Default workflow

[drtconway]

Hi Janis,

It would make it easier to package up workflows if there was a way, either explicitly, or by convention of allowing the specification of a default workflow/tool in a file containing multiple workflows/tools.

Some possibilities include:

• Inherit from DefaultWorkflow, and if the file contains only one such workflow, then use that as the default
• Have a static or virtual method default_workflow or something, and if it returns true, then take that as the default workflow
• First or last workflow in the file
• define a variable default_janis_workflow or similar, and use that if specified.

Thinking about how it might work in practice, the following seems like a reasonable way to keep it modular, so that importing things down the track works neatly:

class MyHelperTool(PythonTool):
    ...

class Phase1(Workflow):
    ...

class Phase2(Workflow):
    ...

class MyExcellentWorkflow(Workflow):
    ...

class MainWorkflow(MyExcellentWorkflow, DefaultWorkflow):
    # May need to call init on the superclass, I guess
    pass

Thus a client that wants to use MyExcellentWorkflow as a component can import it, without inheriting the defaultness. Note that the usage pattern is not specific to the DefaultWorkflow way of specifying which thing is the default.

[illusional]

Hey @drtconway, from your previous similar issue, I don't think I've handled this process very well in the past. I've come up with the following new process in https://github.com/PMCC-BioinformaticsCore/janis-assistant/pull/30, which follows the procedure:

1. If a name is defined:
   • Force parse every token with a case-insensitive match
   • If a single item is returned from a case-sensitive match, then use that
2. If multiple workflows are defined in the same file, use the last defined workflow
   • This covers the existing If a single workflow is defined, use that case
3. If no tools were found, raise an Exception
4. If multiple tools are defined in the file, use the last one:
   • If a name was defined, warn the user that the case-insensitive match returned no results and we'll use the last one
   • Otherwise, just tell the user we'll use the last defined tool

What do you think?

[drtconway]

Using the last defined tool isn't too bad, but it does mean that rearranging code can change the semantics. I like the idea of explicitly marking a tool/workflow as the default one because it means that cosmetic changes to my code don't change the semantics. It's not something to die in a ditch over though.

Could a decorator come to the rescue?

@default
class MyExcellentWorkflow(Workflow):
    ...

On reflection, the explicit tagging could actually be done in a complementary and orthogonal way to the rules you give above, though if you had multiple workflows tagged as default, you should probably warn.

[illusional]

My main concern with annotations is that they're sticky through imports, so:

from registry import MyExcellentWorkflow # myexcellentworkflow is tagged with @default

@default
class MyOtherAwesomeWorkflow(Workflow):
    pass

Janis sees two default workflows, as it can't discern between tokens imported or defined. Unless you wanted to do something like this:

class MyAwesomeWorkflow(Workflow):
    ...

@default
class _MyAwesomeWorkflowDontImportThisOne(Workflow)
    ...

But I think that's less elegant.

You're right, it can work in complement to that in the PR, so I'll merge that for now while we keep discussion this.

[drtconway]

I agree the sticky problem makes it less elegant, but I do still like the idea of explicitly marking entrypoint workflows.

It's not unlike Python's __main__ thing.

[illusional]

What if you exported a specific keyword from your workflow, something like:

__JANIS_ENTRYPOINT = MyAwesomeWorkflow

[drtconway]

That seems like a reasonable approach.

[illusional]

Hi Tom, as discussed this was implemented and released in Janis-assistant, as in my previous comment, you can export __JANIS_ENTRYPOINT, and Janis will use that UNLESS the --name parameter is specified:

__JANIS_ENTRYPOINT = MyAwesomeWorkflow