def testSearchVariantAnnotations(self):
request = protocol.SearchVariantAnnotationsRequest()
request.variantAnnotationSetId = self.variantAnnotationSetId
request.pageSize = self.pageSize
request.referenceName = self.referenceName
request.referenceId = self.referenceId
request.effects = []
request.start = self.start
request.end = self.end
self.httpClient.searchVariantAnnotations(
self.variantAnnotationSetId,
referenceName=self.referenceName,
start=self.start,
end=self.end,
effects=[],
referenceId=self.referenceId)
self.httpClient._runSearchRequest.assert_called_once_with(
request, "variantannotations",
protocol.SearchVariantAnnotationsResponse)
with self.assertRaises(exceptions.BadRequestException):
self.httpClient.searchVariantAnnotations(
self.variantAnnotationSetId,
referenceName=self.referenceName,
start=self.start,
end=self.end,
effects=[{"term": "just a term"}, {"id": "an id"}],
referenceId=self.referenceId)
def searchVariantAnnotations(self,
variantAnnotationSetId,
referenceName=None,
referenceId=None,
start=None,
end=None,
effects=[]):
"""
Returns an iterator over the Annotations fulfilling the specified
conditions from the specified AnnotationSet.
"""
request = protocol.SearchVariantAnnotationsRequest()
request.variantAnnotationSetId = variantAnnotationSetId
request.referenceName = referenceName
request.referenceId = referenceId
request.start = start
request.end = end
request.effects = effects
for effect in request.effects:
if 'id' not in effect:
raise exceptions.BadRequestException(
"Each ontology term should have an id set")
request.pageSize = self._pageSize
return self._runSearchRequest(
request, "variantannotations",
protocol.SearchVariantAnnotationsResponse)
def search_variant_annotations(self,
variant_annotation_set_id,
reference_name="",
reference_id="",
start=0,
end=0,
effects=[]):
"""
Returns an iterator over the Variant Annotations fulfilling
the specified conditions from the specified VariantSet.
:param str variant_annotation_set_id: The ID of the
:class:`ga4gh.protocol.VariantAnnotationSet` of interest.
:param int start: Required. The beginning of the window (0-based,
inclusive) for which overlapping variants should be returned.
Genomic positions are non-negative integers less than reference
length. Requests spanning the join of circular genomes are
represented as two requests one on each side of the join
(position 0).
:param int end: Required. The end of the window (0-based, exclusive)
for which overlapping variants should be returned.
:param str reference_name: The name of the
:class:`ga4gh.protocol.Reference` we wish to return variants from.
:return: An iterator over the
:class:`ga4gh.protocol.VariantAnnotation` objects
defined by the query parameters.
:rtype: iter
"""
request = protocol.SearchVariantAnnotationsRequest()
request.variant_annotation_set_id = variant_annotation_set_id
request.reference_name = reference_name
request.reference_id = reference_id
request.start = start
request.end = end
for effect in effects:
request.effects.add().CopyFrom(protocol.OntologyTerm(**effect))
for effect in request.effects:
if not effect.id:
raise exceptions.BadRequestException(
"Each ontology term should have an id set")
request.page_size = pb.int(self._page_size)
return self._run_search_request(
request, "variantannotations",
protocol.SearchVariantAnnotationsResponse)
def testVariantAnnotationsSearch(self):
dataset = self.dataRepo.getDatasets()[0]
variantAnnotationSet = dataset.getVariantAnnotationSets()[0]
self.assertIsNotNone(variantAnnotationSet)
request = protocol.SearchVariantAnnotationsRequest()
path = '/variantannotations/search'
request.start = 0
request.end = 1000000
request.pageSize = 1
request.referenceName = "1"
request.effects = None
request.variantAnnotationSetId = variantAnnotationSet.getId()
response = self.sendJsonPostRequest(path, request.toJsonString())
responseData = protocol.SearchVariantAnnotationSetsResponse. \
fromJsonString(response.data)
self.assertIsNotNone(responseData.nextPageToken,
"Expected more than one page of results")
request = protocol.SearchVariantAnnotationsRequest()
request.variantAnnotationSetId = variantAnnotationSet.getId()
request.start = 0
request.end = 10
request.referenceName = "1"
request.effects = [{"id": "ThisIsNotAnEffect"}]
response = self.sendJsonPostRequest(path, request.toJsonString())
responseData = protocol.SearchVariantAnnotationsResponse. \
fromJsonString(response.data)
self.assertEquals(len(responseData.variantAnnotations), 0,
"There should be no results for a nonsense effect")
request = protocol.SearchVariantAnnotationsRequest()
request.variantAnnotationSetId = variantAnnotationSet.getId()
request.start = 0
request.end = 10
request.referenceName = "1"
response = self.sendJsonPostRequest(path, request.toJsonString())
responseData = protocol.SearchVariantAnnotationsResponse. \
fromJsonString(response.data)
self.assertGreater(len(responseData.variantAnnotations), 0)
for ann in responseData.variantAnnotations:
self.assertGreater(len(ann.transcriptEffects), 0,
("When no effects are requested ensure "
"some transcript effects are still present"))
request = protocol.SearchVariantAnnotationsRequest()
request.variantAnnotationSetId = variantAnnotationSet.getId()
request.start = 0
request.end = 5
request.referenceName = "1"
request.effects = [{"id": "SO:0001627"}, {"id": "B4DID"}]
response = self.sendJsonPostRequest(path, request.toJsonString())
responseData = protocol.SearchVariantAnnotationsResponse. \
fromJsonString(response.data)
responseLength = len(responseData.variantAnnotations)
self.assertGreater(responseLength, 0,
"There should be some results for a known effect")
for ann in responseData.variantAnnotations:
effectPresent = False
for effect in ann.transcriptEffects:
for featureType in effect.effects:
if featureType.id in map(lambda e: e['id'],
request.effects):
effectPresent = True
self.assertEquals(True, effectPresent,
"The ontology term should appear at least once")
request = protocol.SearchVariantAnnotationsRequest()
request.variantAnnotationSetId = variantAnnotationSet.getId()
request.start = 0
request.end = 5
request.referenceName = "1"
request.effects = [{"id": "B4DID"}, {"id": "SO:0001627"}]
response = self.sendJsonPostRequest(path, request.toJsonString())
responseData = protocol.SearchVariantAnnotationsResponse. \
fromJsonString(response.data)
self.assertEqual(len(responseData.variantAnnotations), responseLength,
"Order shall not affect results")
for ann in responseData.variantAnnotations:
effectPresent = False
for effect in ann.transcriptEffects:
for featureType in effect.effects:
if featureType.id in map(lambda e: e['id'],
request.effects):
effectPresent = True
self.assertEquals(True, effectPresent,
"The ontology term should appear at least once")
request = protocol.SearchVariantAnnotationsRequest()
request.variantAnnotationSetId = variantAnnotationSet.getId()
request.start = 0
request.end = 5
request.referenceName = "1"
request.effects = [{"id": "SO:0001627"}]
response = self.sendJsonPostRequest(path, request.toJsonString())
responseData = protocol.SearchVariantAnnotationsResponse. \
fromJsonString(response.data)
self.assertGreater(
len(responseData.variantAnnotations), 0,
"There should be some results for a good effect ID")
for ann in responseData.variantAnnotations:
effectPresent = False
for effect in ann.transcriptEffects:
for featureType in effect.effects:
if featureType.id in map(lambda e: e['id'],
request.effects):
effectPresent = True
self.assertEquals(True, effectPresent,
"The ontology term should appear at least once")
request = protocol.SearchVariantAnnotationsRequest()
request.variantAnnotationSetId = variantAnnotationSet.getId()
request.start = 0
request.end = 10
request.referenceName = "1"
request.effects = [{"id": "SO:0001627"}, {"id": "SO:0001791"}]
response = self.sendJsonPostRequest(path, request.toJsonString())
responseData = protocol.SearchVariantAnnotationsResponse. \
fromJsonString(response.data)
self.assertGreater(len(responseData.variantAnnotations), 0)
