Merge remaining SVN discvr19.1 changes (#9)

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/RefNtSequenceModel.java

@@ -30,7 +30,6 @@
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.files.FileContentService;
 import org.labkey.api.security.User;
-import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.util.MemTracker;
 import org.labkey.api.writer.PrintWriters;
 
@@ -75,6 +74,9 @@ public class RefNtSequenceModel implements Serializable
     private String _aliases;
     private String _comments;
     private Integer _seqLength;
+    private Date _datedisabled;
+    private String _disabledby;
+
     private String _container;
     private Integer _createdby;
     private Date _created;
@@ -365,6 +367,26 @@ public void setJobId(Integer jobId)
         _jobId = jobId;
     }
 
+    public Date getDatedisabled()
+    {
+        return _datedisabled;
+    }
+
+    public void setDatedisabled(Date datedisabled)
+    {
+        _datedisabled = datedisabled;
+    }
+
+    public String getDisabledby()
+    {
+        return _disabledby;
+    }
+
+    public void setDisabledby(String disabledby)
+    {
+        _disabledby = disabledby;
+    }
+
     public byte[] getSequenceBases()
     {
         if (_sequenceBytes == null)

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java

@@ -31,6 +31,7 @@
 import java.io.IOException;
 import java.util.Collection;
 import java.util.List;
+import java.util.Set;
 
 /**
  * User: bimber
@@ -92,4 +93,6 @@ static public void setInstance(SequenceAnalysisService instance)
     abstract public File writeAllCellHashingBarcodes(File webserverDir) throws PipelineJobException;
 
     abstract public String createReferenceLibrary(List<Integer> sequenceIds, Container c, User u, String name, String assemblyId, String description, boolean skipCacheIndexes, boolean skipTriggers) throws IOException;
+
+    abstract public String createReferenceLibrary(List<Integer> sequenceIds, Container c, User u, String name, String assemblyId, String description, boolean skipCacheIndexes, boolean skipTriggers, Set<GenomeTrigger> extraTriggers) throws IOException;
 }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AbstractAlignmentStepProvider.java

@@ -28,7 +28,7 @@
  * Date: 6/14/2014
  * Time: 2:44 PM
  */
-abstract public class AbstractAlignmentStepProvider<StepType extends AlignmentStep> extends AbstractPipelineStepProvider<StepType>
+abstract public class AbstractAlignmentStepProvider<StepType extends AlignmentStep> extends AbstractPipelineStepProvider<StepType> implements AlignmentStepProvider
 {
     public static String ALIGNMENT_MODE_PARAM = "alignmentMode";
     public static String SUPPORT_MERGED_UNALIGNED = "supportsMergeUnaligned";

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignmentStep.java

@@ -63,6 +63,9 @@ default boolean supportsMetrics()
 
     public boolean supportsGzipFastqs();
 
+    @Override
+    AlignmentStepProvider getProvider();
+
     default String getAlignmentDescription()
     {
         return "Aligner: " + getProvider().getName();

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignmentStepProvider.java

@@ -0,0 +1,9 @@
+package org.labkey.api.sequenceanalysis.pipeline;
+
+public interface AlignmentStepProvider extends PipelineStepProvider
+{
+    default boolean shouldRunIdxstats()
+    {
+        return true;
+    }
+}

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractAlignmentPipelineStep.java

@@ -0,0 +1,21 @@
+package org.labkey.api.sequenceanalysis.run;
+
+import org.labkey.api.sequenceanalysis.pipeline.AlignmentStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+
+abstract public class AbstractAlignmentPipelineStep<Wrapper extends CommandWrapper> extends AbstractCommandPipelineStep<Wrapper>
+{
+    private AlignmentStepProvider _provider;
+
+    public AbstractAlignmentPipelineStep(AlignmentStepProvider provider, PipelineContext ctx, Wrapper wrapper)
+    {
+        super(provider, ctx, wrapper);
+        _provider = provider;
+    }
+
+    @Override
+    public AlignmentStepProvider getProvider()
+    {
+        return _provider;
+    }
+}

SequenceAnalysis/resources/external/scRNAseq/seuratWrapper.sh

@@ -19,7 +19,7 @@ if [ ! -z $SEQUENCEANALYSIS_MAX_RAM ];then
 fi
 
 if [ ! -z SEQUENCEANALYSIS_MAX_THREADS ];then
-    ENV_OPTS=${ENV_OPTS}" -e SEQUENCEANALYSIS_MAX_THREADS"
+    ENV_OPTS=${ENV_OPTS}" -e SEQUENCEANALYSIS_MAX_THREADS="${SEQUENCEANALYSIS_MAX_THREADS}
 fi
 
 sudo $DOCKER pull bimberlab/oosap

SequenceAnalysis/resources/views/variantProcessing.view.xml

@@ -9,5 +9,6 @@
 
 
         <dependency path="SequenceAnalysis/window/SaveAnalysisAsTemplateWindow.js"/>
+        <dependency path="ux/ItemSelector/MultiSelect.js"/>
     </dependencies>
 </view>

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

@@ -228,6 +228,95 @@ Ext4.define('SequenceAnalysis.panel.VariantProcessingPanel', {
             }]
         }];
 
+		var ddGroup = Ext4.id() + '-dd';
+		results.variantMerging = [{
+			description: 'This will run GATK\'s CombineVariants on the set of VCF files',
+			label: 'Merge Variants',
+			name: 'CombineVCFs',
+			parameters: [{
+				fieldXtype: 'checkbox',
+				name: 'doCombine',
+				label: 'Combine VCFs Prior To Processing',
+				description: 'If checked, the VCFs will be merged into a single VCF before processing.',
+				defaultValue: false,
+				additionalExtConfig: {
+					listeners: {
+						change: function (field, val) {
+							val = !!val;
+
+							var field1 = field.up('panel').down('textfield');
+							var field2 = field.up('panel').down('multiselect');
+							var field3 = field.up('panel').down('hidden');
+
+							field1.isToolParam = val;
+							field1.allowBlank = !val;
+
+							field2.isToolParam = val;
+							field3.isToolParam = val;
+
+							field1.setVisible(val);
+							field2.setVisible(val);
+						}
+					}
+				}
+			},{
+				fieldXtype: 'textfield',
+				name: 'fileBaseName',
+				label: 'Filename',
+				description: 'This is the basename that will be used for the output gzipped VCF',
+				commandLineParam: false,
+				additionalExtConfig: {
+					hidden: true,
+					isToolParam: false,
+					width: 500,
+					allowBlank: true //toggle value based on checkbox
+				},
+				defaultValue: null
+			},{
+				fieldXtype: 'hidden',
+				name: 'doSplitJobs',
+				label: 'Split Jobs',
+				description: 'If combine is selected, jobs should not be split',
+				commandLineParam: false,
+				additionalExtConfig: {
+					hidden: true,
+					isToolParam: false,
+					name: 'doSplitJobs',  //override the more specific name auto-assigned
+					getToolParameterValue: function(){
+						var ret = this.getValue();
+
+						return ret ? JSON.parse(ret) : ret;
+					}
+				},
+				defaultValue: false
+			},{
+				name: 'priority',
+				fieldXtype: 'multiselect',
+				additionalExtConfig: {
+					hidden: true,
+					isToolParam: false,
+					store: this.outputFileStore,
+					fieldLabel: 'Merge Priority Order',
+					style: 'padding: 10px;padding-bottom: 30px;',
+					border: true,
+					width: 500,
+					autoScroll: true,
+					helpPopup: 'This is the priority order in which files will be merged, top being highest priority',
+					displayField: 'name',
+					valueField: 'rowid',
+					multiSelect: false,
+					dragGroup: ddGroup,
+					dropGroup: ddGroup,
+					getToolParameterValue: function(){
+						var val = this.setupValue(this.store.getRange());
+						val = val == null ? null : val.join(this.delimiter);
+
+						return val;
+					}
+				}
+			}]
+		}];
+
 		var items = [];
         if (this.showGenotypeGVCFs){
             items.push({
@@ -239,6 +328,18 @@ Ext4.define('SequenceAnalysis.panel.VariantProcessingPanel', {
                 toolConfig: results
             })
         }
+        else {
+			items.push({
+				xtype: 'sequenceanalysis-analysissectionpanel',
+				title: 'Merge VCFs',
+				stepType: 'variantMerging',
+				singleTool: false,
+				toolIdx: 0,
+				sectionDescription: 'This section allows you to optionally merge the input VCFs prior to processing',
+				toolConfig: results
+			})
+		}
+
 		items.push({
 			xtype: 'sequenceanalysis-analysissectionpanel',
 			title: 'Variant Preprocessing',
@@ -277,14 +378,20 @@ Ext4.define('SequenceAnalysis.panel.VariantProcessingPanel', {
 		}
 
 		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)) {
+			console.log('split jobs set');
+			json.doSplitJobs = !!values.doSplitJobs;
+		}
 
 		LABKEY.Ajax.request({
 			url: LABKEY.ActionURL.buildURL('sequenceanalysis', 'runSequenceHandler'),
-			jsonData: {
-				handlerClass: 'org.labkey.sequenceanalysis.' + (this.showGenotypeGVCFs ? 'analysis.GenotypeGVCFHandler' : 'pipeline.ProcessVariantsHandler'),
-				outputFileIds: this.outputFileIds,
-				params: Ext4.encode(values)
-			},
+			jsonData: json,
 			scope: this,
 			success: function(){
 				Ext4.Msg.hide();

SequenceAnalysis/resources/web/SequenceAnalysis/sequenceanalysisButtons.js

@@ -321,7 +321,7 @@ SequenceAnalysis.Buttons = new function(){
                 dataRegionSelectionKey: 'query',
                 '.select': checked,
                 returnURL: window.location.pathname + window.location.search
-            }, 'GET');
+            });
         },
 
         goToAction: function(href, params, method){