[ARVADOS] updated: 2.1.0-1095-gc2aceca33
Git user
git at public.arvados.org
Fri Jul 23 18:04:39 UTC 2021
Summary of changes:
apps/workbench/Gemfile | 3 -
apps/workbench/Gemfile.lock | 99 ++++-----
apps/workbench/config/boot.rb | 1 -
apps/workbench/test/integration/logins_test.rb | 5 +-
build/package-build-dockerfiles/centos7/Dockerfile | 2 +-
.../package-build-dockerfiles/debian10/Dockerfile | 2 +-
.../ubuntu1604/Dockerfile | 2 +-
.../ubuntu1804/Dockerfile | 2 +-
.../ubuntu2004/Dockerfile | 2 +-
build/package-test-dockerfiles/centos7/Dockerfile | 2 +-
build/package-test-dockerfiles/debian10/Dockerfile | 2 +-
.../package-test-dockerfiles/ubuntu1604/Dockerfile | 2 +-
.../package-test-dockerfiles/ubuntu1804/Dockerfile | 2 +-
.../package-test-dockerfiles/ubuntu2004/Dockerfile | 2 +-
build/rails-package-scripts/arvados-api-server.sh | 2 +-
build/rails-package-scripts/postinst.sh | 21 +-
build/run-build-packages.sh | 4 +-
build/run-tests.sh | 6 +-
build/version-at-commit.sh | 10 +-
doc/_config.yml | 3 +-
doc/_includes/_create_superuser_token.liquid | 2 +-
doc/_includes/_install_rails_command.liquid | 4 +-
doc/admin/config-migration.html.textile.liquid | 8 +-
doc/admin/keep-recovering-data.html.textile.liquid | 2 +-
...restricting-upload-download.html.textile.liquid | 169 ++++++++++++++
doc/admin/storage-classes.html.textile.liquid | 8 +-
.../token-expiration-policy.html.textile.liquid | 4 +-
doc/admin/upgrading.html.textile.liquid | 8 +-
.../methods/container_requests.html.textile.liquid | 1 +
doc/api/methods/containers.html.textile.liquid | 1 +
doc/api/tokens_sso.html.textile.liquid | 78 -------
doc/architecture/dispatchcloud.html.textile.liquid | 99 +++++++++
doc/architecture/dispatchcloud.svg | 1 +
doc/install/arvbox.html.textile.liquid | 6 +-
.../install-dispatch-cloud.html.textile.liquid | 2 +
.../install-arv-git-httpd.html.textile.liquid | 4 +-
doc/install/install-keep-web.html.textile.liquid | 2 +-
...nstall-manual-prerequisites.html.textile.liquid | 8 +-
doc/install/salt-multi-host.html.textile.liquid | 32 ++-
doc/install/salt-single-host.html.textile.liquid | 2 +-
doc/install/salt-vagrant.html.textile.liquid | 2 +-
doc/install/salt.html.textile.liquid | 106 +++++++--
doc/sdk/go/example.html.textile.liquid | 2 +-
doc/user/cwl/costanalyzer.html.textile.liquid | 50 +++--
doc/user/cwl/cwl-runner.html.textile.liquid | 2 +-
.../cwl/federated-workflows.html.textile.liquid | 2 +-
.../topics/storage-classes.html.textile.liquid | 14 +-
go.mod | 6 +-
go.sum | 18 ++
lib/boot/passenger.go | 4 +-
lib/boot/supervisor.go | 5 +
lib/cloud/ec2/ec2.go | 28 +++
lib/cloud/ec2/ec2_test.go | 14 +-
lib/config/config.default.yml | 100 +++++----
lib/config/deprecated.go | 12 -
lib/config/export.go | 9 +-
lib/config/generated_config.go | 100 +++++----
lib/config/load.go | 32 ++-
lib/config/load_test.go | 32 ++-
lib/controller/handler_test.go | 28 ---
lib/controller/localdb/login.go | 21 +-
lib/controller/localdb/login_oidc.go | 19 +-
lib/controller/localdb/login_oidc_test.go | 13 +-
lib/controller/rpc/conn_test.go | 7 +-
lib/costanalyzer/cmd.go | 19 +-
lib/costanalyzer/costanalyzer.go | 242 ++++++++++++++-------
lib/costanalyzer/costanalyzer_test.go | 54 +++--
lib/crunchrun/crunchrun.go | 42 +++-
lib/crunchrun/crunchrun_test.go | 90 +++++---
lib/crunchrun/docker.go | 15 +-
lib/crunchrun/executor.go | 6 +-
lib/crunchrun/executor_test.go | 7 +
lib/crunchrun/singularity.go | 11 +-
lib/install/deps.go | 4 +-
sdk/cwl/arvados_cwl/__init__.py | 2 +-
sdk/cwl/arvados_cwl/arvtool.py | 11 +-
sdk/cwl/arvados_cwl/fsaccess.py | 2 +-
sdk/cwl/arvados_cwl/runner.py | 11 +-
sdk/cwl/setup.py | 5 +-
...ling-slash-dir.cwl => 17801-runtime-outdir.cwl} | 2 +-
sdk/cwl/tests/17858-pack-visit-crash.cwl | 17 ++
.../tests/17879-ignore-sbg-fields-job.yml} | 3 +-
sdk/cwl/tests/17879-ignore-sbg-fields.cwl | 37 ++++
sdk/cwl/tests/arvados-tests.yml | 46 ++++
sdk/cwl/tests/test_submit.py | 47 ++--
sdk/go/arvados/api.go | 17 ++
sdk/go/arvados/config.go | 20 +-
sdk/go/arvados/container.go | 2 +
sdk/go/arvados/fs_backend.go | 7 +-
sdk/go/arvados/fs_base.go | 47 +++-
sdk/go/arvados/fs_collection.go | 40 +++-
sdk/go/arvados/fs_collection_test.go | 53 +++--
sdk/go/arvados/fs_site.go | 6 +
sdk/go/arvados/fs_site_test.go | 45 +++-
sdk/go/arvadostest/fixtures.go | 3 +
sdk/go/arvadostest/oidc_provider.go | 8 +-
sdk/go/keepclient/keepclient.go | 44 ++--
sdk/go/keepclient/keepclient_test.go | 43 ++--
sdk/go/keepclient/support.go | 90 ++++++--
sdk/python/arvados/commands/put.py | 34 +--
sdk/python/tests/run_test_server.py | 13 +-
sdk/python/tests/test_arv_put.py | 31 ++-
services/api/Gemfile | 7 -
services/api/Gemfile.lock | 115 ++++------
.../api/app/assets/stylesheets/application.css | 2 +-
.../api/app/controllers/application_controller.rb | 2 +-
.../app/controllers/user_sessions_controller.rb | 24 +-
services/api/app/models/container.rb | 12 +-
services/api/app/models/container_request.rb | 29 ++-
.../api/app/views/layouts/application.html.erb | 3 -
services/api/app/views/static/intro.html.erb | 17 +-
.../api/app/views/static/login_failure.html.erb | 2 +-
.../api/app/views/user_sessions/failure.html.erb | 2 +-
services/api/config/arvados_config.rb | 19 --
services/api/config/boot.rb | 1 -
services/api/config/environment.rb | 1 -
services/api/config/initializers/omniauth_init.rb | 23 --
...621204455_add_container_output_storage_class.rb | 10 +
services/api/db/structure.sql | 55 ++---
services/api/lib/josh_id.rb | 58 -----
services/api/test/fixtures/container_requests.yml | 30 ++-
services/api/test/fixtures/containers.yml | 24 +-
services/api/test/fixtures/jobs.yml | 2 +-
services/api/test/fixtures/pipeline_instances.yml | 64 +++---
services/api/test/fixtures/pipeline_templates.yml | 30 +--
.../arvados/v1/job_reuse_controller_test.rb | 2 +-
.../functional/user_sessions_controller_test.rb | 10 +-
services/api/test/helpers/git_test_helper.rb | 6 +-
.../api/test/integration/login_workflow_test.rb | 2 +-
.../api/test/integration/user_sessions_test.rb | 16 +-
services/api/test/test.git.tar | Bin 143360 -> 143360 bytes
services/api/test/test_helper.rb | 1 -
services/api/test/unit/commit_test.rb | 14 +-
services/api/test/unit/container_request_test.rb | 90 ++++++++
services/api/test/unit/job_test.rb | 2 +-
services/arv-git-httpd/gitolite_test.go | 6 +-
services/arv-git-httpd/integration_test.go | 5 +-
services/arv-git-httpd/server_test.go | 26 +--
.../crunch-dispatch-local/crunch-dispatch-local.go | 33 ++-
.../crunch-dispatch-local_test.go | 8 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 1 +
services/fuse/arvados_fuse/__init__.py | 8 -
services/fuse/arvados_fuse/command.py | 19 +-
services/fuse/arvados_fuse/fusedir.py | 39 ++--
services/fuse/tests/test_mount.py | 29 +++
services/fuse/tests/test_tmp_collection.py | 10 +
services/keep-web/cache.go | 69 ++++--
services/keep-web/handler.go | 142 +++++++++++-
services/keep-web/handler_test.go | 194 ++++++++++++++++-
services/keep-web/s3.go | 62 +++++-
services/keep-web/s3_test.go | 22 +-
services/keep-web/server_test.go | 4 +-
services/keepproxy/keepproxy.go | 193 +++++++++++-----
services/keepproxy/keepproxy_test.go | 187 +++++++++++++---
tools/arvbox/bin/arvbox | 36 ++-
tools/arvbox/lib/arvbox/docker/Dockerfile.demo | 7 +-
tools/arvbox/lib/arvbox/docker/api-setup.sh | 6 +-
tools/arvbox/lib/arvbox/docker/common.sh | 24 +-
.../lib/arvbox/docker/service/api/run-service | 6 +-
.../docker/service/crunch-dispatch-local/run | 17 +-
.../lib/arvbox/docker/service/gitolite/run-service | 2 +-
.../lib/arvbox/docker/service/ready/run-service | 2 +-
.../arvbox/lib/arvbox/docker/service/workbench/run | 2 +-
.../arvbox/docker/service/workbench/run-service | 10 +-
.../arvbox/docker/service/workbench2/run-service | 6 +-
.../multiple_hostnames/states/snakeoil_certs.sls | 2 +-
.../single_hostname/states/snakeoil_certs.sls | 2 +-
.../local.params.example.multiple_hosts | 5 +-
...l.params.example.single_host_multiple_hostnames | 5 +-
...ocal.params.example.single_host_single_hostname | 5 +-
tools/salt-install/provision.sh | 142 ++++++++----
tools/user-activity/arvados_user_activity/main.py | 20 ++
172 files changed, 3104 insertions(+), 1344 deletions(-)
create mode 100644 doc/admin/restricting-upload-download.html.textile.liquid
delete mode 100644 doc/api/tokens_sso.html.textile.liquid
create mode 100644 doc/architecture/dispatchcloud.html.textile.liquid
create mode 100644 doc/architecture/dispatchcloud.svg
copy sdk/cwl/tests/{10380-trailing-slash-dir.cwl => 17801-runtime-outdir.cwl} (92%)
create mode 100644 sdk/cwl/tests/17858-pack-visit-crash.cwl
copy sdk/{cli/test/binstub_docker_noop/docker.io => cwl/tests/17879-ignore-sbg-fields-job.yml} (84%)
mode change 100755 => 100644
create mode 100644 sdk/cwl/tests/17879-ignore-sbg-fields.cwl
delete mode 100644 services/api/config/initializers/omniauth_init.rb
create mode 100644 services/api/db/migrate/20210621204455_add_container_output_storage_class.rb
delete mode 100644 services/api/lib/josh_id.rb
mode change 120000 => 100755 tools/arvbox/lib/arvbox/docker/service/crunch-dispatch-local/run
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commit c2aceca339ec3a6f3d853865cebd0efe348ff518
Merge: 5bffa5d23 e1cee0a8e
Author: Ward Vandewege <ward at curii.com>
Date: Fri Jul 23 14:04:16 2021 -0400
17755: Merge branch 'main' into 17755-add-singularity-to-compute-image
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward at curii.com>
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