Fix merge conflicts

Author: bbimber

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

@@ -101,26 +101,31 @@ public List<SequenceOutput> getSequenceOutputs()
         return Collections.unmodifiableList(_sequenceOutputs);
     }
 
+    @Override
     public void addSequenceOutput(File file, String label, String category, @Nullable Integer readsetId, @Nullable Integer analysisId, @Nullable Integer genomeId, @Nullable String description)
     {
         _sequenceOutputs.add(new SequenceOutput(file, label, category, readsetId, analysisId, genomeId, description));
     }
 
+    @Override
     public void addInput(File input, String role)
     {
         _inputs.add(Pair.of(input, role));
     }
 
+    @Override
     public void addOutput(File output, String role)
     {
         _outputs.add(Pair.of(output, role));
     }
 
+    @Override
     public void addIntermediateFile(File file)
     {
         addIntermediateFile(file, null);
     }
 
+    @Override
     public void addIntermediateFile(File file, String role)
     {
         if (role != null)
@@ -136,6 +141,11 @@ public void addPicardMetricsFile(Readset rs, File metricFile, File inputFile)
 
     public void addPicardMetricsFile(Readset rs, File metricFile, PicardMetricsOutput.TYPE type)
     {
+        if (!metricFile.exists())
+        {
+            throw new IllegalArgumentException("File does not exist: " + metricFile.getPath());
+        }
+
         _picardMetricsFiles.add(new PipelineStepOutput.PicardMetricsOutput(metricFile, type, rs.getRowId()));
     }
 

SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.322-12.323.sql

@@ -0,0 +1,20 @@
+UPDATE sequenceanalysis.quality_metrics SET metricname = 'Mean Read Length' WHERE metricname = 'Avg Read Length';
+
+UPDATE sequenceanalysis.quality_metrics SET category = 'Readset' WHERE category IS NULL and metricname IN (
+  'Total Reads',
+  'Min Read Length',
+  'Max Read Length',
+  'Mean Read Length',
+  'Total Bases',
+  'Total MBases',
+  'Total GBases',
+  'Total Q10 Bases',
+  'Total Q20 Bases',
+  'Total Q30 Bases',
+  'Total Q40 Bases',
+  'Pct Q10',
+  'Pct Q20',
+  'Pct Q30',
+  'Pct Q40'
+);
+

SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.322-12.323.sql

@@ -0,0 +1,20 @@
+UPDATE sequenceanalysis.quality_metrics SET metricname = 'Mean Read Length' WHERE metricname = 'Avg Read Length';
+
+UPDATE sequenceanalysis.quality_metrics SET category = 'Readset' WHERE category IS NULL and metricname IN (
+  'Total Reads',
+  'Min Read Length',
+  'Max Read Length',
+  'Mean Read Length',
+  'Total Bases',
+  'Total MBases',
+  'Total GBases',
+  'Total Q10 Bases',
+  'Total Q20 Bases',
+  'Total Q30 Bases',
+  'Total Q40 Bases',
+  'Pct Q10',
+  'Pct Q20',
+  'Pct Q30',
+  'Pct Q40'
+);
+

SequenceAnalysis/resources/schemas/sequenceanalysis.xml

@@ -1177,7 +1177,7 @@
                 <isHidden>true</isHidden>
             </column>
             <column columnName="instrument_run_id">
-                <columnTitle>Instrument Run</columnTitle>
+                <columnTitle>Batch/Run</columnTitle>
                 <fk>
                     <fkDbSchema>sequenceanalysis</fkDbSchema>
                     <fkTable>instrument_runs</fkTable>

SequenceAnalysis/resources/views/sequenceAnalysisDetails.html

@@ -17,6 +17,7 @@
             '<div style="margin-bottom: 10px;"></div>' +
             //'<div id="analysisNav_'+webpart.wrapperDivId+'"></div>' +
             //'<br>' +
+            '<div id="outputs_'+webpart.wrapperDivId+'"></div>' +
             '<div id="qualityMetrics_'+webpart.wrapperDivId+'"></div>' +
             '<div style="margin-bottom: 10px;"></div>' +
             '<div id="readsetDiv_'+webpart.wrapperDivId+'"/>'
@@ -52,6 +53,15 @@
         successCallback: onSuccess
     });
 
+    LDK.Utils.getReadOnlyQWP({
+        title: 'Outputs',
+        schemaName: 'sequenceanalysis',
+        queryName: 'outputfiles',
+        maxRows: 20,
+        containerPath: Laboratory.Utils.getQueryContainerPath(),
+        filterArray: [LABKEY.Filter.create('analysis_id', analysisId, LABKEY.Filter.Types.EQUAL)]
+    }).render('outputs_'+webpart.wrapperDivId);
+
     LDK.Utils.getReadOnlyQWP({
         title: 'Quality Metrics',
         schemaName: 'sequenceanalysis',

SequenceAnalysis/resources/web/SequenceAnalysis/panel/IlluminaSampleExportPanel.js

@@ -99,25 +99,30 @@ Ext4.define('SequenceAnalysis.panel.IlluminaSampleExportPanel', {
                         allowBlank: false,
                         displayField: 'name',
                         valueField: 'name',
+                        value: 'FASTQ Only',
                         store: Ext4.create('LABKEY.ext4.data.Store', {
                             schemaName: 'sequenceanalysis',
                             queryName: 'illumina_applications',
                             columns: '*',
                             autoLoad: true,
                             listeners: {
+                                scope: this,
                                 load: function(store){
                                     var rec = LDK.StoreUtils.createModelInstance(store, {
                                         name: 'Custom'
                                     });
                                     store.add(rec);
+
+                                    var field = this.down('#application');
+                                    field.fireEvent('change', field, field.getValue());
                                 }
                             }
                         }),
                         listeners: {
                             scope: this,
                             change: function(field, val){
                                 var kitField = field.up('panel').down('#sampleKit');
-                                if (!val || val == 'Custom'){
+                                if (!val || val === 'Custom'){
                                     kitField.setDisabled(true);
                                     return;
                                 }
@@ -171,6 +176,12 @@ Ext4.define('SequenceAnalysis.panel.IlluminaSampleExportPanel', {
                         helpPopup: 'Leave blank for single-end reads',
                         itemId: 'cycles2',
                         fieldLabel: 'Cycles Read 2'
+                    },{
+                        xtype: 'checkbox',
+                        itemId: 'nameUsingRowId',
+                        fieldLabel: 'Name FASTA Using Row Id',
+                        value: true,
+                        helpPopup: 'If checked, the FASTQs will be named using the numeric rowId, which can make import more automatic.  If unchecked, they will be named using readset name.'
                     },{
                         xtype: 'combo',
                         itemId: 'genomeFolder',
@@ -591,6 +602,7 @@ Ext4.define('SequenceAnalysis.panel.IlluminaSampleExportPanel', {
 
         var genomeFolder = '';
         var genomeField = this.down('#genomeFolder');
+        var nameUsingRowId = this.down('#nameUsingRowId').getValue();
         if (genomeField.getValue()){
             var recIdx = genomeField.store.find(genomeField.valueField, genomeField.getValue());
             var rec = genomeField.store.getAt(recIdx);
@@ -599,7 +611,7 @@ Ext4.define('SequenceAnalysis.panel.IlluminaSampleExportPanel', {
 
         var sampleColumns = [
             ['Sample_ID', 'rowid'],
-            ['Sample_Name', 'name'],
+            ['Sample_Name', 'name', function(row) { return nameUsingRowId ? 's_' + row.rowid : row.name; }],
             ['Sample_Plate', ''],
             ['Sample_Well', ''],
             ['Sample_Project', ''],
@@ -621,7 +633,13 @@ Ext4.define('SequenceAnalysis.panel.IlluminaSampleExportPanel', {
             var toAdd = [];
             Ext4.each(sampleColumns, function(col){
                 if (col.length > 2){
-                    toAdd.push(col[2]);
+                    if (Ext4.isFunction(col[2])) {
+                        toAdd.push(col[2](row));
+                    }
+                    else {
+                        toAdd.push(col[2]);
+                    }
+
                 }
                 else {
                     toAdd.push(row[col[1]]);

SequenceAnalysis/resources/web/SequenceAnalysis/panel/SequenceImportPanel.js

@@ -2335,8 +2335,8 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                         }).show(btn);
                     }
                 }, {
-                    text: 'Assign To Instrument Run',
-                    tooltip: 'Click to assign the selected rows to an existing or new instrument run',
+                    text: 'Assign To Instrument Run/Batch',
+                    tooltip: 'Click to assign the selected rows to an existing or new instrument run or batch',
                     scope: this,
                     handler: function (btn) {
                         var grid = btn.up('grid');

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java

@@ -342,6 +342,7 @@ private void processContainer(Container c, Logger log) throws IOException
                     if (!d.getFile().exists())
                     {
                         log.error("expected output file does not exist: " + d.getFile().getPath());
+                        continue;
                     }
 
                     //also verify indexes

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java

@@ -161,7 +161,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 12.322;
+        return 12.323;
     }
 
     @Override

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisUpgradeCode.java

@@ -2,8 +2,9 @@
 
 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.apache.logging.log4j.Logger;
+import org.biojava3.core.exceptions.CompoundNotFoundError;
 import org.biojava3.core.sequence.DNASequence;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.CompareType;
@@ -199,9 +200,28 @@ public void updateBarcodeRC(final ModuleContext moduleContext)
             ts.forEachResults(rs -> {
                 Map<String, Object> r = new CaseInsensitiveHashMap<>();
                 r.put("tag_name", rs.getString(FieldKey.fromString("tag_name")));
-                DNASequence seq = new DNASequence(rs.getString(FieldKey.fromString("sequence")));
-                r.put("reverse_complement", seq.getReverseComplement().getSequenceAsString());
-                toUpdate.add(r);
+                if (StringUtils.isEmpty(rs.getString(FieldKey.fromString("sequence"))))
+                {
+                    return;
+                }
+
+                try
+                {
+                    String[] sequences = rs.getString(FieldKey.fromString("sequence")).split(",");
+                    List<String> rcs = new ArrayList<>();
+                    for (String s : sequences)
+                    {
+                        DNASequence seq = new DNASequence(s);
+                        rcs.add(seq.getReverseComplement().getSequenceAsString());
+                    }
+
+                    r.put("reverse_complement", StringUtils.join(rcs, ","));
+                    toUpdate.add(r);
+                }
+                catch (CompoundNotFoundError e)
+                {
+                    _log.error("Unable to reverse complement barcode: " + rs.getString(FieldKey.fromString("sequence")), e);
+                }
             });
 
             toUpdate.forEach(row -> {