From 8df19b0f76599ef51e776cc7861eb6bc121d5cca Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Wed, 14 Sep 2016 13:38:15 +0000
Subject: [PATCH] added possibility to provide pre-computed checksums in a txt
file
SVN: 37078
---
.../register-flowlane/register-flowlane.py | 19 +++++++++++++++++--
1 file changed, 17 insertions(+), 2 deletions(-)
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/register-flowlane/register-flowlane.py b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/register-flowlane/register-flowlane.py
index 5c1b0519ae2..e733f9640a5 100644
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/register-flowlane/register-flowlane.py
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/register-flowlane/register-flowlane.py
@@ -58,6 +58,7 @@ CRC32_PATH='lib/crc32'
if System.getProperty('os.name') == 'Mac OS X':
CRC32_PATH='lib/a.out'
NOHUP_REGEX = 'nohup*.txt'
+CHECKSUMS_REGEX = 'checksums.txt'
COMMAND_LINE_INVOCATION = 'Command-line invocation'
MISMATCH_REGEX = r'(barcode-mismatches) ([0-9])'
mismatch_dict = {0: 'NONE', 1:'ONE', 2:'TWO'}
@@ -122,6 +123,8 @@ def writeMetadataFile(transaction, folder_name, meta_data_file_name, sequencing_
Writes a file of meta data related to one sample
'''
+ incoming_path = transaction.getIncoming().getAbsolutePath()
+
sequencing_sample_properties_list = sequencing_sample_properties_dict.keys()
sequencing_sample_properties_list.sort()
@@ -154,8 +157,19 @@ def writeMetadataFile(transaction, folder_name, meta_data_file_name, sequencing_
meta_data_file.write(k.encode('utf-8') + "\t" + fcMetaDataDict[k].encode('utf-8') + "\n")
meta_data_file.write("\nFASTQ_FILES\n".encode('utf-8'))
- for file in fastqFileList:
- meta_data_file.write(os.path.basename(file) + "\t" + str(CRC32_from_file(file, transaction)) + "\n")
+
+ checksums_file = get_file_names(incoming_path, CHECKSUMS_REGEX)
+ if checksums_file:
+ with open(checksums_file[0]) as checksums:
+ for line in checksums:
+ meta_data_file.write(line)
+ else:
+ print("File " + str(checksums_file) + " not found!")
+
+ # Use slow fall back solution
+ for file in fastqFileList:
+ print("Using fall back solution for creation of CRC32 checksums")
+ meta_data_file.write(os.path.basename(file) + "\t" + str(CRC32_from_file(file, transaction)) + "\n")
meta_data_file.write("\nDATASET PROPERTIES\n".encode('utf-8'))
# Data Set Property:
@@ -414,6 +428,7 @@ def process(transaction):
if nohup_file:
command_line_list, mismatches = get_mismatches(nohup_file)
+
# get all fastqs
fastq_files = get_file_names(incoming_path, FASTQ_GZ_PATTERN)
--
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