Skips the physical file removal process for datasets stored in user-defined object stores. These storage locations cannot be resolved by the cleanup script, so the database records are updated while the external files remain intact to prevent potential errors or data loss.
No root pnpm-lock.yaml is shipped, so `pnpm install --frozen-lockfile`
fails with ERR_PNPM_NO_LOCKFILE (hit locally via planemo). The dev
branch is unaffected -- client/pnpm-lock.yaml exists.
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.
This statement is prepared for SQLAlchemy but executed via psycopg2 in
the `pgcleanup.py` script. For psycopg2, the "%" character should be replaced
with %% (see docs
https://www.psycopg.org/docs/usage.html#passing-parameters-to-sql-queries).
SQLAlchemy already takes care of it automatically.
davelopez