From ee6510523d68f82f2fd387618d8e21d56ccc6732 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Wed, 25 Oct 2023 12:07:08 +0300
Subject: Implement "GET /metadata/species".

* gn3/api/metadata.py (list_species): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 gn3/api/metadata.py | 44 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

(limited to 'gn3/api/metadata.py')

diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index 3731cc1..bbf6a74 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -1283,3 +1283,47 @@ CONSTRUCT {
     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": {
+                "data": "@graph",
+                "type": "@type",
+                "id": "@id",
+                "skos": "http://www.w3.org/2004/02/skos/core#",
+                "gnt": "http://genenetwork.org/term/",
+                "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+                "name": "rdfs:label",
+                "family": "gnt:family",
+                "shortName": "gnt:shortName",
+                "alternateName": "skos:altLabel",
+                "taxonomicId": "skos:notation",
+                "fullName": "skos:prefLabel",
+            },
+        })
+    except (RemoteDisconnected, URLError):
+        return jsonify({})
-- 
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