[ARVADOS] updated: 1.3.0-3019-g505c8fa50
Git user
git at public.arvados.org
Tue Aug 25 20:41:40 UTC 2020
Summary of changes:
apps/workbench/Gemfile | 24 +-
apps/workbench/Gemfile.lock | 140 ++---
.../app/controllers/application_controller.rb | 1 -
apps/workbench/app/models/application_record.rb | 7 -
apps/workbench/app/models/arvados_base.rb | 6 +
apps/workbench/bin/bundle | 2 +-
apps/workbench/bin/setup | 6 +-
apps/workbench/bin/update | 3 +
{services/api => apps/workbench}/bin/yarn | 3 +-
apps/workbench/config/application.default.yml | 1 -
apps/workbench/config/application.rb | 7 +-
apps/workbench/config/boot.rb | 1 +
.../config/initializers/content_security_policy.rb | 0
.../config/initializers/new_framework_defaults.rb | 3 -
.../initializers/new_framework_defaults_5_1.rb | 18 +
.../initializers/new_framework_defaults_5_2.rb | 0
apps/workbench/config/routes.rb | 2 +-
apps/workbench/config/secrets.yml | 18 +-
build/rails-package-scripts/README.md | 2 +-
build/rails-package-scripts/arvados-api-server.sh | 4 +-
build/rails-package-scripts/prerm.sh | 1 -
build/run-build-docker-jobs-image.sh | 20 +-
build/run-build-packages-python-and-ruby.sh | 1 -
build/run-tests.sh | 30 +-
doc/_config.yml | 29 +-
doc/_includes/_0_filter_py.liquid | 35 --
doc/_includes/_alert-incomplete.liquid | 11 -
doc/_includes/_alert_stub.liquid | 11 -
doc/_includes/_arv_copy_expectations.liquid | 12 -
doc/_includes/_concurrent_hash_script_py.liquid | 88 ----
doc/_includes/_crunch1only_begin.liquid | 8 -
doc/_includes/_example_docker.liquid | 34 --
doc/_includes/_install_compute_docker.liquid | 2 +-
doc/_includes/_install_git.liquid | 9 -
doc/_includes/_install_rails_reconfigure.liquid | 17 -
doc/_includes/_install_ruby_and_bundler_sso.liquid | 69 ---
doc/_includes/_install_runit.liquid | 19 -
doc/_includes/_pipeline_deprecation_notice.liquid | 9 -
doc/_includes/_run_command_foreach_example.liquid | 46 --
doc/_includes/_run_command_simple_example.liquid | 43 --
doc/_includes/_run_md5sum_py.liquid | 24 -
doc/_includes/_ssh_addkey.liquid | 6 +-
.../_tutorial_bwa_sortsam_pipeline.liquid | 78 ---
doc/_includes/_tutorial_cluster_name.liquid | 9 -
doc/_includes/_tutorial_expectations.liquid | 2 +-
doc/_includes/_tutorial_hash_script_py.liquid | 50 --
...1only_end.liquid => _tutorial_hello_cwl.liquid} | 8 +-
doc/_includes/_tutorial_submit_job.liquid | 25 -
doc/_includes/_what_is_cwl.liquid | 2 +-
doc/admin/scoped-tokens.html.textile.liquid | 6 +
.../token-expiration-policy.html.textile.liquid | 62 +++
doc/admin/user-management-cli.html.textile.liquid | 64 ++-
doc/architecture/federation.html.textile.liquid | 2 +-
.../pipeline_templates/gatk-exome-fq-snp.json | 175 ------
doc/examples/pipeline_templates/rtg-fq-snp.json | 76 ---
doc/examples/ruby/list-active-nodes.rb | 16 -
...opy_pipeline_from_curoverse.html.textile.liquid | 68 ---
.../install-compute-node.html.textile.liquid | 5 +-
.../install-dispatch-cloud.html.textile.liquid | 71 +++
doc/sdk/java-v2/example.html.textile.liquid | 2 +-
doc/sdk/python/cookbook.html.textile.liquid | 31 +-
doc/sdk/python/events.html.textile.liquid | 2 +-
doc/sdk/ruby/example.html.textile.liquid | 2 +-
.../firstpipeline.html.textile.liquid | 94 ----
.../getting_started/nextsteps.html.textile.liquid | 12 -
.../publicproject.html.textile.liquid | 133 -----
.../getting_started/sharedata.html.textile.liquid | 102 ----
doc/start/index.html.textile.liquid | 133 -----
doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml | 6 +-
doc/user/cwl/bwa-mem/bwa-mem-input-uuids.yml | 6 +-
doc/user/cwl/bwa-mem/bwa-mem.cwl | 6 +-
doc/user/cwl/cwl-run-options.html.textile.liquid | 24 +-
doc/user/cwl/cwl-runner.html.textile.liquid | 190 +++++--
doc/user/cwl/cwl-style.html.textile.liquid | 2 +-
doc/user/cwl/cwl-versions.html.textile.liquid | 4 +-
.../check-environment.html.textile.liquid | 10 +-
.../ssh-access-unix.html.textile.liquid | 22 +-
.../ssh-access-windows.html.textile.liquid | 14 +-
.../vm-login-with-webshell.html.textile.liquid | 4 +
.../getting_started/workbench.html.textile.liquid | 12 +-
doc/user/index.html.textile.liquid | 2 +-
doc/user/topics/arv-copy.html.textile.liquid | 91 ++--
doc/user/topics/arv-docker.html.textile.liquid | 155 ++----
doc/user/topics/arv-web.html.textile.liquid | 106 ----
doc/user/topics/keep.html.textile.liquid | 2 +-
...rial-gatk-variantfiltration.html.textile.liquid | 173 ------
doc/user/topics/tutorial-job1.html.textile.liquid | 214 --------
.../add-new-repository.html.textile.liquid | 2 +-
.../git-arvados-guide.html.textile.liquid | 36 +-
...l-keep-collection-lifecycle.html.textile.liquid | 44 +-
.../tutorial-keep-get.html.textile.liquid | 93 ++--
...torial-keep-mount-gnu-linux.html.textile.liquid | 21 +-
.../tutorial-keep-mount-os-x.html.textile.liquid | 10 +-
...tutorial-keep-mount-windows.html.textile.liquid | 4 +-
.../tutorials/tutorial-keep.html.textile.liquid | 61 ++-
...tutorial-workflow-workbench.html.textile.liquid | 16 +-
.../writing-cwl-workflow.html.textile.liquid | 120 +----
go.mod | 14 +-
go.sum | 38 ++
lib/boot/supervisor.go | 2 +-
lib/cloud/azure/azure.go | 283 +++++++---
lib/cloud/azure/azure_test.go | 3 +-
lib/config/config.default.yml | 31 +-
lib/config/export.go | 48 +-
lib/config/generated_config.go | 31 +-
lib/controller/federation/federation_test.go | 2 +-
lib/controller/localdb/login_ldap_test.go | 2 +-
lib/dispatchcloud/dispatcher_test.go | 4 +-
lib/dispatchcloud/scheduler/run_queue.go | 2 +
lib/dispatchcloud/scheduler/run_queue_test.go | 5 +-
lib/dispatchcloud/scheduler/sync.go | 6 +-
lib/dispatchcloud/test/queue.go | 30 +-
lib/dispatchcloud/test/stub_driver.go | 84 ++-
sdk/cli/arvados-cli.gemspec | 3 +-
sdk/go/arvados/config.go | 2 +
sdk/go/arvados/fs_base.go | 27 +-
sdk/go/arvados/fs_collection.go | 62 ++-
sdk/go/arvados/fs_collection_test.go | 22 +-
sdk/go/arvados/fs_deferred.go | 21 +-
sdk/go/arvados/fs_lookup.go | 58 +-
sdk/go/arvados/fs_project.go | 3 +-
sdk/go/arvados/fs_project_test.go | 43 +-
sdk/go/arvados/fs_site.go | 41 +-
sdk/go/arvados/fs_site_test.go | 11 +-
sdk/go/keepclient/keepclient_test.go | 1 +
services/api/.gitignore | 3 +-
.../app/controllers/user_sessions_controller.rb | 5 +
services/api/app/models/api_client.rb | 9 +-
services/api/config/application.rb | 2 +-
services/api/config/arvados_config.rb | 1 +
.../api/lib/tasks/manage_long_lived_tokens.rake | 61 +++
.../functional/user_sessions_controller_test.rb | 23 +-
services/api/test/unit/api_client_test.rb | 41 +-
services/arv-git-httpd/gitolite_test.go | 2 +-
services/arv-web/README | 6 -
services/arv-web/arv-web.py | 256 ---------
services/arv-web/sample-cgi-app/docker_image | 1 -
services/arv-web/sample-cgi-app/public/.htaccess | 3 -
services/arv-web/sample-cgi-app/public/index.cgi | 4 -
services/arv-web/sample-cgi-app/tmp/.keepkeep | 0
services/arv-web/sample-rack-app/config.ru | 8 -
services/arv-web/sample-rack-app/docker_image | 1 -
services/arv-web/sample-rack-app/public/.keepkeep | 0
services/arv-web/sample-rack-app/tmp/.keepkeep | 0
services/arv-web/sample-static-page/docker_image | 1 -
.../arv-web/sample-static-page/public/index.html | 10 -
services/arv-web/sample-static-page/tmp/.keepkeep | 0
services/arv-web/sample-wsgi-app/docker_image | 1 -
services/arv-web/sample-wsgi-app/passenger_wsgi.py | 7 -
services/arv-web/sample-wsgi-app/public/.keepkeep | 0
services/arv-web/sample-wsgi-app/tmp/.keepkeep | 0
services/keep-web/handler.go | 47 +-
services/keep-web/main.go | 3 +-
services/keep-web/s3.go | 452 ++++++++++++++++
services/keep-web/s3_test.go | 584 +++++++++++++++++++++
services/keep-web/server.go | 6 +-
services/keep-web/server_test.go | 2 +-
tools/arvbox/bin/arvbox | 3 +-
tools/compute-images/arvados-images-azure.json | 8 +-
tools/compute-images/build.sh | 11 +-
tools/copy-tutorial/copy-tutorial.sh | 25 +
161 files changed, 2729 insertions(+), 3188 deletions(-)
delete mode 100644 apps/workbench/app/models/application_record.rb
copy {services/api => apps/workbench}/bin/yarn (90%)
copy {services/api => apps/workbench}/config/initializers/content_security_policy.rb (100%)
create mode 100644 apps/workbench/config/initializers/new_framework_defaults_5_1.rb
copy {services/api => apps/workbench}/config/initializers/new_framework_defaults_5_2.rb (100%)
delete mode 100644 doc/_includes/_0_filter_py.liquid
delete mode 100644 doc/_includes/_alert-incomplete.liquid
delete mode 100644 doc/_includes/_alert_stub.liquid
delete mode 100644 doc/_includes/_arv_copy_expectations.liquid
delete mode 100644 doc/_includes/_concurrent_hash_script_py.liquid
delete mode 100644 doc/_includes/_crunch1only_begin.liquid
delete mode 100644 doc/_includes/_example_docker.liquid
delete mode 100644 doc/_includes/_install_git.liquid
delete mode 100644 doc/_includes/_install_rails_reconfigure.liquid
delete mode 100644 doc/_includes/_install_ruby_and_bundler_sso.liquid
delete mode 100644 doc/_includes/_install_runit.liquid
delete mode 100644 doc/_includes/_pipeline_deprecation_notice.liquid
delete mode 100644 doc/_includes/_run_command_foreach_example.liquid
delete mode 100644 doc/_includes/_run_command_simple_example.liquid
delete mode 100644 doc/_includes/_run_md5sum_py.liquid
delete mode 100644 doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid
delete mode 100644 doc/_includes/_tutorial_cluster_name.liquid
delete mode 100644 doc/_includes/_tutorial_hash_script_py.liquid
rename doc/_includes/{_crunch1only_end.liquid => _tutorial_hello_cwl.liquid} (50%)
delete mode 100644 doc/_includes/_tutorial_submit_job.liquid
create mode 100644 doc/admin/token-expiration-policy.html.textile.liquid
delete mode 100644 doc/examples/pipeline_templates/gatk-exome-fq-snp.json
delete mode 100644 doc/examples/pipeline_templates/rtg-fq-snp.json
delete mode 100755 doc/examples/ruby/list-active-nodes.rb
delete mode 100644 doc/install/copy_pipeline_from_curoverse.html.textile.liquid
delete mode 100644 doc/start/getting_started/firstpipeline.html.textile.liquid
delete mode 100644 doc/start/getting_started/nextsteps.html.textile.liquid
delete mode 100644 doc/start/getting_started/publicproject.html.textile.liquid
delete mode 100644 doc/start/getting_started/sharedata.html.textile.liquid
delete mode 100644 doc/start/index.html.textile.liquid
delete mode 100644 doc/user/topics/arv-web.html.textile.liquid
delete mode 100644 doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
delete mode 100644 doc/user/topics/tutorial-job1.html.textile.liquid
create mode 100644 services/api/lib/tasks/manage_long_lived_tokens.rake
delete mode 100644 services/arv-web/README
delete mode 100755 services/arv-web/arv-web.py
delete mode 100644 services/arv-web/sample-cgi-app/docker_image
delete mode 100644 services/arv-web/sample-cgi-app/public/.htaccess
delete mode 100755 services/arv-web/sample-cgi-app/public/index.cgi
delete mode 100644 services/arv-web/sample-cgi-app/tmp/.keepkeep
delete mode 100644 services/arv-web/sample-rack-app/config.ru
delete mode 100644 services/arv-web/sample-rack-app/docker_image
delete mode 100644 services/arv-web/sample-rack-app/public/.keepkeep
delete mode 100644 services/arv-web/sample-rack-app/tmp/.keepkeep
delete mode 100644 services/arv-web/sample-static-page/docker_image
delete mode 100644 services/arv-web/sample-static-page/public/index.html
delete mode 100644 services/arv-web/sample-static-page/tmp/.keepkeep
delete mode 100644 services/arv-web/sample-wsgi-app/docker_image
delete mode 100644 services/arv-web/sample-wsgi-app/passenger_wsgi.py
delete mode 100644 services/arv-web/sample-wsgi-app/public/.keepkeep
delete mode 100644 services/arv-web/sample-wsgi-app/tmp/.keepkeep
create mode 100644 services/keep-web/s3.go
create mode 100644 services/keep-web/s3_test.go
create mode 100755 tools/copy-tutorial/copy-tutorial.sh
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commit 505c8fa50631201e289cc55230d46fdf52fa2055
Merge: b4091adb7 a7631a1cc
Author: Tom Clegg <tom at tomclegg.ca>
Date: Tue Aug 25 16:41:21 2020 -0400
16314: Merge branch 'master'
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at tomclegg.ca>
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