Read pipeline params from the URL in more places

Author: bbimber

SequenceAnalysis/resources/web/SequenceAnalysis/panel/AlignmentImportPanel.js

@@ -86,7 +86,8 @@ Ext4.define('SequenceAnalysis.panel.AlignmentImportPanel', {
                 helpPopup: 'Description for this run, such as detail about the source of the alignments (optional)',
                 itemId: 'jobDescription',
                 name: 'jobDescription',
-                allowBlank: true
+                allowBlank: true,
+                value: LABKEY.ActionURL.getParameter('jobDescription')
             },{
                 fieldLabel: 'Delete Intermediate Files',
                 helpPopup: 'Check to delete the intermediate files created by this pipeline.  In general these are not needed and it will save disk space.  These files might be useful for debugging though.',

SequenceAnalysis/resources/web/SequenceAnalysis/panel/AnalysisSectionPanel.js

@@ -570,7 +570,7 @@ Ext4.define('SequenceAnalysis.panel.AnalysisSectionPanel', {
         return [];
     },
 
-    applySavedValues: function(values){
+    applySavedValues: function(values, allowUrlOverride){
         if (this.stepType){
             var tools = values[this.stepType] ? values[this.stepType].split(';') : [];
             this.setActiveTools(tools);
@@ -585,6 +585,10 @@ Ext4.define('SequenceAnalysis.panel.AnalysisSectionPanel', {
                 if (Ext4.isDefined(values[name])){
                     p.setValue(values[name]);
                 }
+
+                if (allowUrlOverride && LABKEY.ActionURL.getParameter(name)) {
+                    p.setValue(LABKEY.ActionURL.getParameter(name));
+                }
             }, this);
         }
     },

SequenceAnalysis/resources/web/SequenceAnalysis/panel/BaseSequencePanel.js

@@ -269,6 +269,9 @@ Ext4.define('SequenceAnalysis.panel.BaseSequencePanel', {
                                                     return;
                                                 }
 
+                                                // If auto-loading, assume we want to read the URL
+                                                thePanel.down('#readUrlParams').setValue(true);
+
                                                 var recIdx = store.find('name', LABKEY.ActionURL.getParameter('template'));
                                                 if (recIdx > -1) {
                                                     thePanel.down('labkey-combo').setValue(store.getAt(recIdx));
@@ -297,6 +300,12 @@ Ext4.define('SequenceAnalysis.panel.BaseSequencePanel', {
                                 helpPopup: 'By default, the pipelines jobs and their outputs will be created in the workbook you selected. However, in certain cases, such as bulk submission of many jobs, it might be preferable to submit each job to the source folder/workbook for each input. Checking this box will enable this.',
                                 fieldLabel: 'Submit Jobs to Same Folder/Workbook as Readset',
                                 labelWidth: 200
+                            },{
+                                xtype: 'checkbox',
+                                itemId: 'readUrlParams',
+                                helpPopup: 'If true, any parameters provided on the URL with the same name as a parameter in the JSON will be read and override the template.',
+                                fieldLabel: 'Read Parameters From URL',
+                                labelWidth: 200
                             }]
                         }],
                         buttons: [{
@@ -353,7 +362,8 @@ Ext4.define('SequenceAnalysis.panel.BaseSequencePanel', {
                                 delete json.submitJobToReadsetContainer;
                             }
 
-                            win.sequencePanel.applySavedValues(json);
+                            var readUrlParams = win.down('#readUrlParams').getValue();
+                            win.sequencePanel.applySavedValues(json, readUrlParams);
 
                             var submitJobToReadsetContainer = win.sequencePanel.down('[name="submitJobToReadsetContainer"]');
                             if (submitJobToReadsetContainer) {
@@ -386,7 +396,7 @@ Ext4.define('SequenceAnalysis.panel.BaseSequencePanel', {
         }
     },
 
-    applySavedValues: function(values){
+    applySavedValues: function(values, allowUrlOverride){
         //allows for subclasses to exclude this panel
         var alignPanel = this.down('sequenceanalysis-alignmentpanel');
         if (alignPanel) {
@@ -395,7 +405,7 @@ Ext4.define('SequenceAnalysis.panel.BaseSequencePanel', {
 
         var sections = this.query('sequenceanalysis-analysissectionpanel');
         Ext4.Array.forEach(sections, function(s){
-            s.applySavedValues(values);
+            s.applySavedValues(values, allowUrlOverride);
         }, this);
 
         // For top-level properties:

SequenceAnalysis/resources/web/SequenceAnalysis/panel/SequenceAnalysisPanel.js

@@ -300,7 +300,8 @@ Ext4.define('SequenceAnalysis.panel.SequenceAnalysisPanel', {
                 height: 100,
                 helpPopup: 'Description for this analysis (optional)',
                 name: 'jobDescription',
-                allowBlank:true
+                allowBlank: true,
+                value: LABKEY.ActionURL.getParameter('jobDescription')
             },{
                 fieldLabel: 'Delete Intermediate Files',
                 helpPopup: 'Check to delete the intermediate files created by this pipeline.  In general these are not needed and it will save disk space.  These files might be useful for debugging though.',

SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantProcessingPanel.js

@@ -61,7 +61,8 @@ Ext4.define('SequenceAnalysis.panel.VariantProcessingPanel', {
 				height: 100,
 				helpPopup: 'Description for this analysis (optional)',
 				name: 'jobDescription',
-				allowBlank:true
+				allowBlank: true,
+				value: LABKEY.ActionURL.getParameter('jobDescription')
 			},{
 				xtype: 'sequenceanalysis-variantscattergatherpanel',
 				width: 620,

singlecell/resources/web/singlecell/panel/SingleCellProcessingPanel.js

@@ -58,7 +58,8 @@ Ext4.define('SingleCell.panel.SingleCellProcessingPanel', {
                 height: 100,
                 helpPopup: 'Description for this analysis (optional)',
                 name: 'jobDescription',
-                allowBlank:true
+                allowBlank:true,
+                value: LABKEY.ActionURL.getParameter('jobDescription')
             },{
                 xtype: 'combo',
                 name: 'submissionType',