[ARVADOS] updated: 1.3.0-611-g9a7e2a24f
Git user
git at public.curoverse.com
Wed Mar 27 14:02:51 UTC 2019
Summary of changes:
.../controllers/container_requests_controller.rb | 2 +-
apps/workbench/app/helpers/application_helper.rb | 11 +-
build/package-build-dockerfiles/debian8/Dockerfile | 2 +
build/package-test-dockerfiles/debian8/Dockerfile | 2 +
build/run-library.sh | 11 +-
build/run-tests.sh | 652 +++++++++++++--------
.../{bwa-mem-input.yml => bwa-mem-input-mixed.yml} | 11 +
doc/user/cwl/bwa-mem/bwa-mem-input-uuids.yml | 21 +
doc/user/cwl/cwl-runner.html.textile.liquid | 6 +-
lib/cloud/azure/azure.go | 7 +-
lib/controller/cmd.go | 2 +-
lib/controller/handler_test.go | 2 +-
lib/controller/proxy.go | 1 +
lib/dispatchcloud/cmd.go | 14 +-
lib/dispatchcloud/container/queue.go | 84 ++-
lib/dispatchcloud/dispatcher.go | 34 +-
lib/dispatchcloud/dispatcher_test.go | 49 +-
lib/dispatchcloud/driver.go | 32 +-
lib/dispatchcloud/scheduler/fix_stale_locks.go | 1 -
lib/dispatchcloud/scheduler/interfaces.go | 2 +-
lib/dispatchcloud/scheduler/run_queue_test.go | 39 +-
lib/dispatchcloud/scheduler/sync.go | 27 +-
lib/dispatchcloud/test/queue.go | 13 +-
lib/dispatchcloud/test/stub_driver.go | 102 ++--
lib/dispatchcloud/worker/pool.go | 99 ++--
lib/dispatchcloud/worker/runner.go | 154 +++++
lib/dispatchcloud/worker/worker.go | 235 +++++---
lib/dispatchcloud/worker/worker_test.go | 9 +-
lib/service/cmd.go | 32 +-
lib/service/cmd_test.go | 78 +++
lib/service/error.go | 38 ++
sdk/cli/arvados-cli.gemspec | 4 +-
sdk/cwl/arvados_cwl/__init__.py | 2 +-
sdk/cwl/arvados_cwl/arvcontainer.py | 10 +-
sdk/cwl/arvados_cwl/executor.py | 4 +-
sdk/cwl/arvados_cwl/fsaccess.py | 40 +-
sdk/cwl/arvados_cwl/pathmapper.py | 3 +
sdk/cwl/arvados_cwl/runner.py | 89 ++-
sdk/cwl/arvados_cwl/util.py | 4 +-
...> submit_test_job_with_inconsistent_uuids.json} | 4 +-
... => submit_test_job_with_mismatched_uuids.json} | 7 +-
...st_job.json => submit_test_job_with_uuids.json} | 6 +-
sdk/cwl/tests/test_container.py | 14 +-
sdk/cwl/tests/test_submit.py | 132 ++++-
sdk/go/arvados/client.go | 15 +
sdk/go/arvados/config.go | 53 ++
sdk/go/keepclient/discover.go | 8 +-
sdk/ruby/arvados.gemspec | 2 +-
services/api/test/integration/groups_test.rb | 30 +-
services/crunch-run/background.go | 13 +-
services/crunch-run/crunchrun.go | 9 +-
services/crunch-run/crunchrun_test.go | 2 +-
services/fuse/arvados_fuse/__init__.py | 62 ++
services/fuse/arvados_fuse/crunchstat.py | 99 ++--
services/fuse/setup.py | 3 +-
tools/arvbox/bin/arvbox | 85 ++-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 8 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.dev | 1 +
tools/arvbox/lib/arvbox/docker/common.sh | 1 +
tools/arvbox/lib/arvbox/docker/createusers.sh | 17 +-
tools/arvbox/lib/arvbox/docker/devenv.sh | 12 +
tools/arvbox/lib/arvbox/docker/service/nginx/run | 127 +++-
.../lib/arvbox/docker/service/nginx/run-service | 119 ----
.../crunchstat_summary/command.py | 30 +-
.../crunchstat_summary/dygraphs.py | 4 +-
.../crunchstat_summary/reader.py | 10 +-
.../crunchstat_summary/summarizer.py | 66 ++-
.../crunchstat_summary/webchart.py | 10 +-
...4-dz642-lymtndkpy39eibk-arv-mount.txt.gz.report | 4 +-
...-dz642-lymtndkpy39eibk-crunchstat.txt.gz.report | 3 +-
...ainer_9tee4-dz642-lymtndkpy39eibk.txt.gz.report | 3 +-
.../tests/logfile_20151204190335.txt.gz.report | 3 +-
.../tests/logfile_20151210063411.txt.gz.report | 3 +-
.../tests/logfile_20151210063439.txt.gz.report | 3 +-
tools/crunchstat-summary/tests/test_examples.py | 36 +-
75 files changed, 2104 insertions(+), 828 deletions(-)
copy doc/user/cwl/bwa-mem/{bwa-mem-input.yml => bwa-mem-input-mixed.yml} (54%)
create mode 100755 doc/user/cwl/bwa-mem/bwa-mem-input-uuids.yml
create mode 100644 lib/dispatchcloud/worker/runner.go
create mode 100644 lib/service/cmd_test.go
create mode 100644 lib/service/error.go
copy sdk/cwl/tests/{submit_test_job.json => submit_test_job_with_inconsistent_uuids.json} (68%)
copy sdk/cwl/tests/{submit_test_job.json => submit_test_job_with_mismatched_uuids.json} (67%)
copy sdk/cwl/tests/{submit_test_job.json => submit_test_job_with_uuids.json} (63%)
create mode 100755 tools/arvbox/lib/arvbox/docker/devenv.sh
mode change 120000 => 100755 tools/arvbox/lib/arvbox/docker/service/nginx/run
delete mode 100755 tools/arvbox/lib/arvbox/docker/service/nginx/run-service
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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 9a7e2a24f5f3d261e554ac3815b7e2a4c2e24503
Merge: 40adb6fe8 e030e175b
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Wed Mar 27 09:41:37 2019 -0400
Merge branch '14669-java-sdk-v2' into 14670-new-java-sdk-docs
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
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