Files endpoint fails for hosted published workflow with test parameter json

Bug Report

When viewing a published hosted workflow that has a test parameter JSON, there is an error fetching the version’s files using the GA4GH API. If the hosted workflow has no JSON, then there is no error.

Interestingly, although I see the error in Chrome, I haven’t found yet how the UI’s behavior has changed. 😦

This endpoint also fails in production, but the UI in production never invokes that API.

Steps to reproduce the behaviour

1. curl 'https://staging.dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fdockstore.org%2Fcoverbeck%2Fhelloworld/versions/4/CWL/files'
2. Yields {"code":500,"message":"There was an error processing your request. It has been logged (ID 0ead45002d64e786)."}

On the server side:

ERROR [2019-02-05 18:50:10,919] io.dropwizard.jersey.errors.LoggingExceptionMapper: Error handling a request: 9e9b2bcd57255637
! java.lang.IllegalArgumentException: 'other' is different type of Path
! at sun.nio.fs.UnixPath.relativize(UnixPath.java:416)
! at sun.nio.fs.UnixPath.relativize(UnixPath.java:43)
! at io.swagger.api.impl.ToolsApiServiceImpl.lambda$getToolFiles$9(ToolsApiServiceImpl.java:722)
! at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
! at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1380)
! at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
! at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
! at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
! at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
! at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
! at io.swagger.api.impl.ToolsApiServiceImpl.getToolFiles(ToolsApiServiceImpl.java:727)
! at io.swagger.api.impl.ToolsApiServiceImpl.toolsIdVersionsVersionIdTypeFilesGet(ToolsApiServiceImpl.java:652)
! at io.swagger.api.ToolsApi.toolsIdVersionsVersionIdTypeFilesGet(ToolsApi.java:201)
! at sun.reflect.GeneratedMethodAccessor78.invoke(Unknown Source)
! at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
! at java.lang.reflect.Method.invoke(Method.java:498)
! at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)

┆Issue is synchronized with this Jira Bug ┆Fix Versions: Dockstore 1.6 ┆Issue Number: DOCK-254 ┆Sprint: Backlog ┆Issue Type: Bug

[garyluu]

The UI needs to call that endpoint in order to get the wget command in the launch tab. The call is done so in develop and staging whereas production currently may end up with an incorrect command.

[coverbeck]

Confirmed that it is fixed in 1.6.0-rc.0; curling the endpoint now returns a JSON object:

curl "https://staging.dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fdockstore.org%2Fcoverbeck%2Fhelloworld/versions/3/CWL/files"
[{"file_type":"PRIMARY_DESCRIPTOR","path":"Dockstore.cwl"},{"file_type":"TEST_FILE","path":"test.cwl.json"}]