def testReadGroupSetsSearch(self):
path = '/readgroupsets/search'
for dataset in self.backend.getDatasets():
readGroupSets = dataset.getReadGroupSets()
request = protocol.SearchReadGroupSetsRequest()
request.datasetId = dataset.getId()
self.verifySearchMethod(request, path,
protocol.SearchReadGroupSetsResponse,
readGroupSets,
self.verifyReadGroupSetsEqual)
# Check if we can search for the readGroupSet with a good name.
for readGroupSet in readGroupSets:
request = protocol.SearchReadGroupSetsRequest()
request.datasetId = dataset.getId()
request.name = readGroupSet.getLocalId()
self.verifySearchMethod(request, path,
protocol.SearchReadGroupSetsResponse,
[readGroupSet],
self.verifyReadGroupSetsEqual)
# Check if we can search for the readGroupSet with a bad name.
for badId in self.getBadIds():
request = protocol.SearchReadGroupSetsRequest()
request.datasetId = dataset.getId()
request.name = badId
self.verifySearchResultsEmpty(
request, path, protocol.SearchReadGroupSetsResponse)
for badId in self.getBadIds():
request = protocol.SearchReadGroupSetsRequest()
request.datasetId = badId
self.verifySearchMethodFails(request, path)
def testReads(self):
# search read group sets
path = utils.applyVersion('/readgroupsets/search')
request = protocol.SearchReadGroupSetsRequest()
request.datasetId = 'simulatedDataset1'
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(response.status_code, 200)
responseData = protocol.SearchReadGroupSetsResponse.fromJsonString(
response.data)
readGroupSets = responseData.readGroupSets
self.assertEqual(len(readGroupSets), 1)
# search reads
path = utils.applyVersion('/reads/search')
request = protocol.SearchReadsRequest()
readGroupId = readGroupSets[0].readGroups[0].id
request.readGroupIds = [readGroupId]
request.referenceId = "chr1"
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(response.status_code, 200)
responseData = protocol.SearchReadsResponse.fromJsonString(
response.data)
alignments = responseData.alignments
self.assertEqual(len(alignments), self.numAlignmentsPerReadGroup)
for alignment in alignments:
self.assertEqual(alignment.readGroupId, readGroupId)
def testSearchReadGroupSets(self):
request = protocol.SearchReadGroupSetsRequest()
request.datasetId = self.datasetId
request.name = self.objectName
request.pageSize = self.pageSize
self.httpClient.searchReadGroupSets(
self.datasetId, name=self.objectName)
self.httpClient._runSearchRequest.assert_called_once_with(
request, "readgroupsets", protocol.SearchReadGroupSetsResponse)
def testSearchReadGroupSets(self):
request = protocol.SearchReadGroupSetsRequest()
request.dataset_id = self.datasetId
request.name = self.objectName
request.bio_sample_id = self.bioSampleId
request.page_size = self.pageSize
self.httpClient.search_read_group_sets(self.datasetId,
name=self.objectName,
bio_sample_id=self.bioSampleId)
self.httpClient._run_search_request.assert_called_once_with(
request, "readgroupsets", protocol.SearchReadGroupSetsResponse)
def searchReadGroupSets(self, datasetId, name=None):
"""
Returns an iterator over the ReadGroupSets fulfilling the specified
conditions from the specified Dataset.
:param str name: Only ReadGroupSets matching the specified name
will be returned.
:return: An iterator over the :class:`ga4gh.protocol.ReadGroupSet`
objects defined by the query parameters.
:rtype: iter
"""
request = protocol.SearchReadGroupSetsRequest()
request.datasetId = datasetId
request.name = name
request.pageSize = self._pageSize
return self._runSearchRequest(
request, "readgroupsets", protocol.SearchReadGroupSetsResponse)
def searchReadGroupSets(self, datasetId, name=None, bioSampleId=None):
"""
Returns an iterator over the ReadGroupSets fulfilling the specified
conditions from the specified Dataset.
:param str name: Only ReadGroupSets matching the specified name
will be returned.
:param str bioSampleId: Only ReadGroups matching the specified
bioSample will be included in the response.
:return: An iterator over the :class:`ga4gh.protocol.ReadGroupSet`
objects defined by the query parameters.
:rtype: iter
"""
request = protocol.SearchReadGroupSetsRequest()
request.dataset_id = datasetId
request.name = pb.string(name)
request.bio_sample_id = pb.string(bioSampleId)
request.page_size = pb.int(self._pageSize)
return self._runSearchRequest(
request, "readgroupsets", protocol.SearchReadGroupSetsResponse)
def createSearchReadGroupSetsRequest(self):
request = protocol.SearchReadGroupSetsRequest()
setCommaSeparatedAttribute(request, self.args, 'datasetIds')
request.name = self.args.name
return request
def createSearchReadGroupSetsRequest(self):
request = protocol.SearchReadGroupSetsRequest()
request.datasetId = self.args.datasetId
request.name = self.args.name
return request
