From d0d08d513e403f7836da450a1d05eaeb89a5ba30 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Wed, 23 Nov 2022 12:19:02 +0300
Subject: Create a new REST endpoint for fetching a phenotype's metadata

* gn3/api/general.py: (dataset_metadata) Delete.
* gn3/api/metadata.py: Import Blueprint, jsonify, current_app,
SPARQLWrapper and get_dataset_metadata.
(metadata): New Blueprint
(jsonify_dataset_metadata): New function/end-point.
* gn3/app.py: Import metadata
(create_app): Register metadata blueprint.
---
 gn3/api/general.py  |  5 +----
 gn3/api/metadata.py | 22 ++++++++++++++++++++++
 gn3/app.py          |  3 +++
 3 files changed, 26 insertions(+), 4 deletions(-)
 create mode 100644 gn3/api/metadata.py

diff --git a/gn3/api/general.py b/gn3/api/general.py
index 68b128b..f904ffe 100644
--- a/gn3/api/general.py
+++ b/gn3/api/general.py
@@ -69,7 +69,4 @@ def run_r_qtl(geno_filestr, pheno_filestr):
            f"{geno_filestr} {pheno_filestr}")
     return jsonify(run_cmd(cmd)), 201
 
-@general.route("/dataset/<accession_id>")
-def dataset_metadata(accession_id):
-    """Return info as JSON for dataset with ACCESSION_ID."""
-    return jsonify(rdf.get_dataset_metadata(accession_id).data)
+
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
new file mode 100644
index 0000000..4fe9e67
--- /dev/null
+++ b/gn3/api/metadata.py
@@ -0,0 +1,22 @@
+"""API for fetching metadata using an API"""
+from flask import Blueprint
+from flask import jsonify
+from flask import current_app
+
+from SPARQLWrapper import SPARQLWrapper
+
+from gn3.db.rdf import get_dataset_metadata
+
+
+metadata = Blueprint("metadata", __name__)
+
+
+@metadata.route("/dataset/<accession_id>", methods=["GET"])
+def jsonify_dataset_metadata(accession_id):
+    """Fetch a dataset's metadata given it's ACCESSION_ID"""
+    return jsonify(get_dataset_metadata(
+        SPARQLWrapper(current_app
+                      .config
+                      .get("SPARQL_ENDPOINT")),
+        accession_id
+    ).data)
diff --git a/gn3/app.py b/gn3/app.py
index 6c7e483..a187e54 100644
--- a/gn3/app.py
+++ b/gn3/app.py
@@ -18,6 +18,8 @@ from gn3.api.ctl import ctl
 from gn3.api.async_commands import async_commands
 from gn3.api.menu import menu
 from gn3.api.search import search
+from gn3.api.metadata import metadata
+
 
 def create_app(config: Union[Dict, str, None] = None) -> Flask:
     """Create a new flask object"""
@@ -53,4 +55,5 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask:
     app.register_blueprint(async_commands, url_prefix="/api/async_commands")
     app.register_blueprint(menu, url_prefix="/api/menu")
     app.register_blueprint(search, url_prefix="/api/search")
+    app.register_blueprint(metadata, url_prefix="/api/metadata")
     return app
-- 
cgit v1.2.3