[ARVADOS] updated: 1.3.0-1357-g765305463
Git user
git at public.curoverse.com
Tue Jul 16 16:30:09 UTC 2019
Summary of changes:
.../app/controllers/actions_controller.rb | 2 +-
.../app/controllers/application_controller.rb | 18 +-
.../app/controllers/collections_controller.rb | 35 +-
.../controllers/container_requests_controller.rb | 2 +-
.../app/controllers/containers_controller.rb | 2 +-
.../app/controllers/healthcheck_controller.rb | 2 +-
apps/workbench/app/controllers/jobs_controller.rb | 4 +-
.../controllers/pipeline_instances_controller.rb | 2 +-
.../controllers/pipeline_templates_controller.rb | 2 +-
.../app/controllers/projects_controller.rb | 6 +-
apps/workbench/app/controllers/users_controller.rb | 2 +-
.../app/controllers/virtual_machines_controller.rb | 13 +-
.../app/controllers/work_units_controller.rb | 2 +-
.../app/controllers/workflows_controller.rb | 2 +-
apps/workbench/app/helpers/application_helper.rb | 8 +-
apps/workbench/app/helpers/collections_helper.rb | 2 +-
apps/workbench/app/mailers/issue_reporter.rb | 4 +-
.../app/mailers/request_shell_access_reporter.rb | 4 +-
apps/workbench/app/models/arvados_api_client.rb | 38 +-
apps/workbench/app/models/repository.rb | 6 +-
.../api_client_authorizations/_show_help.html.erb | 2 +-
.../app/views/application/_breadcrumbs.html.erb | 2 +-
.../app/views/application/_report_error.html.erb | 2 +-
.../views/application/_report_issue_popup.html.erb | 4 +-
.../app/views/application/_show_sharing.html.erb | 2 +-
.../app/views/collections/show_file_links.html.erb | 2 +-
.../_getting_started_popup.html.erb | 2 +-
apps/workbench/app/views/jobs/_show_log.html.erb | 4 +-
.../app/views/layouts/application.html.erb | 10 +-
apps/workbench/app/views/layouts/body.html.erb | 38 +-
.../_collections_notification.html.erb | 6 +-
.../notifications/_jobs_notification.html.erb | 7 +-
.../notifications/_pipelines_notification.html.erb | 6 +-
.../app/views/projects/_show_dashboard.html.erb | 6 +-
.../app/views/repositories/_show_help.html.erb | 6 +-
.../app/views/user_agreements/index.html.erb | 2 +-
.../app/views/users/_add_ssh_key_popup.html.erb | 2 +-
.../app/views/users/_current_token.html.erb | 4 +-
.../app/views/users/_setup_popup.html.erb | 2 +-
apps/workbench/app/views/users/_ssh_keys.html.erb | 2 +-
apps/workbench/app/views/users/_tables.html.erb | 4 +-
.../app/views/users/_virtual_machines.html.erb | 6 +-
apps/workbench/app/views/users/profile.html.erb | 31 +-
apps/workbench/app/views/users/welcome.html.erb | 8 +-
.../app/views/virtual_machines/_show_help.html.erb | 2 +-
.../app/views/virtual_machines/webshell.html.erb | 2 +-
.../app/views/work_units/_show_log.html.erb | 2 +-
apps/workbench/config/application.default.yml | 208 +----------
apps/workbench/config/application.rb | 5 +-
apps/workbench/config/arvados_config.rb | 194 ++++++++++
apps/workbench/config/load_config.rb | 71 ----
apps/workbench/fpm-info.sh | 4 +-
.../api => apps/workbench}/lib/config_loader.rb | 141 ++++----
apps/workbench/lib/config_validators.rb | 36 +-
.../api => apps/workbench}/lib/tasks/config.rake | 0
apps/workbench/lib/tasks/config_check.rake | 23 --
apps/workbench/lib/tasks/config_dump.rake | 10 -
.../test/controllers/actions_controller_test.rb | 4 +-
.../controllers/application_controller_test.rb | 20 +-
.../controllers/collections_controller_test.rb | 30 +-
.../container_requests_controller_test.rb | 2 +-
.../test/controllers/disabled_api_test.rb | 2 +-
.../test/controllers/projects_controller_test.rb | 26 +-
.../test/controllers/users_controller_test.rb | 4 +-
.../test/integration/anonymous_access_test.rb | 8 +-
.../test/integration/application_layout_test.rb | 27 +-
apps/workbench/test/integration/download_test.rb | 4 +-
apps/workbench/test/integration/errors_test.rb | 6 +-
apps/workbench/test/integration/jobs_test.rb | 2 +-
.../test/integration/link_account_test.rb | 22 +-
.../test/integration/pipeline_instances_test.rb | 3 +-
apps/workbench/test/integration/projects_test.rb | 10 +-
.../test/integration/report_issue_test.rb | 4 +-
.../test/integration/user_profile_test.rb | 26 +-
.../test/integration/user_settings_menu_test.rb | 4 +-
apps/workbench/test/integration/websockets_test.rb | 4 +-
apps/workbench/test/integration/work_units_test.rb | 2 +-
apps/workbench/test/integration_helper.rb | 4 +-
.../collection_unit_test.rb | 2 +-
apps/workbench/test/test_helper.rb | 13 +-
apps/workbench/test/unit/user_test.rb | 2 +-
apps/workbench/test/unit/work_unit_test.rb | 2 +-
build/package-build-dockerfiles/Makefile | 14 +-
build/package-build-dockerfiles/centos7/Dockerfile | 8 +-
build/package-build-dockerfiles/debian8/Dockerfile | 8 +-
build/package-build-dockerfiles/debian9/Dockerfile | 8 +-
.../ubuntu1404/Dockerfile | 8 +-
.../ubuntu1604/Dockerfile | 8 +-
.../ubuntu1804/Dockerfile | 8 +-
build/package-test-dockerfiles/Makefile | 10 +-
build/package-test-dockerfiles/debian8/Dockerfile | 28 --
.../package-test-dockerfiles/ubuntu1404/Dockerfile | 26 --
build/rails-package-scripts/postinst.sh | 6 +-
build/run-build-packages-one-target.sh | 7 +-
build/run-build-packages-python-and-ruby.sh | 2 +-
build/run-build-packages.sh | 28 +-
build/run-library.sh | 34 +-
build/run-tests.sh | 146 ++++----
cmd/arvados-client/cmd.go | 9 +-
cmd/arvados-server/cmd.go | 18 +-
doc/_config.yml | 2 +
...min_list_collections_without_property_py.liquid | 2 +-
...property_to_collections_under_project_py.liquid | 4 +-
.../_admin_update_collection_property_py.liquid | 8 +-
doc/admin/cloudtest.html.textile.liquid | 71 ++++
doc/admin/config-migration.html.textile.liquid | 31 +-
doc/admin/troubleshooting.html.textile.liquid | 74 ++++
doc/admin/upgrading.html.textile.liquid | 4 +
doc/api/methods.html.textile.liquid | 13 +-
doc/api/methods/groups.html.textile.liquid | 28 +-
doc/install/index.html.textile.liquid | 2 +-
doc/install/install-api-server.html.textile.liquid | 154 ++++----
.../install-dispatch-cloud.html.textile.liquid | 31 +-
...nstall-manual-prerequisites.html.textile.liquid | 10 +-
.../install-nodemanager.html.textile.liquid | 2 +-
.../install-workbench-app.html.textile.liquid | 60 +++-
doc/sdk/cli/reference.html.textile.liquid | 2 +-
doc/user/composer/composer.html.textile.liquid | 2 +-
doc/user/cwl/cwl-extensions.html.textile.liquid | 2 +-
doc/user/topics/arv-docker.html.textile.liquid | 78 +---
lib/cloud/cloudtest/cmd.go | 145 ++++++++
lib/cloud/cloudtest/tester.go | 393 ++++++++++++++++++++
lib/cloud/cloudtest/tester_test.go | 97 +++++
lib/cmd/cmd.go | 13 +-
lib/cmdtest/leakcheck.go | 2 +-
lib/config/cmd.go | 72 ++--
lib/config/cmd_test.go | 46 ++-
lib/config/config.default.yml | 197 +++++++++-
lib/config/deprecated.go | 51 ++-
lib/config/export.go | 186 ++++++----
lib/config/export_test.go | 5 +-
lib/config/generated_config.go | 197 +++++++++-
lib/config/load.go | 158 +++++++--
lib/config/load_test.go | 179 +++++++++-
lib/controller/federation/conn.go | 310 ++++++++++++++++
lib/controller/federation_test.go | 179 ++++++----
lib/controller/handler.go | 12 +-
lib/controller/handler_test.go | 8 +-
lib/controller/proxy.go | 19 +-
lib/controller/railsproxy/railsproxy.go | 52 +++
lib/controller/router/checker_test.go | 32 ++
lib/controller/router/error.go | 18 +
lib/controller/router/request.go | 173 +++++++++
lib/controller/router/request_test.go | 206 +++++++++++
lib/controller/router/response.go | 151 ++++++++
lib/controller/router/router.go | 283 +++++++++++++++
lib/controller/router/router_test.go | 395 +++++++++++++++++++++
lib/controller/rpc/conn.go | 266 ++++++++++++++
lib/controller/rpc/conn_test.go | 79 +++++
lib/controller/server_test.go | 7 +-
lib/dispatchcloud/container/queue_test.go | 2 +-
lib/dispatchcloud/dispatcher_test.go | 8 +-
lib/dispatchcloud/driver.go | 9 +-
lib/dispatchcloud/ssh_executor/executor.go | 25 +-
lib/dispatchcloud/worker/pool.go | 4 +-
lib/dispatchcloud/worker/verify.go | 14 +-
lib/service/cmd.go | 19 +-
sdk/cwl/arvados_cwl/fsaccess.py | 6 +-
sdk/cwl/setup.py | 7 +-
sdk/go/arvados/api.go | 105 ++++++
sdk/go/arvados/api_client_authorization.go | 8 +-
sdk/go/arvados/client.go | 66 +++-
sdk/go/arvados/collection.go | 37 +-
sdk/go/arvados/config.go | 40 ++-
sdk/go/arvados/context.go | 24 ++
sdk/go/arvados/error.go | 4 +
sdk/go/arvados/fs_backend.go | 1 -
sdk/go/arvados/fs_collection.go | 7 +-
sdk/go/arvados/fs_project_test.go | 47 ++-
sdk/go/arvados/group.go | 6 +-
sdk/go/arvados/link.go | 14 +-
sdk/go/arvados/log.go | 16 +-
sdk/go/arvados/node.go | 4 +-
sdk/go/arvados/resource_list.go | 35 +-
sdk/go/arvados/resource_list_test.go | 11 +
sdk/go/arvados/specimen.go | 23 ++
sdk/go/arvados/user.go | 6 +-
sdk/go/arvados/workflow.go | 14 +-
sdk/go/arvadostest/api.go | 135 +++++++
sdk/go/arvadostest/fixtures.go | 4 +-
sdk/go/auth/auth.go | 12 +-
sdk/go/auth/handlers.go | 8 +-
sdk/go/httpserver/error.go | 5 +-
sdk/go/httpserver/logger.go | 28 +-
sdk/go/httpserver/logger_test.go | 14 +-
sdk/go/httpserver/metrics.go | 2 +-
sdk/go/keepclient/keepclient.go | 4 +-
sdk/pam/setup.py | 7 +-
sdk/python/tests/nginx.conf | 2 +-
sdk/python/tests/run_test_server.py | 25 +-
.../api/app/controllers/application_controller.rb | 12 +-
.../controllers/arvados/v1/groups_controller.rb | 3 +
services/api/app/models/collection.rb | 10 +-
services/api/config/arvados_config.rb | 48 ++-
services/api/config/config.default.yml | 1 -
services/api/config/initializers/lograge.rb | 15 +
services/api/fpm-info.sh | 4 +-
services/api/test/fixtures/collections.yml | 30 +-
services/api/test/fixtures/container_requests.yml | 2 +-
.../test/functional/application_controller_test.rb | 19 +-
.../arvados/v1/schema_controller_test.rb | 2 +-
.../api/test/integration/login_workflow_test.rb | 8 +-
services/api/test/unit/collection_test.rb | 17 +
services/crunch-run/crunchrun.go | 4 +-
services/fuse/setup.py | 9 +-
services/health/main.go | 2 +-
services/keep-balance/collection_test.go | 2 +-
services/keep-balance/server.go | 10 +-
services/keep-web/cache.go | 6 +-
services/keep-web/cadaver_test.go | 3 +-
services/keep-web/handler_test.go | 21 +-
services/keep-web/server.go | 6 +-
services/keepproxy/keepproxy.go | 2 +-
services/keepstore/handlers.go | 7 +-
services/login-sync/Gemfile.lock | 6 +-
services/nodemanager/setup.py | 7 +-
services/ws/session_v0_test.go | 28 +-
tools/arvbox/bin/arvbox | 13 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 4 +-
tools/arvbox/lib/arvbox/docker/api-setup.sh | 27 +-
.../{service/controller/run => cluster-config.sh} | 24 +-
tools/arvbox/lib/arvbox/docker/common.sh | 5 +
tools/arvbox/lib/arvbox/docker/createusers.sh | 2 +
tools/arvbox/lib/arvbox/docker/go-setup.sh | 3 +
.../lib/arvbox/docker/service/certificate/run | 29 +-
.../lib/arvbox/docker/service/controller/run | 75 +---
tools/arvbox/lib/arvbox/docker/service/nginx/run | 18 +-
.../lib/arvbox/docker/service/sso/run-service | 2 +-
.../arvbox/lib/arvbox/docker/service/workbench/run | 1 +
.../arvbox/docker/service/workbench/run-service | 20 +-
.../crunchstat_summary/dygraphs.py | 27 +-
.../crunchstat_summary/summarizer.py | 40 ++-
.../crunchstat_summary/webchart.py | 11 +-
...4-dz642-lymtndkpy39eibk-arv-mount.txt.gz.report | 1 +
...-dz642-lymtndkpy39eibk-crunchstat.txt.gz.report | 4 +-
...ainer_9tee4-dz642-lymtndkpy39eibk.txt.gz.report | 2 +
.../tests/logfile_20151204190335.txt.gz.report | 1 +
.../tests/logfile_20151210063411.txt.gz.report | 1 +
.../tests/logfile_20151210063439.txt.gz.report | 1 +
tools/crunchstat-summary/tests/test_examples.py | 2 +-
240 files changed, 5804 insertions(+), 1735 deletions(-)
create mode 100644 apps/workbench/config/arvados_config.rb
delete mode 100644 apps/workbench/config/load_config.rb
copy {services/api => apps/workbench}/lib/config_loader.rb (61%)
copy {services/api => apps/workbench}/lib/tasks/config.rake (100%)
delete mode 100644 apps/workbench/lib/tasks/config_check.rake
delete mode 100644 apps/workbench/lib/tasks/config_dump.rake
delete mode 100644 build/package-test-dockerfiles/debian8/Dockerfile
delete mode 100644 build/package-test-dockerfiles/ubuntu1404/Dockerfile
create mode 100644 doc/admin/cloudtest.html.textile.liquid
create mode 100644 doc/admin/troubleshooting.html.textile.liquid
create mode 100644 lib/cloud/cloudtest/cmd.go
create mode 100644 lib/cloud/cloudtest/tester.go
create mode 100644 lib/cloud/cloudtest/tester_test.go
create mode 100644 lib/controller/federation/conn.go
create mode 100644 lib/controller/railsproxy/railsproxy.go
create mode 100644 lib/controller/router/checker_test.go
create mode 100644 lib/controller/router/error.go
create mode 100644 lib/controller/router/request.go
create mode 100644 lib/controller/router/request_test.go
create mode 100644 lib/controller/router/response.go
create mode 100644 lib/controller/router/router.go
create mode 100644 lib/controller/router/router_test.go
create mode 100644 lib/controller/rpc/conn.go
create mode 100644 lib/controller/rpc/conn_test.go
create mode 100644 sdk/go/arvados/api.go
create mode 100644 sdk/go/arvados/context.go
create mode 100644 sdk/go/arvados/specimen.go
create mode 100644 sdk/go/arvadostest/api.go
delete mode 120000 services/api/config/config.default.yml
copy tools/arvbox/lib/arvbox/docker/{service/controller/run => cluster-config.sh} (86%)
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commit 7653054635e3f4f84da3f2b6862cd2c02fbe3fd4
Merge: e4e38ac6a 99240b3eb
Author: Eric Biagiotti <ebiagiotti at veritasgenetics.com>
Date: Tue Jul 16 12:29:04 2019 -0400
Merge branch 'master' into 14965-arv-mount-py-three
refs #14965
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti at veritasgenetics.com>
diff --cc services/fuse/setup.py
index 0bc4a0b65,0439d7d0c..ae1aa019b
--- a/services/fuse/setup.py
+++ b/services/fuse/setup.py
@@@ -38,9 -43,9 +43,9 @@@ setup(name='arvados_fuse'
('share/doc/arvados_fuse', ['agpl-3.0.txt', 'README.rst']),
],
install_requires=[
- 'arvados-python-client >= 0.1.20151118035730',
- 'llfuse >=1.2, <=1.3.6',
+ 'arvados-python-client{}'.format(pysdk_dep),
- # llfuse 1.3.4 fails to install via pip
- 'llfuse >=1.2, <1.3.4',
++ 'llfuse >= 1.3.6',
+ 'future',
'python-daemon',
'ciso8601 >= 2.0.0',
'setuptools',
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