2.3 release (#59)

* source bashrc in entrypoint * submit jobs request propagate returned error messages * get request response json * catch nonzero exit subprocess on git status if not register code not in repo * typo * catch subprocess nonzero exit in defaultvalues handler * report no git repo error to user * don't convert inputs to lower case * register algo config req params check for none * register commit check for r and matlab file exts * update architecture docs for submit jobs, add for dps info * add toastify error on register responses * toastify error for other submit jobs requests * dependency * copy bashrc to bash_profile in entrypoint * add toastify error for default vals in register * testing register result * more register toastify errors Co-authored-by: echyam <[email protected]>
MAAP-Project · Jun 3, 2020 · f85ed63 · f85ed63
1 parent 9485be4
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diff --git a/dps_info/documentation.md b/dps_info/documentation.md
@@ -0,0 +1,15 @@
+## DPS Info Extension Documentation & Architecture
+### Architecture
+<img alt="architecture diagram" src="dps_info_architecture.png" width="350">
+
+#### 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
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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 = "<pre>" + result + "</pre>";
+  if ( isXML === undefined || (! isXML) ){ 
+    textarea.innerHTML = '<pre>' + result + '</pre>';
     // console.log(textarea);
   } else {
-    var xml = "<root><content><p>"+result+"</p></content></root>";
+    var xml = '<root><content><p>'+result+'</p></content></root>';
     var options = {indentation: '  ', stripComments: true, collapseContent: false};
     var formattedXML = format(xml,options); 
     textarea.innerHTML = formattedXML;
@@ -543,16 +549,16 @@ export function popupText(result:string,title:string,fn?:any) {
   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';
 
   // console.log(result);
-  textarea.innerHTML = "<pre>" + result + "</pre>";
+  textarea.innerHTML = '<pre>' + result + '</pre>';
   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
@@ -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