[ARVADOS] updated: 544222127959aed73c0fd90cb50813fe2c65bceb
Git user
git at public.curoverse.com
Tue Aug 30 16:42:26 EDT 2016
Summary of changes:
.../controllers/container_requests_controller.rb | 45 +-
apps/workbench/app/helpers/application_helper.rb | 143 ++++++
.../views/container_requests/_show_inputs.html.erb | 40 ++
.../test/integration/container_requests_test.rb | 99 ++++
apps/workbench/test/integration/projects_test.rb | 2 +-
apps/workbench/test/integration/work_units_test.rb | 2 +-
build/run-build-docker-jobs-image.sh | 18 +-
docker/.gitignore | 2 -
docker/README.md | 81 ---
docker/api/.gitolite.rc | 191 -------
docker/api/Dockerfile | 75 ---
docker/api/apache2_foreground.sh | 7 -
docker/api/apache2_vhost.in | 50 --
docker/api/application.yml.in | 67 ---
docker/api/apt.arvados.org.list | 2 -
docker/api/arvados-clients.yml.in | 6 -
docker/api/config_databases.sh.in | 15 -
docker/api/crunch-dispatch-run.sh | 24 -
docker/api/database.yml.in | 25 -
docker/api/keep_proxy.json | 6 -
docker/api/keep_server_0.json.in | 6 -
docker/api/keep_server_1.json.in | 6 -
docker/api/munge.key | Bin 1024 -> 0 bytes
docker/api/munge.sh | 3 -
docker/api/omniauth.rb.in | 18 -
docker/api/passenger.sh | 7 -
docker/api/setup-gitolite.sh.in | 73 ---
docker/api/setup.sh.in | 82 ---
docker/api/slurm.conf.in | 60 ---
docker/api/superuser_token.in | 1 -
docker/api/supervisor.conf | 43 --
docker/arv-web/Dockerfile | 15 -
docker/arv-web/apache2_foreground.sh | 8 -
docker/arv-web/apache2_vhost | 19 -
docker/arvdock | 559 ---------------------
docker/base/Dockerfile | 43 --
docker/base/apt.arvados.org.list | 2 -
docker/bcbio-nextgen/Dockerfile | 47 --
docker/build.sh | 41 --
docker/build_tools/Makefile | 281 -----------
docker/build_tools/build.rb | 232 ---------
docker/build_tools/config.rb | 74 ---
docker/compute/Dockerfile | 29 --
docker/compute/fuse.conf | 10 -
docker/compute/munge.sh | 3 -
docker/compute/setup.sh.in | 27 -
docker/compute/supervisor.conf | 28 --
docker/compute/wrapdocker | 90 ----
docker/config.yml.example | 91 ----
docker/doc/Dockerfile | 29 --
docker/doc/apache2_foreground.sh | 7 -
docker/doc/apache2_vhost.in | 11 -
docker/install_sdk.sh | 13 -
docker/java-bwa-samtools/Dockerfile | 23 -
docker/keep/Dockerfile | 14 -
docker/keep/keep_signing_secret.in | 1 -
docker/keep/run-keep.in | 11 -
docker/keepproxy/Dockerfile | 12 -
docker/keepproxy/run-keepproxy.in | 15 -
docker/mkimage-debootstrap.sh | 240 ---------
docker/passenger/Dockerfile | 19 -
docker/postgresql/Dockerfile | 35 --
docker/postgresql/pg_hba.conf | 15 -
docker/postgresql/postgresql.conf | 20 -
docker/shell/Dockerfile | 24 -
docker/shell/fuse.conf | 10 -
docker/shell/setup.sh.in | 19 -
docker/shell/superuser_token.in | 1 -
docker/shell/supervisor.conf | 15 -
docker/slurm/Dockerfile | 12 -
docker/slurm/munge.key | Bin 1024 -> 0 bytes
docker/slurm/slurm.conf.in | 60 ---
docker/slurm/supervisor.conf | 7 -
docker/sso/Dockerfile | 32 --
docker/sso/apache2_foreground.sh | 7 -
docker/sso/apache2_vhost.in | 50 --
docker/sso/application.yml.in | 30 --
docker/sso/database.yml.in | 22 -
docker/sso/seeds.rb.in | 9 -
docker/workbench/.gitignore | 3 -
docker/workbench/Dockerfile | 37 --
docker/workbench/apache2_foreground.sh | 7 -
docker/workbench/apache2_vhost.in | 35 --
docker/workbench/application.yml.in | 29 --
docker/workbench/production.rb.in | 91 ----
docker/workbench/secret_token.rb.in | 7 -
docker/workbench/workbench_rails_env.in | 1 -
sdk/cwl/arvados_cwl/fsaccess.py | 5 +
services/api/app/models/arvados_model.rb | 6 +
services/api/app/models/container_request.rb | 4 +-
services/api/test/fixtures/container_requests.yml | 416 +++++++++++++++
services/api/test/fixtures/workflows.yml | 4 +-
services/api/test/unit/container_request_test.rb | 6 +-
services/keepstore/keepstore.go | 2 +-
services/keepstore/s3_volume.go | 3 -
95 files changed, 767 insertions(+), 3450 deletions(-)
create mode 100644 apps/workbench/app/views/container_requests/_show_inputs.html.erb
create mode 100644 apps/workbench/test/integration/container_requests_test.rb
delete mode 100644 docker/.gitignore
delete mode 100644 docker/README.md
delete mode 100644 docker/api/.gitolite.rc
delete mode 100644 docker/api/Dockerfile
delete mode 100755 docker/api/apache2_foreground.sh
delete mode 100644 docker/api/apache2_vhost.in
delete mode 100644 docker/api/application.yml.in
delete mode 100644 docker/api/apt.arvados.org.list
delete mode 100644 docker/api/arvados-clients.yml.in
delete mode 100755 docker/api/config_databases.sh.in
delete mode 100755 docker/api/crunch-dispatch-run.sh
delete mode 100644 docker/api/database.yml.in
delete mode 100644 docker/api/keep_proxy.json
delete mode 100644 docker/api/keep_server_0.json.in
delete mode 100644 docker/api/keep_server_1.json.in
delete mode 100644 docker/api/munge.key
delete mode 100755 docker/api/munge.sh
delete mode 100644 docker/api/omniauth.rb.in
delete mode 100755 docker/api/passenger.sh
delete mode 100755 docker/api/setup-gitolite.sh.in
delete mode 100755 docker/api/setup.sh.in
delete mode 100644 docker/api/slurm.conf.in
delete mode 100644 docker/api/superuser_token.in
delete mode 100644 docker/api/supervisor.conf
delete mode 100644 docker/arv-web/Dockerfile
delete mode 100755 docker/arv-web/apache2_foreground.sh
delete mode 100644 docker/arv-web/apache2_vhost
delete mode 100755 docker/arvdock
delete mode 100644 docker/base/Dockerfile
delete mode 100644 docker/base/apt.arvados.org.list
delete mode 100644 docker/bcbio-nextgen/Dockerfile
delete mode 100755 docker/build.sh
delete mode 100644 docker/build_tools/Makefile
delete mode 100755 docker/build_tools/build.rb
delete mode 100755 docker/build_tools/config.rb
delete mode 100644 docker/compute/Dockerfile
delete mode 100644 docker/compute/fuse.conf
delete mode 100755 docker/compute/munge.sh
delete mode 100755 docker/compute/setup.sh.in
delete mode 100644 docker/compute/supervisor.conf
delete mode 100755 docker/compute/wrapdocker
delete mode 100644 docker/config.yml.example
delete mode 100644 docker/doc/Dockerfile
delete mode 100755 docker/doc/apache2_foreground.sh
delete mode 100644 docker/doc/apache2_vhost.in
delete mode 100755 docker/install_sdk.sh
delete mode 100644 docker/java-bwa-samtools/Dockerfile
delete mode 100644 docker/keep/Dockerfile
delete mode 100644 docker/keep/keep_signing_secret.in
delete mode 100755 docker/keep/run-keep.in
delete mode 100644 docker/keepproxy/Dockerfile
delete mode 100755 docker/keepproxy/run-keepproxy.in
delete mode 100755 docker/mkimage-debootstrap.sh
delete mode 100644 docker/passenger/Dockerfile
delete mode 100644 docker/postgresql/Dockerfile
delete mode 100644 docker/postgresql/pg_hba.conf
delete mode 100644 docker/postgresql/postgresql.conf
delete mode 100644 docker/shell/Dockerfile
delete mode 100644 docker/shell/fuse.conf
delete mode 100755 docker/shell/setup.sh.in
delete mode 100644 docker/shell/superuser_token.in
delete mode 100644 docker/shell/supervisor.conf
delete mode 100644 docker/slurm/Dockerfile
delete mode 100644 docker/slurm/munge.key
delete mode 100644 docker/slurm/slurm.conf.in
delete mode 100644 docker/slurm/supervisor.conf
delete mode 100644 docker/sso/Dockerfile
delete mode 100755 docker/sso/apache2_foreground.sh
delete mode 100644 docker/sso/apache2_vhost.in
delete mode 100644 docker/sso/application.yml.in
delete mode 100644 docker/sso/database.yml.in
delete mode 100644 docker/sso/seeds.rb.in
delete mode 100644 docker/workbench/.gitignore
delete mode 100644 docker/workbench/Dockerfile
delete mode 100755 docker/workbench/apache2_foreground.sh
delete mode 100644 docker/workbench/apache2_vhost.in
delete mode 100644 docker/workbench/application.yml.in
delete mode 100644 docker/workbench/production.rb.in
delete mode 100644 docker/workbench/secret_token.rb.in
delete mode 100644 docker/workbench/workbench_rails_env.in
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commit 544222127959aed73c0fd90cb50813fe2c65bceb
Merge: d980abb 5d70974
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Aug 30 16:42:19 2016 -0400
Merge branch 'master' into 9799-nonadmin-logs
Conflicts:
apps/workbench/test/integration/application_layout_test.rb
diff --cc apps/workbench/test/integration/work_units_test.rb
index fb5bc63,63ba275..f842d12
--- a/apps/workbench/test/integration/work_units_test.rb
+++ b/apps/workbench/test/integration/work_units_test.rb
@@@ -55,76 -55,4 +55,76 @@@ class WorkUnitsTest < ActionDispatch::I
assert_no_selector "a[href=\"#{link}\"]"
end
end
+
+ [
+ ['jobs', 'running_job_with_components', true],
+ ['pipeline_instances', 'components_is_jobspec', false],
+ ['containers', 'running', false],
+ ['container_requests', 'running', true],
+ ].each do |type, fixture, cancelable|
+ test "cancel button for #{type}/#{fixture}" do
+ if cancelable
+ need_selenium 'to cancel'
+ end
+
+ obj = api_fixture(type)[fixture]
+ visit page_with_token "active", "/#{type}/#{obj['uuid']}"
+
+ assert_text 'created_at'
+ if cancelable
+ assert_selector 'button', text: 'Cancel'
+ click_button 'Cancel'
+ wait_for_ajax
+ end
+ assert_no_selector 'button', text: 'Cancel'
+ end
+ end
+
+ [
+ ['jobs', 'running_job_with_components'],
+ ['pipeline_instances', 'has_component_with_completed_jobs'],
+ ['container_requests', 'running'],
+ ['container_requests', 'completed'],
+ ].each do |type, fixture|
+ test "edit description for #{type}/#{fixture}" do
+ obj = api_fixture(type)[fixture]
+ visit page_with_token "active", "/#{type}/#{obj['uuid']}"
+
+ within('.arv-description-as-subtitle') do
+ find('.fa-pencil').click
+ find('.editable-input textarea').set('*Textile description for object*')
+ find('.editable-submit').click
+ end
+ wait_for_ajax
+
+ # verify description
+ assert page.has_no_text? '*Textile description for object*'
+ assert page.has_text? 'Textile description for object'
+ end
+ end
+
+ [
+ ['Two Part Pipeline Template', 'part-one', 'Provide a value for the following'],
- ['Workflow with input specifications', 'this work has inputs specified', 'This container is uncommitted'],
++ ['Workflow with input specifications', 'this workflow has inputs specified', 'Provide a value for the following'],
+ ].each do |template_name, preview_txt, process_txt|
+ test "run a process using template #{template_name} from dashboard" do
+ visit page_with_token('admin')
+ assert_text 'Recent pipelines and processes' # seeing dashboard now
+
+ within('.recent-processes-actions') do
+ assert page.has_link?('All processes')
+ find('a', text: 'Run a pipeline').click
+ end
+
+ # in the chooser, verify preview and click Next button
+ within('.modal-dialog') do
+ find('.selectable', text: template_name).click
+ assert_text preview_txt
+ find('.btn', text: 'Next: choose inputs').click
+ end
+
+ # in the process page now
+ assert_text process_txt
+ end
+ end
end
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