[ARVADOS] updated: 2.1.0-1216-g7af0535d3
Git user
git at public.arvados.org
Tue Aug 17 20:12:21 UTC 2021
Summary of changes:
apps/workbench/app/views/layouts/body.html.erb | 6 -
.../test/integration/application_layout_test.rb | 2 -
build/package-build-dockerfiles/Makefile | 8 +-
.../{ubuntu1604 => debian11}/Dockerfile | 8 +-
build/package-test-dockerfiles/Makefile | 8 +-
.../{ubuntu1604 => debian11}/Dockerfile | 12 +-
.../ubuntu1604/etc-apt-preferences.d-arvados | 3 -
...ckages-debian8.sh => test-packages-debian11.sh} | 0
build/package-testing/test-packages-debian9.sh | 1 -
build/package-testing/test-packages-ubuntu1404.sh | 1 -
build/package-testing/test-packages-ubuntu1604.sh | 1 -
build/run-build-packages-one-target.sh | 4 +
build/run-build-packages.sh | 2 +
build/run-library.sh | 11 +-
cmd/arvados-server/arvados-controller.service | 3 -
cmd/arvados-server/arvados-dispatch-cloud.service | 3 -
...roller.service => arvados-dispatch-lsf.service} | 7 +-
cmd/arvados-server/arvados-ws.service | 3 -
cmd/arvados-server/cmd.go | 2 +
doc/_config.yml | 3 +
doc/_includes/_install_ruby_and_bundler.liquid | 2 -
doc/admin/storage-classes.html.textile.liquid | 29 +-
doc/admin/upgrading.html.textile.liquid | 16 +-
doc/api/keep-web-urls.html.textile.liquid | 4 +-
.../install-dispatch.html.textile.liquid | 112 +++++++
.../install-dispatch.html.textile.liquid | 2 +-
.../install-keep-balance.html.textile.liquid | 4 +-
doc/install/install-keep-web.html.textile.liquid | 2 +-
...nstall-manual-prerequisites.html.textile.liquid | 58 +++-
doc/install/packages.html.textile.liquid | 1 +
doc/install/singularity.html.textile.liquid | 42 +++
doc/user/cwl/cwl-extensions.html.textile.liquid | 38 ++-
doc/user/cwl/cwl-run-options.html.textile.liquid | 10 +-
doc/user/topics/arv-copy.html.textile.liquid | 4 +-
doc/user/topics/arv-docker.html.textile.liquid | 8 +-
.../topics/storage-classes.html.textile.liquid | 16 +-
lib/boot/supervisor.go | 5 +
lib/config/config.default.yml | 59 +++-
lib/config/export.go | 7 +
lib/config/generated_config.go | 59 +++-
lib/config/load.go | 53 ++++
lib/config/load_test.go | 121 +++++++-
lib/controller/integration_test.go | 69 +++++
lib/crunchrun/crunchrun.go | 20 +-
lib/crunchrun/crunchrun_test.go | 31 +-
lib/crunchrun/docker.go | 13 +-
lib/crunchrun/executor.go | 8 +-
lib/crunchrun/executor_test.go | 3 +-
lib/crunchrun/singularity.go | 203 +++++++++++--
lib/lsf/dispatch.go | 322 +++++++++++++++++++++
lib/lsf/dispatch_test.go | 156 ++++++++++
lib/lsf/lsfcli.go | 92 ++++++
lib/lsf/lsfqueue.go | 108 +++++++
lib/service/cmd.go | 8 +
sdk/cwl/arvados_cwl/__init__.py | 15 +-
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.0.yml | 29 ++
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.1.yml | 28 ++
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml | 29 ++
sdk/cwl/arvados_cwl/arvcontainer.py | 9 +
sdk/cwl/arvados_cwl/arvtool.py | 10 +-
sdk/cwl/arvados_cwl/context.py | 1 +
sdk/cwl/arvados_cwl/executor.py | 16 +-
sdk/cwl/fpm-info.sh | 3 -
sdk/cwl/tests/test_container.py | 97 ++++++-
sdk/cwl/tests/test_submit.py | 71 ++++-
...r_resources.cwl => submit_storage_class_wf.cwl} | 6 +-
sdk/go/arvados/collection.go | 33 +--
sdk/go/arvados/config.go | 19 +-
sdk/go/arvados/container.go | 3 +
sdk/go/arvados/fs_base.go | 4 +-
sdk/go/arvadostest/fixtures.go | 7 +-
sdk/go/dispatch/dispatch.go | 35 ++-
sdk/go/dispatch/dispatch_test.go | 3 +-
sdk/go/health/aggregator_test.go | 1 +
sdk/go/httpserver/id_generator.go | 1 +
sdk/go/keepclient/keepclient.go | 6 +-
sdk/go/keepclient/keepclient_test.go | 9 +-
sdk/go/keepclient/support.go | 2 +-
sdk/python/arvados/commands/arv_copy.py | 11 +-
sdk/python/arvados/commands/keepdocker.py | 3 +
sdk/python/arvados/commands/put.py | 22 +-
sdk/python/tests/test_arv_copy.py | 5 +-
sdk/python/tests/test_arv_put.py | 84 +++---
.../api/app/controllers/application_controller.rb | 12 +-
services/api/app/mailers/user_notifier.rb | 7 +-
services/api/app/models/collection.rb | 8 +-
services/api/app/models/container.rb | 4 +-
services/api/app/models/container_request.rb | 2 +-
services/api/config/arvados_config.rb | 13 +
.../config/initializers/request_id_middleware.rb | 25 ++
.../api/lib/tasks/manage_long_lived_tokens.rake | 60 ++--
.../test/functional/application_controller_test.rb | 25 --
services/api/test/integration/errors_test.rb | 27 ++
services/api/test/unit/collection_test.rb | 30 ++
services/api/test/unit/container_request_test.rb | 22 +-
services/api/test/unit/user_notifier_test.rb | 2 +
services/arv-git-httpd/arvados-git-httpd.service | 3 -
.../crunch-dispatch-local/crunch-dispatch-local.go | 5 +-
.../crunch-dispatch-local.service | 3 -
.../crunch-dispatch-local_test.go | 12 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 40 +--
.../crunch-dispatch-slurm.service | 3 -
.../crunch-dispatch-slurm_test.go | 35 +--
.../dockercleaner/arvados-docker-cleaner.service | 3 -
services/dockercleaner/fpm-info.sh | 3 -
services/fuse/arvados_fuse/fusedir.py | 84 ++++--
services/health/arvados-health.service | 3 -
services/keep-balance/balance.go | 72 ++---
services/keep-balance/balance_run_test.go | 73 ++---
services/keep-balance/balance_test.go | 12 +-
services/keep-balance/block_state.go | 50 ++++
services/keep-balance/block_state_test.go | 94 ++++++
services/keep-balance/collection.go | 305 ++++++++++++-------
services/keep-balance/collection_test.go | 73 ++---
services/keep-balance/integration_test.go | 34 ++-
services/keep-balance/keep-balance.service | 3 -
services/keep-balance/main.go | 35 ++-
services/keep-balance/main_test.go | 21 +-
services/keep-balance/server.go | 17 +-
services/keep-web/keep-web.service | 3 -
services/keepproxy/keepproxy.service | 3 -
services/keepproxy/keepproxy_test.go | 19 +-
services/keepstore/handler_test.go | 65 ++++-
services/keepstore/handlers.go | 7 +
services/keepstore/keepstore.service | 3 -
services/keepstore/volume.go | 22 ++
services/login-sync/bin/arvados-login-sync | 4 +-
.../multi_host/aws/pillars/arvados.sls | 10 -
128 files changed, 2942 insertions(+), 749 deletions(-)
rename build/package-build-dockerfiles/{ubuntu1604 => debian11}/Dockerfile (78%)
rename build/package-test-dockerfiles/{ubuntu1604 => debian11}/Dockerfile (69%)
delete mode 100644 build/package-test-dockerfiles/ubuntu1604/etc-apt-preferences.d-arvados
rename build/package-testing/{test-packages-debian8.sh => test-packages-debian11.sh} (100%)
delete mode 120000 build/package-testing/test-packages-debian9.sh
delete mode 120000 build/package-testing/test-packages-ubuntu1404.sh
delete mode 120000 build/package-testing/test-packages-ubuntu1604.sh
copy cmd/arvados-server/{arvados-controller.service => arvados-dispatch-lsf.service} (78%)
create mode 100644 doc/install/crunch2-lsf/install-dispatch.html.textile.liquid
create mode 100644 doc/install/singularity.html.textile.liquid
create mode 100644 lib/lsf/dispatch.go
create mode 100644 lib/lsf/dispatch_test.go
create mode 100644 lib/lsf/lsfcli.go
create mode 100644 lib/lsf/lsfqueue.go
copy sdk/cwl/tests/wf/{submit_wf_runner_resources.cwl => submit_storage_class_wf.cwl} (87%)
create mode 100644 services/api/config/initializers/request_id_middleware.rb
create mode 100644 services/keep-balance/block_state_test.go
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commit 7af0535d3b0d7960152b06b7211c26bfd7b208cb
Merge: 6ef187b88 b059ddba2
Author: Ward Vandewege <ward at curii.com>
Date: Tue Aug 17 16:12:10 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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