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Investigate WDL parsing fails to parse some previously verified workflows from draft-2

See original GitHub issue

Bug Report

Expected behaviour

TBD

Actual behaviour

Hmmm, seeing parse errors with some previously working verified tools. https://staging.dockstore.org/containers/quay.io/pancancer/pcawg-bwa-mem-workflow:2.7.0?tab=files and https://staging.dockstore.org/containers/quay.io/pancancer/pcawg-sanger-cgp-workflow:2.1.0?tab=files (have to click on WDL tabs while in “My Workflows” stack traces look like the following, but don’t seem to abort the whole refresh (it is still 200 status code)

14:33:56
INFO [2019-08-20 14:33:56,887] io.dockstore.webservice.helpers.AbstractImageRegistry: quay.io/pancancer/pcawg-bwa-mem-workflow ICGC-TCGA-PanCancer : Parsing WDL...
INFO [2019-08-20 14:33:56,887] io.dockstore.webservice.helpers.AbstractImageRegistry: quay.io/pancancer/pcawg-bwa-mem-workflow ICGC-TCGA-PanCancer : Parsing WDL...

14:33:56
ERROR [2019-08-20 14:33:56,894] io.dockstore.webservice.languages.WDLHandler: Unable to parse WDL file /Dockstore.wdl

14:33:56
! wdl.draft3.parser.WdlParser$SyntaxError: ERROR: Sibling nodes have conflicting names:

14:33:56
!
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14:33:56
! WdlTask defined here (line 1, col 6):
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14:33:56
!
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14:33:56
! task Seqware_BWA_Workflow {
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14:33:56
! ^

14:33:56
!

14:33:56
! WdlWorkflow statement defined here (line 43, col 10):

14:33:56
!

14:33:56
! workflow Seqware_BWA_Workflow {

14:33:56
! ^

14:33:56
!

14:33:56
! at io.dockstore.common.WdlBridge.getBundleFromContent(WdlBridge.scala:322)

14:33:56
! at io.dockstore.common.WdlBridge.getMetadata(WdlBridge.scala:100)

Probably need to see if these are legitimate draft-2 WDL only and to mark them as such if need be.

Environment (Browser or OS and Dockstore version)

API - 1.7.0-beta.5 UI - 2.4.0-beta.4

┆Issue is synchronized with this Jira Story ┆Epic: Update cwltool/cromwell 1.7.0 ┆Fix Versions: Dockstore 1.8 ┆Issue Number: DOCK-916 ┆Sprint: Seabright Sprint 18 Skipjack ┆Issue Type: Story

Issue Analytics

State:
Created 4 years ago
Comments:17 (11 by maintainers)

Top GitHub Comments

1reaction

NatalieEOcommented, Sep 16, 2019

Seems like for bwa-mem and sanger , just need to change the task name so that it is not the same and the workflow name https://gist.github.com/scottfrazer/0131dc01fb31a451f624d664a9b095bf#fully-qualified-names

delly and dkfz don’t have wdl parts?

1reaction

agduncan94commented, Sep 16, 2019

After playing around with a few different workflows, the code seems to properly choose the right language type (draft-2 vs 1.0)

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