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Bug or null handling during rewrite of json

See original GitHub issue

Describe the bug

I’m getting the following error when testing the dockstore interaction with cwltool for updates to an existing tool (new arguments). Files are pulled from FTP addresses before this error occurs, the error also occur if json file references local files:

10:25:35.810 [main] ERROR io.dockstore.client.cli.ArgumentUtility - null
10:25:35.813 [main] ERROR io.dockstore.client.cli.ArgumentUtility - java.lang.NullPointerException
	at io.github.collaboratory.cwl.CWLClient.createUpdatedInputsAndOutputsJson(CWLClient.java:963)
	at io.github.collaboratory.cwl.CWLClient.provisionInputFiles(CWLClient.java:244)
	at io.dockstore.client.cli.nested.BaseLanguageClient.launchPipeline(BaseLanguageClient.java:164)
	at io.github.collaboratory.cwl.CWLClient.launch(CWLClient.java:289)
	at io.dockstore.client.cli.nested.AbstractEntryClient.launchCwl(AbstractEntryClient.java:1185)
	at io.dockstore.client.cli.nested.AbstractEntryClient.checkEntryFile(AbstractEntryClient.java:815)
	at io.dockstore.client.cli.nested.AbstractEntryClient.launch(AbstractEntryClient.java:1132)
	at io.dockstore.client.cli.nested.AbstractEntryClient.processEntryCommands(AbstractEntryClient.java:278)
	at io.dockstore.client.cli.Client.run(Client.java:715)
	at io.dockstore.client.cli.Client.main(Client.java:614)

Runs cleanly via cwltool if files are made local in advance.

To Reproduce

curl points to head of feature/dockstoreLayerOnly of dockstore-cgpmap at time of writing:

curl -L https://github.com/cancerit/dockstore-cgpmap/archive/352e2fd7371fee01c555992ff813452a303d23f0.tar.gz | tar zx
cd dockstore-cgpmap*
docker build -t quay.io/wtsicgp/dockstore-cgpmap:3.2.0 .
dockstore tool --script launch --local-entry cwls/cgpmap-bamBaiOut.cwl --json examples/cgpmap/bamBaiOut/bam_in.json

Expected behavior

No error, workflow runs.

Screenshots NA

Desktop (please complete the following information):

OS: NA
Browser: NA
Version:

Built following quick-start on 2020-09-03 (cwltool is very old in that document)

$ dockstore --version
Dockstore version 1.9.0
You are running the latest stable version...
If you wish to upgrade to the latest unstable version, please use the following command:
   dockstore --upgrade-unstable
$ java --version
openjdk 11.0.8 2020-07-14
OpenJDK Runtime Environment (build 11.0.8+10-post-Ubuntu-0ubuntu118.04.1)
OpenJDK 64-Bit Server VM (build 11.0.8+10-post-Ubuntu-0ubuntu118.04.1, mixed mode, sharing)
$ cwltool --version
/home/ubuntu/.local/bin/cwltool 1.0.20190621234233

┆Issue is synchronized with this Jira Story ┆Fix Versions: Dockstore 1.9.X ┆Issue Number: DOCK-1563 ┆Sprint: Sprint 44- Sea Horse ┆Issue Type: Story