UI for creating methods?

bofallonbofallon Salt Lake City, UtahMember

Hi - I'm trying to create a new, very simple task (just 'hello world', really), and have read the Tool Developer Basics gdoc. However, I couldn't help but notice that there's also a big "Create New Method...." button in the firecloud UI under the Method Repository tab. I've tried this and was able to upload a .wdl file and it appear successful, although I haven't been able to create a method configuration for it so far. Is the UI method creation feature still under development, or should I be able to use it in place of making API calls via the firecloud API?

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Answers

  • jneffjneff BostonMember, Broadie, Moderator admin

    Hello,

    Method Configurations can be created from the Method Configurations tab within a workspace.

    From the Method Repo, you could export your method (WDL) to a workspace. Or from the Method Configurations tab within a workspace, you could click Import Configuration... and then select your method (WDL).

    Once a method is imported/exported to a workspace, you can edit the inputs and outputs using the Method Configurations tab>Edit this page>Save. Then you could Publish the Method Configuration to the Method Repo.

    Let us know if this works for you.

    Thanks,
    Jason

  • bofallonbofallon Salt Lake City, UtahMember

    Thanks for the response. I've uploaded a WDL via the UI and saved it successfully (I think), but heading to the Method Configurations tab, clicking the "Import configuration" button, then selecting my newly created method, and finally clicking "Import" doesn't seem to have any effect. A brief loading gif appears and then disappears, but no new entry is made in the method configurations list, and no errors or warning messages appear. The only other option is to cancel. It's probable that I botched the WDL somehow since this is my first attempt, but in order to test it I'll need a configuration, right?

  • bofallonbofallon Salt Lake City, UtahMember

    Thanks! I've done that already and it's valid WDL.

  • esalinasesalinas BroadMember, Broadie ✭✭✭
  • bofallonbofallon Salt Lake City, UtahMember

    No, I'll check it out though, looks useful.
    I'm worried we might've gotten away from the original questions. It looks like new Methods can be created by uploading a WDL into the UI, is that correct? If so, is there documentation on how best to do this, as I'm running into an issue creating a new method configuration for my newly-uploaded method (described above), and I'm not sure how to diagnose or fix this issue.

  • esalinasesalinas BroadMember, Broadie ✭✭✭

    @bofallon which version of wdltool are you using?

  • jneffjneff BostonMember, Broadie, Moderator admin
    edited November 2016

    Yes, methods can be created by uploading a WDL into the UI. This is covered briefly in our user guide > Uploading Methods through the UI, though it's unlikely to address your specific issue.

    I suspect Eddie suggested you run local Cromwell to further test your WDL in case a WDL-related error is preventing you from importing your method to a workspace. Before uploading WDL workflows, you should use wdltool to validate syntax AND test with local Cromwell. Running local Cromwell is helpful for testing the WDL file against a JSON input file.

    I'm sorry that the testing steps were not clearer as you read through the Tool Dev Basics doc. The attached workshop materials for Tool Developers covers these steps.

    We are also curious what version of wdltool you were using as an outdated version might not have caught a syntax error.

  • esalinasesalinas BroadMember, Broadie ✭✭✭

    @bofallon , can you share with us the WDL?

    -eddie

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