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John Chilton
27800b4e33
- Allow parameter inputs to be optional.
- Allow parameter inputs to have default values (if optional).
- Allow data and collection parameter to be optional.
- Unimplemented but new abstractions should allow having users specify extensions manually if they'd like for data and collection parameters.
The previous workflow Module interface would more or less persist Galaxy's "Tool State" directly into the database. The tool state framework persists state in an un-typed fashion (e.g. the optional value for data inputs would be 'True' instead of True). The Format 2 YAML that we would like to publish to Galaxy and export from Galaxy would much more cleanly represent this as actual boolean values.
The problem gets even worse with parameter inputs where we want the default value to be settable only if optional is True. This requires a conditional in the "Tool Form" language - so the persisted value would be nested structures without typing. For instance - instead of ``{default: 5, parameter_type: "integer", "optional": true}`` that we might want to store into the database or read from a workflow definition file, the framework would require something like ``{"parameter_type": "integer", "parameter_defintion": {"optional": {"optional": "True", {"specify_optional": {"specify_default": "True", "default": "5"}}}}}``.
My preference may have been to have plugins defined in the client that just produce the minimal JSON - but I didn't know how to implement that and Sam's preference was that the client use the tool form framework for everything on the side panel anyway though.
As a result, this commit adds abstractions to separate module tool state (for commiunicating with client and tied to tool form rendering) from abstract export state - loaded from the API when not coming from the tool and stored in database.
To summarize workflow module changes...
- module.get_inputs can build complex tool form parameteras (unchanged)
- module.state is always the tool form state (unchanged)
- module.get_export_state is added to get the abstract state for export and for reasoning about internally
- module.recover_state now assumes recovery from abstract step state until from_tool_form=True is supplied
- API entry points tied to the tool form (build_module) just pass through from_tool_form by default.
- The client now sends from_tool_form into the API whenever it serializes the workflow state for re-saving
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Galaxy Quickstart
=================
Galaxy requires Python 2.7 To check your python version, run:
.. code:: console
$ python -V
Python 2.7.3
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
Configuration & Tools
=====================
You may wish to make changes from the default configuration. This can be
done in the ``config/galaxy.ini`` file.
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>`_ .
Roadmap
=============================
Interested in the next steps for Galaxy? Take a look at the `roadmap <https://github.com/galaxyproject/galaxy/projects/8>`__.