Fix typos in method args

emgapi/management/commands/populate_metagenomics_exchange.py

@@ -104,15 +104,14 @@ def process_to_index_and_update_records(self, analyses_to_index_and_update):
         ):
             jobs_to_update = []
             for annotation_job in page:
-
                 sequence_accession = ""
                 if annotation_job.run:
                     sequence_accession = annotation_job.run.accession
                 if annotation_job.assembly:
                     sequence_accession = annotation_job.assembly.accession
 
                 metadata = self.mgx_api.generate_metadata(
-                    mgya=annotation_job.accession, run_accession=sequence_accession
+                    mgya=annotation_job.accession, sequence_accession=sequence_accession
                 )
                 registry_id, metadata_match = self.mgx_api.check_analysis(
                     mgya=annotation_job.accession,
@@ -129,7 +128,8 @@ def process_to_index_and_update_records(self, analyses_to_index_and_update):
                         continue
 
                     response = self.mgx_api.add_analysis(
-                        mgya=annotation_job.accession, run_accession=annotation_job.run
+                        mgya=annotation_job.accession,
+                        sequence_accession=annotation_job.run,
                     )
                     if response.ok:
                         logging.info(f"Successfully added {annotation_job}")
@@ -193,15 +193,14 @@ def process_to_delete_records(self, analyses_to_delete):
             jobs_to_update = []
 
             for annotation_job in page:
-
                 sequence_accession = ""
                 if annotation_job.run:
                     sequence_accession = annotation_job.run.accession
                 if annotation_job.assembly:
                     sequence_accession = annotation_job.assembly.accession
 
                 metadata = self.mgx_api.generate_metadata(
-                    mgya=annotation_job.accession, run_accession=annotation_job.run
+                    mgya=annotation_job.accession, sequence_accession=sequence_accession
                 )
                 registry_id, _ = self.mgx_api.check_analysis(
                     mgya=annotation_job.accession,

tests/me/test_metagenomics_exchange.py

@@ -1,32 +1,29 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import pytest
-import logging
+from unittest import mock
 
+import pytest
+import requests
+import responses
 from django.conf import settings
 
 from emgapi.metagenomics_exchange import MetagenomicsExchangeAPI
 
-import requests
-import responses
-from unittest import mock
-
 
 class TestME:
-
     def test_check_existing_analysis_me(self):
         me_api = MetagenomicsExchangeAPI()
-        source_id = "MGYA00293719"
-        seq_id = "ERR3063408"
-        return_values = me_api.check_analysis(source_id, seq_id, True)
+        mgya = "MGYA00293719"
+        sequence_accession = "ERR3063408"
+        return_values = me_api.check_analysis(mgya, sequence_accession)
         assert return_values[0]
 
     def test_check_not_existing_analysis_me(self):
         me_api = MetagenomicsExchangeAPI()
         source_id = "MGYA10293719"
         seq_id = "ERR3063408"
-        return_values = me_api.check_analysis(source_id, seq_id, True)
+        return_values = me_api.check_analysis(source_id, seq_id)
         assert not return_values[0]
 
     @pytest.mark.skip(reason="Error on ME API side")
@@ -35,9 +32,7 @@ def test_post_existing_analysis_me(self):
         source_id = "MGYA00293719"
         # Should return -> https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/409
         with pytest.raises(requests.HTTPError, match="401 Client Error"):
-            me_api.add_analysis(
-                mgya=source_id, run_accession="ERR3063408", public=True
-            ).json()
+            me_api.add_analysis(mgya=source_id, sequence_accession="ERR3063408").json()
 
     @responses.activate
     def test_mock_post_new_analysis(self):
@@ -48,7 +43,7 @@ def test_mock_post_new_analysis(self):
         responses.add(responses.POST, url, json={"success": True}, status=201)
 
         response = me_api.add_analysis(
-            mgya="MGYA00593709", run_accession="SRR3960575", public=True
+            mgya="MGYA00593709", sequence_accession="SRR3960575"
         )
 
         assert response.status_code == 201

tests/me/test_populate_metagenomics_exchange.py

@@ -42,8 +42,10 @@ def test_population_dry_mode(self, caplog):
         assert "Dry-mode run: no addition to real ME for MGYA00466090" in caplog.text
         assert "Dry-mode run: no addition to real ME for MGYA00466091" in caplog.text
         assert "Processing 1 analyses to remove" in caplog.text
-        assert "MGYA00005678 doesn't exist in the registry, nothing to delete" in caplog.text
-
+        assert (
+            "MGYA00005678 doesn't exist in the registry, nothing to delete"
+            in caplog.text
+        )
 
     @pytest.mark.usefixtures("run_multiple_analysis_me")
     @mock.patch("emgapi.metagenomics_exchange.MetagenomicsExchangeAPI.add_analysis")
@@ -56,16 +58,18 @@ def test_add_new_analysis(self, mock_check_analysis, mock_add_analysis, caplog):
         """
         pipeline = 4.1
         registry_id = "MGX1"
+
         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
 
         def mock_check_process(*args, **kwargs):
-            if 'metadata' in kwargs:
+            if "metadata" in kwargs:
                 return None, True
             else:
                 return registry_id, True
@@ -84,14 +88,10 @@ def mock_check_process(*args, **kwargs):
         assert ajob.last_mgx_indexed
         assert ajob.mgx_accession == registry_id
 
-
     @pytest.mark.usefixtures("run_multiple_analysis_me")
     @mock.patch("emgapi.metagenomics_exchange.MetagenomicsExchangeAPI.check_analysis")
     @mock.patch("emgapi.metagenomics_exchange.MetagenomicsExchangeAPI.delete_analysis")
-    def test_removals(self,
-                      mock_delete_analysis,
-                      mock_check_analysis,
-                      caplog):
+    def test_removals(self, mock_delete_analysis, mock_check_analysis, caplog):
         """
         Test delete process.
         1 analysis should be removed and updated indexed field in DB
@@ -100,10 +100,7 @@ def test_removals(self,
         mock_check_analysis.return_value = True, True
         mock_delete_analysis.return_value = True
 
-        call_command(
-            "populate_metagenomics_exchange",
-            pipeline=pipeline
-        )
+        call_command("populate_metagenomics_exchange", pipeline=pipeline)
         assert "Indexing 0 new analyses" in caplog.text
         assert "Processing 1 analyses to remove" in caplog.text
         assert "Deleting MGYA00005678" in caplog.text
@@ -114,10 +111,7 @@ def test_removals(self,
     @pytest.mark.usefixtures("run_multiple_analysis_me")
     @mock.patch("emgapi.metagenomics_exchange.MetagenomicsExchangeAPI.check_analysis")
     @mock.patch("emgapi.metagenomics_exchange.MetagenomicsExchangeAPI.patch_analysis")
-    def test_update(self,
-                    mock_patch_analysis,
-                    mock_check_analysis,
-                    caplog):
+    def test_update(self, mock_patch_analysis, mock_check_analysis, caplog):
         """
         Test update process for job that was indexed before updated.
         MGX accession and last_mgx_indexed should be updated
@@ -138,5 +132,3 @@ def test_update(self,
         ajob = AnalysisJob.objects.filter(pipeline__release_version=pipeline).first()
         assert ajob.last_mgx_indexed.date() == timezone.now().date()
         assert ajob.mgx_accession == registry_id
-
-