diff options
| -rw-r--r-- | gn3/db/rdf.py | 45 |
1 files changed, 32 insertions, 13 deletions
diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py index bb9f1b4..5b62b46 100644 --- a/gn3/db/rdf.py +++ b/gn3/db/rdf.py @@ -25,7 +25,7 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX ncbiTaxon: <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=> PREFIX up: <http://purl.uniprot.org/core/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> - +PREFIX publication: <http://genenetwork.org/publication/> """ @@ -33,23 +33,40 @@ def sparql_query( sparql_conn: SPARQLWrapper, query: str, ) -> Tuple[MonadicDict, ...]: """Run a SPARQL query and return the bound variables.""" + def __add_value_to_dict(key, value, my_dict): + _values = set() + if key in my_dict: + if isinstance(my_dict[key], list): + _values = set(my_dict[key]) + else: + _values = set([my_dict[key]]) + _values.add(value) + if _values: + return list(_values) + return value + sparql_conn.setQuery(query) sparql_conn.setReturnFormat(JSON) - parsed_response = MonadicDict() + parsed_response: dict = {} results = sparql_conn.queryAndConvert()["results"]["bindings"] # type: ignore if results: for result in results: if "s" in result: # A CONSTRUCT - parsed_response[ - get_url_local_name( - result["p"]["value"] # type: ignore - ) - ] = Just(result["o"]["value"]) # type: ignore + key = get_url_local_name( + result["p"]["value"] # type: ignore + ) + value = result["o"]["value"] # type: ignore + parsed_response[key] = __add_value_to_dict( + key, value, parsed_response + ) elif "key" in result: # A SELECT parsed_response[ result["key"] # type: ignore - ] = Just(result["value"]) # type: ignore - return (parsed_response,) + ] = __add_value_to_dict( + result["key"], result["value"], # type: ignore + parsed_response + ) + return (MonadicDict(parsed_response),) def get_url_local_name(string: str) -> str: @@ -133,10 +150,12 @@ CONSTRUCT { name=name ) )[0].items(): - if key.endswith("Url") or key == "geoSeries": - response[key] = value - else: - response[key] = value.map(get_url_local_name) + response[key] = value + if isinstance(value, str) and not ( + key.endswith("Url") or key == "geoSeries" + ): + response[key] = value.map(get_url_local_name) # type: ignore + return response return response |