+
+#### sourcefiles
+- index.ts: instantiate & export jupyter extensions
+- activate.ts: contains all extension activate functions
+- panel.ts: contains skeleton code for a basic side panel in jupyter lab, wth a commented-out example activate function (extension must be instantiated and exported as well)
+- jobinfo.ts: 1) creates a widget for listing DPS jobs associated with the user in table; 2) creates a main area jupyter widget for easy UI in listing, describing, and executing algorithms; (1) and (2) are NOT synchronized; the table in (1) is organized as:
+
+| Job Id | Status | Algorithm |
+| ------ | ------ | --------- |
+
+- funcs.ts: common functions across classes & API calls in jobinfo.ts
+- request.ts: class and functions utility for making http requests and reading their responses
diff --git a/dps_info/dps_info_architecture.png b/dps_info/dps_info_architecture.png
new file mode 100644
index 00000000..a31d99d5
Binary files /dev/null and b/dps_info/dps_info_architecture.png differ
diff --git a/entrypoint.sh b/entrypoint.sh
index a9527cf0..a076630a 100755
--- a/entrypoint.sh
+++ b/entrypoint.sh
@@ -27,5 +27,6 @@ env | grep _ >> /etc/environment
# Add conda bin to path
export PATH=$PATH:/opt/conda/bin
+cp /root/.bashrc ~/.bash_profile
jupyter lab --ip=0.0.0.0 --port=3100 --allow-root --NotebookApp.token='' --LabApp.base_url=$PREVIEW_URL --no-browser --debug
diff --git a/submit_jobs/documentation.md b/submit_jobs/documentation.md
index 7461f612..dc91e694 100644
--- a/submit_jobs/documentation.md
+++ b/submit_jobs/documentation.md
@@ -5,14 +5,9 @@
#### sourcefiles
- index.ts: instantiate & export jupyter extensions
- fields.json: required parameters for each DPS/MAS function that calls the MAAP API
-- funcs.ts: common functions across classes & API calls; includes extension activate functions (except for side panels)
+- activate.ts: contains all extension activate functions
+- funcs.ts: common functions across classes & API calls
- selector.ts: widget that creates a dropdown menu for selecting from a prepopulated list of choices
- widgets.ts: contains common widgets for executing DPS/MAS cals to MAAP API; includes 2 dialog popup functions widgets depend on
-- panel.ts: contains skeleton code for a basic side panel in jupyter lab, wth a commented-out example activate function (extension must be instantiated and exported as well)
-- jobinfo.ts: 1) creates a widget for listing DPS jobs associated with the user in table; 2) creates a main area jupyter widget for easy UI in listing, describing, and executing algorithms; format in (1):
-
-| Job Id | Status | Algorithm |
-| ------ | ------ | --------- |
-
- request.ts: class and functions utility for making http requests and reading their responses
- dialog.ts: customize more dialog types & popup functions from the base class/function in @jupyterlab/apputils
diff --git a/submit_jobs/src/activate.ts b/submit_jobs/src/activate.ts
index 8ed2b4a7..2c2350cd 100644
--- a/submit_jobs/src/activate.ts
+++ b/submit_jobs/src/activate.ts
@@ -4,6 +4,7 @@ import { ILauncher } from '@jupyterlab/launcher';
import { IFileBrowserFactory } from "@jupyterlab/filebrowser";
import { IMainMenu } from '@jupyterlab/mainmenu';
import { Menu } from '@phosphor/widgets';
+import { INotification } from 'jupyterlab_toastify';
import { InputWidget, RegisterWidget, popupText } from './widgets';
import { ProjectSelector } from './selector';
import { popup, popupResult } from './dialogs';
@@ -68,47 +69,54 @@ export function activateRegisterAlgorithm(
// send request to defaultvalueshandler
let getValuesFn = function(resp:Object) {
console.log('getValuesFn');
- let configPath = resp['config_path'] as string;
- let defaultValues = resp['default_values'] as Object;
- let prevConfig = resp['previous_config'] as boolean;
+ console.log(resp['status_code']);
+ if (resp['status_code'] != 200) {
+ // error
+ popupText(resp['result'],'Error Registering Algorithm');
+ INotification.error(resp['result']);
+ } else {
+ let configPath = resp['config_path'] as string;
+ let defaultValues = resp['default_values'] as Object;
+ let prevConfig = resp['previous_config'] as boolean;
- if (defaultValues['inputs'] == undefined) {
- defaultValues['inputs'] = [];
- }
- if (defaultValues['description'] == undefined) {
- defaultValues['description'] = '';
- }
-
- console.log(defaultValues);
+ if (defaultValues['inputs'] == undefined) {
+ defaultValues['inputs'] = [];
+ }
+ if (defaultValues['description'] == undefined) {
+ defaultValues['description'] = '';
+ }
- let subtext = 'Auto-generated algorithm configuration:';
- if (prevConfig) {
- subtext = 'Current algorithm configuration:';
- }
+ console.log(defaultValues);
- // register function to be called
- // popup read-only default values
- let registerfn = function() {
- console.log('registerfn testing');
- let w = new RegisterWidget(registerFields,username,defaultValues,subtext,configPath);
- w.setPredefinedFields(defaultValues);
- console.log(w);
- popup(w);
- }
+ let subtext = 'Auto-generated algorithm configuration:';
+ if (prevConfig) {
+ subtext = 'Current algorithm configuration:';
+ }
- // check if algorithm already exists
- // ok -> call registeralgorithmhandler
- // cancel -> edit template at algorithm_config.yaml (config_path)
- algorithmExists(defaultValues['algo_name'],defaultValues['version'],defaultValues['environment']).then((algoExists) => {
- console.log('algo Exists');
- console.log(algoExists);
- if (algoExists != undefined && algoExists) {
- popupText('WARNING Algorithm name and version already exists. \n If you continue, the previously registered algorithm \nwill be LOST','Overwrite Algorithm?',registerfn);
- // ask user if they want to continue
- } else {
- registerfn()
+ // register function to be called
+ // popup read-only default values
+ let registerfn = function() {
+ console.log('registerfn testing');
+ let w = new RegisterWidget(registerFields,username,defaultValues,subtext,configPath);
+ w.setPredefinedFields(defaultValues);
+ console.log(w);
+ popup(w);
}
- });
+
+ // check if algorithm already exists
+ // ok -> call registeralgorithmhandler
+ // cancel -> edit template at algorithm_config.yaml (config_path)
+ algorithmExists(defaultValues['algo_name'],defaultValues['version'],defaultValues['environment']).then((algoExists) => {
+ console.log('algo Exists');
+ console.log(algoExists);
+ if (algoExists != undefined && algoExists) {
+ popupText('WARNING Algorithm name and version already exists. \n If you continue, the previously registered algorithm \nwill be LOST','Overwrite Algorithm?',registerfn);
+ // ask user if they want to continue
+ } else {
+ registerfn()
+ }
+ });
+ }
};
inputRequest('defaultValues','Register Algorithm',{'code_path':path},getValuesFn);
},
diff --git a/submit_jobs/src/funcs.ts b/submit_jobs/src/funcs.ts
index 5087fc62..03fd1bbe 100644
--- a/submit_jobs/src/funcs.ts
+++ b/submit_jobs/src/funcs.ts
@@ -1,4 +1,5 @@
import { PageConfig } from '@jupyterlab/coreutils'
+import { INotification } from 'jupyterlab_toastify';
import { request, RequestResult } from './request';
import { popupResultText } from './widgets';
@@ -49,10 +50,8 @@ export function inputRequest(endpt:string,title:string,inputs:{[k:string]:string
// add params
for (let key in inputs) {
var fieldValue = inputs[key];
-
- if(key !== 'proxy-ticket')
- fieldValue = fieldValue.toLowerCase();
-
+ // if(key !== 'proxy-ticket')
+ // fieldValue = fieldValue.toLowerCase();
requestUrl.searchParams.append(key.toLowerCase(), fieldValue);
}
console.log(requestUrl.href);
@@ -70,6 +69,9 @@ export function inputRequest(endpt:string,title:string,inputs:{[k:string]:string
console.log('fn defined');
fn(json_response);
}
+ } else {
+ var json_response:any = res.json();
+ INotification.error(json_response['result']);
}
});
}
diff --git a/submit_jobs/src/widgets.ts b/submit_jobs/src/widgets.ts
index ccbe0545..b933e70b 100644
--- a/submit_jobs/src/widgets.ts
+++ b/submit_jobs/src/widgets.ts
@@ -337,8 +337,14 @@ export class InputWidget extends Widget {
let json_response:any = res.json();
// console.log(json_response);
me._responseText = me._responseText + '\n' + json_response['result'];
+ if (json_response['status_code'] != 200) {
+ INotification.error(me._responseText);
+ }
} else {
- me._responseText = "Error Sending Request.";
+ let json_response:any = res.json();
+ // console.log(json_response);
+ me._responseText = "Error Sending Request:\n" + json_response['result'];
+ INotification.error(me._responseText);
}
console.log("updating");
me.updateSearchResults();
@@ -382,13 +388,13 @@ export class RegisterWidget extends InputWidget {
subtxt.style.flexDirection = 'column';
subtxt.innerHTML = subtext;
this.node.appendChild(subtxt);
- this.node.appendChild(document.createElement("BR"));
+ this.node.appendChild(document.createElement('BR'));
}
for (var field of this.fields) {
// textarea for inputs field in register
- if (field == "inputs") {
- var fieldLabel = document.createElement("Label");
+ if (field == 'inputs') {
+ var fieldLabel = document.createElement('Label');
fieldLabel.innerHTML = field;
this.node.appendChild(fieldLabel);
@@ -413,7 +419,7 @@ export class RegisterWidget extends InputWidget {
this.node.appendChild(fieldInputs);
} else {
- var fieldLabel = document.createElement("Label");
+ var fieldLabel = document.createElement('Label');
fieldLabel.innerHTML = field;
this.node.appendChild(fieldLabel);
@@ -429,7 +435,7 @@ export class RegisterWidget extends InputWidget {
}
// BREAK
- var x = document.createElement("BR");
+ var x = document.createElement('BR');
this.node.appendChild(x)
// footer text - edit config at path
@@ -496,7 +502,7 @@ export class WidgetResult extends Widget {
// update panel text on resolution of result popup
getValue() {
console.log('checking popup resolution fn');
- if (this.okfn != undefined) {
+ if (typeof this.okfn === "function") {
console.log(this.okfn);
try{
this.okfn();
@@ -515,18 +521,18 @@ export function popupResultText(result:string,title:string,fn?:any,isXML?:boolea
body.style.display = 'flex';
body.style.flexDirection = 'column';
- var textarea = document.createElement("div");
+ var textarea = document.createElement('div');
textarea.id = 'result-text';
textarea.style.display = 'flex';
textarea.style.flexDirection = 'column';
var format = require('xml-formatter');
// console.log(result);
- if ( isXML == undefined || (! isXML) ){
- textarea.innerHTML = "" + result + ""; + if ( isXML === undefined || (! isXML) ){ + textarea.innerHTML = '
' + result + ''; // console.log(textarea); } else { - var xml = "
"+result+"
'+result+'
" + result + ""; + textarea.innerHTML = '
' + result + ''; body.appendChild(textarea); // console.log(body); - if (fn == undefined) { + if (fn === undefined) { popupTitle(new Widget({node:body}),title); } else { popupTitle(new WidgetResult(body,fn),title); diff --git a/submit_jobs/submit_jobs/handlers.py b/submit_jobs/submit_jobs/handlers.py index 9d948e0c..df28fab8 100644 --- a/submit_jobs/submit_jobs/handlers.py +++ b/submit_jobs/submit_jobs/handlers.py @@ -123,7 +123,7 @@ def get(self,**params): # only description and inputs are allowed to be empty for f in ['algo_name','version','environment','run_command','repository_url','docker_url']: - if config[f] == '': + if config[f] == '' or config[f] == None: self.finish({"status_code": 412, "result": "Error: Register field {} cannot be empty".format(f)}) return @@ -151,19 +151,21 @@ def get(self,**params): os.chdir(proj_path) # get git status - git_status_out = subprocess.check_output("git status --branch --porcelain", shell=True).decode("utf-8") - logger.debug(git_status_out) + try: + git_status_out = subprocess.check_output("git status --branch --porcelain", shell=True).decode("utf-8") + logger.debug(git_status_out) # is there a git repo? - if 'not a git repository' in git_status_out: - self.finish({"status_code": 412, "result": "Error: \n{}".format(git_status_out)}) + except: + # subprocess could also error out (nonzero exit code) + self.finish({"status_code": 412, "result": "Error: \nThe code you want to register is not saved in a git repository."}) return git_status = git_status_out.splitlines()[1:] git_status = [e.strip() for e in git_status] - # filter for unsaved python files - unsaved = list(filter(lambda e: ( (e.split('.')[-1] in ['ipynb','py','sh','jl']) and (e[0] in ['M','?']) ), git_status)) + # filter for unsaved python, julia, matlab shell files + unsaved = list(filter(lambda e: ( (e.split('.')[-1] in ['ipynb','py','sh','jl','r','m','mat']) and (e[0] in ['M','?']) ), git_status)) if len(unsaved) != 0: self.finish({"status_code": 412, "result": "Error: Notebook(s) and/or script(s) have not been committed\n{}".format('\n'.join(unsaved))}) return @@ -1221,8 +1223,19 @@ def get(self): proj_path = '/projects/'+params['code_path'] proj_path = '/'.join(proj_path.split('/')[:-1]) os.chdir(proj_path) - repo_url = subprocess.check_output("git remote get-url origin", shell=True).decode('utf-8').strip() - # logger.debug(repo_url) + + # try to get git remote url + try: + repo_url = subprocess.check_output("git remote get-url origin", shell=True).decode('utf-8').strip() + logger.debug(repo_url) + print('reop url is {}'.format(repo_url)) + + # is there a git repo? + except: + # subprocess could also error out (nonzero exit code) + self.finish({"status_code": 412, "result": "Error: \nThe code you want to register is not saved in a git repository."}) + return + vals = {} code_path = params['code_path'] @@ -1265,7 +1278,7 @@ def get(self): logger.debug(settings) # outputs: algo_name, version, environment, repository_url, dockerfile_path - self.finish({"status_code": 200, "default_values":settings, "config_path":config_path, "previous_config":prev_config}) + self.finish({"status_code": 200, "result": "Got default values.", "default_values":settings, "config_path":config_path, "previous_config":prev_config}) class ListJobsHandler(IPythonHandler): # inputs: username diff --git a/submit_jobs/submit_jobs_architecture.png b/submit_jobs/submit_jobs_architecture.png index 9f73b578..94ab1f7d 100644 Binary files a/submit_jobs/submit_jobs_architecture.png and b/submit_jobs/submit_jobs_architecture.png differ