def _testSearchMethod(self, repoIteratorMethod, clientSearchMethod):
repoObjs = list(repoIteratorMethod())
numRepoObjs = len(repoObjs)
pageSizes = self._getPageSizes(numRepoObjs)
for pageSize in pageSizes:
self._client.set_page_size(pageSize)
clientObjs = list(clientSearchMethod())
for repoObj, clientObj in utils.zipLists(repoObjs, clientObjs):
self._assertEqual(repoObj, clientObj)
def _testSearchMethod(self, repoIteratorMethod, clientSearchMethod):
repoObjs = list(repoIteratorMethod())
numRepoObjs = len(repoObjs)
pageSizes = self._getPageSizes(numRepoObjs)
for pageSize in pageSizes:
self._client.set_page_size(pageSize)
clientObjs = list(clientSearchMethod())
for repoObj, clientObj in utils.zipLists(repoObjs, clientObjs):
self._assertEqual(repoObj, clientObj)
def verifyObjectList(self, gaObjects, datamodelObjects, getMethod):
"""
Verifies that the specified list of protocol objects corresponds
to the specified list of datamodel objects.
"""
for gaObject, datamodelObject in utils.zipLists(
gaObjects, datamodelObjects):
self.assertEqual(gaObject, datamodelObject.toProtocolElement())
otherGaObject = getMethod(gaObject.id)
self.assertEqual(gaObject, otherGaObject)
def testSearchFeatures(self):
repoFeatureSets = self._repo.allFeatureSets()
for repoFeatureSet in repoFeatureSets:
repoFeatures = list(repoFeatureSet.getFeatures())
numFeatures = len(repoFeatures)
featureSetId = repoFeatureSet.getId()
pageSizes = self._getPageSizes(numFeatures)
for pageSize in pageSizes:
features = list(self._client.search_features(featureSetId))
for repoFeature, feature in utils.zipLists(
repoFeatures, features):
self.assertEqual(repoFeature, feature)
def testSearchFeatures(self):
repoFeatureSets = self._repo.allFeatureSets()
for repoFeatureSet in repoFeatureSets:
repoFeatures = list(repoFeatureSet.getFeatures())
numFeatures = len(repoFeatures)
featureSetId = repoFeatureSet.getId()
pageSizes = self._getPageSizes(numFeatures)
for pageSize in pageSizes:
features = list(self._client.search_features(featureSetId))
for repoFeature, feature in utils.zipLists(
repoFeatures, features):
self.assertEqual(repoFeature, feature)
def _testSearchMethodInContainer(self, containerAccessorMethod,
clientSearchMethod,
containerIteratorMethod):
for container in containerIteratorMethod:
containerId = container.getId()
repoObjs = getattr(container, containerAccessorMethod)()
numRepoObjs = len(repoObjs)
pageSizes = self._getPageSizes(numRepoObjs)
for pageSize in pageSizes:
self._client.set_page_size(pageSize)
clientObjs = list(clientSearchMethod(containerId))
for repoObj, clientObj in utils.zipLists(repoObjs, clientObjs):
self._assertEqual(repoObj, clientObj)
def testSearchReferences(self):
repoReferenceSets = self._repo.getReferenceSets()
for repoReferenceSet in repoReferenceSets:
referenceSetId = repoReferenceSet.getId()
repoReferences = repoReferenceSet.getReferences()
numRefs = len(repoReferences)
pageSizes = self._getPageSizes(numRefs)
for pageSize in pageSizes:
self._client.set_page_size(pageSize)
references = list(
self._client.search_references(referenceSetId))
for repoReference, reference in utils.zipLists(
repoReferences, references):
self._assertEqual(repoReference, reference)
def testSearchPhenotypes(self):
phenotypeAssociationSets = self._repo.allPhenotypeAssociationSets()
for phenotypeAssociationSet in phenotypeAssociationSets:
repoAssociations = list(phenotypeAssociationSet.getAssociations())
numAssociations = len(repoAssociations)
phenotypeAssociationSetId = phenotypeAssociationSet.getId()
pageSizes = self._getPageSizes(numAssociations)
for pageSize in pageSizes:
clientPhenotypes = list(self._client.search_phenotype
(phenotypeAssociationSetId))
for repoAssociation, clientPhenotype in utils.zipLists(
repoAssociations, clientPhenotypes):
self.assertEqual(repoAssociation.phenotype,
clientPhenotype)
def _testSearchMethodInContainer(
self, containerAccessorMethod, clientSearchMethod,
containerIteratorMethod):
for container in containerIteratorMethod:
containerId = container.getId()
repoObjs = getattr(container, containerAccessorMethod)()
numRepoObjs = len(repoObjs)
pageSizes = self._getPageSizes(numRepoObjs)
for pageSize in pageSizes:
self._client.set_page_size(pageSize)
clientObjs = list(clientSearchMethod(containerId))
for repoObj, clientObj in utils.zipLists(
repoObjs, clientObjs):
self._assertEqual(repoObj, clientObj)
def testSearchReferences(self):
repoReferenceSets = self._repo.getReferenceSets()
for repoReferenceSet in repoReferenceSets:
referenceSetId = repoReferenceSet.getId()
repoReferences = repoReferenceSet.getReferences()
numRefs = len(repoReferences)
pageSizes = self._getPageSizes(numRefs)
for pageSize in pageSizes:
self._client.set_page_size(pageSize)
references = list(
self._client.search_references(referenceSetId))
for repoReference, reference in utils.zipLists(
repoReferences, references):
self._assertEqual(repoReference, reference)
def testSearchPhenotypes(self):
phenotypeAssociationSets = self._repo.allPhenotypeAssociationSets()
for phenotypeAssociationSet in phenotypeAssociationSets:
repoAssociations = list(phenotypeAssociationSet.getAssociations())
numAssociations = len(repoAssociations)
phenotypeAssociationSetId = phenotypeAssociationSet.getId()
pageSizes = self._getPageSizes(numAssociations)
for pageSize in pageSizes:
clientPhenotypes = list(
self._client.search_phenotype(phenotypeAssociationSetId))
for repoAssociation, clientPhenotype in utils.zipLists(
repoAssociations, clientPhenotypes):
self.assertEqual(repoAssociation.phenotype,
clientPhenotype)
def testSearchVariants(self):
for variantSet in self._repo.allVariantSets():
referenceSet = variantSet.getReferenceSet()
referenceName = referenceSet.getLocalId()
variantSetId = variantSet.getId()
repoVariants = list(
variantSet.getVariants(referenceName, 0, 2**32))
numRepoVariants = len(repoVariants)
pageSizes = self._getPageSizes(numRepoVariants)
for pageSize in pageSizes:
self._client.set_page_size(pageSize)
variants = self._client.search_variants(variantSetId)
for repoVariant, variant in utils.zipLists(
repoVariants, variants):
self._assertEqual(repoVariant, variant)
def testSearchVariants(self):
for variantSet in self._repo.allVariantSets():
referenceSet = variantSet.getReferenceSet()
referenceName = referenceSet.getLocalId()
variantSetId = variantSet.getId()
repoVariants = list(variantSet.getVariants(referenceName, 0,
2**32))
numRepoVariants = len(repoVariants)
pageSizes = self._getPageSizes(numRepoVariants)
for pageSize in pageSizes:
self._client.set_page_size(pageSize)
variants = self._client.search_variants(variantSetId)
for repoVariant, variant in utils.zipLists(
repoVariants, variants):
self._assertEqual(repoVariant, variant)
def testAllReads(self):
for dmDataset in self.dataRepo.getDatasets():
for dmReadGroupSet in dmDataset.getReadGroupSets():
dmReferenceSet = dmReadGroupSet.getReferenceSet()
for dmReadGroup in dmReadGroupSet.getReadGroups():
for dmReference in dmReferenceSet.getReferences():
# TODO fix these coordinates.
start = 0
end = 10
dmReads = list(dmReadGroup.getReadAlignments(
dmReference, start, end))
reads = list(self.client.searchReads(
[dmReadGroup.getId()], dmReference.getId(),
start, end))
self.assertGreater(len(reads), 0)
for dmRead, read in utils.zipLists(dmReads, reads):
self.assertEqual(dmRead, read)
def testPrograms(self):
# test that program info is set correctly
readGroupSet = self._gaObject
for readGroup in readGroupSet.getReadGroups():
readGroupInfo = self._readGroupInfos[readGroup.getLocalId()]
gaPrograms = readGroup.getPrograms()
htslibPrograms = readGroupInfo.programs
for gaProgram, htslibProgram in utils.zipLists(
gaPrograms, htslibPrograms):
self.assertEqual(gaProgram.id, htslibProgram.get('ID'))
self.assertEqual(gaProgram.commandLine,
htslibProgram.get('CL', None))
self.assertEqual(gaProgram.name, htslibProgram.get('PN', None))
self.assertEqual(gaProgram.prevProgramId,
htslibProgram.get('PP', None))
self.assertEqual(gaProgram.version,
htslibProgram.get('VN', None))
def testSearchReads(self):
for repoReadGroup in self._repo.allReadGroups():
repoReferenceSet = \
repoReadGroup._parentContainer.getReferenceSet()
for repoReference in repoReferenceSet.getReferences():
referenceId = repoReference.getId()
readGroupId = repoReadGroup.getId()
repoReads = list(
repoReadGroup.getReadAlignments(repoReference))
numRepoReads = len(repoReads)
pageSizes = self._getPageSizes(numRepoReads)
for pageSize in pageSizes:
self._client.set_page_size(pageSize)
reads = list(
self._client.search_reads([readGroupId], referenceId))
for repoRead, read in utils.zipLists(repoReads, reads):
self.assertEqual(repoRead, read)
def testSearchReads(self):
for repoReadGroup in self._repo.allReadGroups():
repoReferenceSet = \
repoReadGroup._parentContainer.getReferenceSet()
for repoReference in repoReferenceSet.getReferences():
referenceId = repoReference.getId()
readGroupId = repoReadGroup.getId()
repoReads = list(
repoReadGroup.getReadAlignments(repoReference))
numRepoReads = len(repoReads)
pageSizes = self._getPageSizes(numRepoReads)
for pageSize in pageSizes:
self._client.set_page_size(pageSize)
reads = list(self._client.search_reads(
[readGroupId], referenceId))
for repoRead, read in utils.zipLists(
repoReads, reads):
self.assertEqual(repoRead, read)
def testSearchVariantAnnotations(self):
for variantAnnotationSet in self._repo.allVariantAnnotationSets():
variantAnnotationSetId = variantAnnotationSet.getId()
variantSet = variantAnnotationSet._parentContainer
referenceSet = variantSet.getReferenceSet()
referenceName = referenceSet.getLocalId()
repoVariantAnnotations = list(
variantAnnotationSet.getVariantAnnotations(
referenceName, 0, 2**32))
numRepoVariantAnnotations = len(repoVariantAnnotations)
pageSizes = self._getPageSizes(numRepoVariantAnnotations)
for pageSize in pageSizes:
self._client.set_page_size(pageSize)
variantAnnotations = self._client.search_variant_annotations(
variantAnnotationSetId, referenceName=referenceName)
for repoVa, va in utils.zipLists(
repoVariantAnnotations, variantAnnotations):
self._assertEqual(repoVa, va)
def testSearchVariantAnnotations(self):
for variantAnnotationSet in self._repo.allVariantAnnotationSets():
variantAnnotationSetId = variantAnnotationSet.getId()
variantSet = variantAnnotationSet._parentContainer
referenceSet = variantSet.getReferenceSet()
referenceName = referenceSet.getLocalId()
repoVariantAnnotations = list(
variantAnnotationSet.getVariantAnnotations(
referenceName, 0, 2**32))
numRepoVariantAnnotations = len(repoVariantAnnotations)
pageSizes = self._getPageSizes(numRepoVariantAnnotations)
for pageSize in pageSizes:
self._client.set_page_size(pageSize)
variantAnnotations = self._client.search_variant_annotations(
variantAnnotationSetId, referenceName=referenceName)
for repoVa, va in utils.zipLists(repoVariantAnnotations,
variantAnnotations):
self._assertEqual(repoVa, va)
def testPrograms(self):
# test that program info is set correctly
readGroupSet = self._gaObject
for readGroup in readGroupSet.getReadGroups():
readGroupInfo = self._readGroupInfos[readGroup.getLocalId()]
gaPrograms = readGroup.getPrograms()
htslibPrograms = readGroupInfo.programs
for gaProgram, htslibProgram in utils.zipLists(
gaPrograms, htslibPrograms):
self.assertEqual(
gaProgram.id, htslibProgram.get('ID'))
self.assertEqual(
gaProgram.command_line, htslibProgram.get('CL', None))
self.assertEqual(
gaProgram.name, htslibProgram.get('PN', None))
self.assertEqual(
gaProgram.prev_program_id, htslibProgram.get('PP', None))
self.assertEqual(
gaProgram.version, htslibProgram.get('VN', None))
def assertAlignmentListsEqual(
self, gaAlignments, pysamAlignments, readGroupInfo):
for gaAlignment, pysamAlignment in utils.zipLists(
gaAlignments, pysamAlignments):
self.assertAlignmentsEqual(
gaAlignment, pysamAlignment, readGroupInfo)
def assertAlignmentListsEqual(self, gaAlignments, pysamAlignments,
readGroupInfo):
for gaAlignment, pysamAlignment in utils.zipLists(
gaAlignments, pysamAlignments):
self.assertAlignmentsEqual(gaAlignment, pysamAlignment,
readGroupInfo)