[ARVADOS] updated: 3386dd9826cf143d078aa8985726516932fafa5b

Git user git at public.curoverse.com
Fri Apr 1 11:31:45 EDT 2016


Summary of changes:
 build/run-build-packages-python-and-ruby.sh | 198 ++++++++++++++++++++++
 build/run-build-packages.sh                 |   2 +-
 crunch_scripts/cwl-runner                   |  91 +++++++++++
 docker/jobs/Dockerfile                      |   6 +-
 docker/jobs/apt.arvados.org.list            |   2 +-
 sdk/cli/bin/crunch-job                      |  17 +-
 sdk/cwl/arvados_cwl/__init__.py             | 244 ++++++++++++++++++++++++----
 sdk/cwl/setup.py                            |   4 +-
 sdk/cwl/test_with_arvbox.sh                 |   3 +
 sdk/cwl/tests/input/blorp.txt               |   1 +
 sdk/cwl/tests/submit_test_job.json          |   6 +
 sdk/cwl/tests/test_submit.py                |  60 +++++++
 sdk/cwl/tests/tool/blub.txt                 |   1 +
 sdk/cwl/tests/tool/submit_tool.cwl          |  19 +++
 sdk/cwl/tests/wf/submit_wf.cwl              |  16 ++
 sdk/python/arvados/commands/keepdocker.py   |  10 +-
 sdk/python/arvados/commands/run.py          |  26 ++-
 sdk/python/setup.py                         |   1 +
 services/api/app/models/job.rb              |   3 +-
 19 files changed, 648 insertions(+), 62 deletions(-)
 create mode 100755 build/run-build-packages-python-and-ruby.sh
 create mode 100755 crunch_scripts/cwl-runner
 create mode 100644 sdk/cwl/tests/input/blorp.txt
 create mode 100644 sdk/cwl/tests/submit_test_job.json
 create mode 100644 sdk/cwl/tests/test_submit.py
 create mode 100644 sdk/cwl/tests/tool/blub.txt
 create mode 100644 sdk/cwl/tests/tool/submit_tool.cwl
 create mode 100644 sdk/cwl/tests/wf/submit_wf.cwl

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commit 3386dd9826cf143d078aa8985726516932fafa5b
Merge: 92c876d 9bf2ba2
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Fri Apr 1 10:01:39 2016 -0400

    Merge branch 'master' into 8857-cwl-job-reuse
    
    Conflicts:
    	sdk/cwl/arvados_cwl/__init__.py

diff --cc sdk/cwl/arvados_cwl/__init__.py
index 339b91c,511f173..ab8d725
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@@ -403,10 -520,24 +530,26 @@@ class ArvCwlRunner(object)
          self.uploaded[src] = pair
  
      def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
+         self.debug = args.debug
+ 
+         if args.quiet:
+             logger.setLevel(logging.WARN)
+             logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
+ 
+         useruuid = self.api.users().current().execute()["uuid"]
+         self.project_uuid = args.project_uuid if args.project_uuid else useruuid
+         self.pipeline = None
+ 
+         if args.submit:
+             runnerjob = RunnerJob(self, tool, job_order, args.enable_reuse)
+             if not args.wait:
+                 runnerjob.run()
+                 return
+ 
          events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
  
 +        self.debug = args.debug
 +        self.ignore_docker_for_reuse = args.ignore_docker_for_reuse
          self.fs_access = CollectionFsAccess(input_basedir)
  
          kwargs["fs_access"] = self.fs_access
@@@ -484,13 -631,25 +643,28 @@@ def main(args, stdout, stderr, api_clie
      exgroup.add_argument("--disable-reuse", action="store_false",
                          default=True, dest="enable_reuse",
                          help="")
+ 
      parser.add_argument("--project-uuid", type=str, help="Project that will own the workflow jobs")
 +    parser.add_argument("--ignore-docker-for-reuse", action="store_true",
 +                        help="Ignore Docker image version when deciding whether to reuse past jobs.",
 +                        default=False)
  
+     exgroup = parser.add_mutually_exclusive_group()
+     exgroup.add_argument("--submit", action="store_true", help="Submit workflow to run on Arvados.",
+                         default=True, dest="submit")
+     exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits jobs to Arvados).",
+                         default=True, dest="submit")
+ 
+     exgroup = parser.add_mutually_exclusive_group()
+     exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
+                         default=True, dest="wait")
+     exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner job and exit.",
+                         default=True, dest="wait")
+ 
      try:
-         runner = ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
+         if api_client is None:
+             api_client=arvados.api('v1', model=OrderedJsonModel())
+         runner = ArvCwlRunner(api_client)
      except Exception as e:
          logger.error(e)
          return 1

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