1.7.0-beta.2 writeStreamAsZip NullPointerException with quay.io/pancancer/pcawg-bwa-mem-workflow

Bug Report

Expected behaviour

https://staging.dockstore.org/containers/quay.io/pancancer/pcawg-bwa-mem-workflow:2.7.0?tab=info should run /dockstore tool launch --entry quay.io/pancancer/pcawg-bwa-mem-workflow:2.7.0 --json Dockstore_cwl.json with dockstore 1.7.0-beta.2 pointed at staging

Actual behaviour

gluu@ODL-GARYLUU:~/Seqware-BWA-Workflow$ ./dockstore tool launch --entry quay.io/pancancer/pcawg-bwa-mem-workflow:2.7.0 --json Dockstore_cwl.json 
dockstore needs to be on PATH for certain commands to work (like --upgrade)
[##################################################] 100%
Created temporary working directory at '/tmp/1565279086032-0'
11:44:46.380 [main] ERROR io.dockstore.client.cli.ArgumentUtility - The tool entry does not exist. Did you mean to launch a local tool or a workflow?
11:44:46.382 [main] ERROR io.dockstore.client.cli.ArgumentUtility - io.swagger.client.ApiException: {"code":500,"message":"There was an error processing your request. It has been logged (ID 5c0879d8bbd2fd97)."}
	at io.swagger.client.ApiClient.invokeAPI(ApiClient.java:718)
	at io.dockstore.client.cli.SwaggerUtility.getArbitraryURL(SwaggerUtility.java:43)
	at io.dockstore.client.cli.nested.ToolClient.downloadTargetEntry(ToolClient.java:663)
	at io.dockstore.client.cli.nested.BaseLanguageClient.initializeWorkingDirectoryWithFiles(BaseLanguageClient.java:223)
	at io.github.collaboratory.cwl.CWLClient.downloadFiles(CWLClient.java:271)
	at io.dockstore.client.cli.nested.BaseLanguageClient.launchPipeline(BaseLanguageClient.java:150)
	at io.github.collaboratory.cwl.CWLClient.launch(CWLClient.java:289)
	at io.dockstore.client.cli.nested.AbstractEntryClient.launchCwl(AbstractEntryClient.java:1200)
	at io.dockstore.client.cli.nested.AbstractEntryClient.launch(AbstractEntryClient.java:1160)
	at io.dockstore.client.cli.nested.AbstractEntryClient.processEntryCommands(AbstractEntryClient.java:278)
	at io.dockstore.client.cli.Client.run(Client.java:711)
	at io.dockstore.client.cli.Client.main(Client.java:611)

Webservice has:

ERROR [2019-08-08 15:44:46,377] io.dropwizard.jersey.errors.LoggingExceptionMapper: Error handling a request: 5c0879d8bbd2fd97
! java.lang.NullPointerException: null
! at io.dockstore.webservice.helpers.EntryVersionHelper.writeStreamAsZip(EntryVersionHelper.java:352)
! at io.dockstore.webservice.resources.DockerRepoResource.lambda$getToolZip$15(DockerRepoResource.java:1110)

Steps to reproduce the behaviour

• git clone ICGC-TCGA-PanCancer/Seqware-BWA-Workflow
• git checkout 2.7.0
• download dockstore 1.7.0-beta.2
• ./dockstore tool launch --entry quay.io/pancancer/pcawg-bwa-mem-workflow:2.7.0 --json Dockstore_cwl.json

More notes: It doesn’t work for 1.6.0 pointed at production either

┆Issue is synchronized with this Jira Story ┆Fix Versions: Dockstore 1.7 ┆Issue Number: DOCK-884 ┆Sprint: Backlog ┆Issue Type: Story

[garyluu]

Doesn’t happen with other workflow versions or other workflows btw. But the other workflow versions fail further down the line for other reasons.

[cricketsloan]

➤ Walt Shands commented:

I ran the workflow using

~/Documents/UCSC/DOCK-884-testing/Seqware-BWA-Workflow => dockstore --version Dockstore version 1.7.0-beta.7 The latest stable version is 1.6.0 You are currently on the latest unstable version. If you wish to upgrade to the latest stable version, please use the following command: dockstore --upgrade-stable ~/Documents/UCSC/DOCK-884-testing/Seqware-BWA-Workflow => java -version java version “12.0.2” 2019-07-16 Java™ SE Runtime Environment (build 12.0.2+10) Java HotSpot™ 64-Bit Server VM (build 12.0.2+10, mixed mode, sharing) ~/Documents/UCSC/DOCK-884-testing/Seqware-BWA-Workflow => cwltool --version /usr/local/bin/cwltool 1.0.20190621234233

The workflow run did not generate the error mentioned in the ticket; however it did fail with the following error; which seems to be internal to the workflow:

[ERROR] command: seqware bundle launch --dir /home/seqware/Seqware-BWA-Workflow/target/Workflow_Bundle_BWA_2.6.8_SeqWare_1.1.1/ --engine whitestar --ini /TRYxTd/datastore/workflow.ini --no-metadata exited with code: 15 None Traceback (most recent call last): File “/home/seqware/Seqware-BWA-Workflow/run_seqware_workflow.py”, line 375, in <module> main() File “/home/seqware/Seqware-BWA-Workflow/run_seqware_workflow.py”, line 338, in main execute(cmd) File “/home/seqware/Seqware-BWA-Workflow/run_seqware_workflow.py”, line 298, in execute raise TypeError: exceptions must be old-style classes or derived from BaseException, not NoneType INFO [job Seqware-BWA-Workflow] Max memory used: 0MiB ERROR [job Seqware-BWA-Workflow] Job error: Error collecting output for parameter ‘merged_output_bai’: …/…/…/…/…/…/var/folders/vj/xky2f9pn64q6__y6w2kpjx4m0000gn/T/1566930435343-0/Dockstore.cwl:94:7: Did not find output file with glob pattern: ‘[‘datastore/hg19.chr22.5x.normal.bam.bai’]’ WARNING [job Seqware-BWA-Workflow] completed permanentFail WARNING Final process status is permanentFail