WebAPI 3.0 compatablity Branch

js/Application.js

@@ -51,8 +51,6 @@ define(
 						|| sharedState.CohortDefinition.dirtyFlag().isDirty()
 						|| sharedState.IRAnalysis.dirtyFlag().isDirty()
 						|| sharedState.CohortPathways.dirtyFlag().isDirty()
-						|| sharedState.estimationAnalysis.dirtyFlag().isDirty()
-						|| sharedState.predictionAnalysis.dirtyFlag().isDirty()
 						|| sharedState.CohortCharacterization.dirtyFlag().isDirty()
 					);
 				});
@@ -118,45 +116,26 @@ define(
 					httpService.setUnauthorizedHandler(() => authApi.resetAuthParams());
 					httpService.setUserTokenGetter(() => authApi.getAuthorizationHeader());
 
+					const exp = authApi.tokenExpirationDate();
+					const now = new Date();
+
+					if (!exp || exp <= now) { authApi.resetAuthParams(); } else { await authApi.refreshToken(); }
+
 					try{
+						await authApi.loadUserInfo();
 						await i18nService.getAvailableLocales();
 					} catch (e) {
 						reject(e.message);
 					}
 
-					if (config.userAuthenticationEnabled) {
-						try {
-							// Routes to welcome are part of auth flow, loadUserInfo in this case is unnecessary and fails. 
-							// More importantly it can trigger an infinite loop when skipLoginEnabled is enabled.
-							if (!window.location.href.includes("/welcome/")) {
-								await authApi.loadUserInfo();
-							}
-						} catch (e) {
-							reject(e.message);
-						}
-
-					}
 					authApi.isAuthenticated.subscribe(executionService.checkExecutionEngineStatus);
 					this.attachGlobalEventListeners();
 					await executionService.checkExecutionEngineStatus(authApi.isAuthenticated());
 
-					// Add user interaction listener that keeps refreshing the token as long
-					// as the user is active (either moving mouse, navigating with keyboard and/or typing):
-					var userInteractionCount = 0;
-					console.log("Adding user interaction listeners...");
+					// Add user interaction listeners to reset idle timeout
+					// (throttled inside resetIdleTimeout to at most once per minute)
 					["mouseover", "keydown", "focusin"].forEach(eventType => {
-						window.addEventListener(eventType, (event) => {
-							userInteractionCount++;
-							if (userInteractionCount % 30 == 0) {
-								console.log(">>> Checking user token....");
-								userInteractionCount = 0;
-								// Refresh the Atlas token if it is close to expiring:
-								if (authApi.isAuthenticated() && this.timeToExpire() < config.refreshTokenThreshold) {
-									console.log(">>> Token close to expiring. Refreshing user token....");
-									authApi.refreshToken();
-								}
-							}
-						});
+						window.addEventListener(eventType, () => authApi.resetIdleTimeout());
 					});
 
 					resolve();
@@ -198,39 +177,15 @@ define(
 			initServiceInformation() {
 				console.info('Initializing service information');
 				return new Promise((resolve, reject) => {
-					const serviceCacheKey = 'ATLAS|' + config.api.url;
-					const cachedService = lscache.get(serviceCacheKey);
-
-					if (cachedService && cachedService.sources) {
-						console.info('cached service');
-						config.api.sources = cachedService;
-						sourceApi.setSharedStateSources(cachedService.sources);
-						resolve();
-					} else {
-						sharedState.sources([]);
-
-						if (config.userAuthenticationEnabled && !authApi.isAuthenticated()) {
-							this.authSubscription = authApi.isAuthenticated.subscribe(async (isAuthed) => {
-								if (isAuthed) {
-									sharedState.appInitializationStatus(await sourceApi.initSourcesConfig());
-									this.authSubscription.dispose();
-									console.info('Re-initialized service information');
-								}
-							});
-							sharedState.appInitializationStatus(constants.applicationStatuses.running);
+					sourceApi.initSourcesConfig()
+						.then(function (appStatus) {
+							sharedState.appInitializationStatus(appStatus);
+							console.info('Init sources from server');
 							resolve();
-							return;
-						} else {
-							sourceApi.initSourcesConfig()
-								.then(function (appStatus) {
-									sharedState.appInitializationStatus(appStatus);
-									console.info('Init sources from server');
-									resolve();
-								});
-						}
-					}
+						});
 				});
 			}
+
 			checkOAuthError() {
 				let hash = window.location.hash;
 				if (hash && hash.includes("oauth_error_email")) {

js/components/ac-access-denied.html

@@ -1,8 +1,6 @@
-<div data-bind="css: classes(), visible: !isAuthenticated || !isPermitted()">
-    <!-- ko if: isAuthenticated && !isPermitted() -->
+<div data-bind="css: classes(), visible: !isPermitted()">
+    <!-- ko if: message --><span data-bind="text: message"></span> <!-- /ko -->
+    <!-- ko if: !isPermitted() -->
         <forbidden />
     <!-- /ko -->
-    <!-- ko ifnot: isAuthenticated -->
-        <unauthenticated />
-    <!-- /ko -->
 </div>

js/components/ac-access-denied.js

@@ -15,7 +15,7 @@ define([
 	class AccessDenied extends Component {
 		constructor(params) {
 			super(params);
-			this.isAuthenticated = params.isAuthenticated;
+			this.message = params.message;
 			this.isPermitted = params.isPermitted || (() => false);
 		}
 	}

js/components/atlas-state.js

@@ -37,7 +37,7 @@ define(['knockout', 'lscache', 'services/job/jobDetail', 'assets/ohdsi.util', 'c
 		state.currentVocabularyVersion(state.defaultVocabularyVersion());
 	}
 
-	state.sourceKeyOfVocabUrl = ko.computed(() => {
+	state.sourceKeyOfVocabUrl = ko.pureComputed(() => {
 		return state.vocabularyUrl() ? state.vocabularyUrl().replace(/\/$/, '').split('/').pop() : null;
 	});
 
@@ -84,24 +84,6 @@ define(['knockout', 'lscache', 'services/job/jobDetail', 'assets/ohdsi.util', 'c
 	};
 	state.CohortPathways.dirtyFlag = ko.observable(new ohdsiUtil.dirtyFlag(state.CohortPathways.current()));
 
-
-	state.estimationAnalysis = {
-		current: ko.observable(null),
-		analysisPath: null,
-		selectedId: ko.observable(null),
-		comparisons: ko.observableArray(),
-	}
-	state.estimationAnalysis.dirtyFlag = ko.observable(new ohdsiUtil.dirtyFlag(state.estimationAnalysis.current()));
-
-	state.predictionAnalysis = {
-		current: ko.observable(null),
-		analysisPath: null,
-		selectedId: ko.observable(null),
-		targetCohorts: ko.observableArray(),
-		outcomeCohorts: ko.observableArray(),
-	}
-	state.predictionAnalysis.dirtyFlag = ko.observable(new ohdsiUtil.dirtyFlag(state.predictionAnalysis.current()));
-
 	state.availableLocales = ko.observableArray();
 	state.locale = ko.observable();
 	state.localeSettings = ko.observable();

js/components/atlas.cohort-editor.html

@@ -1,4 +1,4 @@
-<div class="paddedWrapper">
+<div class="paddedWrapper" data-bind="if: $component.currentCohortDefinition">
 	<!-- contenteditableSwitch must be placed AFTER contentEditable to override 'contenteditable' attribute -->
 	<div class="divtext cohort-description" data-bind="contentEditable: currentCohortDefinition().description, contenteditableSwitch: canEdit(), placeholder: ko.i18n('components.atlasCohortEditor.enterCohortPlaceholder', 'Enter the cohort definition description here')"></div>
 	<div data-bind="eventListener: [

js/components/circe/components/ConceptSetBrowser.js

@@ -88,10 +88,10 @@ define([
 
 		self.isAuthenticated = authApi.isAuthenticated;
 		self.canReadConceptsets = ko.pureComputed(function () {
-		  return (appConfig.userAuthenticationEnabled && self.isAuthenticated() && authApi.isPermittedReadConceptsets()) || !appConfig.userAuthenticationEnabled;
+		  return true; // TODO: do not need permission to list entities
 		});
 		self.canReadCohorts = ko.pureComputed(function () {
-		  return (config.userAuthenticationEnabled && self.isAuthenticated() && authApi.isPermittedReadCohorts()) || !config.userAuthenticationEnabled;
+		  return true; // TODO: do not need permissions to list entities
 		});
 
 		self.loadConceptSetsFromRepository = function (url) {

js/components/cohortbuilder/components/ConceptSetSelectorTemplate.html

@@ -38,17 +38,6 @@
 					<span data-bind="text:ko.i18n('components.conceptSetSelector.clearConceptSet','Clear Concept Set')"></span>
 				</a></li>
 		</ul>
-		<ul>
-			<!-- ko if: previewVisible -->
-			<div onclick="event.stopPropagation();" class="undraggable"
-				style="border: solid 1px black;padding:5px; z-index: 999; background-color:white; position: absolute; max-height:200px; overflow-y:auto"
-				data-bind="style: { top: `${previewTop()}px`, left: `${previewLeft()}px`}">
-				<div style="background-color:#aaa; font-weight: bold" data-bind="text: previewConceptSet().name"></div>
-				<conceptset-quickview params="conceptSet: previewConceptSet"></conceptset-quickview>
-			</div>
-			<!-- /ko -->
-		</ul>
-
 	</div>
 
 </div>

js/components/conceptAddBox/concept-add-box.js

@@ -37,7 +37,7 @@ define([
       super(params);
       this.activeConceptSet = params.activeConceptSet || sharedState.activeConceptSet;
       this.canCreateConceptSet = ko.pureComputed(function () {
-				return ((AuthAPI.isAuthenticated() && AuthAPI.isPermittedCreateConceptset()) || !config.userAuthenticationEnabled);
+				return AuthAPI.isPermittedCreateConceptset();
 			});
       this.isActive = params.isActive || ko.observable(true);
       this.onSubmit = params.onSubmit;

js/components/conceptset/expression.js

@@ -41,7 +41,7 @@ define([
 			this.loading = params.loading;
 			this.authApi = authApi;
 			this.canCreateConceptSet = ko.computed( () => {
-				return ((this.authApi.isAuthenticated() && this.authApi.isPermittedCreateConceptset()) || !config.userAuthenticationEnabled);
+				return this.authApi.isPermittedCreateConceptset();
 			});
 			this.newConceptSetName = ko.observable();
 			this.saveConceptSetShow = ko.observable();

js/components/conceptsetmodal/conceptSetSaveModal.js

@@ -38,7 +38,7 @@ define(['knockout', 'appConfig', 'services/AuthAPI', 'services/ConceptSet', 'com
         );
         this.isNameUnique = ko.observable(false);
 
-        this.canCreate = ko.pureComputed(() => (authApi.isAuthenticated() && authApi.isPermittedCreateConceptset()) || !config.userAuthenticationEnabled);
+        this.canCreate = ko.pureComputed(() => authApi.isPermittedCreateConceptset());
         this.canSave = ko.pureComputed(() => this.canCreate() && this.conceptSetName() && this.conceptSetName().length > 0 && this.isNameUnique());
       }
 

js/components/security/access/configure-access-modal.js

@@ -20,16 +20,16 @@ define([
 			this.isModalShown = params.isModalShown;
 			this.isLoading = ko.observable(false);
 
-		        this.writeRoleName = ko.observable();
-		        this.writeAccessList = ko.observable([]);		    
+			this.writeRoleName = ko.observable();
+			this.writeAccessList = ko.observable([]);
 			this.writeRoleSuggestions = ko.observable([]);
 			this.writeRoleOptions = ko.computed(() => this.writeRoleSuggestions().map(r => r.name));
 			this.writeRoleSearch = ko.observable();
-		        this.writeRoleSearch.subscribe(str => this.loadWriteRoleSuggestions(str));
+			this.writeRoleSearch.subscribe(str => this.loadWriteRoleSuggestions(str));
 
-		        this.readAccessList = ko.observable([]);
-		        this.readRoleName = ko.observable();		    
-		        this.readRoleSuggestions = ko.observable([]);
+			this.readAccessList = ko.observable([]);
+			this.readRoleName = ko.observable();
+			this.readRoleSuggestions = ko.observable([]);
 			this.readRoleOptions = ko.computed(() => this.readRoleSuggestions().map(r => r.name));
 			this.readRoleSearch = ko.observable();
 			this.readRoleSearch.subscribe(str => this.loadReadRoleSuggestions(str));
@@ -58,7 +58,7 @@ define([
 				}
 			];
 
-		        this.writeAccessColumns = [
+			this.writeAccessColumns = [
 				{
 					class: this.classes('access-tbl-col-id'),
 					title: ko.i18n('writeAccessColumns.id', 'ID'),
@@ -81,13 +81,13 @@ define([
 
 		async _loadReadAccessList() {
 			let accessList = await this.loadAccessListFn('READ');
-		        accessList = accessList.map(a => ({ ...a, revoke: () => this.revokeRoleAccess(a.id, 'READ') }));
+			accessList = accessList.map(a => ({ ...a, revoke: () => this.revokeRoleAccess(a.id, 'READ') }));
 			this.readAccessList(accessList);
 		}
 
-	        async _loadWriteAccessList() {
+		async _loadWriteAccessList() {
 			let accessList = await this.loadAccessListFn('WRITE');
-		        accessList = accessList.map(a => ({ ...a, revoke: () => this.revokeRoleAccess(a.id, 'WRITE') }));
+			accessList = accessList.map(a => ({ ...a, revoke: () => this.revokeRoleAccess(a.id, 'WRITE') }));
 			this.writeAccessList(accessList);
 		}
 
@@ -96,16 +96,16 @@ define([
 			this.readRoleSuggestions(res);
 		}
 
-	    	async loadWriteRoleSuggestions() {
+		async loadWriteRoleSuggestions() {
 			const res = await this.loadRoleSuggestionsFn(this.writeRoleSearch());
 			this.writeRoleSuggestions(res);
 		}
 
 		async loadAccessList() {
 			this.isLoading(true);
 			try {
-			        await this._loadReadAccessList();
-			        await this._loadWriteAccessList();
+				await this._loadReadAccessList();
+				await this._loadWriteAccessList();
 			} catch (ex) {
 				console.log(ex);
 			}
@@ -115,28 +115,28 @@ define([
 		async grantAccess(perm_type) {
 			this.isLoading(true);
 			try {
-			       if (perm_type == 'WRITE'){
-				   const role = this.writeRoleSuggestions().find(r => r.name === this.writeRoleName());
-			           await this.grantAccessFn(role.id,'WRITE');
-				   await this._loadWriteAccessList();
-				   this.writeRoleName('');
-  			       } else {
-				   const role = this.readRoleSuggestions().find(r => r.name === this.readRoleName());
-			   	   await this.grantAccessFn(role.id,'READ');
-				   await this._loadReadAccessList();
-				   this.readRoleName('');
-			       }
+				if (perm_type == 'WRITE') {
+					const role = this.writeRoleSuggestions().find(r => r.name === this.writeRoleName());
+					await this.grantAccessFn(role.id, 'WRITE');
+					await this._loadWriteAccessList();
+					this.writeRoleName('');
+				} else {
+					const role = this.readRoleSuggestions().find(r => r.name === this.readRoleName());
+					await this.grantAccessFn(role.id, 'READ');
+					await this._loadReadAccessList();
+					this.readRoleName('');
+				}
 			} catch (ex) {
 				console.log(ex);
 			}
 			this.isLoading(false);
 		}
 
-	        async revokeRoleAccess(roleId, perm_type) {
+		async revokeRoleAccess(roleId, perm_type) {
 			this.isLoading(true);
-		        try {
-			    await this.revokeAccessFn(roleId, perm_type);
-			    await this.loadAccessList();
+			try {
+				await this.revokeAccessFn(roleId, perm_type);
+				await this.loadAccessList();
 			} catch (ex) {
 				console.log(ex);
 			}

js/components/security/access/const.js

@@ -8,8 +8,6 @@ define([], function () {
 		FE_ANALYSIS: 'FE_ANALYSIS',
 		INCIDENCE_RATE: 'INCIDENCE_RATE',
 		SOURCE: 'SOURCE',
-		ESTIMATION: 'ESTIMATION',
-		PREDICTION: 'PREDICTION',
 		REUSABLE: 'REUSABLE'
 	};
 

js/components/tags/modal/tags-modal.js

@@ -205,7 +205,7 @@ define([
                 await this.assignTagFn(tag);
                 tag.assigned = true;
                 this.assignedTagsList.unshift(tag);
-                if (tag.groups.filter(tg => tg.id === this.currentTagGroup().id).length > 0) {
+                if (this.currentTagGroup() && tag.groups.filter(tg => tg.id === this.currentTagGroup().id).length > 0) {
                     this.tagsInGroupList.valueHasMutated();
                 }
             } catch (ex) {
@@ -245,7 +245,7 @@ define([
                 const savedTag = savedTagRes.data;
                 await this.assignTag(savedTag);
                 this.allTagsList().unshift(savedTag);
-                if (this.newCustomTagGroup() === this.currentTagGroup().id) {
+                if (this.currentTagGroup() && this.newCustomTagGroup() === this.currentTagGroup().id) {
                     this.tagsInGroupList().unshift(savedTag);
                     this.sortByAssigned(this.tagsInGroupList);
                     this.tagsInGroupList.valueHasMutated();

js/components/userbar/user-bar.js

@@ -61,10 +61,10 @@ define([
 					componentParams: this.userJobParams,
 				});
 				this.selectedTabKey(constants.jobTypes.USER_JOB.title);
-				this.jobNotificationsPending = ko.computed(() => this.userJobParams.jobListing().filter(j => !j.viewed()).length);
+				this.jobNotificationsPending = ko.pureComputed(() => this.userJobParams.jobListing().filter(j => !j.viewed()).length);
 			} else {
 				this.selectedTabKey(constants.jobTypes.ALL_JOB.title);
-				this.jobNotificationsPending = ko.computed(() => this.allJobParams.jobListing().filter(j => !j.viewed()).length);
+				this.jobNotificationsPending = ko.pureComputed(() => this.allJobParams.jobListing().filter(j => !j.viewed()).length);
 				this.allJobParams.jobNameClick = this.jobNameClick.bind(this);
 			}
 			this.tabs.push({
@@ -73,7 +73,7 @@ define([
 				componentName: 'user-bar-jobs',
 				componentParams: this.allJobParams,
 			});
-			this.jobsCount = ko.computed(() => {
+			this.jobsCount = ko.pureComputed(() => {
 				if (this.selectedTabKey() === constants.jobTypes.USER_JOB.title) {
 					return this.userJobParams.jobListing().length;
 				}