Implement "GET /species".

* gn3/api/metadata.py (list_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
genenetwork · Oct 24, 2023 · 671c7c7 · 671c7c7
1 parent ad979ed
commit 671c7c7
Showing 1 changed file with 42 additions and 0 deletions.
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
@@ -620,3 +620,45 @@ def get_ncbi_genewiki_entries(symbol):
             context)
     except (RemoteDisconnected, URLError):
         return jsonify({})
+
+
+@metadata.route("/species", methods=["GET"])
+def list_species():
+    """List all species"""
+    try:
+        sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT"))
+        sparql.setQuery(Template("""
+$prefix
+
+CONSTRUCT {
+        ?species ?predicate ?object .
+} WHERE {
+        ?species ^skos:member gnc:Species ;
+                 ?predicate ?object .
+        VALUES ?predicate {
+               rdfs:label skos:prefLabel
+               skos:altLabel gnt:shortName
+               gnt:family skos:notation
+        }
+
+}
+""").substitute(prefix=RDF_PREFIXES))
+        results = sparql.queryAndConvert()
+        results = json.loads(
+            results.serialize(format="json-ld")
+        )
+        return jsonld.compact(results, {
+            "@context": PREFIXES | {
+                "data": "@graph",
+                "type": "@type",
+                "id": "@id",
+                "name": "rdfs:label",
+                "family": "gnt:family",
+                "shortName": "gnt:shortName",
+                "alternateName": "skos:altLabel",
+                "taxonomicId": "skos:notation",
+                "preferredName": "skos:prefLabel",
+            },
+        })
+    except (RemoteDisconnected, URLError):
+        return jsonify({})