Cohort and analyses execution / generation listings extensions with a button to publish/download Shiny applications

js/components/analysisExecution/analysis-execution-list.html

@@ -100,6 +100,23 @@ <h2 data-bind="css: classes('title'), text: ko.i18n('components.analysisExecutio
             <span data-bind="text: ko.i18nformat('components.analysisExecution.buttons.allExecutions', 'All executions (<%=submissions%>)', {submissions: submissions().length})"></span>
           </button>
         </li>
+ 			<!-- ko if: $component.config.shinyEnabled -->
+      <div class="btn-group">
+        <button class="btn btn-sm btn-primary dropdown-toggle" data-toggle="dropdown"
+          data-bind="attr: {disabled: !$component.isResultsViewPermitted(sourceKey) || $component.runningExecutionStatuses.includes(status()) || submissions().length < 1}">
+          <i class="fa fa-network-wired"></i>
+          <span data-bind="text: 'Shiny App'"></span>
+          <span class="caret"></span>
+        </button>
+        <ul class="dropdown-menu dropdown-menu-right" data-bind="foreach: $component.shinyOptions">
+          <li>
+            <a data-bind="click: () => $data.action($parent)" href="#">
+              <div class="optionText" data-bind="text: ko.i18n($data.title, $data.defaultTitle)"></div>
+            </a>
+          </li>
+        </ul>
+      </div>
+			<!-- /ko -->
       </ul>
     </div>
     <ul data-bind="css: classes('result-list')">

js/components/analysisExecution/analysis-execution-list.js

@@ -8,8 +8,11 @@ define([
   'services/Source',
   'services/JobDetailsService',
   'services/file',
+  'services/http',
+  'moment',
   'lodash',
   'const',
+  'components/analysisExecution/shiny-const',
   'text!./analysis-execution-list.html',
   'less!./analysis-execution-list.less',
   'components/modal-exit-message',
@@ -23,8 +26,11 @@ define([
   SourceService,
   JobDetailsService,
   FileService,
+  httpService,
+  moment,
   lodash,
   consts,
+  shinyConsts,
 	view
 ) {
   class AnalysisExecutionList extends Component {
@@ -89,6 +95,7 @@ define([
       this.executionResultModes = consts.executionResultModes;
       this.isExecutionDesignShown = ko.observable(false);
       this.executionDesign = ko.observable(null);
+      this.config = config;
 
       this.sourcesColumn = [{
           render: (s, p, d) => {
@@ -147,6 +154,67 @@ define([
       );
 
       this.isViewGenerationsPermitted && this.startPolling();
+      this.shinyOptions = [
+				{
+					action: this.downloadShinyApp,
+					title: 'components.shiny.button.menu.download',
+					defaultTitle: 'Download'
+				},
+				{
+					action: this.publishShinyApp,
+					title: 'components.shiny.button.menu.publish',
+					defaultTitle: 'Publish'
+				}
+			];
+    }
+
+    downloadShinyApp = (source) => {
+      let submission = this.findLatestSubmission(source.sourceKey);
+      let submissionId;
+      if (submission) {
+        submissionId = submission.id;
+      }
+
+      let resultsPathPrefix = this.resultsPathPrefix;
+      let apiPath = (resultsPathPrefix && resultsPathPrefix.includes('characterizations'))
+        ? shinyConsts.apiPaths.downloadShinyCC(submissionId, source.sourceKey)
+        : shinyConsts.apiPaths.downloadShinyPW(submissionId, source.sourceKey);
+
+      FileService.loadZipNoRename(
+        config.api.url + apiPath
+      )
+        .catch((e) => console.error("error when downloading: " + e))
+        .finally(() => this.loading(false));
+    }
+
+    publishShinyApp = async (source) => {
+      this.loading = true;
+      let submission = this.findLatestSubmission(source.sourceKey);
+      let submissionId;
+      if (submission) {
+        submissionId = submission.id;
+      }
+
+      let resultsPathPrefix = this.resultsPathPrefix;
+      let apiPath = (resultsPathPrefix && resultsPathPrefix.includes('characterizations'))
+        ? shinyConsts.apiPaths.publishShinyCC(submissionId, source.sourceKey)
+        : shinyConsts.apiPaths.publishShinyPW(submissionId, source.sourceKey);
+
+      let alertPrefix = (resultsPathPrefix && resultsPathPrefix.includes('characterizations'))
+        ? "Characterization"
+        : "Pathway";
+
+      try {
+        await httpService.doGet(config.api.url + apiPath);
+        alert("Cohort " + alertPrefix + " report is published");
+      } catch (e) {
+        console.error('An error has occurred when publishing', e);
+        if (e.status === 403) {
+          alert('Permission denied');
+        } else {
+          alert('Unexpected error occurred when publishing');
+        }
+      }
     }
 
     startPolling() {

js/components/analysisExecution/shiny-const.js

@@ -0,0 +1,13 @@
+define(
+    (require, exports) => {
+        const apiPaths = {
+            downloadShinyCC: (id, sourceKey) => `shiny/download/cohort_characterization/${id}/${sourceKey}`,
+            publishShinyCC: (id, sourceKey) => `shiny/publish/cohort_characterization/${id}/${sourceKey}`,
+            downloadShinyPW: (id, sourceKey) => `shiny/download/cohort_pathway/${id}/${sourceKey}`,
+            publishShinyPW: (id, sourceKey) => `shiny/publish/cohort_pathway/${id}/${sourceKey}`,
+        };
+        return {
+            apiPaths
+        };
+    }
+);

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

@@ -790,6 +790,22 @@ <h3 data-bind="text: ko.i18n('cohortDefinitions.cohortDefinitionManager.panels.a
 											? ko.i18n('cohortDefinitions.cohortDefinitionManager.panels.hideReports', 'Hide Reports')
 											: ko.i18n('cohortDefinitions.cohortDefinitionManager.panels.viewReports', 'View Reports'))"></span>
 		</button>
+		<!-- ko if: $component.config.shinyEnabled -->
+		<div class="btn-group">
+			<button class="btn btn-sm btn-primary dropdown-toggle" data-toggle="dropdown" data-bind="attr: {disabled: $component.isSourceRunning($data) || !isValid()}">
+				<i class="fa fa-network-wired"></i>
+				<span data-bind="text: 'Shiny App'"></span>
+				<span class="caret"></span>
+			</button>
+			<ul class="dropdown-menu dropdown-menu-right" data-bind="foreach: $component.shinyOptions">
+				<li>
+					<a data-bind="click: () => $data.action($parent)" href="#">
+						<div class="optionText" data-bind="text: ko.i18n($data.title, $data.defaultTitle)"></div>
+					</a>
+				</li>
+			</ul>
+		</div>
+		<!-- /ko -->
 	</div>
 </script>
 

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

@@ -6,6 +6,7 @@ define(['jquery', 'knockout', 'text!./cohort-definition-manager.html',
 	'services/ConceptSet',
 	'services/Permission',
 	'services/Tags',
+	'moment',
 	'components/conceptset/utils',
 	'utils/DatatableUtils',
 	'components/cohortbuilder/CohortExpression',
@@ -70,6 +71,7 @@ define(['jquery', 'knockout', 'text!./cohort-definition-manager.html',
 	conceptSetService,
 	PermissionService,
 	TagsService,
+	moment,
 	conceptSetUitls,
 	datatableUtils,
 	CohortExpression,
@@ -213,6 +215,7 @@ define(['jquery', 'knockout', 'text!./cohort-definition-manager.html',
 			this.reportCohortDefinitionId = ko.observable();
 			this.reportSourceKey = ko.observable();
 			this.reportReportName = ko.observable();
+			this.loading = ko.observable(false);
 			this.loadingReport = ko.observable(false);
 			this.reportTriggerRun = ko.observable(false);
 			this.tabMode = sharedState.CohortDefinition.mode;
@@ -849,6 +852,19 @@ define(['jquery', 'knockout', 'text!./cohort-definition-manager.html',
 
 			}
 
+			this.shinyOptions = [
+				{
+					action: this.downloadShinyApp,
+					title: 'components.shiny.button.menu.download',
+					defaultTitle: 'Download'
+				},
+				{
+					action: this.publishShinyApp,
+					title: 'components.shiny.button.menu.publish',
+					defaultTitle: 'Publish'
+				}
+			];
+
 			PermissionService.decorateComponent(this, {
 				entityTypeGetter: () => entityType.COHORT_DEFINITION,
 				entityIdGetter: () => this.currentCohortDefinition().id(),
@@ -1181,6 +1197,29 @@ define(['jquery', 'knockout', 'text!./cohort-definition-manager.html',
 			}
 		}
 
+		downloadShinyApp(source) {
+			FileService.loadZipNoRename(
+				config.api.url + constants.paths.downloadShiny(this.currentCohortDefinition().id(), source.sourceKey)
+			)
+				.catch((e) => console.error("error when downloading: " + e))
+				.finally(() => this.loading(false));
+		}
+
+		async publishShinyApp(source) {
+			this.loading = true;
+			try {
+				await httpService.doGet(config.api.url + constants.paths.publishShiny(this.currentCohortDefinition().id(), source.sourceKey));
+				alert("Cohort is published");
+			} catch (e) {
+				console.error('An error has occurred when publishing', e);
+				if (e.status === 403) {
+					alert('Permission denied');
+				} else {
+					alert('Unexpected error occurred when publishing');
+				}
+			}
+		}
+
 		onRouterParamsChanged(params) {
 			let { cohortDefinitionId, conceptSetId, selectedSourceId, mode = 'definition', sourceKey, sampleId, version } = params;
 			this.cohortDefinitionIdOnRoute(cohortDefinitionId)

js/pages/cohort-definitions/const.js

@@ -45,6 +45,8 @@ define(
 
     const paths = {
       details: id => `/cohortdefinition/${id}`,
+      downloadShiny: (id, sourceKey) => `shiny/download/cohort/${id}/${sourceKey}`,
+      publishShiny: (id, sourceKey) => `shiny/publish/cohort/${id}/${sourceKey}`,
     };
 
 		const getPeriodTypeFilter = (chosenPeriods) => ({

js/pages/incidence-rates/components/iranalysis/components/results.html

@@ -150,6 +150,22 @@ <h3 data-bind="css: classes('report-title'), text: getSourceName()"></h3>
 			<button class="btn btn-sm btn-primary" data-bind="attr: {'disabled': !$data.info() || !$data.info().executionInfo.isValid || !$component.hasSourceAccess($data.source.sourceKey)}, click: () => $component.selectSource($data)">
 				<i class="fa fa-eye"></i> <span data-bind="text: 'View Reports'"></span>
 			</button>
+			<!-- ko if: $component.config.shinyEnabled -->
+			<div class="btn-group">
+				<button class="btn btn-sm btn-primary dropdown-toggle" data-toggle="dropdown" data-bind="attr: {disabled: !$data.info() || !$data.info().executionInfo.isValid || !$component.hasSourceAccess($data.source.sourceKey) || $component.isInProgress($data)}">
+					<i class="fa fa-network-wired"></i>
+					<span data-bind="text: 'Shiny App'"></span>
+					<span class="caret"></span>
+				</button>
+				<ul class="dropdown-menu dropdown-menu-right" data-bind="foreach: $component.shinyOptions">
+					<li>
+						<a data-bind="click: () => $data.action($parent)" href="#">
+							<div class="optionText" data-bind="text: ko.i18n($data.title, $data.defaultTitle)"></div>
+						</a>
+					</li>
+				</ul>
+			</div>
+			<!-- /ko -->
 			<button data-bind="attr: {'disabled': !$data.info() || !$data.info().executionInfo.isValid || !$component.hasSourceAccess($data.source.sourceKey)}, visible: $component.isEditable()" class="btn btn-sm btn-danger removeResult">
 				<i class="fa fa-trash"></i>
 			</button>

js/pages/incidence-rates/components/iranalysis/components/results.js

@@ -2,6 +2,10 @@ define([
 	'knockout',
 	'jquery',
 	'text!./results.html',
+	'appConfig',
+	'services/file',
+	'services/http',
+	'moment',
 	'utils/AutoBind',
 	'services/IRAnalysis',
 	'pages/incidence-rates/const',
@@ -19,6 +23,10 @@ define([
 	ko,
 	$,
 	view,
+	config,
+	FileService,
+	httpService,
+	moment,
 	AutoBind,
 	IRAnalysisService,
 	constants,
@@ -27,7 +35,7 @@ define([
 	authApi,
 	Component,
 	commonUtils,
-	sharedState
+	sharedState,
 ) {
 
 	class IRAnalysisResultsViewer extends AutoBind(Component) {
@@ -49,6 +57,7 @@ define([
 			this.cancelExecution = params.cancelExecution;
 			this.stoppingSources = params.stoppingSources;
 			this.criticalCount = params.criticalCount;
+			this.config = config;
 
 			this.dirtyFlag = params.dirtyFlag;
 			this.analysisCohorts = params.analysisCohorts;
@@ -149,6 +158,42 @@ define([
 				className: 'generation-buttons-column',
 				render: () => `<span data-bind="template: { name: 'generation-buttons', data: $data }"></span>`
 			}];
+			this.shinyOptions = [
+				{
+					action: this.downloadShinyApp,
+					title: 'components.shiny.button.menu.download',
+					defaultTitle: 'Download'
+				},
+				{
+					action: this.publishShinyApp,
+					title: 'components.shiny.button.menu.publish',
+					defaultTitle: 'Publish'
+				}
+			];
+		}
+
+		downloadShinyApp(source) {
+			let analysisId = source.info().executionInfo.id.analysisId;
+			FileService.loadZipNoRename(
+				config.api.url + constants.apiPaths.downloadShiny(analysisId, source.source.sourceKey)
+			)
+				.catch((e) => console.error("error when downloading: " + e))
+				.finally(() => this.isLoading(false));
+		}
+
+		async publishShinyApp(source) {
+			this.loading = true;
+			try {
+				await httpService.doGet(config.api.url + constants.apiPaths.publishShiny(source.info().executionInfo.id.analysisId, source.source.sourceKey));
+				alert("Incidence Rate report is published");
+			} catch (e) {
+				console.error('An error has occurred when publishing', e);
+				if (e.status === 403) {
+					alert('Permission denied');
+				} else {
+					alert('Unexpected error occurred when publishing');
+				}
+			}
 		}
 
 		reportDisabledReason(source) {

js/pages/incidence-rates/const.js

@@ -4,6 +4,8 @@ define(
       root: '/iranalysis/',
       analysis: id => `/iranalysis${typeof id !== 'undefined' ? `/${id}` : ''}`,
       createAnalysis: () => '/iranalysis/0',
+      downloadShiny: (id, sourceKey) => `shiny/download/incidence/${id}/${sourceKey}`,
+      publishShiny: (id, sourceKey) => `shiny/publish/incidence/${id}/${sourceKey}`,
     };
 
     const status = {