diff options
| -rw-r--r-- | gn3/db/rdf.py | 18 |
1 files changed, 11 insertions, 7 deletions
diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py index f1312e3..7ed80b1 100644 --- a/gn3/db/rdf.py +++ b/gn3/db/rdf.py @@ -9,21 +9,23 @@ from string import Template from SPARQLWrapper import JSON, SPARQLWrapper from pymonad.maybe import Just from gn3.monads import MonadicDict -from gn3.settings import SPARQL_ENDPOINT -def sparql_query(query: str) -> Tuple[MonadicDict, ...]: +def sparql_query( + sparql_conn: SPARQLWrapper, query: str +) -> Tuple[MonadicDict, ...]: """Run a SPARQL query and return the bound variables.""" - sparql = SPARQLWrapper(SPARQL_ENDPOINT) - sparql.setQuery(query) - sparql.setReturnFormat(JSON) - results = sparql.queryAndConvert() + sparql_conn.setQuery(query) + sparql_conn.setReturnFormat(JSON) + results = sparql_conn.queryAndConvert() if _r := results["results"]["bindings"]: # type: ignore return (*(MonadicDict(bindings) for bindings in _r),) # type: ignore return (MonadicDict(),) -def get_dataset_metadata(accession_id: str) -> MonadicDict: +def get_dataset_metadata( + sparql_conn: SPARQLWrapper, accession_id: str +) -> MonadicDict: """Return info about dataset with ACCESSION_ID.""" # Check accession_id to protect against query injection. # TODO: This function doesn't yet return the names of the actual dataset @@ -94,6 +96,7 @@ WHERE { if not ( # Expecting only one result sparql_result := sparql_query( + sparql_conn, Template(query).substitute(accession_id=accession_id) )[0] ): @@ -103,6 +106,7 @@ WHERE { result[key] = value.bind(lambda x: Just(x["value"])) investigator_query_result = sparql_query( + sparql_conn, Template( """ PREFIX gn: <http://genenetwork.org/> |