[ARVADOS] updated: 4ccbea9ef440a7e4252b0df5e710dcb767831c60
Git user
git at public.curoverse.com
Mon Apr 24 23:50:54 EDT 2017
Summary of changes:
.../app/assets/javascripts/edit_collection.js | 12 ++
.../app/controllers/keep_disks_controller.rb | 1 +
apps/workbench/app/controllers/users_controller.rb | 1 +
apps/workbench/app/helpers/application_helper.rb | 2 +
apps/workbench/app/models/arvados_base.rb | 4 +
apps/workbench/app/models/arvados_resource_list.rb | 8 ++
apps/workbench/app/models/job.rb | 2 +-
apps/workbench/app/models/pipeline_instance.rb | 7 +-
apps/workbench/app/models/proxy_work_unit.rb | 1 +
apps/workbench/app/models/workflow.rb | 8 ++
.../app/views/collections/_show_files.html.erb | 14 ++-
.../app/views/workflows/_show_recent.html.erb | 65 ++++++++++
.../container_requests_controller_test.rb | 21 ++++
.../workbench/test/integration/collections_test.rb | 1 +
.../test/integration/container_requests_test.rb | 12 ++
apps/workbench/test/integration/work_units_test.rb | 24 ++++
.../test/unit/arvados_resource_list_test.rb | 8 ++
apps/workbench/test/unit/link_test.rb | 3 +
apps/workbench/test/unit/pipeline_instance_test.rb | 3 +
apps/workbench/test/unit/work_unit_test.rb | 3 +
build/run-build-packages.sh | 2 -
build/run-library.sh | 2 +
build/run-tests.sh | 2 +-
sdk/cli/bin/crunch-job | 8 +-
sdk/cli/test/binstub_arv-mount/arv-mount | 1 +
.../test/binstub_clean_fail/{mount => arv-mount} | 0
sdk/cli/test/test_crunch-job.rb | 4 +-
sdk/cwl/arvados_cwl/__init__.py | 37 +++---
sdk/cwl/arvados_cwl/crunch_script.py | 12 +-
sdk/cwl/arvados_cwl/fsaccess.py | 32 +++--
sdk/cwl/arvados_cwl/runner.py | 2 +-
sdk/cwl/setup.py | 2 +-
sdk/cwl/tests/listing-job.yml | 3 +
sdk/cwl/tests/test_container.py | 12 +-
sdk/cwl/tests/test_fsaccess.py | 28 +++++
sdk/cwl/tests/test_job.py | 9 +-
sdk/go/crunchrunner/crunchrunner.go | 66 +++++-----
sdk/go/crunchrunner/crunchrunner_test.go | 51 ++++----
sdk/go/dispatch/throttle_test.go | 29 +++--
sdk/python/arvados/_ranges.py | 6 +-
sdk/python/arvados/arvfile.py | 83 ++++++++++---
sdk/python/arvados/commands/get.py | 16 ++-
sdk/python/tests/test_arv_get.py | 49 ++++++--
sdk/python/tests/test_arvfile.py | 134 ++++++++++++++++++++-
sdk/python/tests/test_stream.py | 7 +-
...1_add_created_by_job_task_index_to_job_tasks.rb | 5 +
...0170419173712_add_object_owner_index_to_logs.rb | 5 +
...esting_container_index_to_container_requests.rb | 5 +
services/api/db/structure.sql | 29 ++++-
services/keep-web/handler.go | 14 +++
services/keep-web/handler_test.go | 31 +++++
51 files changed, 711 insertions(+), 175 deletions(-)
create mode 100644 apps/workbench/app/views/workflows/_show_recent.html.erb
create mode 100755 sdk/cli/test/binstub_arv-mount/arv-mount
rename sdk/cli/test/binstub_clean_fail/{mount => arv-mount} (100%)
create mode 100644 sdk/cwl/tests/listing-job.yml
create mode 100644 sdk/cwl/tests/test_fsaccess.py
create mode 100644 services/api/db/migrate/20170419173031_add_created_by_job_task_index_to_job_tasks.rb
create mode 100644 services/api/db/migrate/20170419173712_add_object_owner_index_to_logs.rb
create mode 100644 services/api/db/migrate/20170419175801_add_requesting_container_index_to_container_requests.rb
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commit 4ccbea9ef440a7e4252b0df5e710dcb767831c60
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Tue Apr 25 00:50:31 2017 -0300
10111: Tests added
diff --git a/apps/workbench/test/controllers/container_requests_controller_test.rb b/apps/workbench/test/controllers/container_requests_controller_test.rb
index 70e042c..6f5a6da 100644
--- a/apps/workbench/test/controllers/container_requests_controller_test.rb
+++ b/apps/workbench/test/controllers/container_requests_controller_test.rb
@@ -56,4 +56,25 @@ class ContainerRequestsControllerTest < ActionController::TestCase
assert_equal completed_cr['cmd'], copied_cr['cmd']
assert_equal completed_cr['runtime_constraints']['ram'], copied_cr['runtime_constraints'][:ram]
end
+
+ [
+ ['completed', true],
+ ['running', true],
+ ['queued', true],
+ ['uncommitted', false],
+ ].each do |cr_fixture, should_show|
+ test "provenance tab should #{should_show ? '' : 'not'} be shown on #{cr_fixture} container requests" do
+ cr = api_fixture('container_requests')[cr_fixture]
+ assert_not_nil cr
+ get(:show,
+ {id: cr['uuid']},
+ session_for(:active))
+ assert_response :success
+ if should_show
+ assert_includes @response.body, "href=\"#Provenance\""
+ else
+ assert_not_includes @response.body, "href=\"#Provenance\""
+ end
+ end
+ end
end
diff --git a/apps/workbench/test/integration/container_requests_test.rb b/apps/workbench/test/integration/container_requests_test.rb
index bd3a813..46f7e17 100644
--- a/apps/workbench/test/integration/container_requests_test.rb
+++ b/apps/workbench/test/integration/container_requests_test.rb
@@ -109,4 +109,16 @@ class ContainerRequestsTest < ActionDispatch::IntegrationTest
assert_text 'This workflow does not need any further inputs'
page.assert_selector 'a', text: 'Run'
end
+
+ test "Provenance graph shown on committed container requests" do
+ cr = api_fixture('container_requests', 'completed')
+ visit page_with_token("active", "/container_requests/#{cr['uuid']}")
+ assert page.has_text? 'Provenance'
+ click_link 'Provenance'
+ wait_for_ajax
+ # Check for provenance graph existance
+ page.assert_selector '#provenance_svg'
+ page.assert_selector 'ellipse+text', text: cr['name'], visible: false
+ page.assert_selector 'g.node>title', text: cr['uuid'], visible: false
+ end
end
commit c043e133b2646037ed630d571e91dbf77344f855
Merge: 93c9287 bf5d77b
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Mon Apr 24 17:07:19 2017 -0300
10111: Merge branch 'master' into 10111-cr-provenance-graph
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