[ARVADOS] updated: dcca309415bc0683f57f38ad65c30b539d80e191
Git user
git at public.curoverse.com
Fri Dec 16 11:20:39 EST 2016
Summary of changes:
apps/workbench/lib/tasks/config_dump.rake | 6 +
build/libcloud-pin | 2 +-
build/run-build-packages.sh | 9 +-
build/run-tests.sh | 12 +-
doc/_config.yml | 10 +-
doc/_includes/_register_cwl_workflow.liquid | 21 --
doc/install/install-ws.html.textile.liquid | 204 ++++++++++++++
doc/user/cwl/cwl-extensions.html.textile.liquid | 56 ++++
.../cwl/cwl-run-options.html.textile.liquid} | 44 ++-
doc/user/cwl/cwl-runner.html.textile.liquid | 206 +++++---------
doc/user/cwl/cwl-style.html.textile.liquid | 2 +
.../examples/crunch-examples.html.textile.liquid | 2 +
.../getting_started/workbench.html.textile.liquid | 2 +-
.../reference/job-pipeline-ref.html.textile.liquid | 2 +
doc/user/topics/arv-docker.html.textile.liquid | 12 +-
doc/user/topics/run-command.html.textile.liquid | 2 +
...nning-pipeline-command-line.html.textile.liquid | 2 +-
...nning-workflow-command-line.html.textile.liquid | 17 --
.../running-external-program.html.textile.liquid | 2 +-
.../tutorial-submit-job.html.textile.liquid | 2 +-
.../writing-cwl-workflow.html.textile.liquid | 186 ++++++++++++-
sdk/cwl/arvados_cwl/__init__.py | 28 +-
sdk/cwl/arvados_cwl/arvcontainer.py | 102 ++++---
sdk/cwl/arvados_cwl/arvjob.py | 6 -
sdk/cwl/arvados_cwl/fsaccess.py | 84 ++++++
sdk/cwl/arvados_cwl/pathmapper.py | 2 +
sdk/cwl/arvados_cwl/runner.py | 12 +-
sdk/cwl/setup.py | 7 +-
sdk/cwl/tests/test_job.py | 6 +
sdk/cwl/tests/test_submit.py | 203 ++++++++++++--
sdk/cwl/tests/test_urljoin.py | 56 ++++
sdk/cwl/tests/wf/expect_arvworkflow.cwl | 24 ++
sdk/cwl/tests/wf/expect_packed.cwl | 2 +-
.../wf/{submit_wf.cwl => submit_keepref_wf.cwl} | 13 +-
sdk/go/arvados/client.go | 97 ++++++-
sdk/go/arvados/log.go | 25 ++
sdk/go/config/load.go | 5 +
sdk/go/ctxlog/log.go | 59 +++++
sdk/go/stats/duration.go | 35 +++
sdk/go/stats/duration_test.go | 23 ++
sdk/python/arvados/commands/put.py | 3 +
sdk/python/arvados/keep.py | 4 +-
sdk/python/setup.py | 1 -
sdk/python/tests/nginx.conf | 16 ++
sdk/python/tests/run_test_server.py | 71 ++++-
sdk/python/tests/test_events.py | 29 +-
services/api/config/application.default.yml | 1 +
services/api/lib/tasks/config_dump.rake | 6 +
services/fuse/arvados_fuse/__init__.py | 30 +--
services/fuse/arvados_fuse/command.py | 2 +
services/fuse/tests/mount_test_base.py | 2 +
services/fuse/tests/test_retry.py | 2 +-
services/keepstore/logging_router.go | 22 +-
services/nodemanager/arvnodeman/launcher.py | 5 +-
.../keepproxy.service => ws/arvados-ws.service} | 6 +-
services/ws/config.go | 40 +++
services/ws/doc.go | 55 ++++
services/ws/event.go | 65 +++++
services/ws/event_source.go | 216 +++++++++++++++
services/ws/handler.go | 235 ++++++++++++++++
services/ws/main.go | 67 +++++
services/ws/permission.go | 94 +++++++
services/ws/router.go | 140 ++++++++++
services/ws/session.go | 33 +++
services/ws/session_v0.go | 295 +++++++++++++++++++++
services/ws/session_v1.go | 14 +
66 files changed, 2683 insertions(+), 361 deletions(-)
create mode 100644 apps/workbench/lib/tasks/config_dump.rake
delete mode 100644 doc/_includes/_register_cwl_workflow.liquid
create mode 100644 doc/install/install-ws.html.textile.liquid
create mode 100644 doc/user/cwl/cwl-extensions.html.textile.liquid
rename doc/{_includes/_arvados_cwl_runner.liquid => user/cwl/cwl-run-options.html.textile.liquid} (51%)
delete mode 100644 doc/user/topics/running-workflow-command-line.html.textile.liquid
create mode 100644 sdk/cwl/tests/test_urljoin.py
create mode 100644 sdk/cwl/tests/wf/expect_arvworkflow.cwl
copy sdk/cwl/tests/wf/{submit_wf.cwl => submit_keepref_wf.cwl} (70%)
create mode 100644 sdk/go/arvados/log.go
create mode 100644 sdk/go/ctxlog/log.go
create mode 100644 sdk/go/stats/duration.go
create mode 100644 sdk/go/stats/duration_test.go
create mode 100644 services/api/lib/tasks/config_dump.rake
copy services/{keepproxy/keepproxy.service => ws/arvados-ws.service} (55%)
create mode 100644 services/ws/config.go
create mode 100644 services/ws/doc.go
create mode 100644 services/ws/event.go
create mode 100644 services/ws/event_source.go
create mode 100644 services/ws/handler.go
create mode 100644 services/ws/main.go
create mode 100644 services/ws/permission.go
create mode 100644 services/ws/router.go
create mode 100644 services/ws/session.go
create mode 100644 services/ws/session_v0.go
create mode 100644 services/ws/session_v1.go
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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 dcca309415bc0683f57f38ad65c30b539d80e191
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Fri Dec 16 13:19:37 2016 -0300
10383: Error out when using --name and --update-collection together.
diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py
index 133b363..38e4349 100644
--- a/sdk/python/arvados/commands/put.py
+++ b/sdk/python/arvados/commands/put.py
@@ -811,6 +811,9 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
if args.stream or args.raw:
logger.error("Cannot use --name with --stream or --raw")
sys.exit(1)
+ elif args.update_collection:
+ logger.error("Cannot use --name with --update-collection")
+ sys.exit(1)
collection_name = args.name
else:
collection_name = "Saved at {} by {}@{}".format(
commit 409d130ddcc4b76def5fa8d61d2584725c61152a
Merge: 55e9587 ba57b65
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Thu Dec 15 19:04:07 2016 -0300
10383: Merge branch 'master' into 10383-arv-put-incremental-upload
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