Subset ' + (i) + ':
'; 20 | cohortsSummary += currentQuery; 21 | cohortsSummary += '
'; 22 | } 23 | } 24 | if (!cohortsSummary) { 25 | cohortsSummary = '
WARNING: No subsets have been selected! Please go to the "Comparison" tab and select your subsets.'; 26 | } 27 | 28 | span.innerHTML = cohortsSummary; 29 | } 30 | 31 | // Trigger for update is clicking the SmartR panel item. Maybe there is a more elegant way? 32 | $scope.$evalAsync(function() { 33 | _showCohortInfo(); // set it one time initially 34 | $('#resultsTabPanel__smartRPanel').on('click', function() { 35 | _showCohortInfo(); 36 | }); 37 | }); 38 | } 39 | }; 40 | 41 | }]); 42 | -------------------------------------------------------------------------------- /web-app/js/smartR/_angular/directives/downloadResultsButton.js: -------------------------------------------------------------------------------- 1 | //# sourceURL=downloadResultsButton.js 2 | 3 | window.smartRApp.directive('downloadResultsButton', ['rServeService', function(rServeService) 4 | { 5 | function downloadFile(data) { 6 | var link = jQuery('') 7 | .attr('href', rServeService.urlForFile(data.executionId, 'analysis_data.zip')) 8 | .attr('download', 'analysis_data.zip') 9 | .css('display', 'none'); 10 | jQuery('body').append(link); 11 | link[0].click(); 12 | link.remove(); 13 | } 14 | 15 | return { 16 | restrict: 'E', 17 | scope: { 18 | disabled: '=' 19 | }, 20 | template: 21 | '' + 22 | '', 23 | link: function(scope, element) { 24 | 25 | var template_btn = element.children()[0]; 26 | var template_msg = element.children()[1]; 27 | 28 | template_btn.disabled = scope.disabled; 29 | 30 | scope.$watch('disabled', function (newValue) { 31 | template_btn.disabled = newValue; 32 | }, true); 33 | 34 | template_btn.onclick = function() { 35 | 36 | template_msg.innerHTML = 'Download data, please wait _'; 37 | 38 | rServeService.startScriptExecution({ 39 | taskType: 'downloadData', 40 | arguments: {} 41 | }).then( 42 | function (data){ 43 | // download file 44 | template_msg.innerHTML = ''; 45 | downloadFile(data); 46 | }, 47 | function (msg){ 48 | template_msg.innerHTML = 'Failure: ' + msg; 49 | } 50 | ) 51 | }; 52 | } 53 | }; 54 | }]); 55 | -------------------------------------------------------------------------------- /web-app/js/smartR/_angular/directives/ngTranscludeReplace.js: -------------------------------------------------------------------------------- 1 | //# sourceURL=ngTranscludeReplace.js 2 | 3 | 'use strict'; 4 | 5 | window.smartRApp.directive('ngTranscludeReplace', ['$log', function ($log) { 6 | return { 7 | terminal: true, 8 | restrict: 'EA', 9 | 10 | link: function ($scope, $element, $attr, ctrl, transclude) { 11 | if (!transclude) { 12 | $log.error('orphan', 13 | 'Illegal use of ngTranscludeReplace directive in the template! ' + 14 | 'No parent directive that requires a transclusion found. '); 15 | return; 16 | } 17 | transclude(function (clone) { 18 | if (clone.length) { 19 | $element.replaceWith(clone); 20 | } 21 | else { 22 | $element.remove(); 23 | } 24 | }); 25 | } 26 | }; 27 | }]); 28 | -------------------------------------------------------------------------------- /web-app/js/smartR/_angular/directives/preprocessButton.js: -------------------------------------------------------------------------------- 1 | //# sourceURL=preprocessButton.js 2 | 3 | 'use strict'; 4 | 5 | window.smartRApp.directive('preprocessButton', [ 6 | 'rServeService', 7 | '$rootScope', 8 | function(rServeService, $rootScope) { 9 | return { 10 | restrict: 'E', 11 | scope: { 12 | running: '=?', 13 | params: '=?', 14 | showSummaryStats: '=', 15 | summaryData: '=', 16 | allSamples: '=?', 17 | numberOfRows: '=?', 18 | projection: '@?' 19 | }, 20 | templateUrl: $rootScope.smartRPath + '/js/smartR/_angular/templates/preprocessButton.html', 21 | link: function(scope, element) { 22 | 23 | var template_btn = element.children()[0]; 24 | var template_msg = element.children()[1]; 25 | 26 | var _onSuccess = function() { 27 | template_msg.innerHTML = 'Task complete! Go to the "Run Analysis" tab to continue.'; 28 | template_btn.disabled = false; 29 | scope.running = false; 30 | }; 31 | 32 | var _onFail = function(msg) { 33 | template_msg.innerHTML = 'Error: ' + msg; 34 | template_btn.disabled = false; 35 | scope.running = false; 36 | }; 37 | 38 | // we add this conditional $watch because there is some crazy promise resolving for allSamples 39 | // going on. This is a workaround which observes allSamples and uses it as criteria for successful 40 | // completion. FIXME 41 | scope.$watch('summaryData', function(newValue) { 42 | if (scope.summaryData && 43 | scope.showSummaryStats && 44 | scope.running && 45 | Object.keys(newValue).indexOf('subsets') !== -1) { 46 | scope.allSamples = newValue.allSamples; 47 | scope.numberOfRows = newValue.numberOfRows; 48 | _onSuccess(); 49 | } 50 | }, true); 51 | 52 | var _showSummaryStats = function() { 53 | template_msg.innerHTML = 'Execute summary statistics, please wait _'; 54 | rServeService.executeSummaryStats('preprocess', scope.projection).then( 55 | function (data) { 56 | scope.summaryData = data.result; // this will trigger $watch 57 | }, 58 | _onFail 59 | ); 60 | }; 61 | 62 | template_btn.onclick = function() { 63 | scope.summaryData = {}; 64 | scope.disabled = true; 65 | scope.running = true; 66 | template_msg.innerHTML = 'Preprocessing, please wait _'; 67 | 68 | var params = scope.params ? scope.params : {}; 69 | rServeService.preprocess(params).then( 70 | scope.showSummaryStats ? _showSummaryStats : _onSuccess, 71 | _onFail 72 | ); 73 | }; 74 | } 75 | }; 76 | }]); 77 | -------------------------------------------------------------------------------- /web-app/js/smartR/_angular/directives/runButton.js: -------------------------------------------------------------------------------- 1 | //# sourceURL=runButton.js 2 | 3 | 'use strict'; 4 | 5 | window.smartRApp.directive('runButton', [ 6 | '$rootScope', 7 | 'rServeService', 8 | 'smartRUtils', 9 | function($rootScope, rServeService, smartRUtils) { 10 | return { 11 | restrict: 'E', 12 | scope: { 13 | running: '=?', 14 | storage: '=storeResultsIn', 15 | script: '@scriptToRun', 16 | name: '@buttonName', 17 | filename: '@?', 18 | params: '=?argumentsToUse', 19 | waitMessage: '@?' 20 | }, 21 | templateUrl: $rootScope.smartRPath + '/js/smartR/_angular/templates/runButton.html', 22 | link: function(scope, element) { 23 | var params = scope.params ? scope.params : {}; 24 | if (!scope.waitMessage) { 25 | scope.waitMessage = 'Creating plot, please wait'; 26 | } 27 | 28 | var template_btn = element.children()[0], 29 | template_msg = element.children()[1]; 30 | 31 | var _onSuccess = function(data) { 32 | scope.storage = data; 33 | template_msg.innerHTML = ''; 34 | scope.disabled = false; 35 | scope.running = false; 36 | }; 37 | 38 | var _onFail = function(msg) { 39 | template_msg.innerHTML = 'Error: ' + msg; 40 | scope.disabled = false; 41 | scope.running = false; 42 | }; 43 | 44 | var _prepareResults = function(response) { 45 | if (scope.filename) { 46 | // when filename is specified it is assumed that results are serialized 47 | // if results are serialized, we need to deserialized them by 48 | // downloading the results files. 49 | rServeService.downloadJsonFile(response.executionId, scope.filename).then( 50 | function(d) { _onSuccess(d.data); }, 51 | _onFail 52 | ); 53 | } else { 54 | _onSuccess(JSON.parse(response.result.artifacts.value)); 55 | } 56 | }; 57 | 58 | template_btn.onclick = function() { 59 | smartRUtils.cleanUp(); 60 | scope.disabled = true; 61 | scope.storage = {}; 62 | scope.running = true; 63 | template_msg.innerHTML = scope.waitMessage + ' _'; 64 | 65 | rServeService.startScriptExecution({ 66 | taskType: scope.script, 67 | arguments: params 68 | }).then( 69 | _prepareResults, 70 | _onFail 71 | ); 72 | }; 73 | } 74 | }; 75 | }]); 76 | -------------------------------------------------------------------------------- /web-app/js/smartR/_angular/directives/sortingCriteria.js: -------------------------------------------------------------------------------- 1 | //# sourceURL=sortingCriteria.js 2 | 3 | 'use strict'; 4 | 5 | window.smartRApp.directive('sortingCriteria', [ 6 | '$rootScope', 7 | function($rootScope) { 8 | return { 9 | restrict: 'E', 10 | scope: { 11 | criteria : '=', 12 | samples: '=', 13 | subsets: '=' 14 | }, 15 | templateUrl: $rootScope.smartRPath + '/js/smartR/_angular/templates/sortingCriteria.html' 16 | }; 17 | } 18 | ]); 19 | -------------------------------------------------------------------------------- /web-app/js/smartR/_angular/directives/summaryStatistics.js: -------------------------------------------------------------------------------- 1 | //# sourceURL=summaryStatistics.js 2 | 3 | 'use strict'; 4 | 5 | window.smartRApp.directive('summaryStats', [ 6 | '$rootScope', 7 | function($rootScope) { 8 | return { 9 | restrict: 'E', 10 | scope: { 11 | summaryData: '=' 12 | }, 13 | templateUrl: $rootScope.smartRPath + '/js/smartR/_angular/templates/summaryStatistics.html' 14 | }; 15 | } 16 | ]); 17 | -------------------------------------------------------------------------------- /web-app/js/smartR/_angular/directives/tabContainer.js: -------------------------------------------------------------------------------- 1 | //# sourceURL=tabContainer.js 2 | 3 | 'use strict'; 4 | 5 | window.smartRApp.directive('tabContainer', 6 | ['$rootScope', 'smartRUtils', '$timeout', function($rootScope, smartRUtils, $timeout) { 7 | return { 8 | restrict: 'E', 9 | transclude: true, 10 | templateUrl: $rootScope.smartRPath + '/js/smartR/_angular/templates/tabContainer.html', 11 | controller: function($scope) { 12 | $scope.tabs = []; 13 | this.addTab = function(tab) { 14 | $scope.tabs.push(tab); 15 | }; 16 | }, 17 | link: function() { 18 | $timeout(function() { // init jQuery UI tabs after DOM has rendered 19 | $('#heim-tabs').tabs(); 20 | }); 21 | } 22 | }; 23 | }]); 24 | -------------------------------------------------------------------------------- /web-app/js/smartR/_angular/directives/workflowControls.js: -------------------------------------------------------------------------------- 1 | //# sourceURL=workflowControls.js 2 | 3 | 'use strict'; 4 | 5 | window.smartRApp.directive('workflowControls', [ 6 | '$rootScope', 7 | 'smartRUtils', 8 | function($rootScope, smartRUtils) { 9 | return { 10 | restrict: 'E', 11 | transclude: true, 12 | templateUrl: $rootScope.smartRPath + '/js/smartR/_angular/templates/workflowControls.html', 13 | link: function(scope, element) { 14 | var controls = element.children()[0]; 15 | var scrollbarWidth = smartRUtils.getScrollBarWidth(); 16 | controls.style.bottom = scrollbarWidth + 'px'; 17 | controls.style.right = scrollbarWidth + 105 + 'px'; 18 | } 19 | }; 20 | } 21 | ]); 22 | -------------------------------------------------------------------------------- /web-app/js/smartR/_angular/directives/workflowTab.js: -------------------------------------------------------------------------------- 1 | //# sourceURL=workflowTab.js 2 | 3 | 'use strict'; 4 | 5 | window.smartRApp.directive('workflowTab', ['smartRUtils', function(smartRUtils) { 6 | return { 7 | restrict: 'E', 8 | scope: { 9 | name: '@tabName', 10 | disabled: '=' 11 | }, 12 | require: '^tabContainer', 13 | transclude: true, 14 | template: '
2 |
18 |
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/web-app/js/smartR/_angular/templates/boxplot.html:
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1 |
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/web-app/js/smartR/_angular/templates/conceptBox.html:
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1 |
3 |
4 |
5 | Biomarker can be a gene, pathway, mirID or UniProtID.
6 |
17 |
7 |
16 | -
8 | 9 | {{biomarker.type}} 10 | {{biomarker.name}} 11 | {{biomarker.synonyms}} 12 |13 | 14 |
2 |
3 |
4 | Drag at least {{min}} node(s) into the box
5 | Select at most {{max}} node(s)
6 | Node(s) do not have the correct type
7 | Nodes must have the same platform 8 |
15 |
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/web-app/js/smartR/_angular/templates/fetchButton.html:
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/web-app/js/smartR/_angular/templates/heatmap.html:
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1 | 4 | Drag at least {{min}} node(s) into the box
5 | Select at most {{max}} node(s)
6 | Node(s) do not have the correct type
7 | Nodes must have the same platform 8 |
10 |
11 |
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34 | 40 |
41 | 34 | 40 |
8 | Analysis name in IPA: {{ ipaState.analysisName }}
9 |
10 |
11 |
12 |
64 |
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/web-app/js/smartR/_angular/templates/linegraph.html:
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1 | Limma
13 | Canonical Pathways
14 | Upstream Regulators
15 | Tox Functions
16 | Networks
17 | Diseases and Bio Functions
18 | Analysis Ready Molecules
19 |
20 |
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27 |
32 |
33 |
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26 |
27 | Ranking Criteria:
2 |
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26 |
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45 |
46 |
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/web-app/js/smartR/_angular/templates/summaryStatistics.html:
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1 | | Plot | 5 |Labels | 6 |Subset 1 | 7 |Subset 2 | 8 |
|---|---|---|---|
13 |
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/web-app/js/smartR/_angular/templates/workflowControls.html:
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/web-app/js/smartR/_angular/templates/workflowWarnings.html:
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1 | -
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- 4 | 6 | {{tab.name}} 7 | 8 | 9 |
2 | {{text}}
3 |
4 |
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/web-app/js/smartR/_angular/viz/plotlyBoxplot.js:
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1 | //# sourceURL=plotlyBoxplot.js
2 |
3 | 'use strict';
4 |
5 | window.smartRApp.directive('boxplot', [
6 | 'smartRUtils',
7 | 'rServeService',
8 | '$rootScope',
9 | function(smartRUtils, rServeService, $rootScope) {
10 |
11 | return {
12 | restrict: 'E',
13 | scope: {
14 | data: '='
15 | },
16 | templateUrl: $rootScope.smartRPath + '/js/smartR/_angular/templates/boxplot.html',
17 | link: function (scope, element) {
18 | var vizDiv = element.children()[0];
19 | /**
20 | * Watch data model (which is only changed by ajax calls when we want to (re)draw everything)
21 | */
22 | scope.$watch('data', function () {
23 | $(vizDiv).empty();
24 | if (! $.isEmptyObject(scope.data)) {
25 | createBoxplot(scope, vizDiv);
26 | }
27 | });
28 | }
29 | };
30 |
31 | function createBoxplot(scope, vizDiv) {
32 | var cf = crossfilter(scope.data.dataMatrix);
33 | var byValue = cf.dimension(function(d) { return d.value; });
34 | var byBioMarker = cf.dimension(function(d) { return d.bioMarker; });
35 |
36 | var plotData = [];
37 | smartRUtils.unique(smartRUtils.getValuesForDimension(byBioMarker)).forEach(function(bioMarker) {
38 | byBioMarker.filterExact(bioMarker);
39 | plotData.push({
40 | type: 'box',
41 | y: smartRUtils.getValuesForDimension(byValue),
42 | name: bioMarker,
43 | boxpoints: 'all',
44 | boxmean: 'sd',
45 | jitter: 0.5
46 | });
47 | byBioMarker.filterAll();
48 | });
49 |
50 | var title = 'Boxplots (' + scope.data.transformation + ')';
51 | title += scope.data.pValue ? ' ANOVA pValue = ' + scope.data.pValue : '';
52 | var layout = {
53 | title: title,
54 | height: 800
55 | };
56 | Plotly.newPlot(vizDiv, plotData, layout);
57 | }
58 | }]);
59 |
60 |
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/web-app/js/smartR/smartR.js:
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1 | 'use strict';
2 |
3 | // Avoid `console` errors in browsers that lack a console.
4 | (function() {
5 | var method;
6 | var noop = function () {};
7 | var methods = [
8 | 'assert', 'clear', 'count', 'debug', 'dir', 'dirxml', 'error',
9 | 'exception', 'group', 'groupCollapsed', 'groupEnd', 'info', 'log',
10 | 'markTimeline', 'profile', 'profileEnd', 'table', 'time', 'timeEnd',
11 | 'timeline', 'timelineEnd', 'timeStamp', 'trace', 'warn'
12 | ];
13 | var length = methods.length;
14 | console = (window.console = window.console || {}); // jshint ignore:line
15 |
16 | while (length--) {
17 | method = methods[length];
18 |
19 | // Only stub undefined methods.
20 | if (!console[method]) {
21 | console[method] = noop;
22 | }
23 | }
24 | }());
25 |
26 | window.smartRPanel = new Ext.Panel({
27 | id: 'smartRPanel',
28 | title: 'SmartR',
29 | region: 'center',
30 | split: true,
31 | height: 90,
32 | layout: 'fit',
33 | collapsible: true,
34 | autoScroll: true,
35 | tbar: new Ext.Toolbar({
36 | id: 'smartRToolbar',
37 | title: 'R Scripts',
38 | items: []
39 | }),
40 | listeners: {
41 | render: function (panel) {
42 | /**
43 | * WORKAROUND : code below is needed to reorder the javascript script load that're broken due to
44 | * ExtJS panel
45 | */
46 | // start workaround
47 | var updater = panel.getUpdater();
48 | updater.on('update', function() {
49 | var panelBody = jQuery(arguments[0].dom);
50 | var scripts = panelBody.children('script');
51 | scripts.remove(); // remove scripts from panel body
52 | panelBody.append(scripts); // re-append again
53 | });
54 | updater.update({
55 | url: pageInfo.basePath + '/smartR/index',
56 | method: 'POST',
57 | scripts: false });
58 | // end workaround
59 | }
60 | }
61 | });
62 |
63 | window.addSmartRPanel = function addSmartRPanel(parentPanel) {
64 | parentPanel.insert(4, window.smartRPanel);
65 | };
66 |
67 | function cleanUpSmartR() {
68 | var d3tips = document.getElementsByClassName('d3-tip');
69 | Array.prototype.forEach.call(d3tips, function(el) { // d3tips is array-like object
70 | el.parentNode.removeChild(el);
71 | });
72 | }
73 | cleanUpSmartR();
74 |
75 |
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