[ARVADOS] updated: 1.3.0-1224-g231a86fd3
Git user
git at public.curoverse.com
Thu Jun 27 14:51:17 UTC 2019
Summary of changes:
.../app/assets/javascripts/components/edit_tags.js | 51 ++-
.../app/views/projects/_container_summary.html.erb | 42 +++
.../app/views/projects/_show_dashboard.html.erb | 10 +
build/run-tests.sh | 44 ++-
cmd/arvados-server/cmd.go | 2 +
doc/_config.yml | 4 +-
...min_list_collections_without_property_py.liquid | 15 +
...property_to_collections_under_project_py.liquid | 36 ++
.../_admin_update_collection_property_py.liquid | 22 ++
doc/_includes/_install_compute_docker.liquid | 2 +-
doc/_includes/_install_postgres_database.liquid | 31 +-
doc/_includes/_mount_types.liquid | 2 +-
doc/_includes/_navbar_top.liquid | 2 +-
...llection-managed-properties.html.textile.liquid | 85 +++++
doc/admin/upgrading.html.textile.liquid | 31 +-
doc/install/install-postgresql.html.textile.liquid | 8 +-
doc/sdk/index.html.textile.liquid | 2 +-
.../collection-versioning.html.textile.liquid | 2 +-
lib/cloud/cloudtest/cmd.go | 153 +++++++++
lib/cloud/cloudtest/tester.go | 377 +++++++++++++++++++++
lib/cloud/cloudtest/tester_test.go | 97 ++++++
lib/config/config.default.yml | 16 +-
lib/config/export.go | 3 +
lib/config/generated_config.go | 16 +-
lib/controller/federation.go | 2 +-
lib/dispatchcloud/dispatcher.go | 15 +
lib/dispatchcloud/dispatcher_test.go | 9 +-
lib/dispatchcloud/driver.go | 15 +-
lib/dispatchcloud/scheduler/interfaces.go | 3 +-
lib/dispatchcloud/scheduler/run_queue_test.go | 5 +-
lib/dispatchcloud/scheduler/sync.go | 1 +
lib/dispatchcloud/ssh_executor/executor.go | 25 +-
lib/dispatchcloud/worker/pool.go | 39 ++-
lib/dispatchcloud/worker/verify.go | 14 +-
sdk/cwl/arvados_cwl/executor.py | 15 +-
sdk/cwl/arvados_cwl/pathmapper.py | 20 +-
sdk/cwl/arvados_cwl/runner.py | 5 +-
...13976-keepref-wf.cwl => 15295-bad-keep-ref.cwl} | 7 +-
sdk/cwl/tests/arvados-tests.yml | 6 +
sdk/cwl/tests/badkeep.yml | 3 +
sdk/go/arvados/config.go | 7 +-
.../src/main/java/org/arvados/sdk/Arvados.java | 2 +-
.../arvados/v1/containers_controller.rb | 3 +-
services/api/app/models/arvados_model.rb | 24 ++
services/api/app/models/collection.rb | 38 +++
services/api/app/models/container.rb | 61 ++--
...0523180148_add_trigram_index_for_text_search.rb | 44 +++
services/api/db/structure.sql | 67 +++-
services/api/lib/record_filters.rb | 8 +
services/api/test/fixtures/containers.yml | 1 +
.../arvados/v1/containers_controller_test.rb | 2 +-
services/api/test/unit/arvados_model_test.rb | 24 ++
services/api/test/unit/collection_test.rb | 61 ++++
services/keep-balance/balance_test.go | 3 +-
tools/arvbox/bin/arvbox | 6 +
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 2 +-
tools/arvbox/lib/arvbox/docker/api-setup.sh | 2 +-
.../lib/arvbox/docker/runit-docker/runit-docker.c | 2 +-
58 files changed, 1449 insertions(+), 145 deletions(-)
create mode 100644 apps/workbench/app/views/projects/_container_summary.html.erb
create mode 100644 doc/_includes/_admin_list_collections_without_property_py.liquid
create mode 100644 doc/_includes/_admin_set_property_to_collections_under_project_py.liquid
create mode 100644 doc/_includes/_admin_update_collection_property_py.liquid
create mode 100644 doc/admin/collection-managed-properties.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
copy sdk/cwl/tests/{13976-keepref-wf.cwl => 15295-bad-keep-ref.cwl} (54%)
create mode 100644 sdk/cwl/tests/badkeep.yml
create mode 100644 services/api/db/migrate/20190523180148_add_trigram_index_for_text_search.rb
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commit 231a86fd3f7e30e9f66d71d92ad7c26578637e37
Merge: 3a2857440 10d70a1c0
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Thu Jun 27 10:50:58 2019 -0400
14287: Merge branch 'master'
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
diff --cc services/api/test/unit/collection_test.rb
index e75ad5d77,c2bf94fe7..2dd6eedcf
--- a/services/api/test/unit/collection_test.rb
+++ b/services/api/test/unit/collection_test.rb
@@@ -1013,20 -1013,64 +1013,81 @@@ class CollectionTest < ActiveSupport::T
assert_empty Collection.where(uuid: uuid)
end
+ test "empty names are exempt from name uniqueness" do
+ act_as_user users(:active) do
+ c1 = Collection.new(name: nil, manifest_text: '', owner_uuid: groups(:aproject).uuid)
+ assert c1.save
+ c2 = Collection.new(name: '', manifest_text: '', owner_uuid: groups(:aproject).uuid)
+ assert c2.save
+ c3 = Collection.new(name: '', manifest_text: '', owner_uuid: groups(:aproject).uuid)
+ assert c3.save
+ c4 = Collection.new(name: 'c4', manifest_text: '', owner_uuid: groups(:aproject).uuid)
+ assert c4.save
+ c5 = Collection.new(name: 'c4', manifest_text: '', owner_uuid: groups(:aproject).uuid)
+ assert_raises(ActiveRecord::RecordNotUnique) do
+ c5.save
+ end
+ end
+ end
++
+ test "create collections with managed properties" do
+ Rails.configuration.Collections.ManagedProperties = {
+ 'default_prop1' => {'Value' => 'prop1_value'},
+ 'responsible_person_uuid' => {'Function' => 'original_owner'}
+ }
+ # Test collection without initial properties
+ act_as_user users(:active) do
+ c = create_collection 'foo', Encoding::US_ASCII
+ assert c.valid?
+ assert_not_empty c.properties
+ assert_equal 'prop1_value', c.properties['default_prop1']
+ assert_equal users(:active).uuid, c.properties['responsible_person_uuid']
+ end
+ # Test collection with default_prop1 property already set
+ act_as_user users(:active) do
+ c = Collection.create(manifest_text: ". d41d8cd98f00b204e9800998ecf8427e 0:34:foo.txt\n",
+ properties: {'default_prop1' => 'custom_value'})
+ assert c.valid?
+ assert_not_empty c.properties
+ assert_equal 'custom_value', c.properties['default_prop1']
+ assert_equal users(:active).uuid, c.properties['responsible_person_uuid']
+ end
+ # Test collection inside a sub project
+ act_as_user users(:active) do
+ c = Collection.create(manifest_text: ". d41d8cd98f00b204e9800998ecf8427e 0:34:foo.txt\n",
+ owner_uuid: groups(:asubproject).uuid)
+ assert c.valid?
+ assert_not_empty c.properties
+ assert_equal users(:active).uuid, c.properties['responsible_person_uuid']
+ end
+ end
+
+ test "update collection with protected managed properties" do
+ Rails.configuration.Collections.ManagedProperties = {
+ 'default_prop1' => {'Value' => 'prop1_value', 'Protected' => true},
+ }
+ act_as_user users(:active) do
+ c = create_collection 'foo', Encoding::US_ASCII
+ assert c.valid?
+ assert_not_empty c.properties
+ assert_equal 'prop1_value', c.properties['default_prop1']
+ # Add new property
+ c.properties['prop2'] = 'value2'
+ c.save!
+ c.reload
+ assert_equal 'value2', c.properties['prop2']
+ # Try to change protected property's value
+ c.properties['default_prop1'] = 'new_value'
+ assert_raises(ArvadosModel::PermissionDeniedError) do
+ c.save!
+ end
+ # Admins are allowed to change protected properties
+ act_as_system_user do
+ c.properties['default_prop1'] = 'new_value'
+ c.save!
+ c.reload
+ assert_equal 'new_value', c.properties['default_prop1']
+ end
+ end
+ end
end
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