Merge pull request #362 from EBI-Metagenomics/Hotfix/Anaylses-Discrep…

…ancies

Hotfix/anaylses discrepancies

.github/workflows/test.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: [3.9]
 
     steps:
     - uses: actions/checkout@v3
@@ -35,7 +35,7 @@ jobs:
 
     - name: 🔧 - Install Dependencies
       run: |
-        pip install install .[tests]
+        pip install .[tests]
         pip freeze
 
     - name: Check for unmigrated code changes

emgapi/models.py

@@ -1698,10 +1698,11 @@ def available(self, request=None):
         - all           | has access to public analyses
         - authenticated | has access to public and private analyses they own
 
-        Filtered out analyses for SUPPRESSED samples
+        Filtered out analyses for SUPPRESSED studies
         """
         query_filters = {
             "all": [
+                Q(study__is_suppressed=False),
                 Q(study__is_private=False),
                 Q(run__is_private=False) | Q(assembly__is_private=False),
                 Q(is_suppressed=False),

emgcli/settings.py

@@ -128,12 +128,12 @@
         },
     },
     'loggers': {
-        'emgena': { 
+        'emgena': {
             'handlers': ['notify'],
             'level': 'INFO',
             'propagate': False
         },
-        'emgapianns.management.commands': { 
+        'emgapianns.management.commands': {
             'handlers': ['default', 'console'],
             'level': 'INFO',
             'propagate': False
@@ -339,8 +339,8 @@ def create_secret_key(var_dir):
 if 'ena' in DATABASES and 'ena_pro' not in DATABASES:
     DATABASES['ena_pro'] = DATABASES['ena']
 
-# this is required to use the djang-mysql QS Hints 
-# https://django-mysql.readthedocs.io/en/latest/queryset_extensions.html?highlight=DJANGO_MYSQL_REWRITE_QUERIES#query-hints 
+# this is required to use the djang-mysql QS Hints
+# https://django-mysql.readthedocs.io/en/latest/queryset_extensions.html?highlight=DJANGO_MYSQL_REWRITE_QUERIES#query-hints
 DJANGO_MYSQL_REWRITE_QUERIES = True
 
 try:

pyproject.toml

@@ -71,12 +71,12 @@ tests = [
     "pytest==6.2.5",
     "pytest-django==4.4.0",
     "pytest-xdist==2.3.0",
-    "model_bakery==1.3.2",
+    "model_bakery==1.17.0",
     "mock_services==0.3.1",
     "mongomock==3.23.0",
     "jsonapi-client==0.9.9",
     "pytest-cov==2.12.1",
-    "pandas==1.3.2",
+    "pandas==2.2.1",
     "responses==0.23.1",
     "Faker==19.6.2",
 ]

tests/webuploader/test_study_summary_generator.py

@@ -19,7 +19,7 @@
 import pandas as pd
 import pytest
 from model_bakery import baker
-from pandas.util.testing import assert_frame_equal
+from pandas.testing import assert_frame_equal
 
 from emgapianns.management.lib import study_summary_generator  # noqa: E402