def _retrieveAllSamplesWithTypeAndParent(self, sampleType, parentSampleId,
parentSampleType):
"""
Retrieve all samples belonging to current experiment
sample and collection having specified type.
"""
if _DEBUG:
self._logger.info("Retrieving samples of type " + sampleType +
" with parent sample with id " + parentSampleId +
" and type " + parentSampleType)
# The samples are of type 'sampleType'
searchCriteria = SearchCriteria()
searchCriteria.addMatchClause(
MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
sampleType))
# The samples have given parent
expSampleCriteria = SearchCriteria()
expSampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
parentSampleType))
expSampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
parentSampleId))
searchCriteria.addSubCriteria(
SearchSubCriteria.createSampleParentCriteria(expSampleCriteria))
# Now search
samples = searchService.searchForSamples(searchCriteria)
# Return the samples
return samples
def _getChildSamples(parentSampleType, parentSamplePermId, sampleType):
"""Return the samples of given type for specified parent sample."""
# The samples are of type 'sampleType'
searchCriteria = SearchCriteria()
searchCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
sampleType)
)
# The samples have given parent
expSampleCriteria = SearchCriteria()
expSampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
parentSampleType)
)
expSampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.PERM_ID,
parentSamplePermId)
)
searchCriteria.addSubCriteria(
SearchSubCriteria.createSampleParentCriteria(expSampleCriteria)
)
# Now search
samples = searchService.searchForSamples(searchCriteria)
# Return the samples
return samples
def _retrieveAllSamplesWithType(self, sampleType):
"""
Retrieve all samples belonging to current experiment
sample and collection having specified type.
"""
# The samples are of type 'sampleType'
searchCriteria = SearchCriteria()
searchCriteria.addMatchClause(
MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
sampleType))
# The samples have parent _EXPERIMENT_SAMPLE
expSampleCriteria = SearchCriteria()
expSampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
self._expSampleType))
expSampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(MatchClauseAttribute.PERM_ID,
self._expSamplePermId))
searchCriteria.addSubCriteria(
SearchSubCriteria.createSampleParentCriteria(expSampleCriteria))
# Now search
samples = searchService.searchForSamples(searchCriteria)
# Return the samples
return samples
def _getChildSamples(parentSampleType, parentSamplePermId, sampleType):
"""Return the samples of given type for specified parent sample."""
# The samples are of type 'sampleType'
searchCriteria = SearchCriteria()
searchCriteria.addMatchClause(
MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
sampleType))
# The samples have given parent
expSampleCriteria = SearchCriteria()
expSampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
parentSampleType))
expSampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(MatchClauseAttribute.PERM_ID,
parentSamplePermId))
searchCriteria.addSubCriteria(
SearchSubCriteria.createSampleParentCriteria(expSampleCriteria))
# Now search
samples = searchService.searchForSamples(searchCriteria)
# Return the samples
return samples
def _getMicroscopySampleTypeSample(self):
# Search sample of type MICROSCOPY_SAMPLE_TYPE with specified CODE
sampleCriteria = SearchCriteria()
sampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
self._sampleType)
)
sampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.PERM_ID,
self._samplePermId)
)
# Search parent sample of type MICROSCOPY_EXPERIMENT with specified permId
sampleParentCriteria = SearchCriteria()
sampleParentCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
self._expSampleType))
sampleParentCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.PERM_ID,
self._expSamplePermId))
# Add the parent sample subcriteria
sampleCriteria.addSubCriteria(
SearchSubCriteria.createSampleParentCriteria(
sampleParentCriteria
)
)
# Search
samples = searchService.searchForSamples(sampleCriteria)
if len(samples) == 0:
samples = []
self._message = "Could not retrieve MICROSCOPY_SAMPLE_TYPE sample with id " + \
self._sampleId + " for parent sample MICROSCOPY_EXPERIMENT with id " + \
self._expSampleId + " from COLLECTION experiment " + self._collectionId + "."
self._logger.error(self._message)
return samples
if _DEBUG:
self._logger.info("Retrieved " + str(len(samples)) + \
" samples of type MICROSCOPY_SAMPLE_TYPE " + \
"for parent sample MICROSCOPY_EXPERIMENT " +
"with ID " + self._expSamplePermId)
# Return
return samples[0]
def _getMicroscopySampleTypeSample(self):
# Search sample of type MICROSCOPY_SAMPLE_TYPE with specified CODE
sampleCriteria = SearchCriteria()
sampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
self._sampleType)
)
sampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.PERM_ID,
self._samplePermId)
)
# Search parent sample of type MICROSCOPY_EXPERIMENT with specified permId
sampleParentCriteria = SearchCriteria()
sampleParentCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
self._expSampleType))
sampleParentCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.PERM_ID,
self._expSamplePermId))
# Add the parent sample subcriteria
sampleCriteria.addSubCriteria(
SearchSubCriteria.createSampleParentCriteria(
sampleParentCriteria
)
)
# Search
samples = searchService.searchForSamples(sampleCriteria)
if len(samples) == 0:
samples = []
self._message = "Could not retrieve MICROSCOPY_SAMPLE_TYPE sample with id " + \
self._sampleId + " for parent sample MICROSCOPY_EXPERIMENT with id " + \
self._expSampleId + " from COLLECTION experiment " + self._collectionId + "."
self._logger.error(self._message)
return samples
if _DEBUG:
self._logger.info("Retrieved " + str(len(samples)) + \
" samples of type MICROSCOPY_SAMPLE_TYPE " + \
"for parent sample MICROSCOPY_EXPERIMENT " +
"with ID " + self._expSamplePermId)
# Return
return samples[0]
def _getSamples(self, expSampleType, expSamplePermId, sampleType):
"""
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 [].
"""
if _DEBUG:
self._logger.info("* Requested experiment sample type: " + expSampleType)
self._logger.info("* Requested experiment sample permId: " + expSamplePermId)
self._logger.info("* Requested sample type: " + sampleType)
# Search samples of type MICROSCOPY_SAMPLE_TYPE
sampleCriteria = SearchCriteria()
sampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
sampleType)
)
# Search parent sample of type MICROSCOPY_EXPERIMENT with specified permId
sampleParentCriteria = SearchCriteria()
sampleParentCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
expSampleType))
sampleParentCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.PERM_ID,
expSamplePermId))
# Add the parent sample subcriteria
sampleCriteria.addSubCriteria(
SearchSubCriteria.createSampleParentCriteria(
sampleParentCriteria
)
)
# Search
samples = searchService.searchForSamples(sampleCriteria)
# Return
return samples
def _getSamples(self, expSampleType, expSamplePermId, sampleType):
"""
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 [].
"""
if _DEBUG:
self._logger.info("* Requested experiment sample type: " + expSampleType)
self._logger.info("* Requested experiment sample permId: " + expSamplePermId)
self._logger.info("* Requested sample type: " + sampleType)
# Search samples of type MICROSCOPY_SAMPLE_TYPE
sampleCriteria = SearchCriteria()
sampleCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
sampleType)
)
# Search parent sample of type MICROSCOPY_EXPERIMENT with specified permId
sampleParentCriteria = SearchCriteria()
sampleParentCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.TYPE,
expSampleType))
sampleParentCriteria.addMatchClause(
MatchClause.createAttributeMatch(
MatchClauseAttribute.PERM_ID,
expSamplePermId))
# Add the parent sample subcriteria
sampleCriteria.addSubCriteria(
SearchSubCriteria.createSampleParentCriteria(
sampleParentCriteria
)
)
# Search
samples = searchService.searchForSamples(sampleCriteria)
# Return
return samples
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
