From 181bcc9670ed534f52fa9eb95b12c34ce1eee378 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Tue, 15 Sep 2015 12:07:46 +0000
Subject: [PATCH] little bug fixes
SVN: 34648
---
.../register-flowlane/register-flowlane.py | 39 ++++++++++++-------
1 file changed, 25 insertions(+), 14 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 073256eee86..03637f2546b 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
@@ -26,9 +26,11 @@ Manuel Kohler
import os
import shutil
import re
+import sys
import subprocess
from collections import OrderedDict
from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+from java.lang import System;
# The following module is located in the path defined in the datastore_server.conf
# Look for: -Dpython.path}
from gfb_utils import *
@@ -49,8 +51,8 @@ NCBI_ORGANISM_TAXONOMY='NCBI_ORGANISM_TAXONOMY'
PHIX_TAXONOMY_ID='10847'
DEFAULT_INDEX='NoIndex'
CRC32_PATH='lib/crc32'
-CRC32_PATH='lib/a.out'
-
+if System.getProperty('os.name') == 'Mac OS X':
+ CRC32_PATH='lib/a.out'
def checkOnFileSize(file):
return os.stat(file).st_size == 0
@@ -129,13 +131,15 @@ def extraCopySciCore (sample_space, filePath, destinationFolder=""):
Handles the extra copies of the data for transfer with datamover for SCICORE
'''
- dropBoxFolder = '/Users/kohleman/tmp/scicore'
- #dropBoxFolder = '/links/shared/dsu/dss/customers/biozentrum_scicore/drop-box'
+ dropBoxFolder = '/links/shared/dsu/dss/customers/biozentrum_scicore/drop-box'
+ if System.getProperty('os.name') == 'Mac OS X':
+ dropBoxFolder = '/Users/kohleman/tmp/scicore'
# 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", "BIOZENTRUM_SPANG",
+ SPACE_LIST = ["DUW_SALZBURGER", "BIOZENTRUM_HANDSCHIN", "BIOZENTRUM_ZAVOLAN",
+ "BIOZENTRUM_KELLER", "BIOZENTRUM_NIMWEGEN", "BSSE_DBM_BIOZENTRUM_NEUROSTEMX",
+ "UNI_BASEL_STPH_UTZINGER", "UNI_BASEL_STPH_GAGNEUX",
+ "BIOZENTRUM_PAPASSOTIROPOULOS_BEERENWINKEL", "BIOZENTRUM_SPANG",
"BIOZENTRUM_JENAL"]
basename = os.path.basename(filePath)
@@ -144,10 +148,10 @@ def extraCopySciCore (sample_space, filePath, destinationFolder=""):
dirname = os.path.join(dropBoxFolder, destinationFolder)
if not os.path.exists(dirname):
os.mkdir(dirname)
- print("COPYING " + filePath + " TO " + dirname)
+ print("COPYING " + filePath + " TO SCICORE FOLDER " + dirname)
shutil.copy(filePath, dirname)
else:
- print(sample_space + " not in SPACE_LIST. Sample will not be copied to BC2.")
+ print(sample_space + " not in SPACE_LIST. Sample will not be copied to BC2.\n")
def get_sample_properties (transaction, sample):
@@ -202,6 +206,8 @@ def renameFiles (fastq_files, undetermined, flow_cell_id):
def put_files_to_dataset (transaction, dataSet, fastq_files, folder_name, flow_cell_id, sample_space, undetermined):
for file in fastq_files:
+ print("SAMPLE_SPACE")
+ print(sample_space)
extraCopySciCore (sample_space, file, folder_name)
transaction.moveFile(file, dataSet, folder_name)
@@ -217,11 +223,11 @@ def split_incoming_folder_name (name):
flowLane = split[-1]
undetermined = False
- # expected Undetermined_H0W8YBGXX
- elif (len(split) == 2):
+ # expected Undetermined_H0W8YBGX_1
+ elif (len(split) == 3):
sample_code = ''
- flowCellId = split[-1]
- flowLane = '1'
+ flowCellId = split[-2]
+ flowLane = split[-1]
undetermined = True
# MiSeq BSSE_QGF_36097_000000000_AH4PH_1
@@ -282,6 +288,7 @@ def process_regular_samples(transaction, name, sample_code, flowLane, fastq_file
def process_undetermined(transaction, undetermined, name, flowCellId, flowLane, fastq_files, first_fastq_file, search_service, fcMetaDataDict, parents, dataSet):
sample_space = ""
newFastqFiles = []
+ sample_space_list = []
lane_parents = searchParents(search_service, parents)
print "Found " + str(lane_parents.size()) + " parents"
newFastqFiles = renameFiles(fastq_files, undetermined, flowCellId)
@@ -291,6 +298,7 @@ def process_undetermined(transaction, undetermined, name, flowCellId, flowLane,
sample_code = parent_sample.getCode()
experiment = parent_sample.getExperiment()
sample_space = parent.getSpace()
+ sample_space_list.append(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
@@ -310,7 +318,10 @@ def process_undetermined(transaction, undetermined, name, flowCellId, flowLane,
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, sample_space, [], flowLane)
-
+
+ sample_space_set = set(sample_space_list)
+ sample_space_set.remove("PHIX")
+ sample_space = sample_space_set.pop()
return newFastqFiles, sample_space
def process(transaction):
--
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