def testGenotypeSearchFeaturePagingAll(self):
"""
Loop through all pages
"""
request = self._createPagingRequest()
request.page_size = 1
feature_set_id = request.feature_set_id
postUrl = "features/search"
response = self.sendSearchRequest(postUrl, request,
protocol.SearchFeaturesResponse)
self.assertEqual(1, len(response.features))
self.assertIsNotNone(response.next_page_token)
print("NEXT PAGE TOKEN: ")
print(response.next_page_token)
pageCount = 1
while response.next_page_token:
previous_id = response.features[0].id
request = protocol.SearchFeaturesRequest()
request.feature_set_id = feature_set_id
request.page_size = 1
request.page_token = response.next_page_token
request.name = "KIT *wild"
response = self.sendSearchRequest(postUrl, request,
protocol.SearchFeaturesResponse)
self.assertEqual(1, len(response.features))
self.assertNotEqual(previous_id, response.features[0].id)
pageCount += 1
self.assertEqual(3, pageCount)
def testGenotypesSearchByNameKIT(self):
request = protocol.SearchFeaturesRequest()
datasetName, featureSet = self.getCGDDataSetFeatureSet()
request.feature_set_id = featureSet.id
request.name = \
"KIT *wild"
postUrl = "features/search"
response = self.sendSearchRequest(postUrl, request,
protocol.SearchFeaturesResponse)
self.assertEqual(3, len(response.features))
def testSearchFeatures(self):
featureSets = self.getAllFeatureSets()
for featureSet in featureSets:
path = "features/search"
request = protocol.SearchFeaturesRequest()
request.feature_set_id = featureSet.id
request.start = 0
request.end = 2**16
request.feature_types.extend(["exon"])
request.reference_name = "chr1"
responseData = self.sendSearchRequest(
path, request, protocol.SearchFeaturesResponse)
for feature in responseData.features:
self.assertIn(
feature.feature_type.term,
request.feature_types,
"Term should be present {} {} \n{}\n{}".format(
feature.feature_type.term,
request.feature_types,
feature, request))
path = "features/search"
request = protocol.SearchFeaturesRequest()
request.feature_set_id = featureSet.id
request.start = 0
request.end = 2**16
request.feature_types.extend(["gene", "exon"])
request.reference_name = "chr1"
responseData = self.sendSearchRequest(
path, request, protocol.SearchFeaturesResponse)
for feature in responseData.features:
self.assertIn(feature.feature_type.term, request.feature_types)
request = protocol.SearchFeaturesRequest()
request.feature_set_id = featureSet.id
request.start = 0
request.end = 2**16
request.feature_types.extend(["exon"])
request.reference_name = "chr1"
responseData = self.sendSearchRequest(
path, request, protocol.SearchFeaturesResponse)
for feature in responseData.features:
self.assertIn(feature.feature_type.term, request.feature_types)
def testGenotypesSearchByNameError(self):
"""
Search for feature by name with a malformed regular expression.
"""
# setup phenotype query
request = protocol.SearchFeaturesRequest()
datasetName, featureSet = self.getCGDDataSetFeatureSet()
request.feature_set_id = featureSet.id
request.name = "*" # invalid regular expression
postUrl = "features/search"
response = self.sendJsonPostRequest(postUrl, protocol.toJson(request))
self.assertEqual(400, response.status_code)
def testGenotypesSearchByName(self):
# setup phenotype query
request = protocol.SearchFeaturesRequest()
datasetName, featureSet = self.getCGDDataSetFeatureSet()
request.feature_set_id = featureSet.id
request.name = "RET M918T missense mutation"
postUrl = "features/search"
response = self.sendSearchRequest(postUrl, request,
protocol.SearchFeaturesResponse)
self.assertEqual(1, len(response.features))
self.assertEqual(
"http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=965",
datamodel.FeatureCompoundId.parse(
response.features[0].id).featureId)
self.assertEqual(request.name, response.features[0].name)
def testSearchFeaturesByGeneSymbol(self):
ran = False
featureSets = self.getAllFeatureSets()
for featureSet in featureSets:
path = "features/search"
request = protocol.SearchFeaturesRequest()
request.feature_set_id = featureSet.id
request.gene_symbol = "BAD GENE SYMBOL"
responseData = self.sendSearchRequest(
path, request, protocol.SearchFeaturesResponse)
self.assertEqual(0, len(responseData.features))
request.gene_symbol = "DDX11L16"
responseData = self.sendSearchRequest(
path, request, protocol.SearchFeaturesResponse)
for feature in responseData.features:
ran = True
self.assertEqual(feature.gene_symbol, request.gene_symbol)
self.assertTrue(ran)
def testSearchFeaturesByName(self):
ran = False
featureSets = self.getAllFeatureSets()
for featureSet in featureSets:
path = "features/search"
request = protocol.SearchFeaturesRequest()
request.feature_set_id = featureSet.id
request.name = "BAD NAME"
responseData = self.sendSearchRequest(
path, request, protocol.SearchFeaturesResponse)
self.assertEqual(0, len(responseData.features))
request.name = "exon:ENSTR0000507418.3:5"
responseData = self.sendSearchRequest(
path, request, protocol.SearchFeaturesResponse)
for feature in responseData.features:
ran = True
self.assertEqual(feature.name, request.name)
self.assertTrue(ran)
def testSearchFeatures(self):
request = protocol.SearchFeaturesRequest()
request.feature_set_id = self.featureSetId
request.parent_id = self.parentId
request.page_size = self.pageSize
request.reference_name = self.referenceName
request.start = self.start
request.end = self.end
request.name = self.objectName
request.gene_symbol = self.geneSymbol
request.feature_types.append(self.feature)
self.httpClient.search_features(self.featureSetId,
parent_id=self.parentId,
reference_name=self.referenceName,
start=self.start,
end=self.end,
feature_types=[self.feature],
name=self.objectName,
gene_symbol=self.geneSymbol)
self.httpClient._run_search_request.assert_called_once_with(
request, "features", protocol.SearchFeaturesResponse)
def search_features(self,
feature_set_id=None,
parent_id="",
reference_name="",
start=0,
end=0,
feature_types=[],
name="",
gene_symbol=""):
"""
Returns the result of running a search_features method
on a request with the passed-in parameters.
:param str feature_set_id: ID of the feature Set being searched
:param str parent_id: ID (optional) of the parent feature
:param str reference_name: name of the reference to search
(ex: "chr1")
:param int start: search start position on reference
:param int end: end position on reference
:param feature_types: array of terms to limit search by (ex: "gene")
:param str name: only return features with this name
:param str gene_symbol: only return features on this gene
:return: an iterator over Features as returned in the
SearchFeaturesResponse object.
"""
request = protocol.SearchFeaturesRequest()
request.feature_set_id = feature_set_id
request.parent_id = parent_id
request.reference_name = reference_name
request.name = name
request.gene_symbol = gene_symbol
request.start = start
request.end = end
request.feature_types.extend(feature_types)
request.page_size = pb.int(self._page_size)
return self._run_search_request(request, "features",
protocol.SearchFeaturesResponse)
def _createPagingRequest(self):
request = protocol.SearchFeaturesRequest()
datasetName, featureSet = self.getCGDDataSetFeatureSet()
request.feature_set_id = featureSet.id
request.name = "KIT *wild"
return request
