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 01718c90fc55cb3028c852f1c55c43f1af708529..9a21b89532a3f2000ca9a2ab3067b92ad8a561aa 100755 --- a/deep_sequencing_unit/dist/etc/data-set-handler-lane.py +++ b/deep_sequencing_unit/dist/etc/data-set-handler-lane.py @@ -19,7 +19,7 @@ from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria FASTQ_GZ_PATTERN = "*.fastq.gz" METADATA_FILE_SUFFIX = "_metadata.tsv" -AFFILIATION= {'FMI': '/links/shared/dsu-dss/dss/customers/fmi/','BIOCENTER_BASEL': '/links/shared/dsu-dss/dss/customers/biozentrum/'} +AFFILIATION= {'FMI': '/links/shared/dsu-dss/dss/customers/fmi/drop-box/','BIOCENTER_BASEL': '/links/shared/dsu-dss/dss/customers/biozentrum/drop-box/'} AFFILIATION_PROPERTY_NAME='AFFILIATION' # ------------------------------------------------------------------------------- @@ -90,9 +90,19 @@ name = incoming.getName() # expected incoming Name, e.g.: Project_110715_SN792_0054_BC035RACXX_1 split=name.split("_") if (len(split) == 6): - incoming_sample=split[1]+ '_'+ split[2] + '_' + split[3] + '_' + split[4]+ ':' + split[-1] + runningDate = split[1] + sequencerId = split[2] + sequentialNumber = split[3] + hiseqTray = split[4][0] + flowCellId = split[4][1:] + flowLane = split[-1] + incoming_sample=runningDate+ '_'+ sequencerId + '_' + sequentialNumber + '_' + hiseqTray + flowCellId + ':' + flowLane +# expected Project_120112_63537AAXX_1 if (len(split) ==4): - incoming_sample=split[1]+ '_'+ split[2] + ':' + split[-1] + runningDate = split[1] + flowCellId = split[2] + flowLane = split[-1] + incoming_sample=runningDate+ '_'+ flowCellId + ':' + flowLane # ------------------------------------------------------------------------------- @@ -156,11 +166,20 @@ for f in range(0,len(folders)): code = property.getPropertyType().getSimpleCode() parentPropertyTypes.append(code) parentPropertiesMap[code] = property + try: + barcode = parentPropertiesMap['BARCODE'] + #print(str(barcode)) + except: + barcode = "NoIndex" + # just use the first six nucleotides for the naming + strBarcode=str(barcode).split()[-1][:-1] parentPropertyTypes.sort() - nameOfFile = parentCode + METADATA_FILE_SUFFIX + # BSSE-DSU-1754_C0364ACXX_CTTGTAA_L007_R1_001.fastq.gz + nameOfFile = parentCode + "_" + flowCellId + "_" + strBarcode + "_L00" + flowLane +METADATA_FILE_SUFFIX - if (parentCode == folders[f].split('_')[-1]): + if (parentCode == folders[f].split('_')[1]): + 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