def testReferencesSearch(self):
path = '/references/search'
for referenceSet in self.backend.getReferenceSets():
references = referenceSet.getReferences()
request = protocol.SearchReferencesRequest()
request.referenceSetId = referenceSet.getId()
self.verifySearchMethod(request, path,
protocol.SearchReferencesResponse,
references, self.verifyReferencesEqual)
for badId in self.getBadIds():
request = protocol.SearchReferencesRequest()
request.referenceSetId = badId
self.verifySearchMethodFails(request, path)
def testReferences(self):
# search for reference sets
path = utils.applyVersion('/referencesets/search')
request = protocol.SearchReferenceSetsRequest()
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(response.status_code, 200)
responseData = protocol.SearchReferenceSetsResponse.fromJsonString(
response.data)
referenceSets = responseData.referenceSets
self.assertEqual(self.numReferenceSets, len(referenceSets))
# search for references
path = utils.applyVersion('/references/search')
request = protocol.SearchReferencesRequest()
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(response.status_code, 200)
responseData = protocol.SearchReferencesResponse.fromJsonString(
response.data)
references = responseData.references
self.assertEqual(
self.numReferenceSets * self.numReferencesPerReferenceSet,
len(references))
for referenceSet in referenceSets:
# fetch the reference set
path = utils.applyVersion('/referencesets/{}'.format(
referenceSet.id))
response = self.app.get(path)
self.assertEqual(response.status_code, 200)
fetchedReferenceSet = protocol.ReferenceSet.fromJsonString(
response.data)
self.assertEqual(fetchedReferenceSet, referenceSet)
self.assertEqual(len(fetchedReferenceSet.referenceIds),
self.numReferencesPerReferenceSet)
for referenceId in referenceSet.referenceIds:
# fetch the reference
path = utils.applyVersion('/references/{}'.format(referenceId))
response = self.app.get(path)
self.assertEqual(response.status_code, 200)
fetchedReference = protocol.Reference.fromJsonString(
response.data)
self.assertEqual(fetchedReference.id, referenceId)
# fetch the bases
path = utils.applyVersion(
'/references/{}/bases'.format(referenceId))
args = protocol.ListReferenceBasesRequest().toJsonDict()
response = self.app.get(path, data=args)
self.assertEqual(response.status_code, 200)
bases = protocol.ListReferenceBasesResponse.fromJsonString(
response.data)
self.assertEqual(len(bases.sequence), 200)
self.assertEqual(set(bases.sequence), set(['A', 'C', 'T',
'G']))
calculatedDigest = hashlib.md5(bases.sequence).hexdigest()
self.assertEqual(calculatedDigest,
fetchedReference.md5checksum)
def testSearchReferences(self):
request = protocol.SearchReferencesRequest()
request.referenceSetId = self.referenceSetId
request.pageSize = self.pageSize
request.accession = self.accession
request.md5checksum = self.md5checksum
self.httpClient.searchReferences(
self.referenceSetId, accession=self.accession,
md5checksum=self.md5checksum)
self.httpClient._runSearchRequest.assert_called_once_with(
request, "references", protocol.SearchReferencesResponse)
def searchReferences(self,
referenceSetId,
accession=None,
md5checksum=None):
"""
Returns an iterator over the References fulfilling the specified
conditions from the specified Dataset.
:param str accession: TODO
:param str md5checksum: TODO
:return: An iterator over the :class:`ga4gh.protocol.Reference`
objects defined by the query parameters.
"""
request = protocol.SearchReferencesRequest()
request.referenceSetId = referenceSetId
request.accession = accession
request.md5checksum = md5checksum
request.pageSize = self._pageSize
return self._runSearchRequest(request, "references",
protocol.SearchReferencesResponse)
def searchReferences(
self, referenceSetId, accession=None, md5checksum=None):
"""
Returns an iterator over the References fulfilling the specified
conditions from the specified Dataset.
:param str referenceSetId: The ReferenceSet to search.
:param str accession: If not None, return the references for which the
`accession` matches this string (case-sensitive, exact match).
:param str md5checksum: If not None, return the references for which
the `md5checksum` matches this string (case-sensitive, exact
match).
:return: An iterator over the :class:`ga4gh.protocol.Reference`
objects defined by the query parameters.
"""
request = protocol.SearchReferencesRequest()
request.referenceSetId = referenceSetId
request.accession = accession
request.md5checksum = md5checksum
request.pageSize = self._pageSize
return self._runSearchRequest(
request, "references", protocol.SearchReferencesResponse)
def sendReferencesSearch(self):
path = "/references/search"
request = protocol.SearchReferencesRequest()
response = self.sendPostRequest(path, request)
return response
def requestFactory():
request = protocol.SearchReferencesRequest()
request.referenceSetId = referenceSet.getId()
return request
def createSearchReferencesRequest(self):
request = protocol.SearchReferencesRequest()
setCommaSeparatedAttribute(request, self.args, 'accessions')
setCommaSeparatedAttribute(request, self.args, 'md5checksums')
return request
