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 4b6a2ce34560667f14c2bdceb36082d1ea97252e..0aa2807a57778bc00cd373152d0cab9da1b73886 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 @@ -19,6 +19,7 @@ import subprocess from time import * from datetime import * from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria +from __builtin__ import file FASTQ_GZ_PATTERN = "*.fastq.gz" METADATA_FILE_SUFFIX = "_metadata.tsv" @@ -51,7 +52,14 @@ def getThreadProperties(transaction): pass return threadPropertyDict +def checkOnFileSize(file): + return os.stat(file).st_size == 0 + def CRC32_from_file(filename, transaction): + + if checkOnFileSize(filename): + raise Exception("FILE " + filename + " IS EMPTY!") + threadPropertyDict = getThreadProperties(transaction) absolutePath = os.path.dirname(os.path.realpath(threadPropertyDict['script-path'])) fullPathCrc32 = (os.path.join(absolutePath, CRC32_PATH)) @@ -170,8 +178,8 @@ def extraCopySciCore (affiliation_name, 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 = '/tmp/scicore' +# dropBoxFolder = '/links/shared/dsu/dss/customers/biozentrum_scicore/drop-box' basename = os.path.basename(filePath) print("extraCopySciCore")