needed for tests

SVN: 34519

deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/jython-lib/gfb_utils.py

+import os
+import time
+import fnmatch
+from time import *
+from datetime import *
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+
+# HISEQ_DICT = {'HISEQ_4000': 'Illumina HiSeq 4000',
+#                   'HISEQ_3000': 'Illumina HiSeq 3000',
+#                   'HISEQ_2500': 'Illumina HiSeq 2500',
+#                   'HISEQ_2000': 'Illumina HiSeq 2000',
+#                   'HISEQ_X': 'Illumina HiSeq X'
+#                   }
+# NEXTSEQ_DICT = {'NEXTSEQ_500': 'Illumina NextSeq 500'}
+# MISEQ_DICT = {'MISEQ': 'Illumina MiSeq'}
+# UNIDENTIFIED_DICT = {'UNIDENTIFIED': 'Unidentified'}
+
+# Instead of using Enum:
+class Sequencers:
+    HISEQ_4000, HISEQ_3000, HISEQ_2500, HISEQ_2000, HISEQ_X, NEXTSEQ_500, MISEQ , UNIDENTIFIED= \
+        ('Illumina HiSeq 4000','Illumina HiSeq 3000','Illumina HiSeq 2500','Illumina HiSeq 2000',
+         'Illumina HiSeq X', 'Illumina NextSeq 500', 'Illumina MiSeq', 'Unidentified')
+
+HISEQ_LIST = [Sequencers.HISEQ_2000, Sequencers.HISEQ_2500, Sequencers.HISEQ_3000, Sequencers.HISEQ_4000, Sequencers.HISEQ_X]
+
+
+def get_model(run_id):
+    """
+    Guesses the sequencer model from the run folder name
+
+    Current Naming schema for Illumina run folders, as far as I know,
+    no documentation found on this, Illumina introduced a field called
+    <InstrumentID> on the NextSeq runParameters.xml. That might be an
+    option for the future. Alternatively a combination of the fields
+    <ApplicationName> and <ApplicationVersion>.
+
+    MiSeq: 150130_M01761_0114_000000000-ACUR0
+    NextSeq: 150202_NS500318_0047_AH3KLMBGXX
+    HiSeq 2000: 130919_SN792_0281_BD2CHRACXX
+    HiSeq 2500: 150203_D00535_0052_AC66RWANXX
+    HiSeq 3000: 150724_J00121_0017_AH2VYMBBXX
+    HiSeq 4000: 150210_K00111_0013_AH2372BBXX
+    HiSeq X: 141121_ST-E00107_0356_AH00C3CCXX
+    """
+    date, machine_id, run_number, fc_string = os.path.basename(run_id).split("_")
+
+    if machine_id.startswith("NS"):
+        model = Sequencers.NEXTSEQ_500
+    elif machine_id.startswith("M"):
+        model = Sequencers.MISEQ
+    elif machine_id.startswith("D"):
+        model = Sequencers.HISEQ_2500
+    elif machine_id.startswith("SN"):
+        model = Sequencers.HISEQ_2000
+    elif machine_id.startswith("J"):
+        model = Sequencers.HISEQ_3000
+    elif machine_id.startswith("K"):
+        model = Sequencers.HISEQ_4000
+    elif machine_id.startswith("ST"):
+        model = Sequencers.HISEQ_X
+    else:
+        model = Sequencers.UNIDENTIFIED
+    return model
+
+
+def get_thread_properties(transaction):
+    threadPropertyDict = {}
+    threadProperties = transaction.getGlobalState().getThreadParameters().getThreadProperties()
+    for key in threadProperties:
+        try:
+            threadPropertyDict[key] = threadProperties.getProperty(key)
+        except:
+            pass
+    return threadPropertyDict
+
+
+def create_openbis_timestamp(file):
+    '''
+    Creates a openBIS compatible time stamp of a file time stamp
+    '''
+    mtime = os.path.getmtime(file)
+    lt = localtime(mtime)
+    tz = localtime().tm_hour - gmtime().tm_hour
+    return (strftime("%Y-%m-%d %H:%M:%S GMT" + "%+.2d" % tz + ":00", lt))
+
+
+def create_openbis_timestamp_now():
+  '''
+  Create an openBIS conform timestamp
+  '''
+  tz=localtime()[3]-gmtime()[3]
+  d=datetime.now()
+  return d.strftime("%Y-%m-%d %H:%M:%S GMT"+"%+.2d" % tz+":00")
+
+
+def search_unique_sample(transaction, sample_code): 
+
+    search_service = transaction.getSearchService()
+    sc = SearchCriteria()
+    sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sample_code));
+    found_sample = search_service.searchForSamples(sc)
+    try:
+        assert found_sample.size() == 1
+    except AssertionError:
+        print (str(found_sample.size()) + ' samples found which match the criterias: '+ sample_code)
+    return found_sample
+
+
+def get_file_names(path, pattern):
+    '''
+    Gets all files matching a PATTERN in a path recursively
+    and returns the result as a list
+    '''
+    matches = []
+    for root, dirnames, filenames in os.walk(path):
+        for filename in fnmatch.filter(filenames, pattern):
+            matches.append(os.path.join(root, filename))
+    matches.sort()
+    return(matches)
+