"""API for fetching metadata using an API""" from string import Template from http.client import RemoteDisconnected from urllib.error import URLError from flask import Blueprint from flask import jsonify from flask import current_app from SPARQLWrapper import SPARQLWrapper from gn3.db.rdf import get_dataset_metadata from gn3.db.rdf import get_publication_metadata from gn3.db.rdf import get_phenotype_metadata from gn3.db.rdf import get_genotype_metadata from gn3.db.rdf import sparql_query from gn3.db.rdf import RDF_PREFIXES metadata = Blueprint("metadata", __name__) @metadata.route("/dataset/<name>", methods=["GET"]) def dataset(name): """Fetch a dataset's metadata given it's ACCESSION_ID""" try: return jsonify( get_dataset_metadata( SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")), name, ).data ) # The virtuoso server is misconfigured or it isn't running at all except (RemoteDisconnected, URLError): return jsonify({}) @metadata.route("/publication/<name>", methods=["GET"]) def publication(name): """Fetch a publication's metadata given it's ACCESSION_ID""" try: if "unpublished" in name: name = f"gn:{name}" else: name = f"publication:{name}" return jsonify( get_publication_metadata( SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")), name, ).data ) # The virtuoso server is misconfigured or it isn't running at all except (RemoteDisconnected, URLError): return jsonify({}) @metadata.route("/phenotype/<name>", methods=["GET"]) def phenotype(name): """Fetch a phenotype's metadata given it's name""" try: return jsonify( get_phenotype_metadata( SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")), name, ).data ) # The virtuoso server is misconfigured or it isn't running at all except (RemoteDisconnected, URLError): return jsonify({}) @metadata.route("/genotype/<name>", methods=["GET"]) def genotype(name): """Fetch a genotype's metadata given it's name""" try: return jsonify( get_genotype_metadata( SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")), name, ).data ) # The virtuoso server is misconfigured or it isn't running at all except (RemoteDisconnected, URLError): return jsonify({}) @metadata.route("/genewiki/<symbol>", methods=["GET"]) def get_genewiki_entries(symbol): """Fetch the GN and NCBI GeneRIF entries""" try: gn_entries = sparql_query( sparql_conn=SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")), query=Template(""" $rdf_prefixes SELECT ?author ?geneCategory (STR(?gnEntry) AS ?entry) (STR(?createdOn) AS ?created) (GROUP_CONCAT(DISTINCT ?pmid; SEPARATOR=',') AS ?PubMedId) ?weburl WHERE { ?generif gn:symbol ?symbol . ?generif gn:geneWikiEntryOfGn _:gnEntry . _:gnEntry gn:geneWikiEntry ?gnEntry; dct:creator ?author; dct:created ?createdOn . OPTIONAL { _:gnEntry gn:geneCategory ?geneCategory } . OPTIONAL { _:gnEntry foaf:homepage ?weburl } . OPTIONAL { _:gnEntry dct:source ?pmid} . OPTIONAL { ?generif gn:wikiEntryOfSpecies ?speciesName . ?species gn:name ?speciesName ; gn:binomialName ?speciesBinomialName . } . FILTER( lcase(?symbol) = '$symbol' ) } GROUP BY ?author ?createdOn ?gnEntry ?generif ?symbol ?weburl ?geneCategory ORDER BY ASC(?createdOn)""").substitute(rdf_prefixes=RDF_PREFIXES, symbol=str(symbol).lower())) ncbi_entries = sparql_query( sparql_conn=SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")), query=Template(""" $rdf_prefixes SELECT ?speciesBinomialName (STR(?gnEntry) AS ?entry) (STR(?createdOn) AS ?createdOn) (GROUP_CONCAT(DISTINCT REPLACE(STR(?pmid), pubmed:, ''); SEPARATOR=',') AS ?PubMedId) ?generif WHERE { ?generif gn:symbol ?symbol . ?generif gn:geneWikiEntryOfNCBI [ gn:geneWikiEntry ?gnEntry ; dct:created ?createdOn ; dct:source ?pmid ] . OPTIONAL { ?generif gn:wikiEntryOfSpecies ?speciesName . ?species gn:name ?speciesName ; gn:binomialName ?speciesBinomialName . } . FILTER( lcase(?symbol) = '$symbol' ) } GROUP BY ?createdOn ?gnEntry ?generif ?symbol ?speciesBinomialName ORDER BY ASC(?createdOn)""").substitute(rdf_prefixes=RDF_PREFIXES, symbol=str(symbol).lower())) return jsonify({ "gn_entries": list(map(lambda x: x.data, gn_entries)), "ncbi_entries": list(map(lambda x: x.data, ncbi_entries)), }) except (RemoteDisconnected, URLError): return jsonify({ "gn_entries": {}, "ncbi_entries": {}, })