From b5af2bed2007ae6a0ad3a5ab81254b01090b134b Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Fri, 30 Jan 2015 16:31:23 +0000
Subject: [PATCH] several minor bug fixes
SVN: 33363
---
.../create-flowcell-hiseq.py | 21 +-
.../export-meta-data/export-meta-data.py | 464 ++++++++++
.../dss/drop-boxes/export-meta-data/lib/crc32 | Bin 0 -> 13196 bytes
.../export-meta-data/plugin.properties | 12 +
.../plugin.properties | 2 +-
.../read-demultiplex-stats-nextseq.py | 833 +++++++-----------
.../read_demultiplex_stats.java | 526 +++++++++++
.../read-demultiplex-stats.py | 11 +-
.../plugin.properties | 2 +-
.../register-dummy/plugin.properties | 11 +
.../register-dummy/register-dummy.py | 56 ++
.../drop-boxes/register-lane-hiseq/lib/crc32 | Bin 13196 -> 10567 bytes
.../drop-boxes/register-lane-miseq/lib/crc32 | Bin 13196 -> 10567 bytes
.../register-lane-miseq.py | 2 +-
.../register-lane-nextseq/lib/crc32 | Bin 13196 -> 10567 bytes
.../register-lane-nextseq/lib/crc32_v2.c | 206 +++++
.../register-lane-nextseq.py | 1 +
17 files changed, 1600 insertions(+), 547 deletions(-)
create mode 100644 deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/export-meta-data/export-meta-data.py
create mode 100755 deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/export-meta-data/lib/crc32
create mode 100644 deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/export-meta-data/plugin.properties
create mode 100644 deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read_demultiplex_stats.java
create mode 100644 deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-dummy/plugin.properties
create mode 100644 deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-dummy/register-dummy.py
create mode 100644 deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-nextseq/lib/crc32_v2.c
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/create-flowcell-hiseq/create-flowcell-hiseq.py b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/create-flowcell-hiseq/create-flowcell-hiseq.py
index 304ca8cd411..7a6945be12e 100644
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/create-flowcell-hiseq/create-flowcell-hiseq.py
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/create-flowcell-hiseq/create-flowcell-hiseq.py
@@ -37,7 +37,6 @@ from time import *
from datetime import *
import xml.etree.ElementTree as etree
from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
-from os.path import isfile
IS_HISEQ_RUN=False
RUNPARAMETERS = 'runParameters.xml'
@@ -144,12 +143,6 @@ def setFcProperty(searchId, dict, newFlowCell, runInfo):
# -----------------------------------------------------------------------------
-def checkIfFileExists (filePath):
- if not os.path.isfile(filePath):
- return False
- else:
- return True
-
def process(transaction):
incoming = transaction.getIncoming()
incomingPath = incoming.getAbsolutePath()
@@ -159,16 +152,8 @@ def process(transaction):
name = incoming.getName()
split=name.split("_")
- runInfoFile = os.path.join(incomingPath, RUNINFO)
- runParametersFile = os.path.join(incomingPath, RUNPARAMETERS)
-
- if not (checkIfFileExists(runInfoFile)):
- raise IOError ("File not found: " + RUNINFO)
- if not (checkIfFileExists(runParametersFile)):
- raise IOError ("File not found: " + RUNPARAMETERS)
-
# Parse the RunInfo.xml file
- runInfo = parseXmlFile(runInfoFile)
+ runInfo = parseXmlFile(incomingPath + '/' + RUNINFO)
maxLanes = runInfo.getAllchildren('FlowcellLayout')[0].attrib[RUNINFO_XML['LANECOUNT']]
# Search for the sample and check if there is already sample with this name
@@ -194,10 +179,10 @@ def process(transaction):
run = runInfo.getAllchildren('Run')[0].attrib
if (run['Id'] != name):
raise NameError('Flowcell names do not match between directory name '+ name +
- ' and ' + RUNINFO + ' property file: ' + run['Id'])
+ ' and ' + RUNINFO + 'property file: ' + run['Id'])
# The HiSeq is providing more infos, which we will parse here:
- runParameters = parseXmlFile(runParametersFile)
+ runParameters = parseXmlFile(incomingPath + '/' + RUNPARAMETERS)
addVocabularyTerm(transaction, "PIPELINE_VERSION", runParameters.getXmlElement(RUNPARAMETERS_XML['RTAVERSION']))
newFlowCell.setPropertyValue("ILLUMINA_PIPELINE_VERSION", runParameters.getXmlElement(RUNPARAMETERS_XML['RTAVERSION']))
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/export-meta-data/export-meta-data.py b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/export-meta-data/export-meta-data.py
new file mode 100644
index 00000000000..f5253bc0874
--- /dev/null
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/export-meta-data/export-meta-data.py
@@ -0,0 +1,464 @@
+'''
+Processes each flow lane of a Sequencing run
+
+Expects as incoming folder:
+BSSE_QGF_22266_H0W8YBGXX_1
+or
+Undetermined_H0W8YBGXX
+
+Note:
+print statements go to: ~openbis/sprint/datastore_server/log/startup_log.txt
+'''
+
+import os
+import fnmatch
+import time
+import shutil
+import re
+import subprocess
+from time import *
+from datetime import *
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+from ch.systemsx.cisd.openbis.dss.generic.shared import DataSourceQueryService
+
+FASTQ_GZ_PATTERN = "*.fastq.gz"
+METADATA_FILE_SUFFIX = "_metadata.tsv"
+AFFILIATION= {'FMI': '/links/shared/dsu/dss/customers/fmi/drop-box/',
+ 'BIOCENTER_BASEL': '/links/shared/dsu/dss/customers/biozentrum/drop-box/',
+ 'NEUROSTEMX': '/links/shared/dsu/dss/customers/biozentrum/drop-box/',
+ 'SWISS_TPH' : '/links/shared/dsu/dss/customers/biozentrum/drop-box/'}
+AFFILIATION_PROPERTY_NAME='AFFILIATION'
+INDEX1='BARCODE'
+INDEX2='INDEX2'
+EXTERNAL_SAMPLE_NAME='EXTERNAL_SAMPLE_NAME'
+INDEXREAD1='INDEXREAD'
+INDEXREAD2='INDEXREAD2'
+SAMPLE_TYPE = 'SAMPLE_TYPE'
+SAMPLE_CODE = 'SAMPLE_CODE'
+NCBI_ORGANISM_TAXONOMY='NCBI_ORGANISM_TAXONOMY'
+PHIX_TAXONOMY_ID='10847'
+DEFAULT_INDEX='NoIndex'
+CRC32_PATH='lib/crc32'
+
+# -------------------------------------------------------------------------------
+
+def getThreadProperties(transaction):
+ threadPropertyDict = {}
+ threadProperties = transaction.getGlobalState().getThreadParameters().getThreadProperties()
+ for key in threadProperties:
+ try:
+ threadPropertyDict[key] = threadProperties.getProperty(key)
+ except:
+ pass
+ return threadPropertyDict
+
+def CRC32_from_file(filename, transaction):
+ threadPropertyDict = getThreadProperties(transaction)
+ absolutePath = os.path.dirname(os.path.realpath(threadPropertyDict['script-path']))
+ fullPathCrc32 = (os.path.join(absolutePath, CRC32_PATH))
+ if os.path.exists(fullPathCrc32):
+ args = [fullPathCrc32, filename]
+ p = subprocess.Popen(args, stdout=subprocess.PIPE)
+ cksum = (p.communicate()[0])
+ print("Calculated crc32 checksum for: "+ os.path.basename(filename) + " " + cksum)
+ else:
+ cksum = 0 & 0xFFFFFFFF
+ return cksum
+
+def getFileNames(path):
+ '''
+ 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, FASTQ_GZ_PATTERN):
+ matches.append(os.path.join(root, filename))
+ matches.sort()
+ return(matches)
+
+def writeMetadataFile(transaction, folder_name, meta_data_file_name, sequencing_sample_properties_dict,
+ fcMetaDataDict, experiment, affiliation_name, fastqFileList, flowLane):
+ '''
+ Writes a file of meta data related to one sample
+ '''
+
+ sequencing_sample_properties_list = sequencing_sample_properties_dict.keys()
+ sequencing_sample_properties_list.sort()
+
+ expId = experiment.getExperimentIdentifier()
+ try:
+ meta_data_file = open(meta_data_file_name,'w')
+ for propertyType in sequencing_sample_properties_list:
+ if (propertyType in [u'FLOW_CELL_PROPERTIES']):
+ continue
+ if propertyType in [SAMPLE_TYPE] or propertyType in [SAMPLE_CODE]:
+ meta_data_file.write(propertyType.encode('utf-8') + "\t" +
+ str(sequencing_sample_properties_dict[propertyType])+ "\n")
+ else:
+ meta_data_file.write(propertyType.encode('utf-8') + "\t" +
+ sequencing_sample_properties_dict[propertyType].encode('utf-8').replace('\n',',') + "\n")
+
+ meta_data_file.write("EXPERIMENT\t" + expId + "\n".encode('utf-8'))
+ meta_data_file.write("\nFLOWCELL PROPERTIES\n".encode('utf-8'))
+ fcMetaDataDict["LANE_NUMBER"] = flowLane
+ keys = fcMetaDataDict.keys()
+ keys.sort()
+
+ sequencer_vocabulary_description = get_vocabulary_descriptions(transaction, 'SEQUENCER')
+ meta_data_file.write('SEQUENCER_MODEL' + "\t" + sequencer_vocabulary_description[fcMetaDataDict['SEQUENCER']].encode('utf-8') + "\n")
+
+ for k in keys:
+ 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")
+
+ except IOError:
+ print ('File error, could not write '+ file)
+ finally:
+ meta_data_file.close()
+
+ destinationFolder = folder_name
+ #extraCopy (affiliation_name, meta_data_file_name)
+ #extraCopySciCore (affiliation_name, meta_data_file_name, destinationFolder)
+
+def create_openbis_timestamp ():
+ '''
+ 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 sortedDictValues(adict):
+ '''
+ Given a dictionary it returns the values of this dict sorted
+ by the keys
+ d = {2:1, 4:1, 1:1, 100:3, 3:5}
+ sortedDictValues(d)
+ [1, 1, 5, 1, 3]
+ '''
+ keys = adict.keys()
+ keys.sort()
+ return map(adict.get, keys)
+
+# -------------------------------------------------------------------------------
+
+def extraCopy (affiliation_name, path):
+ '''
+ @deprecated: replaced with extraCopySciCore
+ Handles the extra copies of the data for transfer with datamover via the
+ bc2 network to the FMI and BIOCENTER
+ For the BIOCENTER there is a folder created in which all data gets into
+ '''
+ if (affiliation_name in AFFILIATION):
+ if (affiliation_name == 'BIOCENTER_BASEL' or affiliation_name == 'NEUROSTEMX' ):
+ dirname = AFFILIATION[affiliation_name] + datetime.now().strftime("%Y-%m-%d")
+ if not os.path.exists(dirname):
+ os.mkdir(dirname)
+ shutil.copy(path, dirname)
+ else:
+ shutil.copy(path, AFFILIATION[affiliation_name])
+
+# -------------------------------------------------------------------------------
+
+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'
+ basename = os.path.basename(filePath)
+
+ print("extraCopySciCore")
+ print basename
+ print affiliation_name
+
+ if (affiliation_name in ['BIOCENTER_BASEL', 'NEUROSTEMX', 'SWISS_TPH']):
+ dirname = os.path.join(dropBoxFolder, destinationFolder)
+ if not os.path.exists(dirname):
+ os.mkdir(dirname)
+ print("COPYING " + filePath + " TO " + dirname)
+ shutil.copy(filePath, dirname)
+
+# -------------------------------------------------------------------------------
+
+def get_sample_properties (transaction, sample):
+
+ sample_properties_dict = {}
+ # returns Map<String, String>
+ sample_properties = sample.getSample().getProperties()
+ sequencing_sample_type = sample.getSampleType()
+ sequencing_sample_code = sample.getCode()
+ sample_properties_dict[SAMPLE_TYPE] = sequencing_sample_type
+ sample_properties_dict[SAMPLE_CODE] = sequencing_sample_code
+
+ for property in sample_properties:
+ code = property.getPropertyType().getSimpleCode()
+ sample_properties_dict[code] = property.tryGetAsString()
+
+ return sample_properties_dict
+
+# -------------------------------------------------------------------------------
+
+def searchParents (search_service, parents):
+
+ # search for the parents
+ sc = SearchCriteria()
+ # set the Search Criteria to an OR condition, default is AND
+ sc.setOperator(SearchCriteria.SearchOperator.MATCH_ANY_CLAUSES)
+ # Get the codes for all parents
+ for parent in parents:
+ parentSubCode = parent.getSubCode()
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, parentSubCode));
+ # all parents of the flow lane
+ foundParents = search_service.searchForSamples(sc)
+
+ return foundParents
+
+# -------------------------------------------------------------------------------
+
+def sanitizeString(myString):
+ return re.sub('[^A-Za-z0-9]+', '_', myString)
+
+# -------------------------------------------------------------------------------
+
+def searchSample (sample_code, search_service):
+ sc = SearchCriteria()
+ print('Searching sample: '+ str(sample_code))
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sample_code));
+ foundSamples = search_service.searchForSamples(sc)
+ return foundSamples
+
+
+def renameFiles (fastq_files, undetermined, flow_cell_id):
+
+ newFastqFileList = []
+ for file in fastq_files:
+ if undetermined:
+ folder = os.path.dirname(file)
+ fileName = os.path.basename(file)
+ filepart, suffix = fileName.split('.',1)
+ new_file = folder + "/" + flow_cell_id + '_' + filepart + "." + suffix
+ print ("Renaming file " + file + " to " + new_file)
+ os.rename(file, new_file)
+ else:
+ new_file = file
+ newFastqFileList.append(new_file)
+ return newFastqFileList
+
+# -------------------------------------------------------------------------------
+
+def put_files_to_dataset (transaction, dataSet, fastq_files, folder_name, flow_cell_id, affiliation_name, undetermined):
+
+ for file in fastq_files:
+ extraCopySciCore (affiliation_name, file, folder_name)
+ transaction.moveFile(file, dataSet, folder_name)
+
+# -------------------------------------------------------------------------------
+
+def split_incoming_folder_name (name):
+ split=name.split("_")
+
+ # expected incoming Name, e.g.: BSSE_QGF_22266_H0W8YBGXX_1
+ if (len(split) == 5):
+ sample_code = '-'.join([split[0], split[1], split[2]])
+ flowCellId = split[3]
+ flowLane = split[-1]
+ undetermined = False
+
+ # expected Undetermined_H0W8YBGXX
+ if (len(split) == 2):
+ sample_code = ''
+ flowCellId = split[-1]
+ flowLane = "1"
+ undetermined = True
+
+ incoming_sample = flowCellId + ':' + flowLane
+ return sample_code, flowCellId, flowLane, incoming_sample, undetermined
+
+# -------------------------------------------------------------------------------
+
+def get_vocabulary_descriptions (transaction, vocabulary_name):
+ vocabulary_descriptions_dict = {}
+ vocabulary = transaction.getVocabulary(vocabulary_name)
+ vocabulary_terms = vocabulary.getTerms()
+ for term in vocabulary_terms:
+ vocabulary_descriptions_dict[term.getCode()] = term.getDescription()
+ return vocabulary_descriptions_dict
+
+# -------------------------------------------------------------------------------
+
+def process(transaction):
+
+ undetermined = False
+
+ print("\n" + str(datetime.now()))
+
+ incomingPath = transaction.getIncoming().getAbsolutePath()
+ name = transaction.getIncoming().getName()
+ # Get the search service
+ search_service = transaction.getSearchService()
+
+ def searchSampleInSpace (type, search_service):
+
+ spaceCode = "UNI_BASEL_GAGNEUX"
+ sc = SearchCriteria()
+# print('Searching sample: '+ str(code))
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.SPACE, spaceCode));
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, type));
+ foundSamples = search_service.searchForSamples(sc)
+ return foundSamples
+
+ samples = searchSampleInSpace("ILLUMINA_SEQUENCING", search_service)
+ print(samples.size())
+
+
+
+
+ for sample in samples[0:5]:
+
+ sequencing_sample_properties_dict = get_sample_properties (transaction, sample)
+ meta_data_file_name = sequencing_sample_properties_dict["SAMPLE_CODE"] + METADATA_FILE_SUFFIX
+
+ sampleName = sequencing_sample_properties_dict["SAMPLE_CODE"]
+
+ print(meta_data_file_name)
+ print(sequencing_sample_properties_dict)
+
+ flowCellId = "150109_D00535_0042_AHB2K0ADXX"
+
+ flowcell_sample_immutable = searchSample (flowCellId, search_service)
+ fcMetaDataDict = get_sample_properties(transaction, flowcell_sample_immutable[0])
+
+ experiment = sample.getExperiment()
+ affiliation_name = "dummy"
+ flowLane = "1"
+ newFastqFiles = ["/tmp/hello.txt", "/tmp/bio.txt"]
+
+ meta_data_file_path = '/tmp/metadata_'+ sampleName
+
+ DATA_SOURCE = "pathinfo_dev"
+ QUERY = """
+ SELECT ds.code as "data_set_code", dsf.*
+ FROM data_sets ds, data_set_files dsf
+ WHERE ds.code = ?{1} AND dsf.dase_id = ds.id
+ """
+
+ dsqs = DataSourceQueryService()
+
+ dsqs.select(DATA_SOURCE, QUERY)
+ #results = queryService.select(DATA_SOURCE, QUERY, ['20150108225105804-60446532'])
+ print(results)
+
+
+ writeMetadataFile(transaction, sampleName, meta_data_file_path, sequencing_sample_properties_dict,
+ fcMetaDataDict, experiment, affiliation_name, newFastqFiles, flowLane)
+
+# sample_code, flowCellId, flowLane, incoming_sample, undetermined = split_incoming_folder_name (name)
+#
+# # get all fastqs
+# fastq_files=getFileNames(incomingPath)
+#
+# # BSSE-QGF-22266-H0W8YBGXX-1-654-BC3-TTAGGC_S1_L001_R1_001.fastq.gz
+# # BSSE-QGF-22051-H0T25AGXX-1-1-1-TAAGGCGA-CTCTCTAT_S46_L001_R1_001.fastq.gz
+# first_fastq_file = os.path.basename(fastq_files[0])
+#
+# flowcell_sample_immutable = searchSample (flowCellId, search_service)
+# fcMetaDataDict = get_sample_properties(transaction, flowcell_sample_immutable[0])
+# foundLane = searchSample (incoming_sample, search_service)
+#
+# # there should be only one sample because it is unique within one Flow Cell
+# if (len(foundLane) > 1):
+# raise Exception("More than one sample found! No unique code: " + incoming_sample)
+# elif (len(foundLane) == 0):
+# raise Exception("No matching sample found for: " + incoming_sample)
+# else :
+# sample = foundLane[0].getSample()
+# parents = sample.getParents()
+#
+# # Create a data set and set type
+# dataSet = transaction.createNewDataSet("FASTQ_GZ")
+# dataSet.setMeasuredData(False)
+# dataSet.setPropertyValue(INDEX1, DEFAULT_INDEX)
+# dataSet.setPropertyValue(INDEX2, DEFAULT_INDEX)
+# dirName = transaction.createNewDirectory(dataSet,name)
+#
+# if not undetermined:
+# newFastqFiles = fastq_files
+# foundSample = searchSample (sample_code, search_service)
+# sequencing_sample = foundSample[0].getSample()
+# experiment = sequencing_sample.getExperiment()
+# sequencing_sample_code = sequencing_sample.getCode()
+# print("sequencing_sample_code: "+ sequencing_sample_code)
+#
+# sequencing_sample_properties_dict = get_sample_properties (transaction, foundSample[0])
+#
+# if (INDEX1 in sequencing_sample_properties_dict) and (fcMetaDataDict[INDEXREAD1] > 0):
+# #print(sequencing_sample_properties_dict[INDEX1])
+# dataSet.setPropertyValue(INDEX1, sequencing_sample_properties_dict[INDEX1])
+# if (INDEX2 in sequencing_sample_properties_dict) and (fcMetaDataDict[INDEXREAD2] > 0):
+# dataSet.setPropertyValue(INDEX2, sequencing_sample_properties_dict[INDEX2])
+# dataSet.setPropertyValue(EXTERNAL_SAMPLE_NAME, sequencing_sample_properties_dict[EXTERNAL_SAMPLE_NAME])
+#
+# if (AFFILIATION_PROPERTY_NAME in sequencing_sample_properties_dict):
+# affiliation_name = sequencing_sample_properties_dict[AFFILIATION_PROPERTY_NAME]
+#
+# filepart, suffix = first_fastq_file.split('.',1)
+# meta_data_file_name = filepart.rsplit('_',2)[0] + METADATA_FILE_SUFFIX
+# # get a file from the IDataSetRegistrationTransaction so it is automatically part of the data set
+# meta_data_file_path = transaction.createNewFile(dataSet, name, meta_data_file_name)
+# writeMetadataFile(transaction, name, meta_data_file_path, sequencing_sample_properties_dict,
+# fcMetaDataDict, experiment, affiliation_name, fastq_files, flowLane)
+#
+# # Undetermined Files
+# else:
+# affiliation_name = ""
+# affiliation_for_Undetermined = ""
+# newFastqFiles = []
+# lane_parents = searchParents (search_service, parents)
+# newFastqFiles = renameFiles(fastq_files, undetermined, flowCellId)
+# for parent in lane_parents:
+# sequencing_sample_properties_dict = get_sample_properties (transaction, parent)
+# parent_sample = parent.getSample()
+# sample_code = parent_sample.getCode()
+# experiment = parent_sample.getExperiment()
+# if (AFFILIATION_PROPERTY_NAME in sequencing_sample_properties_dict):
+# affiliation_name = sequencing_sample_properties_dict[AFFILIATION_PROPERTY_NAME]
+#
+# # Special Sample Types without index (e.g. ILLUMINA_SEQUENCING_NEUROSTEMX_SINGLECELL) are caught here.
+# # as those samples do not have a NCBI ORGANISM TAXONOMY
+# if NCBI_ORGANISM_TAXONOMY not in sequencing_sample_properties_dict:
+# print(sample_code + ": Processing Sample without NCBI ORGANISM TAXONOMY: ILLUMINA_SEQUENCING_NEUROSTEMX_SINGLECELL")
+# meta_data_file_path = transaction.createNewFile(dataSet, name, sample_code + '_' + flowCellId + '_' + first_fastq_file.split('.')[0] + METADATA_FILE_SUFFIX)
+# writeMetadataFile(transaction, name, meta_data_file_path, sequencing_sample_properties_dict,
+# fcMetaDataDict, experiment, affiliation_name, newFastqFiles, flowLane)
+# affiliation_for_Undetermined = affiliation_name
+#
+# elif (INDEX1 not in sequencing_sample_properties_dict) and (INDEX2 not in sequencing_sample_properties_dict) and \
+# (sequencing_sample_properties_dict[NCBI_ORGANISM_TAXONOMY] != PHIX_TAXONOMY_ID):
+# print('NONINDEXED sample and Taxonomy id is NOT' + PHIX_TAXONOMY_ID +', probably a pool: ' + sample_code)
+# meta_data_file_path = transaction.createNewFile(dataSet, name, sample_code + '_' + flowCellId + '_' + first_fastq_file.split('.')[0] + METADATA_FILE_SUFFIX)
+# writeMetadataFile(transaction, name, meta_data_file_path, sequencing_sample_properties_dict,
+# fcMetaDataDict, experiment, affiliation_name, newFastqFiles, flowLane)
+# affiliation_for_Undetermined = affiliation_name
+# # PARENTS:
+# else:
+# # Create Parent Meta data
+# 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, affiliation_name, [], flowLane)
+# continue
+#
+# put_files_to_dataset (transaction, dataSet, newFastqFiles, name, flowCellId, affiliation_for_Undetermined, undetermined)
+#
+# if foundLane.size() > 0:
+# sa = transaction.getSampleForUpdate(foundLane[0].getSampleIdentifier())
+# sa.setPropertyValue("DATA_TRANSFERRED", create_openbis_timestamp())
+# dataSet.setSample(foundLane[0])
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/export-meta-data/lib/crc32 b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/export-meta-data/lib/crc32
new file mode 100755
index 0000000000000000000000000000000000000000..ffaf277227c6dfb0dae3fbe751d9db158bd5ae29
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diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/export-meta-data/plugin.properties b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/export-meta-data/plugin.properties
new file mode 100644
index 00000000000..6e3d93e5e91
--- /dev/null
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/export-meta-data/plugin.properties
@@ -0,0 +1,12 @@
+#
+# Drop box for registering a flow cell output as a data set
+#
+# Variables:
+# incoming-root-dir
+# Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/export-meta-data
+incoming-data-completeness-condition = marker-file
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+script-path = export-meta-data.py
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/plugin.properties b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/plugin.properties
index af28b8443a7..102a5fe3f83 100644
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/plugin.properties
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/plugin.properties
@@ -2,7 +2,7 @@
# Variables:
# incoming-root-dir
# Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/read-demultiplex-stats-nextseq
+incoming-dir = ${incoming-root-dir}/read-demultiplex-stats-nextseq
incoming-data-completeness-condition = marker-file
top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
script-path = read-demultiplex-stats-nextseq.py
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read-demultiplex-stats-nextseq.py b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read-demultiplex-stats-nextseq.py
index 4be28cc09e8..50bdbc493a0 100755
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read-demultiplex-stats-nextseq.py
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read-demultiplex-stats-nextseq.py
@@ -1,545 +1,328 @@
'''
- @copyright: 2012 ETH Zuerich, CISD
-
- @license:
- Licensed under the Apache License, Version 2.0 (the "License");
- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
-
-
-@author: Manuel Kohler
-
-XML Structur which is processed:
-
-<?xml version="1.0"?>
-<Summary>
- <Lane index="8">
- <Sample index="lane8">
- <Barcode index="Undetermined">
- <Tile index="1101">
- <Read index="1">
- <Raw>
- <Yield>1921250</Yield>
- <YieldQ30>949680</YieldQ30>
- <ClusterCount>38425</ClusterCount>
- <ClusterCount0MismatchBarcode>0</ClusterCount0MismatchBarcode>
- <ClusterCount1MismatchBarcode>0</ClusterCount1MismatchBarcode>
- <QualityScoreSum>40995660</QualityScoreSum>
- </Raw>
- <Pf>
- <Yield>945450</Yield>
- <YieldQ30>854815</YieldQ30>
- <ClusterCount>18909</ClusterCount>
- <ClusterCount0MismatchBarcode>0</ClusterCount0MismatchBarcode>
- <ClusterCount1MismatchBarcode>0</ClusterCount1MismatchBarcode>
- <QualityScoreSum>33815505</QualityScoreSum>
- </Pf>
- </Read>
- </Tile>
- [...]
-
-@note:
-print statements go to: <openBIS_HOME>/datastore_server/log/startup_log.txt
-'''
-
-import time
-import os
-import fnmatch
-import xml.etree.ElementTree as etree
-from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
-from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria
-
-
-class parseXmlFile:
-
- def __init__(self, xmlFile):
- self.xmlFile = xmlFile
- self.tree = etree.parse(self.xmlFile)
- self.root = self.tree.getroot()
-
-# -----------------------------------------------------------------------------
-
-class qcValues(object):
- def __init__(self, Yield = 0, YieldQ30 = 0, ClusterCount = 0,
- ClusterCount0MismatchBarcode = 0, ClusterCount1MismatchBarcode = 0,
- QualityScoreSum = 0, *args, **kwargs):
- self.Yield = Yield
- self.YieldQ30 = YieldQ30
- self.ClusterCount = ClusterCount
- self.ClusterCount0MismatchBarcode = ClusterCount0MismatchBarcode
- self.ClusterCount1MismatchBarcode = ClusterCount1MismatchBarcode
- self.QualityScoreSum = QualityScoreSum
-
- def __str__(self):
- return "Yield: %s, YieldQ30: %s, ClusterCount: %s, ClusterCount0MismatchBarcode: %s," \
- " CusterCount1MismatchBarcode: %s, QualityScoreSum: %s" \
- % (self.Yield, self.YieldQ30, self.ClusterCount, self.ClusterCount0MismatchBarcode,
- self.ClusterCount1MismatchBarcode, self.QualityScoreSum)
-
-class sample:
- def __init__(self, Lane = 0, Sample = '', Barcode = '', Tile = '', Read = '', rawqc = qcValues([]),
- pfqc = qcValues([]), *args, **kwargs):
- self.Lane = Lane
- self.Sample = Sample
- self.Barcode = Barcode
- self.Tile = Tile
- self.Read = Read
- self.rawqc = rawqc
- self.pfqc = pfqc
-
- def __str__(self):
- return "Lane: %s, Sample: %s, Barcode: %s, Tile: %s, Read: %s, rawqc: %s, pfqc: %s" \
- % (self.Lane, self.Sample, self.Barcode, self.Tile, self.Read, self.rawqc, self.pfqc)
-
-# -----------------------------------------------------------------------------
-
-class Statistics:
- def __init__(self, lane = 0, sampleName = "", index1 = "NoIndex", index2 = "NoIndex", pfYieldSum = 0,
- rawYieldSum = 0, pfPercentage = 0.0, rawReadsSum = 0, pfReadsSum = 0,
- pfYieldQ30Sum = 0, qualityScoreSum = 0, rawPercentageReadsPerLane = 0.0,
- pfYieldQ30Percentage = 0.0, pfsumQualityScore = 0, pfmeanQualityScore = 0.0):
- self.lane = lane
- self.sampleName = sampleName
- self.index1 = index1
- self.index2 = index2
- self.pfYieldSum = pfYieldSum
- self.rawYieldSum = rawYieldSum
- self.pfPercentage = pfPercentage
- self.rawReadsSum = rawReadsSum
- self.pfReadsSum = pfReadsSum
- self.pfYieldQ30Sum = pfYieldQ30Sum
- self.qualityScoreSum = qualityScoreSum
- self.rawPercentageReadsPerLane = rawPercentageReadsPerLane
- self.pfYieldQ30Percentage = pfYieldQ30Percentage
- self.pfsumQualityScore = pfsumQualityScore
- self.pfmeanQualityScore = pfmeanQualityScore
-
- def __str__(self):
- return "lane: %s, sampleName: %s, index1: %s, index2: %s, pfYieldSum: %s, pfPercentage: %s," \
- " rawReadsSum: %s, pfReadsSum: %s," \
- " rawPercentageReadsPerLane: %s, pfYieldQ30Percentage: %s," \
- " pfmeanQualityScore: %s" \
- % (self.lane, self.sampleName, self.index1, self.index2, self.pfYieldSum, self.pfPercentage,
- self.rawReadsSum, self.pfReadsSum,
- self.rawPercentageReadsPerLane, self.pfYieldQ30Percentage, self.pfmeanQualityScore)
-
- def calculatePercentagePF (self, rawYield = 0, pfYield = 1):
- try:
- return round(float(pfYield) / float(rawYield) * 100, 2)
- except:
- return 0.0
-
- def calulateMeanQualityScore (self, pfqualityScoreSum = 0, pfYield = 1):
- try:
- return round (float(pfqualityScoreSum) / float(pfYield), 2)
- except:
- return 0.0
-
- def calculateYieldQ30Percentage (self, pfYieldQ30 = 0, pfYield = 1):
- try:
- return round (float(pfYieldQ30) / float(pfYield) * 100, 2)
- except:
- return 0.0
-
-# -----------------------------------------------------------------------------
-
-def xml2Memory(DEMULTIPLEX_XML):
- '''
- Parse the XML file and put all values in a memory structure:
- List of:
- lane, sample, barcode, tile, read, qcRawList, qcPfList
- '''
-
- RAW_TAG = "Raw"
- PF_TAG = "Pf"
-
- sampleList = []
-
- xml = parseXmlFile(DEMULTIPLEX_XML)
- r = xml.tree.getroot()
-
- for lane in r.getchildren():
- for mysample in lane:
- for barcode in mysample:
- for tile in barcode:
- for read in tile:
-
- qcRaw = qcValues()
- qcPf = qcValues()
- qcRawList = []
- qcPfList = []
-
- # Read out the Raw fields
- raw = read.find(RAW_TAG)
- for child in raw.getchildren():
- # equivalent to a Java reflection
- setattr(qcRaw, child.tag, int(child.text))
-
- # Read out the Pf fields
- pf = read.find(PF_TAG)
- for child in pf.getchildren():
- # equivalent to a Java reflection
- setattr(qcPf, child.tag, int(child.text))
-
- qcRawList.append(qcRaw)
- qcPfList.append(qcPf)
-
- singleElement = sample ()
-
- setattr(singleElement, lane.tag, lane.attrib)
- setattr(singleElement, mysample.tag, mysample.attrib)
- setattr(singleElement, barcode.tag, barcode.attrib)
- setattr(singleElement, tile.tag, tile.attrib)
- setattr(singleElement, read.tag, read.attrib)
- singleElement.rawqc = qcRawList
- singleElement.pfqc = qcPfList
-
- sampleList.append(singleElement)
- return sampleList
-
-# -----------------------------------------------------------------------------
-
-def calculateStatistics(listofSamples):
- '''
- Structure of 'listofSamples'
- Lane: {'index': '6'}, Sample: {'index': 'BSSE-QGF-3524_C0NKPACXX'}, Barcode: {'index': 'TGACCA'},
- Tile: {'index': '2307'}, Read: {'index': '1'}, rawqc:<mem>, pfqc:<mem>
- '''
-
- numberOfTiles = len(listofSamples)
-
- tile = sample()
- raw = qcValues ()
- pf = qcValues ()
- stats = Statistics()
-
- for tile in listofSamples:
- raw = tile.rawqc[0]
- pf = tile.pfqc[0]
-
- stats.pfYieldSum += pf.Yield
- stats.rawYieldSum += raw.Yield
- stats.rawReadsSum += raw.ClusterCount
- stats.pfReadsSum += pf.ClusterCount
- stats.pfYieldQ30Sum += pf.YieldQ30
- stats.qualityScoreSum += pf.QualityScoreSum
-
- # Can not be set here, needs to be calculated later
- #stats.rawPercentageReadsPerLane = rawPercentageReadsPerLane
- stats.pfPercentage = stats.calculatePercentagePF(stats.rawYieldSum, stats.pfYieldSum)
- stats.pfYieldQ30Percentage = stats.calculateYieldQ30Percentage(stats.pfYieldQ30Sum, stats.pfYieldSum)
- stats.pfmeanQualityScore = stats.calulateMeanQualityScore(stats.qualityScoreSum, stats.pfYieldSum)
- stats.lane = listofSamples[0].Lane.values()[0]
- stats.sampleName = listofSamples[0].Sample.values()[0]
- index = listofSamples[0].Barcode.values()[0]
- try:
- stats.index1, stats.index2 = index.split("-")
- except:
- stats.index1 = index
- return stats
-
-# -----------------------------------------------------------------------------
-
-
-def rawReadSumPerSamples(stat):
- '''
- Creates a dictionary with the lanes as keys
- The values are a list where the elements are a dictionary again.
- This dictionary has the sample names as key and the RawReadSum as value.
-
- Example:
- {4': [{'BSSE-QGF-3434_C0NKPACXX': 248999502}], '7': [{'lane7': 123921974},
- {'BSSE-QGF-3527_C0NKPACXX': 38587703}, {'BSSE-QGF-3529_C0NKPACXX': 30130893},
- {'BSSE-QGF-3528_C0NKPACXX': 34519296}, {'BSSE-QGF-3526_C0NKPACXX': 34980179}]}
- '''
-
- laneDict = {}
- for e in stat:
- if e.lane not in laneDict:
- laneDict[e.lane] = [{e.sampleName:e.rawReadsSum}]
- else:
- laneDict[e.lane].append({e.sampleName:e.rawReadsSum})
- return laneDict
-
-# -----------------------------------------------------------------------------
-
-def createSumRawReadsPerLane(laneDict):
- '''
- Creates a dictionary with lane as key and sum of Raw Reads as value:
- {'1': 183180877, '3': 244968562, '2': 191496395, '5': 193466239, '4': 248999502,
- '7': 262140045, '6': 257136830, '8': 209948449}
- '''
- sumRawReadsDict = {}
- for lane in laneDict:
- sumRawReads = 0
- for sampleNameDict in laneDict[lane]:
- sumRawReads += sampleNameDict.values()[0]
-
- sumRawReadsDict[lane] = sumRawReads
- return sumRawReadsDict
-
-# -----------------------------------------------------------------------------
-
-def createPercentagePerLane(laneDict, sumRawReadsDict):
- '''
- Creates a dictionary with the sample Name as key and the percentage of raw reads related to
- all reads in the same lane
- {'lane7': 47.27, 'BSSE-QGF-3433_C0NKPACXX': 100.0, 'BSSE-QGF-3666_C0NKPACXX': 54.12}
- '''
-
- relRawReadsDict = {}
- for lane in laneDict:
- for sampleName in laneDict[lane]:
- relRawReadsDict[sampleName.keys()[0]] = round(float(sampleName.values()[0]) /
- float(sumRawReadsDict[lane]) * 100, 2)
- return relRawReadsDict
-
-# -----------------------------------------------------------------------------
-
-def locate(pattern, root):
- '''Locate all files matching supplied filename pattern in and below
- supplied root directory.'''
- for path, dirs, files in os.walk(os.path.abspath(root)):
- for filename in fnmatch.filter(files, pattern):
- yield os.path.join(path, filename)
-
-# -----------------------------------------------------------------------------
-
-def getVocabulary(transaction, vocabularyCode):
-
- vocabularyTermList = []
- vocabulary = transaction.getSearchService().searchForVocabulary(vocabularyCode)
- if (vocabulary is None):
- print 'VOCABULARY %s does not exist' % (vocabularyCode)
- else:
- print "Getting VOCABULARY: " + vocabulary.getCode()
- for term in vocabulary.getTerms():
- vocabularyTermList.append(term.getCode())
- vocabularyTermList.sort()
- return vocabularyTermList
+@copyright: 2012 ETH Zuerich, CISD
-# -----------------------------------------------------------------------------
+@license:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
-def getFlowCellMetaData (transaction,flowCellId):
+ http://www.apache.org/licenses/LICENSE-2.0
- def sortedDictValues(adict):
- keys = adict.keys()
- keys.sort()
- return map(adict.get, keys)
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- search = transaction.getSearchService()
- sc = SearchCriteria()
- print('Searching FlowCell: '+ str(flowCellId))
- sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, flowCellId));
- foundFlowCells = search.searchForSamples(sc)
+@author: Fabian Gemperle
- try:
- assert foundFlowCells.size() == 1
- except AssertionError:
- print (str(foundFlowCells.size()) + \
- ' flow cells found which match the criterias: '+ flowCellId)
+@note: print statements go to ~/openbis/servers/datastore_server/log/startup_log.txt
- fcPropertiesDict = {}
- fcPropertyTypes = []
-
- fcProperties = foundFlowCells[0].getSample().getProperties()
- for property in fcProperties:
- code = property.getPropertyType().getSimpleCode()
- fcPropertyTypes.append(code)
- fcPropertiesDict[code] = property.getValue()
-
- fcPropertyTypes.sort()
- return fcPropertiesDict, fcPropertyTypes
+'''
+import time
+import math
+import os
+import fnmatch
+# Load Java-Library to import XML data:
+import read_demultiplex_stats
+# Load openBIS-Libraries:
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria
-# -----------------------------------------------------------------------------
def process(transaction):
'''
- Main
+ Main method in corresponding openBIS dropbox
'''
- FASTQ_DATA_SET_TYPE='FASTQ_GZ'
- DEMUX_FILE='Flowcell_demux_summary.xml'
- NO_INDEX='NOINDEX'
- UNDETERMINED='UNDETERMINED'
-
- incomingPath = transaction.getIncoming().getPath()
- name = transaction.getIncoming().getName()
-
- print('\n'+time.ctime())
-
- fcPropertiesDict, fcPropertyTypes = getFlowCellMetaData(transaction, name)
- print fcPropertiesDict
- print fcPropertyTypes
-
- search_service = transaction.getSearchService()
-
- FileGenerator= locate(DEMUX_FILE, incomingPath)
- DEMULTIPLEX_XML = FileGenerator.next()
-
- sampleList = xml2Memory(DEMULTIPLEX_XML)
-
- sa = sample()
- sampleDict = {}
-
- # key = sample name, value = sample()
- for element in range(0, len(sampleList)):
- sa = sampleList[element]
- # Check if new sample
- if (sa.Sample is not sampleList[element - 1].Sample):
- sampleName = sa.Sample.values()[0]
- sampleDict[sampleName] = [sa]
+ # Constants:
+ XML_FILENAME = 'ConversionStats.xml'
+ TYPE_DATASET = 'FASTQ_GZ'
+ INDEX_NO = 'NOINDEX'
+ INDEX_UNKNOWN = 'UNKNOWN'
+ INDEX_EMPTY = ''
+ CODE_INDEX1 = 'BARCODE'
+ CODE_INDEX2 = 'INDEX2'
+ CODE_INDEX1LENGTH = 'INDEXREAD'
+ CODE_INDEX2LENGTH = 'INDEXREAD2'
+
+ ##########################################################
+ def locate(pattern, root):
+ '''Locate all files matching supplied filename pattern in and below supplied root directory.'''
+ for path, dirs, files in os.walk(os.path.abspath(root)):
+ for filename in fnmatch.filter(files, pattern):
+ yield os.path.join(path, filename)
+
+ ##########################################################
+ def getInfoVocabularyTerms(vocabularyCode):
+ '''
+ Get information about Terms of certain Vocabulary in openBIS.
+ Input:
+ - vocabularyCode: code of Vocabulary to be investigated
+ Output:
+ - vocabularyTerms: list of Terms in Vocabulary
+ '''
+ vocabulary = transaction.getSearchService().searchForVocabulary(vocabularyCode)
+
+ vocabularyTerms = []
+ if (vocabulary is None):
+ print '\nOCCURRED EXCEPTION: Vocabulary %s does not exist' % (vocabularyCode)
else:
- sampleDict[sampleName].append(sa)
-
- stat = [calculateStatistics(sampleDict[mysample]) for mysample in sampleDict]
-
- # calculate the relative amount of reads per index
- laneDict = rawReadSumPerSamples(stat)
- sumRawReadsDict = createSumRawReadsPerLane(laneDict)
- relRawReadsDict = createPercentagePerLane(laneDict, sumRawReadsDict)
-
- # set the values in the object
- for mye in stat:
- mye.rawPercentageReadsPerLane = relRawReadsDict[mye.sampleName]
-
- def sampleSearch(Code=''):
- sc = SearchCriteria()
- numberOfLanes = 0
- sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, Code));
- search_service = transaction.getSearchService()
- foundSample = search_service.searchForSamples(sc)
- if foundSample.size() > 0:
- # Search for contained samples
- sampleSc = SearchCriteria()
- sampleSc.addSubCriteria(SearchSubCriteria.createSampleContainerCriteria(sc))
- foundContainedSamples = search_service.searchForSamples(sampleSc)
- numberOfLanes = foundContainedSamples.size()
- return foundSample, foundContainedSamples, numberOfLanes
-
-#--------------------------------------------------------------------------------------------------------------------------------------
-
- def searchDataSetsofSample(sample, index1, index2, DATA_SET_TYPE):
- sc = SearchCriteria()
- sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sample));
- search_service = transaction.getSearchService()
- foundSample = search_service.searchForSamples(sc)
-
- dataSetSc = SearchCriteria()
- # set the Search Criteria to an OR condition, default is AND
- #dataSetSc.setOperator(SearchCriteria.SearchOperator.MATCH_ANY_CLAUSES)
- dataSetSc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, DATA_SET_TYPE))
- dataSetSc.addMatchClause(SearchCriteria.MatchClause.createPropertyMatch("BARCODE", index1 ))
- dataSetSc.addMatchClause(SearchCriteria.MatchClause.createPropertyMatch("INDEX2", index2))
- dataSetSc.addSubCriteria(SearchSubCriteria.createSampleCriteria(sc))
- foundDataSets = search_service.searchForDataSets(dataSetSc)
- print "foundDataSets.size() "+ str(foundDataSets.size())
+ for term in vocabulary.getTerms():
+ vocabularyTerms.append(term.getCode())
+ vocabularyTerms.sort()
+
+ return vocabularyTerms
+
+ ##########################################################
+ def getInfoSampleProperties(sampleCode):
+ '''
+ Get information about Properties of certain Sample in openBIS.
+ Input:
+ - sampleCode: code of Sample to be investigated
+ Outputs:
+ - propertiesCode: list of Properties' codes
+ - propertiesCodeValue: dictionary of Properties' codes and values
+ '''
+ ss = transaction.getSearchService()
+
+ scSample = SearchCriteria()
+ scSample.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode));
+ foundSamples = ss.searchForSamples(scSample)
+
+ propertiesCode = []
+ propertiesCodeValue = {}
+ try:
+ assert foundSamples.size() == 1
+ properties = foundSamples[0].getSample().getProperties()
+ for p in properties:
+ codeProperty = p.getPropertyType().getSimpleCode()
+ propertiesCode.append(codeProperty)
+ propertiesCodeValue[codeProperty] = p.getValue()
+ propertiesCode.sort()
+ except AssertionError:
+ print ('\nOCCURRED EXCEPTION: ' + str(foundSamples.size()) + ' Samples found which match the criteria code \"' + sampleCode + '\".')
+
+ return propertiesCode, propertiesCodeValue
+
+ ##########################################################
+ def getInfoDataSetPropertiesOfSample(sampleCode):
+ '''
+ Get information about Properties of some DataSet of certain Sample in openBIS.
+ Input:
+ - sampleCode: code of DataSet's Sample to be investigated
+ Outputs:
+ - propertiesCode: list of Properties' codes
+ - propertiesCodeValue: dictionary of Properties' codes and values
+ '''
+ ss = transaction.getSearchService()
+
+ scSample = SearchCriteria()
+ scSample.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode));
+ #foundSamples = ss.searchForSamples(scSample)
+
+ scDataSet = SearchCriteria()
+ scDataSet.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, TYPE_DATASET))
+ scDataSet.addSubCriteria(SearchSubCriteria.createSampleCriteria(scSample))
+ foundDataSets = ss.searchForDataSets(scDataSet)
+
+ propertiesCode = []
+ propertiesCodeValue = {}
+ try:
+ assert foundDataSets.size() > 0
+ codeProperties = foundDataSets[0].getAllPropertyCodes()
+ for cp in codeProperties:
+ propertiesCode.append(cp)
+ propertiesCodeValue[cp] = foundDataSets[0].getPropertyValue(cp)
+ propertiesCode.sort()
+ except AssertionError:
+ print ('\nOCCURRED EXCEPTION: ' + str(foundDataSets.size()) + ' DataSets found which Sample match the criteria code \"' + sampleCode + '\" and type \"' + TYPE_DATASET + '\".')
+
+ return propertiesCode, propertiesCodeValue
+
+ ##########################################################
+ def getIndexesOfDataSetsOfSample(sampleFlowLaneCode):
+ '''
+ Get both indexes (parts of barcode) of all DataSets of certain FlowLane-Sample in openBIS.
+ Inputs:
+ - sampleFlowLaneCode: code of DataSet's Sample
+ Outputs:
+ - indexes1: list of first index of DataSets
+ - indexes2: list of second index of DataSets
+ '''
+ ss = transaction.getSearchService()
+
+ scSample = SearchCriteria()
+ scSample.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleFlowLaneCode));
+ #foundSamples = ss.searchForSamples(scSample)
+
+ scDataSet = SearchCriteria()
+ scDataSet.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, TYPE_DATASET))
+ scDataSet.addSubCriteria(SearchSubCriteria.createSampleCriteria(scSample))
+ foundDataSets = ss.searchForDataSets(scDataSet)
+
+ indexes1 = []
+ indexes2 = []
+ try:
+ assert foundDataSets.size() > 0
+ except AssertionError:
+ print ('\nOCCURRED EXCEPTION: ' + str(foundDataSets.size()) + ' DataSets found which Sample match the criteria code \"' + sampleFlowLaneCode + '\" and type \"' + TYPE_DATASET + '\".')
for ds in foundDataSets:
- print "Index1 for found Data Set" + ds.getDataSetCode() + " " + ds.getPropertyValue('BARCODE')
- print "Index2 for found Data Set" + ds.getDataSetCode() + " " + ds.getPropertyValue('INDEX2')
-
- return foundDataSets
-
-#--------------------------------------------------------------------------------------------------------------------------------------
-
- def getIndexesofDataSetsofSample(sample, DATA_SET_TYPE):
-
- index1List = []
- index2List = []
- sc = SearchCriteria()
- sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sample));
- search_service = transaction.getSearchService()
- foundSample = search_service.searchForSamples(sc)
-
- dataSetSc = SearchCriteria()
- dataSetSc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, DATA_SET_TYPE))
- dataSetSc.addSubCriteria(SearchSubCriteria.createSampleCriteria(sc))
- foundDataSets = search_service.searchForDataSets(dataSetSc)
+ indexes1.append(ds.getPropertyValue(CODE_INDEX1))
+ indexes2.append(ds.getPropertyValue(CODE_INDEX2))
+
+ return indexes1, indexes2
+
+ ##########################################################
+ def searchDataSetsOfSample(sampleFlowLaneCode, index1, index2):
+ '''
+ Search DataSets by corresponding indexes (parts of barcode) of certain FlowLane-Sample in openBIS.
+ Inputs:
+ - sampleFlowLaneCode: code of DataSet's Sample
+ - index1: first index of DataSet
+ - index2: second index of DataSet
+ Output:
+ - foundDataSets: DataSets corresponding to inputs and constant TYPE_DATASET
+ '''
+ ss = transaction.getSearchService()
+
+ scSample = SearchCriteria()
+ scSample.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleFlowLaneCode));
+ #foundSample = ss.searchForSamples(scSample)
+
+ scDataSet = SearchCriteria()
+ scDataSet.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, TYPE_DATASET))
+ scDataSet.addMatchClause(SearchCriteria.MatchClause.createPropertyMatch(CODE_INDEX1, index1))
+ scDataSet.addMatchClause(SearchCriteria.MatchClause.createPropertyMatch(CODE_INDEX2, index2))
+ scDataSet.addSubCriteria(SearchSubCriteria.createSampleCriteria(scSample))
+ foundDataSets = ss.searchForDataSets(scDataSet)
for ds in foundDataSets:
- index1List.append(ds.getPropertyValue('BARCODE'))
- index2List.append(ds.getPropertyValue('INDEX2'))
- return index1List, index2List
-
-
- flowcell, lanes, numberOfLanes = sampleSearch(name)
+ print "Index1 of found DataSet " + ds.getDataSetCode() + ": " + ds.getPropertyValue(CODE_INDEX1)
+ print "Index2 of found DataSet " + ds.getDataSetCode() + ": " + ds.getPropertyValue(CODE_INDEX2)
- index1Length = fcPropertiesDict['INDEXREAD']
- index2Length = fcPropertiesDict['INDEXREAD2']
-
- for mystat in stat:
- laneCode = flowcell[0].getCode() + ":" + mystat.lane
- searchIndex1 = mystat.index1.upper()
- searchIndex2 = mystat.index2.upper()
- print '\n'
- print mystat
-
- index1List, index2List = getIndexesofDataSetsofSample(laneCode, FASTQ_DATA_SET_TYPE)
- print "Searching for "+ searchIndex1 + " in " + str(index1List)
- print "Searching for "+ searchIndex2 + " in " + str(index2List)
-
- if searchIndex1 not in (NO_INDEX):
- if searchIndex1 not in (UNDETERMINED):
- if index1Length > 7:
- searchIndex1List = [ index1 for index1 in index1List if searchIndex1 in index1]
- else:
- searchIndex1List = [ index1 for index1 in index1List if searchIndex1 in index1[:-2]]
- try:
- if len(searchIndex1List) > 1:
- if searchIndex1List[0].startswith(searchIndex1):
- searchIndex1 = searchIndex1List[0]
- else:
- searchIndex1 = searchIndex1List[1]
- else:
- searchIndex1 = searchIndex1List[0]
- print searchIndex1
- except:
- searchIndex1 = 'MISSING'
- else:
- searchIndex1 = NO_INDEX
- if searchIndex2 not in (NO_INDEX):
- if searchIndex2 not in (UNDETERMINED):
- if index2Length > 7:
- searchIndex2 = [ index2 for index2 in index2List if searchIndex2 in index2]
- else:
- searchIndex2 = [ index2 for index2 in index2List if searchIndex2 in index2[:-2]]
- try:
- searchIndex2 = searchIndex2[0]
- except:
- searchIndex1 = 'MISSING'
- else:
- searchIndex2 = NO_INDEX
-
- print "searchIndex1 " + str(searchIndex1)
- print "searchIndex2 " + str(searchIndex2)
+ return foundDataSets
- # Search for a data set with those two indices
- DataSet = searchDataSetsofSample(laneCode, searchIndex1, searchIndex2, FASTQ_DATA_SET_TYPE)
+ ##########################################################
+ def reversecomplement(sequence):
+ '''
+ Reverse sequence and replace each nucleotide by its complement.
+ Input:
+ - sequence: sequence of nucleotides
+ Output:
+ - reverse_complement_sequence: reversed and complemented sequence
+ '''
+ lookup_table = {'A': 'T', 'T': 'A', 'G': 'C', 'C': 'G'}
+ reverse_complement_sequence = ''
+ for nucleotide in reversed(sequence):
+ reverse_complement_sequence += lookup_table[nucleotide]
+ return reverse_complement_sequence
+
+ ##########################################################
+
+ print('\nPROCESS RUNNING '+time.ctime())
+ incomingPath = transaction.getIncoming().getPath()
+ FileGenerator= locate(XML_FILENAME, incomingPath)
+ xmlfile = FileGenerator.next()
+ print "File: " + xmlfile
+
+ # Import data of XML file (independent of openBIS data):
+ JavaClassToProcessXML = read_demultiplex_stats() # this function is implemented as Class in Java:
+ samplestatisticslist = JavaClassToProcessXML.importXMLdata_and_calculateStatistics(xmlfile)
+ if len(samplestatisticslist) == 0:
+ print "\nNo Projects/Samples/Barcodes are contained in XML-file " + xmlfile + "!"
+ return
+
+ # Prepare links between XML and openBIS w.r.t. Samples:
+ codeSampleFlowCell = samplestatisticslist[0].Flowcell # expect just one equal FlowCell of all imported datasets
+ codeSampleFlowLane = samplestatisticslist[0].Flowcell + ":1" # expect just one equal FlowLane of all imported datasets
+
+ # Just get information of openBIS about Properties in Sample of FlowCell and corresponding FlowLane:
+ #propertiesCode, propertiesCodeValue = getInfoSampleProperties(codeSampleFlowCell)
+ #print "\nCode of Properties in FlowCell Sample "+codeSampleFlowCell+":\n", propertiesCode, "\n", propertiesCodeValue
+ #propertiesCode, propertiesCodeValue = getInfoSampleProperties(codeSampleFlowLane)
+ #print "\nCode of Properties in FlowLane Sample "+codeSampleFlowLane+":\n", propertiesCode, "\n", propertiesCodeValue
+
+ # Just get information of openBIS about Properties in one of the DataSets of FlowLane:
+ #propertiesCode, propertiesCodeValue = getInfoDataSetPropertiesOfSample(codeSampleFlowLane)
+ #print "\nCode of Properties in one of DataSets in Sample "+codeSampleFlowLane+" having Type "+TYPE_DATASET+":\n", propertiesCode, "\n", propertiesCodeValue
+
+ # Just get information of openBIS about Terms in some Vocabulary:
+ #vocabularyCode = CODE_INDEX1 # CODE_INDEX1 CODE_INDEX2
+ #vocabularyTerms = getInfoVocabularyTerms(vocabularyCode)
+ #print "\nTerms in Vocabulary "+vocabularyCode+":\n", vocabularyTerms
+
+ # Prepare links between XML and openBIS w.r.t to indexes in DataSet (openBIS):
+ index1list, index2list = getIndexesOfDataSetsOfSample(codeSampleFlowLane)
+ propertiesCode, propertiesCodeValue = getInfoSampleProperties(codeSampleFlowCell)
+ index1length = int(propertiesCodeValue[CODE_INDEX1LENGTH])
+ index2length = int(propertiesCodeValue[CODE_INDEX2LENGTH])
+
+ nprocessedDataSets = 0
+ for s in samplestatisticslist:
+ print "\nContent in XML file:\n", s
+ print "Connection to openBIS:"
+
+ # Prepare link between XML and openBIS w.r.t to indexes in Barcode (XML):
+ indexes = s.Barcode.split("-")
+ if len(indexes) == 1: # only first part in Barcode
+ index1search = indexes[0].upper()
+ index2search = INDEX_EMPTY
+ elif len(indexes) == 2: # both parts in Barcode
+ index1search = indexes[0].upper()
+ index2search = indexes[1].upper()
+ else:
+ index1search = INDEX_EMPTY
+ index2search = INDEX_EMPTY
+
+ # Set link between XML and openBIS w.r.t to indexes in DataSet (openBIS):
+ if index1search == INDEX_EMPTY or index1search == INDEX_UNKNOWN:
+ index1 = INDEX_NO
+ else: # Hint: just two cases were known about index1length, that is 8 or 6
+ if index1length > 7:
+ index1 = [ index1 for index1 in index1list if index1search == index1 ]
+ else: # for smaller indexlength, the index is by 1 shorter in XML-file than in openBIS
+ index1 = [ index1 for index1 in index1list if index1search == index1[:index1length] ]
+ try:
+ index1 = index1[0]
+ except:
+ print '\nOCCURRED EXCEPTION: First index \"' + index1search + '\" of Barcode in XML file has no corresponding DataSet in openBIS!'
+ index1 = 'MISSING'
+ if index2search == INDEX_EMPTY or index2search == INDEX_UNKNOWN:
+ index2 = INDEX_NO
+ else: # Hint: just one case was known about index2length, that is 8
+ if index2length > 7: # second and larger index must be reversed and complemented in contrast to first or smaller index
+ index2 = [ index2 for index2 in index2list if reversecomplement(index2search) == index2 ]
+ else: # second and smaller index is unknown how to handle
+ index2 = [ index2 for index2 in index2list if reversecomplement(index2search) == index2 ]
+ try:
+ index2 = index2[0]
+ except:
+ print '\nOCCURRED EXCEPTION: Second index \"' + index2search + '\" of Barcode in XML file has no corresponding DataSet in openBIS!'
+ index2 = 'MISSING'
+
+ # Get DataSet of openBIS corresponding to Project/Sample/Barcode of XML file:
+ correspondingDataSet = searchDataSetsOfSample(codeSampleFlowLane, index1, index2)
try:
- assert DataSet.size() == 1
- except AssertionError:
- print (str(DataSet.size()) + ' data sets found which match the criterias: '+
- str(laneCode), searchIndex1, searchIndex2)
- continue
-
- sa = transaction.getDataSetForUpdate(DataSet[0].getDataSetCode())
- sa.setPropertyValue('YIELD_MBASES', str(mystat.pfYieldSum))
- sa.setPropertyValue('RAW_YIELD_MBASES', str(mystat.rawYieldSum))
- sa.setPropertyValue('PERCENTAGE_PASSED_FILTERING',str(mystat.pfPercentage))
- sa.setPropertyValue('PF_READS_SUM',str(mystat.pfReadsSum))
- sa.setPropertyValue('RAW_READS_SUM',str(mystat.rawReadsSum))
- sa.setPropertyValue('PERCENTAGE_RAW_CLUSTERS_PER_LANE', str(mystat.rawPercentageReadsPerLane))
- sa.setPropertyValue('PFYIELDQ30PERCENTAGE', str(mystat.pfYieldQ30Percentage))
- sa.setPropertyValue('PFMEANQUALITYSCORE', str(mystat.pfmeanQualityScore))
-
- print "Modified data sets properties of: " + DataSet[0].getDataSetCode()
-
- print "DONE"
+ assert correspondingDataSet.size() == 1
+ except AssertionError:
+ print ('\nOCCURRED EXCEPTION: ' + str(correspondingDataSet.size()) + ' DataSets found which Sample match the criteria index1 \"' + str(index1) + '\" and index2 \"' + str(index2) + '\" and code \"' + codeSampleFlowLane + '\" and type \"' + TYPE_DATASET + '\".')
+ continue
+
+ # Modify Properties of corresponding DataSet:
+ # (method setPropertyValue requires Strings as Input, but Number format must fit to Properties already defined in openBIS)
+ ds = transaction.getDataSetForUpdate(correspondingDataSet[0].getDataSetCode())
+ ds.setPropertyValue('YIELD_MBASES', str(int(s.Mega_PfYield)))
+ ds.setPropertyValue('RAW_YIELD_MBASES', str(int(s.Mega_RawYield)))
+ ds.setPropertyValue('PERCENTAGE_PASSED_FILTERING',str(s.Percentage_PfClusterCount_RawClusterCount))
+ ds.setPropertyValue('PF_READS_SUM',str(int(s.Sum_PfClusterCount))) # convert first to Integer, then to String
+ ds.setPropertyValue('RAW_READS_SUM',str(int(s.Sum_RawClusterCount))) # convert first to Integer, then to String
+ ds.setPropertyValue('PERCENTAGE_RAW_CLUSTERS_PER_LANE', str(s.Percentage_RawClusterCount_AllRawClusterCounts))
+ ds.setPropertyValue('PFYIELDQ30PERCENTAGE', str(s.Percentage_PfYieldQ30_PfYield))
+ ds.setPropertyValue('PFMEANQUALITYSCORE', str(s.Fraction_PfQualityScoreSum_PfYield))
+ print "Properties in DataSet \"" + correspondingDataSet[0].getDataSetCode() + "\" are modified."
+ nprocessedDataSets += 1
+
+ print "\n", nprocessedDataSets, " openBIS-DataSets were processed."
+ print len(samplestatisticslist), " XML-Projects/-Samples/-Barcodes were processed."
+ print("PROCESS DONE "+time.ctime())
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read_demultiplex_stats.java b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read_demultiplex_stats.java
new file mode 100644
index 00000000000..818ca97b511
--- /dev/null
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats-nextseq/read_demultiplex_stats.java
@@ -0,0 +1,526 @@
+/*
+@copyright: 2012 ETH Zuerich, CISD
+
+@license:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+@author: Fabian Gemperle
+
+@note: This Class is in Jython importable as Java-Library after compiling it.
+ In compilation 4 Class files arise:
+ - read_demultiplex_stats.class
+ - read_demultiplex_stats$SampleItem.class
+ - read_demultiplex_stats$Sample.class
+ - read_demultiplex_stats$Statistics.class
+*/
+
+import java.util.List;
+import java.util.ArrayList;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamConstants;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.InputStream;
+
+//##########################################################
+
+public final class read_demultiplex_stats {
+
+ public List<Statistics> samplestatisticslist = new ArrayList<Statistics>();
+
+ public read_demultiplex_stats() {
+ // This Class-Constructor is unnecessary???
+ }
+
+ public List<Statistics> importXMLdata_and_calculateStatistics(String XMLfile) {
+ /*Parse corresponding XML file, put all values into a memory structure, calculate statistics overall samples.
+ Output: samplestatisticslist (list of Sample-Statistics-Objects)
+ Input: XMLfile having structure of file ConversionStats.xml (Example of 1.10.2014):
+ <?xml version="1.0" encoding="utf-8"?> => Assumptions about XML structure:
+ <Stats> => Element is singlechild
+ <Flowcell flowcell-id="H0YVKBGXX"> => Element is singlechild
+ <Project name="BSSE_QGF_23096_H0YVKBGXX_1"> => Element is one of many children, additionally there is summary-element with attribute name="all"
+ <Sample name="BSSE_QGF_23096_H0YVKBGXX_1_PZ27_PZ33_CelSEQ_"> => Element is singlechild except second summary-element with attribute name="all"
+ <Barcode name="unknown"> => Element is singlechild except second summary-element with attribute name="all"
+ <Lane number="1"> => Element is one of several children
+ <Tile number="11101"> => Element is one of many children
+ <Raw> => Element is singlechild
+ <ClusterCount>328653</ClusterCount> => Element is singlechild
+ <Read number="1"> => Element is one of several children
+ <Yield>24977628</Yield> => Element is singlechild
+ <YieldQ30>16162292</YieldQ30> => Element is singlechild
+ <QualityScoreSum>703070796</QualityScoreSum> => Element is singlechild
+ </Read>
+ <Read number="2"> => Element is one of several children
+ <Yield>24977628</Yield> => Element is singlechild
+ <YieldQ30>16233173</YieldQ30> => Element is singlechild
+ <QualityScoreSum>699507245</QualityScoreSum> => Element is singlechild
+ </Read>
+ </Raw>
+ <Pf> => Element is singlechild
+ <ClusterCount>302121</ClusterCount> => Element is singlechild
+ <Read number="1"> => Element is one of several children
+ <Yield>22961196</Yield> => Element is singlechild
+ <YieldQ30>15842531</YieldQ30> => Element is singlechild
+ <QualityScoreSum>686898532</QualityScoreSum> => Element is singlechild
+ </Read>
+ <Read number="2"> => Element is one of several children
+ <Yield>22961196</Yield> => Element is singlechild
+ <YieldQ30>16233173</YieldQ30> => Element is singlechild
+ <QualityScoreSum>699507245</QualityScoreSum> => Element is singlechild
+ </Read>
+ </Pf>
+ </Tile>
+ <Tile number="11102">
+ [...]
+ */
+
+ try {
+
+ // temporary variables (frequently changing during XML-read-in):
+ String errormessage = "";
+ int event = 0;
+ int skip = 0;
+ String curflowcellname = "";
+ String curprojectname = "";
+ String cursamplename = "";
+ String curbarcodename = "";
+ double curlanenumber = Double.NaN; // obvious double, but could be turned into int
+ double curtilenumber = Double.NaN; // obvious double, but could be turned into int
+ Sample cursample = null;
+ Statistics curstatistics = null;
+ SampleItem currawitem = null;
+ SampleItem curpfitem = null;
+
+ InputStream xmlfile = new FileInputStream(XMLfile);
+ XMLInputFactory xmlfactory = XMLInputFactory.newInstance();
+ XMLStreamReader xmlparser = xmlfactory.createXMLStreamReader(xmlfile);
+
+ // Start-Tag "Stats":
+ event = xmlparser.nextTag(); // Assumption: just white space or comments are aside explicit start-tag
+ if (event != XMLStreamConstants.START_ELEMENT || !xmlparser.getLocalName().equals("Stats")) {
+ errormessage = "STRANGE ERROR IN METHOD importXMLdata_and_calculateStatistics WHEN READING IN XMLFILE. => CHECK CODE AND XMLFILE-STRUCTURE!";
+ //System.out.println(errormessage);
+ throw new Exception(errormessage);
+ }
+ //System.out.println("\nStart-Element with tag " + xmlparser.getLocalName() + " with " + xmlparser.getAttributeCount() + " attributes with first attribute: " + xmlparser.getAttributeLocalName(0) +" = " + xmlparser.getAttributeValue(0));
+
+ // Loop over potential Tags "Flowcell":
+ event = xmlparser.nextTag(); // Assumption: just white spaces or comments are aside start- or end-tag
+ List<Statistics> samplestatistics = new ArrayList<Statistics>();
+ boolean doimport = true;
+ while (doimport) {
+
+ // concerning tag Flowcell:
+ if (event == XMLStreamConstants.START_ELEMENT && xmlparser.getLocalName().equals("Flowcell")) {
+ //System.out.println("\nStart-Element with tag " + xmlparser.getLocalName() + " with " + xmlparser.getAttributeCount() + " attributes with first attribute: " + xmlparser.getAttributeLocalName(0) +" = " + xmlparser.getAttributeValue(0));
+ curflowcellname = xmlparser.getAttributeValue(0); // Assumption: Flowcell-attribute flowcell-id is just string
+ event = xmlparser.nextTag();
+ } else if (event == XMLStreamConstants.END_ELEMENT && xmlparser.getLocalName().equals("Flowcell")) {
+ curflowcellname = "";
+ event = xmlparser.nextTag();
+
+ // concerning tag Project:
+ } else if (event == XMLStreamConstants.START_ELEMENT && xmlparser.getLocalName().equals("Project")) {
+ //System.out.println("\nStart-Element with tag " + xmlparser.getLocalName() + " with " + xmlparser.getAttributeCount() + " attributes with first attribute: " + xmlparser.getAttributeLocalName(0) +" = " + xmlparser.getAttributeValue(0));
+ if (xmlparser.getAttributeValue(0).equals("all")) {
+ // skip the current XML element and all of its following subelements:
+ skip = 1;
+ while (skip > 0) {
+ event = xmlparser.next();
+ switch (event) {
+ case XMLStreamConstants.END_ELEMENT: skip -= 1;
+ break; // break-command after each case is necessary in switch-statement
+ case XMLStreamConstants.START_ELEMENT: skip += 1;
+ break; // break-command after each case is necessary in switch-statement
+ default: skip += 0; // text elements, spaces, ...
+ break; // break-command after each case is necessary in switch-statement
+ }
+ }
+ } else {
+ curprojectname = xmlparser.getAttributeValue(0); // Assumption: Project-attribute name is just string
+ }
+ event = xmlparser.nextTag();
+ } else if (event == XMLStreamConstants.END_ELEMENT && xmlparser.getLocalName().equals("Project")) {
+ curprojectname = "";
+ event = xmlparser.nextTag();
+
+ // concerning tag Sample:
+ } else if (event == XMLStreamConstants.START_ELEMENT && xmlparser.getLocalName().equals("Sample")) {
+ //System.out.println("\nStart-Element with tag " + xmlparser.getLocalName() + " with " + xmlparser.getAttributeCount() + " attributes with first attribute: " + xmlparser.getAttributeLocalName(0) +" = " + xmlparser.getAttributeValue(0));
+ if (xmlparser.getAttributeValue(0).equals("all")) {
+ // skip the current XML element and all of its following subelements:
+ skip = 1;
+ while (skip > 0) {
+ event = xmlparser.next();
+ switch (event) {
+ case XMLStreamConstants.END_ELEMENT: skip -= 1;
+ break; // break-command after each case is necessary in switch-statement
+ case XMLStreamConstants.START_ELEMENT: skip += 1;
+ break; // break-command after each case is necessary in switch-statement
+ default: skip += 0; // text elements, spaces, ...
+ break; // break-command after each case is necessary in switch-statement
+ }
+ }
+ } else {
+ cursamplename = xmlparser.getAttributeValue(0); // Assumption: Sample-attribute name is just string
+ }
+ event = xmlparser.nextTag();
+ } else if (event == XMLStreamConstants.END_ELEMENT && xmlparser.getLocalName().equals("Sample")) {
+ cursamplename = "";
+ event = xmlparser.nextTag();
+
+ // concerning tag Barcode (which is as well the start/end of Project-/Sample-Entry):
+ } else if (event == XMLStreamConstants.START_ELEMENT && xmlparser.getLocalName().equals("Barcode")) {
+ //System.out.println("\nStart-Element with tag " + xmlparser.getLocalName() + " with " + xmlparser.getAttributeCount() + " attributes with first attribute: " + xmlparser.getAttributeLocalName(0) +" = " + xmlparser.getAttributeValue(0));
+ if (xmlparser.getAttributeValue(0).equals("all")) {
+ // skip the current XML element and all of its following subelements:
+ skip = 1;
+ while (skip > 0) {
+ event = xmlparser.next();
+ switch (event) {
+ case XMLStreamConstants.END_ELEMENT: skip -= 1;
+ break; // break-command after each case is necessary in switch-statement
+ case XMLStreamConstants.START_ELEMENT: skip += 1;
+ break; // break-command after each case is necessary in switch-statement
+ default: skip += 0; // text elements, spaces, ...
+ break; // break-command after each case is necessary in switch-statement
+ }
+ }
+ } else {
+ curbarcodename = xmlparser.getAttributeValue(0); // Assumption: Barcode-attribute name is just string
+ cursample = new Sample();
+ cursample.Flowcell = curflowcellname;
+ cursample.Project = curprojectname;
+ cursample.Sample = cursamplename;
+ cursample.Barcode = curbarcodename;
+ }
+ event = xmlparser.nextTag();
+ } else if (event == XMLStreamConstants.END_ELEMENT && xmlparser.getLocalName().equals("Barcode")) {
+ // Statistics 1st step: calculate individual statistics per sample:
+ curstatistics = new Statistics(cursample);
+ samplestatisticslist.add(curstatistics);
+ cursample = null;
+ curstatistics = null;
+ curbarcodename = "";
+ event = xmlparser.nextTag();
+
+ // concerning Lane:
+ } else if (event == XMLStreamConstants.START_ELEMENT && xmlparser.getLocalName().equals("Lane")) {
+ //System.out.println("\nStart-Element with tag " + xmlparser.getLocalName() + " with " + xmlparser.getAttributeCount() + " attributes with first attribute: " + xmlparser.getAttributeLocalName(0) +" = " + xmlparser.getAttributeValue(0));
+ curlanenumber = Double.parseDouble(xmlparser.getAttributeValue(0)); // Assumption:Lane-attribute number is always numeric
+ event = xmlparser.nextTag();
+ } else if (event == XMLStreamConstants.END_ELEMENT && xmlparser.getLocalName().equals("Lane")) {
+ curlanenumber = Double.NaN;
+ event = xmlparser.nextTag();
+
+ // concerning Tile with all its sub-elements:
+ } else if (event == XMLStreamConstants.START_ELEMENT && xmlparser.getLocalName().equals("Tile")) {
+ //System.out.println("\nStart-Element with tag " + xmlparser.getLocalName() + " with " + xmlparser.getAttributeCount() + " attributes with first attribute: " + xmlparser.getAttributeLocalName(0) +" = " + xmlparser.getAttributeValue(0));
+ curtilenumber = Double.parseDouble(xmlparser.getAttributeValue(0)); // Assumption: Tile-attribute number is always numeric
+ // concerning Raw with Assumption: Raw-element is singlechild:
+ xmlparser.nextTag();
+ //System.out.println("\nStart-Element with tag " + xmlparser.getLocalName());
+ currawitem = new SampleItem();
+ currawitem.Type = "Raw";
+ currawitem.Lane = curlanenumber;
+ currawitem.Tile = curtilenumber;
+ xmlparser.nextTag();
+ currawitem.ClusterCount = Double.parseDouble(xmlparser.getElementText()); // Assumption: ClusterCount-element is numeric singlechild
+ //System.out.println("\nValue: ClusterCount=" + currawitem.ClusterCount);
+ xmlparser.nextTag();
+ while (event == XMLStreamConstants.START_ELEMENT && xmlparser.getLocalName().equals("Read")) { // Assumption: at least or more than 1 Read-element
+ //System.out.println("\nStart-Element with tag " + xmlparser.getLocalName() + " with " + xmlparser.getAttributeCount() + " attributes with first attribute: " + xmlparser.getAttributeLocalName(0) +" = " + xmlparser.getAttributeValue(0));
+ xmlparser.nextTag();
+ currawitem.YieldList.add(Double.parseDouble(xmlparser.getElementText())); // Assumption: Yield-element is numeric singlechild
+ xmlparser.nextTag();
+ currawitem.YieldQ30List.add(Double.parseDouble(xmlparser.getElementText())); // Assumption: YieldQ30List-element is numeric singlechild
+ xmlparser.nextTag();
+ currawitem.QualityScoreSumList.add(Double.parseDouble(xmlparser.getElementText())); // Assumption: QualityScoreSumList-element is numeric singlechild
+ xmlparser.nextTag();
+ xmlparser.nextTag();
+ //System.out.println("Values in Read: Yield=" + currawitem.YieldList.get(currawitem.YieldList.size()-1) + ", YieldQ30=" + currawitem.YieldQ30List.get(currawitem.YieldQ30List.size()-1) + ", QualityScoreSum=" + currawitem.QualityScoreSumList.get(currawitem.QualityScoreSumList.size()-1));
+ }
+ //System.out.println("\nRaw-SampleItem " + currawitem);
+ cursample.RawList.add(currawitem);
+ currawitem = null;
+ // concerning Pf with Assumption that entire Pf-element is structured same as Raw:
+ xmlparser.nextTag();
+ //System.out.println("\nStart-Element with tag " + xmlparser.getLocalName());
+ curpfitem = new SampleItem();
+ curpfitem.Type = "Pf";
+ curpfitem.Lane = curlanenumber;
+ curpfitem.Tile = curtilenumber;
+ xmlparser.nextTag();
+ curpfitem.ClusterCount = Double.parseDouble(xmlparser.getElementText());
+ //System.out.println("\nValue: ClusterCount=" + curpfitem.ClusterCount);
+ xmlparser.nextTag();
+ while (event == XMLStreamConstants.START_ELEMENT && xmlparser.getLocalName().equals("Read")) {
+ //System.out.println("\nStart-Element with tag " + xmlparser.getLocalName() + " with " + xmlparser.getAttributeCount() + " attributes with first attribute: " + xmlparser.getAttributeLocalName(0) +" = " + xmlparser.getAttributeValue(0));
+ xmlparser.nextTag();
+ curpfitem.YieldList.add(Double.parseDouble(xmlparser.getElementText()));
+ xmlparser.nextTag();
+ curpfitem.YieldQ30List.add(Double.parseDouble(xmlparser.getElementText()));
+ xmlparser.nextTag();
+ curpfitem.QualityScoreSumList.add(Double.parseDouble(xmlparser.getElementText()));
+ xmlparser.nextTag();
+ xmlparser.nextTag();
+ //System.out.println("Values in Read: Yield=" + curpfitem.YieldList.get(curpfitem.YieldList.size()-1) + ", YieldQ30=" + curpfitem.YieldQ30List.get(curpfitem.YieldQ30List.size()-1) + ", QualityScoreSum=" + curpfitem.QualityScoreSumList.get(curpfitem.QualityScoreSumList.size()-1));
+ }
+ //System.out.println("\nPf-SampleItem " + curpfitem);
+ cursample.PfList.add(curpfitem);
+ curpfitem = null;
+ // attain end of current Tile and afterwards continue in next Tile/Lane/Barcode/Sample/Project:
+ event = xmlparser.nextTag();
+ } else if (event == XMLStreamConstants.END_ELEMENT && xmlparser.getLocalName().equals("Tile")) {
+ curtilenumber = Double.NaN;
+ event = xmlparser.nextTag();
+
+ // concerning finish of reading in XML or hit upon error due XML content:
+ } else if (event == XMLStreamConstants.END_ELEMENT && xmlparser.getLocalName().equals("Stats")) {
+ // this final part of while loop is just for analyzing potential errors, but
+ // could be removed and changed in: while xmlparser.getLocalName() != 'Stats'
+ doimport = false;
+ } else {
+ doimport = false;
+ errormessage = "STRANGE ERROR IN METHOD importXMLdata_and_calculateStatistics WHEN READING IN XMLFILE. => CHECK CODE AND XMLFILE-STRUCTURE!";
+ //System.out.println(errormessage);
+ throw new Exception(errormessage);
+ }
+
+ }
+ xmlparser.close();
+
+ } catch (FileNotFoundException | XMLStreamException e) {
+ System.out.println("OCCURRED EXCEPTION " + e.toString());
+ e.printStackTrace();
+ } catch (IllegalArgumentException e) {
+ System.out.println("OCCURRED EXCEPTION " + e.toString());
+ e.printStackTrace();
+ } catch (Exception e) { // catch any other exception
+ System.out.println("OCCURRED EXCEPTION " + e.toString());
+ e.printStackTrace();
+ } finally { // anyway adapt statistics and return output (It would be empty list due to constructor of this object)
+ // Statistics 2nd step: adapt single sample's statistics including entire list of samples
+ for (Statistics s : samplestatisticslist) {
+ s.adaptStatisticsWithRespectToAllSamples(samplestatisticslist);
+ }
+ return samplestatisticslist;
+ }
+
+ }
+
+//##########################################################
+
+ public class SampleItem {
+ /*
+ Object of an item in sample including
+ - the corresponding type Raw or Pf
+ - the index of corresponding Lane, Tile
+ - measured value of ClusterCount and values in Lists (w.r.t. Read) of Yield, YieldQ30, QualityScoreSum
+ */
+
+ public String Type = "";
+ // Define unknown numerical value. Type double could be exchanged with int, but double is necessary to initialize NaN-value.
+ public double Lane = Double.NaN;
+ public double Tile = Double.NaN;
+ public double ClusterCount = Double.NaN;
+ // Define unknown ArrayList of numerical values with changeable List size. Type Double(object) instead of double(primitive) is necessary in Lists.
+ public List<Double> YieldList = new ArrayList<Double>();
+ public List<Double> YieldQ30List = new ArrayList<Double>();
+ public List<Double> QualityScoreSumList = new ArrayList<Double>();
+
+ public String toString() {
+ return "Type: " + this.Type + ", Lane: " + (long)this.Lane + ", Tile: " + (long)this.Tile
+ + ", ClusterCount: " + (long)this.ClusterCount + ", YieldList: " + this.YieldList
+ + ", YieldQ30List: " + this.YieldQ30List + ", QualityScoreSumList: " + this.QualityScoreSumList;
+ }
+
+ }
+
+//##########################################################
+
+ public class Sample {
+ /*
+ Object of an entire sample including
+ - the name of Flowcell, Project, Sample, Barcode
+ - the list of Raw and Pf SampleItem-Objects
+ */
+
+ public String Flowcell = "";
+ public String Project = "";
+ public String Sample = "";
+ public String Barcode = "";
+ // Define unknown ArrayList of SampleItems:
+ public List<SampleItem> RawList = new ArrayList<SampleItem>();
+ public List<SampleItem> PfList = new ArrayList<SampleItem>();
+
+ public String toString() {
+ return "Flowcell: " + this.Flowcell + ", Project: " + this.Project + ", Sample: " + this.Sample + ", Barcode: " + this.Barcode
+ + ", RawList: " + this.RawList + ", PfList: " + this.PfList;
+ }
+
+ }
+
+//##########################################################
+
+ public class Statistics extends Sample {
+ /*
+ Object of Statistics within one single sample inherited from Sample-Object
+ */
+
+ public double Sum_RawClusterCount = Double.NaN; // obvious double, but could be turned into int
+ public double Sum_PfClusterCount = Double.NaN; // obvious double, but could be turned into int
+ public double Sum_RawYield = Double.NaN;
+ public double Sum_PfYield = Double.NaN;
+ public double Sum_RawYieldQ30 = Double.NaN;
+ public double Sum_PfYieldQ30 = Double.NaN;
+ public double Sum_RawQualityScoreSum = Double.NaN;
+ public double Sum_PfQualityScoreSum = Double.NaN;
+ public double Mega_RawYield = Double.NaN; // obvious double, but could be turned into int
+ public double Mega_PfYield = Double.NaN; // obvious double, but could be turned into int
+ public double Percentage_PfYield_RawYield = Double.NaN;
+ public double Percentage_PfYieldQ30_PfYield = Double.NaN;
+ public double Fraction_PfQualityScoreSum_PfYield = Double.NaN;
+ public double Percentage_PfClusterCount_RawClusterCount = Double.NaN;
+ public double Percentage_RawClusterCount_AllRawClusterCounts = Double.NaN;
+
+ public Statistics(Sample sample) {
+ /*
+ Constructor of derived class
+ Initialization: Already initialized Sample-Object is necessary argument.
+ */
+
+ super();
+ Flowcell = sample.Flowcell;
+ Project = sample.Project;
+ Sample = sample.Sample;
+ Barcode = sample.Barcode;
+ RawList = sample.RawList;
+ PfList = sample.PfList;
+
+ if (RawList.size()>0) Sum_RawClusterCount = 0;
+ for (SampleItem s : RawList) Sum_RawClusterCount += s.ClusterCount;
+ if (PfList.size()>0) Sum_PfClusterCount = 0;
+ for (SampleItem s : PfList) Sum_PfClusterCount += s.ClusterCount;
+ if (RawList.size()>0) Sum_RawYield = 0;
+ for (SampleItem s : RawList) for (double d : s.YieldList) Sum_RawYield += d;
+ if (PfList.size()>0) Sum_PfYield = 0;
+ for (SampleItem s : PfList) for (double d : s.YieldList) Sum_PfYield += d;
+ if (RawList.size()>0) Sum_RawYieldQ30 = 0;
+ for (SampleItem s : RawList) for (double d : s.YieldQ30List) Sum_RawYieldQ30 += d;
+ if (PfList.size()>0) Sum_PfYieldQ30 = 0;
+ for (SampleItem s : PfList) for (double d : s.YieldQ30List) Sum_PfYieldQ30 += d;
+ if (RawList.size()>0) Sum_RawQualityScoreSum = 0;
+ for (SampleItem s : RawList) for (double d : s.QualityScoreSumList) Sum_RawQualityScoreSum += d;
+ if (PfList.size()>0) Sum_PfQualityScoreSum = 0;
+ for (SampleItem s : PfList) for (double d : s.QualityScoreSumList) Sum_PfQualityScoreSum += d;
+// Mega_RawYield = calculate_MegaUnit(Sum_RawYield);
+// Mega_PfYield = calculate_MegaUnit(Sum_PfYield);
+
+ Mega_RawYield = Sum_RawYield;
+ Mega_PfYield = Sum_PfYield;
+
+ Percentage_PfYield_RawYield = calculate_Percentage(Sum_PfYield,Sum_RawYield);
+ Percentage_PfYieldQ30_PfYield = calculate_Percentage(Sum_PfYieldQ30,Sum_PfYield);
+ Fraction_PfQualityScoreSum_PfYield = calculate_Fraction(Sum_PfQualityScoreSum,Sum_PfYield);
+ Percentage_PfClusterCount_RawClusterCount = calculate_Percentage(Sum_PfClusterCount,Sum_RawClusterCount);
+ // Calculation of attribute "Percentage_RawClusterCount_AllRawClusterCounts" needs statistics of all other included samples. => After initializing this object, apply method: adaptStatisticsWithRespectToAllSamples(statisticslist)
+ }
+
+ public String toString() {
+ return "Flowcell: " + this.Flowcell + ", Project: " + this.Project + ", Sample: " + this.Sample + ", Barcode: " + this.Barcode
+ + ", Raw Clusters: " + (long)this.Sum_RawClusterCount + ", Mbases Raw Yield: " + this.Mega_RawYield
+ + ", % Raw Clusters overall: " + this.Percentage_RawClusterCount_AllRawClusterCounts
+ + ", Pf Clusters: " + (long)this.Sum_PfClusterCount + ", Mbases Pf Yield: " + this.Mega_PfYield
+ + ", % PfYield/RawYield: " + this.Percentage_PfYield_RawYield
+ + ", % PfYieldQ30/PfYield: " + this.Percentage_PfYieldQ30_PfYield
+ + ", Mean Pf Quality Score: " + this.Fraction_PfQualityScoreSum_PfYield
+ + ", % Passes Filtering: " + this.Percentage_PfClusterCount_RawClusterCount;
+ }
+
+ public void adaptStatisticsWithRespectToAllSamples(List<Statistics> statisticslist) {
+ /*
+ This Statistics-Object (corresponding to one sample) is adapted by employing a list of
+ Statistics-Objects corresponding to all samples influencing the statistics of single sample.
+ Input: statisticslist contains all Statistics-Objects
+ */
+ if (statisticslist.size()==0) { // here it additionally should be checked, if calling object is included ...
+ Percentage_RawClusterCount_AllRawClusterCounts = Double.NaN;
+ String errormessage = "INPUT ARGUMENT statisticslist MUST BE LIST OF Statistics OBJECTS INCLUDING THE CALLING OBJECT IN METHOD adaptStatisticsWithRespectToAllSamples!";
+ //System.out.println(errormessage);
+ throw new IllegalArgumentException(errormessage); // Exception reasonable since otherwise wrong results.
+ } else {
+ double sum_allrawclustercounts = 0;
+ for (Statistics s : statisticslist) sum_allrawclustercounts += s.Sum_RawClusterCount;
+ Percentage_RawClusterCount_AllRawClusterCounts = calculate_Percentage(Sum_RawClusterCount, sum_allrawclustercounts);
+ }
+ }
+
+ public double calculate_MegaUnit(double x) {
+ double z;
+ if (x == Double.POSITIVE_INFINITY || x == Double.NEGATIVE_INFINITY || Double.isNaN(x)) {
+ z = Double.NaN;
+ String errormessage = "INPUT ARGUMENT WAS UNREASONABLE IN METHOD calculate_MegaUnit! x = " + x + " (Values were in Sample " + Sample + ")";
+ //System.out.println(errormessage);
+ //throw new IllegalArgumentException(errormessage);
+ } else {
+ z = x/1000000;
+ }
+ return z;
+ }
+
+ public double calculate_Percentage(double x, double y) {
+ double z = x/y;
+ if (z == Double.POSITIVE_INFINITY || z == Double.NEGATIVE_INFINITY || Double.isNaN(z)) {
+ z = Double.NaN;
+ String errormessage = "INPUT ARGUMENT WAS UNREASONABLE IN METHOD calculate_Percentage! x = " + x + ", y = " + y + " (Values were in Sample " + Sample + ")";
+ //System.out.println(errormessage);
+ //throw new IllegalArgumentException(errormessage);
+ } else {
+ z = 100*z;
+ }
+ return z;
+ }
+
+ public double calculate_Fraction(double x, double y) {
+ double z = x/y;
+ if (z == Double.POSITIVE_INFINITY || z == Double.NEGATIVE_INFINITY || Double.isNaN(z)) {
+ z = Double.NaN;
+ String errormessage = "INPUT ARGUMENT WAS UNREASONABLE IN METHOD calculate_Fraction! x = " + x + ", y = " + y + " (Values were in Sample " + Sample + ")";
+ //System.out.println(errormessage);
+ //throw new IllegalArgumentException(errormessage);
+ }
+ return z;
+ }
+
+ public double roundspecific(double x, int places) {
+ double z;
+ if (places < 0 || places > 13 || x == Double.POSITIVE_INFINITY || x == Double.NEGATIVE_INFINITY || Double.isNaN(x)) {
+ z = Double.NaN;
+ String errormessage = "INPUT ARGUMENT WAS UNREASONABLE IN METHOD roundspecific! x = " + x + ", places = " + places + " (Values were in Sample " + Sample + ")";
+ //System.out.println(errormessage);
+ //throw new IllegalArgumentException(errormessage);
+ } else {
+ double factor = Math.pow(10, places);
+ z = Math.round(x * factor);
+ z = z / factor;
+ }
+ return z;
+ }
+
+ }
+
+}
\ No newline at end of file
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats/read-demultiplex-stats.py b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats/read-demultiplex-stats.py
index b6c0cc3a544..3e86dfcf7a4 100755
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats/read-demultiplex-stats.py
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/read-demultiplex-stats/read-demultiplex-stats.py
@@ -499,7 +499,16 @@ def process(transaction):
else:
searchIndex1 = [ index1 for index1 in index1List if searchIndex1 in index1[:-1]]
try:
- searchIndex1 = searchIndex1[0]
+ if len(searchIndex1) > 1:
+ print("AMBIGIOUS INDEX FOUND!")
+ print(searchIndex1)
+ if searchIndex1[0].startswith(mystat.index1.upper()):
+ searchIndex1 = searchIndex1[0]
+ else:
+ searchIndex1 = searchIndex1[1]
+ else:
+ searchIndex1 = searchIndex1[0]
+
except:
searchIndex1 = 'MISSING'
else:
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-cluster-alignment-java/plugin.properties b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-cluster-alignment-java/plugin.properties
index 35b2b5253d0..f3d4bd413ad 100644
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-cluster-alignment-java/plugin.properties
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-cluster-alignment-java/plugin.properties
@@ -3,5 +3,5 @@ top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JavaT
program-class = ch.systemsx.cisd.etlserver.registrator.api.v2.AlignmentJavaDataSetRegistrationDropboxV2
#program-class = AlignmentJavaDataSetRegistrationDropboxV2
storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-incoming-dir-create = true
+incoming-dir-create = false
incoming-data-completeness-condition = auto-detection
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-dummy/plugin.properties b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-dummy/plugin.properties
new file mode 100644
index 00000000000..ad9cc236b38
--- /dev/null
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-dummy/plugin.properties
@@ -0,0 +1,11 @@
+#
+# Drop box for registering a flow cell output as a data set
+#
+# Variables:
+# incoming-root-dir
+# Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/register-dummy
+incoming-data-completeness-condition = marker-file
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+script-path = register-dummy.py
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-dummy/register-dummy.py b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-dummy/register-dummy.py
new file mode 100644
index 00000000000..01a2eec1e4f
--- /dev/null
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-dummy/register-dummy.py
@@ -0,0 +1,56 @@
+'''
+@copyright:
+2014 ETH Zuerich, CISD
+
+@license:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+@author:
+Manuel Kohler
+'''
+
+import os
+import shutil
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria
+
+
+def splitFolderName (folderName):
+ runFolder, lane = folderName.rsplit("_", 1)
+ return runFolder + ":" + lane
+
+def searchSample (transaction, sampleCode):
+ # Get the search service
+ search_service = transaction.getSearchService()
+
+ print("Searching for " + sampleCode)
+ # Search for the sample
+ sc = SearchCriteria()
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
+ foundSamples = search_service.searchForSamples(sc)
+ assert(len(foundSamples), 1)
+ return foundSamples[0]
+
+def process(transaction):
+
+ # expected incoming folder names:
+ # 120917_SN792_0158_AC125KACXX_4
+
+ incomingFolder = transaction.getIncoming().getName()
+ flowLaneName = splitFolderName(incomingFolder)
+ flowLane = searchSample(transaction, flowLaneName)
+
+ dataSet = transaction.createNewDataSet("ALIGNMENT")
+ dataSet.setMeasuredData(False)
+ dataSet.setSample(flowLane)
+ transaction.moveFile(transaction.getIncoming().getPath(), dataSet)
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-hiseq/lib/crc32 b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-hiseq/lib/crc32
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diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-miseq/register-lane-miseq.py b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-miseq/register-lane-miseq.py
index 56d96799ca6..985022f203b 100644
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-miseq/register-lane-miseq.py
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-miseq/register-lane-miseq.py
@@ -25,8 +25,8 @@ AFFILIATION_PROPERTY_NAME='AFFILIATION'
INDEX1='BARCODE'
INDEX2='INDEX2'
EXTERNAL_SAMPLE_NAME='EXTERNAL_SAMPLE_NAME'
+
DEFAULT_INDEX='NoIndex'
-CRC32_PATH='lib/crc32'
# -------------------------------------------------------------------------------
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-nextseq/lib/crc32 b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-nextseq/lib/crc32
index ffaf277227c6dfb0dae3fbe751d9db158bd5ae29..7959ca94a1fa61e47c2e4df815bb35fceb7bd809 100755
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diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-nextseq/lib/crc32_v2.c b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-nextseq/lib/crc32_v2.c
new file mode 100644
index 00000000000..b38d22d40f6
--- /dev/null
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/dss/drop-boxes/register-lane-nextseq/lib/crc32_v2.c
@@ -0,0 +1,206 @@
+/*----------------------------------------------------------------------------*\
+ * CRC-32 version 2.0.0 by Craig Bruce, 2006-04-29.
+ *
+ * This program generates the CRC-32 values for the files named in the
+ * command-line arguments. These are the same CRC-32 values used by GZIP,
+ * PKZIP, and ZMODEM. The Crc32_ComputeBuf() can also be detached and
+ * used independently.
+ *
+ * THIS PROGRAM IS PUBLIC-DOMAIN SOFTWARE.
+ *
+ * Based on the byte-oriented implementation "File Verification Using CRC"
+ * by Mark R. Nelson in Dr. Dobb's Journal, May 1992, pp. 64-67.
+ *
+ * v1.0.0: original release.
+ * v1.0.1: fixed printf formats.
+ * v1.0.2: fixed something else.
+ * v1.0.3: replaced CRC constant table by generator function.
+ * v1.0.4: reformatted code, made ANSI C. 1994-12-05.
+ * v2.0.0: rewrote to use memory buffer & static table, 2006-04-29.
+\*----------------------------------------------------------------------------*/
+
+#include <stdio.h>
+#include <stdlib.h>
+
+/*----------------------------------------------------------------------------*\
+ * Local functions
+\*----------------------------------------------------------------------------*/
+
+static int Crc32_ComputeFile( FILE *file, unsigned long *outCrc32 );
+
+static unsigned long Crc32_ComputeBuf( unsigned long inCrc32, const void *buf,
+ size_t bufLen );
+
+/*----------------------------------------------------------------------------*\
+ * NAME:
+ * main() - main function for CRC-32 generation
+ * DESCRIPTION:
+ * Computes the CRC-32 value for the set of files named in the command-
+ * line arguments.
+ * ARGUMENTS:
+ * argc - command-line-argument count
+ * argv - command-line-argument strings
+ * RETURNS:
+ * err - 0 on success or executes exit(1) on error
+ * ERRORS:
+ * - file errors
+\*----------------------------------------------------------------------------*/
+
+int main( int argc, const char *argv[] )
+{
+ FILE *file = NULL;
+ const char *filename;
+ unsigned long argIdx;
+ unsigned long crc32;
+ int err;
+
+ /** compute crcs **/
+ if (argc < 2) {
+ /** read from 'stdin' if no arguments given **/
+ err = Crc32_ComputeFile( stdin, &crc32 );
+ if (err == -1) goto ERR_EXIT;
+ printf("crc32 = 0x%08lX for (stdin)\n", crc32 );
+ } else {
+ /** report named files in sequence **/
+ for (argIdx=1; argIdx < argc; argIdx++) {
+ filename = argv[argIdx];
+ file = fopen( filename, "rb" );
+ if (file == NULL) {
+ fprintf( stderr, "error opening file \"%s\"!\n", filename );
+ goto ERR_EXIT;
+ }
+ err = Crc32_ComputeFile( file, &crc32 );
+ if (err == -1) goto ERR_EXIT;
+ /*printf("crc32 = 0x%08lX for \"%s\"\n", crc32, filename );*/
+ printf("%08lX", crc32);
+ err = fclose( file );
+ file = NULL;
+ if (err == EOF) {
+ fprintf( stderr, "error closing file \"%s\"!\n", filename );
+ goto ERR_EXIT;
+ }
+ }
+ }
+ return( 0 );
+
+ /** error exit **/
+ERR_EXIT:
+ if (file != NULL) fclose( file );
+ exit( 1 );
+}
+
+/*----------------------------------------------------------------------------*\
+ * NAME:
+ * Crc32_ComputeFile() - compute CRC-32 value for a file
+ * DESCRIPTION:
+ * Computes the CRC-32 value for an opened file.
+ * ARGUMENTS:
+ * file - file pointer
+ * outCrc32 - (out) result CRC-32 value
+ * RETURNS:
+ * err - 0 on success or -1 on error
+ * ERRORS:
+ * - file errors
+\*----------------------------------------------------------------------------*/
+
+static int Crc32_ComputeFile( FILE *file, unsigned long *outCrc32 )
+{
+# define CRC_BUFFER_SIZE 8192
+ unsigned char buf[CRC_BUFFER_SIZE];
+ size_t bufLen;
+
+ /** accumulate crc32 from file **/
+ *outCrc32 = 0;
+ while (1) {
+ bufLen = fread( buf, 1, CRC_BUFFER_SIZE, file );
+ if (bufLen == 0) {
+ if (ferror(file)) {
+ fprintf( stderr, "error reading file\n" );
+ goto ERR_EXIT;
+ }
+ break;
+ }
+ *outCrc32 = Crc32_ComputeBuf( *outCrc32, buf, bufLen );
+ }
+ return( 0 );
+
+ /** error exit **/
+ERR_EXIT:
+ return( -1 );
+}
+
+/*----------------------------------------------------------------------------*\
+ * NAME:
+ * Crc32_ComputeBuf() - computes the CRC-32 value of a memory buffer
+ * DESCRIPTION:
+ * Computes or accumulates the CRC-32 value for a memory buffer.
+ * The 'inCrc32' gives a previously accumulated CRC-32 value to allow
+ * a CRC to be generated for multiple sequential buffer-fuls of data.
+ * The 'inCrc32' for the first buffer must be zero.
+ * ARGUMENTS:
+ * inCrc32 - accumulated CRC-32 value, must be 0 on first call
+ * buf - buffer to compute CRC-32 value for
+ * bufLen - number of bytes in buffer
+ * RETURNS:
+ * crc32 - computed CRC-32 value
+ * ERRORS:
+ * (no errors are possible)
+\*----------------------------------------------------------------------------*/
+
+static unsigned long Crc32_ComputeBuf( unsigned long inCrc32, const void *buf,
+ size_t bufLen )
+{
+ static const unsigned long crcTable[256] = {
+ 0x00000000,0x77073096,0xEE0E612C,0x990951BA,0x076DC419,0x706AF48F,0xE963A535,
+ 0x9E6495A3,0x0EDB8832,0x79DCB8A4,0xE0D5E91E,0x97D2D988,0x09B64C2B,0x7EB17CBD,
+ 0xE7B82D07,0x90BF1D91,0x1DB71064,0x6AB020F2,0xF3B97148,0x84BE41DE,0x1ADAD47D,
+ 0x6DDDE4EB,0xF4D4B551,0x83D385C7,0x136C9856,0x646BA8C0,0xFD62F97A,0x8A65C9EC,
+ 0x14015C4F,0x63066CD9,0xFA0F3D63,0x8D080DF5,0x3B6E20C8,0x4C69105E,0xD56041E4,
+ 0xA2677172,0x3C03E4D1,0x4B04D447,0xD20D85FD,0xA50AB56B,0x35B5A8FA,0x42B2986C,
+ 0xDBBBC9D6,0xACBCF940,0x32D86CE3,0x45DF5C75,0xDCD60DCF,0xABD13D59,0x26D930AC,
+ 0x51DE003A,0xC8D75180,0xBFD06116,0x21B4F4B5,0x56B3C423,0xCFBA9599,0xB8BDA50F,
+ 0x2802B89E,0x5F058808,0xC60CD9B2,0xB10BE924,0x2F6F7C87,0x58684C11,0xC1611DAB,
+ 0xB6662D3D,0x76DC4190,0x01DB7106,0x98D220BC,0xEFD5102A,0x71B18589,0x06B6B51F,
+ 0x9FBFE4A5,0xE8B8D433,0x7807C9A2,0x0F00F934,0x9609A88E,0xE10E9818,0x7F6A0DBB,
+ 0x086D3D2D,0x91646C97,0xE6635C01,0x6B6B51F4,0x1C6C6162,0x856530D8,0xF262004E,
+ 0x6C0695ED,0x1B01A57B,0x8208F4C1,0xF50FC457,0x65B0D9C6,0x12B7E950,0x8BBEB8EA,
+ 0xFCB9887C,0x62DD1DDF,0x15DA2D49,0x8CD37CF3,0xFBD44C65,0x4DB26158,0x3AB551CE,
+ 0xA3BC0074,0xD4BB30E2,0x4ADFA541,0x3DD895D7,0xA4D1C46D,0xD3D6F4FB,0x4369E96A,
+ 0x346ED9FC,0xAD678846,0xDA60B8D0,0x44042D73,0x33031DE5,0xAA0A4C5F,0xDD0D7CC9,
+ 0x5005713C,0x270241AA,0xBE0B1010,0xC90C2086,0x5768B525,0x206F85B3,0xB966D409,
+ 0xCE61E49F,0x5EDEF90E,0x29D9C998,0xB0D09822,0xC7D7A8B4,0x59B33D17,0x2EB40D81,
+ 0xB7BD5C3B,0xC0BA6CAD,0xEDB88320,0x9ABFB3B6,0x03B6E20C,0x74B1D29A,0xEAD54739,
+ 0x9DD277AF,0x04DB2615,0x73DC1683,0xE3630B12,0x94643B84,0x0D6D6A3E,0x7A6A5AA8,
+ 0xE40ECF0B,0x9309FF9D,0x0A00AE27,0x7D079EB1,0xF00F9344,0x8708A3D2,0x1E01F268,
+ 0x6906C2FE,0xF762575D,0x806567CB,0x196C3671,0x6E6B06E7,0xFED41B76,0x89D32BE0,
+ 0x10DA7A5A,0x67DD4ACC,0xF9B9DF6F,0x8EBEEFF9,0x17B7BE43,0x60B08ED5,0xD6D6A3E8,
+ 0xA1D1937E,0x38D8C2C4,0x4FDFF252,0xD1BB67F1,0xA6BC5767,0x3FB506DD,0x48B2364B,
+ 0xD80D2BDA,0xAF0A1B4C,0x36034AF6,0x41047A60,0xDF60EFC3,0xA867DF55,0x316E8EEF,
+ 0x4669BE79,0xCB61B38C,0xBC66831A,0x256FD2A0,0x5268E236,0xCC0C7795,0xBB0B4703,
+ 0x220216B9,0x5505262F,0xC5BA3BBE,0xB2BD0B28,0x2BB45A92,0x5CB36A04,0xC2D7FFA7,
+ 0xB5D0CF31,0x2CD99E8B,0x5BDEAE1D,0x9B64C2B0,0xEC63F226,0x756AA39C,0x026D930A,
+ 0x9C0906A9,0xEB0E363F,0x72076785,0x05005713,0x95BF4A82,0xE2B87A14,0x7BB12BAE,
+ 0x0CB61B38,0x92D28E9B,0xE5D5BE0D,0x7CDCEFB7,0x0BDBDF21,0x86D3D2D4,0xF1D4E242,
+ 0x68DDB3F8,0x1FDA836E,0x81BE16CD,0xF6B9265B,0x6FB077E1,0x18B74777,0x88085AE6,
+ 0xFF0F6A70,0x66063BCA,0x11010B5C,0x8F659EFF,0xF862AE69,0x616BFFD3,0x166CCF45,
+ 0xA00AE278,0xD70DD2EE,0x4E048354,0x3903B3C2,0xA7672661,0xD06016F7,0x4969474D,
+ 0x3E6E77DB,0xAED16A4A,0xD9D65ADC,0x40DF0B66,0x37D83BF0,0xA9BCAE53,0xDEBB9EC5,
+ 0x47B2CF7F,0x30B5FFE9,0xBDBDF21C,0xCABAC28A,0x53B39330,0x24B4A3A6,0xBAD03605,
+ 0xCDD70693,0x54DE5729,0x23D967BF,0xB3667A2E,0xC4614AB8,0x5D681B02,0x2A6F2B94,
+ 0xB40BBE37,0xC30C8EA1,0x5A05DF1B,0x2D02EF8D };
+ unsigned long crc32;
+ unsigned char *byteBuf;
+ size_t i;
+
+ /** accumulate crc32 for buffer **/
+ crc32 = inCrc32 ^ 0xFFFFFFFF;
+ byteBuf = (unsigned char*) buf;
+ for (i=0; i < bufLen; i++) {
+ crc32 = (crc32 >> 8) ^ crcTable[ (crc32 ^ byteBuf[i]) & 0xFF ];
+ }
+ return( crc32 ^ 0xFFFFFFFF );
+}
+
+/*----------------------------------------------------------------------------*\
+ * END OF MODULE: crc32.c
+\*----------------------------------------------------------------------------*/
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 d357a6a02f1..4b6a2ce3456 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
@@ -360,6 +360,7 @@ def process(transaction):
meta_data_file_path = transaction.createNewFile(dataSet, name, meta_data_file_name)
writeMetadataFile(transaction, name, meta_data_file_path, sequencing_sample_properties_dict,
fcMetaDataDict, experiment, affiliation_name, fastq_files, flowLane)
+ affiliation_for_Undetermined = affiliation_name
# Undetermined Files
else:
--
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