[ARVADOS] updated: 1.1.3-260-g53ce9b6
Git user
git at public.curoverse.com
Mon Mar 26 11:22:46 EDT 2018
Summary of changes:
apps/workbench/Gemfile | 19 +-
apps/workbench/Gemfile.lock | 270 +++++++++++----------
apps/workbench/app/models/container_work_unit.rb | 2 +-
.../pipeline_instances/_running_component.html.erb | 4 +-
.../views/work_units/_component_detail.html.erb | 2 +-
apps/workbench/config/application.default.yml | 2 +-
apps/workbench/config/initializers/mime_types.rb | 1 +
.../test/controllers/disabled_api_test.rb | 3 +
.../controllers/healthcheck_controller_test.rb | 3 +
.../test/integration/anonymous_access_test.rb | 6 +-
apps/workbench/test/test_helper.rb | 6 +-
build/build.list | 6 +-
.../package-testing/test-package-python-cwltest.sh | 1 +
.../test-package-python27-python-cwltest.sh | 4 +-
build/package-testing/test-packages-debian9.sh | 41 +---
build/run-build-packages-one-target.sh | 17 +-
build/run-build-packages.sh | 19 +-
build/run-tests.sh | 10 +-
doc/_config.yml | 1 +
doc/_includes/_tutorial_expectations.liquid | 2 +-
.../install-compute-node.html.textile.liquid | 2 +-
doc/install/migrate-docker19.html.textile.liquid | 2 +-
doc/sdk/python/arvados-fuse.html.textile.liquid | 64 +++++
doc/sdk/python/cookbook.html.textile.liquid | 42 ++++
doc/user/cwl/cwl-extensions.html.textile.liquid | 12 +-
.../tutorial-keep-mount.html.textile.liquid | 2 +-
lib/dispatchcloud/node_size.go | 43 ++--
sdk/cwl/arvados_cwl/__init__.py | 30 ++-
sdk/cwl/arvados_cwl/arv-cwl-schema.yml | 20 ++
sdk/cwl/arvados_cwl/arvcontainer.py | 56 ++++-
sdk/cwl/arvados_cwl/crunch_script.py | 1 +
sdk/cwl/arvados_cwl/runner.py | 5 +-
sdk/cwl/setup.py | 2 +-
sdk/cwl/tests/arvados-tests.yml | 12 +
sdk/cwl/tests/secret_test_job.yml | 1 +
sdk/cwl/tests/test_container.py | 135 ++++++++++-
sdk/cwl/tests/test_submit.py | 202 ++++++++++++++-
sdk/cwl/tests/wf/secret_job.cwl | 20 ++
sdk/cwl/tests/wf/secret_wf.cwl | 21 ++
sdk/go/arvados/keep_service.go | 34 ++-
sdk/python/arvados/__init__.py | 6 +-
sdk/python/arvados/collection.py | 6 +
sdk/python/arvados/commands/migrate19.py | 2 +-
sdk/python/arvados/commands/put.py | 35 ++-
sdk/python/tests/test_arv_put.py | 90 ++++++-
services/api/Gemfile | 10 +-
services/api/Gemfile.lock | 205 ++++++++--------
.../api/app/controllers/application_controller.rb | 3 +-
.../arvados/v1/container_requests_controller.rb | 1 +
.../arvados/v1/containers_controller.rb | 10 +
.../controllers/arvados/v1/schema_controller.rb | 2 +-
services/api/app/models/arvados_model.rb | 87 ++++---
services/api/app/models/blob.rb | 6 +-
services/api/app/models/commit.rb | 4 +-
services/api/app/models/container.rb | 91 +++++--
services/api/app/models/container_request.rb | 50 +++-
services/api/app/models/job.rb | 2 +-
services/api/config/initializers/lograge.rb | 12 +
services/api/config/routes.rb | 1 +
...180228220311_add_secret_mounts_to_containers.rb | 8 +
...80313180114_change_container_priority_bigint.rb | 5 +
services/api/db/structure.sql | 20 +-
.../request_error.rb} | 2 +-
services/api/test/fixtures/containers.yml | 27 +++
.../v1/container_requests_controller_test.rb | 74 +++++-
.../arvados/v1/containers_controller_test.rb | 22 +-
services/api/test/helpers/container_test_helper.rb | 15 ++
services/api/test/unit/container_request_test.rb | 235 +++++++++++++-----
services/api/test/unit/container_test.rb | 30 ++-
.../crunch-dispatch-slurm_test.go | 18 +-
services/crunch-dispatch-slurm/slurm.go | 9 +-
services/crunch-dispatch-slurm/squeue.go | 42 +++-
services/crunch-dispatch-slurm/squeue_test.go | 59 ++++-
services/crunch-run/crunchrun.go | 100 ++++++--
services/crunch-run/crunchrun_test.go | 161 +++++++++++-
services/crunch-run/logging_test.go | 9 +-
services/crunch-run/upload.go | 1 +
services/crunch-run/upload_test.go | 27 ++-
services/keep-balance/balance.go | 108 +++++++--
services/keep-balance/balance_run_test.go | 128 ++++++++--
services/keep-balance/balance_test.go | 48 +++-
services/keep-balance/block_state.go | 12 +-
services/keep-balance/keep_service.go | 26 ++
services/keepstore/azure_blob_volume.go | 2 +-
services/keepstore/handlers.go | 4 +-
services/keepstore/mounts_test.go | 10 +-
services/keepstore/pull_worker_test.go | 2 +-
services/keepstore/volume.go | 24 +-
services/nodemanager/arvnodeman/jobqueue.py | 4 +-
tools/arvbox/bin/arvbox | 4 +-
.../arvbox/lib/arvbox/docker/service/workbench/run | 4 +-
.../arvbox/docker/service/workbench/run-service | 3 +-
92 files changed, 2289 insertions(+), 702 deletions(-)
create mode 120000 build/package-testing/test-package-python-cwltest.sh
copy tools/arvbox/lib/arvbox/docker/logger => build/package-testing/test-package-python27-python-cwltest.sh (74%)
mode change 100755 => 120000 build/package-testing/test-packages-debian9.sh
create mode 100644 doc/sdk/python/arvados-fuse.html.textile.liquid
create mode 100644 sdk/cwl/tests/secret_test_job.yml
create mode 100644 sdk/cwl/tests/wf/secret_job.cwl
create mode 100644 sdk/cwl/tests/wf/secret_wf.cwl
create mode 100644 services/api/db/migrate/20180228220311_add_secret_mounts_to_containers.rb
create mode 100644 services/api/db/migrate/20180313180114_change_container_priority_bigint.rb
copy services/api/{app/helpers/commit_ancestors_helper.rb => lib/request_error.rb} (74%)
create mode 100644 services/api/test/helpers/container_test_helper.rb
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commit 53ce9b61336c5385eb2250267efa69613b5eaec7
Merge: add8af3 f728be2
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Mon Mar 26 17:07:07 2018 +0200
Merge branch 'master' of git.curoverse.com:arvados into 13076-r-autogen-api
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
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