[ARVADOS] created: 05f94a7837527f79df122e9942eaab166e987b15
Git user
git at public.curoverse.com
Wed Jan 4 09:26:25 EST 2017
at 05f94a7837527f79df122e9942eaab166e987b15 (commit)
commit 05f94a7837527f79df122e9942eaab166e987b15
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Wed Jan 4 11:25:20 2017 -0300
10223: Added support to CR output_name on cwl-runner. Updated test.
diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index dbbd83d..edf8c26 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -237,6 +237,7 @@ class RunnerContainer(Runner):
command = ["arvados-cwl-runner", "--local", "--api=containers"]
if self.output_name:
command.append("--output-name=" + self.output_name)
+ container_req["output_name"] = self.output_name
if self.output_tags:
command.append("--output-tags=" + self.output_tags)
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index a39972b..17b864b 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -469,6 +469,7 @@ class TestSubmit(unittest.TestCase):
logging.exception("")
stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-name="+output_name, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
+ stubs.expect_container_spec["output_name"] = output_name
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
commit f81427c5f93c159d26c3125aaa7ede4c5986dd07
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Mon Jan 2 18:14:33 2017 -0300
10223: Added output_name column to container_request. When being finalized, if output_name is set then the output
collection will be named accordingly. If there is a unique index violation, a date is added to its name.
Also, added output_name to CR search index.
diff --git a/services/api/app/models/container_request.rb b/services/api/app/models/container_request.rb
index f92fa21..4555820 100644
--- a/services/api/app/models/container_request.rb
+++ b/services/api/app/models/container_request.rb
@@ -35,18 +35,19 @@ class ContainerRequest < ArvadosModel
t.add :environment
t.add :expires_at
t.add :filters
+ t.add :log_uuid
t.add :mounts
t.add :name
+ t.add :output_name
t.add :output_path
+ t.add :output_uuid
t.add :priority
t.add :properties
t.add :requesting_container_uuid
t.add :runtime_constraints
+ t.add :scheduling_parameters
t.add :state
t.add :use_existing
- t.add :output_uuid
- t.add :log_uuid
- t.add :scheduling_parameters
end
# Supported states for a container request
@@ -90,15 +91,34 @@ class ContainerRequest < ArvadosModel
['output', 'log'].each do |out_type|
pdh = c.send(out_type)
next if pdh.nil?
+ if self.output_name and out_type == 'output'
+ coll_name = self.output_name
+ else
+ coll_name = "Container #{out_type} for request #{uuid}"
+ end
manifest = Collection.where(portable_data_hash: pdh).first.manifest_text
- coll = Collection.create!(owner_uuid: owner_uuid,
- manifest_text: manifest,
- portable_data_hash: pdh,
- name: "Container #{out_type} for request #{uuid}",
- properties: {
- 'type' => out_type,
- 'container_request' => uuid,
- })
+ begin
+ coll = Collection.create!(owner_uuid: owner_uuid,
+ manifest_text: manifest,
+ portable_data_hash: pdh,
+ name: coll_name,
+ properties: {
+ 'type' => out_type,
+ 'container_request' => uuid,
+ })
+ rescue ActiveRecord::RecordNotUnique => rn
+ ActiveRecord::Base.connection.execute 'ROLLBACK'
+ raise unless out_type == 'output' and self.output_name
+ # Postgres specific unique name check. See ApplicationController#create for
+ # a detailed explanation.
+ raise unless rn.original_exception.is_a? PG::UniqueViolation
+ err = rn.original_exception
+ detail = err.result.error_field(PG::Result::PG_DIAG_MESSAGE_DETAIL)
+ raise unless /^Key \(owner_uuid, name\)=\([a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15}, .*?\) already exists\./.match detail
+ # Output collection name collision detected: append a timestamp.
+ coll_name = "#{self.output_name} #{Time.now.getgm.strftime('%FT%TZ')}"
+ retry
+ end
if out_type == 'output'
out_coll = coll.uuid
else
@@ -269,7 +289,8 @@ class ContainerRequest < ArvadosModel
:container_image, :cwd, :description, :environment,
:filters, :mounts, :name, :output_path, :priority,
:properties, :requesting_container_uuid, :runtime_constraints,
- :state, :container_uuid, :use_existing, :scheduling_parameters
+ :state, :container_uuid, :use_existing, :scheduling_parameters,
+ :output_name
when Committed
if container_uuid.nil?
@@ -281,14 +302,16 @@ class ContainerRequest < ArvadosModel
end
# Can update priority, container count, name and description
- permitted.push :priority, :container_count, :container_count_max, :container_uuid, :name, :description
+ permitted.push :priority, :container_count, :container_count_max, :container_uuid,
+ :name, :description
if self.state_changed?
# Allow create-and-commit in a single operation.
permitted.push :command, :container_image, :cwd, :description, :environment,
:filters, :mounts, :name, :output_path, :properties,
:requesting_container_uuid, :runtime_constraints,
- :state, :container_uuid, :use_existing, :scheduling_parameters
+ :state, :container_uuid, :use_existing, :scheduling_parameters,
+ :output_name
end
when Final
diff --git a/services/api/db/migrate/20161223090712_add_output_name_to_container_requests.rb b/services/api/db/migrate/20161223090712_add_output_name_to_container_requests.rb
new file mode 100644
index 0000000..0e6adfb
--- /dev/null
+++ b/services/api/db/migrate/20161223090712_add_output_name_to_container_requests.rb
@@ -0,0 +1,9 @@
+class AddOutputNameToContainerRequests < ActiveRecord::Migration
+ def up
+ add_column :container_requests, :output_name, :string, :default => nil
+ end
+
+ def down
+ remove_column :container_requests, :output_name
+ end
+end
diff --git a/services/api/db/migrate/20170102153111_add_output_name_to_container_request_search_index.rb b/services/api/db/migrate/20170102153111_add_output_name_to_container_request_search_index.rb
new file mode 100644
index 0000000..0bd7c47
--- /dev/null
+++ b/services/api/db/migrate/20170102153111_add_output_name_to_container_request_search_index.rb
@@ -0,0 +1,21 @@
+class AddOutputNameToContainerRequestSearchIndex < ActiveRecord::Migration
+ def up
+ begin
+ remove_index :container_requests, :name => 'container_requests_search_index'
+ rescue
+ end
+ add_index :container_requests,
+ ["uuid", "owner_uuid", "modified_by_client_uuid", "modified_by_user_uuid", "name", "state", "requesting_container_uuid", "container_uuid", "container_image", "cwd", "output_path", "output_uuid", "log_uuid", "output_name"],
+ name: "container_requests_search_index"
+ end
+
+ def down
+ begin
+ remove_index :container_requests, :name => 'container_requests_search_index'
+ rescue
+ end
+ add_index :container_requests,
+ ["uuid", "owner_uuid", "modified_by_client_uuid", "modified_by_user_uuid", "name", "state", "requesting_container_uuid", "container_uuid", "container_image", "cwd", "output_path", "output_uuid", "log_uuid"],
+ name: "container_requests_search_index"
+ end
+end
diff --git a/services/api/db/structure.sql b/services/api/db/structure.sql
index 7ee7ea6..fb32872 100644
--- a/services/api/db/structure.sql
+++ b/services/api/db/structure.sql
@@ -294,7 +294,8 @@ CREATE TABLE container_requests (
use_existing boolean DEFAULT true,
scheduling_parameters text,
output_uuid character varying(255),
- log_uuid character varying(255)
+ log_uuid character varying(255),
+ output_name character varying(255) DEFAULT NULL::character varying
);
@@ -1527,7 +1528,7 @@ CREATE INDEX container_requests_full_text_search_idx ON container_requests USING
-- Name: container_requests_search_index; Type: INDEX; Schema: public; Owner: -; Tablespace:
--
-CREATE INDEX container_requests_search_index ON container_requests USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name, state, requesting_container_uuid, container_uuid, container_image, cwd, output_path, output_uuid, log_uuid);
+CREATE INDEX container_requests_search_index ON container_requests USING btree (uuid, owner_uuid, modified_by_client_uuid, modified_by_user_uuid, name, state, requesting_container_uuid, container_uuid, container_image, cwd, output_path, output_uuid, log_uuid, output_name);
--
@@ -2706,4 +2707,8 @@ INSERT INTO schema_migrations (version) VALUES ('20161115171221');
INSERT INTO schema_migrations (version) VALUES ('20161115174218');
-INSERT INTO schema_migrations (version) VALUES ('20161213172944');
\ No newline at end of file
+INSERT INTO schema_migrations (version) VALUES ('20161213172944');
+
+INSERT INTO schema_migrations (version) VALUES ('20161223090712');
+
+INSERT INTO schema_migrations (version) VALUES ('20170102153111');
\ No newline at end of file
diff --git a/services/api/test/unit/container_request_test.rb b/services/api/test/unit/container_request_test.rb
index c4d1efe..1f65c01 100644
--- a/services/api/test/unit/container_request_test.rb
+++ b/services/api/test/unit/container_request_test.rb
@@ -505,6 +505,41 @@ class ContainerRequestTest < ActiveSupport::TestCase
assert_equal prev_container_uuid, cr.container_uuid
end
+ test "Set up output collection on finalized container request" do
+ set_user_from_auth :active
+ output_name = 'Test output collection'
+ cr = create_minimal_req!(priority: 1,
+ state: ContainerRequest::Committed,
+ output_name: output_name)
+ cr.reload
+ act_as_system_user do
+ c = Container.find_by_uuid(cr.container_uuid)
+ c.update_attributes!(state: Container::Locked)
+ c.update_attributes!(state: Container::Running)
+ c.update_attributes!(state: Container::Complete,
+ exit_code: 0,
+ output: '1f4b0bc7583c2a7f9102c395f4ffc5e3+45',
+ log: 'fa7aeb5140e2848d39b416daeef4ffc5+45')
+ end
+ cr.reload
+ output_coll = Collection.find_by_uuid(cr.output_uuid)
+ assert_not_nil output_coll
+ assert_equal output_coll.name, output_name
+ # Now ask for a second CR, equal to the first one so it will reuse the container
+ cr2 = create_minimal_req!(priority: 1,
+ state: ContainerRequest::Uncommitted,
+ output_name: output_name)
+ cr2.state = ContainerRequest::Committed
+ cr2.save
+ assert_equal ContainerRequest::Final, cr2.state
+ output_coll_2 = Collection.find_by_uuid(cr2.output_uuid)
+ # Make sure the resulting output collection name include the original name
+ # plus the date
+ assert_not_equal output_coll_2.name, output_coll.name
+ assert output_coll_2.name.include? output_name
+ assert_match /\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}Z/, output_coll_2.name
+ end
+
test "Finalize committed request when reusing a finished container" do
set_user_from_auth :active
cr = create_minimal_req!(priority: 1, state: ContainerRequest::Committed)
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