get_submission_docker.cwl

#!/usr/bin/env cwl-runner
#
# Extract the submitted Docker repository and Docker digest
#
cwlVersion: v1.0
class: CommandLineTool
baseCommand: python

inputs:
  - id: submissionid
    type: int
  - id: synapse_config
    type: File

arguments:
  - valueFrom: get_submission_docker.py
  - valueFrom: $(inputs.submissionid)
    prefix: -s
  - valueFrom: results.json
    prefix: -r
  - valueFrom: $(inputs.synapse_config.path)
    prefix: -c

requirements:
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing:
      - entryname: get_submission_docker.py
        entry: |
          #!/usr/bin/env python
          import synapseclient
          import argparse
          import json
          import os
          parser = argparse.ArgumentParser()
          parser.add_argument("-s", "--submissionid", required=True, help="Submission ID")
          parser.add_argument("-r", "--results", required=True, help="download results info")
          parser.add_argument("-c", "--synapse_config", required=True, help="credentials file")
          args = parser.parse_args()
          syn = synapseclient.Synapse(configPath=args.synapse_config)
          syn.login()
          sub = syn.getSubmission(args.submissionid, downloadLocation=".")
          if sub.entity.concreteType != 'org.sagebionetworks.repo.model.docker.DockerRepository':
            raise Exception('Expected DockerRepository type but found '+sub.entity.entityType)
          result = {'docker_repository':sub.get("dockerRepositoryName",""),'docker_digest':sub.get("dockerDigest",""),'entityid':sub.entity.id}
          with open(args.results, 'w') as o:
            o.write(json.dumps(result))
     
outputs:
  - id: docker_repository
    type: string
    outputBinding:
      glob: results.json
      loadContents: true
      outputEval: $(JSON.parse(self[0].contents)['docker_repository'])
  - id: docker_digest
    type: string
    outputBinding:
      glob: results.json
      loadContents: true
      outputEval: $(JSON.parse(self[0].contents)['docker_digest'])
  - id: entityid
    type: string
    outputBinding:
      glob: results.json
      loadContents: true
      outputEval: $(JSON.parse(self[0].contents)['entityid'])