Merge pull request #18250 from mvdbeek/test_robustness

[24.0] Skip tests if toolshed, dx.doi not responding

lib/galaxy/managers/citations.py

@@ -55,6 +55,7 @@ def _raw_get_bibtex(self, doi):
         # content encoding from the Content-Type header (res.encoding), and if
         # that fails, falls back to guessing from the content itself (res.apparent_encoding).
         # The guessed encoding is sometimes wrong, better to default to utf-8.
+        res.raise_for_status()
         if res.encoding is None:
             res.encoding = "utf-8"
         return res.text

lib/galaxy_test/driver/uses_shed.py

@@ -4,9 +4,12 @@
 import string
 import tempfile
 from typing import ClassVar
+from unittest import SkipTest
 
 from galaxy.app import UniverseApplication
 from galaxy.model.base import transaction
+from galaxy.util.tool_shed.tool_shed_registry import DEFAULT_TOOL_SHED_URL
+from galaxy.util.unittest_utils import is_site_up
 from galaxy_test.base.populators import DEFAULT_TIMEOUT
 from galaxy_test.base.uses_shed_api import UsesShedApi
 from galaxy_test.driver.driver_util import (
@@ -47,6 +50,8 @@ def _app(self) -> UniverseApplication: ...
 
     @classmethod
     def configure_shed(cls, config):
+        if not is_site_up(DEFAULT_TOOL_SHED_URL):
+            raise SkipTest(f"Test depends on [{DEFAULT_TOOL_SHED_URL}] being up and it appears to be down.")
         cls.shed_tools_dir = tempfile.mkdtemp()
         cls.shed_tool_data_dir = tempfile.mkdtemp()
         cls._test_driver.temp_directories.extend([cls.shed_tool_data_dir, cls.shed_tools_dir])

test/unit/app/managers/test_CitationsManager_db.py

@@ -1,3 +1,6 @@
+from unittest import SkipTest
+
+import requests
 from beaker.cache import CacheManager
 from beaker.util import parse_cache_config_options
 
@@ -29,8 +32,11 @@ def test_DoiCache(url_factory):  # noqa: F811
     with create_and_drop_database(db_url):
         doi_cache = MockDoiCache(galaxy.config.GalaxyAppConfiguration(override_tempdir=False), db_url)
         assert is_cache_empty(db_url, "doi")
-        assert "Jörg" in doi_cache.get_bibtex("10.1093/bioinformatics/bts252")
-        assert "Özkurt" in doi_cache.get_bibtex("10.1101/2021.12.24.474111")
+        try:
+            assert "Jörg" in doi_cache.get_bibtex("10.1093/bioinformatics/bts252")
+            assert "Özkurt" in doi_cache.get_bibtex("10.1101/2021.12.24.474111")
+        except requests.exceptions.RequestException as e:
+            raise SkipTest(f"dx.doi failed to respond: {e}")
         assert not is_cache_empty(db_url, "doi")
         doi_cache._cache.clear()
         assert is_cache_empty(db_url, "doi")

test/unit/app/test_galaxy_install.py

@@ -17,8 +17,10 @@
 from galaxy.tool_shed.unittest_utils import StandaloneInstallationTarget
 from galaxy.tool_shed.util.repository_util import check_for_updates
 from galaxy.util.tool_shed.tool_shed_registry import DEFAULT_TOOL_SHED_URL
+from galaxy.util.unittest_utils import skip_if_site_down
 
 
+@skip_if_site_down(DEFAULT_TOOL_SHED_URL)
 def test_against_production_shed(tmp_path: Path):
     repo_owner = "iuc"
     repo_name = "featurecounts"