antonkulaga / cromwell-client Goto Github PK

Hi,

For better visualization, the client doesn't display the prefixes present in the original json input files, but this produces an issue when debugging. When one inputs the json displayed on the client, the workflow fails due to wrong input.

Thank you

Thanks for this! Just tried using the docker command in README. I verified that I can see Cromwell Swagger on localhost:8080, but when trying to connect using cromwell-client I get:
running workflow at http://127.0.0.1:8080 failed
Exceeded configured max-open-requests value of [32]. This means that the request queue of this pool (HostConnectionPoolSetup(127.0.0.1,8080,ConnectionPoolSetup(ConnectionPoolSettings(512,0,5,32,1,Duration.Inf,100 milliseconds,2 minutes,30 seconds,ClientConnectionSettings(Some(User-Agent: akka-http/10.1.11),30 seconds,2 minutes,512,None,WebSocketSettings(<function0>,ping,Duration.Inf,akka.http.impl.settings.WebSocketSettingsImpl$$$Lambda$153/1984513847@29dfcd54),List(),ParserSettings(2048,16,64,64,8192,64,8388608,8388608,256,1048576,Strict,RFC6265,true,Set(),Full,Error,Map(If-Range -> 0, If-Modified-Since -> 0, If-Unmodified-Since -> 0, default -> 12, Content-MD5 -> 0, Date -> 0, If-Match -> 0, If-None-Match -> 0, User-Agent -> 32),false,true,akka.util.ConstantFun$$$Lambda$42/1795960102@39d055a7,akka.util.ConstantFun$$$Lambda$42/1795960102@39d055a7,akka.util.ConstantFun$$$Lambda$43/1027591600@74f495e4),None,TCPTransport),New,1 second),akka.http.scaladsl.HttpConnectionContext$@277f2c96,akka.event.MarkerLoggingAdapter@354212da))) has completely filled up because the pool currently does not process requests fast enough to handle the incoming request load. Please retry the request later. See http://doc.akka.io/docs/akka-http/current/scala/http/client-side/pool-overflow.html for more information.
Let me know how I can help debug?

Hi,

The cromwell-client sometimes doesn't display the workflows when the limit of workflows to display is 25. However, when changing the limit to 50 it displays it.

Files added to dependencies

cromwell-client_1 | 2022-08-20 20:16:31.318Z info [UserActor] VALIDATING WDL at http://cromwell:8000 - (UserActor.scala:107)
cromwell-client_1 | written dependency as temp file /tmp/8610569505943648695/align_reads.wdl
cromwell-client_1 | written dependency as temp file /tmp/8610569505943648695/clean_reads.wdl

Validation output:
Failed to import 'clean_reads.wdl' (reason 1 of 1): Failed to resolve 'clean_reads.wdl' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Relative path
Failed to import 'align_reads.wdl' (reason 1 of 1): Failed to resolve 'align_reads.wdl' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Relative path

Run results in successful execution, so it is a validation issue. I wasn't able to pinpoint the root cause of the failed validation.
In https://github.com/antonkulaga/cromwell-client/blob/master/client/jvm/src/main/scala/group/research/aging/cromwell/client/CromwellClientJVMSpecific.scala
calls to produce dependencies parameter in postWorkflowStrings and validateWorkflow are identical:
zipDependencies(wdlDependencies).map(f=>ByteBuffer.wrap(f.loadBytes))

Comment says * Created by antonkulaga on 2/18/17. There is an issue with Cromwell reported sometime later: broadinstitute/cromwell#5182 might be related.

hello,

I'm getting 404 when I try to get output files.

http://10.142.0.5:8001/cromwell/cromwell-executions/WholeGenomeGermlineSingleSample/93594b55-4e1f-4831-99bd-0a6df7f9a70a/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/bde5e5b5-e4cd-4cf2-b4f8-1d2d9db6df26/call-CollectUnsortedReadgroupBamQualityMetrics/shard-0/execution/stdout

Inside the docker container it works:

ls /data/cromwell-executions/WholeGenomeGermlineSingleSample/93594b55-4e1f-4831-99bd-0a6df7f9a70a/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/bde5e5b5-e4cd-4cf2-b4f8-1d2
d9db6df26/call-CollectUnsortedReadgroupBamQualityMetrics/shard-0/execution/stdout

The storage is mounted inside from a blob storage

version: '3.8'
services:
  cromwell-client:
    image: quay.io/comp-bio-aging/cromwell-web:latest
    environment:
      - CROMWELL=http://cromwell:8000
      - CROMWELL_LOGS=/data/sources/cromwell-client/logs
    ports:
      - 8001:8001
    volumes:
      - /mnt/coab/cromwell-executions:/data/cromwell-executions:ro
      - /mnt/coab/cromwell-workflow-logs:/data/cromwell-workflow-logs:ro

networks:
  default:
    name: cromwellazure_default
    external: true