Upgraded to ATTED-II API v5

api/resources/proxy.py

@@ -9,12 +9,12 @@
 request_headers = {"user-agent": "BAR API", "accept": "application/json"}
 
 
-@bar_proxy.route("/atted_api4/<string:gene_id>/<int:top_n>")
-class ATTEDApi4(Resource):
+@bar_proxy.route("/atted_api5/<string:gene_id>/<int:top_n>")
+class ATTEDApi5(Resource):
     @bar_proxy.param("gene_id", _in="path", default="At1g01010")
     @bar_proxy.param("top_n", _in="path", default=5)
     def get(self, gene_id="", top_n=""):
-        """This end point is a proxy for ATTED-II api version 4.
+        """This end point is a proxy for ATTED-II api version 5.
         This is used by ThaleMine.
         This end point is currently not cached.
         """
@@ -30,7 +30,7 @@ def get(self, gene_id="", top_n=""):
 
         # Now query the web service
         payload = {"gene": gene_id, "topN": top_n}
-        resp = requests.get("https://atted.jp/cgi-bin/api4.cgi", params=payload, headers=request_headers)
+        resp = requests.get("https://atted.jp/api5/", params=payload, headers=request_headers)
 
         # I think the remote API always returns status 200, so skip status checking
         return resp.json()

tests/data/get_atted_api4.json → tests/data/get_atted_api5.json

@@ -5,7 +5,6 @@
     "entrez_gene_id": [
       839580
     ],
-    "type": null,
     "value": null,
     "topN": 5,
     "database": "Ath-u.c4-0",
@@ -14,36 +13,32 @@
   "result_set": [
     {
       "entrez_gene_id": 839580,
+      "type": "z",
       "results": [
         {
           "gene": 842367,
           "other_id": "At1g60730",
-          "mutual_rank": 793.88,
-          "logit_score": 4.5801
+          "z": 4.5801
         },
         {
           "gene": 838288,
           "other_id": "At1g17170",
-          "mutual_rank": 968.79,
-          "logit_score": 4.2795
+          "z": 4.2795
         },
         {
           "gene": 817498,
           "other_id": "At2g29490",
-          "mutual_rank": 1006.44,
-          "logit_score": 4.2216
+          "z": 4.2216
         },
         {
           "gene": 829559,
           "other_id": "At4g34131",
-          "mutual_rank": 1014.08,
-          "logit_score": 4.2101
+          "z": 4.2101
         },
         {
           "gene": 825091,
           "other_id": "At3g59220",
-          "mutual_rank": 1119.2,
-          "logit_score": 4.0597
+          "z": 4.0597
         }
       ],
       "other_id": "At1g01010"

tests/resources/test_proxy.py

@@ -7,29 +7,29 @@ class TestIntegrations(TestCase):
     def setUp(self):
         self.app_client = app.test_client()
 
-    def test_get_atted_api4(self):
+    def test_get_atted_api5(self):
         """This tests the data returned by the Atted proxy
         :return:
         """
         # Valid data
-        response = self.app_client.get("/proxy/atted_api4/At1g01010/5")
+        response = self.app_client.get("/proxy/atted_api5/At1g01010/5")
         # Note: pytest is running from project root. So path is relative to project root
-        with open("tests/data/get_atted_api4.json") as json_file:
+        with open("tests/data/get_atted_api5.json") as json_file:
             expected = load(json_file)
         self.assertEqual(response.json, expected)
 
         # Invalid gene
-        response = self.app_client.get("/proxy/atted_api4/At1g0101x/5")
+        response = self.app_client.get("/proxy/atted_api5/At1g0101x/5")
         expected = {"wasSuccessful": False, "error": "Invalid gene id"}
         self.assertEqual(response.json, expected)
 
         # If no data, the service should return this response
-        response = self.app_client.get("/proxy/atted_api4/At1g01011/5")
+        response = self.app_client.get("/proxy/atted_api5/At1g01011/5")
 
         expected = {"error": "No gene ID specified.", "status_code": 400}
         self.assertEqual(response.json, expected)
 
         # Invalid topN count
-        response = self.app_client.get("proxy/atted_api4/At1g01010/9999999999999999999")
+        response = self.app_client.get("proxy/atted_api5/At1g01010/9999999999999999999")
         expected = {"wasSuccessful": False, "error": "Invalid count"}
         self.assertEqual(response.json, expected)