[ARVADOS] updated: 2.1.0-248-g045e3127c
Git user
git at public.arvados.org
Wed Jan 6 14:52:46 UTC 2021
Summary of changes:
.gitignore | 2 +
.licenseignore | 4 +
CONTRIBUTING.md | 2 +-
.../app/controllers/application_controller.rb | 2 +-
.../controllers/container_requests_controller.rb | 63 ++-
.../app/controllers/trash_items_controller.rb | 12 +-
apps/workbench/app/controllers/users_controller.rb | 12 +
.../app/controllers/work_units_controller.rb | 1 +
apps/workbench/app/helpers/application_helper.rb | 5 +
apps/workbench/app/models/container_request.rb | 24 +
apps/workbench/app/models/user.rb | 2 +-
.../_extra_tab_line_buttons.html.erb | 47 +-
.../views/container_requests/_show_inputs.html.erb | 18 +-
apps/workbench/app/views/users/profile.html.erb | 21 +-
.../container_requests_controller_test.rb | 23 +-
apps/workbench/test/integration/work_units_test.rb | 4 +-
build/README | 4 +-
build/build-dev-docker-jobs-image.sh | 12 +-
build/package-build-dockerfiles/Makefile | 19 +-
build/package-build-dockerfiles/centos7/Dockerfile | 12 +-
.../{debian9 => ubuntu2004}/Dockerfile | 7 +-
build/package-test-dockerfiles/Makefile | 18 +-
.../{debian9 => ubuntu2004}/Dockerfile | 6 +-
...age-rh-python36-python-arvados-python-client.sh | 2 +-
...ges-debian10.sh => test-packages-ubuntu2004.sh} | 0
build/rails-package-scripts/README.md | 4 +-
build/rails-package-scripts/arvados-sso-server.sh | 13 -
build/rails-package-scripts/postinst.sh | 9 +-
build/run-build-docker-images.sh | 65 ++-
build/run-build-docker-jobs-image.sh | 55 +-
build/run-build-packages-one-target.sh | 15 +-
build/run-build-packages-python-and-ruby.sh | 13 +-
build/run-build-packages-sso.sh | 158 ------
build/run-build-packages.sh | 9 +-
build/run-library.sh | 67 +--
build/version-at-commit.sh | 5 +-
cmd/arvados-client/cmd.go | 2 +
doc/Gemfile | 2 +-
doc/Gemfile.lock | 2 +-
doc/_config.yml | 9 +
doc/_includes/_compute_ping_rb.liquid | 290 -----------
doc/_includes/_example_sdk_go.liquid | 8 +-
doc/_includes/_install_ruby_and_bundler.liquid | 14 +-
doc/_includes/_tutorial_hello_cwl.liquid | 7 +-
doc/admin/config.html.textile.liquid | 2 +-
doc/admin/federation.html.textile.liquid | 4 +-
doc/admin/upgrading.html.textile.liquid | 20 +-
doc/admin/user-activity.html.textile.liquid | 101 ++++
doc/api/keep-s3.html.textile.liquid | 89 ++++
doc/api/keep-web-urls.html.textile.liquid | 75 +++
doc/api/keep-webdav.html.textile.liquid | 103 ++++
doc/api/methods.html.textile.liquid | 6 +-
doc/api/methods/collections.html.textile.liquid | 2 +-
doc/api/methods/groups.html.textile.liquid | 2 +
doc/api/methods/jobs.html.textile.liquid | 16 +-
.../methods/pipeline_templates.html.textile.liquid | 16 +-
.../arvados-on-kubernetes-GKE.html.textile.liquid | 8 -
...ados-on-kubernetes-minikube.html.textile.liquid | 6 +-
.../arvados-on-kubernetes.html.textile.liquid | 4 -
doc/install/arvbox.html.textile.liquid | 19 +-
.../install-dispatch.html.textile.liquid | 2 +-
doc/install/index.html.textile.liquid | 6 +-
doc/install/install-api-server.html.textile.liquid | 19 +-
.../install-compute-ping.html.textile.liquid | 14 -
doc/install/install-keep-web.html.textile.liquid | 4 +-
...nstall-manual-prerequisites.html.textile.liquid | 4 +-
doc/install/install-postgresql.html.textile.liquid | 10 +-
doc/install/new_cluster_checklist_AWS.xlsx | Bin 5647 -> 5712 bytes
doc/install/new_cluster_checklist_Azure.xlsx | Bin 5666 -> 5748 bytes
doc/install/new_cluster_checklist_slurm.xlsx | Bin 5645 -> 5669 bytes
doc/install/packages.html.textile.liquid | 7 +-
doc/install/salt-multi-host.html.textile.liquid | 110 ++++
doc/install/salt-single-host.html.textile.liquid | 215 ++++++++
doc/install/salt-vagrant.html.textile.liquid | 127 +++++
doc/install/salt.html.textile.liquid | 29 ++
doc/sdk/cli/install.html.textile.liquid | 2 +-
doc/sdk/cli/reference.html.textile.liquid | 2 +
doc/sdk/go/example.html.textile.liquid | 4 +-
.../python/arvados-cwl-runner.html.textile.liquid | 8 +-
doc/sdk/python/arvados-fuse.html.textile.liquid | 10 +-
doc/sdk/python/cookbook.html.textile.liquid | 31 ++
doc/sdk/python/sdk-python.html.textile.liquid | 10 +-
doc/sdk/ruby/index.html.textile.liquid | 2 +-
doc/user/composer/composer.html.textile.liquid | 2 +-
doc/user/cwl/cwl-extensions.html.textile.liquid | 2 +-
.../git-arvados-guide.html.textile.liquid | 2 +-
.../tutorials/wgs-tutorial.html.textile.liquid | 4 +-
doc/zenweb-liquid.rb | 14 +-
docker/jobs/Dockerfile | 2 +-
docker/jobs/apt.arvados.org-dev.list | 2 +-
docker/jobs/apt.arvados.org-stable.list | 2 +-
docker/jobs/apt.arvados.org-testing.list | 2 +-
docker/migrate-docker19/Dockerfile | 2 +-
lib/boot/postgresql.go | 4 +-
lib/boot/supervisor.go | 9 +-
lib/cloud/ec2/ec2.go | 6 +-
lib/cmd/cmd.go | 2 +-
lib/config/cmd_test.go | 6 +-
lib/config/config.default.yml | 7 +-
lib/config/deprecated_test.go | 18 +-
lib/config/export.go | 1 -
lib/config/generated_config.go | 7 +-
lib/config/load.go | 18 +
lib/config/load_test.go | 41 +-
lib/controller/api/routable.go | 13 +
lib/controller/auth_test.go | 126 +++++
lib/controller/fed_collections.go | 12 +-
lib/controller/fed_containers.go | 12 +-
lib/controller/fed_generic.go | 34 +-
lib/controller/federation.go | 13 +-
lib/controller/federation/conn.go | 21 +-
lib/controller/federation_test.go | 4 +-
lib/controller/handler.go | 7 +-
lib/controller/integration_test.go | 158 ++++++
lib/controller/localdb/login_oidc.go | 201 +++++++-
lib/controller/localdb/login_oidc_test.go | 224 ++------
lib/controller/localdb/login_testuser.go | 2 +-
lib/controller/railsproxy/railsproxy.go | 3 +-
lib/controller/rpc/conn_test.go | 6 +-
.../command.go => costanalyzer/cmd.go} | 8 +-
lib/costanalyzer/costanalyzer.go | 568 +++++++++++++++++++++
lib/costanalyzer/costanalyzer_test.go | 325 ++++++++++++
lib/crunchrun/background.go | 4 +-
lib/crunchrun/crunchrun.go | 76 +--
lib/crunchrun/crunchrun_test.go | 32 +-
lib/crunchrun/logging.go | 2 +-
lib/crunchrun/logging_test.go | 6 +-
lib/ctrlctx/db.go | 1 +
lib/dispatchcloud/container/queue.go | 6 +-
lib/dispatchcloud/test/ssh_service.go | 2 +
lib/install/deps.go | 8 +-
lib/mount/command.go | 1 +
lib/service/cmd.go | 4 +-
lib/service/cmd_test.go | 9 +-
lib/service/tls.go | 2 +-
sdk/R/R/Collection.R | 3 +-
sdk/R/README.Rmd | 20 +-
sdk/cli/arvados-cli.gemspec | 3 +-
sdk/cwl/arvados_cwl/__init__.py | 2 +-
sdk/cwl/arvados_cwl/arvcontainer.py | 7 +-
sdk/cwl/arvados_cwl/arvdocker.py | 6 +-
sdk/cwl/arvados_cwl/arvworkflow.py | 2 +-
sdk/cwl/arvados_cwl/executor.py | 2 +-
sdk/cwl/arvados_cwl/pathmapper.py | 4 +-
sdk/cwl/arvados_cwl/runner.py | 21 +-
sdk/cwl/arvados_cwl/task_queue.py | 77 ---
sdk/cwl/arvados_version.py | 43 +-
sdk/cwl/fpm-info.sh | 2 +-
sdk/cwl/gittaggers.py | 48 --
sdk/cwl/setup.py | 2 +-
sdk/cwl/test_with_arvbox.sh | 6 +-
sdk/cwl/tests/federation/arvboxcwl/fed-config.cwl | 3 +-
sdk/cwl/tests/federation/arvboxcwl/start.cwl | 2 +-
sdk/cwl/tests/test_submit.py | 42 +-
sdk/cwl/tests/test_tq.py | 2 +-
sdk/cwl/tests/tool/submit_tool.cwl | 2 +-
sdk/cwl/tests/tool/tool_with_sf.cwl | 2 +-
sdk/cwl/tests/wf/16169-step.cwl | 2 +-
sdk/cwl/tests/wf/expect_arvworkflow.cwl | 2 +-
sdk/cwl/tests/wf/expect_packed.cwl | 2 +-
sdk/cwl/tests/wf/expect_upload_packed.cwl | 2 +-
sdk/cwl/tests/wf/secret_wf.cwl | 2 +-
sdk/cwl/tests/wf/submit_wf_packed.cwl | 2 +-
sdk/dev-jobs.dockerfile | 4 +-
sdk/go/arvados/client.go | 7 +-
sdk/go/arvados/config.go | 9 +-
sdk/go/arvados/container.go | 4 +-
sdk/go/arvados/fs_collection.go | 9 +-
sdk/go/arvados/link.go | 2 +-
sdk/go/arvadosclient/arvadosclient.go | 34 +-
sdk/go/arvadostest/api.go | 80 +--
sdk/go/arvadostest/db.go | 1 +
sdk/go/arvadostest/fixtures.go | 25 +-
sdk/go/arvadostest/oidc_provider.go | 174 +++++++
sdk/go/auth/auth.go | 2 +-
sdk/go/blockdigest/blockdigest.go | 6 +-
sdk/go/blockdigest/blockdigest_test.go | 4 +-
sdk/go/blockdigest/testing.go | 2 +-
sdk/go/keepclient/hashcheck.go | 32 +-
sdk/go/keepclient/keepclient.go | 37 +-
sdk/go/keepclient/keepclient_test.go | 50 +-
sdk/go/keepclient/root_sorter_test.go | 14 +-
sdk/go/keepclient/support.go | 72 +--
sdk/go/manifest/manifest.go | 70 +--
sdk/python/README.rst | 4 +-
sdk/python/arvados/api.py | 4 +
sdk/python/arvados/keep.py | 6 +-
sdk/python/arvados/util.py | 61 +++
sdk/python/arvados_version.py | 39 +-
sdk/python/gittaggers.py | 29 --
sdk/python/tests/fed-migrate/README | 4 +-
sdk/python/tests/fed-migrate/fed-migrate.cwl | 6 +-
sdk/python/tests/fed-migrate/fed-migrate.cwlex | 6 +-
sdk/python/tests/fed-migrate/superuser-tok.cwl | 2 +-
sdk/python/tests/run_test_server.py | 16 +-
sdk/python/tests/test_util.py | 137 +++++
sdk/ruby/arvados.gemspec | 3 +-
sdk/ruby/lib/arvados.rb | 33 +-
.../api/app/controllers/application_controller.rb | 6 +-
.../v1/api_client_authorizations_controller.rb | 8 +-
.../arvados/v1/collections_controller.rb | 40 +-
.../arvados/v1/container_requests_controller.rb | 4 +-
.../controllers/arvados/v1/groups_controller.rb | 25 +-
.../app/controllers/arvados/v1/jobs_controller.rb | 8 +-
.../controllers/arvados/v1/schema_controller.rb | 2 +-
.../app/controllers/arvados/v1/users_controller.rb | 26 +-
services/api/app/middlewares/arvados_api_token.rb | 2 +-
.../api/app/models/api_client_authorization.rb | 244 +++++----
services/api/app/models/arvados_model.rb | 65 ++-
services/api/app/models/collection.rb | 23 +-
services/api/app/models/link.rb | 2 +
services/api/app/models/user.rb | 98 ++--
services/api/config/arvados_config.rb | 7 +-
.../20201103170213_refresh_trashed_groups.rb | 17 +
.../migrate/20201105190435_refresh_permissions.rb | 15 +
...02174753_fix_collection_versions_timestamps.rb} | 8 +-
services/api/db/structure.sql | 19 +-
.../20200501150153_permission_table_constants.rb | 2 +-
services/api/lib/create_superuser_token.rb | 2 +-
services/api/lib/current_api_client.rb | 3 +
.../api/lib/fix_collection_versions_timestamps.rb | 43 ++
services/api/lib/update_permissions.rb | 10 +-
services/api/script/rails | 2 +-
services/api/test/fixtures/collections.yml | 104 +++-
services/api/test/fixtures/container_requests.yml | 234 ++++++++-
services/api/test/fixtures/containers.yml | 147 ++++++
.../arvados/v1/collections_controller_test.rb | 2 +-
.../arvados/v1/groups_controller_test.rb | 39 +-
.../arvados/v1/schema_controller_test.rb | 2 +-
.../api/test/integration/collections_api_test.rb | 78 +++
services/api/test/integration/remote_user_test.rb | 57 ++-
services/api/test/test_helper.rb | 1 +
services/api/test/unit/collection_test.rb | 76 ++-
.../api/test/unit/create_superuser_token_test.rb | 27 +-
services/api/test/unit/log_test.rb | 14 +
services/api/test/unit/user_test.rb | 5 +-
.../crunch-dispatch-local.service} | 8 +-
.../fpm-info.sh} | 3 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 2 +-
services/dockercleaner/arvados_version.py | 35 +-
services/dockercleaner/fpm-info.sh | 2 +-
services/dockercleaner/gittaggers.py | 1 -
services/fuse/README.rst | 2 +-
services/fuse/arvados_version.py | 39 +-
services/fuse/gittaggers.py | 1 -
services/keep-web/cache.go | 8 +-
services/keep-web/doc.go | 156 +-----
services/keep-web/handler.go | 59 ++-
services/keep-web/handler_test.go | 35 +-
services/keep-web/s3.go | 297 +++++++++--
services/keep-web/s3_test.go | 248 ++++++++-
services/keep-web/s3aws_test.go | 77 +++
services/keep-web/server_test.go | 19 +-
services/keepproxy/keepproxy.go | 77 +--
services/keepstore/keepstore.go | 4 +-
services/login-sync/arvados-login-sync.gemspec | 3 +-
services/ws/doc.go | 2 +-
tools/arvbox/bin/arvbox | 6 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 2 +
tools/arvbox/lib/arvbox/docker/Dockerfile.demo | 11 +
tools/arvbox/lib/arvbox/docker/api-setup.sh | 6 +-
tools/arvbox/lib/arvbox/docker/cluster-config.sh | 4 +-
tools/arvbox/lib/arvbox/docker/common.sh | 1 +
tools/arvbox/lib/arvbox/docker/go-setup.sh | 17 +-
tools/arvbox/lib/arvbox/docker/keep-setup.sh | 38 +-
tools/arvbox/lib/arvbox/docker/runsu.sh | 3 +
.../lib/arvbox/docker/service/api/run-service | 6 +-
.../lib/arvbox/docker/service/doc/run-service | 7 +-
.../lib/arvbox/docker/service/gitolite/run-service | 8 +-
.../arvbox/docker/service/keepproxy/run-service | 23 -
tools/arvbox/lib/arvbox/docker/service/nginx/run | 14 +
.../lib/arvbox/docker/service/vm/run-service | 6 +
.../arvbox/docker/service/workbench/run-service | 36 +-
.../arvbox/docker/service/workbench2/run-service | 6 +
tools/compute-images/scripts/base.sh | 2 +-
tools/crunchstat-summary/arvados_version.py | 39 +-
tools/crunchstat-summary/gittaggers.py | 1 -
tools/salt-install/README.md | 20 +
tools/salt-install/Vagrantfile | 42 ++
tools/salt-install/provision.sh | 285 +++++++++++
tools/salt-install/single_host/arvados.sls | 159 ++++++
.../salt-install/single_host/docker.sls | 7 +-
tools/salt-install/single_host/locale.sls | 14 +
.../single_host/nginx_api_configuration.sls | 28 +
.../single_host/nginx_controller_configuration.sls | 58 +++
.../single_host/nginx_keepproxy_configuration.sls | 57 +++
.../single_host/nginx_keepweb_configuration.sls | 57 +++
tools/salt-install/single_host/nginx_passenger.sls | 24 +
.../single_host/nginx_webshell_configuration.sls | 74 +++
.../single_host/nginx_websocket_configuration.sls | 58 +++
.../single_host/nginx_workbench2_configuration.sls | 48 ++
.../single_host/nginx_workbench_configuration.sls | 73 +++
tools/salt-install/single_host/postgresql.sls | 42 ++
tools/salt-install/tests/hasher-workflow-job.yml | 10 +
tools/salt-install/tests/hasher-workflow.cwl | 65 +++
.../salt-install/tests/hasher.cwl | 25 +-
tools/salt-install/tests/run-test.sh | 68 +++
.../salt-install/tests/test.txt | 2 +-
tools/sync-groups/sync-groups.go | 10 +-
tools/sync-groups/sync-groups_test.go | 8 -
{services/fuse => tools/user-activity}/MANIFEST.in | 1 -
tools/user-activity/README.rst | 5 +
agpl-3.0.txt => tools/user-activity/agpl-3.0.txt | 0
.../arvados_user_activity/__init__.py | 2 -
tools/user-activity/arvados_user_activity/main.py | 152 ++++++
tools/user-activity/arvados_version.py | 58 +++
.../user-activity/bin/arv-user-activity | 5 +-
.../fpm-info.sh | 0
.../{crunchstat-summary => user-activity}/setup.py | 25 +-
309 files changed, 7281 insertions(+), 2484 deletions(-)
rename build/package-build-dockerfiles/{debian9 => ubuntu2004}/Dockerfile (81%)
rename build/package-test-dockerfiles/{debian9 => ubuntu2004}/Dockerfile (87%)
copy build/package-testing/{test-packages-debian10.sh => test-packages-ubuntu2004.sh} (100%)
delete mode 100644 build/rails-package-scripts/arvados-sso-server.sh
delete mode 100755 build/run-build-packages-sso.sh
delete mode 100644 doc/_includes/_compute_ping_rb.liquid
create mode 100644 doc/admin/user-activity.html.textile.liquid
create mode 100644 doc/api/keep-s3.html.textile.liquid
create mode 100644 doc/api/keep-web-urls.html.textile.liquid
create mode 100644 doc/api/keep-webdav.html.textile.liquid
delete mode 100644 doc/install/install-compute-ping.html.textile.liquid
create mode 100644 doc/install/salt-multi-host.html.textile.liquid
create mode 100644 doc/install/salt-single-host.html.textile.liquid
create mode 100644 doc/install/salt-vagrant.html.textile.liquid
create mode 100644 doc/install/salt.html.textile.liquid
create mode 100644 lib/controller/auth_test.go
copy lib/{deduplicationreport/command.go => costanalyzer/cmd.go} (77%)
create mode 100644 lib/costanalyzer/costanalyzer.go
create mode 100644 lib/costanalyzer/costanalyzer_test.go
delete mode 100644 sdk/cwl/arvados_cwl/task_queue.py
delete mode 100644 sdk/cwl/gittaggers.py
create mode 100644 sdk/go/arvadostest/oidc_provider.go
delete mode 100644 sdk/python/gittaggers.py
create mode 100644 services/api/db/migrate/20201103170213_refresh_trashed_groups.rb
create mode 100644 services/api/db/migrate/20201105190435_refresh_permissions.rb
copy services/api/db/migrate/{20200602141328_fix_roles_projects.rb => 20201202174753_fix_collection_versions_timestamps.rb} (53%)
create mode 100644 services/api/lib/fix_collection_versions_timestamps.rb
copy services/{crunch-dispatch-slurm/crunch-dispatch-slurm.service => crunch-dispatch-local/crunch-dispatch-local.service} (73%)
copy services/{api/app/helpers/jobs_helper.rb => crunch-dispatch-local/fpm-info.sh} (78%)
delete mode 120000 services/dockercleaner/gittaggers.py
delete mode 120000 services/fuse/gittaggers.py
create mode 100644 services/keep-web/s3aws_test.go
delete mode 120000 tools/crunchstat-summary/gittaggers.py
create mode 100644 tools/salt-install/README.md
create mode 100644 tools/salt-install/Vagrantfile
create mode 100755 tools/salt-install/provision.sh
create mode 100644 tools/salt-install/single_host/arvados.sls
copy apps/workbench/app/controllers/keep_services_controller.rb => tools/salt-install/single_host/docker.sls (62%)
create mode 100644 tools/salt-install/single_host/locale.sls
create mode 100644 tools/salt-install/single_host/nginx_api_configuration.sls
create mode 100644 tools/salt-install/single_host/nginx_controller_configuration.sls
create mode 100644 tools/salt-install/single_host/nginx_keepproxy_configuration.sls
create mode 100644 tools/salt-install/single_host/nginx_keepweb_configuration.sls
create mode 100644 tools/salt-install/single_host/nginx_passenger.sls
create mode 100644 tools/salt-install/single_host/nginx_webshell_configuration.sls
create mode 100644 tools/salt-install/single_host/nginx_websocket_configuration.sls
create mode 100644 tools/salt-install/single_host/nginx_workbench2_configuration.sls
create mode 100644 tools/salt-install/single_host/nginx_workbench_configuration.sls
create mode 100644 tools/salt-install/single_host/postgresql.sls
create mode 100644 tools/salt-install/tests/hasher-workflow-job.yml
create mode 100644 tools/salt-install/tests/hasher-workflow.cwl
copy sdk/cwl/tests/stdout.cwl => tools/salt-install/tests/hasher.cwl (50%)
create mode 100755 tools/salt-install/tests/run-test.sh
copy sdk/cwl/tests/__init__.py => tools/salt-install/tests/test.txt (95%)
copy {services/fuse => tools/user-activity}/MANIFEST.in (72%)
create mode 100644 tools/user-activity/README.rst
copy agpl-3.0.txt => tools/user-activity/agpl-3.0.txt (100%)
copy services/api/config/initializers/andand.rb => tools/user-activity/arvados_user_activity/__init__.py (84%)
create mode 100755 tools/user-activity/arvados_user_activity/main.py
create mode 100644 tools/user-activity/arvados_version.py
copy services/dockercleaner/tests/__init__.py => tools/user-activity/bin/arv-user-activity (63%)
mode change 100644 => 100755
copy tools/{crunchstat-summary => user-activity}/fpm-info.sh (100%)
copy tools/{crunchstat-summary => user-activity}/setup.py (52%)
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commit 045e3127cb48845c7d988d01488c055f02ae2ec3
Merge: 4cc84d125 cc0e5b0c7
Author: Ward Vandewege <ward at curii.com>
Date: Wed Jan 6 09:52:13 2021 -0500
16106: Merge branch 'master' into 16106-azure-spot-instance-support
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward at curii.com>
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