Arvados

@ 54a93a3d

• Added workbench/test/diagnostics/container_request_test.rb

• The test executes the workflow uuid(s) configured in the "diagnostics" section

• Obviously, this requires a Crunch2 environment, hence currently this test can be used in 9tee4 environment

• To aid testing, in 9tee4 environment, I added an "Arvados tutorial" public project and added the tutorial CWL workflow. This can be used to configure the diagnostics test in jenkins

• To review using 9tee4 environment:

1. Add the following to your workbench application.yml file

diagnostics:
  secret_token: nicelongrandomlygeneratedsecrettoken
  arvados_workbench_url: https://workbench.9tee4.arvadosapi.com
  user_tokens:
    active: yourtokengoeshere
  container_requests_to_test:
    container_request_1:
      workflow_uuid: 9tee4-7fd4e-tyhlr6qigdl7oel
      input_paths: []
      max_wait_seconds: 300

2. Use the following command to run:

 RAILS_ENV=diagnostics bundle exec rake TEST=test/diagnostics/container_request_test.rb

Just a small comment: Should the pipeline diagnostics test be updated as the container request regarding the assertion of the "Pause" button?
Ran the diag test locally (on OSX didn't work, started Firefox and got a timeout 60secs later, worked on Virtualbox) and got the "Timeout" error:

  1) Error:
ContainerRequestTest#test_run_container_request:_container_request_1:
Timeout::Error: execution expired
    test/diagnostics_test_helper.rb:21:in `visit_page_with_token'
    test/diagnostics_test_helper.rb:73:in `block in wait_until_page_has'
    test/diagnostics_test_helper.rb:71:in `wait_until_page_has'
    test/diagnostics/container_request_test.rb:46:in `block (2 levels) in <class:ContainerRequestTest>'
    test/test_helper.rb:299:in `run'

... so it's all good until 9tee4 get it's env updates.

Ran the test again, with 9tee4 updated. All good, so LGTM!

I couldn't find a way to copy to other people's projects from the workbench so I ended up doing:

arv-copy --src settings --dst settings --project-uuid 9tee4-j7d0g-fgfwayv3uiv7b38 9tee4-4zz18-1mmqp9ag92paj69

as my admin account from the shell

radika take a look at

apps/workbench/app/controllers/work_units_controller.rb: attrs['command'] = ["arvados-cwl-runner", "--local", "--api=containers", "/var/lib/cwl/workflow.json#main", "/var/lib/cwl/cwl.input.json"]

where is that /var/lib/ referring to? ... this is failing