Add delete and patch commands with tests to ME API

emgapi/metagenomics_exchange.py

@@ -50,13 +50,13 @@ def post_request(self, endpoint: str, data: dict):
         response.raise_for_status()
         return response
 
-    def delete_request(self, endpoint: str, data: dict):
+    def delete_request(self, endpoint: str):
         headers = {
             "Accept": "application/json",
             "Authorization": self.__token,
         }
         response = requests.delete(
-            f"{self.base_url}/{endpoint}", json=data, headers=headers
+            f"{self.base_url}/{endpoint}", headers=headers
         )
         response.raise_for_status()
         return response
@@ -104,15 +104,16 @@ def check_analysis(self, source_id: str, public: bool) -> bool:
         return False
 
     def delete_analysis(self, registry_id: str):
-        data = {"registryID": registry_id}
-        response = self.delete_request(endpoint="datasets", data=data)
+        response = self.delete_request(endpoint=f"datasets/{registry_id}")
         if response.ok:
-            logging.info(f"{registry_id} was deleted")
+            logging.info(f"{registry_id} was deleted with {response.status_code}")
             return True
         else:
             if response.status_code == 400:
                 logging.error(f"Bad request for {registry_id}")
             elif response.status_code == 401:
+                logging.error(f"Failed to authenticate for {registry_id}")
+            else:
                 logging.error(f"{response.message} for {registry_id}")
             return False
 

tests/me/test_metagenomics_exchange.py

@@ -11,17 +11,18 @@
 import responses
 
 class TestME:
-    def test_check_existing_analysis(self):
+
+    def test_check_existing_analysis_me(self):
         me_api = MetagenomicsExchangeAPI()
         source_id = "MGYA00293719"
         assert me_api.check_analysis(source_id, True)
 
-    def test_check_not_existing_analysis(self):
+    def test_check_not_existing_analysis_me(self):
         me_api = MetagenomicsExchangeAPI(broker="MAR")
         source_id = "MGYA00293719"
         assert not me_api.check_analysis(source_id, True)
 
-    def test_post_existing_analysis(self):
+    def test_post_existing_analysis_me(self):
         me_api = MetagenomicsExchangeAPI()
         source_id = "MGYA00293719"
         # Should return -> https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/409
@@ -39,4 +40,45 @@ def test_mock_post_new_analysis(self):
         response = me_api.add_analysis(mgya="MGYA00593709", run_accession="SRR3960575", public=True)
 
         assert response.status_code == 201
-        assert response.json() == {'success': True}
+        assert response.json() == {'success': True}
+
+    @responses.activate
+    def test_mock_delete_analysis_from_me(self):
+        me_api = MetagenomicsExchangeAPI()
+        registry_id = "MGX0000780"
+        endpoint = f"datasets/{registry_id}"
+        url = settings.ME_API + f"/{endpoint}"
+
+        responses.add(responses.DELETE, url, json={'success': True}, status=201)
+        response = me_api.delete_request(endpoint)
+
+        assert response.status_code == 201
+        assert response.json() == {'success': True}
+
+
+    def test_wrong_delete_request_me(self):
+        me_api = MetagenomicsExchangeAPI()
+        registry_id = "MGX0000780"
+        endpoint = f"dataset/{registry_id}"
+
+        with pytest.raises(requests.HTTPError, match="404 Client Error"):
+            me_api.delete_request(endpoint)
+
+    def test_patch_analysis_me(self):
+        me_api = MetagenomicsExchangeAPI()
+        registry_id = "MGX0000788"
+        mgya = "MGYA00593709"
+        run_accession = "SRR3960575"
+        public = False
+
+        data = {
+            "confidence": "full",
+            "endPoint": f"https://www.ebi.ac.uk/metagenomics/analyses/{mgya}",
+            "method": ["other_metadata"],
+            "sourceID": mgya,
+            "sequenceID": run_accession,
+            "status": "public" if public else "private",
+            "brokerID": "EMG",
+        }
+        assert me_api.patch_analysis(registry_id, data)
+

tests/me/test_mgx_api.py

@@ -13,7 +13,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
+"""
 import pytest
 
 from unittest.mock import patch
@@ -24,7 +24,7 @@
 
 from emgapi.metagenomics_exchange import MetagenomicsExchangeAPI
 from emgapi.models import AnalysisJob, MetagenomicsExchange, ME_Broker
-"""
+
 @pytest.mark.django_db
 class TestMeAPI:
     @patch("emgapi.metagenomics_exchange.MetagenomicsExchangeAPI.post_request")