Merge pull request #152 from BimberLab/22.3_fb_merge

Merge discvr-21.11 to discvr-22.3

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/model/ReadData.java

@@ -56,6 +56,8 @@ public interface ReadData extends Serializable
 
     public Integer getModifiedBy();
 
+    public Integer getTotalReads();
+
     public String getSra_accession();
 
     public boolean isArchived();

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

@@ -83,6 +83,11 @@ public interface PipelineStepProvider<StepType extends PipelineStep>
      */
     public ToolParameterDescriptor getParameterByName(String name);
 
+    default boolean hasParameter(String name)
+    {
+        return getParameterByName(name) != null;
+    }
+
     /**
      * Creates the JSON object sent to the client that is used to build the client UI
      */

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

@@ -4,7 +4,6 @@
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.PipelineJobService;
@@ -30,6 +29,11 @@ public SamSorter(@Nullable Logger logger)
     }
 
     public File execute(File input, @Nullable File output, SAMFileHeader.SortOrder sortOrder) throws PipelineJobException
+    {
+        return execute(input, output, sortOrder, null);
+    }
+
+    public File execute(File input, @Nullable File output, SAMFileHeader.SortOrder sortOrder, @Nullable List<String> extraArgs) throws PipelineJobException
     {
         getLogger().info("Sorting SAM/BAM: " + input.getPath());
 
@@ -50,7 +54,7 @@ public File execute(File input, @Nullable File output, SAMFileHeader.SortOrder s
         }
         else if (sortOrder != SAMFileHeader.SortOrder.coordinate)
         {
-            throw new PipelineJobException("Improper sort order: " + sortOrder.name());
+            getLogger().debug("Using sort order: " + sortOrder.name());
         }
 
         Integer threads = SequencePipelineService.get().getMaxThreads(getLogger());
@@ -71,6 +75,11 @@ else if (sortOrder != SAMFileHeader.SortOrder.coordinate)
         params.add("-T");
         params.add(tmpDir);
 
+        if (extraArgs != null)
+        {
+            params.addAll(extraArgs);
+        }
+
         params.add("-o");
         params.add(output.getPath());
 

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

@@ -65,6 +65,11 @@ public Class getProcessorClass()
 
     public String getName();
 
+    default String getAnalysisType(PipelineJob job)
+    {
+        return getName();
+    }
+
     public String getDescription();
 
     /**

SequenceAnalysis/resources/queries/sequenceanalysis/outputfiles.js

@@ -14,3 +14,17 @@ function beforeDelete(row, errors){
         errors._form = 'You cannot directly delete analyses.  To delete these records, use the delete button above the analysis grid.';
     }
 }
+
+function beforeInsert(row, errors){
+    beforeUpsert(row, errors);
+}
+
+function beforeUpdate(row, errors){
+    beforeUpsert(row, errors);
+}
+
+function beforeUpsert(row, errors) {
+    if (row.dataid && typeof row.dataid == 'string') {
+        row.dataid = triggerHelper.createExpData(row.dataid);
+    }
+}

SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.328-12.329.sql

@@ -0,0 +1,19 @@
+CREATE INDEX IDX_asj_status_container_alignment_id_ref_nt_id ON sequenceanalysis.alignment_summary_junction (
+	status ASC,
+	container ASC,
+	alignment_id ASC,
+	ref_nt_id ASC
+);
+
+CREATE INDEX IDX_readData_readset ON sequenceanalysis.readData (
+	readset ASC
+)
+INCLUDE(fileid1, fileid2, runid);
+
+CREATE INDEX IDX_quality_metrics_metricname_dataid_readset ON sequenceanalysis.quality_metrics (
+	metricName ASC,
+	dataId ASC,
+	readset ASC
+)
+INCLUDE(metricValue);
+

SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.328-12.329.sql

@@ -0,0 +1,19 @@
+CREATE NONCLUSTERED INDEX IDX_asj_status_container_alignment_id_ref_nt_id ON sequenceanalysis.alignment_summary_junction (
+	status ASC,
+	container ASC,
+	alignment_id ASC,
+	ref_nt_id ASC
+);
+
+CREATE NONCLUSTERED INDEX IDX_readData_readset ON sequenceanalysis.readData (
+	readset ASC
+)
+INCLUDE(fileid1, fileid2, runid);
+
+CREATE NONCLUSTERED INDEX IDX_quality_metrics_metricname_dataid_readset ON sequenceanalysis.quality_metrics (
+	metricName ASC,
+	dataId ASC,
+	readset ASC
+)
+INCLUDE(metricValue);
+

SequenceAnalysis/resources/web/SequenceAnalysis/Utils.js

@@ -137,7 +137,7 @@ SequenceAnalysis.Utils = new function(){
                     exonPosition = nt_position - startNT + exon[0];
                     nt_positions.push(exonPosition);
                     exons.push(idx);
-                    if(nt_positions.length == 3)
+                    if(nt_positions.length === 3)
                         return false;  //jump to next exon
 
                     nt_position++;
@@ -152,6 +152,22 @@ SequenceAnalysis.Utils = new function(){
                 nt_positions: nt_positions,
                 exons: exons
             };
+        },
+
+        // https://github.com/overset/javascript-natural-sort/blob/master/naturalSort.js
+        naturalSortFn: function(o1, o2){
+            o1 = SequenceAnalysis.Utils.getNaturalSortValue(o1);
+            o2 = SequenceAnalysis.Utils.getNaturalSortValue(o2);
+
+            if (o1 === o2) {
+                return 0;
+            }
+
+            return o1 < o2 ? -1 : 1;
+        },
+
+        getNaturalSortValue: function(value) {
+            return value ? value.replace(/(\d+)/g, "0000000000$1").replace(/0*(\d{10,})/g, "$1") : value;
         }
     }
 }

SequenceAnalysis/resources/web/SequenceAnalysis/field/SequenceOutputFileSelectorField.js

@@ -49,7 +49,7 @@ Ext4.define('SequenceAnalysis.field.SequenceOutputFileSelectorField', {
                     }
                 }
                 else {
-                    LDK.Utils.logError('unable to find library field in GenomeFileSelectorField');
+                    LDK.Utils.logError('unable to find library field in SequenceOutputFileSelectorField');
                 }
             }
             else if (window && window.libraryId){

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
             }];