Modified ME dj function to add new ME records, fixed tests for ME and…

… api

emgapi/management/commands/mgx_api.py

@@ -17,10 +17,9 @@
 import logging
 
 from django.core.management import BaseCommand
-from django.conf import settings
 
 from emgapi.models import AnalysisJob, MetagenomicsExchange, ME_Broker
-from metagenomics_exchange import MetagenomicsExchangeAPI
+from emgapi.metagenomics_exchange import MetagenomicsExchangeAPI
 
 logger = logging.getLogger(__name__)
 
@@ -101,22 +100,24 @@ def handle(self, *args, **options):
         self.assembly_accession = options.get("assembly")
         self.run_accession = options.get("run")
 
-        # FIXME: this command needs adjustments
         broker = options.get("broker")
-        url = settings.ME_API['dev']
-        check_url = url + f'brokers/{self.broker}/datasets'
-        ME = MetagenomicsExchangeAPI()
+        broker_obj = ME_Broker.objects.get_or_create(broker)
+        ME = MetagenomicsExchangeAPI(broker=broker)
         analyses = self._filtering_analyses()
 
         for analysis in analyses:
             MGYA = analysis.accession
             public = not analysis.is_private
             # check is MGYA in ME
-            if ME.check_analysis(url=check_url, sourceID=MGYA, public=public, token=settings.ME_TOKEN):
+            if ME.check_analysis(source_id=MGYA, public=public):
                 logging.info(f"{MGYA} exists in ME")
             else:
                 logging.info(f"{MGYA} does not exist in ME")
-                ME.add_record(url=url, mgya=MGYA, run_accession=analysis.run.accesison, public=public, broker=broker,
-                              token=settings.ME_TOKEN)
+                response = ME.add_record(mgya=MGYA, run_accession=analysis.run, public=public)
+                if response.status_code == 201:
+                    logging.info(f"Populating MetagenomicsExchange table with {MGYA}")
+                    MetagenomicsExchange.objects.get_or_create(analysis, broker=broker_obj)
+                else:
+                    logging.error(f"{MGYA} response exit code: {response.status_code}. No population to DB.")
 
 

emgapi/metagenomics_exchange.py

@@ -53,15 +53,15 @@ def post_request(self, endpoint: str, data: dict):
     def add_record(self, mgya: str, run_accession: str, public: bool):
         data = {
             "confidence": "full",
-            "endPoint": f"https://www.ebi.ac.uk/metagenomics/analyses/mgya",
+            "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": self.broker,
         }
         response = self.post_request(endpoint="datasets", data=data)
-        return response.json()
+        return response
 
     def check_analysis(self, source_id: str, public: bool) -> bool:
         logging.info(f"Check {source_id}")
@@ -75,7 +75,7 @@ def check_analysis(self, source_id: str, public: bool) -> bool:
             datasets = data.get("datasets")
             for item in datasets:
                 if item.get("sourceID") == source_id:
+                    logging.info(f"{source_id} exists")
                     return True
-            logging.info(f"{source_id} exists")
-
+            logging.info(f"{source_id} does not exist")
         return False

emgapi/models.py

@@ -1615,18 +1615,16 @@ class ME_Broker(models.Model):
 
 
 class MetagenomicsExchangeManager(models.Manager):
-    def get_or_create(self, analysis, broker=None):
+    def get_or_create(self, analysis, broker):
         try:
             me_record = MetagenomicsExchange.objects.get(
-                analysis=analysis
+                analysis=analysis, broker=broker
             )
         except ObjectDoesNotExist:
             logging.warning(f"{analysis.accession} not in ME db, creating.")
             me_record = MetagenomicsExchange(
-                analysis=analysis,
+                analysis=analysis, broker=broker
             )
-            if broker:
-                me_record.broker = broker
             me_record.save()
             logging.info(f"Created record ID: {me_record.id}")
         return me_record
@@ -1644,6 +1642,9 @@ class MetagenomicsExchange(models.Model):
     objects = MetagenomicsExchangeManager()
     objects_admin = models.Manager()
 
+    def __str__(self):
+        return f"{self.analysis.job_id} under {self.broker}"
+
 
 class StudyErrorType(models.Model):
     error_id = models.IntegerField(

tests/me/test_metagenomics_exchange.py

@@ -6,7 +6,9 @@
 
 from emgapi.metagenomics_exchange import MetagenomicsExchangeAPI
 
-from requests import HTTPError
+import requests
+import responses
+import settings
 
 
 class TestME:
@@ -24,5 +26,21 @@ def test_post_existing_analysis(self):
         me_api = MetagenomicsExchangeAPI()
         source_id = "MGYA00293719"
         # Should return -> https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/409
-        with pytest.raises(HTTPError, match="409 Client Error"):
-            me_api.add_record(mgya=source_id, run_accession="ERR3063408", public=True)
+        with pytest.raises(requests.HTTPError, match="409 Client Error"):
+            me_api.add_record(mgya=source_id, run_accession="ERR3063408", public=True).json()
+
+    @responses.activate
+    def test_mock_post_new_analysis(self):
+        me_api = MetagenomicsExchangeAPI()
+        endpoint = "datasets"
+        url = settings.ME_API + f"/{endpoint}"
+
+        responses.add(responses.POST, url, json={'success': True}, status=201)
+
+        response = me_api.add_record(mgya="MGYA00593709", run_accession="SRR3960575", public=True)
+
+        assert response.status_code == 201
+        assert response.json() == {'success': True}
+
+
+

tests/me/test_api.py → 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
 
@@ -25,18 +25,21 @@
 
 @pytest.mark.django_db
 class TestMeAPI:
-    @patch("emgapi.management.commands.mgx_api.Command.post_request")
+    @patch("emgapi.metagenomics_exchange.MetagenomicsExchangeAPI.post_request")
+    @pytest.mark.usefixtures(
+        "me_broker",
+        "metagenomics_exchange",
+    )
     def test_new_analysis_population(
             self,
-            mock_post_request,
-            run_multiple_analysis
+            mock_post_request
     ):
         class MockResponse:
             def __init__(self, ok, status_code):
                 self.ok = ok
                 self.status_code = status_code
 
-        mock_post_request.return_value = MockResponse(True, 200)
+        mock_post_request.return_value = MockResponse(True, 201)
         test_run = "ABC01234"
         test_pipeline_version = 5.0
         test_broker = 'EMG'
@@ -49,9 +52,14 @@ def __init__(self, ok, status_code):
         )
         analysis = AnalysisJob.objects.filter(run__accession=test_run).filter(pipeline__pipeline_id=test_pipeline_version).first()
         assert ME_Broker.objects.filter(brokerID=test_broker).count() == 1
-        assert MetagenomicsExchange.objects.filter(analysis=analysis).count() == 1
+        broker_id = ME_Broker.objects.filter(brokerID=test_broker).first().id
+        assert MetagenomicsExchange.objects.filter(analysis=analysis).filter(broker=broker_id).count() == 1
 
-    @patch("emgapi.management.commands.mgx_api.Command.get_request")
+    @pytest.mark.usefixtures(
+        "me_broker",
+        "metagenomics_exchange",
+    )
+    @patch("emgapi.metagenomics_exchange.MetagenomicsExchangeAPI.get_request")
     def test_check_existing_analysis(
             self,
             mock_get_request,
@@ -67,6 +75,7 @@ def __init__(self, ok, status_code, json_data):
 
             def json(self):
                 return self.json_data
+
         test_run = "ABC01234"
         test_pipeline_version = 1.0
         test_broker = 'MAR'
@@ -83,5 +92,5 @@ def json(self):
         )
 
         assert ME_Broker.objects.filter(brokerID=test_broker).count() == 1
-        assert MetagenomicsExchange.objects.filter(analysis=analysis).count() == 1
-    """
+        broker_id = ME_Broker.objects.filter(brokerID=test_broker).first().id
+        assert MetagenomicsExchange.objects.filter(analysis=analysis, broker=broker_id).count() == 1