[ARVADOS] updated: 820cd60245b86032f81fb1265e7f5074aa38ff79
Git user
git at public.curoverse.com
Fri May 19 17:55:27 EDT 2017
Summary of changes:
.../workbench/app/assets/javascripts/filterable.js | 2 +-
.../app/controllers/application_controller.rb | 7 +
.../controllers/container_requests_controller.rb | 61 ++-
.../app/controllers/projects_controller.rb | 20 +-
.../app/controllers/workflows_controller.rb | 4 +
apps/workbench/app/helpers/application_helper.rb | 6 +
apps/workbench/app/helpers/provenance_helper.rb | 109 +++---
apps/workbench/app/models/container.rb | 4 +-
apps/workbench/app/models/container_request.rb | 4 +-
apps/workbench/app/models/container_work_unit.rb | 44 ++-
apps/workbench/app/models/work_unit.rb | 4 +
.../application/_show_text_with_locators.html.erb | 31 ++
.../_show_recent.html.erb | 22 +-
.../container_requests/_show_recent_rows.html.erb | 36 ++
.../app/views/container_requests/index.html.erb | 11 +
.../app/views/projects/_show_tab_contents.html.erb | 2 +-
.../app/views/users/_show_activity.html.erb | 2 +-
.../views/work_units/_component_detail.html.erb | 97 ++++-
.../app/views/work_units/_show_status.html.erb | 19 +-
.../app/views/work_units/_show_table_data.html.erb | 14 +
.../app/views/workflows/_show_definition.html.erb | 48 +++
apps/workbench/app/views/workflows/show.html.erb | 20 +
apps/workbench/fpm-info.sh | 9 +-
.../container_requests_controller_test.rb | 16 +
.../test/controllers/workflows_controller_test.rb | 12 +
.../test/integration/container_requests_test.rb | 28 ++
apps/workbench/test/integration/projects_test.rb | 18 +
apps/workbench/test/integration/work_units_test.rb | 17 +
apps/workbench/test/unit/work_unit_test.rb | 4 +-
.../ubuntu1604/Dockerfile | 2 +-
build/run-build-packages-one-target.sh | 8 +
build/run-library.sh | 8 +-
build/run-tests.sh | 113 +++---
doc/Rakefile | 3 +-
...nstall-manual-prerequisites.html.textile.liquid | 5 +-
sdk/cwl/arvados_cwl/__init__.py | 11 +-
sdk/cwl/arvados_cwl/arvcontainer.py | 26 +-
sdk/cwl/arvados_cwl/arvjob.py | 1 +
sdk/cwl/arvados_cwl/crunch_script.py | 3 +-
sdk/cwl/setup.py | 4 +-
sdk/cwl/tests/test_container.py | 34 +-
sdk/cwl/tests/test_job.py | 2 +-
sdk/go/arvados/container.go | 1 +
sdk/python/arvados/__init__.py | 55 +--
sdk/python/arvados/_normalize_stream.py | 5 +-
sdk/python/arvados/_ranges.py | 8 +-
sdk/python/arvados/api.py | 21 +-
sdk/python/arvados/arvfile.py | 106 +++---
sdk/python/arvados/cache.py | 9 +-
sdk/python/arvados/collection.py | 108 +++---
sdk/python/arvados/commands/_util.py | 2 -
sdk/python/arvados/commands/arv_copy.py | 24 +-
sdk/python/arvados/commands/get.py | 14 +-
sdk/python/arvados/commands/keepdocker.py | 11 +-
sdk/python/arvados/commands/ls.py | 5 +-
sdk/python/arvados/commands/migrate19.py | 21 +-
sdk/python/arvados/commands/put.py | 56 +--
sdk/python/arvados/commands/run.py | 15 +-
sdk/python/arvados/commands/ws.py | 5 +-
sdk/python/arvados/crunch.py | 1 +
sdk/python/arvados/errors.py | 4 +-
sdk/python/arvados/events.py | 31 +-
sdk/python/arvados/keep.py | 104 ++++--
sdk/python/arvados/retry.py | 8 +-
sdk/python/arvados/safeapi.py | 14 +-
sdk/python/arvados/stream.py | 30 +-
sdk/python/arvados/timer.py | 4 +-
sdk/python/arvados/util.py | 8 +-
sdk/python/bin/arv-get | 2 +-
sdk/python/setup.py | 9 +-
sdk/python/tests/arvados_testutil.py | 77 +++-
sdk/python/tests/keepstub.py | 130 +++++--
sdk/python/tests/manifest_examples.py | 5 +-
.../tests/performance/performance_profiler.py | 14 +-
sdk/python/tests/performance/test_a_sample.py | 7 +-
sdk/python/tests/run_test_server.py | 13 +-
sdk/python/tests/test_api.py | 27 +-
sdk/python/tests/test_arv_copy.py | 17 +-
sdk/python/tests/test_arv_get.py | 35 +-
sdk/python/tests/test_arv_keepdocker.py | 39 +-
sdk/python/tests/test_arv_ls.py | 25 +-
sdk/python/tests/test_arv_normalize.py | 25 +-
sdk/python/tests/test_arv_put.py | 79 ++--
sdk/python/tests/test_arv_run.py | 17 +-
sdk/python/tests/test_arv_ws.py | 16 +-
sdk/python/tests/test_arvfile.py | 343 +++++++++--------
sdk/python/tests/test_benchmark_collections.py | 11 +-
sdk/python/tests/test_cache.py | 20 +-
sdk/python/tests/test_collections.py | 410 ++++++++++++++-------
sdk/python/tests/test_errors.py | 21 +-
sdk/python/tests/test_events.py | 52 +--
sdk/python/tests/test_keep_client.py | 164 ++++-----
sdk/python/tests/test_keep_locator.py | 20 +-
sdk/python/tests/test_pipeline_template.py | 3 +-
sdk/python/tests/test_retry.py | 15 +-
sdk/python/tests/test_retry_job_helpers.py | 8 +-
sdk/python/tests/test_stream.py | 50 +--
sdk/python/tests/test_util.py | 6 +-
.../api/app/controllers/application_controller.rb | 32 +-
.../arvados/v1/collections_controller.rb | 4 -
.../arvados/v1/containers_controller.rb | 9 +
.../controllers/arvados/v1/groups_controller.rb | 21 +-
.../controllers/arvados/v1/schema_controller.rb | 7 +
services/api/app/models/arvados_model.rb | 20 +
services/api/app/models/collection.rb | 4 +
services/api/app/models/container.rb | 49 ++-
services/api/app/models/container_request.rb | 4 +
services/api/app/models/job.rb | 91 ++++-
services/api/app/models/pipeline_instance.rb | 4 +
services/api/app/models/pipeline_template.rb | 4 +
services/api/app/models/workflow.rb | 4 +
services/api/config/application.default.yml | 35 +-
services/api/config/application.rb | 2 +
.../api/config/initializers/noop_deep_munge.rb | 10 -
services/api/fpm-info.sh | 2 +-
.../test/fixtures/api_client_authorizations.yml | 7 +
services/api/test/fixtures/container_requests.yml | 33 ++
services/api/test/fixtures/containers.yml | 8 +
.../arvados/v1/containers_controller_test.rb | 23 ++
.../arvados/v1/groups_controller_test.rb | 15 +
services/api/test/integration/groups_test.rb | 13 +
...{noop_deep_munge.rb => noop_deep_munge_test.rb} | 29 +-
services/api/test/unit/container_test.rb | 17 +-
services/api/test/unit/job_test.rb | 18 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 26 +-
.../crunch-dispatch-slurm_test.go | 98 +++--
services/crunch-run/crunchrun.go | 161 ++++++--
services/crunch-run/crunchrun_test.go | 121 +++++-
services/crunch-run/logging.go | 234 +++++++++++-
services/crunch-run/logging_test.go | 43 +++
services/keepstore/azure_blob_volume.go | 5 +
services/keepstore/handlers.go | 52 ++-
services/keepstore/mounts_test.go | 104 ++++++
services/keepstore/pull_worker.go | 87 +++--
services/keepstore/pull_worker_integration_test.go | 25 +-
services/keepstore/pull_worker_test.go | 234 ++++++------
services/keepstore/s3_volume.go | 5 +
services/keepstore/trash_worker.go | 12 +-
services/keepstore/trash_worker_test.go | 29 +-
services/keepstore/volume.go | 65 ++++
services/keepstore/volume_test.go | 4 +
services/keepstore/volume_unix.go | 77 ++++
services/keepstore/work_queue_test.go | 22 +-
services/nodemanager/arvnodeman/jobqueue.py | 8 +-
services/nodemanager/tests/test_jobqueue.py | 2 +-
services/ws/config.go | 25 +-
services/ws/event_source.go | 9 +-
services/ws/server.go | 5 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 3 +-
149 files changed, 3589 insertions(+), 1553 deletions(-)
create mode 100644 apps/workbench/app/views/application/_show_text_with_locators.html.erb
copy apps/workbench/app/views/{pipeline_instances => container_requests}/_show_recent.html.erb (60%)
create mode 100644 apps/workbench/app/views/container_requests/_show_recent_rows.html.erb
create mode 100644 apps/workbench/app/views/container_requests/index.html.erb
create mode 100644 apps/workbench/app/views/work_units/_show_table_data.html.erb
create mode 100644 apps/workbench/app/views/workflows/_show_definition.html.erb
create mode 100644 apps/workbench/app/views/workflows/show.html.erb
mode change 100755 => 100644 sdk/python/arvados/commands/ls.py
delete mode 100644 services/api/config/initializers/noop_deep_munge.rb
rename services/api/test/integration/{noop_deep_munge.rb => noop_deep_munge_test.rb} (63%)
create mode 100644 services/keepstore/mounts_test.go
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commit 820cd60245b86032f81fb1265e7f5074aa38ff79
Author: radhika <radhika at curoverse.com>
Date: Fri May 19 17:55:01 2017 -0400
9587: project#Trash tab displays trashed collections
diff --git a/apps/workbench/app/controllers/projects_controller.rb b/apps/workbench/app/controllers/projects_controller.rb
index 0322b52..4009f12 100644
--- a/apps/workbench/app/controllers/projects_controller.rb
+++ b/apps/workbench/app/controllers/projects_controller.rb
@@ -259,14 +259,18 @@ class ProjectsController < ApplicationController
@next_page_href = nil
end
else
- @objects = @object.contents(order: @order,
- include_trash: true,
- limit: @limit,
- filters: @filters,
- offset: @offset)
- @next_page_href = next_page_href(partial: :contents_rows,
- filters: @filters.to_json,
- order: @order.to_json)
+ contents_args = {order: @order,
+ limit: @limit,
+ filters: @filters,
+ offset: @offset}
+ contents_args[:include_trash] = true if params[:include_trash]
+ @objects = @object.contents(contents_args)
+
+ next_page_args = {partial: :contents_rows,
+ filters: @filters.to_json,
+ order: @order.to_json}
+ next_page_args[:include_trash] = true if params[:include_trash]
+ @next_page_href = next_page_href(next_page_args)
end
preload_links_for_objects(@objects.to_a)
diff --git a/apps/workbench/app/views/projects/_show_tab_contents.html.erb b/apps/workbench/app/views/projects/_show_tab_contents.html.erb
index a33a1cf..b9a9d07 100644
--- a/apps/workbench/app/views/projects/_show_tab_contents.html.erb
+++ b/apps/workbench/app/views/projects/_show_tab_contents.html.erb
@@ -89,7 +89,7 @@
<col width="60%" style="width: 60%;" />
<col width="40%" style="width: 40%;" />
</colgroup>
- <tbody data-infinite-scroller="#<%= tab_pane %>-scroll" data-infinite-content-href="<%= url_for partial: :contents_rows %>" data-infinite-content-params-projecttab="<%= local_assigns.select{|k| [:order, :limit, :filters].include? k }.to_json %>" data-infinite-content-params-attr="projecttab">
+ <tbody data-infinite-scroller="#<%= tab_pane %>-scroll" data-infinite-content-href="<%= url_for partial: :contents_rows %>" data-infinite-content-params-projecttab="<%= local_assigns.select{|k| [:order, :limit, :filters, :include_trash].include? k }.to_json %>" data-infinite-content-params-attr="projecttab">
</tbody>
<thead>
<tr>
diff --git a/apps/workbench/test/integration/projects_test.rb b/apps/workbench/test/integration/projects_test.rb
index 8a47a53..1aa7bf7 100644
--- a/apps/workbench/test/integration/projects_test.rb
+++ b/apps/workbench/test/integration/projects_test.rb
@@ -752,4 +752,22 @@ class ProjectsTest < ActionDispatch::IntegrationTest
assert_text project['name']
end
end
+
+ test 'check trash tab' do
+ visit page_with_token 'active', '/projects'
+ find("#projects-menu").click
+ within('.dropdown-menu') do
+ first('li', text: 'Home').click
+ end
+
+ untrashed_collection = api_fixture('collections')['collection_owned_by_active']
+ trashed_collection = api_fixture('collections')['deleted_on_next_sweep']
+ assert_text untrashed_collection['name']
+ assert_no_text trashed_collection['name']
+
+ # go to Trash tab and verify contents
+ click_link 'Trash'
+ assert_text trashed_collection['name']
+ assert_no_text untrashed_collection['name']
+ end
end
commit 9b949e31f7c37f35b9695e7c35e7bd7d1064ac95
Merge: 35f06a3 49a9c33
Author: radhika <radhika at curoverse.com>
Date: Fri May 19 15:40:47 2017 -0400
Merge branch 'master' into 9587-wb-trash-tab
commit 35f06a3ed12fd7f70879ef5c8c3716d42a3387bb
Merge: a0431de c182087
Author: radhika <radhika at curoverse.com>
Date: Thu May 18 16:10:05 2017 -0400
Merge branch 'master' into 9587-wb-trash-tab
commit a0431de218861e6b1dccde591ba30e88d4d13741
Merge: 541d476 6e5079f
Author: radhika <radhika at curoverse.com>
Date: Wed May 17 14:29:18 2017 -0400
Merge branch 'master' into 9587-wb-trash-tab
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