[ARVADOS] updated: 2.1.0-113-g6bf9e1a4b
Git user
git at public.arvados.org
Wed Nov 18 21:24:13 UTC 2020
Summary of changes:
.licenseignore | 4 +
CONTRIBUTING.md | 2 +-
.../controllers/container_requests_controller.rb | 63 ++++-
.../app/controllers/work_units_controller.rb | 1 +
apps/workbench/app/helpers/application_helper.rb | 5 +
apps/workbench/app/models/container_request.rb | 24 ++
.../_extra_tab_line_buttons.html.erb | 47 +---
.../views/container_requests/_show_inputs.html.erb | 18 +-
.../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 | 33 +--
build/run-build-packages-one-target.sh | 12 +-
build/run-build-packages-sso.sh | 158 -----------
build/run-build-packages.sh | 2 +-
build/run-library.sh | 47 ++--
build/version-at-commit.sh | 5 +-
doc/Gemfile | 2 +-
doc/Gemfile.lock | 2 +-
doc/_config.yml | 8 +
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/upgrading.html.textile.liquid | 10 +-
doc/api/keep-s3.html.textile.liquid | 74 ++++++
doc/api/keep-web-urls.html.textile.liquid | 75 ++++++
doc/api/keep-webdav.html.textile.liquid | 103 ++++++++
doc/api/methods/groups.html.textile.liquid | 2 +
.../install-dispatch.html.textile.liquid | 2 +-
doc/install/index.html.textile.liquid | 6 +-
.../install-compute-ping.html.textile.liquid | 14 -
...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 | 1 -
doc/install/salt-multi-host.html.textile.liquid | 110 ++++++++
doc/install/salt-single-host.html.textile.liquid | 86 ++++++
doc/install/salt-vagrant.html.textile.liquid | 73 ++++++
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/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 +-
doc/zenweb-liquid.rb | 14 +-
docker/jobs/Dockerfile | 2 +-
lib/boot/supervisor.go | 6 +-
lib/cmd/cmd.go | 2 +-
lib/controller/api/routable.go | 13 +
lib/controller/auth_test.go | 126 +++++++++
lib/controller/fed_collections.go | 12 +-
lib/controller/fed_containers.go | 6 +-
lib/controller/fed_generic.go | 34 +--
lib/controller/federation.go | 13 +-
lib/controller/federation/conn.go | 8 +
lib/controller/handler.go | 6 +-
lib/controller/integration_test.go | 81 ++++++
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/crunchrun/background.go | 2 +-
lib/dispatchcloud/container/queue.go | 6 +-
lib/install/deps.go | 4 +-
lib/service/cmd.go | 2 +-
lib/service/cmd_test.go | 9 +-
sdk/R/R/Collection.R | 3 +-
sdk/R/README.Rmd | 20 +-
sdk/cli/arvados-cli.gemspec | 3 +-
sdk/cwl/arvados_version.py | 43 +--
sdk/cwl/fpm-info.sh | 2 +-
sdk/cwl/gittaggers.py | 48 ----
sdk/cwl/test_with_arvbox.sh | 4 +-
sdk/cwl/tests/federation/arvboxcwl/fed-config.cwl | 3 +-
sdk/cwl/tests/federation/arvboxcwl/start.cwl | 2 +-
sdk/cwl/tests/test_submit.py | 6 +-
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 | 8 +-
sdk/go/arvados/container.go | 4 +-
sdk/go/arvados/fs_collection.go | 9 +-
sdk/go/arvados/link.go | 2 +-
sdk/go/arvadosclient/arvadosclient.go | 28 +-
sdk/go/arvadostest/api.go | 80 +++---
sdk/go/arvadostest/oidc_provider.go | 174 +++++++++++++
sdk/go/auth/auth.go | 2 +-
sdk/go/blockdigest/blockdigest.go | 6 +-
sdk/go/blockdigest/testing.go | 2 +-
sdk/go/keepclient/keepclient.go | 37 +--
sdk/go/keepclient/keepclient_test.go | 40 +--
sdk/go/keepclient/root_sorter_test.go | 14 +-
sdk/go/keepclient/support.go | 50 ++--
sdk/python/README.rst | 4 +-
sdk/python/arvados/api.py | 4 +
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/ruby/arvados.gemspec | 3 +-
.../api/app/controllers/application_controller.rb | 6 +-
.../v1/api_client_authorizations_controller.rb | 8 +-
.../arvados/v1/collections_controller.rb | 32 +--
.../arvados/v1/container_requests_controller.rb | 4 +-
.../controllers/arvados/v1/groups_controller.rb | 25 +-
.../app/controllers/arvados/v1/jobs_controller.rb | 8 +-
.../app/controllers/arvados/v1/users_controller.rb | 26 +-
services/api/app/middlewares/arvados_api_token.rb | 2 +-
.../api/app/models/api_client_authorization.rb | 225 +++++++++-------
services/api/app/models/arvados_model.rb | 65 +++--
services/api/app/models/link.rb | 2 +
services/api/app/models/user.rb | 98 ++++---
.../20201103170213_refresh_trashed_groups.rb | 17 ++
.../migrate/20201105190435_refresh_permissions.rb | 15 ++
services/api/db/structure.sql | 18 +-
.../20200501150153_permission_table_constants.rb | 2 +-
services/api/lib/current_api_client.rb | 3 +
services/api/lib/update_permissions.rb | 10 +-
services/api/script/rails | 2 +-
.../arvados/v1/groups_controller_test.rb | 39 ++-
.../arvados/v1/schema_controller_test.rb | 2 +-
services/api/test/integration/remote_user_test.rb | 57 ++--
services/api/test/test_helper.rb | 1 +
services/api/test/unit/user_test.rb | 5 +-
.../crunch-dispatch-local.service} | 8 +-
.../fpm-info.sh} | 3 +-
services/dockercleaner/arvados_version.py | 35 ++-
services/dockercleaner/fpm-info.sh | 2 +-
services/dockercleaner/gittaggers.py | 1 -
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/s3.go | 174 +++++++++++--
services/keep-web/s3_test.go | 66 ++++-
services/keep-web/s3aws_test.go | 77 ++++++
services/keep-web/server_test.go | 1 +
services/keepproxy/keepproxy.go | 37 +--
services/keepstore/keepstore.go | 4 +-
services/login-sync/arvados-login-sync.gemspec | 3 +-
services/ws/doc.go | 2 +-
tools/arvbox/bin/arvbox | 5 +-
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 | 2 +-
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/crunchstat-summary/arvados_version.py | 39 +--
tools/crunchstat-summary/gittaggers.py | 1 -
tools/salt-install/README.md | 20 ++
tools/salt-install/Vagrantfile | 37 +++
tools/salt-install/provision.sh | 235 +++++++++++++++++
tools/salt-install/single_host/arvados.sls | 159 +++++++++++
tools/salt-install/single_host/locale.sls | 14 +
.../single_host/nginx_api_configuration.sls | 28 ++
.../single_host/nginx_controller_configuration.sls | 59 +++++
.../single_host/nginx_keepproxy_configuration.sls | 58 +++++
.../single_host/nginx_keepweb_configuration.sls | 58 +++++
tools/salt-install/single_host/nginx_passenger.sls | 24 ++
.../single_host/nginx_webshell_configuration.sls | 75 ++++++
.../single_host/nginx_websocket_configuration.sls | 59 +++++
.../single_host/nginx_workbench2_configuration.sls | 49 ++++
.../single_host/nginx_workbench_configuration.sls | 74 ++++++
tools/salt-install/single_host/postgresql.sls | 42 +++
tools/sync-groups/sync-groups.go | 10 +-
tools/sync-groups/sync-groups_test.go | 8 -
206 files changed, 3750 insertions(+), 1862 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/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
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/{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
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
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commit 6bf9e1a4b5640f3cdd057810f0c9b8a945bb88bd
Merge: b39f7a614 5d23eb939
Author: Ward Vandewege <ward at curii.com>
Date: Wed Nov 18 16:23:51 2020 -0500
Merge branch 'master' into 16950-add-costanalyzer
refs #16950
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward at curii.com>
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