[ARVADOS] updated: 1.3.0-571-g215d15bc0

[Git user]

Summary of changes:
 .../controllers/container_requests_controller.rb   |   2 +-
 apps/workbench/app/helpers/application_helper.rb   |  11 +-
 build/run-library.sh                               |  11 +-
 build/run-tests.sh                                 | 645 +++++++++++++--------
 .../{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/dispatchcloud/container/queue.go               |  45 +-
 lib/dispatchcloud/dispatcher_test.go               |  20 +-
 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              |  96 ++-
 lib/dispatchcloud/worker/pool.go                   |  87 ++-
 lib/dispatchcloud/worker/runner.go                 | 154 +++++
 lib/dispatchcloud/worker/worker.go                 | 211 ++++---
 lib/dispatchcloud/worker/worker_test.go            |   9 +-
 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/config.go                           |   6 +
 sdk/ruby/arvados.gemspec                           |   2 +-
 services/api/test/integration/groups_test.rb       |  30 +-
 services/crunch-run/background.go                  |   7 +
 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 +
 42 files changed, 1347 insertions(+), 552 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
 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

       via  215d15bc03a38be1965a5d9df21417a3f7eae032 (commit)
       via  a07891c7ac7e90ebdf35ae1812ec03c818fe2a67 (commit)
       via  1c21d98f48d42c453fb8ac2f9869d0240a437d1d (commit)
       via  dbbc5a9078c0fe88160729f3ca8f56673397b106 (commit)
       via  51b136d8f7937b7f16aa8457a6b97c9b0e63d388 (commit)
       via  aed47afc7647f24af6541ff03a0cc0649a5358ee (commit)
       via  c9baf35106d64d8b26741256c145616bfbea9645 (commit)
       via  8c0178f2ff01a284ac4bebbc664b9fb7f64cdc38 (commit)
       via  2e1e5442ae846a026c5de7edb0dd78e09c56b5a7 (commit)
       via  e6f350e56674e3f19d24755b94a22e59cf8478b6 (commit)
       via  b286e013ab8ccc64d06ee107c155a03696fddeed (commit)
       via  41365ac598721e31fc88c462934e0a06cafe2aae (commit)
       via  3384d541acca51c346f8ebfe08b0dc93a33936ff (commit)
       via  19ab7c19fcd56b05ff2d06f7fb4b66a515c90f4b (commit)
       via  1a3075e05722b396b54f61a86348731ce1e0f55f (commit)
       via  96f73954851d44ab715fa0b34861a93c00aa0519 (commit)
       via  c04d16f1482d10d64ddcceba4dcc7ab06032f033 (commit)
       via  90bb5de474c45e0b786f387ecab2277b593e335d (commit)
       via  4013f2bd35cf76d92aeafc4d3b0b4e2fd7a2dd84 (commit)
       via  cd020c016106fbe844501c5f434c16f4def4e08d (commit)
       via  8d660b2b276475f1bd5b56614a28a33a358dd038 (commit)
       via  d924d8bf8b08a009e6fe2c75cf97b8d27ebb6089 (commit)
       via  1c6c860b90c54f1c257ef2016f725176d9cf50c6 (commit)
       via  6582c5afa53258fcb36d682fb690203930b7b2f6 (commit)
       via  2a748e79c3a72454d70e40f39fcad9dabf4943cc (commit)
       via  b268e5520ceed74300b01cc80857e020a8e4ba05 (commit)
       via  db439331ed1888868e97e18a253257c8b40567da (commit)
       via  45974ce224baf26d0a4c445dd1e9322193f1f64f (commit)
       via  1eb77b5c90ea52a516c3b38b7316425f6d7cf4fd (commit)
       via  ca521bb33e933aa097e855897ec960fc72e4d497 (commit)
       via  3ccaff49c9da5721d7ae5fc6c41ae91413f797c4 (commit)
       via  6844ff128e34898eae1a2cc513d8a0bfa4aed545 (commit)
       via  a2bfb6d9f3d9e8675a644e9cc9a1bbcdc79f71e6 (commit)
       via  1ea2e3c4125cf9340e8fde52f338fa814f46c0b6 (commit)
       via  9ecc3c378f694f9bd222c1efd6b75104affdb6e7 (commit)
       via  069f4a9236364c6a3f3e4b022bbd3266de6abda9 (commit)
       via  360ba4426a6074f394abe107a7989acf580c1947 (commit)
       via  58b12d248ed05f8b75b16cee33b0e153e7be71f6 (commit)
       via  35a42c13bc91d5b3cfa8dfb53a0d51fc2c3def82 (commit)
       via  9e8d0cd4d5663e1901a2553babe3910bf0a12896 (commit)
       via  233e184eaf40febfbc9b083bdfdd45a438cc350f (commit)
       via  0be3e2c040d8d785bbd5c3e8d9de62c0fbaee0ec (commit)
       via  dc71f08c4a78e6e53a4da6f88fd054a9e39600ad (commit)
       via  af4ff20376a0b8b39f6120b4d9662449164a501f (commit)
       via  0145b3654f3af993b03719996385dedd2e803c08 (commit)
       via  0e9aa62c7865f092917d3d46b0de4a3dd453b672 (commit)
      from  fb8c51a195f2d9603cb129d8c3a21dc5d700aab3 (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 215d15bc03a38be1965a5d9df21417a3f7eae032
Merge: fb8c51a19 a07891c7a
Author: Eric Biagiotti <ebiagiotti at veritasgenetics.com>
Date:   Thu Mar 21 14:03:16 2019 -0400

    Merge remote-tracking branch 'origin/master' into 14645-fuse-operations-reporting
    
    refs #14645
    
    Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti at veritasgenetics.com>


-----------------------------------------------------------------------


hooks/post-receive
--