add launch study window from sample window

js/pages/characterizations/routes.js

@@ -34,7 +34,7 @@ define(
 						router.setCurrentView('characterizations-list');
 					});
 				}),
-				'cc/characterizations/:id:': characterizationViewEdit,
+				'c/:id:': characterizationViewEdit,
 				'cc/characterizations/:id:/:section:': characterizationViewEdit,
 				'cc/characterizations/:id:/:section:/:subId:': characterizationViewEdit, // for executions
 				'cc/feature-analyses': new AuthorizedRoute(() => {

js/pages/cohort-definitions/cohort-definition-manager.js

@@ -194,6 +194,7 @@ define(['jquery', 'knockout', 'text!./cohort-definition-manager.html',
 	class CohortDefinitionManager extends AutoBind(Clipboard(Page)) {
 		constructor(params) {
 			super(params);
+			const self = this;
 			this.pollTimeoutId = null;
 			this.authApi = authApi;
 			this.config = config;
@@ -237,7 +238,7 @@ define(['jquery', 'knockout', 'text!./cohort-definition-manager.html',
 			this.isFeMaleSample=ko.observable(false);
 			this.isOtherGenderSample=ko.observable(false);
 			//error state
-			this.sampleNameError=ko.pureComputed(() => this.sampleName().trim() == "");
+			this.sampleNameError=ko.pureComputed(() => this.sampleName().trim() ===	 "");
 			this.patientCountError=ko.pureComputed(() => !(this.patientCount() > 0)); // this works because null == 0
 			this.isAgeRange =ko.pureComputed(() => ['between','notBetween'].includes(this.sampleAgeType()));
 			this.firstAgeError = ko.pureComputed(() => this.firstAge() != null && this.firstAge() < 0);
@@ -256,6 +257,21 @@ define(['jquery', 'knockout', 'text!./cohort-definition-manager.html',
 
 			//validation input value
 
+			this.selectedSampleId = ko.observable('');
+			this.selectedSampleName = ko.observable('');
+			this.sampleDataLoading = ko.observable(false);
+			this.sampleData =ko.observableArray([]);
+			this.sampleList = ko.observableArray();
+
+			// validation samples
+
+			this.annotationSets = ko.observableArray([]);
+			this.annotationLinkShown = ko.observable(false);
+			this.annotationSetsLoading = ko.observable(false);
+			this.isAnnotationSetLinking = ko.observable(false);
+			this.isAnnotationSetLoading = ko.observable(false);
+			this.annotationSampleId = ko.observable('');
+
 			//sample list
 			this.sampleListCols = [
 				{
@@ -294,7 +310,7 @@ define(['jquery', 'knockout', 'text!./cohort-definition-manager.html',
 					}
 				}
 			];
-			this.sampleList = ko.observableArray();
+
 
 			// Sample data table
 			this.sampleCols =  [
@@ -315,19 +331,6 @@ define(['jquery', 'knockout', 'text!./cohort-definition-manager.html',
 				}
 			];
 
-			this.selectedSampleId = ko.observable('');
-			this.selectedSampleName = ko.observable('');
-			this.sampleDataLoading = ko.observable(false);
-			this.sampleData =ko.observableArray([]);
-
-			// validation samples
-
-			this.annotationSets = ko.observableArray([]);
-			this.annotationLinkShown = ko.observable(false);
-			this.annotationSetsLoading = ko.observable(false);
-			this.isAnnotationSetLinking = ko.observable(false);
-			this.annotationSampleId = ko.observable('');
-
 			this.annotationSetCols = [
 				{
 					title: 'ID',
@@ -344,8 +347,11 @@ define(['jquery', 'knockout', 'text!./cohort-definition-manager.html',
 				{
 					title: 'Actions',
 					sortable: false,
-					render: function() {
-						return `<button class="btn btn-primary btn-sm annotation-link-btn" title="Link annotation set">Create Study</button><span class="annotation-link-status"></span>`
+					data: 'id',
+					render: (d) => {
+						return `<button class="btn btn-primary btn-sm annotation-link-btn" title="View annotation set">Launch Study</button><span class="annotation-link-status"></span>`;
+
+
 					}
 				}
 			];
@@ -1715,13 +1721,16 @@ define(['jquery', 'knockout', 'text!./cohort-definition-manager.html',
 				this.annotationLinkShown(true);
 				this.annotationSetsLoading(true);
 				this.annotationSampleId(sampleId);
+
 				this.loadAnnotationSets(cohortDefinitionId)
 					.then(res => {
 						this.showAnnotationDataTable(res);
 					})
 					.finally(() => {
 						this.annotationSetsLoading(false);
 					});
+
+
 			} else {
 				this.fetchSampleData({sampleId, sourceKey, cohortDefinitionId});
 			}
@@ -1775,29 +1784,88 @@ define(['jquery', 'knockout', 'text!./cohort-definition-manager.html',
 				this.isAnnotationSetLinking(true);
 				const btn = e.target;
 				const status = btn.nextSibling;
+				status.textContent = "Retrieving study information...";
 				btn.disabled = true;
-				status.textContent = "Creating study...";
-				annotationService.linkAnnotationToSamples({
-					'sampleId': sampleId,
-					'cohortDefinitionId': cohortDefinitionId,
-					'sourceKey': sourceKey,
-					'annotationSetId': d.id
-				})
-					.then(res => {
-						status.textContent = "Study successfully created!";
-						console.log('posted annotation sample link');
-						console.log(res);
+				annotationService.getSetsBySampleId(sampleId)
+					.then((items) => {
+						return items.includes(d['id']);
 					})
-					.catch(error=>{
-						console.error(error);
-						status.textContent = "Error creating study!";
-						btn.disabled = false;
-						alert('Error linking sample to annotations. Please try again later.');
-					})
-					.finally(() => {
-						this.isAnnotationSetLinking(false);
-						this.annotationLinkShown(false);
+					.then((linked) => {
+						if (linked) {
+							status.textContent = "Launching study...";
+							annotationService.getAnnotationsBySampleIdSetId(sampleId, d.id)
+								.then((items) => {
+									if (items.length > 0) {
+										window.location = `#/profiles/${sourceKey}/${items[0].subjectId}/${cohortDefinitionId}/${sampleId}`;
+										location.reload();
+									} else {
+										console.error(error);
+										status.textContent = "Error launching study!";
+										btn.disabled = false;
+										alert('Error launching sample to annotations. Please try again later.');
+									}
+								})
+								.catch(error=>{
+									console.error(error);
+									status.textContent = "Error launching study!";
+									btn.disabled = false;
+									alert('Error launching sample to annotations. Please try again later.');
+								})
+								.finally(() => {
+									this.isAnnotationSetLinking(false);
+									this.annotationLinkShown(false);
+								})
+						}
+						else {
+							status.textContent = "Creating study...";
+							annotationService.linkAnnotationToSamples({
+								'sampleId': sampleId,
+								'cohortDefinitionId': cohortDefinitionId,
+								'sourceKey': sourceKey,
+								'annotationSetId': d.id
+							})
+								.then(res => {
+									status.textContent = "Launching Study...";
+									console.log('posted annotation sample link');
+									console.log(res);
+									annotationService.getAnnotationsBySampleIdSetId(sampleId, d.id)
+										.then((items) => {
+											if (items.length > 0) {
+												window.location = `#/profiles/${sourceKey}/${items[0].subjectId}/${cohortDefinitionId}/${sampleId}`;
+												location.reload();
+											} else {
+												console.error(error);
+												status.textContent = "Error launching study!";
+												btn.disabled = false;
+												alert('Error launching sample to annotations. Please try again later.');
+											}
+										})
+										.catch(error=>{
+											console.error(error);
+											status.textContent = "Error launching study!";
+											btn.disabled = false;
+											alert('Error launching sample to annotations. Please try again later.');
+										})
+										.finally(() => {
+											this.isAnnotationSetLinking(false);
+											this.annotationLinkShown(false);
+										})
+								})
+								.catch(error=>{
+									console.error(error);
+									status.textContent = "Error creating study!";
+									btn.disabled = false;
+									alert('Error linking sample to annotations. Please try again later.');
+								})
+								.finally(() => {
+									this.isAnnotationSetLinking(false);
+									this.annotationLinkShown(false);
+								});
+						}
 					});
+
+
+
 			}
 		}
 

js/pages/profiles/annotation/view-models/Annotation.js

@@ -120,9 +120,11 @@ define(['knockout', './Set', './Result', 'services/Annotation'], function (ko, S
               if (sampleName.indexOf(' ') >=0) {
               sampleName  = sampleName.split(" ").join('_');
             }
-            self.annotationSaving(false );
+            self.annotationSaving(false);
             //window.location = `#/profiles/${sourceKey}/${ko.toJS(annotationView).navigation.nextSubjectId}/${cohortId}/${sampleName}`;
             self.nav.nextLink();
+          }).catch((error) => {
+            self.annotationSaving(false);
           });
       }
     }

js/pages/profiles/annotation/view-models/Content.js

@@ -21,7 +21,7 @@ define(['knockout', './Annotation', 'services/Annotation'], function (ko, Annota
                             });
                     } else {
                         self.annotation = new Annotation(set, personId, cohortId, sourceKey, [], null, annotationView, sampleName);
-                        self.annotationLoaded(false);
+                        self.annotationLoaded(true);
                     }
                 });
         };

js/pages/profiles/annotation/view-models/Navigation.js

@@ -8,11 +8,13 @@ define(['knockout', './Navigation', 'services/Annotation'], function (ko, Naviga
         self.numProfileSamples = ko.observable();
         self.numAnnotations = ko.observable();
         self.navigationLoaded = ko.observable(false);
+        self.sampleId = ko.observable();
+        self.sourceKey = ko.observable(sourceKey);
+        self.cohortId = ko.observable(cohortId);
+        self.personId = ko.observable(personId);
 
         this.prevLink = function() {
-            if (sampleName.indexOf(' ') >= 0) {
-                sampleName= sampleName.split(" ").join('_');
-            }
+
             window.location = `#/profiles/${sourceKey}/${self.prevSubjectId()}/${cohortId}/${sampleName}`;
             location.reload();
         };
@@ -24,19 +26,6 @@ define(['knockout', './Navigation', 'services/Annotation'], function (ko, Naviga
             location.reload();
         };
 
-        // this.prevLink = ko.computed(function() {
-        //   if (sampleName.indexOf(' ') >=0) {
-        //     sampleName  = sampleName.split(" ").join('_');
-        //   }
-        //     return `#/profiles/${sourceKey}/${self.prevSubjectId()}/${cohortId}/${sampleName}`;
-        // }, self);
-
-        // this.nextLink = ko.computed(function() {
-        //   if (sampleName.indexOf(' ') >=0) {
-        //     sampleName  = sampleName.split(" ").join('_');
-        //   }
-        //     return `#/profiles/${sourceKey}/${self.nextSubjectId()}/${cohortId}/${sampleName}`;
-        // }, self);
 
         this.completionPercent = ko.computed(function() {
             return Math.ceil((self.numAnnotations()/self.numProfileSamples())*100);
@@ -45,6 +34,11 @@ define(['knockout', './Navigation', 'services/Annotation'], function (ko, Naviga
         self.initialize = function(sampleName, cohortId, personId, sourceKey) {
             annotationService.getAnnotationNavigation(sampleName, cohortId, personId, sourceKey)
                 .then((navigation) => {
+                    if (sampleName.indexOf(' ') >= 0) {
+                        sampleName= sampleName.split(" ").join('_');
+                    }
+                    self.sampleId(sampleName);
+
                     // const { prevSubjectId, nextSubjectId, nextUnannotatedSubjectId, numProfileSamples, numAnnotations } = navigation;
                     const samples = navigation.elements;
 

js/pages/profiles/const.js

@@ -4,6 +4,7 @@ define(
     const paths = {
       source: sourceKey => `#/profiles/${sourceKey}`,
       person: (sourceKey, personId) => `#/profiles/${sourceKey}/${personId}`,
+      sample: (sourceKey, personId, cohortDefinitionId, sampleId) => `#/profiles/${sourceKey}/${personId}/${cohortDefinitionId}/${sampleId}`,
     };
 
     return {

js/pages/profiles/profile-manager.html

@@ -145,10 +145,10 @@
 										<div data-bind="with: navigation">
 											<div class="btn-group btn-group-justified annotation-next-prev" disable role="group">
 												<div class="btn-group" role="group">
-													<a class="btn btn-default" data-bind="click: prevLink, attr: {disabled: !navigationLoaded() }, html: !navigationLoaded() ? 'Loading': '<span>Prev</span>'" role="button"></a>
+													<a class="btn btn-default btn-prf-annotation-prev" data-bind="click: prevLink, attr: { href: '#/profiles/' + sourceKey() + '/' + prevSubjectId() + '/' + cohortId() + '/' + sampleId(), disabled: !navigationLoaded() }, html: !navigationLoaded() ? 'Loading': '<span>Prev</span>'" role="button"></a>
 												</div>
 												<div class="btn-group" role="group">
-													<a class="btn btn-default" data-bind="click: nextLink, attr: {disabled: !navigationLoaded() }, html: !navigationLoaded() ? 'Loading': '<span>Next</span>'" role="button"></a>
+													<a class="btn btn-default btn-prf-annotation-next" data-bind="click: nextLink, attr: {href: '#/profiles/' + sourceKey() + '/' + nextSubjectId() + '/' + cohortId() + '/' + sampleId(), disabled: !navigationLoaded() }, html: !navigationLoaded() ? 'Loading': '<span>Next</span>'" role="button"></a>
 												</div>
 											</div>
 <!--											<div class="annotation-progress">-->

js/pages/profiles/routes.js

@@ -10,6 +10,7 @@ define(
             params.sourceKey = (path[0] || null);
             params.personId = (path[1] || null);
             params.cohortDefinitionId = (path[2] || null);
+            params.cohortSampleId = (path[3] || null);
 
             router.setCurrentView('profile-manager', params);
           });

js/services/Annotation.js

@@ -81,6 +81,34 @@ define(function (require, exports) {
 
         return response;
     };
+
+    const getSetsBySampleId = function(sampleId) {
+        // http://localhost:8080/WebAPI/annotations?cohortSampleId=6
+        return httpService.doGet(`${config.webAPIRoot}annotations?cohortSampleId=${sampleId}`)
+            .then((resp) => {
+                const sets = new Set();
+                resp.data.forEach((x, i) => {
+                    sets.add(x.questionSetId);
+                });
+                return Array.from(sets);
+            })
+            .catch(er => {
+                console.error("unable to load sets");
+                console.log(er);
+                });
+    };
+
+    const getAnnotationsBySampleIdSetId = function(sampleId, setId) {
+        // http://localhost:8080/WebAPI/annotations?cohortSampleId=6
+        return httpService.doGet(`${config.webAPIRoot}annotations?cohortSampleId=${sampleId}&setId=${setId}`)
+            .then((res) => {
+                return res.data;
+            })
+            .catch(er => {
+                console.error("unable to load sets");
+                console.log(er);
+            });
+    };
 
     const getAnnotationNavigation = function(sampleName, cohort, subject, source) {
       const data = {
@@ -112,6 +140,8 @@ define(function (require, exports) {
 
     return {
         getAnnotationSets,
+        getSetsBySampleId,
+        getAnnotationsBySampleIdSetId,
         getStudySets,
         getSuperTable,
         getStudyResults,