Changes due to modifications of Illumina bcl2fastq 2.17.1.14

- changed the split char of dual-indexed runs to "+"
- ignore additional undetermined statistics added to the XML (ours is complete)

SVN: 34359

deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read-demultiplex-stats-nextseq.py

@@ -46,6 +46,8 @@ def process(transaction):
   CODE_INDEX2 = 'INDEX2'
   CODE_INDEX1LENGTH = 'INDEXREAD'
   CODE_INDEX2LENGTH = 'INDEXREAD2'
+  BARCODE_SPLIT_CHAR = "+"
+
 
   ##########################################################
   def locate(pattern, root):
@@ -287,7 +289,7 @@ def process(transaction):
     print "Connection to openBIS:"
 
     # Prepare link between XML and openBIS w.r.t to indexes in Barcode (XML):
-    indexes = s.Barcode.split("-")
+    indexes = s.Barcode.split(BARCODE_SPLIT_CHAR)
     if len(indexes) == 1: # only first part in Barcode
       index1search = indexes[0].upper()
       index2search = INDEX_EMPTY

deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read_demultiplex_stats.java

@@ -115,8 +115,7 @@ public final class read_demultiplex_stats
             if (event != XMLStreamConstants.START_ELEMENT || !xmlparser.getLocalName().equals("Stats"))
             {
                 errormessage =
-                        "STRANGE ERROR IN METHOD importXMLdata_and_calculateStatistics WHEN READING IN XMLFILE. => CHECK CODE AND XMLFILE-STRUCTURE!";
-                //System.out.println(errormessage);
+                        "STRANGE ERROR IN METHOD importXMLdata_and_calculateStatistics WHEN READING IN XMLFILE. => CHECK CODE AND XMLFILE-STRUCTURE! Got " + event;
                 throw new Exception(errormessage);
             }
             //System.out.println("\nStart-Element with tag " + xmlparser.getLocalName() + " with " + xmlparser.getAttributeCount() + " attributes with first attribute: " + xmlparser.getAttributeLocalName(0) +" = " + xmlparser.getAttributeValue(0));
@@ -127,7 +126,6 @@ public final class read_demultiplex_stats
             boolean doimport = true;
             while (doimport)
             {
-
                 // concerning tag Flowcell:
                 if (event == XMLStreamConstants.START_ELEMENT && xmlparser.getLocalName().equals("Flowcell"))
                 {
@@ -154,13 +152,13 @@ public final class read_demultiplex_stats
                             {
                                 case XMLStreamConstants.END_ELEMENT:
                                     skip -= 1;
-                                    break; // break-command after each case is necessary in switch-statement
+                                    break;
                                 case XMLStreamConstants.START_ELEMENT:
                                     skip += 1;
-                                    break; // break-command after each case is necessary in switch-statement
+                                    break;
                                 default:
                                     skip += 0; // text elements, spaces, ...
-                                    break; // break-command after each case is necessary in switch-statement
+                                    break;
                             }
                         }
                     } else
@@ -337,14 +335,9 @@ public final class read_demultiplex_stats
                 } else
                 {
                     doimport = false;
-                    errormessage =
-                            "STRANGE ERROR IN METHOD importXMLdata_and_calculateStatistics WHEN READING IN XMLFILE. => CHECK CODE AND XMLFILE-STRUCTURE!";
-                    //System.out.println(errormessage);
-                    throw new Exception(errormessage);
+                    System.out.println("Warning: Different XML structure than expectet. Got event: " + event);
                 }
-
             }
-
             xmlparser.close();
 
         } catch (FileNotFoundException | XMLStreamException e)