[21.05] Do not persist tool state when invoking workflow

[mvdbeek]

If the tool_inputs column of the workflow_step is loaded as
MutableJSONType any "accidental" change of values in the dict marks the
object as "dirty" in the sqlalchemy session it is attached to and will
be persisted when the session is being flushed.
Making the column type JSONType instead of MutableJSONType means
that the object is not marked as dirty and will not be persisted in that
case. The correct method to use to actually persist step inputs is
WorkflowModule.save_to_step or setting step.tool_inputs directly. This
fixes #9886 and (probably, wasn't able to reproduce myself) #12081 (comment)

The issue in #9886 is that
when you submit a workflow the step state is converted to a tool state
in
https://github.com/mvdbeek/galaxy/blob/90dff9af5bec8bed1258620e5351d0350e284206/lib/galaxy/workflow/modules.py#L661:

    def step_state_to_tool_state(self, state):
        state = safe_loads(state)
        if "format" in state:
            formats = state["format"]
            if formats:
                formats = ",".join(listify(formats))
                state["format"] = formats
        state = json.dumps(state)
        return state

and safe_loads just returns the same object if the object that is passed
in is not actually a JSON string. So state["format"] = formats
manipulates the step state in place and that gets committed when
flushing the new invocation.

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:

This is tricky to write good tests for. You could revert #9884 and run @dannon's workflow in https://gist.github.com/dannon/d8abf15c848405a7dc15a792149087d3 and make sure that after running it once you don't see "tool_state": "{\"optional\": false, \"format\": [\"f\", \"\", \"\", \"a\", \"\", \"\", \"s\", \"\", \"\", \"t\", \"\", \"\", \"a\"]}", in the tool state. That's what I used to figure out how to fix this.

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[jmchilton]

Thank you!