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-rw-r--r--gn3/api/metadata.py74
1 files changed, 74 insertions, 0 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index f87743b..d542dc6 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -1,4 +1,5 @@
"""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
@@ -9,6 +10,8 @@ from SPARQLWrapper import SPARQLWrapper
from gn3.db.rdf import get_dataset_metadata
from gn3.db.rdf import get_trait_metadata
+from gn3.db.rdf import sparql_query
+from gn3.db.rdf import RDF_PREFIXES
metadata = Blueprint("metadata", __name__)
@@ -42,3 +45,74 @@ def trait_metadata(dataset_name, trait_name):
# 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": {},
+ })