diff options
| -rw-r--r-- | gn3/api/general.py | 4 | ||||
| -rw-r--r-- | gn3/db/datasets.py | 104 | ||||
| -rw-r--r-- | gn3/db/rdf.py | 131 |
3 files changed, 135 insertions, 104 deletions
diff --git a/gn3/api/general.py b/gn3/api/general.py index e0bfc81..68b128b 100644 --- a/gn3/api/general.py +++ b/gn3/api/general.py @@ -7,7 +7,7 @@ from flask import request from gn3.fs_helpers import extract_uploaded_file from gn3.commands import run_cmd -from gn3.db import datasets +from gn3.db import rdf general = Blueprint("general", __name__) @@ -72,4 +72,4 @@ def run_r_qtl(geno_filestr, pheno_filestr): @general.route("/dataset/<accession_id>") def dataset_metadata(accession_id): """Return info as JSON for dataset with ACCESSION_ID.""" - return jsonify(datasets.dataset_metadata(accession_id)) + return jsonify(rdf.get_dataset_metadata(accession_id).data) diff --git a/gn3/db/datasets.py b/gn3/db/datasets.py index 1d2f071..bc5467b 100644 --- a/gn3/db/datasets.py +++ b/gn3/db/datasets.py @@ -1,11 +1,8 @@ """ This module contains functions relating to specific trait dataset manipulation """ -import re -from string import Template -from typing import Any, Dict, List, Optional -from SPARQLWrapper import JSON, SPARQLWrapper -from gn3.settings import SPARQL_ENDPOINT +from typing import Any + def retrieve_probeset_trait_dataset_name( threshold: int, name: str, connection: Any): @@ -264,100 +261,3 @@ def retrieve_trait_dataset(trait_type, trait, threshold, conn): **dataset_fns[trait_type](), **group } - -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) - sparql.setReturnFormat(JSON) - return sparql.queryAndConvert()['results']['bindings'] # type: ignore - -def dataset_metadata(accession_id: str) -> Optional[Dict[str, Any]]: - """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 None - # 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 "$accession_id" ; - rdf:type gn:dataset ; - gn:name ?name . - OPTIONAL { ?dataset gn:datasetGroup ?dataset_group } . - # FIXME: gn:datasetStatus should not be optional. But, some records don't - # have it. - OPTIONAL { ?dataset gn:datasetStatus ?status } . - OPTIONAL { ?dataset gn:title ?title } . - OPTIONAL { ?dataset gn:geoSeries ?geo_series } . -} -""", - """ -PREFIX gn: <http://genenetwork.org/> -SELECT ?platform_name ?normalization_name ?species_name ?inbred_set_name ?tissue_name -WHERE { - ?dataset gn:accessionId "$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 "$accession_id" ; - rdf:type gn:dataset . - OPTIONAL { ?dataset gn:specifics ?specifics . } - OPTIONAL { ?dataset gn:summary ?summary . } - OPTIONAL { ?dataset gn:aboutCases ?about_cases . } - OPTIONAL { ?dataset gn:aboutTissue ?about_tissue . } - OPTIONAL { ?dataset gn:aboutPlatform ?about_platform . } - OPTIONAL { ?dataset gn:aboutDataProcessing ?about_data_processing . } - OPTIONAL { ?dataset gn:notes ?notes . } - OPTIONAL { ?dataset gn:experimentDesign ?experiment_design . } - OPTIONAL { ?dataset gn:contributors ?contributors . } - OPTIONAL { ?dataset gn:citation ?citation . } - OPTIONAL { ?dataset gn:acknowledgment ?acknowledgment . } -} -"""] - result: Dict[str, Any] = {'accession_id': accession_id, - 'investigator': {}} - query_result = {} - for query in queries: - if sparql_result := sparql_query(Template(query).substitute(accession_id=accession_id)): - query_result.update(sparql_result[0]) - else: - return None - for key, value in query_result.items(): - result[key] = value['value'] - investigator_query_result = sparql_query(Template(""" -PREFIX gn: <http://genenetwork.org/> -SELECT ?name ?address ?city ?state ?zip ?phone ?email ?country ?homepage -WHERE { - ?dataset gn:accessionId "$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] - for key, value in investigator_query_result.items(): - result['investigator'][key] = value['value'] - return result diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py new file mode 100644 index 0000000..f1312e3 --- /dev/null +++ b/gn3/db/rdf.py @@ -0,0 +1,131 @@ +"""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 |