[ARVADOS] updated: 50128b53da4003912635b03fb27b5be2c5beaca1
Git user
git at public.curoverse.com
Mon Nov 21 17:29:28 EST 2016
Summary of changes:
.gitignore | 3 +
.../app/controllers/application_controller.rb | 24 +-
.../app/controllers/collections_controller.rb | 13 +-
.../app/controllers/projects_controller.rb | 23 +-
.../controllers/work_unit_templates_controller.rb | 6 +-
.../app/controllers/work_units_controller.rb | 12 +-
apps/workbench/app/models/arvados_base.rb | 6 +-
.../app/views/projects/_show_workflows.html.erb | 5 +
.../test/controllers/disabled_api_test.rb | 63 ++++
.../test/integration/pipeline_instances_test.rb | 13 +-
apps/workbench/test/unit/disabled_api_test.rb | 15 +
build/run-build-docker-jobs-image.sh | 4 +-
build/run-build-packages.sh | 4 +-
build/run-tests.sh | 8 +-
doc/_config.yml | 83 +++--
.../_container_runtime_constraints.liquid | 1 +
doc/_includes/_crunch1only_begin.liquid | 2 +
doc/_includes/_crunch1only_end.liquid | 1 +
doc/_includes/_notebox_begin_warning.liquid | 2 +
doc/_includes/_pipeline_deprecation_notice.liquid | 2 +-
doc/_layouts/default.html.liquid | 2 +-
doc/api/authentication.html.textile.liquid | 40 ---
doc/api/crunch-scripts.html.textile.liquid | 5 +-
doc/api/execution.html.textile.liquid | 27 ++
doc/api/index.html.textile.liquid | 44 +--
doc/api/methods.html.textile.liquid | 120 +++----
.../api_client_authorizations.html.textile.liquid | 54 +++-
doc/api/methods/api_clients.html.textile.liquid | 40 ++-
.../methods/authorized_keys.html.textile.liquid | 43 ++-
doc/api/methods/collections.html.textile.liquid | 55 +++-
.../methods/container_requests.html.textile.liquid | 100 ++++--
doc/api/methods/containers.html.textile.liquid | 76 ++++-
doc/api/methods/groups.html.textile.liquid | 47 +--
doc/api/methods/humans.html.textile.liquid | 39 ++-
doc/api/methods/job_tasks.html.textile.liquid | 55 +++-
doc/api/methods/jobs.html.textile.liquid | 101 ++++--
doc/api/methods/keep_disks.html.textile.liquid | 52 ++-
doc/api/methods/keep_services.html.textile.liquid | 52 +--
doc/api/methods/links.html.textile.liquid | 69 ++--
doc/api/methods/logs.html.textile.liquid | 49 ++-
doc/api/methods/nodes.html.textile.liquid | 50 ++-
.../methods/pipeline_instances.html.textile.liquid | 44 ++-
.../methods/pipeline_templates.html.textile.liquid | 182 ++++++++++-
doc/api/methods/repositories.html.textile.liquid | 45 ++-
doc/api/methods/specimens.html.textile.liquid | 41 ++-
doc/api/methods/traits.html.textile.liquid | 40 ++-
doc/api/methods/users.html.textile.liquid | 67 ++--
.../methods/virtual_machines.html.textile.liquid | 52 +--
doc/api/methods/workflows.html.textile.liquid | 44 ++-
doc/api/permission-model.html.textile.liquid | 143 +++------
doc/api/requests.html.textile.liquid | 349 +++++++++++++++++++++
doc/api/resources.html.textile.liquid | 46 ++-
doc/api/schema/ApiClient.html.textile.liquid | 24 --
.../ApiClientAuthorization.html.textile.liquid | 29 --
doc/api/schema/AuthorizedKey.html.textile.liquid | 24 --
doc/api/schema/Collection.html.textile.liquid | 39 ---
doc/api/schema/Container.html.textile.liquid | 59 ----
.../schema/ContainerRequest.html.textile.liquid | 70 -----
doc/api/schema/Group.html.textile.liquid | 25 --
doc/api/schema/Human.html.textile.liquid | 19 --
doc/api/schema/Job.html.textile.liquid | 69 ----
doc/api/schema/JobTask.html.textile.liquid | 47 ---
doc/api/schema/KeepDisk.html.textile.liquid | 31 --
doc/api/schema/KeepService.html.textile.liquid | 24 --
doc/api/schema/Link.html.textile.liquid | 83 -----
doc/api/schema/Log.html.textile.liquid | 33 --
doc/api/schema/Node.html.textile.liquid | 28 --
.../schema/PipelineInstance.html.textile.liquid | 26 --
.../schema/PipelineTemplate.html.textile.liquid | 161 ----------
doc/api/schema/Repository.html.textile.liquid | 25 --
doc/api/schema/Specimen.html.textile.liquid | 22 --
doc/api/schema/Trait.html.textile.liquid | 22 --
doc/api/schema/User.html.textile.liquid | 30 --
doc/api/schema/VirtualMachine.html.textile.liquid | 21 --
doc/api/schema/Workflow.html.textile.liquid | 23 --
doc/api/storage.html.textile.liquid | 170 ++++++++++
doc/api/tokens.html.textile.liquid | 63 ++++
doc/images/Arvados_Permissions.svg | 4 +
doc/images/Crunch_dispatch.svg | 4 +
doc/images/Keep_manifests.svg | 4 +
doc/images/Keep_reading_writing_block.svg | 4 +
doc/images/Keep_rendezvous_hashing.svg | 4 +
doc/images/Session_Establishment.svg | 4 +
.../install-prerequisites.html.textile.liquid | 4 +-
doc/install/install-keep-web.html.textile.liquid | 2 +-
doc/install/install-keepproxy.html.textile.liquid | 2 +-
doc/sdk/cli/install.html.textile.liquid | 1 -
doc/sdk/go/example.html.textile.liquid | 76 +++++
doc/sdk/go/index.html.textile.liquid | 15 +-
doc/sdk/index.html.textile.liquid | 13 +-
doc/sdk/java/example.html.textile.liquid | 78 +++++
doc/sdk/java/index.html.textile.liquid | 11 +-
doc/sdk/perl/example.html.textile.liquid | 81 +++++
doc/sdk/perl/index.html.textile.liquid | 59 +---
doc/sdk/python/events.html.textile.liquid | 2 +-
doc/sdk/python/example.html.textile.liquid | 51 +++
doc/sdk/python/sdk-python.html.textile.liquid | 3 +-
doc/sdk/ruby/example.html.textile.liquid | 75 +++++
doc/sdk/ruby/index.html.textile.liquid | 74 +----
doc/user/cwl/cwl-runner.html.textile.liquid | 9 +-
.../reference/job-pipeline-ref.html.textile.liquid | 2 +-
doc/user/topics/arv-run.html.textile.liquid | 4 +
...nning-pipeline-command-line.html.textile.liquid | 4 +
.../running-external-program.html.textile.liquid | 4 +-
...tutorial-pipeline-workbench.html.textile.liquid | 4 +
.../tutorial-submit-job.html.textile.liquid | 4 +-
sdk/cli/bin/arv-run-pipeline-instance | 2 +
sdk/cli/bin/crunch-job | 6 +-
sdk/cwl/arvados_cwl/__init__.py | 175 +++++++----
sdk/cwl/arvados_cwl/arvcontainer.py | 28 +-
sdk/cwl/arvados_cwl/arvdocker.py | 26 +-
sdk/cwl/arvados_cwl/arvjob.py | 72 +++--
sdk/cwl/arvados_cwl/arvworkflow.py | 14 +-
sdk/cwl/arvados_cwl/crunch_script.py | 14 +-
sdk/cwl/arvados_cwl/pathmapper.py | 33 +-
sdk/cwl/arvados_cwl/runner.py | 28 +-
sdk/cwl/setup.py | 2 +-
sdk/cwl/test_with_arvbox.sh | 19 +-
sdk/cwl/tests/mock_discovery.py | 13 +
sdk/cwl/tests/test_container.py | 121 ++++---
sdk/cwl/tests/test_job.py | 117 ++++---
sdk/cwl/tests/test_make_output.py | 21 +-
sdk/cwl/tests/test_pathmapper.py | 3 +-
sdk/cwl/tests/test_submit.py | 273 ++++++++++++++--
sdk/go/arvados/container.go | 39 ++-
sdk/python/arvados/events.py | 77 +++--
.../arvados/v1/collections_controller.rb | 2 +-
.../arvados/v1/container_requests_controller.rb | 1 +
.../arvados/v1/containers_controller.rb | 1 +
.../controllers/arvados/v1/groups_controller.rb | 13 +
services/api/app/models/arvados_model.rb | 2 +-
services/api/app/models/container.rb | 11 +-
services/api/app/models/container_request.rb | 47 ++-
services/api/app/models/log.rb | 2 +-
services/api/app/models/node.rb | 30 +-
services/api/config/application.default.yml | 3 +
...43147_add_scheduling_parameters_to_container.rb | 6 +
...add_output_and_log_uuid_to_container_request.rb | 22 ++
..._log_uuids_to_container_request_search_index.rb | 21 ++
services/api/db/structure.sql | 18 +-
services/api/test/fixtures/nodes.yml | 6 +-
.../arvados/v1/collections_controller_test.rb | 43 +++
.../v1/container_requests_controller_test.rb | 22 ++
services/api/test/unit/container_request_test.rb | 77 ++++-
services/api/test/unit/log_test.rb | 10 +-
services/api/test/unit/node_test.rb | 27 ++
services/arv-git-httpd/main.go | 2 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 6 +-
.../crunch-dispatch-slurm_test.go | 2 +-
services/crunch-run/crunchrun.go | 5 +
services/crunch-run/crunchrun_test.go | 22 ++
services/fuse/arvados_fuse/__init__.py | 7 +-
services/keep-web/main.go | 2 +-
services/keepproxy/keepproxy.go | 2 +-
services/keepstore/azure_blob_volume.go | 22 +-
services/keepstore/azure_blob_volume_test.go | 11 +-
services/keepstore/collision.go | 16 +-
services/keepstore/config.go | 9 +
services/keepstore/config_test.go | 9 +
services/keepstore/count.go | 44 +++
services/keepstore/handler_test.go | 25 +-
services/keepstore/handlers.go | 139 +++++---
.../keepstore/handlers_with_generic_volume_test.go | 15 +-
services/keepstore/keepstore.go | 5 +-
services/keepstore/keepstore_test.go | 49 +--
services/keepstore/pull_worker.go | 3 +-
services/keepstore/s3_volume.go | 297 +++++++++++++++---
services/keepstore/s3_volume_test.go | 39 ++-
services/keepstore/trash_worker_test.go | 19 +-
services/keepstore/volume.go | 52 ++-
services/keepstore/volume_generic_test.go | 87 ++---
services/keepstore/volume_test.go | 7 +-
services/keepstore/volume_unix.go | 30 +-
services/keepstore/volume_unix_test.go | 37 +--
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 48 ++-
tools/arvbox/lib/arvbox/docker/common.sh | 6 +-
tools/arvbox/lib/arvbox/docker/crunch-setup.sh | 1 +
.../lib/arvbox/docker/service/ready/run-service | 4 +-
tools/keep-exercise/keep-exercise.go | 19 +-
179 files changed, 4222 insertions(+), 2498 deletions(-)
create mode 100644 apps/workbench/app/views/projects/_show_workflows.html.erb
create mode 100644 apps/workbench/test/controllers/disabled_api_test.rb
create mode 100644 apps/workbench/test/unit/disabled_api_test.rb
create mode 100644 doc/_includes/_crunch1only_begin.liquid
create mode 100644 doc/_includes/_crunch1only_end.liquid
create mode 100644 doc/_includes/_notebox_begin_warning.liquid
delete mode 100644 doc/api/authentication.html.textile.liquid
create mode 100644 doc/api/execution.html.textile.liquid
create mode 100644 doc/api/requests.html.textile.liquid
delete mode 100644 doc/api/schema/ApiClient.html.textile.liquid
delete mode 100644 doc/api/schema/ApiClientAuthorization.html.textile.liquid
delete mode 100644 doc/api/schema/AuthorizedKey.html.textile.liquid
delete mode 100644 doc/api/schema/Collection.html.textile.liquid
delete mode 100644 doc/api/schema/Container.html.textile.liquid
delete mode 100644 doc/api/schema/ContainerRequest.html.textile.liquid
delete mode 100644 doc/api/schema/Group.html.textile.liquid
delete mode 100644 doc/api/schema/Human.html.textile.liquid
delete mode 100644 doc/api/schema/Job.html.textile.liquid
delete mode 100644 doc/api/schema/JobTask.html.textile.liquid
delete mode 100644 doc/api/schema/KeepDisk.html.textile.liquid
delete mode 100644 doc/api/schema/KeepService.html.textile.liquid
delete mode 100644 doc/api/schema/Link.html.textile.liquid
delete mode 100644 doc/api/schema/Log.html.textile.liquid
delete mode 100644 doc/api/schema/Node.html.textile.liquid
delete mode 100644 doc/api/schema/PipelineInstance.html.textile.liquid
delete mode 100644 doc/api/schema/PipelineTemplate.html.textile.liquid
delete mode 100644 doc/api/schema/Repository.html.textile.liquid
delete mode 100644 doc/api/schema/Specimen.html.textile.liquid
delete mode 100644 doc/api/schema/Trait.html.textile.liquid
delete mode 100644 doc/api/schema/User.html.textile.liquid
delete mode 100644 doc/api/schema/VirtualMachine.html.textile.liquid
delete mode 100644 doc/api/schema/Workflow.html.textile.liquid
create mode 100644 doc/api/storage.html.textile.liquid
create mode 100644 doc/api/tokens.html.textile.liquid
create mode 100644 doc/images/Arvados_Permissions.svg
create mode 100644 doc/images/Crunch_dispatch.svg
create mode 100644 doc/images/Keep_manifests.svg
create mode 100644 doc/images/Keep_reading_writing_block.svg
create mode 100644 doc/images/Keep_rendezvous_hashing.svg
create mode 100644 doc/images/Session_Establishment.svg
create mode 100644 doc/sdk/go/example.html.textile.liquid
create mode 100644 doc/sdk/java/example.html.textile.liquid
create mode 100644 doc/sdk/perl/example.html.textile.liquid
create mode 100644 doc/sdk/python/example.html.textile.liquid
create mode 100644 doc/sdk/ruby/example.html.textile.liquid
create mode 100644 sdk/cwl/tests/mock_discovery.py
create mode 100644 services/api/db/migrate/20161111143147_add_scheduling_parameters_to_container.rb
create mode 100644 services/api/db/migrate/20161115171221_add_output_and_log_uuid_to_container_request.rb
create mode 100644 services/api/db/migrate/20161115174218_add_output_and_log_uuids_to_container_request_search_index.rb
create mode 100644 services/api/test/functional/arvados/v1/container_requests_controller_test.rb
create mode 100644 services/keepstore/config_test.go
create mode 100644 services/keepstore/count.go
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commit 50128b53da4003912635b03fb27b5be2c5beaca1
Merge: 0d2d039 e5fd39a
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Mon Nov 21 19:28:14 2016 -0300
10383: Merge branch 'master' into 10383-arv-put-incremental-upload
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