def testToProtocolElement(self):
dataset = datasets.Dataset('dataset1')
term = protocol.OntologyTerm()
term.term = "male genotypic sex"
term.term_id = "PATO:0020001"
# Write out a valid input
print(protocol.toJsonDict(term))
validIndividual = protocol.Individual(name="test",
created="2016-05-19T21:00:19Z",
updated="2016-05-19T21:00:19Z",
sex=term)
validIndividual.attributes.attr['test']. \
values.add().string_value = 'test-info'
# pass through protocol creation
individual = bioMetadata.Individual(dataset, "test")
individual.populateFromJson(protocol.toJson(validIndividual))
gaIndividual = individual.toProtocolElement()
# Verify elements exist
self.assertEqual(gaIndividual.created, validIndividual.created)
self.assertEqual(gaIndividual.updated, validIndividual.updated)
# Invalid input
invalidIndividual = '{"bad:", "json"}'
individual = bioMetadata.Individual(dataset, "test")
# Should fail
self.assertRaises(exceptions.InvalidJsonException,
individual.populateFromJson, invalidIndividual)
def setUp(self):
self.parser = cli_repomanager.RepoManager.getParser()
self.registryPath = 'a/repo/path'
self.datasetName = "datasetName"
self.filePath = 'a/file/path'
self.dirPath = 'a/dir/path/'
self.individualName = "test"
self.biosampleName = "test"
self.individual = protocol.toJson(
protocol.Individual(name="test",
created="2016-05-19T21:00:19Z",
updated="2016-05-19T21:00:19Z"))
self.biosample = protocol.toJson(
protocol.Biosample(name="test",
created="2016-05-19T21:00:19Z",
updated="2016-05-19T21:00:19Z"))
def toProtocolElement(self):
species = None
sex = None
if self.getSpecies():
species = protocol.fromJson(json.dumps(self.getSpecies()),
protocol.OntologyTerm)
if self.getSex():
sex = protocol.fromJson(json.dumps(self.getSex()),
protocol.OntologyTerm)
gaIndividual = protocol.Individual(dataset_id=self._datasetId,
created=self.getCreated(),
updated=self.getUpdated(),
description=self.getDescription(),
id=self.getId(),
name=self.getName(),
species=species,
sex=sex)
self.serializeAttributes(gaIndividual)
return gaIndividual
class RepoManagerEndToEndTest(unittest.TestCase):
datasetName = 'datasetOne'
metadata = {'description': 'aDescription'}
individualName = "test"
biosampleName = "test"
individual = protocol.toJson(protocol.Individual(
name="test",
created="2016-05-19T21:00:19Z",
updated="2016-05-19T21:00:19Z"))
biosample = protocol.toJson(protocol.Biosample(
name="test",
created="2016-05-19T21:00:19Z",
updated="2016-05-19T21:00:19Z"))
attributes = {"key1": "value1", "key2": "value2"}
def setUp(self):
_, self.repoFile = tempfile.mkstemp(
prefix='ga4gh_repo_manager_end2end_test')
os.unlink(self.repoFile)
def tearDown(self):
if os.path.exists(self.repoFile):
os.unlink(self.repoFile)
def _runCmd(self, cmd, *args):
command = [cmd, self.repoFile] + list(args)
cli_repomanager.repo_main(command)
def testEndToEnd(self):
self._runCmd("init")
self._runCmd("add-ontology", paths.ontologyPath)
self._runCmd(
"add-referenceset", paths.faPath,
'-n', paths.referenceSetName,
'-A', json.dumps(self.attributes))
self._runCmd("add-dataset", self.datasetName,
'-A', json.dumps(self.attributes))
self._runCmd("add-biosample",
self.datasetName,
self.biosampleName,
self.biosample)
self._runCmd("add-individual",
self.datasetName,
self.individualName,
self.individual)
self._runCmd(
"add-readgroupset", self.datasetName, "patient1", "sample1", paths.bamPath,
'-R', paths.referenceSetName, '-n', paths.readGroupSetName,
'-A', json.dumps(self.attributes))
self._runCmd(
"add-featureset", self.datasetName, paths.featuresPath,
'-R', paths.referenceSetName, '-O', paths.ontologyName,
'-A', json.dumps(self.attributes))
# ensure we can handle trailing slashes
vcfPath = paths.vcfDirPath + '/'
self._runCmd(
"add-variantset", self.datasetName,
'patient1', 'sample1',
vcfPath, '-R', paths.referenceSetName,
'-A', json.dumps(self.attributes))
variantAnnotationSetName = "vas"
self._runCmd(
"add-variantset", self.datasetName,
'patient1', 'sample1',
paths.annotatedVcfPath, '-R', paths.referenceSetName,
"-aO", paths.ontologyName, "-n", variantAnnotationSetName,
'-A', json.dumps(self.attributes))
phenotypeAssociationSetName = "paSet"
self._runCmd(
"add-phenotypeassociationset",
self.datasetName,
paths.phenotypeAssociationSetPath,
"-n",
phenotypeAssociationSetName,
'-A', json.dumps(self.attributes))
self._runCmd("verify")
self._runCmd("list")
self._runCmd(
"remove-phenotypeassociationset",
self.datasetName, phenotypeAssociationSetName, "-f")
self._runCmd(
"remove-variantset", self.datasetName, paths.variantSetName, "-f")
self._runCmd(
"remove-variantset", self.datasetName, variantAnnotationSetName,
"-f")
self._runCmd(
"remove-readgroupset", self.datasetName,
paths.readGroupSetName, "-f")
self._runCmd(
"remove-featureset", self.datasetName, paths.featureSetName,
"-f")
self._runCmd(
"remove-dataset", self.datasetName, "-f")
self._runCmd(
"remove-referenceset", paths.referenceSetName, "-f")
self._runCmd(
"remove-ontology", paths.ontologyName, "-f")
def testForce(self):
datasetName = 'dataset1'
self._runCmd("init")
self._runCmd("add-dataset", datasetName)
with mock.patch(
'ga4gh.server.cli.repomanager.getRawInput',
lambda x: 'N'):
self._runCmd("remove-dataset", datasetName)
with mock.patch(
'ga4gh.server.cli.repomanager.getRawInput',
lambda x: 'y'):
self._runCmd("remove-dataset", datasetName)
with self.assertRaises(SystemExit):
self._runCmd("remove-dataset", datasetName)