fixes regression bug with EBI Search dump commands, following refacto…

…ring for metagenomics exchange. also adds some simple e2e tests for ebisearch dump commands. (#352)

emgapi/management/commands/ebi_search_analysis_dump.py

@@ -172,9 +172,9 @@ def handle(self, *args, **options):
         analyses: QuerySet = AnalysisJob.objects_dump.available(None)
 
         if not is_full_snapshot:
-            analyses = AnalysisJob.objects_for_indexing.to_add()
+            analyses = AnalysisJob.objects_for_ebisearch_indexing.to_add()
 
-            removals = AnalysisJob.objects_for_indexing.to_delete()
+            removals = AnalysisJob.objects_for_ebisearch_indexing.to_delete()
 
             # produce incremental deletion file
             deletions_file = pathlib.Path(output_dir) / pathlib.Path('analyses-deletes.xml')

emgapi/management/commands/ebi_search_study_dump.py

@@ -71,9 +71,9 @@ def handle(self, *args, **options):
         studies: QuerySet = Study.objects.available(None)
 
         if not is_full_snapshot:
-            studies = Study.objects_for_indexing.to_add()
+            studies = Study.objects_for_ebisearch_indexing.to_add()
 
-            removals = Study.objects_for_indexing.to_delete()
+            removals = Study.objects_for_ebisearch_indexing.to_delete()
 
             # produce incremental deletion file
             deletions_file = pathlib.Path(output_dir) / pathlib.Path('projects-deletes.xml')

emgcli/__init__.py

@@ -1 +1 @@
-__version__: str = "2.4.45"
+__version__: str = "2.4.46"

pyproject.toml

@@ -117,7 +117,7 @@ max-line-length = 119
 """
 
 [tool.bumpversion]
-current_version = "2.4.45"
+current_version = "2.4.46"
 
 [[tool.bumpversion.files]]
 filename = "emgcli/__init__.py"

tests/external_indexing_services/test_ebisearch_dump.py

@@ -0,0 +1,48 @@
+import os
+
+import pytest
+from django.core.management import call_command
+
+from test_utils.emg_fixtures import *  # noqa
+
+@pytest.mark.django_db(transaction=True)
+@pytest.mark.usefixtures("experiment_type")
+class TestEbiSearchDump:
+    def test_dump_studies(self, sample):
+        """Test ebi search dump studies"""
+        call_command(
+            "ebi_search_study_dump", "-o", f"/tmp/emg_dump_studies",
+        )
+        assert os.path.exists(f"/tmp/emg_dump_studies/projects.xml")
+        assert os.path.isfile(f"/tmp/emg_dump_studies/projects.xml")
+        assert os.path.exists(f"/tmp/emg_dump_studies/projects-deletes.xml")
+        assert os.path.isfile(f"/tmp/emg_dump_studies/projects-deletes.xml")
+
+        with open(f"/tmp/emg_dump_studies/projects.xml") as f:
+            dump = f.read()
+            assert "MGYS00001234" in dump
+            assert "<entry_count>1</entry_count>" in dump
+
+        with open(f"/tmp/emg_dump_studies/projects-deletes.xml") as f:
+            dump = f.readlines()
+            assert len(dump) == 5  # i.e. no entries within the xml
+
+    def test_dump_analyses(self, run_v5):
+        """Test ebi search dump analyses"""
+        call_command(
+            "ebi_search_analysis_dump", "-o", f"/tmp/emg_dump_analyses",
+        )
+        assert os.path.exists(f"/tmp/emg_dump_analyses/analyses_0001.xml")
+        assert os.path.isfile(f"/tmp/emg_dump_analyses/analyses_0001.xml")
+        assert os.path.exists(f"/tmp/emg_dump_analyses/analyses-deletes.xml")
+        assert os.path.isfile(f"/tmp/emg_dump_analyses/analyses-deletes.xml")
+
+        with open(f"/tmp/emg_dump_analyses/analyses_0001.xml") as f:
+            dump = f.read()
+            assert "MGYA00001234" in dump
+            assert "<entry_count>1</entry_count>" in dump
+
+        with open(f"/tmp/emg_dump_analyses/analyses-deletes.xml") as f:
+            dump = f.readlines()
+            assert len(dump) == 5  # i.e. no entries within the xml
+