Metadata-Version: 2.4
Name: galaxy-schema
Version: 25.0.3
Summary: Pydantic models for Galaxy
Home-page: https://github.com/galaxyproject/galaxy
Author: Galaxy Project and Community
Author-email: galaxy-committers@lists.galaxyproject.org
License: AFL
Keywords: Galaxy
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Academic Free License (AFL)
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Software Development
Classifier: Topic :: Software Development :: Code Generators
Classifier: Topic :: Software Development :: Testing
Requires-Python: >=3.9
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: galaxy-util
Requires-Dist: pydantic[email]>=2.7.4
Dynamic: license-file


.. image:: https://badge.fury.io/py/galaxy-schema.svg
   :target: https://pypi.org/project/galaxy-schema/



Overview
--------

The Galaxy_ API schema objects.

* Code: https://github.com/galaxyproject/galaxy

.. _Galaxy: http://galaxyproject.org/

History
-------

.. to_doc

-------------------
25.0.3 (2025-09-23)
-------------------

No recorded changes since last release

-------------------
25.0.2 (2025-08-13)
-------------------


=========
Bug fixes
=========

* Correct visualization response schema by `@guerler <https://github.com/guerler>`_ in `#20627 <https://github.com/galaxyproject/galaxy/pull/20627>`_
* Fix dataset serializers and response models by `@arash77 <https://github.com/arash77>`_ in `#20694 <https://github.com/galaxyproject/galaxy/pull/20694>`_

=============
Other changes
=============

* Merge 24.2 into 25.0 by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20681 <https://github.com/galaxyproject/galaxy/pull/20681>`_

-------------------
25.0.1 (2025-06-20)
-------------------

No recorded changes since last release

-------------------
25.0.0 (2025-06-18)
-------------------


=========
Bug fixes
=========

* Better handling of public pages and workflows authored by deleted users by `@jdavcs <https://github.com/jdavcs>`_ in `#19394 <https://github.com/galaxyproject/galaxy/pull/19394>`_

============
Enhancements
============

* Implement tool markdown reports. by `@jmchilton <https://github.com/jmchilton>`_ in `#19054 <https://github.com/galaxyproject/galaxy/pull/19054>`_
* Let file sources choose a path for uploaded files by `@kysrpex <https://github.com/kysrpex>`_ in `#19154 <https://github.com/galaxyproject/galaxy/pull/19154>`_
* Calculate hash for new non-deferred datasets when finishing a job by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19181 <https://github.com/galaxyproject/galaxy/pull/19181>`_
* Fix UP031 errors - Part 4 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19235 <https://github.com/galaxyproject/galaxy/pull/19235>`_
* Update pydantic to 2.10.3 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19326 <https://github.com/galaxyproject/galaxy/pull/19326>`_
* Empower Users to Build More Kinds of Collections, More Intelligently by `@jmchilton <https://github.com/jmchilton>`_ in `#19377 <https://github.com/galaxyproject/galaxy/pull/19377>`_
* Add User-Defined Tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19434 <https://github.com/galaxyproject/galaxy/pull/19434>`_
* Improve asynchronous tasks error handling and reporting by `@davelopez <https://github.com/davelopez>`_ in `#19448 <https://github.com/galaxyproject/galaxy/pull/19448>`_
* Allow to send notifications when Admins cancel jobs by `@davelopez <https://github.com/davelopez>`_ in `#19547 <https://github.com/galaxyproject/galaxy/pull/19547>`_
* Remove tags used by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#19576 <https://github.com/galaxyproject/galaxy/pull/19576>`_
* Generate correct types for Dataset source transformations on backend. by `@jmchilton <https://github.com/jmchilton>`_ in `#19666 <https://github.com/galaxyproject/galaxy/pull/19666>`_
* Define simple models for job messages. by `@jmchilton <https://github.com/jmchilton>`_ in `#19688 <https://github.com/galaxyproject/galaxy/pull/19688>`_
* Show workflow help (and readme?) in run form by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#19736 <https://github.com/galaxyproject/galaxy/pull/19736>`_
* Migrate Page editing controller endpoint to API by `@guerler <https://github.com/guerler>`_ in `#19923 <https://github.com/galaxyproject/galaxy/pull/19923>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#19929 <https://github.com/galaxyproject/galaxy/pull/19929>`_
* Enable ``warn_redundant_casts`` mypy option and drop redundant casts by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20008 <https://github.com/galaxyproject/galaxy/pull/20008>`_
* Add DOI to workflow metadata by `@jdavcs <https://github.com/jdavcs>`_ in `#20033 <https://github.com/galaxyproject/galaxy/pull/20033>`_

-------------------
24.2.4 (2025-06-17)
-------------------


=========
Bug fixes
=========

* ChatGXY Error Handling by `@dannon <https://github.com/dannon>`_ in `#19987 <https://github.com/galaxyproject/galaxy/pull/19987>`_

-------------------
24.2.3 (2025-03-16)
-------------------

No recorded changes since last release

-------------------
24.2.2 (2025-03-08)
-------------------


============
Enhancements
============

* Add bwa_mem2_index directory datatype, framework enhancements for testing directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19694 <https://github.com/galaxyproject/galaxy/pull/19694>`_

-------------------
24.2.1 (2025-02-28)
-------------------

No recorded changes since last release

-------------------
24.2.0 (2025-02-11)
-------------------


=========
Bug fixes
=========

* Drop "Send to cloud" tool and associated cloudauthz code by `@jdavcs <https://github.com/jdavcs>`_ in `#18196 <https://github.com/galaxyproject/galaxy/pull/18196>`_
* Fix issue with generating slug for sharing by `@arash77 <https://github.com/arash77>`_ in `#18986 <https://github.com/galaxyproject/galaxy/pull/18986>`_
* Fix invocation metrics usability by providing job context. by `@jmchilton <https://github.com/jmchilton>`_ in `#19279 <https://github.com/galaxyproject/galaxy/pull/19279>`_

============
Enhancements
============

* Experimental galactic wizard by `@dannon <https://github.com/dannon>`_ in `#15860 <https://github.com/galaxyproject/galaxy/pull/15860>`_
* Feature - stdout live reporting by `@gecage952 <https://github.com/gecage952>`_ in `#16975 <https://github.com/galaxyproject/galaxy/pull/16975>`_
* Add errors fast api by `@arash77 <https://github.com/arash77>`_ in `#18093 <https://github.com/galaxyproject/galaxy/pull/18093>`_
* Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by `@jmchilton <https://github.com/jmchilton>`_ in `#18272 <https://github.com/galaxyproject/galaxy/pull/18272>`_
* Improve datasets permissions API schema typing by `@davelopez <https://github.com/davelopez>`_ in `#18563 <https://github.com/galaxyproject/galaxy/pull/18563>`_
* Improve typing for archived histories API schema by `@davelopez <https://github.com/davelopez>`_ in `#18586 <https://github.com/galaxyproject/galaxy/pull/18586>`_
* Tighten user notification API response types by `@davelopez <https://github.com/davelopez>`_ in `#18599 <https://github.com/galaxyproject/galaxy/pull/18599>`_
* Improve update user API payload schema by `@davelopez <https://github.com/davelopez>`_ in `#18602 <https://github.com/galaxyproject/galaxy/pull/18602>`_
* Improve update history payload schema by `@davelopez <https://github.com/davelopez>`_ in `#18618 <https://github.com/galaxyproject/galaxy/pull/18618>`_
* Improve types around User in schema and client by `@davelopez <https://github.com/davelopez>`_ in `#18645 <https://github.com/galaxyproject/galaxy/pull/18645>`_
* Improve accept header API schema by `@davelopez <https://github.com/davelopez>`_ in `#18668 <https://github.com/galaxyproject/galaxy/pull/18668>`_
* Migrate Visualizations API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18721 <https://github.com/galaxyproject/galaxy/pull/18721>`_
* Backend handling of setting user-role, user-group, and group-role associations by `@jdavcs <https://github.com/jdavcs>`_ in `#18777 <https://github.com/galaxyproject/galaxy/pull/18777>`_
* Update Visualization FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18792 <https://github.com/galaxyproject/galaxy/pull/18792>`_
* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
* Migrate Library Contents API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18838 <https://github.com/galaxyproject/galaxy/pull/18838>`_
* Enable ``ignore-without-code`` mypy error code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18898 <https://github.com/galaxyproject/galaxy/pull/18898>`_
* Decouple user email from role name by `@jdavcs <https://github.com/jdavcs>`_ in `#18966 <https://github.com/galaxyproject/galaxy/pull/18966>`_
* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
* Allow recovering a normalized version of workflow request state from API by `@jmchilton <https://github.com/jmchilton>`_ in `#18985 <https://github.com/galaxyproject/galaxy/pull/18985>`_
* Add job metrics per invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19048 <https://github.com/galaxyproject/galaxy/pull/19048>`_
* Implement workflow parameter validators. by `@jmchilton <https://github.com/jmchilton>`_ in `#19092 <https://github.com/galaxyproject/galaxy/pull/19092>`_
* Access public history in job cache / job search by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19108 <https://github.com/galaxyproject/galaxy/pull/19108>`_
* Always validate hashes when provided by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19110 <https://github.com/galaxyproject/galaxy/pull/19110>`_

-------------------
24.1.4 (2024-12-11)
-------------------


=========
Bug fixes
=========

* Handle error when workflow is unowned in Invocation view by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18730 <https://github.com/galaxyproject/galaxy/pull/18730>`_
* Fix datatype validation of newly built collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18738 <https://github.com/galaxyproject/galaxy/pull/18738>`_
* Fix job summary for optional unset job data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18754 <https://github.com/galaxyproject/galaxy/pull/18754>`_
* Fix ``TypeError`` from Pydantic 2.9.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18788 <https://github.com/galaxyproject/galaxy/pull/18788>`_
* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
* Make all fields optional for HelpForumPost by `@davelopez <https://github.com/davelopez>`_ in `#18839 <https://github.com/galaxyproject/galaxy/pull/18839>`_
* Remove the default `Incoming` suffix in `GenericModel` class by `@davelopez <https://github.com/davelopez>`_ in `#19174 <https://github.com/galaxyproject/galaxy/pull/19174>`_

============
Enhancements
============

* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_

-------------------
24.1.3 (2024-10-25)
-------------------


=========
Bug fixes
=========

* Handle error when workflow is unowned in Invocation view by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18730 <https://github.com/galaxyproject/galaxy/pull/18730>`_
* Fix datatype validation of newly built collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18738 <https://github.com/galaxyproject/galaxy/pull/18738>`_
* Fix job summary for optional unset job data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18754 <https://github.com/galaxyproject/galaxy/pull/18754>`_
* Fix ``TypeError`` from Pydantic 2.9.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18788 <https://github.com/galaxyproject/galaxy/pull/18788>`_
* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
* Make all fields optional for HelpForumPost by `@davelopez <https://github.com/davelopez>`_ in `#18839 <https://github.com/galaxyproject/galaxy/pull/18839>`_

============
Enhancements
============

* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_

-------------------
24.1.2 (2024-09-25)
-------------------


=========
Bug fixes
=========

* Handle error when workflow is unowned in Invocation view by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18730 <https://github.com/galaxyproject/galaxy/pull/18730>`_
* Fix datatype validation of newly built collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18738 <https://github.com/galaxyproject/galaxy/pull/18738>`_
* Fix job summary for optional unset job data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18754 <https://github.com/galaxyproject/galaxy/pull/18754>`_
* Fix ``TypeError`` from Pydantic 2.9.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18788 <https://github.com/galaxyproject/galaxy/pull/18788>`_
* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
* Make all fields optional for HelpForumPost by `@davelopez <https://github.com/davelopez>`_ in `#18839 <https://github.com/galaxyproject/galaxy/pull/18839>`_

============
Enhancements
============

* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_

-------------------
24.1.1 (2024-07-02)
-------------------


============
Enhancements
============

* Visualizing workflow runs with an invocation graph view by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#17413 <https://github.com/galaxyproject/galaxy/pull/17413>`_
* Add `email` notifications channel by `@davelopez <https://github.com/davelopez>`_ in `#17914 <https://github.com/galaxyproject/galaxy/pull/17914>`_
* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17991 <https://github.com/galaxyproject/galaxy/pull/17991>`_
* Add pagination support to Files Source plugins by `@davelopez <https://github.com/davelopez>`_ in `#18059 <https://github.com/galaxyproject/galaxy/pull/18059>`_
* Enable flake8-implicit-str-concat ruff rules by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18067 <https://github.com/galaxyproject/galaxy/pull/18067>`_
* Empower users to bring their own storage and file sources by `@jmchilton <https://github.com/jmchilton>`_ in `#18127 <https://github.com/galaxyproject/galaxy/pull/18127>`_
* Display DOIs in Archived Histories by `@davelopez <https://github.com/davelopez>`_ in `#18134 <https://github.com/galaxyproject/galaxy/pull/18134>`_
* Allow running and editing workflows for specific versions by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18378 <https://github.com/galaxyproject/galaxy/pull/18378>`_

-------------------
24.0.3 (2024-06-28)
-------------------


=========
Bug fixes
=========

* do not expand datasets that are known to be inaccessible by `@martenson <https://github.com/martenson>`_ in `#17818 <https://github.com/galaxyproject/galaxy/pull/17818>`_
* Allow purge query param, deprecate purge body param by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18105 <https://github.com/galaxyproject/galaxy/pull/18105>`_
* Fix deprecated `deprecated` argument by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18119 <https://github.com/galaxyproject/galaxy/pull/18119>`_
* Fix users API serialization when listing users by `@davelopez <https://github.com/davelopez>`_ in `#18329 <https://github.com/galaxyproject/galaxy/pull/18329>`_
* Fix update group API payload model by `@davelopez <https://github.com/davelopez>`_ in `#18374 <https://github.com/galaxyproject/galaxy/pull/18374>`_
* Serialize purged flag for datasets in collections by `@davelopez <https://github.com/davelopez>`_ in `#18420 <https://github.com/galaxyproject/galaxy/pull/18420>`_

-------------------
24.0.2 (2024-05-07)
-------------------

No recorded changes since last release

-------------------
24.0.1 (2024-05-02)
-------------------


=========
Bug fixes
=========

* Fix tag regex pattern by `@jdavcs <https://github.com/jdavcs>`_ in `#18025 <https://github.com/galaxyproject/galaxy/pull/18025>`_
* Fix History Dataset Association creation so that hid is always set by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18036 <https://github.com/galaxyproject/galaxy/pull/18036>`_

-------------------
24.0.0 (2024-04-02)
-------------------


=========
Bug fixes
=========

* Fix Workflow Comment Model for Pydantic 2 by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#17296 <https://github.com/galaxyproject/galaxy/pull/17296>`_
* Add basic model import attribute validation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17628 <https://github.com/galaxyproject/galaxy/pull/17628>`_
* Make latest_workflow_uuid optional by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17629 <https://github.com/galaxyproject/galaxy/pull/17629>`_
* Fix workflow person validation by `@dannon <https://github.com/dannon>`_ in `#17636 <https://github.com/galaxyproject/galaxy/pull/17636>`_
* Make WorkflowInput label, value and uuid optional by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17638 <https://github.com/galaxyproject/galaxy/pull/17638>`_
* Fix step type serialization for StoredWorkflowDetailed models by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17716 <https://github.com/galaxyproject/galaxy/pull/17716>`_
* Fix input parameter step type by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17767 <https://github.com/galaxyproject/galaxy/pull/17767>`_
* Fix optional types in Help Forum API by `@davelopez <https://github.com/davelopez>`_ in `#17832 <https://github.com/galaxyproject/galaxy/pull/17832>`_
* Fix archived histories mixing with active in histories list by `@davelopez <https://github.com/davelopez>`_ in `#17856 <https://github.com/galaxyproject/galaxy/pull/17856>`_

============
Enhancements
============

* port invocation API to fastapi by `@martenson <https://github.com/martenson>`_ in `#16707 <https://github.com/galaxyproject/galaxy/pull/16707>`_
* Python 3.8 as minimum by `@mr-c <https://github.com/mr-c>`_ in `#16954 <https://github.com/galaxyproject/galaxy/pull/16954>`_
* Toward declarative help for Galaxy markdown directives. by `@jmchilton <https://github.com/jmchilton>`_ in `#16979 <https://github.com/galaxyproject/galaxy/pull/16979>`_
* Create pydantic model for the return of show operation -  get: `/api/jobs/{job_id}`  by `@heisner-tillman <https://github.com/heisner-tillman>`_ in `#17153 <https://github.com/galaxyproject/galaxy/pull/17153>`_
* Vueifiy History Grids by `@guerler <https://github.com/guerler>`_ in `#17219 <https://github.com/galaxyproject/galaxy/pull/17219>`_
* Refactor two of the missing invocation routes to FastAPI by `@heisner-tillman <https://github.com/heisner-tillman>`_ in `#17237 <https://github.com/galaxyproject/galaxy/pull/17237>`_
* Migrate models to pydantic 2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17262 <https://github.com/galaxyproject/galaxy/pull/17262>`_
* Combines legacy qv-pattern and advanced filter pattern in history index endpoint by `@guerler <https://github.com/guerler>`_ in `#17368 <https://github.com/galaxyproject/galaxy/pull/17368>`_
* Update to black 2024 stable style by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17391 <https://github.com/galaxyproject/galaxy/pull/17391>`_
* Allow using tool data bundles as inputs to reference data select parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17435 <https://github.com/galaxyproject/galaxy/pull/17435>`_
* Refactor Workflow API routes - Part 1 by `@heisner-tillman <https://github.com/heisner-tillman>`_ in `#17463 <https://github.com/galaxyproject/galaxy/pull/17463>`_
* Consolidate resource grids into tab views by `@guerler <https://github.com/guerler>`_ in `#17487 <https://github.com/galaxyproject/galaxy/pull/17487>`_
* Display workflow invocation counts. by `@jmchilton <https://github.com/jmchilton>`_ in `#17488 <https://github.com/galaxyproject/galaxy/pull/17488>`_
* Filter out subworkflow invocations by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17558 <https://github.com/galaxyproject/galaxy/pull/17558>`_
* Restore histories API behavior for `keys` query parameter by `@davelopez <https://github.com/davelopez>`_ in `#17779 <https://github.com/galaxyproject/galaxy/pull/17779>`_
* Fix datasets API custom keys encoding by `@davelopez <https://github.com/davelopez>`_ in `#17793 <https://github.com/galaxyproject/galaxy/pull/17793>`_

-------------------
23.2.1 (2024-02-21)
-------------------

First release
