def _getDataSetsForExperiment(self):
"""
Return a list of datasets belonging to the experiment and optionally
to the sample. If the sample ID is empty, only the experiment is used
in the search criteria.
If none are found, return [].
"""
# Set search criteria to retrieve all datasets for the experiment.
# If the sample code is set, we also filter by it.
searchCriteria = SearchCriteria()
searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE, "MICROSCOPY_IMG_CONTAINER"))
expCriteria = SearchCriteria()
expCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.PERM_ID, self._experiment.permId))
searchCriteria.addSubCriteria(SearchSubCriteria.createExperimentCriteria(expCriteria))
if self._sample is not None:
self._logger.info("Filter by sample " + self._sampleId)
sampleCriteria = SearchCriteria()
sampleCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.PERM_ID, self._sample.permId))
searchCriteria.addSubCriteria(SearchSubCriteria.createSampleCriteria(sampleCriteria))
dataSets = searchService.searchForDataSets(searchCriteria)
if len(dataSets) == 0:
dataSets = []
self._message = "Could not retrieve datasets for experiment " \
"with id " + self._experimentId
if self._sampleId != "":
self._message = self._message + " and sample with id " + \
self._sampleId
self._logger.error(self._message)
# Return
return dataSets
def _getDataSetsForSample(sampleIdentifier, dataSetType):
"""Return the dataSet of given type for specified sample."""
# Set search criteria to retrieve the dataSet associated with the sample
searchCriteria = SearchCriteria()
searchCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
dataSetType)
)
sampleCriteria = SearchCriteria()
sampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.CODE,
sampleIdentifier)
)
searchCriteria.addSubCriteria(
SearchSubCriteria.createSampleCriteria(
sampleCriteria)
)
dataSetList = searchService.searchForDataSets(searchCriteria)
if len(dataSetList) != 1:
[]
# Return the dataSet
return dataSetList
def _getDataSetForTube(self, tubeCode=None):
"""
Get the datasets belonging to the tube with specified tube code.
If none is found, return [].
If no tubeCode is given, it is assumed that the tube is the passed
entity with code self._entityCode.
"""
if tubeCode is None:
tubeCode = self._entityCode
# Set search criteria to retrieve the dataset contained in the tube
searchCriteria = SearchCriteria()
tubeCriteria = SearchCriteria()
tubeCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, tubeCode))
searchCriteria.addSubCriteria(SearchSubCriteria.createSampleCriteria(tubeCriteria))
dataSets = searchService.searchForDataSets(searchCriteria)
if len(dataSets) == 0:
self._message = "Could not retrieve datasets for tube " \
"with code " + tubeCode + "."
self._logger.error(self._message)
# Return
return dataSets
def _getDataSetForWell(self, wellId=None):
"""
Get the datasets belonging to the well with specified code. If none
are found, return [].
If no wellId is given, it is assumed that the well is the passed
entity with code self._entityId.
"""
if wellId is None:
wellId = self._entityId
# Set search criteria to retrieve the dataset contained in the well
searchCriteria = SearchCriteria()
wellCriteria = SearchCriteria()
wellCriteria.addMatchClause(
MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
wellId))
searchCriteria.addSubCriteria(
SearchSubCriteria.createSampleCriteria(wellCriteria))
dataSets = searchService.searchForDataSets(searchCriteria)
if len(dataSets) == 0:
self._message = "Could not retrieve datasets for well " \
"with code " + wellId + "."
self._logger.error(self._message)
# Return
return dataSets
def _getDataSetForTube(self, tubeCode):
"""
Get the datasets belonging to the tube with specified tube code.
If none is found, return [].
"""
if _DEBUG:
self._logger.info("Searching for tube with code " + tubeCode)
# Set search criteria to retrieve the dataset contained in the tube
searchCriteria = SearchCriteria()
tubeCriteria = SearchCriteria()
tubeCriteria.addMatchClause(
MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
tubeCode))
searchCriteria.addSubCriteria(
SearchSubCriteria.createSampleCriteria(tubeCriteria))
dataSets = searchService.searchForDataSets(searchCriteria)
if _DEBUG:
self._logger.info("Retrieved " + str(len(dataSets)) + \
" datasets for tube with code " + tubeCode)
if len(dataSets) == 0:
self._message = "Could not retrieve datasets for tube " \
"with code " + tubeCode + "."
self._logger.error(self._message)
# Return
return dataSets
def _getDataSetsForExperiment(self):
"""
Return a list of datasets belonging to the experiment and optionally
to the sample. If the sample ID is empty, only the experiment is used
in the search criteria.
If none are found, return [].
"""
# Set search criteria to retrieve all datasets of type MICROSCOPY_IMG_CONTAINER
# for the experiment. If the sample code is set, we also filter by it.
searchCriteria = SearchCriteria()
searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE, "MICROSCOPY_IMG_CONTAINER"))
expCriteria = SearchCriteria()
expCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.PERM_ID, self._experiment.permId))
searchCriteria.addSubCriteria(SearchSubCriteria.createExperimentCriteria(expCriteria))
if self._sample is not None:
self._logger.info("Filter by sample " + self._sampleId)
sampleCriteria = SearchCriteria()
sampleCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.PERM_ID, self._sample.permId))
searchCriteria.addSubCriteria(SearchSubCriteria.createSampleCriteria(sampleCriteria))
dataSets = searchService.searchForDataSets(searchCriteria)
if len(dataSets) == 0:
dataSets = []
self._message = "Could not retrieve datasets for experiment " \
"with id " + self._experimentId
if self._sampleId != "":
self._message = self._message + " and sample with id " + \
self._sampleId
self._logger.error(self._message)
# Return
return dataSets
def _getDataSetForWell(self, wellCode=None):
"""
Get the datasets belonging to the well with specified code. If none
are found, return [].
If no wellCode is given, it is assumed that the well is the passed
entity with code self._entityCode.
"""
if wellCode is None:
wellCode = self._entityCode
# Set search criteria to retrieve the dataset contained in the well
searchCriteria = SearchCriteria()
wellCriteria = SearchCriteria()
wellCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, wellCode))
searchCriteria.addSubCriteria(SearchSubCriteria.createSampleCriteria(wellCriteria))
dataSets = searchService.searchForDataSets(searchCriteria)
if len(dataSets) == 0:
self._message = "Could not retrieve datasets for well " \
"with code " + wellCode + "."
# Return
return dataSets
def _getDataSetsForSample(sampleIdentifier, dataSetType):
"""Return the dataSet of given type for specified sample."""
# Set search criteria to retrieve the dataSet associated with the sample
searchCriteria = SearchCriteria()
searchCriteria.addMatchClause(
MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
dataSetType))
sampleCriteria = SearchCriteria()
sampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
sampleIdentifier))
searchCriteria.addSubCriteria(
SearchSubCriteria.createSampleCriteria(sampleCriteria))
dataSetList = searchService.searchForDataSets(searchCriteria)
if len(dataSetList) != 1:
[]
# Return the dataSet
return dataSetList
def _getAccessoryDataSetsForExperiment(self):
"""
Return a list of datasets belonging to the experiment and optionally
to the sample. If the sample ID is empty, only the experiment is used
in the search criteria.
If none are found, return [].
"""
# Set search criteria to retrieve all datasets of type for the experiment.
# If the sample code is set, we also filter by it.
searchCriteria = SearchCriteria()
searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE, "MICROSCOPY_ACCESSORY_FILE"))
expCriteria = SearchCriteria()
expCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.PERM_ID, self._experiment.permId))
searchCriteria.addSubCriteria(SearchSubCriteria.createExperimentCriteria(expCriteria))
if self._sample is not None:
self._logger.info("Filter by sample " + self._sampleId)
sampleCriteria = SearchCriteria()
sampleCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.PERM_ID, self._sample.permId))
searchCriteria.addSubCriteria(SearchSubCriteria.createSampleCriteria(sampleCriteria))
accessoryDataSets = searchService.searchForDataSets(searchCriteria)
# Append the accessory datasets
if len(accessoryDataSets) != 0:
self._message = "Found " + str(len(accessoryDataSets)) + \
" accessory datasets for experiment " \
"with id " + self._experimentId
if self._sampleId != "":
self._message = self._message + " and sample with id " + \
self._sampleId
self._logger.info(self._message)
# Return
return accessoryDataSets
def _getDataSets(self, expSampleType, expSamplePermId, sampleType, samplePermId,
requestedDatasetType="MICROSCOPY_IMG_CONTAINER"):
"""
Return a list of datasets of requested type belonging to the MICROSCOPY_EXPERIMENT sample
and a specific sample of type MICROSCOPY_SAMPLE_TYPE.
If none are found, return [].
"""
# Only two types of experiment are allowed
assert requestedDatasetType == "MICROSCOPY_IMG_CONTAINER" or requestedDatasetType == "MICROSCOPY_ACCESSORY_FILE", \
"Input argument 'requestedDatasetType' must be one of MICROSCOPY_IMG_CONTAINER or MICROSCOPY_ACCESSORY_FILE."
self._logger.info("_getDataSetsForMicroscopySampleType() called " +
"with requested data type " + requestedDatasetType)
if _DEBUG:
self._logger.info("* Requested dataset type: " + requestedDatasetType)
self._logger.info("* Requested experiment sample type: " + expSampleType)
self._logger.info("* Requested experiment sample permId: " + expSamplePermId)
self._logger.info("* Requested sample type: " + sampleType)
self._logger.info("* Requested sample permId: " + samplePermId)
# Dataset criteria
datasetSearchCriteria = SearchCriteria()
datasetSearchCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
requestedDatasetType)
)
# Add search criteria for sample of type MICROSCOPY_EXPERIMENT with specified CODE
sampleExpCriteria = SearchCriteria()
sampleExpCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
expSampleType))
sampleExpCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.PERM_ID,
expSamplePermId)
)
# Add search criteria for sample of type MICROSCOPY_SAMPLE_TYPE with specified CODE
sampleCriteria = SearchCriteria()
sampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
sampleType)
)
sampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.PERM_ID,
samplePermId)
)
sampleCriteria.addSubCriteria(
SearchSubCriteria.createSampleParentCriteria(
sampleExpCriteria)
)
# Add search for a parent sample of type MICROSCOPY_SAMPLE_TYPE as subcriterion
datasetSearchCriteria.addSubCriteria(
SearchSubCriteria.createSampleCriteria(sampleCriteria)
)
# Retrieve the datasets
dataSets = searchService.searchForDataSets(datasetSearchCriteria)
# Inform
self._logger.info("Retrieved " + str(len(dataSets)) +
" dataSets of type " + requestedDatasetType + ".")
# Return
return dataSets
def _getDataSets(self, expSampleType, expSamplePermId, sampleType, samplePermId,
requestedDatasetType="MICROSCOPY_IMG_CONTAINER"):
"""
Return a list of datasets of requested type belonging to the MICROSCOPY_EXPERIMENT sample
and a specific sample of type MICROSCOPY_SAMPLE_TYPE.
If none are found, return [].
"""
# Only two types of experiment are allowed
assert requestedDatasetType == "MICROSCOPY_IMG_CONTAINER" or requestedDatasetType == "MICROSCOPY_ACCESSORY_FILE", \
"Input argument 'requestedDatasetType' must be one of MICROSCOPY_IMG_CONTAINER or MICROSCOPY_ACCESSORY_FILE."
self._logger.info("_getDataSetsForMicroscopySampleType() called " +
"with requested data type " + requestedDatasetType)
if _DEBUG:
self._logger.info("* Requested dataset type: " + requestedDatasetType)
self._logger.info("* Requested experiment sample type: " + expSampleType)
self._logger.info("* Requested experiment sample permId: " + expSamplePermId)
self._logger.info("* Requested sample type: " + sampleType)
self._logger.info("* Requested sample permId: " + samplePermId)
# Dataset criteria
datasetSearchCriteria = SearchCriteria()
datasetSearchCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
requestedDatasetType)
)
# Add search criteria for sample of type MICROSCOPY_EXPERIMENT with specified CODE
sampleExpCriteria = SearchCriteria()
sampleExpCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
expSampleType))
sampleExpCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.PERM_ID,
expSamplePermId)
)
# Add search criteria for sample of type MICROSCOPY_SAMPLE_TYPE with specified CODE
sampleCriteria = SearchCriteria()
sampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
sampleType)
)
sampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.PERM_ID,
samplePermId)
)
sampleCriteria.addSubCriteria(
SearchSubCriteria.createSampleParentCriteria(
sampleExpCriteria)
)
# Add search for a parent sample of type MICROSCOPY_SAMPLE_TYPE as subcriterion
datasetSearchCriteria.addSubCriteria(
SearchSubCriteria.createSampleCriteria(sampleCriteria)
)
# Retrieve the datasets
dataSets = searchService.searchForDataSets(datasetSearchCriteria)
# Inform
self._logger.info("Retrieved " + str(len(dataSets)) +
" dataSets of type " + requestedDatasetType + ".")
# Return
return dataSets
