Fetch phenotypes from virtuoso

* gn3/api/metadata.py: Import get_phenotype_metadata.
(phenotype): New end-point.
* gn3/db/rdf.py (get_phenotype_metadata): New function.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 16 insertions, 0 deletions

diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index 49c6798..a2eff05 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -10,6 +10,7 @@ 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 sparql_query
 from gn3.db.rdf import RDF_PREFIXES
 
@@ -51,6 +52,21 @@ def publication(name):
         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("/genewiki/<symbol>", methods=["GET"])
 def get_genewiki_entries(symbol):
     """Fetch the GN and NCBI GeneRIF entries"""