From caad4550c927c394f791c96c82ab6a8a991900d1 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Tue, 24 Jul 2012 15:50:54 +0000
Subject: [PATCH] - added flow cell properties to the TSB-based meta data file
SVN: 26176
---
.../dist/etc/data-set-handler-lane.py | 56 ++++++++++++++++---
1 file changed, 49 insertions(+), 7 deletions(-)
diff --git a/deep_sequencing_unit/dist/etc/data-set-handler-lane.py b/deep_sequencing_unit/dist/etc/data-set-handler-lane.py
index 468205cef1f..5e4b0b85810 100755
--- a/deep_sequencing_unit/dist/etc/data-set-handler-lane.py
+++ b/deep_sequencing_unit/dist/etc/data-set-handler-lane.py
@@ -44,7 +44,7 @@ def getFileNames(path=incomingPath):
matches.sort()
return(matches)
-def writeMetadataFile (fileName, parentPropertyTypes, parentPropertiesMap):
+def writeMetadataFile (fileName, parentPropertyTypes, parentPropertiesMap, fcMetaDataDict, fcMetaDataList):
'''
Writes a file of meta date related to one sample
'''
@@ -52,7 +52,14 @@ def writeMetadataFile (fileName, parentPropertyTypes, parentPropertiesMap):
metaDataFile = open(fileName,'w')
for propertyType in parentPropertyTypes:
metaDataFile.write(propertyType.encode('utf-8') + "\t" +
- parentPropertiesMap[propertyType].tryGetAsString().encode('utf-8') + "\n")
+ parentPropertiesMap[propertyType].tryGetAsString().encode('utf-8') + "\n")
+
+ metaDataFile.write("\nFLOWCELL PROPERTIES\n".encode('utf-8'))
+
+ for fcMetaData in fcMetaDataList:
+ metaDataFile.write(fcMetaData.encode('utf-8') + "\t" +
+ fcMetaDataDict[fcMetaData].tryGetAsString().encode('utf-8') + "\n")
+ pass
except IOError:
print ('File error, could not write '+ fileName)
finally:
@@ -108,6 +115,40 @@ if (len(split) ==4):
flowLane = split[-1]
incoming_sample=runningDate+ '_'+ flowCellId + ':' + flowLane
+
+# -------------------------------------------------------------------------------
+
+def getFlowCellMetaData (flowCellId):
+
+ def sortedDictValues(adict):
+ keys = adict.keys()
+ keys.sort()
+ return map(adict.get, keys)
+
+ search = transaction.getSearchService()
+ sc = SearchCriteria()
+ print('Searching FlowCell: '+ str(flowCellId))
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, flowCellId));
+ foundFlowCells = search.searchForSamples(sc)
+
+ try:
+ assert foundFlowCells.size() == 1
+ except AssertionError:
+ print (str(foundFlowCells.size()) + ' flow cells found which match the criterias: '+ flowCellId)
+
+ fcPropertiesDict = {}
+ fcPropertyTypes = []
+
+ fcProperties = foundFlowCells[0].getSample().getProperties()
+ for property in fcProperties:
+ code = property.getPropertyType().getSimpleCode()
+ fcPropertyTypes.append(code)
+ fcPropertiesDict[code] = property
+
+ fcPropertyTypes.sort()
+ return fcPropertiesDict, fcPropertyTypes
+
+
# -------------------------------------------------------------------------------
# Get the search service
@@ -132,7 +173,7 @@ else :
# search for the parents
sc = SearchCriteria()
-# set the Serach Criteria to an OR condition, default is AND
+# set the Search Criteria to an OR condition, default is AND
sc.setOperator(SearchCriteria.SearchOperator.MATCH_ANY_CLAUSES)
# Get the codes for all parents
for parent in parents:
@@ -163,7 +204,7 @@ for f in range(0,len(folders)):
parentProperties = parent.getProperties()
# just get the current code
parentCode = parent.getCode()
- print("Found parent code: "+ parentCode)
+ #print("Found parent code: "+ parentCode)
# reformat Java ArrayList and Sort
parentPropertyTypes = []
@@ -194,7 +235,7 @@ for f in range(0,len(folders)):
completeBarcode=barcode + "-" + index2
parentPropertyTypes.sort()
- # BSSE-DSU-1754_C0364ACXX_CTTGTAA-AACC_L007_R1_001.fastq.gz
+ # BSSE--1754_C0364ACXX_CTTGTAA-AACC_L007_R1_001.fastq.gz
nameOfFile = parentCode + "_" + flowCellId + "_" + completeBarcode + "_L00" + flowLane +METADATA_FILE_SUFFIX
if (parentCode == folders[f].split('_')[1]):
@@ -203,8 +244,9 @@ for f in range(0,len(folders)):
#print("Creating metadata file:" + nameOfFile)
# get a file from the IDataSetRegistrationTransaction so it is automatically part of the data set
pathToFile = transaction.createNewFile(dataSet, folders[f], nameOfFile)
- # use this file path to write to this file
- writeMetadataFile(pathToFile, parentPropertyTypes, parentPropertiesMap)
+
+ fcMetaDataDict, fcMetaDataList = getFlowCellMetaData(incoming_sample.split(":")[0])
+ writeMetadataFile(pathToFile, parentPropertyTypes, parentPropertiesMap, fcMetaDataDict, fcMetaDataList)
affiliation_name = parentPropertiesMap[AFFILIATION_PROPERTY_NAME].tryGetAsString()
extraCopy (affiliation_name, pathToFile)
--
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