def populateFromJson(self, jsonString):
try:
parsed = protocol.fromJson(jsonString, protocol.BioSample)
except:
raise exceptions.InvalidJsonException(jsonString)
self._created = parsed.created
self._updated = parsed.updated
self._description = parsed.description
self._disease = protocol.toJsonDict(parsed.disease)
self._individualId = parsed.individual_id
self._info = {}
for key in parsed.info:
self._info[key] = {"values": protocol.toJsonDict(parsed.info[key])}
return self
def populateFromJson(self, jsonString):
# TODO validate
try:
parsed = protocol.fromJson(jsonString, protocol.Individual)
except:
raise exceptions.InvalidJsonException(jsonString)
self._created = parsed.created
self._updated = parsed.updated
self._description = parsed.description
self._species = protocol.toJsonDict(parsed.species)
self._sex = protocol.toJsonDict(parsed.sex)
self._info = {}
for key in parsed.info:
self._info[key] = {"values": protocol.toJsonDict(parsed.info[key])}
return self
def sendListRequest(self, path, request):
headers = {
'Origin': self.exampleUrl,
}
data = protocol.toJsonDict(request)
response = self.app.post(path, data=data, headers=headers)
return response
def testToProtocolElement(self):
dataset = datasets.Dataset('dataset1')
term = protocol.OntologyTerm()
term.term = "male genotypic sex"
term.id = "PATO:0020001"
term.source_name = "PATO"
term.source_version = pb.string("2015-11-18")
# 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.info['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 verifyParsedOutputsEqualReadGroup(self,
clientIterator,
cliCommand,
cliArguments=""):
cliOutput = self.captureJsonOutput(cliCommand, cliArguments)
clientOutput = [protocol.toJsonDict(gObj) for gObj in clientIterator]
self.assertEqual(clientOutput, cliOutput)
return len(clientOutput)
def _formatExternalIdentifiers(self, element, element_type):
"""
Formats several external identifiers for query
"""
elementClause = None
elements = []
if not issubclass(element.__class__, dict):
element = protocol.toJsonDict(element)
if element['externalIdentifiers']:
for _id in element['externalIdentifiers']:
elements.append(
self._formatExternalIdentifier(_id, element_type))
elementClause = "({})".format(" || ".join(elements))
return elementClause
def _formatOntologyTermObject(self, terms, element_type):
"""
Formats the ontology term object for query
"""
elementClause = None
if not isinstance(terms, collections.Iterable):
terms = [terms]
elements = []
for term in terms:
if not issubclass(term.__class__, dict):
term = protocol.toJsonDict(term)
if term['id']:
elements.append('?{} = <{}> '.format(element_type, term['id']))
else:
elements.append('?{} = <{}> '.format(
element_type, self._toNamespaceURL(term['term'])))
elementClause = "({})".format(" || ".join(elements))
return elementClause
def verifyParsedOutputsEqual(self,
clientIterator,
cliCommand,
cliArguments="",
scrubFunc=None):
"""
Verify that the parsed JSON of all the objects in the specified
client iterator are equal to the parsed JSON from the specified
CLI command.
"""
cliOutput = self.captureJsonOutput(cliCommand, cliArguments)
clientOutput = [protocol.toJsonDict(gObj) for gObj in clientIterator]
if scrubFunc is not None:
# this is a hack to deal with the issue of the timestamps on
# objects being different
scrubFunc(cliOutput, clientOutput)
self.assertEqual(clientOutput, cliOutput)
return len(clientOutput)
def testInstantiation(self):
for class_ in self._getExceptionClasses():
# some exceptions are becoming too complicated to instantiate
# like the rest of the exceptions; just do them manually
if class_ == exceptions.RequestValidationFailureException:
objClass = protocol.SearchReadsRequest
obj = objClass()
obj.start = -1
jsonDict = protocol.toJsonDict(obj)
args = (jsonDict, objClass)
else:
numInitArgs = len(inspect.getargspec(class_.__init__).args) - 1
args = ['arg' for _ in range(numInitArgs)]
instance = class_(*args)
self.assertIsInstance(instance, exceptions.BaseServerException)
message = instance.getMessage()
self.assertIsInstance(message, basestring)
self.assertGreater(len(message), 0)
self.assertEqual(instance.getErrorCode(), class_.getErrorCode())
def testToGA4GH(self):
sample_associations = {
u'environment_label': u'sunitinib',
u'feature_label': u'RET M918T missense mutation',
u'evidence_type': u'http://purl.obolibrary.org/obo/ECO_0000033',
u'feature': {
u'http://purl.obolibrary.org/obo/GENO_0000408':
u'http://www.ncbi.nlm.nih.gov/gene/5979',
u'http://purl.obolibrary.org/obo/GENO_reference_amino_acid':
u'M',
u'http://www.w3.org/1999/02/22-rdf-syntax-ns#type':
u'http://purl.obolibrary.org/obo/SO_0001059',
u'http://biohackathon.org/resource/faldo#location':
u'http://www.monarchinitiative.org/_918918UniProtKB:'
'P07949#P07949-1Region',
u'http://purl.obolibrary.org/obo/GENO_reference_nucleotide':
u'T',
u'http://purl.obolibrary.org/obo/'
'GENO_results_in_amino_acid_change':
u'T',
u'http://purl.obolibrary.org/obo/RO_0002200':
u'http://ohsu.edu/cgd/3774b1d2',
u'http://purl.obolibrary.org/obo/RO_0002205':
u'http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?'
'REQUEST=CCDS&DATA=7200.1',
u'http://purl.obolibrary.org/obo/GENO_altered_nucleotide':
u'C',
u'http://www.w3.org/2000/01/rdf-schema#label':
u'RET M918T missense mutation',
u'id':
u'http://cancer.sanger.ac.uk/cosmic/mutation/'
'overview?id=965',
u'http://www.w3.org/2002/07/owl#sameAs':
u'http://www.ncbi.nlm.nih.gov/SNP/74799832',
},
u'evidence': u'http://ohsu.edu/cgd/sensitivity',
u'environment': {
u'http://purl.obolibrary.org/obo/RO_0002606':
u'http://ohsu.edu/cgd/71fe9f0f',
u'http://www.w3.org/2000/01/rdf-schema#subClassOf':
u'http://purl.obolibrary.org/obo/CHEBI_23888',
u'http://www.w3.org/1999/02/22-rdf-syntax-ns#type':
u'http://www.w3.org/2002/07/owl#Class',
u'http://www.w3.org/2000/01/rdf-schema#label': u'sunitinib',
u'id': u'http://www.drugbank.ca/drugs/DB01268',
},
u'sources': u'http://www.ncbi.nlm.nih.gov/pubmed/21470995|'
'http://www.ncbi.nlm.nih.gov/pubmed/21470995',
u'phenotype': {
u'http://purl.obolibrary.org/obo/BFO_0000159':
u'http://ohsu.edu/cgd/sensitivity',
u'http://www.w3.org/1999/02/22-rdf-syntax-ns#type':
u'http://purl.obolibrary.org/obo/DOID_3969',
u'http://www.w3.org/2000/01/rdf-schema#label':
u'Papillary thyroid carcinoma with sensitivity to therapy',
u'id': u'http://ohsu.edu/cgd/30ebfd1a',
},
u'phenotype_label':
u'Papillary thyroid carcinoma with sensitivity to therapy',
u'id': u'http://ohsu.edu/cgd/fe484b5c',
u'association': u'http://ohsu.edu/cgd/fe484b5c',
}
result = self.phenotypeAssocationSet._toGA4GH(sample_associations)
self.assertEqual(result.__class__.__name__,
'FeaturePhenotypeAssociation')
fpa_dict = protocol.toJsonDict(result)
description = 'Association: genotype:[RET M918T missense mutation]' \
' phenotype:[Papillary thyroid carcinoma with ' \
'sensitivity to therapy] environment:[sunitinib]' \
' evidence:[sensitivity] publications:' \
'[http://www.ncbi.nlm.nih.gov/pubmed/21470995|' \
'http://www.ncbi.nlm.nih.gov/pubmed/21470995]'
self.assertEqual(fpa_dict['description'], description)
self.assertIn('featureIds', fpa_dict.keys())
self.assertIn('evidence', fpa_dict.keys())
self.assertIn('environmentalContexts', fpa_dict.keys())
self.assertEqual(len(fpa_dict['featureIds']), 1)
self.assertEqual(len(fpa_dict['evidence']), 1)
self.assertEqual(len(fpa_dict['environmentalContexts']), 1)