Allow user to insert tool steps to either beginning or end of tool chain (#147)

* Allow user to insert tool steps to either beginning or end of tool chain
* Allow additional values to be saved in singlecell templates

Author: bbimber

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

@@ -128,7 +128,27 @@ Ext4.define('SequenceAnalysis.panel.AnalysisSectionPanel', {
 
             items.push({
                 xtype: 'ldk-linkbutton',
-                text: 'Add',
+                text: 'Add to Start',
+                linkCls: 'labkey-text-link',
+                step: step,
+                handler: function(btn){
+                    var win = btn.up('window');
+                    var owner = win.ownerPanel;
+                    var target = owner.down('#toolConfgPanel');
+
+                    //check if exists
+                    if (!owner.allowDuplicateSteps && target.down('[stepName=' + btn.step.name + ']')) {
+                        Ext4.Msg.alert('Already Added', 'This step has already been added and cannot be used twice.');
+                    }
+                    else {
+                        target.insert(0, owner.getAbbreviatedConfigForItem(btn.step));
+                    }
+                }
+            });
+
+            items.push({
+                xtype: 'ldk-linkbutton',
+                text: 'Add to End',
                 linkCls: 'labkey-text-link',
                 step: step,
                 handler: function(btn){
@@ -144,7 +164,7 @@ Ext4.define('SequenceAnalysis.panel.AnalysisSectionPanel', {
                         target.add(owner.getAbbreviatedConfigForItem(btn.step));
                     }
                 }
-            })
+            });
         }, this);
 
         if (items.length){
@@ -161,7 +181,7 @@ Ext4.define('SequenceAnalysis.panel.AnalysisSectionPanel', {
                 },
                 layout: {
                     type: 'table',
-                    columns: 3
+                    columns: 4
                 },
                 items: items
             }];

SequenceAnalysis/test/src/org/labkey/test/tests/external/labModules/SequenceTest.java

@@ -535,7 +535,7 @@ private void analysisPanelTest() throws Exception
         new Window.WindowFinder(getDriver()).withTitle("Tool Details").waitFor();
         waitAndClick(Ext4Helper.Locators.window("Tool Details").append(Ext4Helper.Locators.ext4Button("Done")));
 
-        List<Ext4CmpRef> btns = _ext4Helper.componentQuery("window ldk-linkbutton[text='Add']", Ext4CmpRef.class);
+        List<Ext4CmpRef> btns = _ext4Helper.componentQuery("window ldk-linkbutton[text='Add to End']", Ext4CmpRef.class);
         for (Ext4CmpRef btn : btns)
         {
             waitAndClick(Locator.id(btn.getId()).append(Locator.tag("a")));
@@ -783,7 +783,7 @@ private void alignmentImportPanelTest(boolean sequencePipelineEnabled) throws Ex
         waitForElement(win);
 
         //NOTE: team city is getting JS errors I cant repro locally.  adding sleep() to see if waiting helps
-        List<Ext4CmpRef> btns = _ext4Helper.componentQuery("window ldk-linkbutton[text='Add']", Ext4CmpRef.class);
+        List<Ext4CmpRef> btns = _ext4Helper.componentQuery("window ldk-linkbutton[text='Add to End']", Ext4CmpRef.class);
         for (Ext4CmpRef btn : btns)
         {
             // Note: BQSR includes a genome selector field, which will log a warning to the server is a genome isnt configured ahead of time.

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

@@ -328,5 +328,15 @@ 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);
     }
 });