diff options
Diffstat (limited to 'gn3/db/rdf/__init__.py')
| -rw-r--r-- | gn3/db/rdf/__init__.py | 17 |
1 files changed, 11 insertions, 6 deletions
diff --git a/gn3/db/rdf/__init__.py b/gn3/db/rdf/__init__.py index 94a5776..f0ac494 100644 --- a/gn3/db/rdf/__init__.py +++ b/gn3/db/rdf/__init__.py @@ -163,18 +163,23 @@ PHENOTYPE_CONTEXT = ( ) -def sparql_construct_query(query: str, endpoint: str) -> dict: +def sparql_query(query: str, endpoint: str, format_type="json-ld") -> dict: """Query virtuoso using a CONSTRUCT query and return a json-ld dictionary""" sparql = SPARQLWrapper(endpoint) + if format_type == "json-ld": + sparql.setQuery(query) + results = sparql.queryAndConvert() + return json.loads(results.serialize(format=format_type)) # type: ignore + # For SELECTs + sparql.setReturnFormat(JSON) sparql.setQuery(query) - results = sparql.queryAndConvert() - return json.loads(results.serialize(format="json-ld")) # type: ignore + return sparql.queryAndConvert()["results"]["bindings"] # type: ignore def query_frame_and_compact(query: str, context: dict, endpoint: str) -> dict: """Frame and then compact the results given a context""" - results = sparql_construct_query(query, endpoint) + results = sparql_query(query, endpoint) return jsonld.compact( jsonld.frame(results, context), context, options={"graph": True} ) @@ -182,13 +187,13 @@ def query_frame_and_compact(query: str, context: dict, endpoint: str) -> dict: def query_and_compact(query: str, context: dict, endpoint: str) -> dict: """Compact the results given a context""" - results = sparql_construct_query(query, endpoint) + results = sparql_query(query, endpoint) return jsonld.compact(results, context, options={"graph": True}) def query_and_frame(query: str, context: dict, endpoint: str) -> dict: """Frame the results given a context""" - results = sparql_construct_query(query, endpoint) + results = sparql_query(query, endpoint) return jsonld.frame(results, context) |