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-rw-r--r--gn3/db/rdf.py131
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diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py
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+"""RDF utilities
+
+This module is a collection of functions that handle SPARQL queries.
+
+"""
+import re
+from typing import Tuple
+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, ...]:
+ """Run a SPARQL query and return the bound variables."""
+ sparql = SPARQLWrapper(SPARQL_ENDPOINT)
+ sparql.setQuery(query)
+ sparql.setReturnFormat(JSON)
+ results = sparql.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:
+ """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
+ # files.
+ pattern = re.compile(r"GN\d+", re.ASCII)
+ if not pattern.fullmatch(accession_id):
+ return MonadicDict()
+ # KLUDGE: We split the SPARQL query because virtuoso is very slow on a
+ # single large query.
+ queries = [
+ """
+PREFIX gn: <http://genenetwork.org/>
+SELECT ?name ?dataset_group ?status ?title ?geo_series
+WHERE {
+ ?dataset gn:accessionId "$accession_id" ;
+ rdf:type gn:dataset .
+ OPTIONAL { ?dataset gn:name ?name } .
+ OPTIONAL { ?dataset gn:datasetGroup ?dataset_group } .
+ # FIXME: gn:datasetStatus should not be optional. But, some records don't
+ # have it.
+ OPTIONAL { ?dataset gn:datasetStatus ?status } .
+ OPTIONAL { ?dataset gn:title ?title } .
+ OPTIONAL { ?dataset gn:geoSeries ?geo_series } .
+}
+""",
+ """
+PREFIX gn: <http://genenetwork.org/>
+SELECT ?platform_name ?normalization_name ?species_name ?inbred_set_name ?tissue_name
+WHERE {
+ ?dataset gn:accessionId "$accession_id" ;
+ rdf:type gn:dataset ;
+ gn:normalization / gn:name ?normalization_name ;
+ gn:datasetOfSpecies / gn:menuName ?species_name ;
+ gn:datasetOfInbredSet / gn:name ?inbred_set_name .
+ OPTIONAL { ?dataset gn:datasetOfTissue / gn:name ?tissue_name } .
+ 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
+ ?citation ?acknowledgment
+WHERE {
+ ?dataset gn:accessionId "$accession_id" ;
+ rdf:type gn:dataset .
+ OPTIONAL { ?dataset gn:specifics ?specifics . }
+ OPTIONAL { ?dataset gn:summary ?summary . }
+ OPTIONAL { ?dataset gn:aboutCases ?about_cases . }
+ OPTIONAL { ?dataset gn:aboutTissue ?about_tissue . }
+ OPTIONAL { ?dataset gn:aboutPlatform ?about_platform . }
+ OPTIONAL { ?dataset gn:aboutDataProcessing ?about_data_processing . }
+ OPTIONAL { ?dataset gn:notes ?notes . }
+ OPTIONAL { ?dataset gn:experimentDesign ?experiment_design . }
+ OPTIONAL { ?dataset gn:contributors ?contributors . }
+ OPTIONAL { ?dataset gn:citation ?citation . }
+ OPTIONAL { ?dataset gn:acknowledgment ?acknowledgment . }
+}
+""",
+ ]
+ result: MonadicDict = MonadicDict(
+ {
+ "accession_id": accession_id,
+ }
+ )
+ query_result: MonadicDict = MonadicDict()
+ for query in queries:
+ if not (
+ # Expecting only one result
+ sparql_result := sparql_query(
+ Template(query).substitute(accession_id=accession_id)
+ )[0]
+ ):
+ return MonadicDict()
+ query_result |= sparql_result
+ for key, value in query_result.items():
+ result[key] = value.bind(lambda x: Just(x["value"]))
+
+ investigator_query_result = sparql_query(
+ Template(
+ """
+PREFIX gn: <http://genenetwork.org/>
+SELECT ?name ?address ?city ?state ?zip ?phone ?email ?country ?homepage
+WHERE {
+ ?dataset gn:accessionId "$accession_id" ;
+ rdf:type gn:dataset ;
+ gn:datasetOfInvestigator ?investigator .
+ OPTIONAL { ?investigator foaf:name ?name . }
+ OPTIONAL { ?investigator gn:address ?address . }
+ OPTIONAL { ?investigator gn:city ?city . }
+ OPTIONAL { ?investigator gn:state ?state . }
+ OPTIONAL { ?investigator gn:zipCode ?zip . }
+ OPTIONAL { ?investigator foaf:phone ?phone . }
+ OPTIONAL { ?investigator foaf:mbox ?email . }
+ OPTIONAL { ?investigator gn:country ?country . }
+ OPTIONAL { ?investigator foaf:homepage ?homepage . }
+}
+ """
+ ).substitute(accession_id=accession_id)
+ )[0]
+ result["investigators"] = Just({
+ key: value.bind(lambda a: a["value"])
+ for key, value in investigator_query_result.items()
+ })
+ return result