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John ChiltonandClaude Opus 4.6
32f49d0f6c
Reuses existing tool <tests> blocks to drive execution through the browser tool form, then verifies outputs with verify() infrastructure. Harness infrastructure (navigates_galaxy.py): - run_tool_test() orchestrates: fetch test def via galaxy_interactor, stage data via stage_inputs(), fill form, execute, verify - Data staging uses stage_inputs() from populators (not bespoke upload), supporting files, collections, binary data, and ftype passthrough - Collection staging converts TestCollectionDef dicts to CWL-like job entries; supports paired, list, and list:paired (nested) types - Job-based output tracking: snapshots pre-execution jobs, finds new job after form submit, fetches outputs by dataset ID via job API - Output collection verification: checks collection_type, element count, and verifies each element's content; supports nested sub-collections - Two-pass input filling: shallow params first (conditionals), then deferred params, data params, collection params last - Type detection via smart components: drilldown, checkbox_select, boolean, color, select, text - Multi-data support: detect FormSelection wrapper, clear auto-selected tags before setting desired value - Smart component selectors in navigation.yml for param type detection and interaction (parameter_checkbox_input, parameter_color_input, parameter_text_input, parameter_drilldown_option, etc.) Test data: - Add test cases to gx_data.xml and gx_repeat_boolean.xml - Fix output name in gx_repeat_data.xml (out_file1 -> output) Test suite (test_tool_form_harness.py) — 30 tests: - Scalar params: int, float, text, select, boolean, color - Composite params: conditional (select + boolean), section, repeat, drilldown, multi-select checkboxes, data column, multi-data - Data: single file, optional absent, multi-output, multi-repeats - Collections: paired, list, list:paired input; paired and list:paired output verification; mixed collection+data; optional absent collection - Integration: simple_constructs, implicit_default_conds Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
:alt: Galaxy Logo
The latest information about Galaxy can be found on the `Galaxy Community Hub <https://galaxyproject.org/>`__.
Community support is available at `Galaxy Help <https://help.galaxyproject.org/>`__.
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:target: https://gitter.im/galaxyproject/Lobby
:alt: Chat on gitter
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:target: https://webchat.freenode.net/?channels=galaxyproject
:alt: Chat on irc
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:alt: Release Documentation
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:target: https://travis-ci.org/galaxyproject/galaxy
:alt: Inspect the test results
Galaxy Quickstart
=================
Galaxy requires Python 3.10 or higher. To check your Python version, run:
.. code:: console
$ python -V
Python 3.10.12
Start Galaxy:
.. code:: console
$ sh run.sh
Once Galaxy completes startup, you should be able to view Galaxy in your
browser at: http://localhost:8080
For more installation details please see: https://getgalaxy.org/
Documentation is available at: https://docs.galaxyproject.org/
Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/
Tools
=====
Tools can be either installed from the Tool Shed or added manually.
For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
Note that not all dependencies for the tools provided in the
``tool_conf.xml.sample`` are included. To install them please visit
"Manage dependencies" in the admin interface.
Issues and Galaxy Development
=============================
Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .