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13 comments

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    Jason Cerrato

    Hi Josh,

    Thanks for reporting this. Are you saying that you are unable to submit jobs in https://portal.firecloud.org/ or https://firecloud.terra.bio/? I have just submitted jobs using both as a test. Are you seeing this happen for any particular workspace? Are you getting back any error messages when attempting to submit using either the old FC UI or FISS? If so, please provide screenshots that may give us a better idea of what you're facing and we'll be happy to take a look.

    Kind regards,

    Jason

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    jgould

    Submissions fail from portal.firecloud.org when the exception: "400 Bad Request": "The request content was malformed:\nExpected String as JsString, but got null"

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    Jason Cerrato

    Can you share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org? Let us know the workspace name, as well as the relevant submission and workflow IDs if any.

    Can you confirm the same error occurs running a workflow on a different workspace? 

    Are you receiving the same error when using FISS?

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    jgould

    I've encountered the same error in multiple workspaces and from multiple users. It seems the error is resolved if you use the data model. The same error is generated when using FISS. Thanks.

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    Jason Cerrato

    Hi Josh,

    Can you share one or more of the workspaces where this happened so that we can try and replicate the issue? If you get to the point of actually being able to submit but it comes back with the error, let us know the submission ID. If you can't even begin to submit, please let us know that too, and write the specific steps taken to achieve that error.

    Are these multiple workspaces using the same workflow(s) or completely different workflows?

    Many thanks,

    Jason

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    jgould

    This happens with any workflow. Steps to reproduce. 

    • Navigate to https://portal.firecloud.org/
    • Create a new workspace or use an existing workspace
    • Import broadgdac/echo from Broad methods repository
    • Uncheck "Configure inputs/outputs using the Workspace Data Model"
    • Enter a string for message input and click "Save"
    • Click "Launch Analysis" and then "Launch"

    The payload {
    methodConfigurationNamespace: "broadgdac",
    methodConfigurationName: "echo",
    entityType: null,
    entityName: null,
    useCallCache: true
    } is submitted to the /submissions endpoint. The response is "400 Bad Request": "The request content was malformed:\nExpected String as JsString, but got null"

     

     

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    Jason Cerrato

    Hi Josh,

    Thank you for that detailed breakdown. I'll be passing this information on to an engineer to take a closer look.

    Kind regards,

    Jason

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    Adam Nichols

    Hi jgould,

    Terra developer here. This is a bug and we have the fix coded up. It looks like our next release might not be until Thursday, March 5.

    In the meantime FISS could possibly work around the issue by omitting the fields instead of setting them to null. I'm not sure what level of involvement you have with the FISS codebase.

    Thanks for reporting and apologies for the inconvenience.

    Best,

    Adam

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    Bo Li

    Hi Adam,

    Will the Terra team continue to maintain the firecloud package or there will be a Terra equivalent?

    Thanks,

    Bo

     

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    Jason Cerrato

    Hi Bo,

    When you say "firecloud package," what package are you referring to? 

    Kind regards,

    Jason

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    Bo Li

    Hi Jason,

    I mean the fiss/firecloud python package. https://github.com/broadinstitute/fiss

    It seems that this package is not maintained since 7 months ago.

    Bo

     

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    Jason Cerrato

    Hi Bo,

    Thanks for the clarification. The FISS package is not created by or maintained by DSP and the Terra team. For questions about FISS, you may want to reach out to David Heiman who is the primary contributor to the project.

    If you have any further questions, please let us know!

    Kind regards,

    Jason

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    Adam Nichols

    jgould we shipped the fix for this last night. Please let us know if you notice any continued issues.

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