Update sequence barcode reverse_complement field automatically

Author: bbimber

SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.321-12.322.sql

@@ -0,0 +1 @@
+SELECT core.executeJavaUpgradeCode('updateBarcodeRC');

SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.321-12.322.sql

@@ -0,0 +1 @@
+SELECT core.executeJavaUpgradeCode('updateBarcodeRC');

SequenceAnalysis/resources/views/illuminaSampleSheetExport.html

@@ -14,7 +14,7 @@
              LABKEY.Filter.create('rowid', pks.join(';'), LABKEY.Filter.Types.EQUALS_ONE_OF)
          ],
          sort: 'rowid,barcode5,barcode3',
-         columns: 'rowid,name,barcode5,barcode3,barcode5/sequence,barcode3/sequence,platform,sampleid',
+         columns: 'rowid,name,barcode5,barcode3,barcode5/sequence,barcode5/reverse_complement,barcode3/sequence,platform,sampleid',
          scope: this,
          success: function(result){
              if(result && result.rows.length){

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

@@ -604,7 +604,7 @@ Ext4.define('SequenceAnalysis.panel.IlluminaSampleExportPanel', {
             ['Sample_Well', ''],
             ['Sample_Project', ''],
             ['I7_Index_ID', 'barcode5'],
-            ['index', 'barcode5/sequence'],
+            ['index', 'barcode5/reverse_complement'],
             ['I5_Index_ID', 'barcode3'],
             ['index2', 'barcode3/sequence'],
             ['Description', ''],

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

@@ -160,7 +160,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 12.321;
+        return 12.322;
     }
 
     @Override

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

@@ -3,19 +3,26 @@
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.log4j.Logger;
+import org.biojava3.core.sequence.DNASequence;
+import org.labkey.api.collections.CaseInsensitiveHashMap;
+import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.DeferredUpgrade;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.Table;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.data.UpgradeCode;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.module.ModuleContext;
+import org.labkey.api.query.FieldKey;
 import org.labkey.api.sequenceanalysis.RefNtSequenceModel;
 import org.labkey.api.util.PageFlowUtil;
 
 import java.io.File;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
@@ -177,4 +184,28 @@ public void appendSequenceLength(final ModuleContext moduleContext)
 
         SequenceAnalysisManager.get().apppendSequenceLength(moduleContext.getUpgradeUser(), _log);
     }
+
+    /** called at 12.321-12.322*/
+    @SuppressWarnings({"UnusedDeclaration"})
+    @DeferredUpgrade
+    public void updateBarcodeRC(final ModuleContext moduleContext)
+    {
+        TableInfo ti = SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_BARCODES);
+        TableSelector ts = new TableSelector(ti, PageFlowUtil.set("tag_name", "sequence"), new SimpleFilter(FieldKey.fromString("reverse_complement"), null, CompareType.ISBLANK), null);
+        if (ts.exists())
+        {
+            List<Map<String, Object>> toUpdate = new ArrayList<>();
+            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);
+            });
+
+            toUpdate.forEach(row -> {
+                Table.update(moduleContext.getUpgradeUser(), ti, row, row.get("tag_name"));
+            });
+        }
+    }
 }