def execute(self):
"""
Catalog reduced data files
"""
config = ConfigParser.RawConfigParser()
config.read('/etc/autoreduce/icat4.cfg')
directory = "/" + self._facilityName + "/" + self._instrumentName + "/" + self._investigationName + "/shared/autoreduce"
logging.info("reduction output directory: %s" % directory)
#set dataset name
dataset = self._factory.create("dataset")
dsType = self._factory.create("datasetType")
dsType.id = config.get('DatasetType', 'reduced')
dataset.type = dsType
dataset.name = self._runNumber
dataset.location = directory
datafiles = []
pattern = '*' + self._runNumber + '*'
for dirpath, dirnames, filenames in os.walk(directory):
listing = glob.glob(os.path.join(dirpath, pattern))
for filepath in listing:
filename =os.path.basename(filepath)
logging.info("Filename: %s" % filename)
datafile = self._factory.create("datafile")
datafile.location = filepath
datafile.name = filename
extension = os.path.splitext(filename)[1][1:]
dfFormat = self._factory.create("datafileFormat")
dfFormat.id = config.get('DatafileFormat', extension)
datafile.datafileFormat = dfFormat
modTime = os.path.getmtime(filepath)
datafile.datafileCreateTime = epochToISO8601(modTime)
datafile.fileSize = os.path.getsize(filepath)
datafiles.append(datafile)
dataset.datafiles = datafiles
dataset.type = dsType
dbDatasets = self._service.search(self._sessionId, "Dataset INCLUDE Datafile [name = '" + str(dataset.name) + "'] <-> Investigation <-> Instrument [name = '" + str(self._instrumentName) + "'] <-> DatasetType [name = 'reduced']")
if len(dbDatasets) == 0:
dbInvestigations = self._service.search(self._sessionId, "Investigation INCLUDE Sample [name = '" + str(self._investigationName) + "'] <-> Instrument [name = '" + self._instrumentName + "'] <-> Dataset [name = '" + str(dataset.name) + "']")
if len(dbInvestigations) == 0:
logging.error("No investigation entry found: try cataloging the raw data first.")
return
else:
investigation = dbInvestigations[0]
if len(dbInvestigations)>1:
logging.error("Multiple investigation entries found: using the first.")
logging.debug("Creating dataset: %s" % datetime.now())
dataset.investigation = investigation
dataset.sample = investigation.samples[0]
self._service.create(self._sessionId, dataset)
elif len(dbDatasets) == 1:
logging.debug("reduced dataset %s is already cataloged, updating reduced dataset... " % (dataset.name))
dbDataset = dbDatasets[0]
# update "one to many" relationships
if hasattr(dbDataset, "datafiles"):
dfs = getattr(dbDataset, "datafiles")
self._service.deleteMany(self._sessionId, dfs)
for df in datafiles:
df.dataset = dbDataset
self._service.createMany(self._sessionId, datafiles)
else:
logging.error("ERROR, there should be only one dataset per run number per type reduced")
def execute(self):
#find facility, investigation_type
config = ConfigParser.RawConfigParser()
config.read('/etc/autoreduce/icat4.cfg')
investigation = self._factory.create("investigation")
#find facility, investigation_type
facility = self._factory.create("facility")
facility.id = config.get('Facility', 'sns')
investigation.facility = facility
invType = self._factory.create("investigationType")
invType.id = config.get('InvestigationType', 'experiment')
investigation.type = invType
totalCounts=0
protonCharge=0
duration=0
entry_count=0
sample = self._factory.create("sample")
sample.name = 'NONE'
#open nexus file
file = nxs.open(self._infilename, 'r')
for name, nxclass in file.entries():
if nxclass == "NXentry" and name != "entry-VETO":
listing = file.getentries()
#investigation name
if listing.has_key('experiment_identifier'):
file.opendata('experiment_identifier')
investigation.name = file.getdata()
file.closedata()
else:
investigation.name = "IPTS-0000"
#investigation title
if listing.has_key('title'):
file.opendata('title')
investigation_title = unicode(file.getdata(), errors='replace')
investigation.title = investigation_title.encode('ascii', 'replace')
file.closedata()
else:
investigation.title = "NONE"
#create dataset
dataset = self._factory.create("dataset")
#investigation run number
if listing.has_key('collection_identifier'):
file.opendata('collection_identifier')
investigation.visitId = str(file.getdata())
file.closedata()
else:
investigation.visitId = "0"
#dataset run number
file.opendata('run_number')
dataset.name = file.getdata()
file.closedata()
#dataset title
if listing.has_key('title'):
file.opendata('title')
dataset_description = unicode(file.getdata(), errors='replace')
dataset.description = dataset_description.encode('ascii', 'replace')
file.closedata()
dsType = self._factory.create("datasetType")
dsType.id = config.get('DatasetType', 'experiment_raw')
dataset.type = dsType
#set dataset start time
if listing.has_key('start_time'):
file.opendata('start_time')
if entry_count == 0:
dataset.startDate = file.getdata()
elif dataset.startDate > file.getdata():
dataset.startDate = file.getdata()
file.closedata()
#set dataset end time
if listing.has_key('end_time'):
file.opendata('end_time')
if entry_count == 0:
dataset.endDate = file.getdata()
elif dataset.endDate < file.getdata():
dataset.endDate = file.getdata()
file.closedata()
#dataset proton_charge
file.opendata('proton_charge')
protonCharge = protonCharge + file.getdata()
file.closedata()
#dataset total_counts
file.opendata('total_counts')
totalCounts = totalCounts + file.getdata()
file.closedata()
#dataset duration
file.opendata('duration')
duration = duration + file.getdata()
file.closedata()
#investigation instrument
file.opengroup('instrument')
file.opendata('name')
for attr,value in file.attrs():
if attr == 'short_name':
instrument = self._factory.create("instrument")
instrument.name = value
instrument.id = config.get('Instrument', value.lower())
investigation.instrument = instrument
file.closedata()
file.closegroup()
if listing.has_key('sample'):
file.opengroup('sample')
listSample = file.getentries()
if listSample.has_key('name'):
file.opendata('name')
# Text stored in the Nexus file is XML escaped
# ICAT unescapes it automatically, so we need to
# do it here if we want to determine whether
# the sample is already in the DB.
sample_name = unicode(file.getdata(), errors='replace')
sample.name = saxutils.unescape(sample_name.encode('ascii', 'replace'))
file.closedata()
else:
sample.name = "NONE"
sampleParameters = []
#set sample nature
if listSample.has_key('nature'):
file.opendata('nature')
nature = file.getdata()
file.closedata()
if nature:
parameterType = self._factory.create("parameterType")
parameterType.id = config.get('ParameterType', 'nature')
parameterType.applicableToSample = config.getboolean('ParameterType', 'nature_applicable_to_sample')
sampleParameter = self._factory.create("sampleParameter")
sampleParameter.type = parameterType
sampleParameter.stringValue = nature
sampleParameters.append(sampleParameter)
if listSample.has_key('identifier'):
file.opendata('identifier')
identifier = file.getdata()
file.closedata()
if identifier:
parameterType = self._factory.create("parameterType")
parameterType.id = config.get('ParameterType', 'identifier')
parameterType.applicableToSample = config.getboolean('ParameterType', 'identifier_applicable_to_sample')
sampleParameter = self._factory.create("sampleParameter")
sampleParameter.type = parameterType
sampleParameter.stringValue = identifier
sampleParameters.append(sampleParameter)
if len(sampleParameters):
sample.parameters = sampleParameters
file.closegroup()
file.close()
#set dataset parameters
parameters = []
#1) parameter proton_charge
if protonCharge:
parameterType = self._factory.create("parameterType")
parameterType.id = config.get('ParameterType', 'proton_charge')
parameterType.applicableToDataset = config.getboolean('ParameterType', 'proton_charge_applicable_to_dataset')
datasetParameter = self._factory.create("datasetParameter")
datasetParameter.type = parameterType
datasetParameter.stringValue = protonCharge
parameters.append(datasetParameter)
#2) parameter total_counts
if totalCounts:
parameterType = self._factory.create("parameterType")
parameterType.id = config.get('ParameterType', 'total_counts')
parameterType.applicableToDataset = config.getboolean('ParameterType', 'total_counts_applicable_to_dataset')
datasetParameter = self._factory.create("datasetParameter")
datasetParameter.type = parameterType
datasetParameter.numericValue = totalCounts
parameters.append(datasetParameter)
#3) parameter duration
if duration:
parameterType = self._factory.create("parameterType")
parameterType.id = config.get('ParameterType', 'duration')
parameterType.applicableToDataset = config.getboolean('ParameterType', 'duration_applicable_to_dataset')
datasetParameter = self._factory.create("datasetParameter")
datasetParameter.type = parameterType
datasetParameter.numericValue = duration
parameters.append(datasetParameter)
dataset.parameters = parameters
dataset.location = self._infilename
datafiles = []
token=self._infilename.split("/")
proposalDir = "/" + token[1] + "/" + token[2] + "/" + token[3]
for dirpath, dirnames, filenames in os.walk(proposalDir):
if dirpath.find("shared") == -1 and dirpath.find("data") == -1:
for filename in [f for f in filenames]:
#if dataset.name in filename and os.path.islink(filename) != False:
if dataset.name in filename:
logging.info("Filename: %s" % filename)
datafile = self._factory.create("datafile")
filepath = os.path.join(dirpath,filename)
extension = os.path.splitext(filename)[1][1:]
datafile.name = filename
datafile.location = filepath
dfFormat = self._factory.create("datafileFormat")
dfFormat.id = config.get('DatafileFormat', extension)
datafile.datafileFormat = dfFormat
modTime = os.path.getmtime(filepath)
datafile.datafileCreateTime = epochToISO8601(modTime)
datafile.fileSize = os.path.getsize(filepath)
datafiles.append(datafile)
dataset.datafiles = datafiles
dbDatasets = self._service.search(self._sessionId, "Dataset INCLUDE Datafile [name = '" + str(dataset.name) + "'] <-> Investigation <-> Instrument [name = '" + str(instrument.name) + "'] <-> DatasetType [name = 'experiment_raw']")
if len(dbDatasets) == 0:
dbInvestigations = self._service.search(self._sessionId, "Investigation INCLUDE Sample [name = '" + investigation.name + "' AND visitId = '" + investigation.visitId + "'] <-> Instrument [name = '" + instrument.name + "']")
if len(dbInvestigations) == 0:
logging.debug("New IPTS: creating investigation, sample, run...")
# create new investigation
invId = self._service.create(self._sessionId, investigation)
investigation.id = invId
# create new sample
sample.investigation = investigation
sampleId = self._service.create(self._sessionId, sample)
sample.id = sampleId
logging.debug(" invId: %s sampleId: %s" % (str(invId), str(sampleId)))
elif len(dbInvestigations) == 1:
investigation = dbInvestigations[0]
dbSamples = investigation.samples
newSample = True
for dbSample in dbSamples:
if dbSample.name == sample.name:
sample.id = dbSample.id
newSample = False
if newSample == True:
logging.debug("New run: existing investigation, creating sample and run...")
sample.investigation = investigation
sampleId = self._service.create(self._sessionId, sample)
sample.id = sampleId
else:
logging.debug("New run: existing investigation and sample, creating run...")
else:
logging.error("ERROR, there should be only one investigation per instrument per investigation name")
# create new dataset
dataset.sample = sample
dataset.investigation = investigation
datasetId = self._service.create(self._sessionId, dataset)
logging.debug(" datasetId: %s" % str(datasetId))
elif len(dbDatasets) == 1:
logging.debug("Run %s is already cataloged, updating catalog..." % dataset.name)
dbDataset = dbDatasets[0]
logging.debug(" datasetId: %s" % str(dbDataset.id))
# update "one to many" relationships
if hasattr(dbDataset, "datafiles"):
dfs = getattr(dbDataset, "datafiles")
self._service.deleteMany(self._sessionId, dfs)
for df in datafiles:
df.dataset = dbDataset
self._service.createMany(self._sessionId, datafiles)
# update "many to one" relationships
ds = self._service.get(self._sessionId, "Dataset INCLUDE 1", dbDataset.id)
investigation.id = ds.investigation.id
dbSamples = self._service.search(self._sessionId, "Sample <-> Investigation [id = '" + str(ds.investigation.id) + "']")
updateSample = True
for sa in dbSamples:
if sa.name == sample.name:
sample = sa
updateSample = False
if updateSample == True:
sample.id = ds.sample.id
sample.investigation = investigation
self._service.update(self._sessionId, sample)
dataset.id = ds.id
dataset.sample = sample
dataset.investigation = investigation
self._service.update(self._sessionId, dataset)
self._service.update(self._sessionId, investigation)
else:
logging.error("ERROR, there should be only one dataset per run number per type experiment_raw")
def execute(self):
"""
Catalog reduced data files
"""
config = ConfigParser.RawConfigParser()
config.read('/etc/autoreduce/icat4.cfg')
directory = "/" + self._facilityName + "/" + self._instrumentName + "/" + self._investigationName + "/shared/autoreduce"
logging.info("reduction output directory: %s" % directory)
#set dataset name
dataset = self._factory.create("dataset")
dsType = self._factory.create("datasetType")
dsType.id = config.get('DatasetType', 'reduced')
dataset.type = dsType
dataset.name = self._runNumber
dataset.location = directory
datafiles = []
pattern = '*' + self._runNumber + '*'
for dirpath, dirnames, filenames in os.walk(directory):
listing = glob.glob(os.path.join(dirpath, pattern))
for filepath in listing:
filename = os.path.basename(filepath)
logging.info("Filename: %s" % filename)
datafile = self._factory.create("datafile")
datafile.location = filepath
datafile.name = filename
extension = os.path.splitext(filename)[1][1:]
dfFormat = self._factory.create("datafileFormat")
dfFormat.id = config.get('DatafileFormat', extension)
datafile.datafileFormat = dfFormat
modTime = os.path.getmtime(filepath)
datafile.datafileCreateTime = epochToISO8601(modTime)
datafile.fileSize = os.path.getsize(filepath)
datafiles.append(datafile)
dataset.datafiles = datafiles
dataset.type = dsType
dbDatasets = self._service.search(
self._sessionId,
"Dataset INCLUDE Datafile [name = '" + str(dataset.name) +
"'] <-> Investigation <-> Instrument [name = '" +
str(self._instrumentName) +
"'] <-> DatasetType [name = 'reduced']")
if len(dbDatasets) == 0:
dbInvestigations = self._service.search(
self._sessionId, "Investigation INCLUDE Sample [name = '" +
str(self._investigationName) + "'] <-> Instrument [name = '" +
self._instrumentName + "'] <-> Dataset [name = '" +
str(dataset.name) + "']")
if len(dbInvestigations) == 0:
logging.error(
"No investigation entry found: try cataloging the raw data first."
)
return
else:
investigation = dbInvestigations[0]
if len(dbInvestigations) > 1:
logging.error(
"Multiple investigation entries found: using the first."
)
logging.debug("Creating dataset: %s" % datetime.now())
dataset.investigation = investigation
dataset.sample = investigation.samples[0]
self._service.create(self._sessionId, dataset)
elif len(dbDatasets) == 1:
logging.debug(
"reduced dataset %s is already cataloged, updating reduced dataset... "
% (dataset.name))
dbDataset = dbDatasets[0]
# update "one to many" relationships
if hasattr(dbDataset, "datafiles"):
dfs = getattr(dbDataset, "datafiles")
self._service.deleteMany(self._sessionId, dfs)
for df in datafiles:
df.dataset = dbDataset
self._service.createMany(self._sessionId, datafiles)
else:
logging.error(
"ERROR, there should be only one dataset per run number per type reduced"
)
def execute(self):
#find facility, investigation_type
config = ConfigParser.RawConfigParser()
config.read('/etc/autoreduce/icat4.cfg')
investigation = self._factory.create("investigation")
#find facility, investigation_type
facility = self._factory.create("facility")
facility.id = config.get('Facility', 'sns')
investigation.facility = facility
invType = self._factory.create("investigationType")
invType.id = config.get('InvestigationType', 'experiment')
investigation.type = invType
totalCounts = 0
protonCharge = 0
duration = 0
entry_count = 0
sample = self._factory.create("sample")
sample.name = 'NONE'
#open nexus file
file = nxs.open(self._infilename, 'r')
for name, nxclass in file.entries():
if nxclass == "NXentry" and name != "entry-VETO":
listing = file.getentries()
#investigation name
if listing.has_key('experiment_identifier'):
file.opendata('experiment_identifier')
investigation.name = file.getdata()
file.closedata()
else:
investigation.name = "IPTS-0000"
#investigation title
if listing.has_key('title'):
file.opendata('title')
investigation_title = unicode(file.getdata(),
errors='replace')
investigation.title = investigation_title.encode(
'ascii', 'replace')
file.closedata()
else:
investigation.title = "NONE"
#create dataset
dataset = self._factory.create("dataset")
#investigation run number
if listing.has_key('collection_identifier'):
file.opendata('collection_identifier')
investigation.visitId = str(file.getdata())
file.closedata()
else:
investigation.visitId = "0"
#dataset run number
file.opendata('run_number')
dataset.name = file.getdata()
file.closedata()
#dataset title
if listing.has_key('title'):
file.opendata('title')
dataset_description = unicode(file.getdata(),
errors='replace')
dataset.description = dataset_description.encode(
'ascii', 'replace')
file.closedata()
dsType = self._factory.create("datasetType")
dsType.id = config.get('DatasetType', 'experiment_raw')
dataset.type = dsType
#set dataset start time
if listing.has_key('start_time'):
file.opendata('start_time')
if entry_count == 0:
dataset.startDate = file.getdata()
elif dataset.startDate > file.getdata():
dataset.startDate = file.getdata()
file.closedata()
#set dataset end time
if listing.has_key('end_time'):
file.opendata('end_time')
if entry_count == 0:
dataset.endDate = file.getdata()
elif dataset.endDate < file.getdata():
dataset.endDate = file.getdata()
file.closedata()
#dataset proton_charge
file.opendata('proton_charge')
protonCharge = protonCharge + file.getdata()
file.closedata()
#dataset total_counts
file.opendata('total_counts')
totalCounts = totalCounts + file.getdata()
file.closedata()
#dataset duration
file.opendata('duration')
duration = duration + file.getdata()
file.closedata()
#investigation instrument
file.opengroup('instrument')
file.opendata('name')
for attr, value in file.attrs():
if attr == 'short_name':
instrument = self._factory.create("instrument")
instrument.name = value
instrument.id = config.get('Instrument', value.lower())
investigation.instrument = instrument
file.closedata()
file.closegroup()
if listing.has_key('sample'):
file.opengroup('sample')
listSample = file.getentries()
if listSample.has_key('name'):
file.opendata('name')
# Text stored in the Nexus file is XML escaped
# ICAT unescapes it automatically, so we need to
# do it here if we want to determine whether
# the sample is already in the DB.
sample_name = unicode(file.getdata(), errors='replace')
sample.name = saxutils.unescape(
sample_name.encode('ascii', 'replace'))
file.closedata()
else:
sample.name = "NONE"
sampleParameters = []
#set sample nature
if listSample.has_key('nature'):
file.opendata('nature')
nature = file.getdata()
file.closedata()
if nature:
parameterType = self._factory.create(
"parameterType")
parameterType.id = config.get(
'ParameterType', 'nature')
parameterType.applicableToSample = config.getboolean(
'ParameterType', 'nature_applicable_to_sample')
sampleParameter = self._factory.create(
"sampleParameter")
sampleParameter.type = parameterType
sampleParameter.stringValue = nature
sampleParameters.append(sampleParameter)
if listSample.has_key('identifier'):
file.opendata('identifier')
identifier = file.getdata()
file.closedata()
if identifier:
parameterType = self._factory.create(
"parameterType")
parameterType.id = config.get(
'ParameterType', 'identifier')
parameterType.applicableToSample = config.getboolean(
'ParameterType',
'identifier_applicable_to_sample')
sampleParameter = self._factory.create(
"sampleParameter")
sampleParameter.type = parameterType
sampleParameter.stringValue = identifier
sampleParameters.append(sampleParameter)
if len(sampleParameters):
sample.parameters = sampleParameters
file.closegroup()
file.close()
#set dataset parameters
parameters = []
#1) parameter proton_charge
if protonCharge:
parameterType = self._factory.create("parameterType")
parameterType.id = config.get('ParameterType', 'proton_charge')
parameterType.applicableToDataset = config.getboolean(
'ParameterType', 'proton_charge_applicable_to_dataset')
datasetParameter = self._factory.create("datasetParameter")
datasetParameter.type = parameterType
datasetParameter.stringValue = protonCharge
parameters.append(datasetParameter)
#2) parameter total_counts
if totalCounts:
parameterType = self._factory.create("parameterType")
parameterType.id = config.get('ParameterType', 'total_counts')
parameterType.applicableToDataset = config.getboolean(
'ParameterType', 'total_counts_applicable_to_dataset')
datasetParameter = self._factory.create("datasetParameter")
datasetParameter.type = parameterType
datasetParameter.numericValue = totalCounts
parameters.append(datasetParameter)
#3) parameter duration
if duration:
parameterType = self._factory.create("parameterType")
parameterType.id = config.get('ParameterType', 'duration')
parameterType.applicableToDataset = config.getboolean(
'ParameterType', 'duration_applicable_to_dataset')
datasetParameter = self._factory.create("datasetParameter")
datasetParameter.type = parameterType
datasetParameter.numericValue = duration
parameters.append(datasetParameter)
dataset.parameters = parameters
dataset.location = self._infilename
datafiles = []
token = self._infilename.split("/")
proposalDir = "/" + token[1] + "/" + token[2] + "/" + token[3]
for dirpath, dirnames, filenames in os.walk(proposalDir):
if dirpath.find("shared") == -1 and dirpath.find("data") == -1:
for filename in [f for f in filenames]:
#if dataset.name in filename and os.path.islink(filename) != False:
if dataset.name in filename:
logging.info("Filename: %s" % filename)
datafile = self._factory.create("datafile")
filepath = os.path.join(dirpath, filename)
extension = os.path.splitext(filename)[1][1:]
datafile.name = filename
datafile.location = filepath
dfFormat = self._factory.create("datafileFormat")
dfFormat.id = config.get('DatafileFormat', extension)
datafile.datafileFormat = dfFormat
modTime = os.path.getmtime(filepath)
datafile.datafileCreateTime = epochToISO8601(modTime)
datafile.fileSize = os.path.getsize(filepath)
datafiles.append(datafile)
dataset.datafiles = datafiles
dbDatasets = self._service.search(
self._sessionId,
"Dataset INCLUDE Datafile [name = '" + str(dataset.name) +
"'] <-> Investigation <-> Instrument [name = '" +
str(instrument.name) +
"'] <-> DatasetType [name = 'experiment_raw']")
if len(dbDatasets) == 0:
dbInvestigations = self._service.search(
self._sessionId,
"Investigation INCLUDE Sample [name = '" + investigation.name +
"' AND visitId = '" + investigation.visitId +
"'] <-> Instrument [name = '" + instrument.name + "']")
if len(dbInvestigations) == 0:
logging.debug(
"New IPTS: creating investigation, sample, run...")
# create new investigation
invId = self._service.create(self._sessionId, investigation)
investigation.id = invId
# create new sample
sample.investigation = investigation
sampleId = self._service.create(self._sessionId, sample)
sample.id = sampleId
logging.debug(" invId: %s sampleId: %s" %
(str(invId), str(sampleId)))
elif len(dbInvestigations) == 1:
investigation = dbInvestigations[0]
dbSamples = investigation.samples
newSample = True
for dbSample in dbSamples:
if dbSample.name == sample.name:
sample.id = dbSample.id
newSample = False
if newSample == True:
logging.debug(
"New run: existing investigation, creating sample and run..."
)
sample.investigation = investigation
sampleId = self._service.create(self._sessionId, sample)
sample.id = sampleId
else:
logging.debug(
"New run: existing investigation and sample, creating run..."
)
else:
logging.error(
"ERROR, there should be only one investigation per instrument per investigation name"
)
# create new dataset
dataset.sample = sample
dataset.investigation = investigation
datasetId = self._service.create(self._sessionId, dataset)
logging.debug(" datasetId: %s" % str(datasetId))
elif len(dbDatasets) == 1:
logging.debug("Run %s is already cataloged, updating catalog..." %
dataset.name)
dbDataset = dbDatasets[0]
logging.debug(" datasetId: %s" % str(dbDataset.id))
# update "one to many" relationships
if hasattr(dbDataset, "datafiles"):
dfs = getattr(dbDataset, "datafiles")
self._service.deleteMany(self._sessionId, dfs)
for df in datafiles:
df.dataset = dbDataset
self._service.createMany(self._sessionId, datafiles)
# update "many to one" relationships
ds = self._service.get(self._sessionId, "Dataset INCLUDE 1",
dbDataset.id)
investigation.id = ds.investigation.id
dbSamples = self._service.search(
self._sessionId, "Sample <-> Investigation [id = '" +
str(ds.investigation.id) + "']")
updateSample = True
for sa in dbSamples:
if sa.name == sample.name:
sample = sa
updateSample = False
if updateSample == True:
sample.id = ds.sample.id
sample.investigation = investigation
self._service.update(self._sessionId, sample)
dataset.id = ds.id
dataset.sample = sample
dataset.investigation = investigation
self._service.update(self._sessionId, dataset)
self._service.update(self._sessionId, investigation)
else:
logging.error(
"ERROR, there should be only one dataset per run number per type experiment_raw"
)
