Update biosample communicator to not retry 404

.gitlab-ci.yml

@@ -4,7 +4,7 @@ stages:
 
 test:
   stage: test
-  image: python:3.8.7-slim-buster
+  image: python:3.8.7-slim-bullseye
   before_script:
     - apt-get update && apt-get install curl default-jre -y
     - mkdir /tmp/nextflow && cd /tmp/nextflow && (curl -s https://get.nextflow.io | bash) && chmod 755 nextflow $$ export PATH=/tmp/:$PATH && cd -
@@ -29,7 +29,7 @@ test:
 
 deploy-python-package-production:
   stage: deploy
-  image: python:3.8.7-slim-buster
+  image: python:3.8.7-slim-bullseye
   script:
     - python setup.py sdist
     - twine upload dist/*
@@ -41,4 +41,3 @@ deploy-python-package-production:
     TWINE_PASSWORD: $PYPI_PASSWORD
   only:
     - tags
-

CHANGELOG.md

@@ -5,7 +5,7 @@ Changelog for ebi_eva_common_pyutils
 ## 0.7.4 (unreleased)
 ---------------------
 
-- Nothing changed yet.
+- Update biosamples communicator to not retry 404s
 
 
 ## 0.7.3 (2025-06-19)

ebi_eva_common_pyutils/biosamples_communicators.py

@@ -25,11 +25,18 @@ class HALNotReadyError(Exception):
     pass
 
 
+# Extends ValueError so clients can still expect ValueErrors to be raised on failed requests,
+# but we have a more specific class internally to know when to retry.
+class HttpErrorRetry(ValueError):
+    pass
+
+
 class HALCommunicator(AppLogger):
     """
     This class helps navigate through REST API that uses the HAL standard.
     """
     acceptable_code = [200, 201]
+    no_retry_code = [404]
 
     def __init__(self, auth_url, bsd_url, username, password):
         self.auth_url = auth_url
@@ -43,9 +50,12 @@ def _validate_response(self, response):
             self.error(response.request.method + ': ' + response.request.url + " with " + str(response.request.body))
             self.error("headers: {}".format(response.request.headers))
             self.error("<{}>: {}".format(response.status_code, response.text))
-            raise ValueError('The HTTP status code ({}) is not one of the acceptable codes ({})'.format(
+            error_msg = 'The HTTP status code ({}) is not one of the acceptable codes ({})'.format(
                 str(response.status_code), str(self.acceptable_code))
-            )
+            if response.status_code in self.no_retry_code:
+                raise ValueError(error_msg)
+            else:
+                raise HttpErrorRetry(error_msg)
         return response
 
     @cached_property
@@ -55,7 +65,7 @@ def token(self):
         self._validate_response(response)
         return response.text
 
-    @retry(exceptions=(ValueError, requests.RequestException), tries=3, delay=2, backoff=1.2, jitter=(1, 3))
+    @retry(exceptions=(HttpErrorRetry, requests.RequestException), tries=3, delay=2, backoff=1.2, jitter=(1, 3))
     def _req(self, method, url, **kwargs):
         """Private method that sends a request using the specified method. It adds the headers required by bsd"""
         headers = kwargs.pop('headers', {})

setup.py

@@ -17,7 +17,7 @@
     url='https://github.com/EBIVariation/eva-common-pyutils',
     keywords=['EBI', 'EVA', 'PYTHON', 'UTILITIES'],
     install_requires=requirements,
-    extras_require={'eva-internal': ['psycopg2-binary', 'pymongo', 'networkx<=2.5']},
+    extras_require={'eva-internal': ['psycopg2-binary', 'pymongo<=3.12', 'networkx<=2.5']},
     classifiers=[
         'Development Status :: 5 - Production/Stable',
         'Intended Audience :: Developers',

tests/common/test_biosamples_communicators.py

@@ -2,7 +2,7 @@
 from unittest import TestCase
 from unittest.mock import Mock, patch, PropertyMock
 
-from ebi_eva_common_pyutils.biosamples_communicators import HALCommunicator, WebinHALCommunicator
+from ebi_eva_common_pyutils.biosamples_communicators import HALCommunicator, WebinHALCommunicator, HttpErrorRetry
 
 
 class TestHALCommunicator(TestCase):
@@ -29,10 +29,22 @@ def test_req(self):
                 headers={'Accept': 'application/hal+json', 'Authorization': 'Bearer token'}
             )
 
+        # 500 should trigger a retry
         with patch.object(HALCommunicator, 'token', new_callable=PropertyMock(return_value='token')), \
                 patch('requests.request') as mocked_request:
             mocked_request.return_value = Mock(status_code=500, request=PropertyMock(url='text'))
-            self.assertRaises(ValueError, self.comm._req, 'GET', 'http://BSD.example.org')
+            self.assertRaises(HttpErrorRetry, self.comm._req, 'GET', 'http://BSD.example.org')
+
+        # 404 should fail with a ValueError, but not trigger a retry
+        with patch.object(HALCommunicator, 'token', new_callable=PropertyMock(return_value='token')), \
+                patch('requests.request') as mocked_request:
+            mocked_request.return_value = Mock(status_code=404, request=PropertyMock(url='text'))
+            try:
+                self.comm._req('GET', 'http://BSD.example.org')
+            except HttpErrorRetry:
+                self.fail('Request should not raise HttpErrorRetry')
+            except ValueError:
+                return
 
     def test_root(self):
         expected_json = {'json': 'values'}