Ensure checkbox values included in JSON even if unchecked

Author: bbimber

.github/workflows/build_latest.yml

@@ -40,5 +40,5 @@ jobs:
           repo_token: "${{ secrets.PAT }}"
           automatic_release_tag: "latest"
           prerelease: true
-          title: "DISCVR Development Build: ${{ fromJson(steps.get_default_branch.outputs.data).default_branch }}"
+          title: "Development Build: ${{ fromJson(steps.get_default_branch.outputs.data).default_branch }}"
           files: /home/runner/work/_temp/_github_home/lkDist/discvr/DISCVR-*

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

@@ -255,8 +255,8 @@ Ext4.define('SequenceAnalysis.panel.SequenceAnalysisPanel', {
             version: 2
         };
 
-        //first add the general params
-        Ext4.apply(json, this.down('#runInformation').getForm().getFieldValues());
+        //first add the general params. Note: include all to ensure we include unchecked checkboxes. Using useDataValues=false to ensure we get the string-serialized value
+        Ext4.apply(json, this.down('#runInformation').getForm().getValues(false, false, false, false));
 
         json['alignment.doAlignment'] = this.down('#doAlignment').getValue();
 
@@ -305,13 +305,15 @@ Ext4.define('SequenceAnalysis.panel.SequenceAnalysisPanel', {
                 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.',
                 name: 'deleteIntermediateFiles',
                 inputValue: true,
+                uncheckedValue: false,
                 checked: true,
                 xtype: 'checkbox'
             },{
                 fieldLabel: 'Copy Inputs To Working Directory?',
                 helpPopup: 'Check to copy the input files to the working directory.  Depending on your environment, this may or may not help performance.',
                 name: 'copyInputsLocally',
                 inputValue: true,
+                uncheckedValue: false,
                 checked: false,
                 xtype: 'checkbox'
             }, this.getSaveTemplateCfg(),{
@@ -320,6 +322,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceAnalysisPanel', {
                 hidden: !LABKEY.Security.currentUser.isAdmin,
                 name: 'submitJobToReadsetContainer',
                 inputValue: true,
+                uncheckedValue: false,
                 checked: false,
                 xtype: 'checkbox'
             }]

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

@@ -407,12 +407,11 @@ Ext4.define('SequenceAnalysis.panel.VariantProcessingPanel', {
 			return;
 		}
 
-		Ext4.Msg.wait('Submitting...');
 		var json = {
 			handlerClass: 'org.labkey.sequenceanalysis.' + (this.showGenotypeGVCFs ? 'analysis.GenotypeGVCFHandler' : 'pipeline.ProcessVariantsHandler'),
 			outputFileIds: this.outputFileIds,
 			params: Ext4.encode(values)
-		}
+		};
 
 		if (Ext4.isDefined(values.doSplitJobs)) {
 			json.doSplitJobs = !!values.doSplitJobs;
@@ -441,6 +440,7 @@ Ext4.define('SequenceAnalysis.panel.VariantProcessingPanel', {
 			}
 		}
 
+		Ext4.Msg.wait('Submitting...');
 		LABKEY.Ajax.request({
 			url: LABKEY.ActionURL.buildURL('sequenceanalysis', actionName),
 			jsonData: json,
@@ -465,8 +465,8 @@ Ext4.define('SequenceAnalysis.panel.VariantProcessingPanel', {
 			version: 2
 		};
 
-		//first add the general params
-		Ext4.apply(json, this.down('#runInformation').getForm().getFieldValues());
+		//first add the general params. Note: include all to ensure we include unchecked checkboxes. Using useDataValues=false to ensure we get the string-serialized value
+		Ext4.apply(json, this.down('#runInformation').getForm().getValues(false, false, false, false));
 
 		//then append each section
 		var sections = this.query('sequenceanalysis-analysissectionpanel');

SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantScatterGatherPanel.js

@@ -61,6 +61,7 @@ Ext4.define('SequenceAnalysis.panel.VariantScatterGatherPanel', {
                                 name: 'scatterGather.allowSplitChromosomes',
                                 fieldLabel: 'Allow Split Contigs',
                                 value: true,
+                                uncheckedValue: false,
                                 inputValue: true,
                                 helpPopup: 'If true, a given chromosome/contig can be split between jobs.  Otherwise chromosomes are always intact across jobs.'
                             });

SequenceAnalysis/resources/web/SequenceAnalysis/window/OutputHandlerWindow.js

@@ -250,7 +250,7 @@ Ext4.define('SequenceAnalysis.window.OutputHandlerWindow', {
             return;
         }
 
-        //Note: include all to ensure we include unchecked checkboxes
+        //Note: include all to ensure we include unchecked checkboxes. Using useDataValues=false to ensure we get the string-serialized value
         var params = this.down('form').getForm().getValues(false, false, false, false);
         var json = {
             handlerType: this.handlerType,