diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read-demultiplex-stats-nextseq.py b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read-demultiplex-stats-nextseq.py index 71bcaafada6931170e0a4807003e59059c17cf14..b66873933cbf7cfa3ec86d19920f94fc1b56c92e 100755 --- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read-demultiplex-stats-nextseq.py +++ b/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 diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read_demultiplex_stats.java b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read_demultiplex_stats.java index dddea50b5cf5ff5aa15e279d9c9d2a9315d33a87..e10a38ce32fc6da382a7ce584d7818bfd493202d 100644 --- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read_demultiplex_stats.java +++ b/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)