diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats/read-demultiplex-stats.py b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats/read-demultiplex-stats.py
index 37026732a852c60e6bd214360a6936a83468ed3c..47668634301a15a27f4ab3102f4927e220f6e57e 100755
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats/read-demultiplex-stats.py
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats/read-demultiplex-stats.py
@@ -389,6 +389,58 @@ def getFlowCellMetaData (transaction,flowCellId):
fcPropertyTypes.sort()
return fcPropertiesDict, fcPropertyTypes
+def getIndexesofDataSetsofSample(transaction, sample, DATA_SET_TYPE):
+
+ index1List = []
+ index2List = []
+ sc = SearchCriteria()
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sample));
+ search_service = transaction.getSearchService()
+ foundSample = search_service.searchForSamples(sc)
+
+ dataSetSc = SearchCriteria()
+ dataSetSc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, DATA_SET_TYPE))
+ dataSetSc.addSubCriteria(SearchSubCriteria.createSampleCriteria(sc))
+ foundDataSets = search_service.searchForDataSets(dataSetSc)
+ for ds in foundDataSets:
+ index1List.append(ds.getPropertyValue('BARCODE'))
+ index2List.append(ds.getPropertyValue('INDEX2'))
+ return index1List, index2List
+
+def searchDataSetsofSample(transaction, sample, index1, index2, DATA_SET_TYPE):
+ sc = SearchCriteria()
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sample));
+ search_service = transaction.getSearchService()
+ foundSample = search_service.searchForSamples(sc)
+
+ dataSetSc = SearchCriteria()
+ # set the Search Criteria to an OR condition, default is AND
+ #dataSetSc.setOperator(SearchCriteria.SearchOperator.MATCH_ANY_CLAUSES)
+ dataSetSc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, DATA_SET_TYPE))
+ dataSetSc.addMatchClause(SearchCriteria.MatchClause.createPropertyMatch("BARCODE", index1 ))
+ dataSetSc.addMatchClause(SearchCriteria.MatchClause.createPropertyMatch("INDEX2", index2))
+ dataSetSc.addSubCriteria(SearchSubCriteria.createSampleCriteria(sc))
+ foundDataSets = search_service.searchForDataSets(dataSetSc)
+ print "foundDataSets.size() "+ str(foundDataSets.size())
+ for ds in foundDataSets:
+ print "Index1 for found Data Set" + ds.getDataSetCode() + " " + ds.getPropertyValue('BARCODE')
+ print "Index2 for found Data Set" + ds.getDataSetCode() + " " + ds.getPropertyValue('INDEX2')
+
+ return foundDataSets
+
+def sampleSearch(transaction, code=''):
+ sc = SearchCriteria()
+ numberOfLanes = 0
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, code));
+ search_service = transaction.getSearchService()
+ foundSample = search_service.searchForSamples(sc)
+ if foundSample.size() > 0:
+ # Search for contained samples
+ sampleSc = SearchCriteria()
+ sampleSc.addSubCriteria(SearchSubCriteria.createSampleContainerCriteria(sc))
+ foundContainedSamples = search_service.searchForSamples(sampleSc)
+ numberOfLanes = foundContainedSamples.size()
+ return foundSample, foundContainedSamples, numberOfLanes
# -----------------------------------------------------------------------------
@@ -403,7 +455,7 @@ def process(transaction):
UNDETERMINED='UNDETERMINED'
incomingPath = transaction.getIncoming().getPath()
- name = transaction.getIncoming().getName().split('-')[0]
+ name, laneNumber = transaction.getIncoming().getName().split('-')
print('\n'+time.ctime())
@@ -420,7 +472,7 @@ def process(transaction):
sa = sample()
sampleDict = {}
- print ("Length Sample List: " + str(len(sampleList)))
+ print ("Length List samples x tiles x surface: " + str(len(sampleList)))
# key = sample name, value = sample()
for element in range(0, len(sampleList)):
@@ -448,66 +500,7 @@ def process(transaction):
for mye in stat:
mye.rawPercentageReadsPerLane = relRawReadsDict[mye.sampleName]
- def sampleSearch(Code=''):
- sc = SearchCriteria()
- numberOfLanes = 0
- sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, Code));
- search_service = transaction.getSearchService()
- foundSample = search_service.searchForSamples(sc)
- if foundSample.size() > 0:
- # Search for contained samples
- sampleSc = SearchCriteria()
- sampleSc.addSubCriteria(SearchSubCriteria.createSampleContainerCriteria(sc))
- foundContainedSamples = search_service.searchForSamples(sampleSc)
- numberOfLanes = foundContainedSamples.size()
- return foundSample, foundContainedSamples, numberOfLanes
-
-#--------------------------------------------------------------------------------------------------------------------------------------
-
- def searchDataSetsofSample(sample, index1, index2, DATA_SET_TYPE):
- sc = SearchCriteria()
- sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sample));
- search_service = transaction.getSearchService()
- foundSample = search_service.searchForSamples(sc)
-
- dataSetSc = SearchCriteria()
- # set the Search Criteria to an OR condition, default is AND
- #dataSetSc.setOperator(SearchCriteria.SearchOperator.MATCH_ANY_CLAUSES)
- dataSetSc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, DATA_SET_TYPE))
- dataSetSc.addMatchClause(SearchCriteria.MatchClause.createPropertyMatch("BARCODE", index1 ))
- dataSetSc.addMatchClause(SearchCriteria.MatchClause.createPropertyMatch("INDEX2", index2))
- dataSetSc.addSubCriteria(SearchSubCriteria.createSampleCriteria(sc))
- foundDataSets = search_service.searchForDataSets(dataSetSc)
- print "foundDataSets.size() "+ str(foundDataSets.size())
- for ds in foundDataSets:
- print "Index1 for found Data Set" + ds.getDataSetCode() + " " + ds.getPropertyValue('BARCODE')
- print "Index2 for found Data Set" + ds.getDataSetCode() + " " + ds.getPropertyValue('INDEX2')
-
- return foundDataSets
-
-#--------------------------------------------------------------------------------------------------------------------------------------
-
- def getIndexesofDataSetsofSample(sample, DATA_SET_TYPE):
-
- index1List = []
- index2List = []
- sc = SearchCriteria()
- sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sample));
- search_service = transaction.getSearchService()
- foundSample = search_service.searchForSamples(sc)
-
- dataSetSc = SearchCriteria()
- dataSetSc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, DATA_SET_TYPE))
- dataSetSc.addSubCriteria(SearchSubCriteria.createSampleCriteria(sc))
- foundDataSets = search_service.searchForDataSets(dataSetSc)
- for ds in foundDataSets:
- index1List.append(ds.getPropertyValue('BARCODE'))
- index2List.append(ds.getPropertyValue('INDEX2'))
- return index1List, index2List
-
-#--------------------------------------------------------------------------------------------------------------------------------------
-
- flowcell, lanes, numberOfLanes = sampleSearch(name)
+ flowcell, lanes, numberOfLanes = sampleSearch(transaction, name)
index1Length = fcPropertiesDict['INDEXREAD']
index2Length = fcPropertiesDict['INDEXREAD2']
@@ -515,9 +508,16 @@ def process(transaction):
full_lane_statistics = lane_statistics()
complete_lane_statistic = full_lane_statistics.caluclate_complete_lane_statistic(stat)
+ print(complete_lane_statistic.pfYieldSum)
# TODO Can we assume that this is always the same lanes, so we take the first one?
lane = lanes[0]
- mutable_lane = transaction.getSampleForUpdate(lane.getSampleIdentifier())
+
+ for lane in lanes:
+ if laneNumber == lane.getSampleIdentifier().split(":")[-1]:
+ mutable_lane = transaction.getSampleForUpdate(lane.getSampleIdentifier())
+ print("Setting Complete Lanes Statistics For: " + lane.getSampleIdentifier())
+ break
+
mutable_lane.setPropertyValue("YIELD_MBASES", str(complete_lane_statistic.pfYieldSum))
mutable_lane.setPropertyValue('RAW_YIELD_MBASES', str(complete_lane_statistic.rawYieldSum))
mutable_lane.setPropertyValue('PERCENTAGE_PASSED_FILTERING',str(complete_lane_statistic.pfPercentage))
@@ -534,7 +534,7 @@ def process(transaction):
print '\n'
print mystat
- index1List, index2List = getIndexesofDataSetsofSample(laneCode, FASTQ_DATA_SET_TYPE)
+ index1List, index2List = getIndexesofDataSetsofSample(transaction, laneCode, FASTQ_DATA_SET_TYPE)
print "Searching for "+ searchIndex1 + " in " + str(index1List)
print "Searching for "+ searchIndex2 + " in " + str(index2List)
@@ -576,7 +576,7 @@ def process(transaction):
print "searchIndex2 " + str(searchIndex2)
# Search for a data set with those two indices
- DataSet = searchDataSetsofSample(laneCode, searchIndex1, searchIndex2, FASTQ_DATA_SET_TYPE)
+ DataSet = searchDataSetsofSample(transaction, laneCode, searchIndex1, searchIndex2, FASTQ_DATA_SET_TYPE)
try:
assert DataSet.size() == 1
except AssertionError: