Suppression propagation fixes (#344)

* fixes progress logging in ena sync scripts

* do not return suppressed study/samples etc

* fixes typo

* 2.4.39

emgapi/models.py

@@ -300,73 +300,78 @@ def available(self, request=None):
         """
         _query_filters = {
             'StudyQuerySet': {
-                'all': [Q(is_private=False),],
+                'all': [Q(is_private=False, is_suppressed=False),],
             },
             'StudyDownloadQuerySet': {
-                'all': [Q(study__is_private=False),],
+                'all': [Q(study__is_private=False, study__is_suppressed=False),],
             },
             'SampleQuerySet': {
-                'all': [Q(is_private=False),],
+                'all': [Q(is_private=False, is_suppressed=False),],
             },
             'RunQuerySet': {
                 'all': [
-                    Q(is_private=False),
+                    Q(is_private=False, is_suppressed=False),
                 ],
             },
             'AssemblyQuerySet': {
                 'all': [
-                    Q(is_private=False),
+                    Q(is_private=False, is_suppressed=False),
                 ],
             },
             'AnalysisJobDownloadQuerySet': {
                 'all': [
-                    Q(job__study__is_private=False),
+                    Q(job__study__is_private=False, job__study__is_suppressed=False),
                     Q(job__run__is_private=False) | Q(job__assembly__is_private=False),
                     Q(job__analysis_status_id=AnalysisStatus.COMPLETED) | Q(job__analysis_status_id=AnalysisStatus.QC_NOT_PASSED)
                 ],
             },
             'AssemblyExtraAnnotationQuerySet': {
                 'all': [
-                    Q(assembly__is_private=False),
+                    Q(assembly__is_private=False, assembly__is_suppressed=False),
                 ],
             },
             'RunExtraAnnotationQuerySet': {
                 'all': [
-                    Q(run__is_private=False),
+                    Q(run__is_private=False, run__is_suppressed=False),
                 ],
             },
         }
 
         if request is not None and request.user.is_authenticated:
             _username = request.user.username
             _query_filters['StudyQuerySet']['authenticated'] = \
-                [Q(submission_account_id__iexact=_username) | Q(is_private=False)]
+                [Q(submission_account_id__iexact=_username) | Q(is_private=False, is_suppressed=False)]
             _query_filters['StudyDownloadQuerySet']['authenticated'] = \
                 [Q(study__submission_account_id__iexact=_username) |
-                 Q(study__is_private=False)]
+                 Q(study__is_private=False, study__is_suppressed=False)]
             _query_filters['SampleQuerySet']['authenticated'] = \
-                [Q(submission_account_id__iexact=_username) | Q(is_private=False)]
+                [Q(submission_account_id__iexact=_username) | Q(is_private=False), Q(is_suppressed=False)]
             _query_filters['RunQuerySet']['authenticated'] = \
                 [Q(study__submission_account_id__iexact=_username, is_private=True) |
-                 Q(is_private=False)]
+                 Q(is_private=False),
+                 Q(is_suppressed=False)]
             _query_filters['AssemblyQuerySet']['authenticated'] = \
                 [Q(samples__studies__submission_account_id__iexact=_username,
                    is_private=True) |
-                 Q(is_private=False)]
+                 Q(is_private=False),
+                 Q(is_suppressed=False)]
             _query_filters['AnalysisJobDownloadQuerySet']['authenticated'] = \
                 [Q(job__study__submission_account_id__iexact=_username,
                    job__is_private=True) |
                  Q(job__study__submission_account_id__iexact=_username,
                    job__assembly__is_private=True) |
-                 Q(job__run__is_private=False) | Q(job__assembly__is_private=False)]
+                 Q(job__run__is_private=False) | Q(job__assembly__is_private=False),
+                 Q(job__is_suppressed=False)]
             _query_filters['AssemblyExtraAnnotationQuerySet']['authenticated'] = \
                 [Q(assembly__samples__studies__submission_account_id__iexact=_username,
                    is_private=True) |
-                 Q(assembly__is_private=False)]
+                 Q(assembly__is_private=False),
+                 Q(assembly__is_suppressed=False)]
             _query_filters['RunExtraAnnotationQuerySet']['authenticated'] = \
                 [Q(run__samples__studies__submission_account_id__iexact=_username,
                    is_private=True) |
-                 Q(run__is_private=False)]
+                 Q(run__is_private=False),
+                 Q(run__is_suppressed=False)]
 
         filters = _query_filters.get(self.__class__.__name__)
 

emgcli/__init__.py

@@ -1 +1 @@
-__version__: str = "2.4.38"
+__version__: str = "2.4.39"

emgena/management/commands/sync_assemblies_with_ena.py

@@ -96,7 +96,7 @@ def handle(self, *args, **kwargs):
                 emg_assemblies_batch,
                 ["is_private", "is_suppressed", "suppression_reason", "suppressed_at"],
             )
-            logging.info(f"Batch {round(assemblies_count / batch_size)} processed.")
+            logging.info(f"Batch {round(offset / batch_size)} of {round(assemblies_count / batch_size)} processed.")
             offset += batch_size
 
         logging.info("Completed")

emgena/management/commands/sync_runs_with_ena.py

@@ -57,7 +57,7 @@ def handle(self, *args, **kwargs):
                 emg_runs_batch,
                 ["is_private", "is_suppressed", "suppression_reason", "suppressed_at"],
             )
-            logging.info(f"Batch {round(runs_count / batch_size)} processed.")
+            logging.info(f"Batch {round(offset / batch_size)} of {round(runs_count / batch_size)} processed.")
             offset += batch_size
 
         logging.info("Completed")

emgena/management/commands/sync_samples_with_ena.py

@@ -69,7 +69,7 @@ def handle(self, *args, **kwargs):
                 emg_samples_batch,
                 ["is_private", "is_suppressed", "suppression_reason", "suppressed_at"],
             )
-            logging.info(f"Batch {round(samples_count / batch_size)} processed.")
+            logging.info(f"Batch {round(offset / batch_size)} of {round(samples_count / batch_size)} processed.")
             offset += batch_size
 
         logging.info("Completed")

emgena/management/commands/sync_studies_with_ena.py

@@ -70,7 +70,7 @@ def handle(self, *args, **kwargs):
                     "public_release_date",
                 ],
             )
-            logging.info(f"Batch {round(studies_count / batch_size)} processed.")
+            logging.info(f"Batch {round(offset / batch_size)} of {round(studies_count / batch_size)} processed.")
             offset += batch_size
 
         logging.info("Completed")

pyproject.toml

@@ -117,7 +117,7 @@ max-line-length = 119
 """
 
 [tool.bumpversion]
-current_version = "2.4.38"
+current_version = "2.4.39"
 
 [[tool.bumpversion.files]]
 filename = "emgcli/__init__.py"

tests/ena/test_sync_samples_with_ena.py

@@ -15,11 +15,9 @@
 # limitations under the License.
 
 import pytest
-import os
 
 from unittest.mock import patch
 
-from django.urls import reverse
 from django.core.management import call_command
 from emgapi.models import Sample, Assembly, AnalysisJob, Run
 

tests/ena/test_sync_studies_with_ena.py

@@ -47,6 +47,9 @@ def test_make_studies_private(self, ena_study_objs_mock, ena_private_studies):
             if study in public_studies:
                 assert study.is_private == True
 
+        assert Study.objects.available(None).count() == 0
+
+
     @patch("emgena.models.Study.objects")
     def test_make_studies_public(self, ena_study_objs_mock, ena_public_studies):
         ena_study_objs_mock.using("era").filter.return_value = ena_public_studies
@@ -67,6 +70,8 @@ def test_make_studies_public(self, ena_study_objs_mock, ena_public_studies):
             if study in private_studies:
                 assert study.is_private == False
 
+        assert Study.objects.available(None).count() == all_studies.count()
+
     @patch("emgena.models.Study.objects")
     def test_suppress_studies(self, ena_study_objs_mock, ena_suppressed_studies):
         ena_study_objs_mock.using("era").filter.return_value = ena_suppressed_studies
@@ -94,6 +99,8 @@ def test_suppress_studies(self, ena_study_objs_mock, ena_suppressed_studies):
                 == study.get_suppression_reason_display().lower()
             )
 
+        assert Study.objects.available(None).count() == 0
+
     @patch("emgena.models.Study.objects")
     def test_suppress_studies_propagation(self, ena_study_objs_mock, ena_suppression_propagation_studies):
         ena_study_objs_mock.using("era").filter.return_value = ena_suppression_propagation_studies