- Extract FavoritesManager (lib/galaxy/managers/favorites.py): owns
normalize / resolve / persist / order logic; controllers in users.py
are now 2 lines each, and trans.sa_session.commit moves out of the
controller layer. Drops the redundant re-normalize on every write
and replaces FavoriteObjectType.X.value == .value defensive dispatch
with enum-identity comparison. Renames the set_favorite_order
endpoint summary away from the ambiguous "top-level" wording.
- Move curated_tool_tags_by_id off the toolbox into ToolsService;
the controller now routes through the service instead of poking
trans.app.toolbox directly. Raw aggregates (curated_tool_tags,
tool_edam_operations, tool_edam_topics) remain on the toolbox since
they're derived from per-tool data.
- Rename /api/tools/tags -> /api/tags/tool_tags (operation_id
tags__tool_tags) to disambiguate from /api/tools/{id}; update the
client store, tests, and the hand-edited OpenAPI schema entry.
(Run `make update-client-api-schema` before pushing to regenerate
the schema in its canonical alphabetical position.)
- Promote inline imports to module-level (ontology_data.py logging,
app/__init__.py configure_tool_tag_mapping); replace
getattr(self.config, "tool_tag_mappings_file", None) with direct
attribute access now that the option is registered in the schema.
- Convert ontology_data's import-time bundled-mapping reads to
lru_cache so the YAML / TSV files load lazily; fix the
Tool._setup_id comment to point at the actual lowercasing site
(Tool.parse around `self_ids = [self.id.lower()]`).
- doc/source/admin/tool_panel.rst: 26.0 -> 26.1.
- scripts/extract_tool_sections_from_api.py: annotate the public
helpers the test suite imports.
- test_to_dict_cache_drops_when_tool_removed now asserts observable
to_dict() output before/after remove, not private cache membership.
- Split test_tool_discovery_landing into focused tests; extract a
helper that opens the discovery view and types the standard filter.
- Move the Playwright drag helper from test_tool_panel_search.py into
TestWithSeleniumMixin.playwright_drag_item_above so future tests
reuse it.
- Client tests: drop the full-string Whoosh equality in
utilities.test.ts; hard-code expected Whoosh strings in
ToolsList.test.ts (drop createWhooshQuery as both sides of the
assertion) and remove the redundant injectTestRouter mount option
(ToolsList.vue only uses the useRouter composable); drop the
FontAwesome data-icon/iconName assertions in ToolPanel.test.ts in
favor of icon-existence checks; replace three near-identical
add/remove favorite tests in ToolsListCard.test.ts with an it.each;
export quoteToolTagValue from Panels/utilities so
filterConversion.test.js imports the real helper instead of
reconstructing it inline; delete the spy-only "loads the curated
tag mapping" test in ToolBoxSearch.test.ts (the gate is covered by
ToolPanel.test.ts's negative case and the favorite-tag rendering
tests cover the positive case end-to-end).
Two related fixes around the admin-facing helper script and admin docs:
* Make the helper script work from any cwd and against any Galaxy
server: `--api-url`, `--output`, `--timeout` argparse flags; raise
`RuntimeError` on transport / decode failures (was a silent no-op);
anchor the default output path on the script location so
`python scripts/extract_tool_sections_from_api.py` works without a
prior `cd`. Default output now points at `config/tool_tag_mappings.yml`
to match the new admin override path.
* Add a "Curated tool tags" section to `doc/source/admin/tool_panel.rst`
documenting the new `tool_tag_mappings_file` option, the new
`tag:"…"` / `ontology:"…"` search syntax, the `?section=` URL
deprecation, and the reindex requirement after changing the mapping.
Nest the prebuilt/hash-check branches inside `if [ $SKIP_CLIENT_BUILD
-eq 0 ]` so the shape mirrors the subsequent build-or-install block.
Per Nicola's review.
The prebuilt client path (GALAXY_INSTALL_PREBUILT_CLIENT=1, used by
planemo) now pulls the matching galaxy-web-client wheel from PyPI and
lets webapp.py pick it up via `import galaxy.web_client`. The
root-level pnpm install is no longer needed for this flow -- the
Galaxy client isn't a JS library, so shipping it as an npm package
was always the wrong shape.
Dev versions don't have a published wheel, so we bail early with a
message pointing users at the source build path.
only directories in `lib/galaxy` & `packages/*/galaxy`
All other files removed or moved to their own module
All references to those files updated, especially galaxy/version.py
Replaces yarn with pnpm throughout the Makefile and common_startup.sh.
The startup script now installs pnpm via conda, corepack, or npm
depending on the environment.
by runnig:
```shell
make pyupgrade
ruff check --fix .
make format
```
Also update ruff configuration to:
- Enable UP006 and UP035 error codes for PEP 585 type annotations
- Ignore UP045 for the packages which need to stay compatible with Python 3.8
- Add tool-util-models paths to those that need to stay compatible with Python 3.8
Updates repository_metadata.tools with new and correct file locations.
The test toolshed moved around `file_path` multiple times since its
inception, and old revisions might point at old location. This is a
simple script that fixes the locations. It has a dry run mode that I've
run successfully:
```
----------------------------------------------------------------------
Dry run complete - no changes made to database
======================================================================
SUMMARY
======================================================================
Total RepositoryMetadata records processed: 25414
RepositoryMetadata with tools: 22497
Total tools examined: 40470
Tools with correct paths (unchanged): 3898
Tools with paths updated: 36572
- Tool file exists on disk: 33297
- Tool file missing (removed in later changeset): 3275
Tools with path construction errors: 0
======================================================================
```
it also write out json files for each repository as backups should
this be needed.
Closes https://github.com/galaxyproject/galaxy/issues/21454
Found by running:
```
make pyupgrade
ruff check --fix .
ruff check --preview --unsafe-fixes --select=F401 --fix .
make format
make update-client-api-schema
```
The bulk of the changes are replacements of typing deprecated aliases
such as `Dict` and `List` with the standard library classes. These
aliases became redundant in Python 3.9 when the corresponding
pre-existing classes were enhanced to support `[]`, see
https://docs.python.org/3/library/typing.html#deprecated-aliases
Also:
- Update the `pyupgrade` Makefile target to use `--py38-plus` for the
packages needed by Pulsar, including the new galaxy-tool-util-models
package.
mvdbeek