Mock the Metagenomics Exchange API

emgapi/metagenomics_exchange.py

@@ -127,8 +127,12 @@ def check_analysis(self, mgya: str, sequence_accession: str, metadata=None):
             Either the Run accession or the Assembly accession related to the MGYA.
 
         Returns:
-        requests.models.Response
-            The response object from the API request.
+        tuple
+            A tuple containing two elements:
+                - analysis_registry_id : str
+                    The analysis registry ID.
+                - metadata_match : boolean
+                    True, if the metadata matchs.
         """
         if not mgya:
             raise ValueError(f"mgya is mandatory.")
@@ -143,7 +147,7 @@ def check_analysis(self, mgya: str, sequence_accession: str, metadata=None):
 
         endpoint = f"sequences/{sequence_accession}/datasets"
         analysis_registry_id = None
-        metadata_match = True
+        metadata_match = False
 
         try:
             response = self.get_request(endpoint=endpoint, params=params)
@@ -171,18 +175,22 @@ def check_analysis(self, mgya: str, sequence_accession: str, metadata=None):
             ]
             logging.info(f"{mgya} exists in ME")
             analysis_registry_id = found_record.get("registryID")
+            if not analysis_registry_id:
+                raise ValueError(f"The Metagenomics Exchange 'registryID' for {mgya} is null.")
+
             if metadata:
                 for metadata_record in metadata:
                     if not (metadata_record in found_record):
-                        metadata_match = False
-                        return analysis_registry_id, metadata_match
+                        return analysis_registry_id, False
                     else:
                         if metadata[metadata_record] != found_record[metadata_record]:
                             metadata_match = False
                             logging.info(
-                                f"Incorrect field {metadata[metadata_record]} != {found_record[metadata_record]})"
+                                f"The metadata doesn't match, for field {metadata[metadata_record]} != {found_record[metadata_record]})"
                             )
-                            return analysis_registry_id, metadata_match
+                        else:
+                            metadata_match = True
+                        return analysis_registry_id, metadata_match
             return analysis_registry_id, metadata_match
 
         return analysis_registry_id, metadata_match

tests/me/test_metagenomics_exchange.py

@@ -1,8 +1,6 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from unittest import mock
-
 import pytest
 import requests
 import responses
@@ -12,18 +10,35 @@
 
 
 class TestME:
-    def test_check_existing_analysis_me(self):
-        me_api = MetagenomicsExchangeAPI()
+
+    @responses.activate
+    def test_check_existing_analysis_me(self, settings):
+        # FIXME: this test doesn't check if the metadata matches or not.
         mgya = "MGYA00293719"
         sequence_accession = "ERR3063408"
-        return_values = me_api.check_analysis(mgya, sequence_accession)
-        assert return_values[0]
+        responses.add(
+            responses.GET,
+            f"{settings.METAGENOMICS_EXCHANGE_API}/sequences/{sequence_accession}/datasets",
+            json={"datasets": [{"sourceID": mgya, "registryID": "MGX_FAKE"}]},
+            status=200,
+        )
+        me_api = MetagenomicsExchangeAPI()
+
+        registry_id, _ = me_api.check_analysis(mgya, sequence_accession)
+        assert registry_id == "MGX_FAKE"
 
+    @responses.activate
     def test_check_not_existing_analysis_me(self):
+        mgya = "MGYA10293719"
+        sequence_accession = "ERR3063408"
+        responses.add(
+            responses.GET,
+            f"{settings.METAGENOMICS_EXCHANGE_API}/sequences/{sequence_accession}/datasets",
+            json={"datasets": []},
+            status=200,
+        )
         me_api = MetagenomicsExchangeAPI()
-        source_id = "MGYA10293719"
-        seq_id = "ERR3063408"
-        return_values = me_api.check_analysis(source_id, seq_id)
+        return_values = me_api.check_analysis(mgya, sequence_accession)
         assert not return_values[0]
 
     @pytest.mark.skip(reason="Error on ME API side")
@@ -62,38 +77,41 @@ def test_mock_delete_analysis_from_me(self):
         assert response.status_code == 201
         assert response.json() == {"success": True}
 
-    def test_wrong_delete_request_me(self):
+    @responses.activate
+    def test_incorrect_delete_request_me(self):
+        # TODO: this test doesn't make much sense
         me_api = MetagenomicsExchangeAPI()
+        responses.add(
+            responses.DELETE,
+            f"{settings.METAGENOMICS_EXCHANGE_API}/dataset/MGX0000780",
+            status=401,
+        )
         registry_id = "MGX0000780"
         endpoint = f"dataset/{registry_id}"
-        assert not me_api.delete_request(endpoint)
+        response = me_api.delete_request(endpoint)
+        assert response.status_code == 401
 
-    @mock.patch("emgapi.metagenomics_exchange.MetagenomicsExchangeAPI.patch_request")
-    def test_patch_analysis_me(self, mock_patch_request):
+    @responses.activate
+    def test_patch_analysis_me(self):
         me_api = MetagenomicsExchangeAPI()
 
-        class MockResponse:
-            def __init__(self, json_data, status_code):
-                self.json_data = json_data
-                self.status_code = status_code
-                self.ok = True
-
-            def json(self):
-                return self.json_data
-
-        mock_patch_request.return_value = MockResponse({}, 200)
         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",
+            "status": "public",
             "brokerID": "EMG",
         }
+
+        responses.add(
+            responses.PATCH,
+            f"{settings.METAGENOMICS_EXCHANGE_API}/datasets/{registry_id}",
+            status=200,
+        )
+
         assert me_api.patch_analysis(registry_id, data)