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Update womtool graph command to support WDL 1.0

See original GitHub issue

Now that we’ve updated our WDLs to 1.0, we’ve found that womtool graph no longer works. It looks like it only supports draft2 and earlier WDL.

test.wdl:

version 1.0

workflow Test { }

$ java -jar womtool-35.jar graph /tmp/test.wdl 
Exception in thread "main" wdl.draft2.parser.WdlParser$SyntaxError: ERROR: Finished parsing without consuming all tokens.

version 1.0
^
     
	at wdl.draft2.parser.WdlParser.parse(WdlParser.java:2330)
	at wdl.draft2.parser.WdlParser.parse(WdlParser.java:2335)
	at wdl.draft2.model.AstTools$.getAst(AstTools.scala:266)
	at wdl.draft2.model.WdlNamespace$.$anonfun$load$1(WdlNamespace.scala:160)
	at scala.util.Try$.apply(Try.scala:209)
	at wdl.draft2.model.WdlNamespace$.load(WdlNamespace.scala:160)
	at wdl.draft2.model.WdlNamespace$.loadUsingSource(WdlNamespace.scala:156)
	at wdl.draft2.model.WdlNamespaceWithWorkflow$.load(WdlNamespace.scala:571)
	at womtool.graph.GraphPrint$.generateWorkflowDigraph(GraphPrint.scala:19)
	at womtool.WomtoolMain$.graph(WomtoolMain.scala:94)
	at womtool.WomtoolMain$.dispatchCommand(WomtoolMain.scala:48)
	at womtool.WomtoolMain$.runWomtool(WomtoolMain.scala:125)
	at womtool.WomtoolMain$.delayedEndpoint$womtool$WomtoolMain$1(WomtoolMain.scala:130)
	at womtool.WomtoolMain$delayedInit$body.apply(WomtoolMain.scala:18)
	at scala.Function0.apply$mcV$sp(Function0.scala:34)
	at scala.Function0.apply$mcV$sp$(Function0.scala:34)
	at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:12)
	at scala.App.$anonfun$main$1$adapted(App.scala:76)
	at scala.collection.immutable.List.foreach(List.scala:389)
	at scala.App.main(App.scala:76)
	at scala.App.main$(App.scala:74)
	at womtool.WomtoolMain$.main(WomtoolMain.scala:18)
	at womtool.WomtoolMain.main(WomtoolMain.scala)

The womgraph command still works, but the output from that command is so verbose it’s unusable for viewing our workflows.

Issue Analytics

State:
Created 5 years ago
Comments:16 (9 by maintainers)

Top GitHub Comments

11reactions

hailiangmeicommented, Jan 23, 2019

Would that be possible to increase the priority of this issue? Would be really nice to easily generate the workflow graph for discussion and presentation purpose. Thanks!

1reaction

tsjsdbdcommented, Oct 17, 2019

We also need this feature, any news fot this ? (it’s been a year 😄 )

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