Changeset 5475

Timestamp:

Jun 5, 2019, 4:21:22 PM (4 years ago)

Author:

Nicklas Nordborg

Message:

References #1142: Create MIPs flow cell and start sequencing

The "Auto-analyze" option should now work for HiSeq. It has not been tested fully. If it works it will most likely try to start a RNAseq demux so it will probably fail soon after that.

Location:

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie

Files:

• extensions/HiSeqSignalHandler.java (added)
• extensions/NextSeqSignalHandler.java (modified) (1 diff)
• extensions/ReggieSignalHandlerFactory.java (modified) (1 diff)
• servlet/SequencingRunServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/extensions/NextSeqSignalHandler.java

@@ -205 +205 @@
             numLanes = Values.getInt(value);
           }
-          else if ("Read1".equals(key) || "Read2".equals(key) || "Index1Read".equals(key))
+          else if ("Read1".equals(key) || "Read2".equals(key) || "Index1Read".equals(key) || "Index2Read".equals(key))
           {
             numReads += Values.getInt(value);

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/extensions/ReggieSignalHandlerFactory.java

@@ -78 +78 @@
       handlers = new SignalHandler[] { new NextSeqSignalHandler(job) };
     }
+    else if ("HiSeq".equals(signalType))
+    {
+      handlers = new SignalHandler[] { new HiSeqSignalHandler(job) };
+    }
     
     return handlers;

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/SequencingRunServlet.java

@@ -62 +62 @@
 import net.sf.basedb.reggie.dao.SequencingRun;
 import net.sf.basedb.reggie.dao.Subtype;
+import net.sf.basedb.reggie.extensions.HiSeqSignalHandler;
 import net.sf.basedb.reggie.extensions.NextSeqSignalHandler;
 import net.sf.basedb.reggie.grid.ScriptUtil;
@@ -386 +387 @@
         Annotationtype.CLUSTER_START.setAnnotationValue(dc, flowCell, startDate);
         Annotationtype.FLOWCELL_ID.setAnnotationValue(dc, flowCell, flowCellBarcode);
+        String flowCellType = (String)Annotationtype.FLOWCELL_TYPE.getAnnotationValue(dc, flowCell);
         
         // Load pool aliquots for all lanes and set creation date
@@ -455 +457 @@
             job.setExternalId(flowCellBarcode);
             
-            // TODO - Add support for HiSeq
-            String signalURI = NextSeqSignalHandler.getSignalUri(flowCellBarcode);
+            String signalURI = "HiSeq".equals(flowCellType) ? 
+              HiSeqSignalHandler.getSignalUri(flowCellBarcode) :
+              NextSeqSignalHandler.getSignalUri(flowCellBarcode);
             job.setSignalTransporter(ExtensionSignalTransporter.class, signalURI);