From: Peter Amstutz <peter.amstutz@curoverse.com>
Date: Mon, 21 Mar 2016 16:37:38 +0000 (-0400)
Subject: Merge branch 'master' into 8654-arv-jobs-cwl-runner
X-Git-Tag: 1.1.0~1022^2~36
X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/f04cfcce18c6e4bd1faf3140ccbc835328580024

Merge branch 'master' into 8654-arv-jobs-cwl-runner
---

f04cfcce18c6e4bd1faf3140ccbc835328580024
diff --cc sdk/cwl/arvados_cwl/__init__.py
index 480d18ef81,5ed83abb92..c0adb33550
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@@ -348,47 -360,11 +364,49 @@@ class ArvCwlRunner(object)
      def add_uploaded(self, src, pair):
          self.uploaded[src] = pair
  
 +    def upload_docker(self, tool):
 +        pass
 +
 +    def submit(self, tool, job_order, input_basedir, args, **kwargs):
 +        files = set()
 +        def visitFiles(self, path):
 +            files.add(path)
 +
 +        adjustFiles(process.scandeps("", tool.tool,
 +                                     set(("run")),
 +                                     set(("$schemas", "path"))),
 +                    visitFiles)
 +        adjustFiles(job_order, visitFiles)
 +
 +        mapper = ArvPathMapper(self, files, "",
 +                               "$(task.keep)/%s",
 +                               "$(task.keep)/%s/%s",
 +                               **kwargs)
 +
 +        job_order = adjustFiles(job_order, lambda p: mapper.mapper(p))
 +
 +        response = self.api.jobs().create(body={
 +            "script": "cwl-runner",
 +            "script_version": "8654-arv-jobs-cwl-runner",
 +            "repository": "arvados",
 +            "script_parameters": job_order,
 +            "runtime_constraints": {
 +                "docker_image": "arvados/jobs"
 +            }
 +        }, find_or_create=args.enable_reuse).execute(num_retries=self.num_retries)
 +        print response["uuid"]
 +        return None
 +
 +
      def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
 +        if args.submit:
 +            self.submit(tool, job_order, input_basedir, args, **kwargs)
 +            return
 +
          events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
  
+         self.debug = args.debug
+ 
          try:
              self.api.collections().get(uuid=crunchrunner_pdh).execute()
          except arvados.errors.ApiError as e: