Greater visibility to submitting jobs to source container when applying template

Author: bbimber

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

@@ -269,6 +269,10 @@ Ext4.define('SequenceAnalysis.panel.BaseSequencePanel', {
                                         Ext4.defer(field.focus, 200, field);
                                     }
                                 }
+                            },{
+                                xtype: 'checkbox',
+                                itemId: 'useReadsetContainer',
+                                fieldLabel: 'Submit Jobs to Same Folder/Workbook as Readset'
                             }]
                         }],
                         buttons: [{
@@ -294,6 +298,12 @@ Ext4.define('SequenceAnalysis.panel.BaseSequencePanel', {
                                     json = Ext4.decode(json);
                                 }
 
+                                var useReadsetContainer = win.down('#useReadsetContainer').getValue();
+                                if (!useReadsetContainer) {
+                                    delete json.useOutputFileContainer;
+                                    delete json.submitJobToReadsetContainer;
+                                }
+
                                 win.sequencePanel.applySavedValues(json);
                                 win.close();
                             }
@@ -354,5 +364,15 @@ Ext4.define('SequenceAnalysis.panel.BaseSequencePanel', {
         Ext4.Array.forEach(sections, function(s){
             s.applySavedValues(values);
         }, this);
+
+        // For top-level properties:
+        Ext4.Array.forEach(['submissionType', 'useOutputFileContainer', 'submitJobToReadsetContainer'], function(val) {
+            if (values[val]) {
+                var field = this.down('[name="' + val + '"]');
+                if (field) {
+                    field.setValue(values[val]);
+                }
+            }
+        }, this);
     }
 });

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

@@ -318,9 +318,8 @@ Ext4.define('SequenceAnalysis.panel.SequenceAnalysisPanel', {
                 checked: false,
                 xtype: 'checkbox'
             }, this.getSaveTemplateCfg(),{
-                fieldLabel: 'Submit Jobs To Same Container As Readset?',
+                fieldLabel: 'Submit Jobs To Same Folder/Workbook As Readset?',
                 helpPopup: 'If checked, each alignment job will be submitted to the container/workbook of the parent readset, rather than this container',
-                hidden: !LABKEY.Security.currentUser.isAdmin,
                 name: 'submitJobToReadsetContainer',
                 inputValue: true,
                 uncheckedValue: false,

singlecell/resources/views/singleCellDataManagement.html

@@ -39,6 +39,9 @@
                     },{
                         name: 'Readsets Assigned to Run Lacking Data',
                         url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'sequence_readsets', 'query.viewName': 'Assigned to Run Lacking Data'})
+                    },{
+                        name: 'Analyses In Novogene-Related Workbook',
+                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'sequence_analyses', 'query.container/title~containsoneof': 'Novogene;shipment'})
                     }]
                 },{
                     header: 'Data Archival',

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

@@ -329,15 +329,5 @@ Ext4.define('SingleCell.panel.SingleCellProcessingPanel', {
 
         errors = Ext4.unique(errors);
         return errors;
-    },
-
-    applySavedValues: function(values){
-        this.callOverridden(arguments);
-
-        Ext4.Array.forEach(['submissionType', 'useOutputFileContainer'], function(val) {
-            if (values[val]) {
-                this.down('[name="' + val + '"]').setValue(values[val]);
-            }
-        }, this);
     }
 });