diff options
Diffstat (limited to 'gn3/db')
-rw-r--r-- | gn3/db/datasets.py | 12 |
1 files changed, 6 insertions, 6 deletions
diff --git a/gn3/db/datasets.py b/gn3/db/datasets.py index c50e148..a41e228 100644 --- a/gn3/db/datasets.py +++ b/gn3/db/datasets.py @@ -3,7 +3,7 @@ This module contains functions relating to specific trait dataset manipulation """ import re from string import Template -from typing import Any, Dict, Optional +from typing import Any, Dict, List, Optional from SPARQLWrapper import JSON, SPARQLWrapper from gn3.settings import SPARQL_ENDPOINT @@ -297,7 +297,7 @@ def retrieve_trait_dataset(trait_type, trait, threshold, conn): **group } -def sparql_query(query: str) -> Dict[str, Any]: +def sparql_query(query: str) -> List[Dict[str, Any]]: """Run a SPARQL query and return the bound variables.""" sparql = SPARQLWrapper(SPARQL_ENDPOINT) sparql.setQuery(query) @@ -328,7 +328,7 @@ WHERE { OPTIONAL { ?dataset gn:geoSeries ?geo_series } . } """, - """ + """ PREFIX gn: <http://genenetwork.org/> SELECT ?platform_name ?normalization_name ?species_name ?inbred_set_name ?tissue_name WHERE { @@ -341,7 +341,7 @@ WHERE { OPTIONAL { ?dataset gn:datasetOfPlatform / gn:name ?platform_name } . } """, - """ + """ PREFIX gn: <http://genenetwork.org/> SELECT ?specifics ?summary ?about_cases ?about_tissue ?about_platform ?about_data_processing ?notes ?experiment_design ?contributors @@ -362,8 +362,8 @@ WHERE { OPTIONAL { ?dataset gn:acknowledgment ?acknowledgment . } } """] - result = {'accession_id': accession_id, - 'investigator': {}} + result: Dict[str, Any] = {'accession_id': accession_id, + 'investigator': {}} query_result = {} for query in queries: if sparql_result := sparql_query(Template(query).substitute(accession_id=accession_id)): |