unable to reference a bucket object directly in method config

birgerbirger Member, Broadie, CGA-mod ✭✭✭

I have a method config that references a file input through a workspace attribute. I wanted to replace the attribute value with an explicit google bucket URL. I got the following error when I saved the updated method config:

Failed at line 1, column 1: workspace.' expected butg' found.

According the documentation available at firecloud.org, I should be able to explicitly reference a file in a method config:

The workaround, of course, is to create another workspace attribute.

Answers

  • thibaultthibault Broad InstituteMember, Broadie, Dev admin

    Does it work if you add quotes around the path? Like "gs://my-bucket/my-file.bam" ?

    I suspect you need to do this because we treat this. and workspace. as special cases and everything else needs to go through our parser. We should make this more clear in the documentation.

  • birgerbirger Member, Broadie, CGA-mod ✭✭✭

    I tried placing quotes. The error message went away, but the value was not highlighted as a link, so I wasn't sure whether it would work. At that point I decided to just create a new workspace attribute and report the problem to the forum.

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    Hello @birger, I wanted to clarify what you were doing when you found this issue.

    From what I understand, you created a workspace attribute that pointed to a specific gs:// url, and when you went to the method configuration to reference that attribute, you typed in workspace.attributeName (for whatever the name of your attribute was), and that's when you got that error message?

    Or, were you trying to directly reference a gs:// URL from the method configuration?

    In either case, this is not the desired behavior. I'm trying to determine whether we need to further clarify our documentation about string usage, or if this is potentially an edge case bug that we need to further diagnose.

  • birgerbirger Member, Broadie, CGA-mod ✭✭✭

    I was trying to directly reference a gs:// URL from a method configuration.

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    Alright, that is definitely a lapse in the documentation. I have updated the section you specified in your original post, and you can find that here.

    After testing it in a private workspace, simply wrapping your gs:// URL in quotes works as expected; the method ran to completion with the proper results. Thank you for bringing this to our attention!

Sign In or Register to comment.