From f1f6bdda69fd98238e25f9113ff3e4fdbb6e79e7 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Wed, 4 Feb 2015 14:06:39 +0000
Subject: [PATCH] - clean up - call the master data export
SVN: 33386
---
.../register-flowcell-hiseq.py | 77 +++++--------------
1 file changed, 21 insertions(+), 56 deletions(-)
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-flowcell-hiseq/register-flowcell-hiseq.py b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-flowcell-hiseq/register-flowcell-hiseq.py
index f82b63d9991..62ab3d79aa3 100644
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-flowcell-hiseq/register-flowcell-hiseq.py
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-flowcell-hiseq/register-flowcell-hiseq.py
@@ -29,68 +29,33 @@ Manuel Kohler
'''
import os
-import shutil
-import glob
-import xml.etree.ElementTree as etree
+import subprocess
from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
-IS_HISEQ_RUN=False
-
-RUNINFO_FOLDER='/links/shared/dsu/dss/register-runstatistics/'
-REGEX_RUNINFO_SAMPLE = '/Data/Status*'
-REGEX_RUNINFO_REPORTS = '/Data/reports'
-MARKER_STRING='.MARKER_is_finished_'
-
-def touch_markerfile(filename):
- try:
- # do a touch
- open(filename, 'w').close()
- except:
- print('Could not touch ' + filename)
-
def process(transaction):
- incomingPath = transaction.getIncoming().getPath()
- name = transaction.getIncoming().getName()
+ args = ['/links/application/dsu/export_QGF_master_data/export_QGF_master_data.sh']
- folders=[]
- folders=os.listdir(incomingPath)
+ try:
+ p = subprocess.Popen(args, stdout=subprocess.PIPE)
+ print(p.communicate()[0])
+ except:
+ print("Could not run: " + str(args))
- split=name.split("_")
- if (len(split) == 4):
- dataSet = transaction.createNewDataSet("ILLUMINA_HISEQ_OUTPUT")
- IS_HISEQ_RUN=True
- if (len(split) == 2):
- dataSet = transaction.createNewDataSet("ILLUMINA_GA_OUTPUT")
+ incomingPath = transaction.getIncoming().getPath()
+ name = transaction.getIncoming().getName()
- #move RunInfo into a different drop box
- #runInfoSample=glob.glob(incomingPath + REGEX_RUNINFO_SAMPLE)
- #runInfoReport=glob.glob(incomingPath + REGEX_RUNINFO_REPORTS)
- #runInfoList = runInfoSample + runInfoReport
- #os.makedirs(RUNINFO_FOLDER + name + '/Data/')
- #for runInfo in runInfoList:
- # try:
- # if os.path.isdir(runInfo):
-# shutil.copytree(runInfo, RUNINFO_FOLDER + name + '/Data/' + os.path.basename(runInfo))
-# else:
-# shutil.copy2(runInfo, RUNINFO_FOLDER + name + '/Data/')
-# except (IOError, os.error), why:
-# print (runInfo, RUNINFO_FOLDER + name, str(why))
+ split=name.split("_")
+ if (len(split) == 4):
+ dataSet = transaction.createNewDataSet("ILLUMINA_HISEQ_OUTPUT")
-# touch_markerfile(RUNINFO_FOLDER+MARKER_STRING+name)
-
- # Create a data set and set type
- dataSet.setMeasuredData(False)
-
- # Get the search service
- search_service = transaction.getSearchService()
-
- # Search for the sample
- sc = SearchCriteria()
- sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, name));
- foundSamples = search_service.searchForSamples(sc)
+ dataSet.setMeasuredData(False)
+
+ search_service = transaction.getSearchService()
+ sc = SearchCriteria()
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, name));
+ foundSamples = search_service.searchForSamples(sc)
- if foundSamples.size() > 0:
- # Add the incoming file into the data set
- transaction.moveFile(incomingPath, dataSet)
- dataSet.setSample(foundSamples[0])
+ if foundSamples.size() > 0:
+ transaction.moveFile(incomingPath, dataSet)
+ dataSet.setSample(foundSamples[0])
\ No newline at end of file
--
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