ruff 0.280.0 has a bug that would turn the imports guarded by `if
TYPE_CHECKING` into their non-string variant, which would break the
runtime. So we can't merge 23.1 into dev without this.
Upgrade syntax using `pyupgrade --py36-plus` .
Manually drop several `six` imports.
Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
Minimum secret key length for Blowfish was increased from 4 to 5 bytes.
First argument to Blowfish.new() must be a bytestring, and the `mode`
argument is no more optional.
Remove unused `encode_id` function from `scripts/api/common.py` .
Documentation updated, then rebuilt with `make config-rebuild` .
In this implementation, all tools contained in repositories will be loaded into the Galaxy tool panel.
The user can specify the following when sending a POST to the new Galaxy API URL:
/api/tool_shed_repositories/new/install_repository_revision
1) an existing tool panel section id for loading tools or a new tool panel section label in which case a new ToolPanelSection will be created for containing the tools.
2) if they want tool dependencies installed along with the repository.
3) if they want repository dependencies installed along with the repository
4) which defined shed-related tool panel config file to use for installed tools
Additional effort is needed to abstract more previously existing functionality out of web controllers.
Add script that is able to create a sequencer configuration for the sample tracking system using API.
- added web api methods to update requests, samples using restful api
- removed the old ad-doc web api
- modified the data transfer code to use this api
- code cleanup
'enable_api = True' in config file. You should not enable the API on
production sites as this code is brand new and may contain serious bugs and
security flaws! Implemented:
* Display libraries
* Display library info
* Display library contents
* Display library content info
* Create library folders
* Upload datasets to a library from a server directory or with a path paste.
* Basic example scripts in scripts/api/
Framework changes that were made to support this:
* API Key interface in User Preferences.
* New api_keys database table for storing users' API Keys.
* New API-specific route mapper in webapp.
* API controllers in galaxy.web.api
* Return handling in reused library_common methods.
* expose_api decorator for API controller methods validates key and ensures
valid JSON format.
* UniverseWebTransaction renamed to GalaxyWebTransaction and subclassed for
GalaxyWebUITransaction and GalaxyWebAPITransaction.
Things that need to be done next:
* Documentation!
* Refactor reused code from library_common and other controllers into an
even-more-generic location and format. The main changes are that the Web UI
returns redirects and rendered templates, whereas the API returns various
HTTP status codes and JSON.
* Implement more functionality.
* The request and response format should be considered alpha and are subject to
change. They will be standardized as the API matures.
Hints to get started can be found in scripts/api/README
Nicola Soranzo