def get_json_doc(self, api, id):
# construct url from id
url = AVAILABLE_API_SOURCES[api]['annotate_syntax'].replace('*', id)
json_doc = fetch_doc_from_api(url)
context = load_context(api)
json_doc.update(context)
self.jsonld_doc = nquads_transform(json_doc)
return json_doc
def compose_query_parameter_from_uri(uri, value, api):
context = load_context(api)
context.pop('root')
query_string = ''
if uri in get_uri_list(context):
path_list = get_uri_list(context)[uri]
for _item in path_list:
query_string = query_string + ' ' + _item + ':' + value + ' OR'
return query_string.strip(' OR')
def get_discrepancy_id(output_file_name, mongo_collection, uri):
src = get_src_db()
context = load_context('mygene.info')
data = src[mongo_collection].find()
with open(output_file_name, 'w') as f:
for _doc in data:
_doc.update(context)
jsonld_doc = nquads_transform(_doc)
rsid = fetch_value_by_uri(jsonld_doc, uri)
if type(rsid) == list:
f.write(_doc['_id'] + "\n")
def uri_to_field_name(uri, api, relation=None):
context = load_context(api)
if relation:
return [
_field for _field, _uri in context["@context"].items()
if uri == _uri["@type"] and relation == _uri["@id"]
]
else:
return [
_field for _field, _uri in context["@context"].items()
if uri == _uri["@type"]
]
def relation_handler():
add_nodes_edges = []
relation_edge = 0
edges= []
for _id in AVAILABLE_IDS.keys():
add_nodes_edges.append({'data': {'id': _id, 'type': 'id'}})
for _api in AVAILABLE_API_SOURCES.keys():
add_nodes_edges.append({'data': {'id': _api, 'type': 'api'}})
if 'annotate_ids' in AVAILABLE_API_SOURCES[_api]:
for annotate_id in AVAILABLE_API_SOURCES[_api]['annotate_ids']:
add_nodes_edges.append({'data': {'id': relation_edge, 'source': annotate_id, 'target': _api, 'label': 'input'}})
relation_edge += 1
if 'jsonld' in AVAILABLE_API_SOURCES[_api]:
context = load_context(_api)
for k, v in context['@context'].items():
_edge = {'data': {'source': find_id_from_uri(v["@type"]), 'target': _api, 'label': v["@id"]}}
if _edge not in edges:
_edge['data']['id'] = relation_edge
add_nodes_edges.append(_edge)
edges.append(_edge)
relation_edge += 1
else:
print(_edge)
return add_nodes_edges
def uri_to_field_name(uri, api):
context = load_context(api)
return [
_field for _field, _uri in context["@context"].items() if _uri == uri
]