def _run_list_reference_bases_page_request(self, request):
url_suffix = "listreferencebases"
url = posixpath.join(self._url_prefix, url_suffix)
response = self._session.post(url,
params=self._get_http_parameters(),
data=protocol.toJson(request))
self._check_response_status(response)
return self._deserialize_response(response.text,
protocol.ListReferenceBasesResponse)
def _run_search_page_request(self, protocol_request, object_name,
protocol_response_class):
url = posixpath.join(self._url_prefix, object_name + '/search')
data = protocol.toJson(protocol_request)
self._logger.debug("request:{}".format(data))
response = self._session.post(url,
params=self._get_http_parameters(),
data=data)
self._check_response_status(response)
return self._deserialize_response(response.text,
protocol_response_class)
def harvest(genes):
datasets = c.search_datasets()
phenotype_association_set_id = None
phenotype_association_set_name = None
for dataset in datasets:
phenotype_association_sets = c.search_phenotype_association_sets(dataset_id=dataset.id)
for phenotype_association_set in phenotype_association_sets:
phenotype_association_set_id = phenotype_association_set.id
phenotype_association_set_name = phenotype_association_set.name
# print 'Found G2P phenotype_association_set:', phenotype_association_set.id, phenotype_association_set.name
break
assert phenotype_association_set_id
assert phenotype_association_set_name
feature_set_id = None
datasets = c.search_datasets()
for dataset in datasets:
featuresets = c.search_feature_sets(dataset_id=dataset.id)
for featureset in featuresets:
if phenotype_association_set_name in featureset.name:
feature_set_id = featureset.id
# print 'Found G2P feature_set:', feature_set_id
break
assert feature_set_id
gene_features = []
for gene in set(genes):
feature_generator = c.search_features(feature_set_id=feature_set_id, name='.*{}.*'.format(gene))
features = list(feature_generator)
if len(features) == 0:
# print "{} Found no features".format(gene)
gene_features.append({'gene': gene})
else:
# print "{} Found {} features in G2P feature_set {}".format(gene, len(features),feature_set_id)
a = []
for f in features:
a.append(json.loads(protocol.toJson(f)))
gene_features.append({'gene': gene, 'features': a})
for gene_feature in gene_features:
if 'features' in gene_feature:
for f in gene_feature['features']:
feature_phenotype_associations = c.search_genotype_phenotype(
phenotype_association_set_id=phenotype_association_set_id,
feature_ids=[f['id']])
associations = list(feature_phenotype_associations)
a = []
for association in associations:
a.append(json.loads(protocol.toJson(association)))
f['associations'] = a
# print "{} has {} associations".format(gene_feature['gene'], len(a))
for gene_feature in gene_features:
gene_feature['ga4gh'] = {}
if 'features' in gene_feature:
gene_feature['ga4gh']['features'] = gene_feature['features']
del gene_feature['features']
yield gene_feature
def _run_list_reference_bases_page_request(self, request):
response_json = self._backend.runListReferenceBases(
protocol.toJson(request))
return self._deserialize_response(response_json,
protocol.ListReferenceBasesResponse)
def _run_search_page_request(self, protocol_request, object_name,
protocol_response_class):
search_method = self._search_method_map[object_name]
response_json = search_method(protocol.toJson(protocol_request))
return self._deserialize_response(response_json,
protocol_response_class)