diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-nextseq/register-lane-nextseq.py b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-nextseq/register-lane-nextseq.py
index 0aa2807a57778bc00cd373152d0cab9da1b73886..5ca8462c770548a1bdf78b973a3e23fc48610e50 100644
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-nextseq/register-lane-nextseq.py
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-nextseq/register-lane-nextseq.py
@@ -23,10 +23,6 @@ from __builtin__ import file
FASTQ_GZ_PATTERN = "*.fastq.gz"
METADATA_FILE_SUFFIX = "_metadata.tsv"
-AFFILIATION= {'FMI': '/links/shared/dsu/dss/customers/fmi/drop-box/',
- 'BIOCENTER_BASEL': '/links/shared/dsu/dss/customers/biozentrum/drop-box/',
- 'NEUROSTEMX': '/links/shared/dsu/dss/customers/biozentrum/drop-box/',
- 'SWISS_TPH' : '/links/shared/dsu/dss/customers/biozentrum/drop-box/'}
AFFILIATION_PROPERTY_NAME='AFFILIATION'
INDEX1='BARCODE'
INDEX2='INDEX2'
@@ -39,6 +35,7 @@ NCBI_ORGANISM_TAXONOMY='NCBI_ORGANISM_TAXONOMY'
PHIX_TAXONOMY_ID='10847'
DEFAULT_INDEX='NoIndex'
CRC32_PATH='lib/crc32'
+CRC32_PATH='lib/a.out'
# -------------------------------------------------------------------------------
@@ -85,7 +82,7 @@ def getFileNames(path):
return(matches)
def writeMetadataFile(transaction, folder_name, meta_data_file_name, sequencing_sample_properties_dict,
- fcMetaDataDict, experiment, affiliation_name, fastqFileList, flowLane):
+ fcMetaDataDict, experiment, sample_space, fastqFileList, flowLane):
'''
Writes a file of meta data related to one sample
'''
@@ -128,8 +125,7 @@ def writeMetadataFile(transaction, folder_name, meta_data_file_name, sequencing_
meta_data_file.close()
destinationFolder = folder_name
- #extraCopy (affiliation_name, meta_data_file_name)
- extraCopySciCore (affiliation_name, meta_data_file_name, destinationFolder)
+ extraCopySciCore (sample_space, meta_data_file_name, destinationFolder)
def create_openbis_timestamp ():
'''
@@ -155,38 +151,22 @@ def create_openbis_timestamp ():
# -------------------------------------------------------------------------------
-def extraCopy (affiliation_name, path):
- '''
- @deprecated: replaced with extraCopySciCore
- Handles the extra copies of the data for transfer with datamover via the
- bc2 network to the FMI and BIOCENTER
- For the BIOCENTER there is a folder created in which all data gets into
- '''
- if (affiliation_name in AFFILIATION):
- if (affiliation_name == 'BIOCENTER_BASEL' or affiliation_name == 'NEUROSTEMX' ):
- dirname = AFFILIATION[affiliation_name] + datetime.now().strftime("%Y-%m-%d")
- if not os.path.exists(dirname):
- os.mkdir(dirname)
- shutil.copy(path, dirname)
- else:
- shutil.copy(path, AFFILIATION[affiliation_name])
-
-# -------------------------------------------------------------------------------
-
-def extraCopySciCore (affiliation_name, filePath, destinationFolder=""):
+def extraCopySciCore (sample_space, filePath, destinationFolder=""):
'''
Handles the extra copies of the data for transfer with datamover for SCICORE
'''
- dropBoxFolder = '/tmp/scicore'
-# dropBoxFolder = '/links/shared/dsu/dss/customers/biozentrum_scicore/drop-box'
+ dropBoxFolder = '/Users/kohleman/tmp/scicore'
+ #dropBoxFolder = '/links/shared/dsu/dss/customers/biozentrum_scicore/drop-box'
+
+ # if a sample is part of this space list then it will be transferred to sciCore
+ SPACE_LIST = ["UNI_BASEL_SALZBURGER", "BIOCENTER_HANDSCHIN", "BIOCENTER_ZAVOLAN",
+ "BIOCENTER_KELLER", "BIOCENTER_SILANDER", "ETHZ_NEUROSTEMX",
+ "UNI_BASEL_UTZINGER", "UNI_BASEL_GAGNEUX"]
+
basename = os.path.basename(filePath)
- print("extraCopySciCore")
- print basename
- print affiliation_name
-
- if (affiliation_name in ['BIOCENTER_BASEL', 'NEUROSTEMX', 'SWISS_TPH']):
+ if (sample_space in SPACE_LIST):
dirname = os.path.join(dropBoxFolder, destinationFolder)
if not os.path.exists(dirname):
os.mkdir(dirname)
@@ -261,10 +241,10 @@ def renameFiles (fastq_files, undetermined, flow_cell_id):
# -------------------------------------------------------------------------------
-def put_files_to_dataset (transaction, dataSet, fastq_files, folder_name, flow_cell_id, affiliation_name, undetermined):
+def put_files_to_dataset (transaction, dataSet, fastq_files, folder_name, flow_cell_id, sample_space, undetermined):
for file in fastq_files:
- extraCopySciCore (affiliation_name, file, folder_name)
+ extraCopySciCore (sample_space, file, folder_name)
transaction.moveFile(file, dataSet, folder_name)
# -------------------------------------------------------------------------------
@@ -358,32 +338,30 @@ def process(transaction):
if (INDEX2 in sequencing_sample_properties_dict) and (fcMetaDataDict[INDEXREAD2] > 0):
dataSet.setPropertyValue(INDEX2, sequencing_sample_properties_dict[INDEX2])
dataSet.setPropertyValue(EXTERNAL_SAMPLE_NAME, sequencing_sample_properties_dict[EXTERNAL_SAMPLE_NAME])
-
- if (AFFILIATION_PROPERTY_NAME in sequencing_sample_properties_dict):
- affiliation_name = sequencing_sample_properties_dict[AFFILIATION_PROPERTY_NAME]
-
+ sample_space = foundSample[0].getSpace()
+
filepart, suffix = first_fastq_file.split('.',1)
meta_data_file_name = filepart.rsplit('_',2)[0] + METADATA_FILE_SUFFIX
# get a file from the IDataSetRegistrationTransaction so it is automatically part of the data set
meta_data_file_path = transaction.createNewFile(dataSet, name, meta_data_file_name)
writeMetadataFile(transaction, name, meta_data_file_path, sequencing_sample_properties_dict,
- fcMetaDataDict, experiment, affiliation_name, fastq_files, flowLane)
- affiliation_for_Undetermined = affiliation_name
+ fcMetaDataDict, experiment, sample_space, fastq_files, flowLane)
+ affiliation_for_Undetermined = sample_space
# Undetermined Files
else:
- affiliation_name = ""
+ sample_space = ""
affiliation_for_Undetermined = ""
newFastqFiles = []
lane_parents = searchParents (search_service, parents)
newFastqFiles = renameFiles(fastq_files, undetermined, flowCellId)
for parent in lane_parents:
- sequencing_sample_properties_dict = get_sample_properties (transaction, parent)
- parent_sample = parent.getSample()
- sample_code = parent_sample.getCode()
- experiment = parent_sample.getExperiment()
- if (AFFILIATION_PROPERTY_NAME in sequencing_sample_properties_dict):
- affiliation_name = sequencing_sample_properties_dict[AFFILIATION_PROPERTY_NAME]
+ sequencing_sample_properties_dict = get_sample_properties (transaction, parent)
+ parent_sample = parent.getSample()
+ sample_code = parent_sample.getCode()
+ experiment = parent_sample.getExperiment()
+ sample_space = parent.getSpace()
+ print(sample_space)
# Special Sample Types without index (e.g. ILLUMINA_SEQUENCING_NEUROSTEMX_SINGLECELL) are caught here.
# as those samples do not have a NCBI ORGANISM TAXONOMY
@@ -391,23 +369,24 @@ def process(transaction):
print(sample_code + ": Processing Sample without NCBI ORGANISM TAXONOMY: ILLUMINA_SEQUENCING_NEUROSTEMX_SINGLECELL")
meta_data_file_path = transaction.createNewFile(dataSet, name, sample_code + '_' + flowCellId + '_' + first_fastq_file.split('.')[0] + METADATA_FILE_SUFFIX)
writeMetadataFile(transaction, name, meta_data_file_path, sequencing_sample_properties_dict,
- fcMetaDataDict, experiment, affiliation_name, newFastqFiles, flowLane)
- affiliation_for_Undetermined = affiliation_name
+ fcMetaDataDict, experiment, sample_space, newFastqFiles, flowLane)
+ affiliation_for_Undetermined = sample_space
- elif (INDEX1 not in sequencing_sample_properties_dict) and (INDEX2 not in sequencing_sample_properties_dict) and \
+ elif (INDEX1 not in sequencing_sample_properties_dict or sequencing_sample_properties_dict[INDEX1]== 'NOINDEX') and \
+ (INDEX2 not in sequencing_sample_properties_dict or sequencing_sample_properties_dict[INDEX2]== 'NOINDEX') and \
(sequencing_sample_properties_dict[NCBI_ORGANISM_TAXONOMY] != PHIX_TAXONOMY_ID):
- print('NONINDEXED sample and Taxonomy id is NOT' + PHIX_TAXONOMY_ID +', probably a pool: ' + sample_code)
+ print('NONINDEXED sample and Taxonomy id is NOT ' + PHIX_TAXONOMY_ID +', probably a pool: ' + sample_code)
meta_data_file_path = transaction.createNewFile(dataSet, name, sample_code + '_' + flowCellId + '_' + first_fastq_file.split('.')[0] + METADATA_FILE_SUFFIX)
writeMetadataFile(transaction, name, meta_data_file_path, sequencing_sample_properties_dict,
- fcMetaDataDict, experiment, affiliation_name, newFastqFiles, flowLane)
- affiliation_for_Undetermined = affiliation_name
+ fcMetaDataDict, experiment, sample_space, newFastqFiles, flowLane)
+ affiliation_for_Undetermined = sample_space
# PARENTS:
else:
# Create Parent Meta data
print(sample_code + ": Create parent meta data file")
meta_data_file_path = transaction.createNewFile(dataSet, name, 'PARENT_' + sample_code + '_' + flowCellId + METADATA_FILE_SUFFIX)
writeMetadataFile(transaction, name, meta_data_file_path, sequencing_sample_properties_dict,
- fcMetaDataDict, experiment, affiliation_name, [], flowLane)
+ fcMetaDataDict, experiment, sample_space, [], flowLane)
continue
put_files_to_dataset (transaction, dataSet, newFastqFiles, name, flowCellId, affiliation_for_Undetermined, undetermined)
@@ -416,3 +395,4 @@ def process(transaction):
sa = transaction.getSampleForUpdate(foundLane[0].getSampleIdentifier())
sa.setPropertyValue("DATA_TRANSFERRED", create_openbis_timestamp())
dataSet.setSample(foundLane[0])
+