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can't launch a method on a pair if another pair has arrays in a field? or integer in col. header?

esalinasesalinas BroadMember, Broadie ✭✭✭

I launched a WDL/method "esalinas/CallingGroupSnapshot ID: 8" on one of two pairs in my workspace. An attached PNG shows that pair #1 of two pairs has fields in the data model filled out from the successful run.

Note that the some of the fields (for example "m1cs") have for their values arrays. See attached TXT file that I downloaded for the pair by clicking the "Download pair data" link. Note too that the column headers ("m1cs") have integers in the string.

I wanted to run the CONFIG on the other pair (#2). So I go to the method configuration tab, find the indicated config, and I click the blue "Launch Analysis ..." button. The "Launch Analysis" dialog box appears.

Because the root entity type is a pair and I want to run it on the config on the other pair I hit the "Pair" filter button. An attached PNG shows the "Pair (2)" button I click. Upon clicking the button, the UI becomes unresponsive. I reproduce the bug but have the console open during the reproduction. In the console, I see "1 is not ISequable".

**_Since I've never seen arrays in the data tab before, I guess that the UI error might be due to arrays in the data entity model for the pair whose WDL run was successful.

Since I've never seen integers in the column headers before, I guess that the UI error might be due to integers in the column header. _**

The UI should continue to respond if there are arrays in the values or integers in the column headers. Either that, or the method configuration output boxes should have prohibited me from putting integers in the names of the outputs (for example "m1cs").

I note that in the WDL I have been forced to dump all outputs because I cannot have an OUTPUT block. If I have the output block I am unable to run the WDL both locally and on firecloud - this is because of cromwell method repo and cromwell executor version discrepancies I believe. Thus, I cannot have the output block and am forced to dump all task outputs back to the data entity model so I cannot stop the arrays from going to the data entity model.

The arrays come from a scatter loop with mutect1, mutect2, and mutect-FC.

Answers

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

    Eddie, Please share your workspace with me (READER privileges are fine since I will be cloning it to run further tests). Also, please make sure I have access to the method you are running.

    thanks,

    Chet.

  • esalinasesalinas BroadMember, Broadie ✭✭✭

    Hi Chet.

    I've made you a READER on broad-firecloud-tcga/EDDIE_CALLING_WS_clone3

    That workspace has this issue.

    I've also made you READER on the method esalinas/CallingGroup/8

    Note that even if you are able to execute the config that it won't run successfully because I've changed the underlying docker environment that the WDL runs in.

    -eddie

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

    Does that mean I won't be able to duplicate the error scenario you describe in this posting?

    -Chet

  • esalinasesalinas BroadMember, Broadie ✭✭✭

    The issue the inability to even select the input to be passed to the config so you should be able to replicate the issue.

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