From 59c8bc53f8aa386a1052478c8553c523bfaaeb3d Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Mon, 20 Nov 2023 17:42:59 +0300
Subject: Attach phenotype endpoints to one function.

* gn3/api/metadata.py (phenotypes): Add "/phenotypes/<group>/<name>"
to this endpoint.
(fetch_phenotype_by_group): Delete.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 gn3/api/metadata.py | 64 +++++------------------------------------------------
 1 file changed, 5 insertions(+), 59 deletions(-)

(limited to 'gn3/api')

diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index b97a4c4..45bef41 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -416,13 +416,14 @@ CONSTRUCT {
     except (RemoteDisconnected, URLError):
         return jsonify({})
 
-
-@metadata.route("/phenotypes/<name>", methods=["GET"])
-def phenotypes(name):
+@metadata.route("/phenotypes/<name>",methods=["GET"])
+@metadata.route("/phenotypes/<group>/<name>", methods=["GET"])
+def phenotypes(name, group=None):
     """Fetch a phenotype's metadata given it's name"""
     try:
         args = request.args
-        dataset = args.get("dataset", "")
+        if group:
+            name = f"{group}_{name}"
         _query = Template("""
 $prefix
 
@@ -476,61 +477,6 @@ CONSTRUCT {
         return jsonify({})
 
 
-@metadata.route("/phenotypes/<group>/<name>", methods=["GET"])
-def fetch_phenotype_by_group(group, name):
-    """Fetch a phenotype's metadata given it's name"""
-    try:
-        args = request.args
-        dataset = args.get("dataset", "")
-        _query = Template("""
-$prefix
-
-CONSTRUCT {
-        ?phenotype ?predicate ?object ;
-                   ?pubPredicate ?pubObject ;
-                   ex:species ?speciesName ;
-                   ex:inbredSet ?inbredSetName ;
-                   ex:dataset ?datasetName .
-} WHERE {
-        ?phenotype rdfs:label "$name" ;
-                   xkos:classifiedUnder ?inbredSet ;
-                   ?predicate ?object .
-        ?inbredSet ^xkos:classifiedUnder ?phenotype ;
-                   (rdfs:label|skos:prefLabel|gnt:code) "$group" ;
-                   xkos:generalizes ?species .
-        ?species skos:prefLabel ?speciesName .
-        FILTER (!regex(str(?predicate), '(classifiedUnder)', 'i')) .
-        OPTIONAL {
-        ?publication ^dct:isReferencedBy ?phenotype ;
-                     rdf:type fabio:ResearchPaper ;
-                     ?pubPredicate ?pubObject .
-        FILTER (!regex(str(?pubPredicate), '(hasPubMedId|type)', 'i')) .
-        } .
-	OPTIONAL {
-	?dataset rdf:type dcat:Dataset ;
-                 xkos:classifiedUnder  ?type;
-		 rdfs:label "$dataset" ;
-		 skos:prefLabel ?datasetName .
-	?type ^skos:member gnc:DatasetType .
-	FILTER(?type = gnc:Phenotype) .
-	}
-}
-""").substitute(prefix=RDF_PREFIXES,
-                group=group,
-                name=name,
-                dataset=dataset)
-        _context = {
-            "@context": PHENOTYPE_CONTEXT,
-            "type": "gnc:Phenotype",
-        }
-        return query_frame_and_compact(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
-
-
 @metadata.route("/genotypes/<name>", methods=["GET"])
 def genotypes(name):
     """Fetch a genotype's metadata given it's name"""
-- 
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