Merge branch 'release_24.0' into release_24.1

lib/galaxy/config/sample/tool_shed.yml.sample

@@ -15,6 +15,10 @@ tool_shed:
   # installation directory.
   #hgweb_config_dir: null
 
+  # Default URL prefix for repositories served via hgweb. If running an
+  # external hgweb server you should set this to an empty string.
+  #hgweb_repo_prefix: repos/
+
   # Allow pushing directly to mercurial repositories directly and
   # without authentication.
   #config_hg_for_dev: null

lib/galaxy/config/schemas/tool_shed_config_schema.yml

@@ -31,6 +31,14 @@ mapping:
           Where the hgweb.config file is stored.
           The default is the Galaxy installation directory.
 
+      hgweb_repo_prefix:
+        type: str
+        required: false
+        default: repos/
+        desc: |
+          Default URL prefix for repositories served via hgweb.
+          If running an external hgweb server you should set this to an empty string.
+
       config_hg_for_dev:
         type: str
         required: false

lib/galaxy/managers/citations.py

@@ -57,6 +57,7 @@ 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/webapps/galaxy/services/dataset_collections.py

@@ -275,7 +275,7 @@ def serialize_element(dsc_element) -> DCESummary:
                     hdca_id=self.encode_id(hdca.id),
                     parent_id=self.encode_id(result["object"]["id"]),
                 )
-            else:
+            elif result["element_type"] == DCEType.hda:
                 result["object"]["accessible"] = self.hda_manager.is_accessible(dsc_element.element_object, trans.user)
             return result
 

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])

lib/tool_shed/util/hgweb_config.py

@@ -19,11 +19,11 @@ class HgWebConfigManager:
     def __init__(self):
         self.hgweb_config_dir = None
         self.in_memory_config = None
+        self.lock = threading.Lock()
 
     def add_entry(self, lhs, rhs):
         """Add an entry in the hgweb.config file for a new repository."""
-        lock = threading.Lock()
-        lock.acquire(True)
+        self.lock.acquire(True)
         try:
             # Since we're changing the config, make sure the latest is loaded into memory.
             self.read_config(force_read=True)
@@ -38,12 +38,11 @@ def add_entry(self, lhs, rhs):
         except Exception as e:
             log.debug("Exception in HgWebConfigManager.add_entry(): %s", unicodify(e))
         finally:
-            lock.release()
+            self.lock.release()
 
     def change_entry(self, old_lhs, new_lhs, new_rhs):
         """Change an entry in the hgweb.config file for a repository - this only happens when the owner changes the name of the repository."""
-        lock = threading.Lock()
-        lock.acquire(True)
+        self.lock.acquire(True)
         try:
             self.make_backup()
             # Remove the old entry.
@@ -55,7 +54,7 @@ def change_entry(self, old_lhs, new_lhs, new_rhs):
         except Exception as e:
             log.debug("Exception in HgWebConfigManager.change_entry(): %s", unicodify(e))
         finally:
-            lock.release()
+            self.lock.release()
 
     def get_entry(self, lhs):
         """Return an entry in the hgweb.config file for a repository"""

lib/tool_shed/util/repository_util.py

@@ -228,7 +228,7 @@ def create_repository(
     # Create the local repository.
     init_repository(repo_path=repository_path)
     # Add an entry in the hgweb.config file for the local repository.
-    lhs = f"repos/{repository.user.username}/{repository.name}"
+    lhs = f"{app.config.hgweb_repo_prefix}{repository.user.username}/{repository.name}"
     app.hgweb_config_manager.add_entry(lhs, repository_path)
     # Create a .hg/hgrc file for the local repository.
     create_hgrc_file(app, repository)

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"