Add check to prevent STAR submission without GTF unless specifically chosen

Author: bbimber

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

@@ -50,7 +50,7 @@ Ext4.define('SequenceAnalysis.panel.AnalysisSectionPanel', {
                         var val = i.additionalExtConfig[prop];
                         if (Ext4.isString(val) && val.match(/^js:/)){
                             val = val.replace(/^js:/, '');
-                            val = eval(val);
+                            val = eval("false || " + val);
 
                             i.additionalExtConfig[prop] = val;
                         }

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

@@ -161,7 +161,7 @@ Ext4.define('SequenceAnalysis.window.OutputHandlerWindow', {
                         var val = i.additionalExtConfig[prop];
                         if (Ext4.isString(val) && val.match(/^js:/)){
                             val = val.replace(/^js:/, '');
-                            val = eval(val);
+                            val = eval("false || " + val);
 
                             i.additionalExtConfig[prop] = val;
                         }

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/StarWrapper.java

@@ -213,6 +213,10 @@ public AlignmentOutput performAlignment(Readset rs, File inputFastq1, @Nullable
                 args.add("--quantMode");
                 args.add("GeneCounts");
             }
+            else
+            {
+                getPipelineCtx().getLogger().info("No GTF was provided, so gene counts will not be created");
+            }
 
             addThreadArgs(args);
             getWrapper().execute(args);
@@ -432,7 +436,11 @@ public Provider()
                     put("extensions", Arrays.asList("gtf", "gff"));
                     put("width", 400);
                     put("allowBlank", true);
+                    put("getErrors", "js:function(){var errors = [];var val = this.getValue();var gtfField = this.up('panel').down('field[name=\"alignment.STAR.generateCounts\"]');if (gtfField && gtfField.getValue()) { errors.push('Must select a GTF when Generate Counts is selected') } return errors;}");
                 }}, null),
+                ToolParameterDescriptor.create("generateCounts", "Generate Counts", "There are rare cases when STAR is used without a GTF, so this field is not required.  If that field is left blank, counts are not generated.  Checking this field prevents job submission unless a GTF is provided.  Uncheck to allow running without a GTF.", "checkbox", new JSONObject(){{
+                    put("checked", true);
+                }}, false),
                 ToolParameterDescriptor.create(LONG_READS, "Reads >500bp", "If the reads are expected to exceed 500bp (per pair), this will use STARlong instead of STAR.", "checkbox", new JSONObject(){{
                     put("checked", false);
                 }}, false),