[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
via 3386dd9826cf143d078aa8985726516932fafa5b (commit)
via 9bf2ba202652163937d79341e855910f8c330d05 (commit)
via 49743c080265b270693154d7a327d0433b0a7dbe (commit)
via 2fa70753122b53e70005c8f7d2d9b0f12588aa2e (commit)
via 98ada97aef7838001ba87af08761b3abd5b011bb (commit)
via d646e4d515fff35c04544f531f5a7bc0a53a79ab (commit)
via c020dd4470a5f8cbcfe15e764553622828f69ab5 (commit)
via cdcddca613c896fd8395a4045c858945451c3fa0 (commit)
via c19a7bbf7af84f0b8d60ebe29ee9365eca36fbbb (commit)
via 9d035125ea1f8b6bd32fa6f862b32ba9308ebc66 (commit)
via c980683a243903babe9cc09cabc71e1c6229fef1 (commit)
via 057a218324fd68bf5b9d034240d225b539b393a6 (commit)
via 505b7680f8ed8f518f1c3368eb4107e493115b23 (commit)
via f7e07c3a28d4f4e1adbd957749bd825e44a2e523 (commit)
via 3fe0e22c8b6edecd2651c5ee4db105a1e19f42e8 (commit)
via 5eabedb88ce741076167efd2305216043dd9abd5 (commit)
via db1fd09c38132bbaf04e6921bdc0de3bf28abe09 (commit)
via 436105d3e249ad8dc55fb618d0d2c0d8ed29b395 (commit)
via c22b3b27841508c534c6b287ef1508841fd892d4 (commit)
via 529a648458ceefc02d77abf470a2005a099d9907 (commit)
via 204bba7b53a2f7eba36782facf6dc8903aee120a (commit)
via 414ab8bf556c08065d8235a80822344ab5265aae (commit)
via 5c1410e60eb06769207dbafd77501bf2fa45a29b (commit)
via 525e930dcb35b440424d53b09a9788fd8726b781 (commit)
via 48a323ca58614b7e2e100fd69fdc8a441d5d0c80 (commit)
via a8af246b8c99b070fc445cda3d3a13bdf0885f24 (commit)
via beaea7361fdfaf3dd220e3f5999fb3c0dfc3e61c (commit)
via d170d92ce35f402b68fc07c7cbeed2d215685837 (commit)
via b8260eb5cdc2c403083d7dbea49c45791a763e9c (commit)
via 9bccc21498bab7e1300af17c5844f868f119bb9c (commit)
via ad775d785386d751e9b8b0d127885b56f3e016ff (commit)
via 67ef6afce1dd158938eebcf6bed9d3edeb9d73a0 (commit)
via 9507b78b62a042013a8c80ed82182a2ca6d45912 (commit)
via 39df0227516440638035168f5f89df4634f37e1a (commit)
via e1655f12ed1cfec6b5763e1db81e7ec8dd0f7a14 (commit)
via 5450d1417a31aaf2f71e16a440fcfee0a06be6c7 (commit)
via f9f7ccc13963e52b60a10d99806b00a1de66833f (commit)
via 133d751f665ccf24fde56d1f8acf23f9a3475927 (commit)
via 8539a6c20fecc7bed02f1c7f81d3d2a1c0974e1f (commit)
via cb6d05e27e37f29ea99cf6e474ee09a1479252e1 (commit)
via 46f5721a767f8e012b3e3183412bb8f9c5ff0ac6 (commit)
via 8f46e1564dd7c4f42fdccc6e5c8222ce8955405e (commit)
via 76c7406f60319da7011ac9797ae32eb22f574d4c (commit)
via 785a877a46f0c6580d46dac179ea2d4c4a6e7de3 (commit)
via 4fecea55bd6dd5befd82bf7ec5dd4fe93bd93cea (commit)
via f04cfcce18c6e4bd1faf3140ccbc835328580024 (commit)
via 8e6e328e8f8985b763e5a26185de769ea3ad904d (commit)
via defc3f65bfeed18d4ca0beb0e2a3aabd0db6cc75 (commit)
via a87af13d2d3461470b89b0811629a077a70c1938 (commit)
via 846a2728f3cfc80efc220a60536dea16b5f0fcbd (commit)
via bdfd1e9f8bc2a3933f6b0bc7afd5cfebd815fd90 (commit)
via 86865a741f902ac008e11d1dec90b87b89822025 (commit)
via 4d5e04d4998d2fe6c33a98bb93e7ec05e559bcbd (commit)
via 30443c31bf020b6f558c4b7d954599b24c1a98ce (commit)
via 83645e26981cf9a01c72096298fd9f8dd0f5309e (commit)
via ca4958ad27277b1d4ae0226382e214fb2b1f2fec (commit)
from 92c876d90253a0db23d40aa125cba335f7bf7e27 (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
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
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list