_GATEWAY_HTTP_USER env var)
-#c.GatewayClient.http_user = None
-
-## The gateway API endpoint for accessing kernel resources
-# (JUPYTER_GATEWAY_KERNELS_ENDPOINT env var)
-#c.GatewayClient.kernels_endpoint = '/api/kernels'
-
-## The gateway API endpoint for accessing kernelspecs
-# (JUPYTER_GATEWAY_KERNELSPECS_ENDPOINT env var)
-#c.GatewayClient.kernelspecs_endpoint = '/api/kernelspecs'
-
-## The gateway endpoint for accessing kernelspecs resources
-# (JUPYTER_GATEWAY_KERNELSPECS_RESOURCE_ENDPOINT env var)
-#c.GatewayClient.kernelspecs_resource_endpoint = '/kernelspecs'
-
-## The time allowed for HTTP request completion. (JUPYTER_GATEWAY_REQUEST_TIMEOUT
-# env var)
-#c.GatewayClient.request_timeout = 60.0
-
-## The url of the Kernel or Enterprise Gateway server where kernel specifications
-# are defined and kernel management takes place. If defined, this Notebook
-# server acts as a proxy for all kernel management and kernel specification
-# retrieval. (JUPYTER_GATEWAY_URL env var)
-#c.GatewayClient.url = None
-
-## For HTTPS requests, determines if server's certificate should be validated or
-# not. (JUPYTER_GATEWAY_VALIDATE_CERT env var)
-#c.GatewayClient.validate_cert = True
-
-## The websocket url of the Kernel or Enterprise Gateway server. If not
-# provided, this value will correspond to the value of the Gateway url with 'ws'
-# in place of 'http'. (JUPYTER_GATEWAY_WS_URL env var)
-#c.GatewayClient.ws_url = None
diff --git a/package.json b/package.json
index 8e155f3b87..61252326c5 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "stochss",
- "version": "2.0.0",
+ "version": "2.0.1",
"description": "",
"main": "webpack.config.js",
"scripts": {
diff --git a/public_models/Brusselator/Brusselator.ipynb b/public_models/Brusselator/Brusselator.ipynb
index b84fa725eb..d9ae8c91c9 100644
--- a/public_models/Brusselator/Brusselator.ipynb
+++ b/public_models/Brusselator/Brusselator.ipynb
@@ -15,13 +15,13 @@
"source": [
"import numpy as np\n",
"import gillespy2\n",
- "from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
- "from gillespy2.core.events import EventAssignment, EventTrigger, Event\n",
- "from gillespy2.solvers.cpp.ssa_c_solver import SSACSolver\n",
- "# from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n",
- "# from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"
+ "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
+ "from gillespy2 import EventAssignment, EventTrigger, Event\n",
+ "from gillespy2 import SSACSolver\n",
+ "# from gillespy2 import VariableSSACSolver\n",
+ "# from gillespy2 import BasicTauLeapingSolver\n",
+ "# from gillespy2 import BasicTauHybridSolver\n",
+ "# from gillespy2 import BasicODESolver"
]
},
{
diff --git a/public_models/Degradation/Degradation.ipynb b/public_models/Degradation/Degradation.ipynb
index b3f58b11ad..0c2c174373 100644
--- a/public_models/Degradation/Degradation.ipynb
+++ b/public_models/Degradation/Degradation.ipynb
@@ -15,13 +15,13 @@
"source": [
"import numpy as np\n",
"import gillespy2\n",
- "from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
- "from gillespy2.core.events import EventAssignment, EventTrigger, Event\n",
- "from gillespy2.solvers.cpp.ssa_c_solver import SSACSolver\n",
- "# from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n",
- "# from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"
+ "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
+ "from gillespy2 import EventAssignment, EventTrigger, Event\n",
+ "from gillespy2 import SSACSolver\n",
+ "# from gillespy2 import VariableSSACSolver\n",
+ "# from gillespy2 import BasicTauLeapingSolver\n",
+ "# from gillespy2 import BasicTauHybridSolver\n",
+ "# from gillespy2 import BasicODESolver"
]
},
{
diff --git a/public_models/Dimerization/Dimerization.ipynb b/public_models/Dimerization/Dimerization.ipynb
index 540b34317c..f038f105f6 100644
--- a/public_models/Dimerization/Dimerization.ipynb
+++ b/public_models/Dimerization/Dimerization.ipynb
@@ -15,13 +15,13 @@
"source": [
"import numpy as np\n",
"import gillespy2\n",
- "from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
- "from gillespy2.core.events import EventAssignment, EventTrigger, Event\n",
- "from gillespy2.solvers.cpp.ssa_c_solver import SSACSolver\n",
- "# from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n",
- "# from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"
+ "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
+ "from gillespy2 import EventAssignment, EventTrigger, Event\n",
+ "from gillespy2 import SSACSolver\n",
+ "# from gillespy2 import VariableSSACSolver\n",
+ "# from gillespy2 import BasicTauLeapingSolver\n",
+ "# from gillespy2 import BasicTauHybridSolver\n",
+ "# from gillespy2 import BasicODESolver"
]
},
{
diff --git a/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.mdl b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.mdl
new file mode 100644
index 0000000000..320f352f31
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.mdl
@@ -0,0 +1 @@
+{"is_spatial":false,"defaultID":8,"defaultMode":"discrete","annotation":"The SIR model is a simple mathematical model of epidemics. An epidemic is when the number of people infected with a disease is increasing in a population. S, I, and R stand for:\n\nS - susceptible: These are people that are not infected with the disease yet. However, they are not immune to it either and so they can become infected with the disease in the future.\nI - infected or infectious: These are people that are infected with the disease and can transmit the disease to susceptible people.\nR - recovered: These are people who have recovered from the disease and are immune, so they can no longer be infected with the disease.\n\nThis model is reasonably predictive for infectious diseases that are transmitted from human to human, and where recovery confers lasting resistance, such as measles, mumps and rubella.\nThese variables (S, I, and R) represent the number of people in each compartment at a particular time. To represent that the number of susceptible, infectious and removed individuals may vary over time (even if the total population size remains constant), we make the precise numbers a function of t (time): S(t), I(t) and R(t). For a specific disease in a specific population, these functions may be worked out in order to predict possible outbreaks and bring them under control.\nAs implied by the variable function of t, the model is dynamic in that the numbers in each compartment may fluctuate over time. The importance of this dynamic aspect is most obvious in an endemic disease with a short infectious period, such as measles in the UK prior to the introduction of a vaccine in 1968. Such diseases tend to occur in cycles of outbreaks due to the variation in number of susceptibles (S(t)) over time. During an epidemic, the number of susceptible individuals falls rapidly as more of them are infected and thus enter the infectious and removed compartments. The disease cannot break out again until the number of susceptibles has built back up, e.g. as a result of offspring being born into the susceptible compartment.\nEach member of the population typically progresses from susceptible to infectious to recovered.","modelSettings":{"endSim":20,"timeStep":0.05,"volume":1},"meshSettings":{"count":2},"species":[{"compID":1,"name":"Susceptible","value":999,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are\n susceptible to infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]},{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]},{"compID":3,"name":"Recovered","value":0,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that have recovered from infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}],"initialConditions":[],"parameters":[{"compID":4,"name":"beta","expression":"0.0083","annotation":"Rate at which a Susceptible species becomes infected\n"},{"compID":5,"name":"gamma","expression":"0.3","annotation":"Rate at which an Infected species recovers from the infection.\n\n"}],"reactions":[{"compID":6,"name":"r1","reactionType":"custom-massaction","summary":"Susceptible+Infected \\rightarrow 2Infected","massaction":true,"propensity":"","annotation":"","subdomains":["subdomain 1:","subdomain 2:"],"rate":{"compID":4,"name":"beta","expression":"8.3","annotation":""},"reactants":[{"ratio":1,"specie":{"compID":1,"name":"Susceptible","value":999,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are\n susceptible to infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}},{"ratio":1,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}],"products":[{"ratio":2,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}]},{"compID":7,"name":"r2","reactionType":"change","summary":"Infected \\rightarrow Recovered","massaction":false,"propensity":"","annotation":"","subdomains":["subdomain 1:","subdomain 2:"],"rate":{"compID":5,"name":"gamma","expression":"0.3","annotation":""},"reactants":[{"ratio":1,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}],"products":[{"ratio":1,"specie":{"compID":3,"name":"Recovered","value":0,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that have recovered from infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}]}],"rules":[],"eventsCollection":[],"functionDefinitions":[]}
\ No newline at end of file
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 1D Parameter Sweep Workflow Incomplete.wkfl/SIR Epidemic Model.mdl b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 1D Parameter Sweep Workflow Incomplete.wkfl/SIR Epidemic Model.mdl
new file mode 100644
index 0000000000..51a3fd2585
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 1D Parameter Sweep Workflow Incomplete.wkfl/SIR Epidemic Model.mdl
@@ -0,0 +1 @@
+{"is_spatial":false,"defaultID":8,"defaultMode":"discrete","annotation":"Susceptible, Infected, Recovered epidemiology (SIR) Model.\n","modelSettings":{"endSim":20,"timeStep":0.05,"volume":1},"meshSettings":{"count":2},"species":[{"compID":1,"name":"Susceptible","value":999,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are\n susceptible to infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]},{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]},{"compID":3,"name":"Recovered","value":0,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that have recovered from infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}],"initialConditions":[],"parameters":[{"compID":4,"name":"beta","expression":"0.0083","annotation":"Rate at which a Susceptible species becomes infected\n"},{"compID":5,"name":"gamma","expression":"0.3","annotation":"Rate at which an Infected species recovers from the infection.\n\n"}],"reactions":[{"compID":6,"name":"r1","reactionType":"custom-massaction","summary":"Susceptible+Infected \\rightarrow 2Infected","massaction":true,"propensity":"","annotation":"","subdomains":["subdomain 1:","subdomain 2:"],"rate":{"compID":4,"name":"beta","expression":"8.3","annotation":""},"reactants":[{"ratio":1,"specie":{"compID":1,"name":"Susceptible","value":999,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are\n susceptible to infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}},{"ratio":1,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}],"products":[{"ratio":2,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}]},{"compID":7,"name":"r2","reactionType":"change","summary":"Infected \\rightarrow Recovered","massaction":false,"propensity":"","annotation":"","subdomains":["subdomain 1:","subdomain 2:"],"rate":{"compID":5,"name":"gamma","expression":"0.3","annotation":""},"reactants":[{"ratio":1,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}],"products":[{"ratio":1,"specie":{"compID":3,"name":"Recovered","value":0,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that have recovered from infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}]}],"rules":[],"eventsCollection":[],"functionDefinitions":[]}
\ No newline at end of file
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 1D Parameter Sweep Workflow Incomplete.wkfl/info.json b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 1D Parameter Sweep Workflow Incomplete.wkfl/info.json
new file mode 100644
index 0000000000..9b302b9385
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 1D Parameter Sweep Workflow Incomplete.wkfl/info.json
@@ -0,0 +1 @@
+{"source_model": "Examples/Example SIR Epidemic Project.proj/SIR Epidemic Model.mdl", "wkfl_model": null, "type": "parameterSweep", "start_time": null}
\ No newline at end of file
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 1D Parameter Sweep Workflow Incomplete.wkfl/settings.json b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 1D Parameter Sweep Workflow Incomplete.wkfl/settings.json
new file mode 100644
index 0000000000..8b4e69e473
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 1D Parameter Sweep Workflow Incomplete.wkfl/settings.json
@@ -0,0 +1 @@
+{"simulationSettings": {"isAutomatic": false, "relativeTol": 0.001, "absoluteTol": 1e-06, "realizations": 20, "algorithm": "SSA", "seed": -1, "tauTol": 0.03}, "parameterSweepSettings": {"is1D": true, "p1Min": 0.004, "p1Max": 0.013, "p1Steps": 15, "p2Min": 0.15, "p2Max": 0.44999999999999996, "p2Steps": 11, "parameterOne": {"compID": 4, "name": "beta", "expression": "0.0083", "annotation": "Rate at which a Susceptible species becomes infected\n"}, "parameterTwo": {"compID": 5, "name": "gamma", "expression": "0.3", "annotation": "Rate at which an Infected species recovers from the infection.\n\n"}, "speciesOfInterest": {"compID": 2, "name": "Infected", "value": 1, "mode": "discrete", "switchTol": 0.03, "switchMin": 100, "isSwitchTol": true, "annotation": "Initial population of a species that are infected\n", "diffusionCoeff": 0, "subdomains": ["subdomain 1:", "subdomain 2:"]}}, "resultsSettings": {"mapper": "final", "reducer": "avg", "outputs": []}}
\ No newline at end of file
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/COMPLETE b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/COMPLETE
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/RUNNING b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/RUNNING
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/SIR Epidemic Model.mdl b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/SIR Epidemic Model.mdl
new file mode 100644
index 0000000000..51a3fd2585
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/SIR Epidemic Model.mdl
@@ -0,0 +1 @@
+{"is_spatial":false,"defaultID":8,"defaultMode":"discrete","annotation":"Susceptible, Infected, Recovered epidemiology (SIR) Model.\n","modelSettings":{"endSim":20,"timeStep":0.05,"volume":1},"meshSettings":{"count":2},"species":[{"compID":1,"name":"Susceptible","value":999,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are\n susceptible to infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]},{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]},{"compID":3,"name":"Recovered","value":0,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that have recovered from infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}],"initialConditions":[],"parameters":[{"compID":4,"name":"beta","expression":"0.0083","annotation":"Rate at which a Susceptible species becomes infected\n"},{"compID":5,"name":"gamma","expression":"0.3","annotation":"Rate at which an Infected species recovers from the infection.\n\n"}],"reactions":[{"compID":6,"name":"r1","reactionType":"custom-massaction","summary":"Susceptible+Infected \\rightarrow 2Infected","massaction":true,"propensity":"","annotation":"","subdomains":["subdomain 1:","subdomain 2:"],"rate":{"compID":4,"name":"beta","expression":"8.3","annotation":""},"reactants":[{"ratio":1,"specie":{"compID":1,"name":"Susceptible","value":999,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are\n susceptible to infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}},{"ratio":1,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}],"products":[{"ratio":2,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}]},{"compID":7,"name":"r2","reactionType":"change","summary":"Infected \\rightarrow Recovered","massaction":false,"propensity":"","annotation":"","subdomains":["subdomain 1:","subdomain 2:"],"rate":{"compID":5,"name":"gamma","expression":"0.3","annotation":""},"reactants":[{"ratio":1,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}],"products":[{"ratio":1,"specie":{"compID":3,"name":"Recovered","value":0,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that have recovered from infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}]}],"rules":[],"eventsCollection":[],"functionDefinitions":[]}
\ No newline at end of file
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/info.json b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/info.json
new file mode 100644
index 0000000000..17a1f7280d
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/info.json
@@ -0,0 +1 @@
+{"source_model": "Examples/Example SIR Epidemic Project.proj/SIR Epidemic Model.mdl", "wkfl_model": "Examples/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/SIR Epidemic Model.mdl", "type": "parameterSweep", "start_time": "Aug 27, 2020 08:34 PM UTC"}
\ No newline at end of file
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/logs.txt b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/logs.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/plots.json b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/plots.json
new file mode 100644
index 0000000000..a9043ba224
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/plots.json
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\ No newline at end of file
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results.json b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results.json
new file mode 100644
index 0000000000..1cea4a4499
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results.json
@@ -0,0 +1 @@
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888.25, 878.7 , 867.2 ,\n 814.95, 807.5 , 798.6 , 830.85, 823.3 , 812.9 , 803.45],\n [949.1 , 891.7 , 927.15, 915.7 , 901.6 , 849.75, 840.5 , 876.3 ,\n 866.5 , 859.2 , 849.4 , 841.85, 833.05, 825.15, 817.1 ],\n [951.85, 943.35, 931.6 , 918.85, 906.15, 898.75, 845.25, 837.1 ,\n 872.1 , 777.85, 814.05, 719.85, 713.65, 705.8 , 699.45],\n [955.35, 942.85, 930.9 , 874.05, 912. , 901.6 , 850.35, 841.55,\n 877.75, 782.3 , 817.75, 725.45, 760.75, 753.45, 747.35],\n [958.6 , 943.75, 935.5 , 878.55, 871.1 , 908.85, 901.4 , 891. ,\n 882.15, 874.4 , 780. , 773.6 , 766.95, 759.2 , 753.15]]), 'var': array([[37480.46 , 125.8475, 186.6275, 31697.66 , 185.09 ,\n 53719.3275, 90726.6275, 69001.26 , 24889.6475, 23759.5475,\n 22688.25 , 40512.8475, 20760.61 , 51738.09 , 61739.1275],\n [ 80.44 , 167.61 , 65633.69 , 172.0875, 274.9475,\n 30065.4275, 184.9 , 27487.74 , 26263.9275, 47471.96 ,\n 81051.6275, 43797.0475, 22349.56 , 21537.29 , 329.91 ],\n [ 90.64 , 162.5475, 68000.9875, 194.1 , 237.64 ,\n 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, 66391.24 , 65246.7475, 63947.06 , 62945.7275]])}, 'avg': {'min': array([[ 0.0074813 , 332.02244389, 285.98503741, 0.02743142,\n 214.54862843, 0.00249377, 0.00498753, 0.00498753,\n 0.00249377, 0.00249377, 0.01246883, 0.01246883,\n 0.00498753, 0.00249377, 0.00498753],\n [401.78304239, 327.97256858, 0.00249377, 249.49625935,\n 220.01496259, 0.01246883, 174.07730673, 0.01496259,\n 0.00498753, 0.00249377, 0.00249377, 0.00249377,\n 0.00249377, 0.00249377, 95.19950125],\n [397.56608479, 327.26932668, 0.00249377, 249.87281796,\n 218.10473815, 0.00249377, 0.00498753, 152.7680798 ,\n 0.0074813 , 0.00498753, 0.01995012, 110.50623441,\n 0.00997506, 0.00997506, 0.00997506],\n [398.12718204, 330.81795511, 281.44638404, 0.01745636,\n 0.00498753, 0.00249377, 0.00249377, 0.00997506,\n 139.86783042, 0.00997506, 0.00498753, 0.00498753,\n 0.00498753, 0.00498753, 0.00249377],\n [407.25187032, 0.01995012, 283.43640898, 247.15461347,\n 216.90274314, 191.55610973, 173.83790524, 156.86783042,\n 0.00498753, 0.00997506, 0.00498753, 0.00498753,\n 0.00498753, 0.00498753, 0.00498753],\n [416.78553616, 341.7755611 , 0.00498753, 0.0074813 ,\n 0.00249377, 0.00249377, 0.00498753, 154.69326683,\n 0.00498753, 132.09975062, 0.0074813 , 0.00498753,\n 0.00498753, 0.00498753, 0.00498753],\n [ 0.00997506, 340.71321696, 281.52369077, 241.87281796,\n 0.00249377, 0.00498753, 0.00249377, 154.7680798 ,\n 141.10473815, 130.31421446, 120.840399 , 0.0074813 ,\n 104.06982544, 97.56109726, 92.18453865],\n [401.87032419, 337.43142145, 282.17206983, 242.77306733,\n 0.00498753, 0.01496259, 164. , 149.41895262,\n 0.00249377, 126.16708229, 117.1446384 , 0.00249377,\n 0.00249377, 0.00249377, 0.00249377],\n [395.8553616 , 324.12219451, 274.94513716, 237.60349127,\n 207.55361596, 183.82044888, 164.73067332, 148.99750623,\n 136.76309227, 125.82543641, 124.77306733, 115.34413965,\n 107.86783042, 0.00249377, 0.00249377],\n [ 0.00249377, 337.7605985 , 0.01496259, 246.79052369,\n 218.90024938, 196.8478803 , 0.00249377, 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781.17206983, 0.99750623,\n 0.99750623, 0.99750623, 0.99750623],\n [512.82543641, 580.95261845, 644.32917706, 670.2394015 ,\n 701.65336658, 738.60598504, 759.34912718, 767.13715711,\n 775.72817955, 799.5286783 , 816.36907731, 826.6159601 ,\n 833.9925187 , 0.99750623, 0.99750623],\n [ 0.99750623, 586.00997506, 0.98503741, 688.82044888,\n 714.55361596, 737.06733167, 0.99750623, 0.98503741,\n 0.99501247, 0.99750623, 819.73566085, 829.58852868,\n 837.80299252, 843.3765586 , 842.83790524],\n [515.03990025, 592.0074813 , 627.80548628, 0.99750623,\n 723.38902743, 742.65336658, 764.83790524, 782.67581047,\n 0.99501247, 0.99750623, 0.99750623, 824.53865337,\n 833.26683292, 840.42144638, 846.49376559],\n [516.7755611 , 0.98254364, 631.44389027, 679.46134663,\n 721.82543641, 0.9925187 , 0.99501247, 783.43142145,\n 797.7680798 , 814.69825436, 818.80299252, 825.49376559,\n 833.10972569, 839.98004988, 846.02244389],\n [523.72069825, 602.60099751, 638.55860349, 679.25436409,\n 723.77306733, 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816.10224439, 828.89276808, 839.2967581 , 845.20448878,\n 852.39900249, 858.58354115, 864.17955112],\n [552.48129676, 622.47630923, 675.57605985, 712.64588529,\n 743.6159601 , 767.50623441, 790.56359102, 812.29925187,\n 824.6084788 , 838.11221945, 844.23441397, 852.22693267,\n 859.52369077, 865.2394015 , 870.3117207 ],\n [567.60349127, 636.46633416, 678.99002494, 731.04488778,\n 744.52618454, 778.49376559, 793.16708229, 815.3042394 ,\n 827.59850374, 840.86533666, 839.01995012, 846.66334165,\n 854.16458853, 860.33665835, 866.16957606],\n [551.37157107, 628.02992519, 678.56608479, 710.37157107,\n 748.32917706, 770.58104738, 786.97506234, 802.21197007,\n 820.3915212 , 831.64089776, 841.44638404, 848.94264339,\n 856.52618454, 863.11471322, 876.05236908],\n [562.71321696, 629.02992519, 677.45386534, 724.66832918,\n 753.53865337, 773.32668329, 796.36658354, 813.7605985 ,\n 830.27930175, 841.25935162, 850.55610973, 859.26932668,\n 866.31670823, 872.64837905, 878.2967581 ],\n [564.81047382, 631.22194514, 679.95012469, 718.97506234,\n 755.06483791, 783.45386534, 800.4713217 , 810.46134663,\n 827.33665835, 837.9201995 , 850.80299252, 859.60099751,\n 867.28927681, 871.19201995, 876.77306733],\n [561.6084788 , 628.42144638, 685.71321696, 719.5436409 ,\n 755.11221945, 784.34164589, 801.88279302, 808.17456359,\n 826.78304239, 836. , 846.02493766, 855.63591022,\n 862.680798 , 868.90024938, 874.72069825],\n [552.64089776, 634.5286783 , 682.65336658, 723.20698254,\n 747.91521197, 774.4638404 , 791.48379052, 809.78054863,\n 827.49625935, 836.99750623, 847.94264339, 857.02493766,\n 863.17955112, 869.72817955, 875.88279302],\n [557.2244389 , 631.86284289, 683.55361596, 718.22693267,\n 749.40648379, 776.09975062, 794.75810474, 812.79052369,\n 826.87032419, 835.7605985 , 849.16458853, 857.26184539,\n 864.38902743, 871.19700748, 876.8478803 ]]), 'avg': array([[465.84413965, 559.28503741, 603.22394015, 607.64451372,\n 672.23815461, 634.05785536, 579.20947631, 624.59600998,\n 718.70972569, 721.76346633, 729.31608479, 699.0574813 ,\n 749.19002494, 678.27805486, 641.73104738],\n [500.85573566, 572.79064838, 553.39825436, 655.08316708,\n 685.65723192, 680.09588529, 732.61421446, 711.23740648,\n 722.54351621, 694.78715711, 628.65760599, 714.46047382,\n 759.35660848, 765.38678304, 810.50436409],\n [512.05511222, 579.36122195, 565.83927681, 668.1861596 ,\n 698.5 , 654.47581047, 714.51084788, 761.59177057,\n 735.86708229, 705.67007481, 755.30922693, 803.50710723,\n 769.93902743, 775.5617207 , 780.85124688],\n [511.24713217, 580.50174564, 636.61408978, 643.64476309,\n 634.19775561, 657.40798005, 681.24102244, 729.2265586 ,\n 782.58466334, 713.01957606, 724.57456359, 732.21209476,\n 736.19563591, 741.80523691, 665.2659601 ],\n [522.77194514, 559.15261845, 641.43528678, 679.96770574,\n 713.74102244, 737.9744389 , 760.08640898, 775.96284289,\n 710.86084788, 759.7765586 , 730.80374065, 738.70947631,\n 743.2361596 , 749.34127182, 754.75673317],\n [518.49451372, 589.16832918, 611.40598504, 652.26571072,\n 644.15099751, 670.28004988, 725.94501247, 779.90199501,\n 754.23690773, 804.29064838, 774.780798 , 743.340399 ,\n 750.00399002, 755.06159601, 760.0946384 ],\n [497.96870324, 596.84713217, 651.67955112, 694.40760599,\n 651.70473815, 713.02680798, 693.18004988, 786.7680798 ,\n 800.33815461, 813.90723192, 823.91745636, 789.56122195,\n 839.47418953, 846.02805486, 850.90024938],\n [530.60261845, 595.95997506, 654.93865337, 696.32693267,\n 691.50336658, 716.34438903, 772.49413965, 787.22157107,\n 761.92705736, 816.68441397, 823.60698254, 791.52381546,\n 798.47331671, 804.78054863, 810.39975062],\n [533.4734414 , 606.90561097, 658.80822943, 698.00548628,\n 727.23815461, 754.54713217, 774.90074813, 790.31471322,\n 804.59962594, 819.62992519, 828.94389027, 836.55274314,\n 843.95623441, 808.60336658, 814.26309227],\n [481.77992519, 606.019202 , 625.44625935, 699.15972569,\n 732.76433915, 754.13703242, 733.98902743, 752.35249377,\n 767.69850374, 778.03017456, 831.62930175, 839.37805486,\n 846.81034913, 854.17568579, 861.44002494],\n [536.53740648, 610.02493766, 659.85623441, 671.30610973,\n 737.83354115, 760.99501247, 781.98665835, 799.05935162,\n 771.62830424, 782.16658354, 792.35261845, 842.96396509,\n 851.26620948, 858.08453865, 864.00648379],\n [537.96583541, 582.4872818 , 661.87992519, 702.79738155,\n 738.07817955, 725.66832918, 743.09837905, 799.88491272,\n 815.05137157, 828.16895262, 837.12793017, 846.81695761,\n 854.4521197 , 860.85648379, 866.72144638],\n [541.7584788 , 615.83640898, 662.93977556, 705.38865337,\n 740.06521197, 765.79800499, 744.96009975, 759.60411471,\n 814.47256858, 743.91259352, 796.81620948, 720.30785536,\n 726.81359102, 732.64925187, 737.8105985 ],\n [537.60349127, 612.56221945, 665.26147132, 670.67568579,\n 737.68466334, 764.43765586, 745.62356608, 761.3819202 ,\n 816.26446384, 745.53578554, 798.55561097, 721.68054863,\n 770.72506234, 776.88154613, 782.29451372],\n [543.91945137, 614.52830424, 668.14563591, 673.05922693,\n 704.48977556, 766.04189526, 783.48703242, 803.52855362,\n 817.60074813, 830.01084788, 757.12605985, 765.14164589,\n 772.15311721, 778.17793017, 783.64426434]]), 'var': array([[ 11489.67157698, 279.73474114, 269.15286883,\n 19877.79014526, 177.4050861 , 44739.74773639,\n 83670.14919248, 68873.09224445, 27216.75905834,\n 27538.35744073, 28231.10931516, 54318.62079121,\n 29696.39513908, 81043.93849821, 102788.05126416],\n [ 136.59758539, 242.35590355, 34095.09221155,\n 173.06420064, 331.64903109, 24439.55947443,\n 184.25525221, 26731.76378169, 27576.09208181,\n 53725.0500266 , 98676.90530911, 56778.97096926,\n 30598.18768042, 31074.90405091, 147.59719459],\n [ 127.11942706, 178.00334281, 35667.50549902,\n 104.08409169, 109.84202368, 47589.25691295,\n 26887.31147896, 144.66414394, 28556.02404531,\n 55316.03267212, 30058.88384587, 120.30873954,\n 31258.38145439, 31732.55807046, 32164.38502701],\n [ 345.65218494, 176.47415352, 179.42226036,\n 21888.09373603, 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6.17877221e+08,\n 5.90779306e+08, 5.64334270e+08, 5.40213737e+08],\n [9.36220297e+06, 1.04248024e+07, 1.06098485e+07, 3.17446952e+08,\n 2.88173175e+07, 1.28170968e+07, 3.04076816e+08, 2.92371424e+08,\n 8.30466739e+06, 4.86670844e+08, 2.34244923e+08, 5.98452324e+08,\n 4.04268550e+08, 3.86179116e+08, 3.70065135e+08],\n [6.67876537e+06, 6.90410114e+06, 5.91340339e+06, 2.98195571e+08,\n 3.01364657e+08, 7.77080079e+06, 1.26904131e+07, 1.43082493e+07,\n 1.17454115e+07, 6.87893387e+06, 4.33760445e+08, 4.12135377e+08,\n 3.90678723e+08, 3.73905182e+08, 3.57377629e+08]])}, 'final': {'min': array([[ 1., 881., 926., 1., 969., 1., 1., 1., 1., 1., 1.,\n 1., 1., 1., 1.],\n [829., 887., 1., 955., 972., 1., 987., 1., 1., 1., 1.,\n 1., 1., 1., 999.],\n [825., 900., 1., 956., 974., 1., 1., 991., 1., 1., 1.,\n 998., 1., 1., 1.],\n [822., 899., 938., 1., 1., 1., 1., 1., 995., 1., 1.,\n 1., 1., 1., 1.],\n [834., 1., 936., 961., 972., 986., 990., 994., 1., 1., 1.,\n 1., 1., 1., 1.],\n [819., 892., 1., 1., 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\ No newline at end of file
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/avg-avg.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/avg-avg.csv
new file mode 100644
index 0000000000..91352105b9
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/avg-avg.csv
@@ -0,0 +1,226 @@
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/avg-max.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/avg-max.csv
new file mode 100644
index 0000000000..8ce893bac1
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/avg-max.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/avg-min.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/avg-min.csv
new file mode 100644
index 0000000000..9d5fc4f58f
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/avg-min.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/avg-var.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/avg-var.csv
new file mode 100644
index 0000000000..bfc900c45d
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/avg-var.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/final-avg.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/final-avg.csv
new file mode 100644
index 0000000000..dc0bd88c56
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/final-avg.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/final-max.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/final-max.csv
new file mode 100644
index 0000000000..947dd86417
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/final-max.csv
@@ -0,0 +1,226 @@
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/final-min.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/final-min.csv
new file mode 100644
index 0000000000..495738397e
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/final-min.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/final-var.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/final-var.csv
new file mode 100644
index 0000000000..913f227b4b
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/final-var.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-avg.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-avg.csv
new file mode 100644
index 0000000000..38ca8fac81
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-avg.csv
@@ -0,0 +1,226 @@
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-max.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-max.csv
new file mode 100644
index 0000000000..721b1bf482
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-max.csv
@@ -0,0 +1,226 @@
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-min.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-min.csv
new file mode 100644
index 0000000000..cc5281c13b
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-min.csv
@@ -0,0 +1,226 @@
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-var.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-var.csv
new file mode 100644
index 0000000000..a7b0b80edf
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-var.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/min-avg.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/min-avg.csv
new file mode 100644
index 0000000000..a6c9e4c7db
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/min-avg.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/min-max.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/min-max.csv
new file mode 100644
index 0000000000..25ba035b4c
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/min-max.csv
@@ -0,0 +1,226 @@
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/min-min.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/min-min.csv
new file mode 100644
index 0000000000..5ca6b427d1
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/min-min.csv
@@ -0,0 +1,226 @@
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/min-var.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/min-var.csv
new file mode 100644
index 0000000000..02174206c5
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/min-var.csv
@@ -0,0 +1,226 @@
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/var-avg.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/var-avg.csv
new file mode 100644
index 0000000000..98124d6b2c
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/var-avg.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/var-max.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/var-max.csv
new file mode 100644
index 0000000000..e1b519dc3b
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/var-max.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/var-min.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/var-min.csv
new file mode 100644
index 0000000000..9c7a8d7f17
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/var-min.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/var-var.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/var-var.csv
new file mode 100644
index 0000000000..c1b54706a8
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/var-var.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/settings.json b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/settings.json
new file mode 100644
index 0000000000..092dbed075
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/settings.json
@@ -0,0 +1 @@
+{"simulationSettings": {"isAutomatic": false, "relativeTol": 0.001, "absoluteTol": 1e-06, "realizations": 20, "algorithm": "SSA", "seed": -1, "tauTol": 0.03}, "parameterSweepSettings": {"is1D": false, "p1Min": 0.004, "p1Max": 0.013, "p1Steps": 15, "p2Min": 0.1, "p2Max": 0.5, "p2Steps": 15, "parameterOne": {"compID": 4, "name": "beta", "expression": "0.0083", "annotation": "Rate at which a Susceptible species becomes infected\n"}, "parameterTwo": {"compID": 5, "name": "gamma", "expression": "0.3", "annotation": "Rate at which an Infected species recovers from the infection.\n\n"}, "speciesOfInterest": {"compID": 2, "name": "Infected", "value": 1, "mode": "discrete", "switchTol": 0.03, "switchMin": 100, "isSwitchTol": true, "annotation": "Initial population of a species that are infected\n", "diffusionCoeff": 0, "subdomains": ["subdomain 1:", "subdomain 2:"]}}, "resultsSettings": {"mapper": "final", "reducer": "avg", "outputs": [{"key": "Recovered-max-var", "stamp": 200727163621, "species": ["Recovered"]}, {"key": "Infected-max-var", "stamp": 200727163636, "species": ["Infected"]}, {"key": "Infected-avg-var", "stamp": 200727163726, "species": ["Infected"]}]}}
\ No newline at end of file
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/COMPLETE b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/COMPLETE
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/RUNNING b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/RUNNING
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/SIR Epidemic Model.mdl b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/SIR Epidemic Model.mdl
new file mode 100644
index 0000000000..51a3fd2585
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/SIR Epidemic Model.mdl
@@ -0,0 +1 @@
+{"is_spatial":false,"defaultID":8,"defaultMode":"discrete","annotation":"Susceptible, Infected, Recovered epidemiology (SIR) Model.\n","modelSettings":{"endSim":20,"timeStep":0.05,"volume":1},"meshSettings":{"count":2},"species":[{"compID":1,"name":"Susceptible","value":999,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are\n susceptible to infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]},{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]},{"compID":3,"name":"Recovered","value":0,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that have recovered from infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}],"initialConditions":[],"parameters":[{"compID":4,"name":"beta","expression":"0.0083","annotation":"Rate at which a Susceptible species becomes infected\n"},{"compID":5,"name":"gamma","expression":"0.3","annotation":"Rate at which an Infected species recovers from the infection.\n\n"}],"reactions":[{"compID":6,"name":"r1","reactionType":"custom-massaction","summary":"Susceptible+Infected \\rightarrow 2Infected","massaction":true,"propensity":"","annotation":"","subdomains":["subdomain 1:","subdomain 2:"],"rate":{"compID":4,"name":"beta","expression":"8.3","annotation":""},"reactants":[{"ratio":1,"specie":{"compID":1,"name":"Susceptible","value":999,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are\n susceptible to infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}},{"ratio":1,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}],"products":[{"ratio":2,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}]},{"compID":7,"name":"r2","reactionType":"change","summary":"Infected \\rightarrow Recovered","massaction":false,"propensity":"","annotation":"","subdomains":["subdomain 1:","subdomain 2:"],"rate":{"compID":5,"name":"gamma","expression":"0.3","annotation":""},"reactants":[{"ratio":1,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}],"products":[{"ratio":1,"specie":{"compID":3,"name":"Recovered","value":0,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that have recovered from infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}]}],"rules":[],"eventsCollection":[],"functionDefinitions":[]}
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/info.json b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/info.json
new file mode 100644
index 0000000000..4fb62a0bac
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/info.json
@@ -0,0 +1 @@
+{"source_model": "Examples/Example SIR Epidemic Project.proj/SIR Epidemic Model.mdl", "wkfl_model": "Examples/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/SIR Epidemic Model.mdl", "type": "gillespy", "start_time": "Aug 27, 2020 08:27 PM UTC", "annotation": "\n\n"}
\ No newline at end of file
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/logs.txt b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/logs.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/plots.json b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/plots.json
new file mode 100644
index 0000000000..260013b25f
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/plots.json
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv0.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv0.csv
new file mode 100644
index 0000000000..fe7e9f8a81
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv0.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv1.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv1.csv
new file mode 100644
index 0000000000..c68a31038b
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv1.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv10.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv10.csv
new file mode 100644
index 0000000000..f313145d92
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv10.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv11.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv11.csv
new file mode 100644
index 0000000000..c34fba3a7c
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv11.csv
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+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv12.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv13.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv13.csv
new file mode 100644
index 0000000000..fd68bf6983
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv13.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv14.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv14.csv
new file mode 100644
index 0000000000..286d0f6bfd
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv14.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv15.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv15.csv
new file mode 100644
index 0000000000..bf2046570f
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv15.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv16.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv16.csv
new file mode 100644
index 0000000000..f6a84ec311
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv16.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv17.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv17.csv
new file mode 100644
index 0000000000..6f90a35e0f
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv17.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv18.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv18.csv
new file mode 100644
index 0000000000..16e16b3f86
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv18.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv19.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv19.csv
new file mode 100644
index 0000000000..67fe14f747
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv19.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv2.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv2.csv
new file mode 100644
index 0000000000..1fb84cd90c
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv2.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv3.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv3.csv
new file mode 100644
index 0000000000..04ef41bff9
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv3.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv4.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv4.csv
new file mode 100644
index 0000000000..81e6ffc0e3
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv4.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv5.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv5.csv
new file mode 100644
index 0000000000..9899343785
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv5.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv6.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv6.csv
new file mode 100644
index 0000000000..ec47dd6663
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv6.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv7.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv7.csv
new file mode 100644
index 0000000000..25ea03dd3f
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv7.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv8.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv8.csv
new file mode 100644
index 0000000000..f4de2b94da
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv8.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv9.csv b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv9.csv
new file mode 100644
index 0000000000..fb2f89c9e8
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv9.csv
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diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/settings.json b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/settings.json
new file mode 100644
index 0000000000..962a83f97e
--- /dev/null
+++ b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/settings.json
@@ -0,0 +1 @@
+{"simulationSettings": {"isAutomatic": false, "relativeTol": 0.001, "absoluteTol": 1e-06, "realizations": 20, "algorithm": "SSA", "seed": -1, "tauTol": 0.03}, "parameterSweepSettings": {"is1D": true, "p1Min": 0, "p1Max": 0, "p1Steps": 11, "p2Min": 0, "p2Max": 0, "p2Steps": 11, "parameterOne": {}, "parameterTwo": {}, "speciesOfInterest": {}}, "resultsSettings": {"mapper": "final", "reducer": "avg", "outputs": [{"key": "stddev", "stamp": 200727162833, "species": ["Susceptible", "Infected", "Recovered"]}, {"key": "stddevran", "stamp": 200727162836, "species": ["Susceptible", "Infected", "Recovered"]}]}}
\ No newline at end of file
diff --git a/public_models/Lotkavolterra_Oscillator/Lotkavolterra_Oscillator.ipynb b/public_models/Lotkavolterra_Oscillator/Lotkavolterra_Oscillator.ipynb
index d8045bf248..3b16d1335d 100644
--- a/public_models/Lotkavolterra_Oscillator/Lotkavolterra_Oscillator.ipynb
+++ b/public_models/Lotkavolterra_Oscillator/Lotkavolterra_Oscillator.ipynb
@@ -15,13 +15,13 @@
"source": [
"import numpy as np\n",
"import gillespy2\n",
- "from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
- "from gillespy2.core.events import EventAssignment, EventTrigger, Event\n",
+ "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
+ "from gillespy2 import EventAssignment, EventTrigger, Event\n",
"# To run a simulation using the SSA Solver simply omit the solver argument from model.run().\n",
- "# from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n",
- "from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"
+ "# from gillespy2 import VariableSSACSolver\n",
+ "# from gillespy2 import BasicTauLeapingSolver\n",
+ "# from gillespy2 import BasicTauHybridSolver\n",
+ "from gillespy2 import BasicODESolver"
]
},
{
diff --git a/public_models/Michaelis_Menten/Michaelis_Menten.ipynb b/public_models/Michaelis_Menten/Michaelis_Menten.ipynb
index 420089680e..95b4129908 100644
--- a/public_models/Michaelis_Menten/Michaelis_Menten.ipynb
+++ b/public_models/Michaelis_Menten/Michaelis_Menten.ipynb
@@ -15,13 +15,13 @@
"source": [
"import numpy as np\n",
"import gillespy2\n",
- "from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
- "from gillespy2.core.events import EventAssignment, EventTrigger, Event\n",
- "from gillespy2.solvers.cpp.ssa_c_solver import SSACSolver\n",
- "# from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n",
- "# from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"
+ "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
+ "from gillespy2 import EventAssignment, EventTrigger, Event\n",
+ "from gillespy2 import SSACSolver\n",
+ "# from gillespy2 import VariableSSACSolver\n",
+ "# from gillespy2 import BasicTauLeapingSolver\n",
+ "# from gillespy2 import BasicTauHybridSolver\n",
+ "# from gillespy2 import BasicODESolver"
]
},
{
diff --git a/public_models/Opioid/Opioid.ipynb b/public_models/Opioid/Opioid.ipynb
index af6fc46c38..1b573b07a8 100644
--- a/public_models/Opioid/Opioid.ipynb
+++ b/public_models/Opioid/Opioid.ipynb
@@ -15,13 +15,13 @@
"source": [
"import numpy as np\n",
"import gillespy2\n",
- "from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
- "from gillespy2.core.events import EventAssignment, EventTrigger, Event\n",
- "from gillespy2.solvers.cpp.ssa_c_solver import SSACSolver\n",
- "# from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n",
- "# from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"
+ "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
+ "from gillespy2 import EventAssignment, EventTrigger, Event\n",
+ "from gillespy2 import SSACSolver\n",
+ "# from gillespy2 import VariableSSACSolver\n",
+ "# from gillespy2 import BasicTauLeapingSolver\n",
+ "# from gillespy2 import BasicTauHybridSolver\n",
+ "# from gillespy2 import BasicODESolver"
]
},
{
diff --git a/public_models/Oregonator/Oregonator.ipynb b/public_models/Oregonator/Oregonator.ipynb
index 1b80682318..6f60bb7a57 100644
--- a/public_models/Oregonator/Oregonator.ipynb
+++ b/public_models/Oregonator/Oregonator.ipynb
@@ -15,13 +15,13 @@
"source": [
"import numpy as np\n",
"import gillespy2\n",
- "from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
- "from gillespy2.core.events import EventAssignment, EventTrigger, Event\n",
+ "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
+ "from gillespy2 import EventAssignment, EventTrigger, Event\n",
"# To run a simulation using the SSA Solver simply omit the solver argument from model.run().\n",
- "# from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n",
- "from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"
+ "# from gillespy2 import VariableSSACSolver\n",
+ "# from gillespy2 import BasicTauLeapingSolver\n",
+ "# from gillespy2 import BasicTauHybridSolver\n",
+ "from gillespy2 import BasicODESolver"
]
},
{
diff --git a/public_models/Schlogl/Schlogl.ipynb b/public_models/Schlogl/Schlogl.ipynb
index 7e619eaea8..9a3a7cfaba 100644
--- a/public_models/Schlogl/Schlogl.ipynb
+++ b/public_models/Schlogl/Schlogl.ipynb
@@ -15,13 +15,13 @@
"source": [
"import numpy as np\n",
"import gillespy2\n",
- "from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
- "from gillespy2.core.events import EventAssignment, EventTrigger, Event\n",
- "from gillespy2.solvers.cpp.ssa_c_solver import SSACSolver\n",
- "# from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n",
- "# from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"
+ "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
+ "from gillespy2 import EventAssignment, EventTrigger, Event\n",
+ "from gillespy2 import SSACSolver\n",
+ "# from gillespy2 import VariableSSACSolver\n",
+ "# from gillespy2 import BasicTauLeapingSolver\n",
+ "# from gillespy2 import BasicTauHybridSolver\n",
+ "# from gillespy2 import BasicODESolver"
]
},
{
diff --git a/public_models/Toggle_Switch/Toggle_Switch.ipynb b/public_models/Toggle_Switch/Toggle_Switch.ipynb
index 74db844951..2847f5fafb 100644
--- a/public_models/Toggle_Switch/Toggle_Switch.ipynb
+++ b/public_models/Toggle_Switch/Toggle_Switch.ipynb
@@ -15,13 +15,13 @@
"source": [
"import numpy as np\n",
"import gillespy2\n",
- "from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
- "from gillespy2.core.events import EventAssignment, EventTrigger, Event\n",
- "from gillespy2.solvers.cpp.ssa_c_solver import SSACSolver\n",
- "# from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n",
- "# from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"
+ "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
+ "from gillespy2 import EventAssignment, EventTrigger, Event\n",
+ "from gillespy2 import SSACSolver\n",
+ "# from gillespy2 import VariableSSACSolver\n",
+ "# from gillespy2 import BasicTauLeapingSolver\n",
+ "# from gillespy2 import BasicTauHybridSolver\n",
+ "# from gillespy2 import BasicODESolver"
]
},
{
diff --git a/public_models/Toggle_Switch/Toggle_Switch1dParamSweep.ipynb b/public_models/Toggle_Switch/Toggle_Switch1dParamSweep.ipynb
index 5c13a12f8b..6f1b54084e 100644
--- a/public_models/Toggle_Switch/Toggle_Switch1dParamSweep.ipynb
+++ b/public_models/Toggle_Switch/Toggle_Switch1dParamSweep.ipynb
@@ -15,13 +15,13 @@
"source": [
"import numpy as np\n",
"import gillespy2\n",
- "from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
- "from gillespy2.core.events import EventAssignment, EventTrigger, Event\n",
+ "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
+ "from gillespy2 import EventAssignment, EventTrigger, Event\n",
"# To run a simulation using the SSA Solver simply omit the solver argument from model.run().\n",
- "from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n",
- "# from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"
+ "from gillespy2 import VariableSSACSolver\n",
+ "# from gillespy2 import BasicTauLeapingSolver\n",
+ "# from gillespy2 import BasicTauHybridSolver\n",
+ "# from gillespy2 import BasicODESolver"
]
},
{
diff --git a/public_models/Toggle_Switch/Toggle_Switch2dParamSweep.ipynb b/public_models/Toggle_Switch/Toggle_Switch2dParamSweep.ipynb
index a6746f9099..5e615baa7e 100644
--- a/public_models/Toggle_Switch/Toggle_Switch2dParamSweep.ipynb
+++ b/public_models/Toggle_Switch/Toggle_Switch2dParamSweep.ipynb
@@ -15,13 +15,13 @@
"source": [
"import numpy as np\n",
"import gillespy2\n",
- "from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
- "from gillespy2.core.events import EventAssignment, EventTrigger, Event\n",
+ "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
+ "from gillespy2 import EventAssignment, EventTrigger, Event\n",
"# To run a simulation using the SSA Solver simply omit the solver argument from model.run().\n",
- "from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n",
- "# from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"
+ "from gillespy2 import VariableSSACSolver\n",
+ "# from gillespy2 import BasicTauLeapingSolver\n",
+ "# from gillespy2 import BasicTauHybridSolver\n",
+ "# from gillespy2 import BasicODESolver"
]
},
{
diff --git a/public_models/Toggle_Switch/Toggle_SwitchSciopeMI.ipynb b/public_models/Toggle_Switch/Toggle_SwitchSciopeMI.ipynb
index 181bea065a..5cc2a7e54e 100644
--- a/public_models/Toggle_Switch/Toggle_SwitchSciopeMI.ipynb
+++ b/public_models/Toggle_Switch/Toggle_SwitchSciopeMI.ipynb
@@ -1 +1 @@
-{"cells":[{"cell_type":"markdown","metadata":{},"source":["# Toggle_Switch"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["import numpy as np\n","import gillespy2\n","from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n","from gillespy2.core.events import EventAssignment, EventTrigger, Event\n","from gillespy2.solvers.cpp.ssa_c_solver import SSACSolver\n","# from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n","# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n","# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n","# from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class Toggle_Switch(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Toggle_Switch\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"alpha1\", expression=10))\n"," self.add_parameter(Parameter(name=\"alpha2\", expression=10))\n"," self.add_parameter(Parameter(name=\"beta\", expression=2))\n"," self.add_parameter(Parameter(name=\"gamma\", expression=2))\n"," self.add_parameter(Parameter(name=\"mu\", expression=1))\n","\n"," # Species\n"," self.add_species(Species(name=\"A\", initial_value=2, mode=\"discrete\"))\n"," self.add_species(Species(name=\"B\", initial_value=2, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"cu\", reactants={}, products={'A': 1}, propensity_function=\"alpha1/(1+pow(B, beta))\"))\n"," self.add_reaction(Reaction(name=\"cv\", reactants={}, products={'B': 1}, propensity_function=\"alpha2/(1+pow(A, gamma))\"))\n"," self.add_reaction(Reaction(name=\"du\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n"," self.add_reaction(Reaction(name=\"dv\", reactants={'B': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n","\n"," # Timespan\n"," self.timespan(np.linspace(0, 250, 251))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = Toggle_Switch()"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["solver = SSACSolver(model=model)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n","# the minimum number of trajectoies needs to be at least 30\n"," kwargs = {\n"," \"solver\":solver,\n"," \"show_labels\":False,\n"," \"number_of_trajectories\":100,\n"," \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06}\n"," }\n"," return kwargs"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from tsfresh.feature_extraction.settings import MinimalFCParameters\n","from sciope.utilities.priors import uniform_prior\n","from sciope.utilities.summarystats import auto_tsfresh\n","from sciope.utilities.distancefunctions import naive_squared\n","from sciope.inference.abc_inference import ABC\n","from sklearn.metrics import mean_absolute_error\n","from dask.distributed import Client"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","\n","# Define simulator function\n","def set_model_parameters(params, model):\n"," \"\"\"para,s - array, need to have the same order as\n"," model.listOfParameters \"\"\"\n"," for e, (pname, p) in enumerate(model.listOfParameters.items()):\n"," model.get_parameter(pname).set_expression(params[e])\n"," return model\n","\n","# Here we use the GillesPy2 Solver\n","def simulator(params, model):\n"," model_update = set_model_parameters(params, model)\n"," \n"," res = model_update.run(**kwargs)\n"," tot_res = np.asarray([x.T for x in res]) # reshape to (N, S, T)\n"," tot_res = tot_res[:,1:, :] # should not contain timepoints\n","\n"," return tot_res\n","\n","# Wrapper, simulator function to abc should should only take one argument (the parameter point)\n","def simulator2(x):\n"," return simulator(x, model=model)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Set up the prior\n","default_param = np.array(list(model.listOfParameters.items()))[:,1] # take default from mode 1 as reference\n","\n","bound = []\n","for exp in default_param:\n"," bound.append(float(exp.expression))\n","\n","# Set the bounds\n","bound = np.array(bound)\n","dmin = bound * 0.1\n","dmax = bound * 2.0\n","\n","# Here we use uniform prior\n","uni_prior = uniform_prior.UniformPrior(dmin, dmax)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# generate some fixed(observed) data based on default parameters of the model\n","fixed_data = model.run(**kwargs)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Reshape the data to (n_points,n_species,n_timepoints) and remove timepoints array\n","fixed_data = np.asarray([x.T for x in fixed_data])\n","fixed_data = fixed_data[:,1:, :]"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Function to generate summary statistics\n","summ_func = auto_tsfresh.SummariesTSFRESH()\n","\n","# Distance\n","ns = naive_squared.NaiveSquaredDistance()\n","\n","# Start abc instance\n","abc = ABC(fixed_data, sim=simulator2, prior_function=uni_prior, summaries_function=summ_func.compute, distance_function=ns)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["c = Client()\n","c"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# First compute the fixed(observed) mean\n","abc.compute_fixed_mean(chunk_size=2)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["res = abc.infer(num_samples=100, batch_size=10, chunk_size=2)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["mae_inference = mean_absolute_error(bound, abc.results[\"inferred_parameters\"])"]}],"metadata":{"kernelspec":{"display_name":"Python 3","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.7.6"}},"nbformat":4,"nbformat_minor":4}
\ No newline at end of file
+{"cells":[{"cell_type":"markdown","metadata":{},"source":["# Toggle_Switch"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["import numpy as np\n","import gillespy2\n","from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n","from gillespy2 import EventAssignment, EventTrigger, Event\n","from gillespy2 import SSACSolver\n","# from gillespy2 import VariableSSACSolver\n","# from gillespy2 import BasicTauLeapingSolver\n","# from gillespy2 import BasicTauHybridSolver\n","# from gillespy2 import BasicODESolver"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class Toggle_Switch(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Toggle_Switch\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"alpha1\", expression=10))\n"," self.add_parameter(Parameter(name=\"alpha2\", expression=10))\n"," self.add_parameter(Parameter(name=\"beta\", expression=2))\n"," self.add_parameter(Parameter(name=\"gamma\", expression=2))\n"," self.add_parameter(Parameter(name=\"mu\", expression=1))\n","\n"," # Species\n"," self.add_species(Species(name=\"A\", initial_value=2, mode=\"discrete\"))\n"," self.add_species(Species(name=\"B\", initial_value=2, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"cu\", reactants={}, products={'A': 1}, propensity_function=\"alpha1/(1+pow(B, beta))\"))\n"," self.add_reaction(Reaction(name=\"cv\", reactants={}, products={'B': 1}, propensity_function=\"alpha2/(1+pow(A, gamma))\"))\n"," self.add_reaction(Reaction(name=\"du\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n"," self.add_reaction(Reaction(name=\"dv\", reactants={'B': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n","\n"," # Timespan\n"," self.timespan(np.linspace(0, 250, 251))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = Toggle_Switch()"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["solver = SSACSolver(model=model)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n","# the minimum number of trajectoies needs to be at least 30\n"," kwargs = {\n"," \"solver\":solver,\n"," \"show_labels\":False,\n"," \"number_of_trajectories\":100,\n"," \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06}\n"," }\n"," return kwargs"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from tsfresh.feature_extraction.settings import MinimalFCParameters\n","from sciope.utilities.priors import uniform_prior\n","from sciope.utilities.summarystats import auto_tsfresh\n","from sciope.utilities.distancefunctions import naive_squared\n","from sciope.inference.abc_inference import ABC\n","from sklearn.metrics import mean_absolute_error\n","from dask.distributed import Client"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","\n","# Define simulator function\n","def set_model_parameters(params, model):\n"," \"\"\"para,s - array, need to have the same order as\n"," model.listOfParameters \"\"\"\n"," for e, (pname, p) in enumerate(model.listOfParameters.items()):\n"," model.get_parameter(pname).set_expression(params[e])\n"," return model\n","\n","# Here we use the GillesPy2 Solver\n","def simulator(params, model):\n"," model_update = set_model_parameters(params, model)\n"," \n"," res = model_update.run(**kwargs)\n"," tot_res = np.asarray([x.T for x in res]) # reshape to (N, S, T)\n"," tot_res = tot_res[:,1:, :] # should not contain timepoints\n","\n"," return tot_res\n","\n","# Wrapper, simulator function to abc should should only take one argument (the parameter point)\n","def simulator2(x):\n"," return simulator(x, model=model)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Set up the prior\n","default_param = np.array(list(model.listOfParameters.items()))[:,1] # take default from mode 1 as reference\n","\n","bound = []\n","for exp in default_param:\n"," bound.append(float(exp.expression))\n","\n","# Set the bounds\n","bound = np.array(bound)\n","dmin = bound * 0.1\n","dmax = bound * 2.0\n","\n","# Here we use uniform prior\n","uni_prior = uniform_prior.UniformPrior(dmin, dmax)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# generate some fixed(observed) data based on default parameters of the model\n","fixed_data = model.run(**kwargs)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Reshape the data to (n_points,n_species,n_timepoints) and remove timepoints array\n","fixed_data = np.asarray([x.T for x in fixed_data])\n","fixed_data = fixed_data[:,1:, :]"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Function to generate summary statistics\n","summ_func = auto_tsfresh.SummariesTSFRESH()\n","\n","# Distance\n","ns = naive_squared.NaiveSquaredDistance()\n","\n","# Start abc instance\n","abc = ABC(fixed_data, sim=simulator2, prior_function=uni_prior, summaries_function=summ_func.compute, distance_function=ns)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["c = Client()\n","c"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# First compute the fixed(observed) mean\n","abc.compute_fixed_mean(chunk_size=2)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["res = abc.infer(num_samples=100, batch_size=10, chunk_size=2)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["mae_inference = mean_absolute_error(bound, abc.results[\"inferred_parameters\"])"]}],"metadata":{"kernelspec":{"display_name":"Python 3","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.7.6"}},"nbformat":4,"nbformat_minor":4}
\ No newline at end of file
diff --git a/public_models/Tyson_Oscillator/Tyson_Oscillator.ipynb b/public_models/Tyson_Oscillator/Tyson_Oscillator.ipynb
index f78abf5c31..53ef2f6e1a 100644
--- a/public_models/Tyson_Oscillator/Tyson_Oscillator.ipynb
+++ b/public_models/Tyson_Oscillator/Tyson_Oscillator.ipynb
@@ -15,13 +15,13 @@
"source": [
"import numpy as np\n",
"import gillespy2\n",
- "from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
- "from gillespy2.core.events import EventAssignment, EventTrigger, Event\n",
- "from gillespy2.solvers.cpp.ssa_c_solver import SSACSolver\n",
- "# from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n",
- "# from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"
+ "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
+ "from gillespy2 import EventAssignment, EventTrigger, Event\n",
+ "from gillespy2 import SSACSolver\n",
+ "# from gillespy2 import VariableSSACSolver\n",
+ "# from gillespy2 import BasicTauLeapingSolver\n",
+ "# from gillespy2 import BasicTauHybridSolver\n",
+ "# from gillespy2 import BasicODESolver"
]
},
{
diff --git a/public_models/Vilar_Oscillator/Vilar_Oscillator.ipynb b/public_models/Vilar_Oscillator/Vilar_Oscillator.ipynb
index 6daacf11b8..7b9774793c 100644
--- a/public_models/Vilar_Oscillator/Vilar_Oscillator.ipynb
+++ b/public_models/Vilar_Oscillator/Vilar_Oscillator.ipynb
@@ -15,13 +15,13 @@
"source": [
"import numpy as np\n",
"import gillespy2\n",
- "from gillespy2.core import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
- "from gillespy2.core.events import EventAssignment, EventTrigger, Event\n",
- "from gillespy2.solvers.cpp.ssa_c_solver import SSACSolver\n",
- "# from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver\n",
- "# from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver\n",
- "# from gillespy2.solvers.numpy.basic_ode_solver import BasicODESolver"
+ "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n",
+ "from gillespy2 import EventAssignment, EventTrigger, Event\n",
+ "from gillespy2 import SSACSolver\n",
+ "# from gillespy2 import VariableSSACSolver\n",
+ "# from gillespy2 import BasicTauLeapingSolver\n",
+ "# from gillespy2 import BasicTauHybridSolver\n",
+ "# from gillespy2 import BasicODESolver"
]
},
{
diff --git a/requirements.txt b/requirements.txt
index 11a30e7c7f..977c2fe9cb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,8 @@
python-libsbml==5.18.0
-gillespy2==1.4.2
-vtk
+python-libsedml==2.0.9
+python-libcombine==0.2.7
+gillespy2==1.5.5
+sciope==0.2
pygmsh==5.0.2
meshio==2.3.10
git+https://github.com/spatialpy/SpatialPy.git@develop
-git+https://github.com/sciope/sciope.git@master
diff --git a/setup.py b/setup.py
index da3aba5e21..17eae6bdcc 100644
--- a/setup.py
+++ b/setup.py
@@ -1,14 +1,49 @@
+# =============================================================================
+# @file __version__.py
+# @brief StochSS version info
+# @license Please see the file named LICENSE in the project directory
+# @website https://github.com/stochss/stochss
+# =============================================================================
+
import setuptools
+import os
+from os import path
+
+
+# Read the contents of auxiliary files.
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+SETUP_DIR = path.dirname(os.path.abspath(__file__))
+
+with open(path.join(SETUP_DIR, 'README.md'), 'r') as f:
+ readme = f.read()
+
+# The following reads the variables without doing an "import handprint",
+# because the latter will cause the python execution environment to fail if
+# any dependencies are not already installed -- negating most of the reason
+# we're using setup() in the first place. This code avoids eval, for security.
+
+version = {}
+with open(path.join(SETUP_DIR, '__version__.py'), 'r') as f:
+ text = f.read().rstrip().splitlines()
+ lines = [line for line in text if line.startswith('__') and '=' in line]
+ for v in lines:
+ setting = v.split('=')
+ version[setting[0].strip()] = setting[1].strip().replace("'", '')
+
+
+# Finally, define our namesake.
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
setuptools.setup(
- name="stochss-singleuser",
- version="2.0.1",
- author="StochSS Team",
- author_email="bdrawert@unca.edu",
- description="StochSS is an integrated development environment (IDE) for simulation of biochemical networks.",
- long_description="StochSS is an integrated development environment (IDE) for simulation of biochemical networks.",
+ name=version['__title__'].lower(),
+ version=version['__version__'],
+ author=version['__author__'],
+ author_email=version['__email__'],
+ description=version['__description__'],
+ long_description=readme,
long_description_content_type="text/markdown",
- url="https://github.com/StochSS/stochss",
+ url=version['__url__'],
packages=setuptools.find_packages(),
classifiers=[
"Programming Language :: Python :: 3",
diff --git a/stochss/dist/stochss-project-browser.html b/stochss/dist/stochss-project-browser.html
new file mode 100644
index 0000000000..f541b7e5b6
--- /dev/null
+++ b/stochss/dist/stochss-project-browser.html
@@ -0,0 +1,4 @@
+`_. All rights reserved.
-
-email: contact@picloud.com
-
-The cloud package is free software; you can redistribute it and/or
-modify it under the terms of the GNU Lesser General Public
-License as published by the Free Software Foundation; either
-version 2.1 of the License, or (at your option) any later version.
-
-This package is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-Lesser General Public License for more details.
-
-You should have received a copy of the GNU Lesser General Public
-License along with this package; if not, see
-http://www.gnu.org/licenses/lgpl-2.1.html
-"""
-
-
-import operator
-import os
-import pickle
-import struct
-import sys
-import types
-from functools import partial
-import itertools
-import cpoyreg
-from copyreg import _extension_registry, _inverted_registry, _extension_cache
-import types
-import dis
-import traceback
-
-#relevant opcodes
-STORE_GLOBAL = chr(dis.opname.index('STORE_GLOBAL'))
-DELETE_GLOBAL = chr(dis.opname.index('DELETE_GLOBAL'))
-LOAD_GLOBAL = chr(dis.opname.index('LOAD_GLOBAL'))
-GLOBAL_OPS = [STORE_GLOBAL, DELETE_GLOBAL, LOAD_GLOBAL]
-
-HAVE_ARGUMENT = chr(dis.HAVE_ARGUMENT)
-EXTENDED_ARG = chr(dis.EXTENDED_ARG)
-
-import logging
-cloudLog = logging.getLogger("Cloud.Transport")
-
-try:
- import ctypes
-except (MemoryError, ImportError):
- logging.warning('Exception raised on importing ctypes. Likely python bug.. some functionality will be disabled', exc_info = True)
- ctypes = None
- PyObject_HEAD = None
-else:
-
- # for reading internal structures
- PyObject_HEAD = [
- ('ob_refcnt', ctypes.c_size_t),
- ('ob_type', ctypes.c_void_p),
- ]
-
-
-from io import StringIO
-
-def xrange_params(xrangeobj):
- """Returns a 3 element tuple describing the xrange start, step, and len respectively
- Note: Only guarentees that elements of xrange are the same. parameters may be different. e.g. xrange(1,1) is interpretted as xrange(0,0); both behave the same though w/ iteration
- """
- xrange_len = len(xrangeobj)
- if not xrange_len: #empty
- return (0,1,0)
- start = xrangeobj[0]
- if xrange_len == 1: #one element
- return start, 1, 1
- return (start, xrangeobj[1] - xrangeobj[0], xrange_len)
-
-def islambda(func):
- return getattr(func,'func_name') == ''
-
-#debug variables intended for developer use:
-printSerialization = False
-printMemoization = False
-
-useForcedImports = True # Should I use forced imports for tracking?
-
-def error_msg(msg, loglevel=logging.WARN, exc_info = 0):
- """Print an error message to pilog if running on cloud; otherwise send to stderr"""
- from .. import _getcloud
- roc = _getcloud().running_on_cloud()
- if roc:
- pilog_module = __import__('pimployee.log', fromlist=['log'])
- pilog_module.pilogger.log(loglevel, msg, exc_info = exc_info)
- else:
- print >> sys.stderr, msg
- if exc_info:
- ei = sys.exc_info()
- traceback.print_exception(ei[0], ei[1], ei[2], None, sys.stderr)
-
-class CloudPickler(pickle.Pickler):
-
- dispatch = copyreg.dispatch_table.copy()
- savedForceImports = False
- savedDjangoEnv = False #hack tro transport django environment
- os_env_vars = [] # OS environment variables to copy over
-
- def __init__(self, file, protocol=None, min_size_to_save= 0):
- pickle.Pickler.__init__(self,file,protocol)
- self.modules = set() #set of modules needed to depickle
- self.globals_ref = {} # map ids to dictionary. used to ensure that functions can share global env
-
- def dump(self, obj):
- # note: not thread safe
- # minimal side-effects, so not fixing
- recurse_limit = 3000
- base_recurse = sys.getrecursionlimit()
- if base_recurse < recurse_limit:
- sys.setrecursionlimit(recurse_limit)
- self.inject_addons()
- try:
- return pickle.Pickler.dump(self, obj)
- except RuntimeError as e:
- if 'recursion' in e.args[0]:
- msg = """Could not pickle object as excessively deep recursion required.
- Try _fast_serialization=2 or contact PiCloud support"""
- raise pickle.PicklingError(msg)
- raise
- finally:
- new_recurse = sys.getrecursionlimit()
- if new_recurse == recurse_limit:
- sys.setrecursionlimit(base_recurse)
-
- def save_buffer(self, obj):
- """Fallback to save_string"""
- pickle.Pickler.save_string(self,str(obj))
- dispatch[buffer] = save_buffer
-
- #block broken objects
- def save_unsupported(self, obj, pack=None):
- raise pickle.PicklingError("Cannot pickle objects of type %s" % type(obj))
- dispatch[types.GeneratorType] = save_unsupported
-
- #python2.6+ supports slice pickling. some py2.5 extensions might as well. We just test it
- try:
- slice(0,1).__reduce__()
- except TypeError: #can't pickle -
- dispatch[slice] = save_unsupported
-
- #itertools objects do not pickle!
- for v in itertools.__dict__.values():
- if type(v) is type:
- dispatch[v] = save_unsupported
-
-
- def save_dict(self, obj):
- """hack fix
- If the dict is a global, deal with it in a special way
- """
- #print('saving', obj)
- if obj is __builtins__:
- self.save_reduce(_get_module_builtins, (), obj=obj)
- else:
- pickle.Pickler.save_dict(self, obj)
- dispatch[pickle.DictionaryType] = save_dict
-
-
- def save_module(self, obj, pack=struct.pack):
- """
- Save a module as an import
- """
- #print('try save import', obj.__name__)
- self.modules.add(obj)
- self.save_reduce(subimport,(obj.__name__,), obj=obj)
- dispatch[types.ModuleType] = save_module #new type
-
- def save_codeobject(self, obj, pack=struct.pack):
- """
- Save a code object
- """
- #print('try to save codeobj: ', obj)
- args = (
- obj.co_argcount, obj.co_nlocals, obj.co_stacksize, obj.co_flags, obj.co_code,
- obj.co_consts, obj.co_names, obj.co_varnames, obj.co_filename, obj.co_name,
- obj.co_firstlineno, obj.co_lnotab, obj.co_freevars, obj.co_cellvars
- )
- self.save_reduce(types.CodeType, args, obj=obj)
- dispatch[types.CodeType] = save_codeobject #new type
-
- def save_function(self, obj, name=None, pack=struct.pack):
- """ Registered with the dispatch to handle all function types.
-
- Determines what kind of function obj is (e.g. lambda, defined at
- interactive prompt, etc) and handles the pickling appropriately.
- """
- write = self.write
-
- name = obj.__name__
- modname = pickle.whichmodule(obj, name)
- #print('which gives %s %s %s' % (modname, obj, name))
- try:
- themodule = sys.modules[modname]
- except KeyError: # eval'd items such as namedtuple give invalid items for their function __module__
- modname = '__main__'
-
- if modname == '__main__':
- themodule = None
-
- if themodule:
- self.modules.add(themodule)
-
- if self.os_env_vars:
-
- # recursion hackery
- os_env_vars = self.os_env_vars
- self.os_env_vars = []
- old_saved_django = self.savedDjangoEnv
- self.savedDjangoEnv = True
-
- write(pickle.MARK)
-
- if isinstance(os_env_vars, dict):
- os_mapping = os_env_vars
- else:
- os_mapping = {}
- for env_var in os_env_vars:
- if env_var in os.environ:
- os_mapping[env_var] = os.environ[env_var]
- self.save_reduce(env_vars_load, (os_mapping,)) # note: nothing sensible to memoize
- write(pickle.POP_MARK)
-
- self.savedDjangoEnv = old_saved_django
-
- if modname == 'cloud.shell':
- # don't save django environment if we are using shell.exec
- self.savedDjangoEnv = True
-
- elif not self.savedDjangoEnv:
- # hack for django - if we detect the settings module, we transport it
- # unfortunately this module is dynamically, not statically, resolved, so
- # dependency analysis never detects it
-
- django_settings = os.environ.get('DJANGO_SETTINGS_MODULE', '')
- if django_settings:
- django_mod = sys.modules.get(django_settings)
- if django_mod:
- cloudLog.debug('Transporting django settings %s during save of %s', django_mod, name)
- self.savedDjangoEnv = True
- self.modules.add(django_mod)
- write(pickle.MARK)
- self.save_reduce(django_settings_load, (django_mod.__name__,), obj=django_mod)
- write(pickle.POP_MARK)
-
-
- # if func is lambda, def'ed at prompt, is in main, or is nested, then
- # we'll pickle the actual function object rather than simply saving a
- # reference (as is done in default pickler), via save_function_tuple.
- if islambda(obj) or obj.func_code.co_filename == '' or themodule == None:
- #Force server to import modules that have been imported in main
- modList = None
- if themodule == None and not self.savedForceImports:
- mainmod = sys.modules['__main__']
- if useForcedImports and hasattr(mainmod,'___pyc_forcedImports__'):
- modList = list(mainmod.___pyc_forcedImports__)
- self.savedForceImports = True
- self.save_function_tuple(obj, modList)
- return
- else: # func is nested
- klass = getattr(themodule, name, None)
- if klass is None or klass is not obj:
- self.save_function_tuple(obj, [themodule])
- return
-
- if obj.__dict__:
- # essentially save_reduce, but workaround needed to avoid recursion
- self.save(_restore_attr)
- write(pickle.MARK + pickle.GLOBAL + modname + '\n' + name + '\n')
- self.memoize(obj)
- self.save(obj.__dict__)
- write(pickle.TUPLE + pickle.REDUCE)
- else:
- write(pickle.GLOBAL + modname + '\n' + name + '\n')
- self.memoize(obj)
- dispatch[types.FunctionType] = save_function
-
- def save_function_tuple(self, func, forced_imports):
- """ Pickles an actual func object.
-
- A func comprises: code, globals, defaults, closure, and dict. We
- extract and save these, injecting reducing functions at certain points
- to recreate the func object. Keep in mind that some of these pieces
- can contain a ref to the func itself. Thus, a naive save on these
- pieces could trigger an infinite loop of save's. To get around that,
- we first create a skeleton func object using just the code (this is
- safe, since this won't contain a ref to the func), and memoize it as
- soon as it's created. The other stuff can then be filled in later.
- """
- save = self.save
- write = self.write
-
- # save the modules (if any)
- if forced_imports:
- write(pickle.MARK)
- save(_modules_to_main)
- #print('forced imports are', forced_imports)
-
- # do not save our own references
- forced_names = [m.__name__ for m in forced_imports if not m.__name__.startswith('cloud')]
- save((forced_names,))
-
- #save((forced_imports,))
- write(pickle.REDUCE)
- write(pickle.POP_MARK)
-
- code, f_globals, defaults, closure, dct, base_globals = self.extract_func_data(func)
-
- save(_fill_function) # skeleton function updater
- write(pickle.MARK) # beginning of tuple that _fill_function expects
-
- # create a skeleton function object and memoize it
- save(_make_skel_func)
- save((code, len(closure), base_globals))
- write(pickle.REDUCE)
- self.memoize(func)
-
- # save the rest of the func data needed by _fill_function
- save(f_globals)
- save(defaults)
- save(closure)
- save(dct)
- write(pickle.TUPLE)
- write(pickle.REDUCE) # applies _fill_function on the tuple
-
- @staticmethod
- def extract_code_globals(co):
- """
- Find all globals names read or written to by codeblock co
- """
- code = co.co_code
- names = co.co_names
- out_names = set()
-
- n = len(code)
- i = 0
- extended_arg = 0
- while i < n:
- op = code[i]
-
- i = i+1
- if op >= HAVE_ARGUMENT:
- oparg = ord(code[i]) + ord(code[i+1])*256 + extended_arg
- extended_arg = 0
- i = i+2
- if op == EXTENDED_ARG:
- extended_arg = oparg*65536
- if op in GLOBAL_OPS:
- out_names.add(names[oparg])
- #print('extracted', out_names, ' from ', names)
- return out_names
-
- def extract_func_data(self, func):
- """
- Turn the function into a tuple of data necessary to recreate it:
- code, globals, defaults, closure, dict
- """
- code = func.func_code
-
- # extract all global ref's
- func_global_refs = CloudPickler.extract_code_globals(code)
- if code.co_consts: # see if nested function have any global refs
- for const in code.co_consts:
- if type(const) is types.CodeType and const.co_names:
- func_global_refs = func_global_refs.union( CloudPickler.extract_code_globals(const))
- # process all variables referenced by global environment
- f_globals = {}
- for var in func_global_refs:
- #Some names, such as class functions are not global - we don't need them
- if func.func_globals.has_key(var):
- f_globals[var] = func.func_globals[var]
-
- # defaults requires no processing
- defaults = func.func_defaults
-
- def get_contents(cell):
- try:
- return cell.cell_contents
- except ValueError as e: #cell is empty error on not yet assigned
- raise pickle.PicklingError('Function to be pickled has free variables that are referenced before assignment in enclosing scope')
-
-
- # process closure
- if func.func_closure:
- closure = map(get_contents, func.func_closure)
- else:
- closure = []
-
- # save the dict
- dct = func.func_dict
-
- if printSerialization:
- outvars = ['code: ' + str(code) ]
- outvars.append('globals: ' + str(f_globals))
- outvars.append('defaults: ' + str(defaults))
- outvars.append('closure: ' + str(closure))
- print('function ', func, 'is extracted to: ', ', '.join(outvars))
-
- base_globals = self.globals_ref.get(id(func.func_globals), {})
- self.globals_ref[id(func.func_globals)] = base_globals
-
- return (code, f_globals, defaults, closure, dct, base_globals)
-
- def save_class_obj(self, cobj, name=None, pack=struct.pack):
- """Save a class object that a reference cannot be provided to"""
-
- #note: Third party types might crash this - add better checks!
- d = dict(cobj.__dict__) #copy dict proxy to a dict
- constructor_dct = {'__doc__' : d.pop('__doc__')}
- if not isinstance(d.get('__dict__', None), property): # don't extract dict that are properties
- d.pop('__dict__',None)
- elif '__dict__' in d:
- constructor_dct['__dict__'] = d.pop('__dict__')
- #pass
-
- d.pop('__weakref__',None) # never needed in serialization
-
- # hack as __new__ is stored differently in the __dict__
- new_override = d.get('__new__', None)
- if new_override:
- constructor_dct['__new__'] = cobj.__new__
- d.pop('__new__', None)
-
- # beginning of class logic
-
- self.save(_fill_class)
-
- self.write(pickle.MARK) # beginning of tuple that _fill_class expects
-
- self.save(type(cobj))
- self.save((cobj.__name__,cobj.__bases__,constructor_dct)) # inject rest of dictionary later
- self.write(pickle.REDUCE)
- self.memoize(cobj)
-
- #print('save %s' % d['__dict__'])
- # save dct needed
- self.save(d)
- self.write(pickle.TUPLE)
- self.write(pickle.REDUCE) # apply _fill_class on tuple
-
- #self.save_reduce(type(cobj), (cobj.__name__, cobj.__bases__, d), obj = cobj)
-
- def save_global(self, obj, name=None, pack=struct.pack):
- write = self.write
- memo = self.memo
-
- if name is None:
- name = obj.__name__
-
- modname = getattr(obj, "__module__", None)
- if modname is None:
- modname = pickle.whichmodule(obj, name)
-
- try:
- __import__(modname)
- themodule = sys.modules[modname]
- except (ImportError, KeyError, AttributeError): #should never occur
- raise pickle.PicklingError(
- "Can't pickle %r: Module %s cannot be found" %
- (obj, modname))
-
- if modname == '__main__':
- themodule = None
-
- if themodule:
- self.modules.add(themodule)
-
- sendRef = True
- typ = type(obj)
- #print('saving', obj, typ)
- try:
- try: #Deal with case when getattribute fails with exceptions
- klass = getattr(themodule, name)
- except (AttributeError):
- if modname == '__builtin__': #new.* are misrepeported
- modname = 'new'
- __import__(modname)
- themodule = sys.modules[modname]
- try:
- klass = getattr(themodule, name)
- except AttributeError as a:
- #print(themodule, name, obj, type(obj))
- raise pickle.PicklingError("Can't pickle builtin %s" % obj)
- else:
- raise
-
- except (ImportError, KeyError, AttributeError):
- if typ == types.TypeType or typ == types.ClassType:
- sendRef = False
- else: #we can't deal with this
- raise
- else:
- if klass is not obj and (typ == types.TypeType or typ == types.ClassType):
- sendRef = False
- if not sendRef:
- self.save_class_obj(obj, name, pack)
- return
-
- if self.proto >= 2:
- code = _extension_registry.get((modname, name))
- if code:
- assert code > 0
- if code <= 0xff:
- write(pickle.EXT1 + chr(code))
- elif code <= 0xffff:
- write("%c%c%c" % (pickle.EXT2, code&0xff, code>>8))
- else:
- write(pickle.EXT4 + pack("= 2 and getattr(func, "__name__", "") == "__newobj__":
- #Added fix to allow transient
- cls = args[0]
- if not hasattr(cls, "__new__"):
- raise pickle.PicklingError(
- "args[0] from __newobj__ args has no __new__")
- if obj is not None and cls is not obj.__class__:
- raise pickle.PicklingError(
- "args[0] from __newobj__ args has the wrong class")
- args = args[1:]
- save(cls)
-
- #Don't pickle transient entries
- if hasattr(obj, '__transient__'):
- transient = obj.__transient__
- state = state.copy()
-
- for k in list(state.keys()):
- if k in transient:
- del state[k]
-
- save(args)
- write(pickle.NEWOBJ)
- else:
- save(func)
- save(args)
- write(pickle.REDUCE)
-
- if obj is not None:
- self.memoize(obj)
-
- # More new special cases (that work with older protocols as
- # well): when __reduce__ returns a tuple with 4 or 5 items,
- # the 4th and 5th item should be iterators that provide list
- # items and dict items (as (key, value) tuples), or None.
-
- if listitems is not None:
- self._batch_appends(listitems)
-
- if dictitems is not None:
- self._batch_setitems(dictitems)
-
- if state is not None:
- #print('obj %s has state %s' % (obj, state))
- save(state)
- write(pickle.BUILD)
-
-
- def save_xrange(self, obj):
- """Save an xrange object in python 2.5
- Python 2.6 supports this natively
- """
- range_params = xrange_params(obj)
- self.save_reduce(_build_xrange,range_params)
-
- #python2.6+ supports xrange pickling. some py2.5 extensions might as well. We just test it
- try:
- xrange(0).__reduce__()
- except TypeError: #can't pickle -- use PiCloud pickler
- dispatch[xrange] = save_xrange
-
- def save_partial(self, obj):
- """Partial objects do not serialize correctly in python2.x -- this fixes the bugs"""
- self.save_reduce(_genpartial, (obj.func, obj.args, obj.keywords))
-
- if sys.version_info < (2,7): #2.7 supports partial pickling
- dispatch[partial] = save_partial
-
-
- def save_file(self, obj):
- """Save a file"""
- from ..transport.adapter import SerializingAdapter
-
- if not hasattr(obj, 'name') or not hasattr(obj, 'mode'):
- raise pickle.PicklingError("Cannot pickle files that do not map to an actual file")
- if obj.name == '':
- return self.save_reduce(getattr, (sys,'stdout'), obj=obj)
- if obj.name == '':
- return self.save_reduce(getattr, (sys,'stderr'), obj=obj)
- if obj.name == '':
- raise pickle.PicklingError("Cannot pickle standard input")
- if hasattr(obj, 'isatty') and obj.isatty():
- raise pickle.PicklingError("Cannot pickle files that map to tty objects")
- if 'r' not in obj.mode:
- raise pickle.PicklingError("Cannot pickle files that are not opened for reading")
- name = obj.name
- try:
- fsize = os.stat(name).st_size
- except OSError:
- raise pickle.PicklingError("Cannot pickle file %s as it cannot be stat" % name)
-
- if obj.closed:
- #create an empty closed string io
- retval = StringIO("")
- retval.close()
- elif not fsize: #empty file
- retval = StringIO("")
- try:
- tmpfile = file(name)
- tst = tmpfile.read(1)
- except IOError:
- raise pickle.PicklingError("Cannot pickle file %s as it cannot be read" % name)
- tmpfile.close()
- if tst != '':
- raise pickle.PicklingError("Cannot pickle file %s as it does not appear to map to a physical, real file" % name)
- elif fsize > SerializingAdapter.max_transmit_data:
- raise pickle.PicklingError("Cannot pickle file %s as it exceeds cloudconf.py's max_transmit_data of %d" %
- (name,SerializingAdapter.max_transmit_data))
- else:
- try:
- tmpfile = file(name)
- contents = tmpfile.read(SerializingAdapter.max_transmit_data)
- tmpfile.close()
- except IOError:
- raise pickle.PicklingError("Cannot pickle file %s as it cannot be read" % name)
- retval = StringIO(contents)
- curloc = obj.tell()
- retval.seek(curloc)
-
- retval.name = name
- self.save(retval) #save stringIO
- self.memoize(obj)
-
- dispatch[file] = save_file
- """Special functions for Add-on libraries"""
-
- def inject_numpy(self):
- numpy = sys.modules.get('numpy')
- if not numpy or not hasattr(numpy, 'ufunc'):
- return
- self.dispatch[numpy.ufunc] = self.__class__.save_ufunc
-
- numpy_tst_mods = ['numpy', 'scipy.special']
- def save_ufunc(self, obj):
- """Hack function for saving numpy ufunc objects"""
- name = obj.__name__
- for tst_mod_name in self.numpy_tst_mods:
- tst_mod = sys.modules.get(tst_mod_name, None)
- if tst_mod:
- if name in tst_mod.__dict__:
- self.save_reduce(_getobject, (tst_mod_name, name))
- return
- raise pickle.PicklingError('cannot save %s. Cannot resolve what module it is defined in' % str(obj))
-
- def inject_timeseries(self):
- """Handle bugs with pickling scikits timeseries"""
- tseries = sys.modules.get('scikits.timeseries.tseries')
- if not tseries or not hasattr(tseries, 'Timeseries'):
- return
- self.dispatch[tseries.Timeseries] = self.__class__.save_timeseries
-
- def save_timeseries(self, obj):
- import scikits.timeseries.tseries as ts
-
- func, reduce_args, state = obj.__reduce__()
- if func != ts._tsreconstruct:
- raise pickle.PicklingError('timeseries using unexpected reconstruction function %s' % str(func))
- state = (1,
- obj.shape,
- obj.dtype,
- obj.flags.fnc,
- obj._data.tostring(),
- ts.getmaskarray(obj).tostring(),
- obj._fill_value,
- obj._dates.shape,
- obj._dates.__array__().tostring(),
- obj._dates.dtype, #added -- preserve type
- obj.freq,
- obj._optinfo,
- )
- return self.save_reduce(_genTimeSeries, (reduce_args, state))
-
- def inject_email(self):
- """Block email LazyImporters from being saved"""
- email = sys.modules.get('email')
- if not email:
- return
- self.dispatch[email.LazyImporter] = self.__class__.save_unsupported
-
- def inject_addons(self):
- """Plug in system. Register additional pickling functions if modules already loaded"""
- self.inject_numpy()
- self.inject_timeseries()
- self.inject_email()
-
- """Python Imaging Library"""
- def save_image(self, obj):
- if not obj.im and obj.fp and 'r' in obj.fp.mode and obj.fp.name \
- and not obj.fp.closed and (not hasattr(obj, 'isatty') or not obj.isatty()):
- #if image not loaded yet -- lazy load
- self.save_reduce(_lazyloadImage,(obj.fp,), obj=obj)
- else:
- #image is loaded - just transmit it over
- self.save_reduce(_generateImage, (obj.size, obj.mode, obj.tostring()), obj=obj)
-
- """
- def memoize(self, obj):
- pickle.Pickler.memoize(self, obj)
- if printMemoization:
- print('memoizing ' + str(obj))
- """
-
-
-
-# Shorthands for legacy support
-
-def dump(obj, file, protocol=2):
- CloudPickler(file, protocol).dump(obj)
-
-def dumps(obj, protocol=2):
- file = StringIO()
-
- cp = CloudPickler(file,protocol)
- cp.dump(obj)
-
- #print('cloud dumped', str(obj), str(cp.modules))
-
- return file.getvalue()
-
-def loads(s):
- return pickle.loads(s)
-
-#hack for __import__ not working as desired
-def subimport(name):
- __import__(name)
- return sys.modules[name]
-
-#hack to load django settings:
-def django_settings_load(name):
- modified_env = False
-
- if 'DJANGO_SETTINGS_MODULE' not in os.environ:
- os.environ['DJANGO_SETTINGS_MODULE'] = name # must set name first due to circular deps
- modified_env = True
- try:
- module = subimport(name)
- except Exception as i:
- error_msg('Could not import django settings %s:' % (name), exc_info = True)
- if modified_env:
- del os.environ['DJANGO_SETTINGS_MODULE']
- else:
- #add project directory to sys,path:
- if hasattr(module,'__file__'):
- dirname = os.path.split(module.__file__)[0] + '/'
- sys.path.append(dirname)
-
- error_msg('Loaded Django settings', logging.DEBUG)
-
-def env_vars_load(env_dct):
- #print('loading environment vars %s' % env_dct)
- for var, value in env_dct.items():
- os.environ[var] = value
- error_msg('Loaded Environment variables %s' % env_dct.keys(), logging.DEBUG)
-
-# restores function attributes
-def _restore_attr(obj, attr):
- for key, val in attr.items():
- setattr(obj, key, val)
- return obj
-
-def _get_module_builtins():
- return pickle.__builtins__
-
-def _modules_to_main(modList):
- """Force every module in modList to be placed into main"""
- if not modList:
- return
-
- main = sys.modules['__main__']
-
- seen_errors = set() # avoid excessive exceptions; cache top-level module failing and reason
- for modname in modList:
- if type(modname) is str:
- try:
- mod = __import__(modname)
- except Exception as i: #catch all...
- key = modname.split('.',1)[0], str(i)
- if key not in seen_errors:
- seen_errors.add(key)
- error_msg('could not import %s\n. Your function may unexpectedly error due to this import failing; \
- Likely due to version mismatch or non-transferred python extension. Specific error was:\n' % modname, exc_info = True)
- else:
- setattr(main,mod.__name__, mod)
- else:
- #REVERSE COMPATIBILITY FOR CLOUD CLIENT 1.5 (WITH EPD)
- #In old version actual module was sent
- setattr(main,modname.__name__, modname)
-
-#object generators:
-def _build_xrange(start, step, len):
- """Built xrange explicitly"""
- return xrange(start, start + step*len, step)
-
-def _genpartial(func, args, kwds):
- if not args:
- args = ()
- if not kwds:
- kwds = {}
- return partial(func, *args, **kwds)
-
-
-def _fill_function(func, globals, defaults, closure, dct):
- """ Fills in the rest of function data into the skeleton function object
- that were created via _make_skel_func().
- """
- func.func_globals.update(globals)
- func.func_defaults = defaults
- func.func_dict = dct
-
- if len(closure) != len(func.func_closure):
- raise pickle.UnpicklingError("closure lengths don't match up")
- for i in range(len(closure)):
- _change_cell_value(func.func_closure[i], closure[i])
-
- return func
-
-def _fill_class(cls, dct):
- """Fill in a class dictionary
- This hack is necessary because functions in class dictionary may reference class
- """
- for key, val in dct.items():
- setattr(cls, key, val)
-
- return cls
-
-def _make_skel_func(code, num_closures, base_globals = None):
- """ Creates a skeleton function object that contains just the provided
- code and the correct number of cells in func_closure. All other
- func attributes (e.g. func_globals) are empty.
- """
- #build closure (cells):
- if not ctypes:
- raise Exception('ctypes failed to import; cannot build function')
-
- cellnew = ctypes.pythonapi.PyCell_New
- cellnew.restype = ctypes.py_object
- cellnew.argtypes = (ctypes.py_object,)
- dummy_closure = tuple(map(lambda i: cellnew(None), range(num_closures)))
-
- if base_globals is None:
- base_globals = {}
- base_globals['__builtins__'] = __builtins__
-
- return types.FunctionType(code, base_globals,
- None, None, dummy_closure)
-
-# this piece of opaque code is needed below to modify 'cell' contents
-cell_changer_code = new.code(
- 1, 1, 2, 0,
- ''.join([
- chr(dis.opmap['LOAD_FAST']), '\x00\x00',
- chr(dis.opmap['DUP_TOP']),
- chr(dis.opmap['STORE_DEREF']), '\x00\x00',
- chr(dis.opmap['RETURN_VALUE'])
- ]),
- (), (), ('newval',), '', 'cell_changer', 1, '', ('c',), ()
-)
-
-def _change_cell_value(cell, newval):
- """ Changes the contents of 'cell' object to newval """
- return types.LambdaType(cell_changer_code, {}, None, (), (cell,))(newval)
-
-"""Constructors for 3rd party libraries
-Note: These can never be renamed due to client compatibility issues"""
-
-def _getobject(modname, attribute):
- mod = __import__(modname)
- return mod.__dict__[attribute]
-
-def _generateImage(size, mode, str_rep):
- """Generate image from string representation"""
- import Image
- i = Image.new(mode, size)
- i.fromstring(str_rep)
- return i
-
-def _lazyloadImage(fp):
- import Image
- fp.seek(0) #works in almost any case
- return Image.open(fp)
-
-"""Timeseries"""
-def _genTimeSeries(reduce_args, state):
- import scikits.timeseries.tseries as ts
- from numpy import ndarray
- from numpy.ma import MaskedArray
-
-
- time_series = ts._tsreconstruct(*reduce_args)
-
- #from setstate modified
- (ver, shp, typ, isf, raw, msk, flv, dsh, dtm, dtyp, frq, infodict) = state
- #print('regenerating %s' % dtyp)
-
- MaskedArray.__setstate__(time_series, (ver, shp, typ, isf, raw, msk, flv))
- _dates = time_series._dates
- #_dates.__setstate__((ver, dsh, typ, isf, dtm, frq)) #use remote typ
- ndarray.__setstate__(_dates,(dsh,dtyp, isf, dtm))
- _dates.freq = frq
- _dates._cachedinfo.update(dict(full=None, hasdups=None, steps=None,
- toobj=None, toord=None, tostr=None))
- # Update the _optinfo dictionary
- time_series._optinfo.update(infodict)
- return time_series
diff --git a/stochss/handlers/util/parameter_sweep.py b/stochss/handlers/util/parameter_sweep.py
index 0ef007ed5a..1676f2dce2 100755
--- a/stochss/handlers/util/parameter_sweep.py
+++ b/stochss/handlers/util/parameter_sweep.py
@@ -13,8 +13,7 @@
except ModuleNotFoundError:
pass
-from gillespy2.solvers.auto.ssa_solver import get_best_ssa_solver
-from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver
+from gillespy2 import VariableSSACSolver
def setup_species_results(c, is_2d):
@@ -146,8 +145,6 @@ def get_data_for_csv(c, keys):
class ParameterSweep1D():
def run(c, settings, verbose=False, is_ssa=False, solver=None):
- if not c.ps_model:
- raise Exception("The parameter sweep has not been configured!")
c.verbose = verbose
results = setup_results(c)
for i,v1 in enumerate(c.p1_range):
@@ -176,7 +173,7 @@ def to_csv(c, path='.', nametag='results_csv', stamp=None, keys=None):
if stamp is None:
now = datetime.now()
stamp = datetime.timestamp(now)
- directory = os.path.join(path, nametag + stamp)
+ directory = os.path.join(path, nametag + str(stamp))
filename = os.path.join(directory, keys+".csv")
if not os.path.exists(directory):
os.mkdir(directory)
@@ -262,8 +259,6 @@ def configure(self, gillespy2_model, settings, trajectories):
class ParameterSweep2D():
def run(c, settings, verbose=False, is_ssa=False, solver=None):
- if not c.ps_model:
- raise Exception("The parameter sweep has not been configured!")
c.verbose = verbose
results = setup_results(c, is_2d=True)
for i,v1 in enumerate(c.p1_range):
@@ -295,7 +290,7 @@ def to_csv(c, path='.', nametag='results_csv', stamp=None, keys=None):
if stamp is None:
now = datetime.now()
stamp = datetime.timestamp(now)
- directory = os.path.join(path, nametag + stamp)
+ directory = os.path.join(path, nametag + str(stamp))
filename = os.path.join(directory, keys+".csv")
if not os.path.exists(directory):
os.mkdir(directory)
diff --git a/stochss/handlers/util/plot_results.py b/stochss/handlers/util/plot_results.py
index fb3d7ccbc5..bd19f8986f 100755
--- a/stochss/handlers/util/plot_results.py
+++ b/stochss/handlers/util/plot_results.py
@@ -4,6 +4,7 @@
import os
import json
import pickle
+import traceback
from os import path
from .stochss_errors import StochSSFileNotFoundError, PlotNotAvailableError
@@ -28,8 +29,9 @@ def read_pickled_results(pickle_path):
results = pickle.load(pickle_file)
return results
except FileNotFoundError as err:
- raise StochSSFileNotFoundError("Could not find the plot file: {0}".format(err))
-
+ raise StochSSFileNotFoundError("Could not find the plot file: {0}".format(err),
+ traceback.format_exc())
+
def get_plot_fig(plots_file_path, plt_key):
'''
@@ -51,15 +53,14 @@ def get_plot_fig(plots_file_path, plt_key):
if os.path.exists(pickle_path):
results = read_pickled_results(pickle_path)
return get_plot_fig_from_results(results, plt_key)
- else:
- raise PlotNotAvailableError("The plot is not available: "+str(err))
+ raise PlotNotAvailableError("The plot is not available: "+str(err), traceback.format_exc())
else:
results = read_pickled_results(pickle_path)
return get_plot_fig_from_results(results, plt_key)
def get_plot_fig_from_results(results, plt_key):
- es_keys = ["stddevran","trajectories","stddev","avg"]
+ es_keys = ["stddevran", "trajectories", "stddev", "avg"]
if plt_key == "stddevran":
plt_fig = results.plotplotly_std_dev_range(return_plotly_figure=True)
@@ -88,7 +89,6 @@ def edit_plot_fig(plt_fig, plt_data):
plt_data : str
The data that needs to be applied to the plot.
'''
- plt_data = json.loads(plt_data)
for key in plt_data.keys():
if key == "title":
plt_fig['layout']['title']['text'] = plt_data[key]
@@ -102,14 +102,13 @@ def plot_results(plots_path, plt_key, plt_data=None):
user_dir = "/home/jovyan"
full_path = path.join(user_dir, plots_path)
-
+
plt_fig = get_plot_fig(full_path, plt_key)
- if type(plt_fig) is str:
+ if isinstance(plt_fig, str):
return plt_fig
if not plt_data:
return json.dumps(plt_fig)
plt_fig = edit_plot_fig(plt_fig, plt_data)
return json.dumps(plt_fig)
-
\ No newline at end of file
diff --git a/stochss/handlers/util/rename.py b/stochss/handlers/util/rename.py
index 2e2ba38cb9..3e6003ec25 100644
--- a/stochss/handlers/util/rename.py
+++ b/stochss/handlers/util/rename.py
@@ -3,12 +3,31 @@
import os
import json
import shutil
+import traceback
try:
from .stochss_errors import StochSSFileNotFoundError, StochSSPermissionsError
except:
from stochss_errors import StochSSFileNotFoundError, StochSSPermissionsError
+def get_file_name(file):
+ '''
+ Get the name of a file object
+
+ Attributes
+ ----------
+ file : str
+ String representation of a file object
+ '''
+ if file.endswith('/'):
+ file = file[:-1]
+ if '/' in file:
+ file = file.split('/').pop()
+ if '.' not in file:
+ return file
+ return '.'.join(file.split('.')[:-1])
+
+
def get_unique_file_name(new_name, dir_path):
'''
Get a unique new name for the target file.
@@ -25,7 +44,7 @@ def get_unique_file_name(new_name, dir_path):
i = 1
if exists:
ext = "." + new_name.split('.').pop()
- name = new_name.split(ext)[0]
+ name = get_file_name(new_name)
if "(" in name and ")" in name:
_i = name.split('(').pop().split(')')[0]
if _i.isdigit():
@@ -74,9 +93,9 @@ def rename(path, new_name):
try:
shutil.move(old_path, new_path)
except FileNotFoundError as err:
- raise StochSSFileNotFoundError("Could not read the file or directory: " + str(err))
+ raise StochSSFileNotFoundError("Could not read the file or directory: " + str(err), traceback.format_exc())
except PermissionError as err:
- raise StochSSPermissionsError("You do not have permission to copy this file or directory: " + str(err))
+ raise StochSSPermissionsError("You do not have permission to copy this file or directory: " + str(err), traceback.format_exc())
if old_path.endswith('/'):
new_path = new_path[:-1]
@@ -93,6 +112,7 @@ def rename(path, new_name):
info_file.truncate()
if changed:
+ new_name = new_path.split('/').pop()
message = "A file already exists with that name, {0} was renamed to {1} in order to prevent a file from being overwriten.".format(old_path.split('/').pop(), new_name)
else:
message = 'Success! {0} was renamed to {1}'.format(old_name, new_name)
diff --git a/stochss/handlers/util/run_model.py b/stochss/handlers/util/run_model.py
index 0b8de45e0d..74d3aea88f 100755
--- a/stochss/handlers/util/run_model.py
+++ b/stochss/handlers/util/run_model.py
@@ -3,10 +3,12 @@
import os
import sys
import json
+import numpy
import argparse
import logging
import pickle
import plotly
+import traceback
from io import StringIO
from gillespy2.core import log
@@ -15,16 +17,11 @@
if type(handler) is logging.StreamHandler:
handler.stream = log_stream
-
-from gillespy2 import Species, Parameter, Reaction, RateRule, Model, AssignmentRule, FunctionDefinition
-
-import numpy
import gillespy2.core.gillespySolver
-from gillespy2.core.events import EventAssignment, EventTrigger, Event
-from gillespy2.core.gillespyError import ModelError, SolverError, DirectoryError, BuildError, ExecutionError
-from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver
-from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver
-from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver
+from gillespy2 import Species, Parameter, Reaction, RateRule, Model, AssignmentRule, FunctionDefinition
+from gillespy2 import EventAssignment, EventTrigger, Event
+from gillespy2 import ModelError, SimulationError, SolverError, DirectoryError, BuildError, ExecutionError
+from gillespy2 import TauLeapingSolver, TauHybridSolver, VariableSSACSolver, SSACSolver
import warnings
warnings.simplefilter("ignore")
@@ -234,7 +231,8 @@ def __init__(self, data, is_ode):
self.species = list(map(lambda s: self.build_specie(s, is_ode), data['species']))
self.parameters = list(map(lambda p: self.build_parameter(p), data['parameters']))
self.reactions = list(map(lambda r: self.build_reaction(r, self.parameters), data['reactions']))
- self.events = list(map(lambda e: self.build_event(e, self.species, self.parameters), data['eventsCollection']))
+ events = list(filter(lambda e: self.is_valid_event(e), data['eventsCollection']))
+ self.events = list(map(lambda e: self.build_event(e, self.species, self.parameters), events))
rate_rules = list(filter(lambda rr: self.is_valid_rate_rule(rr), data['rules']))
assignment_rules = list(filter(lambda rr: self.is_valid_assignment_rule(rr), data["rules"]))
self.rate_rules = list(map(lambda rr: self.build_rate_rules(rr, self.species, self.parameters), rate_rules))
@@ -358,6 +356,19 @@ def build_event_assignment(self, args, species, parameters):
return EventAssignment(variable=variable[0], expression=expression)
+ def is_valid_event(self, event):
+ if event['triggerExpression'] != "":
+ assignments = list(filter(lambda assignment: self.is_valid_assignment(assignment), event['eventAssignments']))
+ if len(assignments) > 0:
+ event['eventAssignments'] = assignments
+ return event
+
+
+ def is_valid_assignment(self, assignment):
+ if assignment['expression'] != "":
+ return assignment
+
+
def is_valid_rate_rule(self, rr):
if rr['type'] == "Rate Rule" and not rr['expression'] == "":
return rr
@@ -423,7 +434,10 @@ def build_stoich_species_dict(self, args):
for stoich_specie in args:
key = stoich_specie['specie']['name']
value = stoich_specie['ratio']
- d[key] = value
+ if key not in d.keys():
+ d[key] = value
+ else:
+ d[key] += value
return d
@@ -450,17 +464,12 @@ def get_models(full_path, name):
stochss_model['name'] = name
is_ode = stochss_model['defaultMode'] == "continuous"
except FileNotFoundError as error:
- print(str(error))
+ print("{0}\n{1}".format(error, traceback.format_exc()))
log.critical("Failed to find the model file: {0}".format(error))
- try:
- _model = ModelFactory(stochss_model, is_ode) # build GillesPy2 model
- gillespy2_model = _model.model
- except Exception as error:
- print(str(error))
- log.error(str(error))
- gillespy2_model = None
-
+ _model = ModelFactory(stochss_model, is_ode) # build GillesPy2 model
+ gillespy2_model = _model.model
+
return gillespy2_model, stochss_model
@@ -475,7 +484,8 @@ def run_model(model_path):
model_path : str
Path to the model file.
'''
- gillespy2_model, stochss_model = get_models(model_path, model_path.split('/').pop().split('.')[0])
+ from rename import get_file_name
+ gillespy2_model, stochss_model = get_models(model_path, get_file_name(model_path))
workflow = GillesPy2Workflow(None, model_path)
results = workflow.run_preview(gillespy2_model, stochss_model)
return results
@@ -511,7 +521,6 @@ def run_solver(model, data, run_timeout, is_ssa=False, solver=None, rate1=None,
def chooseForMe(model, run_timeout, is_ssa, solver, rate1, rate2):
- print("running choose for me")
if solver is None:
solver = model.get_best_solver(precompile=False)
@@ -530,7 +539,7 @@ def chooseForMe(model, run_timeout, is_ssa, solver, rate1, rate2):
def basicODESolver(model, data, run_timeout):
'''
- Run the model with the GillesPy2 BasicODESolver.
+ Run the model with the GillesPy2 ODESolver.
Attributes
----------
@@ -543,7 +552,7 @@ def basicODESolver(model, data, run_timeout):
'''
# print("running ode solver")
results = model.run(
- solver = BasicTauHybridSolver,
+ solver = TauHybridSolver,
timeout = run_timeout,
integrator_options = { 'atol' : data['absoluteTol'], 'rtol' : data['relativeTol']}
)
@@ -563,11 +572,12 @@ def ssaSolver(model, data, run_timeout):
run_timeout : int
Number of seconds until the simulation times out.
'''
- print("running ssa solver")
+ solver = SSACSolver(model=model)
seed = data['seed']
if(seed == -1):
seed = None
results = model.run(
+ solver = solver,
timeout = run_timeout,
number_of_trajectories = data['realizations'],
seed = seed
@@ -594,7 +604,7 @@ def v_ssa_solver(model, data, run_timeout, solver, rate1, rate2):
def basicTauLeapingSolver(model, data, run_timeout):
'''
- Run the model with the GillesPy2 BasicTauLeapingSolver.
+ Run the model with the GillesPy2 TauLeapingSolver.
Attributes
----------
@@ -610,7 +620,7 @@ def basicTauLeapingSolver(model, data, run_timeout):
if(seed == -1):
seed = None
results = model.run(
- solver = BasicTauLeapingSolver,
+ solver = TauLeapingSolver,
timeout = run_timeout,
number_of_trajectories = data['realizations'],
seed = seed,
@@ -621,7 +631,7 @@ def basicTauLeapingSolver(model, data, run_timeout):
def basicTauHybridSolver(model, data, run_timeout):
'''
- Run the model with the GillesPy2 BasicTauHybridSolver.
+ Run the model with the GillesPy2 TauHybridSolver.
Attributes
----------
@@ -637,7 +647,7 @@ def basicTauHybridSolver(model, data, run_timeout):
if(seed == -1):
seed = None
results = model.run(
- solver = BasicTauHybridSolver,
+ solver = TauHybridSolver,
timeout = run_timeout,
number_of_trajectories = data['realizations'],
seed = seed,
@@ -680,7 +690,9 @@ def get_parsed_args():
if 'GillesPy2 simulation exceeded timeout.' in logs:
resp['timeout'] = True
except ModelError as error:
- resp['errors'] = str(error)
+ resp['errors'] = "{0}".format(error)
+ except SimulationError as error:
+ resp['errors'] = "{0}".format(error)
with open(outfile, "w") as fd:
json.dump(resp, fd)
open(outfile + ".done", "w").close()
diff --git a/stochss/handlers/util/run_workflow.py b/stochss/handlers/util/run_workflow.py
index e2b9f2a79b..cc0071ac2a 100755
--- a/stochss/handlers/util/run_workflow.py
+++ b/stochss/handlers/util/run_workflow.py
@@ -8,6 +8,7 @@
import plotly
import argparse
import logging
+import traceback
from shutil import copyfile
from datetime import datetime, timezone, timedelta
@@ -63,7 +64,9 @@ def save_existing_workflow(wkfl, wkfl_type, initialize):
is_new : boolean
Represents whether the workflow is new or not.
'''
- old_model_path = os.path.join(wkfl.wkfl_path, wkfl.mdl_file) # path to the old model
+ with open(wkfl.info_path, 'r') as info_file:
+ file_name = json.load(info_file)['source_model'].split('/').pop()
+ old_model_path = os.path.join(wkfl.wkfl_path, file_name) # path to the old model
os.remove(old_model_path) # remove the old model
try:
copyfile(wkfl.mdl_path, wkfl.wkfl_mdl_path) # copy the new model into the workflow directory
diff --git a/stochss/handlers/util/stochss_errors.py b/stochss/handlers/util/stochss_errors.py
index 061f9c4b4b..00bc72084d 100644
--- a/stochss/handlers/util/stochss_errors.py
+++ b/stochss/handlers/util/stochss_errors.py
@@ -1,74 +1,92 @@
class StochSSAPIError(Exception):
- pass
+
+ def __init__(self, status_code, reason, msg, trace):
+ super().__init__()
+ self.status_code = status_code
+ self.reason = reason
+ self.message = msg
+ self.traceback = trace
class ModelNotFoundError(StochSSAPIError):
- def __init__(self, msg):
- self.status_code = 404
- self.reason = "Model File Not Found"
- self.message = msg
+ def __init__(self, msg, trace=None):
+ super().__init__(404, "Model File Not Found", msg, trace)
class StochSSFileNotFoundError(StochSSAPIError):
- def __init__(self, msg):
- self.status_code = 404
- self.reason = "StochSS File or Directory Not Found"
- self.message = msg
+ def __init__(self, msg, trace=None):
+ super().__init__(404, "StochSS File or Directory Not Found", msg, trace)
class StochSSPermissionsError(StochSSAPIError):
- def __init__(self, msg):
- self.status_code = 403
- self.reason = "Permission Denied"
- self.message = msg
+ def __init__(self, msg, trace=None):
+ super().__init__(403, "Permission Denied", msg, trace)
class ModelNotJSONFormatError(StochSSAPIError):
- def __init__(self, msg):
- self.status_code = 406
- self.reason = "Model Data Not JSON Format"
- self.message = msg
+ def __init__(self, msg, trace=None):
+ super().__init__(406, "Model Data Not JSON Format", msg, trace)
class FileNotJSONFormatError(StochSSAPIError):
- def __init__(self, msg):
- self.status_code = 406
- self.reason = "File Data Not JSON Format"
- self.message = msg
+ def __init__(self, msg, trace=None):
+ super().__init__(406, "File Data Not JSON Format", msg, trace)
class JSONFileNotModelError(StochSSAPIError):
- def __init__(self, msg):
- self.status_code = 406
- self.reason = "JSON File Not StochSS Model Format"
- self.message = msg
+ def __init__(self, msg, trace=None):
+ super().__init__(406, "JSON File Not StochSS Model Format", msg, trace)
class PlotNotAvailableError(StochSSAPIError):
- def __init__(self, msg):
- self.status_code = 406
- self.reason = "Plot Figure Not Available"
- self.message = msg
+ def __init__(self, msg, trace=None):
+ super().__init__(406, "Plot Figure Not Available", msg, trace)
class StochSSWorkflowError(StochSSAPIError):
- def __init__(self, msg):
- self.status_code = 403
- self.reason = "Workflow Errored on Run"
- self.message = msg
+ def __init__(self, msg, trace=None):
+ super().__init__(403, "Workflow Errored on Run", msg, trace)
class StochSSWorkflowNotCompleteError(StochSSAPIError):
- def __init__(self, msg):
- self.status_code = 403
- self.reason = "Workflow Run Not Complete"
- self.message = msg
\ No newline at end of file
+ def __init__(self, msg, trace=None):
+ super().__init__(403, "Workflow Run Not Complete", msg, trace)
+
+
+class StochSSExportCombineError(StochSSAPIError):
+
+ def __init__(self, msg, trace=None):
+ super().__init__(406, "No Completed Workflows Found", msg, trace)
+
+
+class FileNotSBMLFormatError(StochSSAPIError):
+
+ def __init__(self, msg, trace=None):
+ super().__init__(406, "File Not SBML Format", msg, trace)
+
+
+class ImporperMathMLFormatError(StochSSAPIError):
+
+ def __init__(self, msg, trace=None):
+ super().__init__(406, "Imporper Math-ML Format", msg, trace)
+
+
+class FileNotZipArchiveError(StochSSAPIError):
+
+ def __init__(self, msg, trace=None):
+ super().__init__(406, "File Not Zip Archive", msg, trace)
+
+
+class StochSSFileExistsError(StochSSAPIError):
+
+ def __init__(self, msg, trace=None):
+ super().__init__(406, "File Already Exists", msg, trace)
\ No newline at end of file
diff --git a/stochss/handlers/util/upload_file.py b/stochss/handlers/util/upload_file.py
old mode 100644
new mode 100755
index 66e63364e1..b9e14aa2fc
--- a/stochss/handlers/util/upload_file.py
+++ b/stochss/handlers/util/upload_file.py
@@ -2,9 +2,17 @@
import os
import json
-from .rename import get_unique_file_name
-from .convert_sbml_to_model import convert_to_gillespy_model, convert_to_stochss_model
-
+import zipfile
+import shutil
+# from .rename import get_unique_file_name
+# from .convert_sbml_to_model import convert_to_gillespy_model, convert_to_stochss_model
+# try:
+# from stochss_errors import FileNotZipArchiveError
+# except ImportError:
+# from .stochss_errors import FileNotZipArchiveError
+from stochss.handlers.util.rename import get_unique_file_name
+from stochss.handlers.util.convert_sbml_to_model import convert_to_gillespy_model, convert_to_stochss_model
+from stochss.handlers.util.stochss_errors import FileNotZipArchiveError, StochSSFileExistsError
def validate_model(body, file_name):
try:
@@ -12,9 +20,8 @@ def validate_model(body, file_name):
except json.decoder.JSONDecodeError:
return False, False, "The file {0} is not in JSON format.".format(file_name)
- test_keys = ["is_spatial","defaultID","defaultMode","modelSettings","simulationSettings",
- "parameterSweepSettings","species","parameters","reactions","eventsCollection",
- "rules","functionDefinitions","meshSettings","initialConditions"]
+ test_keys = ["species","parameters","reactions","eventsCollection",
+ "rules","functionDefinitions"]
other_keys = []
keys = list(body.keys())
for key in keys:
@@ -22,8 +29,6 @@ def validate_model(body, file_name):
test_keys.remove(key)
else:
other_keys.append(key)
- if len(other_keys):
- return False, True, "The following keys were found in {0} that don't exist within a StochSS model: {1}".format(file_name, ', '.join(other_keys))
if len(test_keys):
return False, True, "The following keys are missing from {0}: {1}".format(file_name, ', '.join(test_keys))
return True, True, ""
@@ -89,12 +94,15 @@ def upload_sbml_file(dir_path, _file_name, name, body):
def unzip_file(full_path, dir_path):
- import zipfile
- import shutil
-
with zipfile.ZipFile(full_path, "r") as zip_file:
+ par_path = os.path.dirname(full_path)
+ member_list = list(map(lambda member: os.path.exists(os.path.join(par_path, member)), zip_file.namelist()))
+ if True in member_list:
+ os.remove(full_path)
+ raise StochSSFileExistsError("Unable to upload {0} as the parent directory in {0} already exists.".format(full_path.split("/").pop()))
zip_file.extractall(dir_path)
- shutil.rmtree(os.path.join(dir_path, "__MACOSX"))
+ if "__MACOSX" in os.listdir(dir_path):
+ shutil.rmtree(os.path.join(dir_path, "__MACOSX"))
def upload_file(dir_path, file_name, name, ext, body, file_type, exts):
@@ -113,7 +121,10 @@ def upload_file(dir_path, file_name, name, ext, body, file_type, exts):
else:
file.write(body)
if ext == "zip":
- unzip_file(full_path, dir_path)
+ try:
+ unzip_file(full_path, dir_path)
+ except zipfile.BadZipFile as err:
+ errors.append(str(err))
dir_path = dir_path.replace("/home/jovyan", "")
if is_valid:
message = "{0} was successfully uploaded to {1}".format(file_name, dir_path)
@@ -168,3 +179,71 @@ def upload(file_data, file_info):
return resp
+
+def upload_from_link(path):
+ import urllib
+
+ user_dir = "/home/jovyan"
+ response = urllib.request.urlopen(path)
+ zip_path = os.path.join(user_dir, path.split('/').pop())
+ if os.path.exists(zip_path):
+ resp = {"message":"Could not upload this file as the {} \
+ already exists".format(path.split("/").pop()),
+ "reason":"Zip Archive Already Exists"}
+ return resp
+ with open(zip_path, "wb") as zip_file:
+ zip_file.write(response.read())
+ try:
+ unzip_file(zip_path, user_dir)
+ except StochSSFileExistsError as err:
+ return {"message":err.message, "reason":err.reason}
+ file_path = get_file_path(user_dir).replace(user_dir+"/", "")
+ target_file = path.split('/').pop()
+ resp = {"message":"Successfully uploaded the file {} to {}".format(target_file,
+ file_path),
+ "file_path":file_path}
+ return resp
+
+
+def get_file_path(path):
+ files = os.listdir(path)
+ paths = list(map(lambda file: os.path.join(path, file), files))
+ return max(paths, key=os.path.getctime)
+
+def get_parsed_args():
+ '''
+ Initializes an argparser to document this script and returns a dict of
+ the arguments that were passed to the script from the command line.
+
+ Attributes
+ ----------
+
+ '''
+ import argparse
+
+ parser = argparse.ArgumentParser(description="Upload a file from an external link")
+ parser.add_argument("file_path", help="The path to the external file.")
+ parser.add_argument("outfile", help="The path to the response file")
+ args = parser.parse_args()
+
+ return args
+
+
+if __name__ == "__main__":
+ args = get_parsed_args()
+ if args.file_path != 'None':
+ resp = upload_from_link(args.file_path)
+ with open(args.outfile, "w") as fd:
+ json.dump(resp, fd)
+ open(args.outfile + ".done", "w").close()
+ else:
+ done = os.path.exists(args.outfile + ".done")
+ if done:
+ with open(args.outfile, 'r') as response_file:
+ resp = json.load(response_file)
+ os.remove(args.outfile)
+ os.remove(args.outfile+".done")
+ else:
+ resp = {}
+ resp['done'] = done
+ print(json.dumps(resp))
diff --git a/stochss/handlers/workflows.py b/stochss/handlers/workflows.py
index c8bffe5715..e57852e37b 100644
--- a/stochss/handlers/workflows.py
+++ b/stochss/handlers/workflows.py
@@ -7,9 +7,11 @@
import logging
import json
import os
+import ast
import subprocess
-from notebook.base.handlers import APIHandler
+import traceback
from json.decoder import JSONDecodeError
+from notebook.base.handlers import APIHandler
from tornado import web
from .util.workflow_status import get_status
@@ -21,14 +23,16 @@
from .util.convert_to_model_inference_notebook import convert_to_mdl_inference_nb
from .util.stochss_errors import StochSSAPIError
from .util.run_workflow import initialize
+from .util.rename import get_file_name
log = logging.getLogger('stochss')
+# pylint: disable=abstract-method
class LoadWorkflowAPIHandler(APIHandler):
'''
########################################################################
- Handler for getting the Workflow's status, info, type, model for the
+ Handler for getting the Workflow's status, info, type, model for the
Workflow manager page.
########################################################################
'''
@@ -45,68 +49,111 @@ async def get(self):
path = self.get_query_argument(name="path")
self.set_header('Content-Type', 'application/json')
user_dir = "/home/jovyan"
- log.debug("Time stamp of the workflow: {0}".format(stamp))
- log.debug("The type of the workflow: {0}".format(wkfl_type))
- log.debug("The path to the workflow/model: {0}".format(path))
- title_types = {"gillespy":"Ensemble Simulation","parameterSweep":"Parameter Sweep"}
- name_types = {"gillespy":"_ES","parameterSweep":"_PS"}
- parent_path = os.path.dirname(path)
+ log.debug("Time stamp of the workflow: %s", stamp)
+ log.debug("The type of the workflow: %s", wkfl_type)
+ log.debug("The path to the workflow/model: %s", path)
+ title_types = {"gillespy":"Ensemble Simulation", "parameterSweep":"Parameter Sweep"}
+ name_types = {"gillespy":"_ES", "parameterSweep":"_PS"}
+ parent_path = self.get_query_argument(name='parentPath', default=os.path.dirname(path))
if path.endswith('.mdl'):
- resp = {"mdlPath":path,"timeStamp":stamp,"type":wkfl_type,
- "status":"new","titleType":title_types[wkfl_type],
- "wkflParPath": parent_path}
- name = path.split('/').pop().split('.')[0]
- resp["wkflName"] = name + name_types[wkfl_type] + stamp
+ resp = {"mdlPath":path, "timeStamp":stamp, "type":wkfl_type,
+ "status":"new", "titleType":title_types[wkfl_type],
+ "wkflParPath": parent_path, "startTime":None}
+ resp["wkflName"] = (get_file_name(path) +
+ name_types[wkfl_type] + stamp)
resp["wkflDir"] = resp['wkflName'] + ".wkfl"
- resp["startTime"] = None
elif path.endswith('.wkfl'):
- resp = {"wkflDir":path.split('/').pop(), "wkflParPath":parent_path}
+ resp = {"wkflDir":path.split('/').pop(), "wkflParPath":parent_path,
+ "wkflName":get_file_name(path)}
resp["status"] = get_status(path)
- name = path.split('/').pop().split('.')[0]
- resp["wkflName"] = name
- try:
- resp["timeStamp"] = "_"+"_".join(name.split('_')[-2:])
- except:
- resp["timeStamp"] = None
+ resp["timeStamp"] = "_"+"_".join(resp['wkflName'].split('_')[-2:])
try:
with open(os.path.join(user_dir, path, "info.json"), "r") as info_file:
info = json.load(info_file)
resp["type"] = info['type']
resp["startTime"] = info['start_time']
- resp["mdlPath"] = info['source_model'] if resp['status'] == "ready" else info['wkfl_model']
+ resp["mdlPath"] = (info['source_model'] if resp['status'] == "ready"
+ else info['wkfl_model'])
resp["titleType"] = title_types[info['type']]
except FileNotFoundError as err:
self.set_status(404)
- error = {"Reason":"Info File Not Found","Message":"Could not find the workflow info file: "+str(err)}
- log.error("Exception information: {0}".format(error))
- self.write(error)
+ error = {"Reason":"Info File Not Found",
+ "Message":"Could not find the workflow info file: "+str(err)}
+ self.respond_with_error(error)
except JSONDecodeError as err:
self.set_status(406)
- error = {"Reason":"File Not JSON Format","Message":"The workflow info file is not JSON decodable: "+str(err)}
- log.error("Exception information: {0}".format(error))
- self.write(error)
+ error = {"Reason":"File Not JSON Format",
+ "Message":"The workflow info file is not JSON decodable: "+str(err)}
+ self.respond_with_error(error)
try:
with open(os.path.join(user_dir, resp['mdlPath']), "r") as model_file:
resp["model"] = json.load(model_file)
- except:
+ self.update_model_data(resp["model"])
+ except FileNotFoundError:
resp["model"] = None
- resp["error"] = {"Reason":"Model Not Found","Message":"Could not find the model file: "+resp['mdlPath']}
- resp["settings"] = self.get_settings(os.path.join(resp['wkflParPath'], resp['wkflDir']), resp['mdlPath'])
- log.debug("Response: {0}".format(resp))
+ resp["error"] = {"Reason":"Model Not Found",
+ "Message":"Could not find the model file: "+resp['mdlPath']}
+ trace = traceback.format_exc()
+ log.error("Exception information: %s\n%s", resp["error"], trace)
+ resp["settings"] = self.get_settings(os.path.join(resp['wkflParPath'], resp['wkflDir']),
+ resp['mdlPath'])
+ log.debug("Response: %s", resp)
self.write(resp)
self.finish()
- def get_settings(self, wkfl_path, mdl_path):
+ @classmethod
+ def update_model_data(cls, data):
+ param_ids = []
+ for param in data['parameters']:
+ param_ids.append(param['compID'])
+ if isinstance(param['expression'], str):
+ try:
+ param['expression'] = ast.literal_eval(param['expression'])
+ except ValueError:
+ pass
+ for reaction in data['reactions']:
+ if reaction['rate'].keys() and isinstance(reaction['rate']['expression'], str):
+ try:
+ reaction['rate']['expression'] = ast.literal_eval(reaction['rate']['expression'])
+ except ValueError:
+ pass
+ for event in data['eventsCollection']:
+ for assignment in event['eventAssignments']:
+ if assignment['variable']['compID'] in param_ids:
+ try:
+ assignment['variable']['expression'] = ast.literal_eval(assignment['variable']['expression'])
+ except ValueError:
+ pass
+ for rule in data['rules']:
+ if rule['variable']['compID'] in param_ids:
+ try:
+ rule['variable']['expression'] = ast.literal_eval(rule['variable']['expression'])
+ except ValueError:
+ pass
+
+
+ @classmethod
+ def get_settings(cls, wkfl_path, mdl_path):
+ '''
+ Get the settings for the workflow.
+
+ Attributes
+ ----------
+ wkfl_path : string
+ The path to the workflow
+ mdl_path : string
+ The path to the model used by the workflow
+ '''
settings_path = os.path.join(wkfl_path, "settings.json")
-
+
if os.path.exists(settings_path):
with open(settings_path, "r") as settings_file:
return json.load(settings_file)
with open("/stochss/stochss_templates/workflowSettingsTemplate.json", "r") as template_file:
settings_template = json.load(template_file)
-
+
if os.path.exists(mdl_path):
with open(mdl_path, "r") as mdl_file:
mdl = json.load(mdl_file)
@@ -115,12 +162,27 @@ def get_settings(self, wkfl_path, mdl_path):
"parameterSweepSettings":mdl['parameterSweepSettings'],
"resultsSettings":settings_template['resultsSettings']}
return settings
- except:
+ except KeyError:
return settings_template
else:
return settings_template
+ def respond_with_error(self, error):
+ '''
+ Respond to the api request with an error
+
+ Attributes
+ ----------
+ error : dict
+ Information on the error being reported
+ '''
+ trace = traceback.format_exc()
+ log.error("Exception information: %s\n%s", error, trace)
+ error['Traceback'] = trace
+ self.write(error)
+
+
class RunWorkflowAPIHandler(APIHandler):
'''
########################################################################
@@ -131,28 +193,30 @@ class RunWorkflowAPIHandler(APIHandler):
async def get(self):
'''
Start running a workflow and record the time in UTC in the workflow_info file.
- Creates workflow directory and workflow_info file if running a new workflow. Copys
+ Creates workflow directory and workflow_info file if running a new workflow. Copys
model into the workflow directory.
Attributes
----------
'''
data = json.loads(self.get_query_argument(name="data"))
- log.debug("Handler query string: {0}".format(data))
+ log.debug("Handler query string: %s", data)
opt_type = data['optType']
wkfl_type = data['type']
model_path = data['mdlPath']
workflow_path = data['wkflPath']
- log.debug("Actions for the workflow: {0}".format(opt_type))
- log.debug("Type of workflow: {0}".format(wkfl_type))
- log.debug("Path to the model: {0}".format(model_path))
- log.debug("Path to the workflow: {0}".format(workflow_path))
- exec_cmd = ["/stochss/stochss/handlers/util/run_workflow.py", "{}".format(model_path), "{0}".format(workflow_path), "{0}".format(wkfl_type) ] # Script commands
+ log.debug("Actions for the workflow: %s", opt_type)
+ log.debug("Type of workflow: %s", wkfl_type)
+ log.debug("Path to the model: %s", model_path)
+ log.debug("Path to the workflow: %s", workflow_path)
+ exec_cmd = ["/stochss/stochss/handlers/util/run_workflow.py",
+ "{}".format(model_path), "{0}".format(workflow_path),
+ "{0}".format(wkfl_type)] # Script commands
opt_type = list(map(lambda el: "-" + el, list(opt_type))) # format the opt_type for argparse
exec_cmd.extend(opt_type) # Add opt_type to exec_cmd
- log.debug("Exec command sent to the subprocess: {0}".format(exec_cmd))
+ log.debug("Exec command sent to the subprocess: %s", exec_cmd)
log.debug('Sending the workflow run cmd')
- pipe = subprocess.Popen(exec_cmd)
+ subprocess.Popen(exec_cmd)
log.debug('The workflow has started')
self.finish()
@@ -173,17 +237,17 @@ async def get(self):
----------
'''
data = json.loads(self.get_query_argument(name="data"))
- log.debug("Handler query string: {0}".format(data))
+ log.debug("Handler query string: %s", data)
opt_type = data['optType']
wkfl_type = data['type']
model_path = data['mdlPath']
workflow_path = data['wkflPath']
settings = data['settings']
- log.debug("Actions for the workflow: {0}".format(opt_type))
- log.debug("Type of workflow: {0}".format(wkfl_type))
- log.debug("Path to the model: {0}".format(model_path))
- log.debug("Path to the workflow: {0}".format(workflow_path))
- kwargs = {"save":True,"settings":settings}
+ log.debug("Actions for the workflow: %s", opt_type)
+ log.debug("Type of workflow: %s", wkfl_type)
+ log.debug("Path to the model: %s", model_path)
+ log.debug("Path to the workflow: %s", workflow_path)
+ kwargs = {"save":True, "settings":settings}
if 'n' in opt_type:
kwargs['new'] = True
else:
@@ -191,11 +255,9 @@ async def get(self):
if 'r' in opt_type:
kwargs['run'] = True
resp = initialize(model_path, workflow_path, wkfl_type, **kwargs)
- log.debug("Response to the command: {0}".format(resp))
+ log.debug("Response to the command: %s", resp)
if resp:
self.write(resp)
- else:
- self.write(errors)
self.finish()
@@ -216,7 +278,7 @@ async def get(self):
workflow_path = self.get_query_argument(name="path")
log.debug('Getting the status of the workflow')
status = get_status(workflow_path)
- log.debug('The status of the workflow is: {0}\n'.format(status))
+ log.debug('The status of the workflow is: %s', status)
self.write(status)
self.finish()
@@ -230,34 +292,40 @@ class PlotWorkflowResultsAPIHandler(APIHandler):
@web.authenticated
async def get(self):
'''
- Retrieve a plot figure of the workflow results based on the plot type
+ Retrieve a plot figure of the workflow results based on the plot type
in the request body.
Attributes
----------
'''
workflow_path = self.get_query_argument(name="path")
- log.debug("The path to the workflow: {0}\n".format(workflow_path))
+ log.debug("The path to the workflow: %s", workflow_path)
body = json.loads(self.get_query_argument(name='data'))
- log.debug("Plot args passed to the plot: {0}\n".format(body))
+ log.debug("Plot args passed to the plot: %s", body)
results_path = os.path.join(workflow_path, 'results/plots.json')
- log.debug("Path to the workflow results: {0}\n".format(results_path))
+ log.debug("Path to the workflow results: %s", results_path)
plt_key = body['plt_key']
- log.debug("Key identifying the requested plot: {0}\n".format(plt_key))
+ log.debug("Key identifying the requested plot: %s", plt_key)
plt_data = body['plt_data']
- log.debug("Title and axis data for the plot: {0}\n".format(plt_data))
+ log.debug("Title and axis data for the plot: %s", plt_data)
self.set_header('Content-Type', 'application/json')
try:
if "None" in plt_data:
plt_fig = plot_results(results_path, plt_key)
else:
- plt_fig = plot_results(results_path, plt_key, plt_data) # Add plot data to the exec cmd if its not "None"
- log.debug("Plot figure: {0}\n".format(plt_fig))
+ # Add plot data to the exec cmd if its not "None"
+ plt_fig = plot_results(results_path, plt_key, plt_data)
+ log.debug("Plot figure: %s", plt_fig)
self.write(plt_fig)
except StochSSAPIError as err:
self.set_status(err.status_code)
- error = {"Reason":err.reason,"Message":err.message}
- log.error("Exception information: {0}\n".format(error))
+ error = {"Reason":err.reason, "Message":err.message}
+ if err.traceback is None:
+ trace = traceback.format_exc()
+ else:
+ trace = err.traceback
+ log.error("Exception information: %s\n%s", error, trace)
+ error['Traceback'] = trace
self.write(error)
self.finish()
@@ -277,24 +345,27 @@ async def get(self):
----------
'''
logs_path = self.get_query_argument(name="path")
- log.debug("Path to the workflow logs file: {0}\n".format(logs_path))
+ log.debug("Path to the workflow logs file: %s", logs_path)
full_path = os.path.join("/home/jovyan/", logs_path)
- log.debug("Full path to the workflow logs file: {0}\n".format(full_path))
+ log.debug("Full path to the workflow logs file: %s", full_path)
try:
with open(full_path, 'r') as log_file:
data = log_file.read()
- log.debug("Contents of the log file: {0}\n".format(data))
+ log.debug("Contents of the log file: %s", data)
if data:
resp = data
else:
resp = "No logs were recoded for this workflow."
- log.debug("Response: {0}\n".format(resp))
+ log.debug("Response: %s", resp)
self.write(resp)
except FileNotFoundError as err:
self.set_status(404)
self.set_header('Content-Type', 'application/json')
- error = {"Reason":"StochSS File or Directory Not Found","Message":"Could not find the workflow log file: "+str(err)}
- log.error("Exception information: {0}\n".format(error))
+ error = {"Reason":"StochSS File or Directory Not Found",
+ "Message":"Could not find the workflow log file: "+str(err)}
+ trace = traceback.format_exc()
+ log.error("Exception information: %s\n%s", error, trace)
+ error['Traceback'] = trace
self.write(error)
self.finish()
@@ -302,7 +373,7 @@ async def get(self):
class WorkflowNotebookHandler(APIHandler):
'''
##############################################################################
- Handler for handling conversions from model (.mdl) file or workflows (.wkfl)
+ Handler for handling conversions from model (.mdl) file or workflows (.wkfl)
to Jupyter Notebook (.ipynb) file for notebook workflows.
##############################################################################
'''
@@ -316,38 +387,122 @@ async def get(self):
'''
log.setLevel(logging.DEBUG)
workflow_type = self.get_query_argument(name="type")
- path = self.get_query_argument(name="path")
+ path = os.path.join("/home/jovyan", self.get_query_argument(name="path"))
settings = None
if path.endswith('.wkfl'):
- name = path.split('/').pop().split('.')[0].replace('-', '_')
+ name = get_file_name(path)
with open(os.path.join(path, "info.json"), "r") as info_file:
info = json.load(info_file)
workflow_type = info['type']
with open(os.path.join(path, "settings.json"), "r") as settings_file:
settings = json.load(settings_file)
if workflow_type == "parameterSweep":
- workflow_type = "1d_parameter_sweep" if settings['parameterSweepSettings']['is1D'] else "2d_parameter_sweep"
+ workflow_type = ("1d_parameter_sweep" if settings['parameterSweepSettings']['is1D']
+ else "2d_parameter_sweep")
+ dest_path = os.path.dirname(path)
path = info['source_model'] if info['wkfl_model'] is None else info['wkfl_model']
- log.debug("Name for the notebook: {0}".format(name))
+ log.debug("Name for the notebook: %s", name)
+ else:
+ dest_path = self.get_query_argument(name="parentPath")
- log.debug("Type of workflow to be run: {0}\n".format(workflow_type))
- log.debug("Path to the model: {0}\n".format(path))
+ log.debug("Type of workflow to be run: %s", workflow_type)
+ log.debug("Path to the model: %s", path)
workflows = {"gillespy":convert_to_notebook,
- "1d_parameter_sweep":convert_to_1d_psweep_nb,
- "2d_parameter_sweep":convert_to_2d_psweep_nb,
- "sciope_model_exploration":convert_to_sciope_me,
- "model_inference":convert_to_mdl_inference_nb}
+ "1d_parameter_sweep":convert_to_1d_psweep_nb,
+ "2d_parameter_sweep":convert_to_2d_psweep_nb,
+ "sciope_model_exploration":convert_to_sciope_me,
+ "model_inference":convert_to_mdl_inference_nb}
try:
- resp = workflows[workflow_type](path, name=name, settings=settings) if settings is not None else workflows[workflow_type](path)
- log.debug("Response: {0}\n".format(resp))
+ resp = (workflows[workflow_type](path, name=name, settings=settings,
+ dest_path=dest_path)
+ if settings is not None else workflows[workflow_type](path,
+ dest_path=dest_path))
+ log.debug("Response: %s", resp)
self.write(resp)
except StochSSAPIError as err:
self.set_status(err.status_code)
self.set_header('Content-Type', 'application/json')
- error = {"Reason":err.reason,"Message":err.message}
- log.error("Exception information: {0}\n".format(error))
+ error = {"Reason":err.reason, "Message":err.message}
+ if err.traceback is None:
+ trace = traceback.format_exc()
+ else:
+ trace = err.traceback
+ log.error("Exception information: %s\n%s", error, trace)
+ error['Traceback'] = trace
self.write(error)
log.setLevel(logging.WARNING)
self.finish()
+
+class SavePlotAPIHandler(APIHandler):
+ '''
+ ##############################################################################
+ Handler for handling conversions from model (.mdl) file or workflows (.wkfl)
+ to Jupyter Notebook (.ipynb) file for notebook workflows.
+ ##############################################################################
+ '''
+ @web.authenticated
+ async def post(self):
+ '''
+ Create a jupyter notebook workflow using a stochss model.
+
+ Attributes
+ ----------
+ '''
+ self.set_header('Content-Type', 'application/json')
+ path = self.get_query_argument(name="path")
+ plot = json.loads(self.request.body.decode())
+ log.debug("The path to the workflow setting file: %s", path)
+ log.debug("The plot to be saved: %s", plot)
+
+ with open(path, "r") as settings_file:
+ settings = json.load(settings_file)
+ log.debug("Original settings: %s", settings)
+
+ settings['resultsSettings']['outputs'].append(plot)
+ log.debug("New settings: %s", settings)
+
+ with open(path, "w") as settings_file:
+ json.dump(settings, settings_file)
+
+ resp = {"message":"The plot was successfully saved", "data":plot}
+ log.debug("Response message: %s", resp)
+ self.write(resp)
+ self.finish()
+
+
+class SaveAnnotationAPIHandler(APIHandler):
+ '''
+ ##############################################################################
+ Handler for saving annotations for workflows.
+ ##############################################################################
+ '''
+ @web.authenticated
+ async def post(self):
+ '''
+ Adds/updates the workflows annotation in the info file.
+
+ Attributes
+ ----------
+ '''
+ self.set_header('Content-Type', 'application/json')
+ path = self.get_query_argument(name="path")
+ annotation = json.loads(self.request.body.decode())['annotation']
+ log.debug("The path to the workflow info file: %s", path)
+ log.debug("The annotation to be saved: %s", annotation)
+
+ with open(path, "r") as info_file:
+ info = json.load(info_file)
+ log.debug("Original info: %s", info)
+
+ info['annotation'] = annotation
+ log.debug("New info: %s", info)
+
+ with open(path, "w") as info_file:
+ json.dump(info, info_file)
+
+ resp = {"message":"The annotation was successfully saved", "data":annotation}
+ log.debug("Response message: %s", resp)
+ self.write(resp)
+ self.finish()
diff --git a/stochss/tests/run_tests.py b/stochss/tests/run_tests.py
index 33c8f82a31..e8ea377acf 100755
--- a/stochss/tests/run_tests.py
+++ b/stochss/tests/run_tests.py
@@ -1,6 +1,8 @@
#!/usr/bin/env python3
-import unittest, sys, os
+import unittest
+import sys
+import os
import argparse
parser = argparse.ArgumentParser()
@@ -15,11 +17,23 @@
import test_model_template
import test_settings_template
import test_convert_sbml
+ import test_upload_file
+ import test_rename
+ import test_generate_zip_file
+ import test_workflow_status
+ import test_ls
+ import test_duplicate
modules = [
test_model_template,
test_settings_template,
- test_convert_sbml
+ test_convert_sbml,
+ test_rename,
+ test_upload_file,
+ test_generate_zip_file,
+ test_workflow_status,
+ test_ls,
+ test_duplicate
]
for module in modules:
diff --git a/stochss/tests/test_duplicate.py b/stochss/tests/test_duplicate.py
new file mode 100644
index 0000000000..80449c7cfa
--- /dev/null
+++ b/stochss/tests/test_duplicate.py
@@ -0,0 +1,325 @@
+import unittest, os, tempfile
+from pathlib import Path
+from handlers.util.duplicate import *
+
+class TestDuplicate(unittest.TestCase):
+
+ #unit tests for method get_unique_file_name
+
+ def test_get_unique_file_name_notcopy_noext(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filename = "test_file"
+ test_filepath = os.path.join(tempdir, test_filename)
+ assert get_unique_file_name(test_filepath) == os.path.join(tempdir,"test_file-copy")
+
+ def test_get_unique_file_name_iscopy_noext(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filename = "test_file-copy"
+ test_filepath = os.path.join(tempdir, test_filename)
+ assert get_unique_file_name(test_filepath) == os.path.join(tempdir, 'test_file-copy(2)')
+
+ def test_get_unique_file_name_notcopy_hasext(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filename = "test_file.sample"
+ test_filepath = os.path.join(tempdir, test_filename)
+ assert get_unique_file_name(test_filepath) == os.path.join(tempdir, 'test_file-copy.sample')
+
+ def test_get_unique_file_name_iscopy_hasext(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filename = "test_file-copy.sample"
+ test_filepath = os.path.join(tempdir, test_filename)
+ assert get_unique_file_name(test_filepath) == os.path.join(tempdir,"test_file-copy(2).sample")
+
+ def test_get_unique_file_name_multiple_copies(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filename = "test_file"
+ test_filepath = os.path.join(tempdir, test_filename)
+ for i in range(2):
+ test_filepath = get_unique_file_name(test_filepath)
+ assert test_filepath == os.path.join(tempdir,"test_file-copy(2)")
+
+ #unit tests for method duplicate
+
+ def test_duplicate_file_not_found_raise_error(self):
+ from handlers.util.stochss_errors import StochSSFileNotFoundError
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filepath = os.path.join(tempdir,"nonexistent_file")
+ with self.assertRaises(StochSSFileNotFoundError):
+ duplicate(test_filepath)
+
+ def test_duplicate_file_not_found_no_new_file(self):
+ from handlers.util.stochss_errors import StochSSFileNotFoundError
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filepath = os.path.join(tempdir,"nonexistent_file")
+ try:
+ duplicate(test_filepath)
+ except StochSSFileNotFoundError:
+ pass
+ tempdir_contents = os.listdir(tempdir)
+ assert len(tempdir_contents) == 0
+
+ def test_duplicate_permission_not_granted_raise_error(self):
+ from handlers.util.stochss_errors import StochSSPermissionsError
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filepath = os.path.join(tempdir,"existent_file")
+ Path(test_filepath).touch()
+ os.chmod(test_filepath,000)
+ with self.assertRaises(StochSSPermissionsError):
+ duplicate(test_filepath)
+
+ def test_duplicate_permission_not_granted_no_new_file(self):
+ from handlers.util.stochss_errors import StochSSPermissionsError
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filepath = os.path.join(tempdir,"existent_file")
+ Path(test_filepath).touch()
+ os.chmod(test_filepath,000)
+ try:
+ duplicate(test_filepath)
+ except StochSSPermissionsError:
+ pass
+ tempdir_contents = os.listdir(tempdir)
+ assert len(tempdir_contents) == 1
+
+
+ def test_duplicate_copy_successful(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filepath = os.path.join(tempdir,"existent_file")
+ Path(test_filepath).touch()
+ duplicate(test_filepath)
+ tempdir_contents = os.listdir(tempdir)
+ assert os.path.isfile(os.path.join(tempdir,'existent_file-copy'))
+
+ #unit tests for method extract_wkfl_model
+
+ def test_extract_wkfl_model_path_changed(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_model_path=os.path.join(tempdir,"test_model")
+ Path(test_model_path).touch()
+ class Test_Workflow:
+ wkfl_mdl_path = ""
+ test_wkfl= Test_Workflow()
+ setattr(test_wkfl,"wkfl_mdl_path",test_model_path)
+ test_extract_target="test_model"
+ extract_wkfl_model(wkfl=test_wkfl,mdl_parent_path=tempdir,model_file=test_extract_target)
+ assert os.path.isfile(os.path.join(tempdir,"test_model(1)"))
+
+ def test_extract_wkfl_model_path_not_changed(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_model_path=os.path.join(tempdir,"test_model")
+ Path(test_model_path).touch()
+ class Test_Workflow:
+ wkfl_mdl_path = ""
+ test_wkfl= Test_Workflow()
+ setattr(test_wkfl,"wkfl_mdl_path",test_model_path)
+ test_extract_target="test_model_extracted"
+ extract_wkfl_model(wkfl=test_wkfl,mdl_parent_path=tempdir,model_file=test_extract_target)
+ assert os.path.isfile(os.path.join(tempdir,test_extract_target))
+
+ def test_extract_wkfl_model_file_not_found_raise_error(self):
+ from handlers.util.stochss_errors import ModelNotFoundError
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_model_path=os.path.join(tempdir,"test_model")
+ class Test_Workflow:
+ wkfl_mdl_path = ""
+ test_wkfl= Test_Workflow()
+ setattr(test_wkfl,"wkfl_mdl_path",test_model_path)
+ with self.assertRaises(ModelNotFoundError):
+ extract_wkfl_model(wkfl=test_wkfl,mdl_parent_path=tempdir,model_file="test_model")
+
+ def test_extract_wkfl_model_file_not_found_no_new_file(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_model_path=os.path.join(tempdir,"test_model")
+ class Test_Workflow:
+ wkfl_mdl_path = ""
+ test_wkfl= Test_Workflow()
+ setattr(test_wkfl,"wkfl_mdl_path",test_model_path)
+ tempdir_contents = os.listdir(tempdir)
+ assert len(tempdir_contents) == 0
+
+ def test_extract_wkfl_model_permission_not_granted_raise_error(self):
+ from handlers.util.stochss_errors import StochSSPermissionsError
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_model_path=os.path.join(tempdir,"test_model")
+ Path(test_model_path).touch()
+ class Test_Workflow:
+ wkfl_mdl_path = ""
+ test_wkfl= Test_Workflow()
+ setattr(test_wkfl,"wkfl_mdl_path",test_model_path)
+ os.chmod(test_model_path,000)
+ with self.assertRaises(StochSSPermissionsError):
+ extract_wkfl_model(wkfl=test_wkfl,mdl_parent_path=tempdir,model_file="test_model")
+
+ def test_extract_wkfl_model_permission_not_granted_no_new_file(self):
+ from handlers.util.stochss_errors import StochSSPermissionsError
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_model_path=os.path.join(tempdir,"test_model")
+ Path(test_model_path).touch()
+ class Test_Workflow:
+ wkfl_mdl_path = ""
+ test_wkfl= Test_Workflow()
+ setattr(test_wkfl,"wkfl_mdl_path",test_model_path)
+ os.chmod(test_model_path,000)
+ try:
+ extract_wkfl_model(wkfl=test_wkfl,mdl_parent_path=tempdir,model_file="test_model")
+ except StochSSPermissionsError:
+ pass
+ tempdir_contents = os.listdir(tempdir)
+ assert len(tempdir_contents) == 1
+
+ #unit tests for method get_wkfl_model_parent_path
+
+ def test_get_wkfl_model_parent_path_model_only(self):
+ assert get_wkfl_model_parent_path("test_path", True, "no wkfl") == "test_path"
+
+ def test_get_wkfl_model_parent_path_does_not_exist(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_model_path=os.path.join(tempdir,"test_model")
+ class Test_Workflow:
+ wkfl_mdl_path = ""
+ mdl_path = ""
+ test_wkfl= Test_Workflow()
+ setattr(test_wkfl, "",test_model_path)
+ assert get_wkfl_model_parent_path("path_does_not_exist", False, test_wkfl) == "path_does_not_exist"
+
+ def test_get_wkfl_model_parent_path_exists(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_dir_path=os.path.join(tempdir,'test_directory')
+ os.mkdir(test_dir_path)
+ test_file_path = os.path.join(test_dir_path,"test_file")
+ class Test_Workflow:
+ mdl_path = ""
+ test_wkfl= Test_Workflow()
+ setattr(test_wkfl, "mdl_path", test_file_path)
+ Path(test_file_path).touch()
+ assert get_wkfl_model_parent_path("path_does_not_exist", False, test_wkfl) == test_dir_path
+
+ #unit tests for method get_model_path
+
+ def test_get_model_path_only_model(self):
+ assert get_model_path("test_wkfl_parent_path", "test_mdl_parent_path", "test_mdl_file", True) == (os.path.join("test_wkfl_parent_path","test_mdl_file"), "")
+
+ def test_get_model_path_wkfl_parent_path_equals_mdl_parent_path_and_exists(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_dual_parent_dir = os.path.join(tempdir, "test_dual_parent_dir")
+ test_model_path = os.path.join(test_dual_parent_dir,"test_model")
+ os.mkdir(test_dual_parent_dir)
+ Path(test_model_path).touch()
+ assert get_model_path(test_dual_parent_dir, test_dual_parent_dir, "test_model", False) == (os.path.join(test_dual_parent_dir,"test_model"), "")
+
+ def test_get_model_path_mdl_file_in_wkfl_parent_path_directory(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_wkfl_parent_dir = os.path.join(tempdir, "test_wkfl_parent_dir")
+ os.mkdir(test_wkfl_parent_dir)
+ test_model_parent_dir = os.path.join(tempdir, "test_model_parent_dir")
+ os.mkdir(test_model_parent_dir)
+ test_model_path = os.path.join(test_wkfl_parent_dir,"test_model")
+ Path(test_model_path).touch()
+ assert get_model_path(test_wkfl_parent_dir, "", "test_model", False) == (os.path.join(test_wkfl_parent_dir,"test_model"), "")
+
+
+ def test_get_model_path_mdl_file_in_mdl_parent_path_directory(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_wkfl_parent_dir = os.path.join(tempdir, "test_wkfl_parent_dir")
+ os.mkdir(test_wkfl_parent_dir)
+ test_model_parent_dir = os.path.join(tempdir, "test_model_parent_dir")
+ os.mkdir(test_model_parent_dir)
+ test_model_path = os.path.join(test_model_parent_dir,"test_model")
+ Path(test_model_path).touch()
+ assert get_model_path(test_wkfl_parent_dir, test_model_parent_dir, "test_model", False) == (os.path.join(test_model_parent_dir,"test_model"), "")
+
+
+ def test_get_model_path_mdl_file_in_mdl_and_wkfl_parent_path_directory(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_wkfl_parent_dir = os.path.join(tempdir, "test_wkfl_parent_dir")
+ os.mkdir(test_wkfl_parent_dir)
+ test_model_parent_dir = os.path.join(tempdir, "test_model_parent_dir")
+ os.mkdir(test_model_parent_dir)
+ test_model_path = os.path.join(test_model_parent_dir,"test_model")
+ Path(test_model_path).touch()
+ test_model_path2 = os.path.join(test_wkfl_parent_dir,"test_model")
+ Path(test_model_path2).touch()
+ assert get_model_path(test_wkfl_parent_dir, test_model_parent_dir, "test_model", False) == (os.path.join(test_wkfl_parent_dir,"test_model"), "")
+
+
+ def test_get_model_path_mdl_file_not_found(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_wkfl_parent_dir = os.path.join(tempdir, "test_wkfl_parent_dir")
+ os.mkdir(test_wkfl_parent_dir)
+ test_model_parent_dir = os.path.join(tempdir, "test_model_parent_dir")
+ os.mkdir(test_model_parent_dir)
+ assert get_model_path(test_wkfl_parent_dir, test_model_parent_dir, "test_model", False) == (os.path.join(test_wkfl_parent_dir,"test_model"), "The model file {0} could not be found. To edit the model or run the workflow you will need to update the path to the model or extract the model from the workflow.".format("test_model"))
+
+
+ #unit tests for method duplicate_wkfl_as_new
+
+ def test_duplicate_wkfl_as_new_wkfl_file_not_found(self):
+ from handlers.util.stochss_errors import StochSSFileNotFoundError
+ with tempfile.TemporaryDirectory() as tempdir:
+ with self.assertRaises(StochSSFileNotFoundError):
+ duplicate_wkfl_as_new(os.path.join(tempdir,"nonexistent_wkfl"), False, "timestamp")
+
+ def test_duplicate_wkfl_as_new_not_JSON_decodable(self):
+ from handlers.util.stochss_errors import FileNotJSONFormatError
+ with tempfile.TemporaryDirectory() as tempdir:
+ Path(os.path.join(tempdir,"info.json")).touch()
+ with self.assertRaises(FileNotJSONFormatError):
+ duplicate_wkfl_as_new(os.path.join(tempdir), False, "timestamp")
+
+
+ def test_duplicate_wkfl_as_new_only_model(self):
+ #from json import load
+ from unittest import mock
+ from handlers.util.run_model import GillesPy2Workflow
+ from handlers.util.stochss_errors import FileNotJSONFormatError
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_dict={"type":"gillespy","source_model":"test_source_model"}
+ test_path = os.path.join(tempdir,"test_wkfl_dir")
+ os.mkdir(test_path)
+ Path(os.path.join(test_path,"info.json")).touch()
+ test_source_model_path = os.path.join(test_path,"test_source_model")
+ Path(test_source_model_path).touch()
+ with mock.patch("handlers.util.run_model.GillesPy2Workflow.get_settings") as mock_settings:
+ mock_settings.return_value = None
+ with mock.patch("json.load") as mock_json:
+ mock_json.return_value = test_dict
+ test_return = duplicate_wkfl_as_new(test_path, True, "timestamp")
+ assert test_return == {'message': 'A copy of the model in {0} has been created'.format(test_path),"mdlPath":os.path.join(tempdir,"test_source_model"),"File":"test_source_model"}
+
+ def test_duplicate_wkfl_as_new_model_file_not_found(self):
+ #from json import load
+ from unittest import mock
+ from handlers.util.run_model import GillesPy2Workflow
+ from handlers.util.stochss_errors import FileNotJSONFormatError
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_dict={"type":"gillespy","source_model":"test_source_model"}
+ test_path = os.path.join(tempdir,"test_wkfl_dir")
+ os.mkdir(test_path)
+ Path(os.path.join(test_path,"info.json")).touch()
+ test_source_model_path = os.path.join(test_path,"test_source_model")
+ Path(test_source_model_path).touch()
+ with mock.patch("handlers.util.run_model.GillesPy2Workflow.get_settings") as mock_settings:
+ mock_settings.return_value = None
+ with mock.patch("json.load") as mock_json:
+ mock_json.return_value = test_dict
+ test_return = duplicate_wkfl_as_new(test_path, False, "timestamp")
+ assert test_return == {'message': 'A new workflow has been created from {0}'.format(test_path), 'wkflPath': test_path+"timestamp.wkfl", 'mdlPath': os.path.join(tempdir,"test_source_model"), 'File': 'test_wkfl_dirtimestamp.wkfl', 'mdl_file': 'test_source_model', 'error': 'The model file test_source_model could not be found. To edit the model or run the workflow you will need to update the path to the model or extract the model from the workflow.'}
+
+ def test_duplicate_wkfl_as_new_model_file_exists(self):
+ #from json import load
+ from unittest import mock
+ from handlers.util.run_model import GillesPy2Workflow
+ from handlers.util.stochss_errors import FileNotJSONFormatError
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_dict={"type":"gillespy","source_model":"test_source_model"}
+ test_path = os.path.join(tempdir,"test_wkfl_dir")
+ os.mkdir(test_path)
+ Path(os.path.join(test_path,"info.json")).touch()
+ test_source_model_path = os.path.join(test_path,"test_source_model")
+ Path(test_source_model_path).touch()
+ Path(os.path.join(tempdir,"test_source_model")).touch()
+ with mock.patch("handlers.util.run_model.GillesPy2Workflow.get_settings") as mock_settings:
+ mock_settings.return_value = None
+ with mock.patch("json.load") as mock_json:
+ mock_json.return_value = test_dict
+ test_return = duplicate_wkfl_as_new(test_path, False, "timestamp")
+ assert test_return == {'message': 'A new workflow has been created from {0}'.format(test_path), 'wkflPath': test_path+"timestamp.wkfl", 'mdlPath': os.path.join(tempdir,"test_source_model"), 'File': 'test_wkfl_dirtimestamp.wkfl', 'mdl_file': 'test_source_model'}
diff --git a/stochss/tests/test_generate_zip_file.py b/stochss/tests/test_generate_zip_file.py
new file mode 100644
index 0000000000..4806ad9173
--- /dev/null
+++ b/stochss/tests/test_generate_zip_file.py
@@ -0,0 +1,68 @@
+import os
+import unittest
+import tempfile
+import handlers.util.generate_zip_file as generate_zip_file
+import handlers.util.stochss_errors as stochss_errors
+
+class TestGenerateZipFile(unittest.TestCase):
+
+ #unit tests for method generate_zip_file
+
+ def test_generate_zip_file(self):
+ test_file = "test_file.foo"
+ test_path = os.path.join("test_path", test_file)
+ test_dir = "test_dir"
+ test_target = "test_target"
+ with unittest.mock.patch("shutil.make_archive") as mock_make_archive:
+ generate_zip_file.generate_zip_file(test_path, test_dir, test_target)
+ correct_filepath = os.path.join(test_dir, "test_file")
+ mock_make_archive.assert_called_with(correct_filepath, 'zip', test_dir, test_target)
+
+ #unit tests for method get_zip_file_data
+
+ def test_get_zip_file_data(self):
+ with unittest.mock.patch("builtins.open", unittest.mock.mock_open(read_data="foo")):
+ assert generate_zip_file.get_zip_file_data("placeholder") == "foo"
+
+ #unit tests for method get_results_csv_dir
+
+ def test_get_results_csv_dir_not_found(self):
+ test_file = "results_csv"
+ test_path = "placeholder"
+ assert generate_zip_file.get_results_csv_dir(test_file, test_path) is None
+
+ def test_get_results_csv_dir_is_found(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_dir = os.path.join(tempdir, "results_csv")
+ os.mkdir(test_dir)
+ assert generate_zip_file.get_results_csv_dir(test_dir, tempdir) == test_dir
+
+ #unit tests for method download_zip
+
+ def test_download_zip_file_invalid_path(self):
+ with self.assertRaises(stochss_errors.StochSSFileNotFoundError):
+ generate_zip_file.download_zip("placeholder_path", "placeholder_action")
+
+ def test_download_zip_file_calls_generate_zip_file(self):
+ test_path = "test_dir/test_path.foo"
+ test_action = "generate"
+ with unittest.mock.patch("os.path.exists"):
+ with unittest.mock.patch("handlers.util.generate_zip_file.get_unique_file_name",\
+ return_value="test_path"):
+ with unittest.mock.patch("handlers.util.generate_zip_file.generate_zip_file")\
+ as mock_generate:
+ generate_zip_file.download_zip(test_path, test_action)
+ mock_generate.assert_called_with("t", os.path.join("/home/jovyan", "test_dir"), \
+ os.path.join("/home/jovyan", test_path))
+
+ def test_download_zip_file_action_generate(self):
+ test_path = "test_dir/test_path.foo"
+ test_action = "generate"
+ test_resp = {"Message":"Successfully created t", "Path":"t",}
+ with unittest.mock.patch("os.path.exists"):
+ with unittest.mock.patch("handlers.util.generate_zip_file.get_unique_file_name",\
+ return_value="test_path"):
+ with unittest.mock.patch("handlers.util.generate_zip_file.generate_zip_file"):
+ assert generate_zip_file.download_zip(test_path, test_action) == test_resp
+
+ #download_zip action resultscsv is not covered pending refactor of user dir from /home/jovyan
diff --git a/stochss/tests/test_ls.py b/stochss/tests/test_ls.py
new file mode 100644
index 0000000000..e5d6f3b7e9
--- /dev/null
+++ b/stochss/tests/test_ls.py
@@ -0,0 +1,228 @@
+"""Unit tests for handlers.util.ls.py"""
+import unittest
+import os
+import tempfile
+from pathlib import Path
+
+import handlers.util.ls as ls
+from handlers.util.stochss_errors import StochSSFileNotFoundError
+
+class TestLS(unittest.TestCase):
+ """Unit test container for handlers.util.ls.py"""
+
+ #unit tests for method get_file_system_data
+
+ def test_get_file_system_data_dir_not_found(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "nonexistent_dir")
+ with self.assertRaises(StochSSFileNotFoundError):
+ ls.get_file_system_data(test_path, tempdir)
+
+ @classmethod
+ def test_get_file_system_data_no_children(cls):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "empty_dir")
+ os.mkdir(test_path)
+ children = ls.get_file_system_data(test_path, tempdir)
+ assert len(children) == 0
+
+ @classmethod
+ def test_get_file_system_data_child_is_wkfl(cls):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "parent_dir")
+ os.mkdir(test_path)
+ test_file_path = os.path.join(test_path, "test_file.wkfl")
+ Path(test_file_path).touch()
+ with unittest.mock.patch("handlers.util.ls.build_child") as mock_build_child:
+ ls.get_file_system_data(test_path, tempdir)
+ mock_build_child.assert_called_once_with \
+ (text="test_file.wkfl", f_type="workflow", p_path=tempdir)
+
+ @classmethod
+ def test_get_file_system_data_child_is_mdl(cls):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "parent_dir")
+ os.mkdir(test_path)
+ test_file_path = os.path.join(test_path, "test_file.mdl")
+ Path(test_file_path).touch()
+ with unittest.mock.patch("handlers.util.ls.build_child") as mock_build_child:
+ ls.get_file_system_data(test_path, tempdir)
+ mock_build_child.assert_called_once_with\
+ (text="test_file.mdl", f_type="nonspatial", p_path=tempdir)
+
+ @classmethod
+ def test_get_file_system_data_child_is_smdl(cls):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "parent_dir")
+ os.mkdir(test_path)
+ test_file_path = os.path.join(test_path, "test_file.smdl")
+ Path(test_file_path).touch()
+ with unittest.mock.patch("handlers.util.ls.build_child") as mock_build_child:
+ ls.get_file_system_data(test_path, tempdir)
+ mock_build_child.assert_called_once_with\
+ (text="test_file.smdl", f_type="spatial", p_path=tempdir)
+
+ @classmethod
+ def test_get_file_system_data_child_is_mesh(cls):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "parent_dir")
+ os.mkdir(test_path)
+ test_file_path = os.path.join(test_path, "test_file.mesh")
+ Path(test_file_path).touch()
+ with unittest.mock.patch("handlers.util.ls.build_child") as mock_build_child:
+ ls.get_file_system_data(test_path, tempdir)
+ mock_build_child.assert_called_once_with\
+ (text="test_file.mesh", f_type="mesh", p_path=tempdir)
+
+ @classmethod
+ def test_get_file_system_data_child_is_ipynb(cls):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "parent_dir")
+ os.mkdir(test_path)
+ test_file_path = os.path.join(test_path, "test_file.ipynb")
+ Path(test_file_path).touch()
+ with unittest.mock.patch("handlers.util.ls.build_child") as mock_build_child:
+ ls.get_file_system_data(test_path, tempdir)
+ mock_build_child.assert_called_once_with\
+ (text="test_file.ipynb", f_type="notebook", p_path=tempdir)
+
+ @classmethod
+ def test_get_file_system_data_child_is_sbml(cls):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "parent_dir")
+ os.mkdir(test_path)
+ test_file_path = os.path.join(test_path, "test_file.sbml")
+ Path(test_file_path).touch()
+ with unittest.mock.patch("handlers.util.ls.build_child") as mock_build_child:
+ ls.get_file_system_data(test_path, tempdir)
+ mock_build_child.assert_called_once_with\
+ (text="test_file.sbml", f_type="sbml-model", p_path=tempdir)
+
+ @classmethod
+ def test_get_file_system_data_child_is_dir(cls):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "parent_dir")
+ os.mkdir(test_path)
+ test_dir_path = os.path.join(test_path, "test_dir")
+ os.mkdir(test_dir_path)
+ with unittest.mock.patch("handlers.util.ls.build_child") as mock_build_child:
+ ls.get_file_system_data(test_path, tempdir)
+ mock_build_child.assert_called_once_with\
+ (text="test_dir", f_type="folder", p_path=tempdir)
+
+ @classmethod
+ def test_get_file_system_data_child_is_other(cls):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "parent_dir")
+ os.mkdir(test_path)
+ test_file_path = os.path.join(test_path, "test_file.foo")
+ Path(test_file_path).touch()
+ with unittest.mock.patch("handlers.util.ls.build_child") as mock_build_child:
+ ls.get_file_system_data(test_path, tempdir)
+ mock_build_child.assert_called_once_with\
+ (text="test_file.foo", f_type="other", p_path=tempdir)
+
+ @classmethod
+ def test_get_file_system_data_child_is_exp(cls):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "parent_dir")
+ os.mkdir(test_path)
+ test_dir_path = os.path.join(test_path, "test_dir.wkgp")
+ os.mkdir(test_dir_path)
+ with unittest.mock.patch("handlers.util.ls.build_child") as mock_build_child:
+ ls.get_file_system_data(test_path, tempdir)
+ mock_build_child.assert_called_once_with\
+ (text="test_dir.wkgp", f_type="workflow-group", p_path=tempdir)
+
+ @classmethod
+ def test_get_file_system_data_child_is_proj(cls):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "parent_dir")
+ os.mkdir(test_path)
+ test_dir_path = os.path.join(test_path, "test_dir.proj")
+ os.mkdir(test_dir_path)
+ with unittest.mock.patch("handlers.util.ls.build_child") as mock_build_child:
+ ls.get_file_system_data(test_path, tempdir)
+ mock_build_child.assert_called_once_with\
+ (text="test_dir.proj", f_type="project", p_path=tempdir)
+
+ #unit tests for method build_child
+
+ @classmethod
+ def test_build_child_top_level(cls):
+ with tempfile.TemporaryDirectory():
+ test_p_path = "none"
+ test_text = "test_text"
+ test_f_type = "test_f_type"
+ assert ls.build_child(text=test_text, f_type=test_f_type, p_path=test_p_path) ==\
+ {"text" : "test_text", "type" : "test_f_type", \
+ "_path" : "test_text", "children" : False}
+
+ @classmethod
+ def test_build_child_sub_level(cls):
+ with tempfile.TemporaryDirectory():
+ test_p_path = "test_p_path"
+ test_text = "test_text"
+ test_f_type = "test_f_type"
+ assert ls.build_child(text=test_text, f_type=test_f_type, p_path=test_p_path) == \
+ {"text" : "test_text", "type" : "test_f_type", \
+ "_path" : os.path.join(test_p_path, test_text), "children" : False}
+
+ @classmethod
+ def test_build_child_wkfl_calls_get_status(cls):
+ with tempfile.TemporaryDirectory():
+ test_p_path = "test_p_path"
+ test_text = "test_text"
+ test_f_type = "workflow"
+ with unittest.mock.patch("handlers.util.ls.get_status") as mock_get_status:
+ ls.build_child(text=test_text, p_path=test_p_path, f_type=test_f_type)
+ mock_get_status.assert_called()
+
+ #unit tests for method build_root
+
+ @classmethod
+ def test_build_root(cls):
+ test_children = "test_children"
+ assert ls.build_root(test_children) ==\
+ [{"text":"/", "type":"root", "_path":"/", \
+ "children":"test_children", "state":{"opened":True}}]
+
+ #unit tests for method check_extension
+
+ @classmethod
+ def test_check_extension_true(cls):
+ test_str = "test"
+ test_target = "target"
+ test_name = test_str + test_target
+ assert ls.check_extension(test_name, test_target)
+
+ @classmethod
+ def test_check_extension_false(cls):
+ test_str = "test"
+ test_target = "target"
+ test_name = test_str
+ assert not ls.check_extension(test_name, test_target)
+
+ #unit tests for method list_files
+
+ @classmethod
+ def test_ls_p_path_none(cls):
+ test_p_path = "none"
+ with unittest.mock.patch("handlers.util.ls.build_root") as mock_build_root:
+ with unittest.mock.patch("handlers.util.ls.get_file_system_data", \
+ return_value="test_return") as mock_get_file_system_data:
+ with unittest.mock.patch("json.dumps"):
+ ls.list_files(p_path=test_p_path)
+ mock_get_file_system_data.assert_called()
+ mock_build_root.assert_called_with("test_return")
+
+ @classmethod
+ def test_ls_p_path_not_none(cls):
+ test_p_path = "test_p_path"
+ test_full_path = os.path.join("/home/jovyan", test_p_path)
+ with unittest.mock.patch("handlers.util.ls.build_root"):
+ with unittest.mock.patch("handlers.util.ls.get_file_system_data", \
+ return_value="test_return") as mock_get_file_system_data:
+ with unittest.mock.patch("json.dumps"):
+ ls.list_files(p_path=test_p_path)
+ mock_get_file_system_data.assert_called_with(test_full_path, test_p_path)
diff --git a/stochss/tests/test_rename.py b/stochss/tests/test_rename.py
new file mode 100644
index 0000000000..7940647080
--- /dev/null
+++ b/stochss/tests/test_rename.py
@@ -0,0 +1,130 @@
+import unittest, os, tempfile
+from pathlib import Path
+from handlers.util.rename import *
+
+class TestRename(unittest.TestCase):
+
+ #unit tests for method get_unique_file_name
+
+ def test_get_unique_file_name_target_does_not_exist(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ gufn_return_filepath = os.path.join(tempdir,"nonexistent_file")
+ gufn_return_tuple = (gufn_return_filepath, False)
+ assert get_unique_file_name("nonexistent_file", tempdir) == (gufn_return_tuple)
+
+ def test_get_unique_file_name_target_exists(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filepath = os.path.join(tempdir,"existent_file")
+ Path(test_filepath).touch()
+ gufn_return_filepath = os.path.join(tempdir,"existent_file(1)")
+ gufn_return_tuple = (gufn_return_filepath, True)
+ assert get_unique_file_name("existent_file", tempdir) == gufn_return_tuple
+
+ def test_get_unique_file_name_numbered_target_exists(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filepath = os.path.join(tempdir,"existent_file(1)")
+ Path(test_filepath).touch()
+ gufn_return_filepath = os.path.join(tempdir,"existent_file(2)")
+ gufn_return_tuple = (gufn_return_filepath, True)
+ assert get_unique_file_name("existent_file(1)", tempdir) == gufn_return_tuple
+
+ def test_get_unique_file_name_with_extension_target_does_not_exist(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ gufn_return_filepath = os.path.join(tempdir,"nonexistent_file.foo")
+ gufn_return_tuple = (gufn_return_filepath, False)
+ assert get_unique_file_name("nonexistent_file.foo", tempdir) == (gufn_return_tuple)
+
+ def test_get_unique_file_name_with_extension_target_exists(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filename = "existent_file.foo"
+ test_filepath = os.path.join(tempdir,test_filename)
+ Path(test_filepath).touch()
+ gufn_return_filepath = os.path.join(tempdir,"existent_file(1).foo")
+ gufn_return_tuple = (gufn_return_filepath, True)
+ assert get_unique_file_name(test_filename, tempdir) == gufn_return_tuple
+
+
+ def test_get_unique_file_name_iterated(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_filename = "existent_file"
+ test_filepath = os.path.join(tempdir, test_filename)
+ Path(test_filepath).touch()
+ for i in range(3):
+ test_filename, placeholder = get_unique_file_name(test_filename, tempdir)
+ Path(test_filename).touch()
+ test_filename = test_filename.split('/').pop()
+ assert len(os.listdir(tempdir)) == 4
+
+ def test_get_unique_file_name_invalid_path(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_dirpath = os.path.join(tempdir,"invalid_directory")
+ with self.assertRaises(FileNotFoundError):
+ get_unique_file_name("nonexistent_file", test_dirpath)
+
+ #unit tests for method rename
+
+ def test_rename_file(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_file = "test_file"
+ test_path = os.path.join(tempdir,test_file)
+ Path(test_path).touch()
+ rename(test_path, "test_file2")
+ test_new_path = os.path.join(tempdir, "test_file2")
+ assert os.path.isfile(test_new_path)
+
+ def test_rename_directory(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_dir = "test_dir"
+ test_path = os.path.join(tempdir, test_dir)
+ os.mkdir(test_path)
+ rename(test_path, "test_dir2")
+ test_new_path = os.path.join(tempdir, "test_dir2")
+ assert os.path.isdir(test_new_path)
+
+ def test_rename_permission_error(self):
+ from handlers.util.stochss_errors import StochSSPermissionsError
+ from unittest import mock
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_dir = "test_dir"
+ test_file = "test_file"
+ test_dir_path = os.path.join(tempdir,test_dir)
+ os.mkdir(test_dir_path)
+ test_path = os.path.join(test_dir_path,test_file)
+ Path(test_path).touch()
+ with mock.patch("shutil.move", side_effect=StochSSPermissionsError('test_error')) as mock_shutil:
+ with self.assertRaises(StochSSPermissionsError):
+ rename(test_path, "test_file2")
+
+ def test_rename_file_not_found_error(self):
+ from handlers.util.stochss_errors import StochSSFileNotFoundError
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_file = "test_file"
+ test_path = os.path.join(tempdir,test_file)
+ with self.assertRaises(StochSSFileNotFoundError):
+ rename(test_path, "test_file2")
+
+ def test_rename_target_exists(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_file = "test_file"
+ test_path = os.path.join(tempdir, test_file)
+ Path(test_path).touch()
+ test_file2 = "test_file2"
+ test_path2 = os.path.join(tempdir, test_file2)
+ Path(test_path2).touch()
+ resp = rename(test_path, "test_file2")
+ assert resp["changed"] == True
+
+ def test_rename_running_wkfl(self):
+ from unittest import mock
+ with tempfile.TemporaryDirectory() as tempdir:
+ with mock.patch("json.dump") as mock_dump:
+ with mock.patch("json.load") as mock_json:
+ with mock.patch('builtins.open', mock.mock_open(read_data="foo")) as m:
+ test_file = "test_file.wkfl"
+ test_path = os.path.join(tempdir, test_file)
+ target_path = os.path.join(tempdir, "test_file2")
+ os.mkdir(test_path)
+ os.mkdir(target_path)
+ Path(os.path.join(target_path,"RUNNING")).touch()
+ rename(test_path, "test_file2")
+ m.assert_called_with(os.path.join(target_path, "info.json"), 'r+')
diff --git a/stochss/tests/test_upload_file.py b/stochss/tests/test_upload_file.py
new file mode 100644
index 0000000000..404c863166
--- /dev/null
+++ b/stochss/tests/test_upload_file.py
@@ -0,0 +1,115 @@
+import os
+import unittest
+from unittest import mock
+import tempfile
+from pathlib import Path
+
+from handlers.util.upload_file import *
+
+class TestUploadFile(unittest.TestCase):
+
+ #unit tests for method validate_model
+
+ def test_validate_model_json_decode_error(self):
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_file = "non_json_file"
+ test_path = os.path.join(tempdir, test_file)
+ Path(test_path).touch()
+ assert validate_model(test_path, test_file) == \
+ (False, False, "The file {0} is not in JSON format.".format(test_file))
+
+ def test_validate_model_valid_keys(self):
+ test_keys = ("is_spatial", "defaultID", "defaultMode", "modelSettings",
+ "simulationSettings", "parameterSweepSettings", "species",
+ "parameters", "reactions", "eventsCollection", "rules",
+ "functionDefinitions", "meshSettings", "initialConditions")
+ class TestKeychain():
+ def keys(self):
+ return test_keys
+
+ complete_keychain = TestKeychain()
+ with mock.patch("json.loads", return_value=complete_keychain):
+ assert validate_model("", "") == (True, True, "")
+
+ def test_validate_model_missing_keys(self):
+ test_keys = ("species","parameters","reactions","eventsCollection",
+ "rules","functionDefinitions")
+
+ class TestKeychain():
+ def keys(self):
+ return ()
+
+ complete_keychain = TestKeychain()
+ with mock.patch("json.loads", return_value=complete_keychain):
+ assert validate_model("", "") == (False, True, \
+ "The following keys are missing from {0}: {1}".format("", ", ".join(test_keys)))
+
+ #unit tests for method upload_model_file
+
+ def test_upload_model_file_is_valid(self):
+ test_valid = True
+ test_json = False
+ test_error = ""
+ predicted_name = ".".join(["some_name", "mdl"])
+ with mock.patch("handlers.util.upload_file.get_unique_file_name",\
+ return_value=("some_path", False)):
+ with mock.patch("handlers.util.upload_file.validate_model",\
+ return_value=(test_valid, test_json, test_error)):
+ with mock.patch("builtins.open", mock.mock_open(read_data="foo")):
+ assert upload_model_file("some_path", "some_file_name", "some_name", None)\
+ ['message'] == "{0} was successfully uploaded to {1}".format(\
+ predicted_name, "some_path")
+
+ def test_upload_model_file_not_valid(self):
+ test_valid = False
+ test_json = False
+ test_error = ""
+ predicted_name = ".".join(["some_name", "json"])
+ with mock.patch("handlers.util.upload_file.get_unique_file_name",\
+ return_value=("some_path", False)):
+ with mock.patch("handlers.util.upload_file.validate_model",\
+ return_value=(test_valid, test_json, test_error)):
+ with mock.patch("builtins.open", mock.mock_open(read_data="foo")):
+ assert upload_model_file("some_path",\
+ "some_file_name", "some_name", None)['message'] ==\
+ "{0} could not be validated as a Model file and was uploaded as {1} to {2}"\
+ .format("some_file_name", predicted_name, "some_path")
+
+ def test_upload_model_file_error(self):
+ test_valid = False
+ test_json = False
+ test_error = "test_error"
+ with mock.patch("handlers.util.upload_file.get_unique_file_name",\
+ return_value=("some_path", False)):
+ with mock.patch("handlers.util.upload_file.validate_model", return_value=\
+ (test_valid, test_json, test_error)):
+ with mock.patch("builtins.open", mock.mock_open(read_data="foo")):
+ assert upload_model_file("some_path", "some_file_name", "some_name", None)\
+ ['errors'] == ['test_error']
+
+ def test_upload_model_file_name_changed(self):
+ test_valid = False
+ test_json = False
+ test_error = ""
+ predicted_name = "some_file"
+ with mock.patch("handlers.util.upload_file.get_unique_file_name",\
+ return_value=(os.path.join("some_parent", "some_file"), True)):
+ with mock.patch("handlers.util.upload_file.validate_model", \
+ return_value=(test_valid, test_json, test_error)):
+ with mock.patch("builtins.open", mock.mock_open(read_data="foo")):
+ assert upload_model_file("some_path", "some_file_name", "some_name", None)['message'] ==\
+ "{0} could not be validated as a Model file and was uploaded as {1} to {2}"\
+ .format("some_file_name", predicted_name, "some_path")
+
+ def test_upload_model_file_json(self):
+ test_valid = True
+ test_json = True
+ test_error = ""
+ with mock.patch("handlers.util.upload_file.get_unique_file_name",\
+ return_value=("some_path", False)):
+ with mock.patch("handlers.util.upload_file.validate_model", return_value=\
+ (test_valid, test_json, test_error)):
+ with mock.patch("builtins.open", mock.mock_open(read_data="foo")):
+ with mock.patch("json.loads", return_value="mock_return") as mock_json_loads:
+ upload_model_file("some_path", "some_file_name", "some_name", None)
+ mock_json_loads.assert_called()
diff --git a/stochss/tests/test_workflow_status.py b/stochss/tests/test_workflow_status.py
new file mode 100644
index 0000000000..36e890c31e
--- /dev/null
+++ b/stochss/tests/test_workflow_status.py
@@ -0,0 +1,52 @@
+import os
+import unittest
+import tempfile
+from pathlib import Path
+
+from handlers.util.workflow_status import get_status
+
+class TestWorkflow_Status(unittest.TestCase):
+
+ #unit tests for method get_status
+
+ def test_get_status_complete(self):
+ from unittest import mock
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "test_dir")
+ os.mkdir(test_path)
+ test_status = "COMPLETE"
+ test_file = os.path.join(test_path, test_status)
+ Path(test_file).touch()
+ with mock.patch("os.path.join",return_value = test_path) as mock_join:
+ assert get_status("") == "complete"
+
+
+ def test_get_status_error(self):
+ from unittest import mock
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "test_dir")
+ os.mkdir(test_path)
+ test_status = "ERROR"
+ test_file = os.path.join(test_path, test_status)
+ Path(test_file).touch()
+ with mock.patch("os.path.join",return_value = test_path) as mock_join:
+ assert get_status("") == "error"
+
+ def test_get_status_running(self):
+ from unittest import mock
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "test_dir")
+ os.mkdir(test_path)
+ test_status = "RUNNING"
+ test_file = os.path.join(test_path, test_status)
+ Path(test_file).touch()
+ with mock.patch("os.path.join",return_value = test_path) as mock_join:
+ assert get_status("") == "running"
+
+ def test_get_status_ready(self):
+ from unittest import mock
+ with tempfile.TemporaryDirectory() as tempdir:
+ test_path = os.path.join(tempdir, "test_dir")
+ os.mkdir(test_path)
+ with mock.patch("os.path.join",return_value = test_path) as mock_join:
+ assert get_status("") == "ready"
diff --git a/stochss_templates/nonSpatialModelTemplate.json b/stochss_templates/nonSpatialModelTemplate.json
index 419ad4695d..894fb677c0 100644
--- a/stochss_templates/nonSpatialModelTemplate.json
+++ b/stochss_templates/nonSpatialModelTemplate.json
@@ -2,6 +2,7 @@
"is_spatial": false,
"defaultID": 1,
"defaultMode": "",
+ "annotation": "",
"modelSettings": {
"endSim": 20,
"timeStep": 0.05,
diff --git a/webpack.config.js b/webpack.config.js
index 8a2215b49f..4534b401c1 100644
--- a/webpack.config.js
+++ b/webpack.config.js
@@ -4,11 +4,14 @@ const HtmlWebpackPlugin = require('html-webpack-plugin');
module.exports = {
mode: 'development',
entry: {
+ home: './client/pages/users-home.js',
quickstart: './client/pages/quickstart.js',
browser: './client/pages/file-browser.js',
editor: './client/pages/model-editor.js',
workflowSelection: './client/pages/workflow-selection.js',
workflowEditor: './client/pages/workflow-manager.js',
+ projectBrowser: './client/pages/project-browser.js',
+ projectManager: './client/pages/project-manager.js'
},
output: {
filename: 'stochss-[name].bundle.js',
@@ -16,6 +19,13 @@ module.exports = {
},
devtool: 'inline-source-map',
plugins: [
+ new HtmlWebpackPlugin({
+ title: 'StochSS | Home',
+ filename: 'stochss-user-home.html',
+ template: 'page_template.pug',
+ name: 'home',
+ inject: false
+ }),
new HtmlWebpackPlugin({
title: 'StochSS | Quickstart',
filename: 'stochss-quickstart.html',
@@ -51,6 +61,20 @@ module.exports = {
name: 'workflowEditor',
inject: false
}),
+ new HtmlWebpackPlugin({
+ title: 'StochSS | Project Browser',
+ filename: 'stochss-project-browser.html',
+ template: 'page_template.pug',
+ name: 'projectBrowser',
+ inject: false
+ }),
+ new HtmlWebpackPlugin({
+ title: 'StochSS | Project Manager',
+ filename: 'stochss-project-manager.html',
+ template: 'page_template.pug',
+ name: 'projectManager',
+ inject: false
+ })
],
optimization: {
splitChunks: {