def testDatasetAttributes(self):
"""
Demonstrates the usage of the Attribute's field on a dataset message.
This field is available on many other messages as well.
"""
key = "numbers_and_strings"
string_value = "hello"
int32_value = 5
double_value = 3.14159
attributes = {key: [string_value, int32_value, double_value]}
dataset = metadata_pb2.Dataset()
myattribute = dataset.attributes.attr[key].values
myattribute.add().string_value = string_value
myattribute.add().int32_value = int32_value
myattribute.add().double_value = double_value
self.assertEqual(dataset.attributes.attr[key].values[0].string_value,
attributes[key][0])
self.assertEqual(dataset.attributes.attr[key].values[1].int32_value,
attributes[key][1])
self.assertEqual(dataset.attributes.attr[key].values[2].double_value,
attributes[key][2])
def search_datasets(request):
"""/datasets/search method request handler"""
if not request.body:
page_size = DEFAULT_PAGE_SIZE
page_token = '0'
else:
try:
request_dict = json_format.Parse(
request.body, metadata_service.SearchDatasetsRequest())
except Exception as e:
return HttpResponseBadRequest(json.dumps(
{"message": e.message.replace("\"", "'")}),
content_type='application/json')
page_size = request_dict.page_size
page_token = request_dict.page_token
if not page_size or page_size == 0:
page_size = DEFAULT_PAGE_SIZE
if not page_token:
page_token = '0'
response = metadata_service.SearchDatasetsResponse()
dataset = metadata.Dataset()
dataset.name = SETNAME
dataset.id = DATASET_ID
dataset.description = 'Variants observed in brca-exchange project'
# TODO uncomment when ga4gh client implements info field otherwise hardcoded values are placed
#dataset.info[SETNAME].append("This set contains variants as stored and mantained by the brca-exchange project")
list_of_sets = []
list_of_sets.append(dataset)
sets = ga4gh_brca_page(list_of_sets, int(page_size), int(page_token))
response.next_page_token
if len(sets) > page_size:
page_token = str(1 + int(page_token))
response.next_page_token = page_token
##############
# TODO Block gets fixed when ga4gh client implements
# info field otherwise hardcoded values are placed
if sets:
response.datasets.extend(sets)
else:
response.next_page_token = ' '
response.datasets.extend([metadata.Dataset()])
##############
return JsonResponse(json_format.MessageToDict(response, False))
def get_dataset(request, dataset_id):
"""/datasets/<dataset id> get dataset via id method"""
if not dataset_id:
return HttpResponseBadRequest(json.dumps(ErrorMessages['datasetId']),
content_type='application/json')
response = metadata_service.GetDatasetRequest()
dataset = metadata.Dataset()
response.dataset_id = dataset_id
dataset.id = DATASET_ID
dataset.name = SETNAME
dataset.description = 'Variants observed in brca-exchange project'
# Needs field for info, still not available from ga4gh client
return JsonResponse(json_format.MessageToDict(dataset, False))
def testTypedAttributes(self):
"""
Demonstrates how to use other types defined in common to create an
attribute message.
"""
dataset = metadata_pb2.Dataset()
ontologyTerm = common_pb2.OntologyTerm()
ontologyTerm.term_id = "test"
ontologyKey = "my_ontology_term"
dataset.attributes.attr[ontologyKey] \
.values.add().ontology_term.MergeFrom(ontologyTerm)
term = dataset.attributes.attr[ontologyKey]
self.assertEqual(term.values[0].ontology_term.term_id,
ontologyTerm.term_id)
experiment = common_pb2.Experiment()
experiment.id = "test"
key = "my_experiment"
dataset.attributes.attr[key] \
.values.add().experiment.MergeFrom(experiment)
self.assertEqual(dataset.attributes.attr[key].values[0].experiment.id,
experiment.id)
def testNestedAttributes(self):
"""
Demonstrates how nested attributes can be used to interchange
arbitrary unstructured, typed data.
"""
dataset = metadata_pb2.Dataset()
key1 = "key1"
key2 = "key2"
string_value = "hello"
int32_value = 32
attributes = {key1: [{key2: [string_value]}, int32_value]}
myAttribute = dataset.attributes.attr[key1].values
nestedAttribute = myAttribute.add().attributes.attr[key2].values
nestedAttribute.add().string_value = string_value
myAttribute.add().int32_value = int32_value
mynested = dataset.attributes.attr[key1]. \
values[0].attributes.attr[key2]
self.assertEqual(mynested.values[0].string_value,
attributes[key1][0][key2][0])
self.assertEqual(dataset.attributes.attr[key1].values[1].int32_value,
attributes[key1][1])
