Handle input params correctly for rerun_invocation()

[simonbray]

No description provided.

[simonbray]

@nsoranzo I found that the params option was not working correctly so I removed it (as params can also be submitted via inputs) - does this look like an okay alternative?

[nsoranzo]

Mmmh, what's not working for you? I notice two issues:

• invocation_details['input_step_parameters'] seems to be never populated by Galaxy, so params_update should actually be just params as in invoke_workflow()
• payload = {'inputs': inputs, 'params': wf_params} should have been payload = {'inputs': inputs, 'parameters': wf_params}

Does that help?

[simonbray]

invocation_details['input_step_parameters'] seems to be never populated by Galaxy, so params_update should actually be just params as in invoke_workflow()

It does, but only if the input parameter is labelled.

payload = {'inputs': inputs, 'params': wf_params} should have been payload = {'inputs': inputs, 'parameters': wf_params}

Whoops, maybe that was it - I'll try that, thanks!

[simonbray]

@nsoranzo it seems that params doesn't work with runtime parameters, can you confirm if that's the case?

[nsoranzo]

Ping @mvdbeek

[simonbray]

At least I couldn't get it to work with a runtime parameter, and the documentation:

        The ``params`` dict should be specified as follows::

          {STEP_ID: PARAM_DICT, ...}

        where PARAM_DICT is::

          {PARAM_NAME: VALUE, ...}

doesn't really make sense for a runtime parameter.

[simonbray]

This seems to make it clear that runtime parameters belong in inputs, not parameters: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/workflow/run_request.py#L282-L285

[simonbray]

@nsoranzo would it be okay if we merge this? I would like to finish https://github.com/galaxyproject/planemo/pull/1140/files and I feel this should be completed first.

I am pretty confident that runtime parameters can only be submitted via inputs, see the two comments above. Also that's how Planemo is doing it: https://github.com/galaxyproject/planemo/blob/master/planemo/galaxy/activity.py#L165

As a result these two lines are needed to 1) get the runtime parameters from the original invocation's input_step_parameters 2) use the workflow_step_ids to match them with the numeric step ids. Then the numeric step ids can be used to update inputs and invoke the new workflow.

I can also split the last two commits into a separate PR if you prefer so we can merge at least the first one (the remapping bit).