[ARVADOS] updated: edc5e4b6645b9b983a85a892bf3d3ad1432a657d
git at public.curoverse.com
git at public.curoverse.com
Wed Oct 1 15:45:23 EDT 2014
Summary of changes:
apps/workbench/Gemfile | 1 +
apps/workbench/Gemfile.lock | 4 +
apps/workbench/app/assets/javascripts/dates.js | 3 +
.../app/assets/stylesheets/application.css.scss | 13 +
.../app/assets/stylesheets/projects.css.scss | 9 +-
.../app/controllers/application_controller.rb | 26 +-
.../app/controllers/collections_controller.rb | 10 +-
.../controllers/pipeline_instances_controller.rb | 18 +-
.../app/controllers/projects_controller.rb | 19 +-
apps/workbench/app/controllers/users_controller.rb | 22 +-
apps/workbench/app/helpers/application_helper.rb | 6 +-
.../app/helpers/pipeline_components_helper.rb | 3 +-
.../app/helpers/pipeline_instances_helper.rb | 115 +++++--
apps/workbench/app/models/arvados_base.rb | 4 +-
apps/workbench/app/models/collection.rb | 2 +-
apps/workbench/app/models/job.rb | 20 +-
apps/workbench/app/models/node.rb | 2 +-
apps/workbench/app/models/pipeline_instance.rb | 8 +-
apps/workbench/app/models/user.rb | 2 +-
apps/workbench/app/models/virtual_machine.rb | 2 +-
.../app/views/application/_content_layout.html.erb | 10 +-
.../views/application/_job_status_label.html.erb | 5 +-
.../{show.html.erb => _title_and_buttons.html.erb} | 22 +-
apps/workbench/app/views/application/show.html.erb | 71 +----
.../collections/_show_source_summary.html.erb | 3 +-
.../workbench/app/views/jobs/_show_recent.html.erb | 2 +-
.../workbench/app/views/jobs/_show_status.html.erb | 110 ++-----
apps/workbench/app/views/jobs/show.html.erb | 32 ++
...unning.html.erb => _running_component.html.erb} | 123 ++------
.../_show_components_json.html.erb | 14 +
.../_show_components_running.html.erb | 252 +++------------
.../views/projects/_compute_node_status.html.erb | 45 ++-
.../views/projects/_compute_node_summary.html.erb | 10 +-
.../app/views/projects/_show_dashboard.html.erb | 103 +++---
.../app/views/users/_manage_repositories.html.erb | 5 +-
apps/workbench/app/views/users/_tables.html.erb | 2 +-
apps/workbench/config/application.default.yml | 16 +-
apps/workbench/config/application.yml.example | 4 +-
apps/workbench/test/diagnostics/pipeline_test.rb | 2 +-
.../test/functional/actions_controller_test.rb | 12 +-
.../test/functional/collections_controller_test.rb | 41 +--
.../pipeline_instances_controller_test.rb | 110 ++++++-
.../test/functional/users_controller_test.rb | 11 +
.../test/integration/pipeline_instances_test.rb | 41 +++
apps/workbench/test/integration/projects_test.rb | 34 +-
.../test/integration/user_profile_test.rb | 2 +-
apps/workbench/test/test_helper.rb | 23 +-
doc/api/methods/nodes.html.textile.liquid | 2 +
doc/api/schema/Job.html.textile.liquid | 1 +
doc/api/schema/Node.html.textile.liquid | 1 +
docker/api/Dockerfile | 3 +-
docker/api/application.yml.in | 2 +
docker/base/Dockerfile | 2 +-
docker/build_tools/build.rb | 1 +
docker/config.yml.example | 5 +
docker/jobs/Dockerfile | 5 +-
docker/passenger/Dockerfile | 6 +-
sdk/cli/Gemfile.lock | 32 +-
sdk/cli/README.textile | 11 -
sdk/cli/arvados-cli.gemspec | 17 +-
sdk/cli/bin/arv-run-pipeline-instance | 74 ++---
sdk/cli/bin/crunch-job | 38 ++-
sdk/go/arvadosclient/arvadosclient_test.go | 8 +-
sdk/go/keepclient/keepclient_test.go | 4 +-
sdk/python/arvados/commands/keepdocker.py | 2 +-
sdk/python/arvados/keep.py | 16 +-
sdk/python/bin/arv-get | 6 +-
sdk/python/setup.py | 22 +-
sdk/python/tests/run_test_server.py | 8 +-
sdk/python/tests/test_keep_client.py | 38 +++
sdk/ruby/arvados.gemspec | 21 +-
.../api/app/controllers/application_controller.rb | 1 +
.../app/controllers/arvados/v1/jobs_controller.rb | 11 +-
.../app/controllers/arvados/v1/nodes_controller.rb | 18 ++
services/api/app/controllers/static_controller.rb | 17 +-
services/api/app/mailers/admin_notifier.rb | 12 -
services/api/app/mailers/user_notifier.rb | 3 +
services/api/app/models/arvados_model.rb | 7 -
services/api/app/models/job.rb | 140 ++++-----
services/api/app/models/node.rb | 12 +
.../admin_notifier/new_inactive_user.text.erb | 4 +-
.../api/app/views/admin_notifier/new_user.text.erb | 4 +-
.../views/user_notifier/account_is_setup.text.erb | 4 +-
services/api/config/application.default.yml | 12 +-
services/api/config/application.yml.example | 2 +
.../db/migrate/20140918153705_add_state_to_job.rb | 23 +-
.../20140924091559_add_job_uuid_to_nodes.rb | 13 +
services/api/db/structure.sql | 9 +-
services/api/lib/has_uuid.rb | 2 +-
services/api/script/crunch-dispatch.rb | 160 ++++++----
services/api/script/rails | 2 +-
services/api/script/update_node_attributes.rb | 106 -------
services/api/test/fixtures/collections.yml | 36 +++
services/api/test/fixtures/jobs.yml | 11 +
services/api/test/fixtures/links.yml | 14 +
services/api/test/fixtures/logs.yml | 9 +
services/api/test/fixtures/nodes.yml | 37 ++-
services/api/test/fixtures/pipeline_instances.yml | 81 +++++
services/api/test/fixtures/pipeline_templates.yml | 27 ++
services/api/test/fixtures/repositories.yml | 5 +
.../arvados/v1/collections_controller_test.rb | 55 +++-
.../arvados/v1/groups_controller_test.rb | 74 +++--
.../functional/arvados/v1/jobs_controller_test.rb | 71 +++--
.../arvados/v1/keep_disks_controller_test.rb | 22 +-
.../functional/arvados/v1/links_controller_test.rb | 26 +-
.../functional/arvados/v1/logs_controller_test.rb | 22 +-
.../functional/arvados/v1/nodes_controller_test.rb | 72 +++++
.../functional/arvados/v1/users_controller_test.rb | 348 ++++-----------------
services/api/test/helpers/users_test_helper.rb | 100 ++++++
services/api/test/integration/groups_test.rb | 42 +++
services/api/test/integration/users_test.rb | 216 +++++++++++++
services/api/test/test_helper.rb | 20 ++
services/api/test/unit/job_test.rb | 49 ++-
services/api/test/unit/log_test.rb | 6 +-
services/api/test/unit/node_test.rb | 6 +
services/api/test/unit/permission_test.rb | 13 +
services/fuse/arvados_fuse/__init__.py | 9 +-
services/fuse/bin/arv-mount | 3 +-
services/fuse/setup.py | 22 +-
services/fuse/tests/test_mount.py | 7 +-
services/keep/tools/traffic_test.py | 4 +-
services/keepproxy/keepproxy_test.go | 2 +-
services/keepstore/handler_test.go | 120 ++++++-
services/keepstore/handlers.go | 76 ++++-
services/keepstore/keepstore.go | 14 +-
125 files changed, 2303 insertions(+), 1597 deletions(-)
copy apps/workbench/app/views/application/{show.html.erb => _title_and_buttons.html.erb} (76%)
create mode 100644 apps/workbench/app/views/jobs/show.html.erb
copy apps/workbench/app/views/pipeline_instances/{_show_components_running.html.erb => _running_component.html.erb} (60%)
delete mode 100644 sdk/cli/README.textile
create mode 100644 services/api/db/migrate/20140924091559_add_job_uuid_to_nodes.rb
delete mode 100755 services/api/script/update_node_attributes.rb
create mode 100644 services/api/test/helpers/users_test_helper.rb
create mode 100644 services/api/test/integration/groups_test.rb
create mode 100644 services/api/test/integration/users_test.rb
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commit edc5e4b6645b9b983a85a892bf3d3ad1432a657d
Merge: 34e461f 359d96e
Author: Tim Pierce <twp at curoverse.com>
Date: Wed Oct 1 15:43:15 2014 -0400
Merge branch 'master' into 3782-large-job-logs
Conflicts:
services/api/test/fixtures/collections.yml
services/api/test/fixtures/jobs.yml
diff --cc apps/workbench/app/controllers/collections_controller.rb
index cc0b3ff,9882fa6..3606ef0
--- a/apps/workbench/app/controllers/collections_controller.rb
+++ b/apps/workbench/app/controllers/collections_controller.rb
@@@ -164,15 -154,15 +166,21 @@@ class CollectionsController < Applicati
ext = File.extname(params[:file])
self.response.headers['Content-Type'] =
Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
- self.response.headers['Content-Length'] = params[:size] if params[:size]
+ if params[:size]
+ size = params[:size].to_i
+ if opts[:maxbytes]
+ size = [size, opts[:maxbytes].to_i].min
+ end
+ self.response.headers['Content-Length'] = size.to_s
+ end
self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
- self.response_body = file_enumerator opts
+ begin
+ file_enumerator(opts).each do |bytes|
+ response.stream.write bytes
+ end
+ ensure
+ response.stream.close
+ end
end
def sharing_scopes
diff --cc services/api/test/fixtures/collections.yml
index ba95b34,817fd5c..d7b2d16
--- a/services/api/test/fixtures/collections.yml
+++ b/services/api/test/fixtures/collections.yml
@@@ -200,16 -212,26 +212,40 @@@ collection_expires_in_future
manifest_text: ". 37b51d194a7513e45b56f6524f2d51f2+3 0:3:expired\n"
name: collection_expires_in_future
+# a collection with a log file that can be parsed by the log viewer
+# This collection hash matches the following log text:
+# 2014-01-01_12:00:01 zzzzz-8i9sb-abcdefghijklmno 0 log message 1
+# 2014-01-01_12:00:02 zzzzz-8i9sb-abcdefghijklmno 0 log message 2
+# 2014-01-01_12:00:03 zzzzz-8i9sb-abcdefghijklmno 0 log message 3
+#
+real_log_collection:
+ uuid: zzzzz-4zz18-op4e2lbej01tcvu
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-09-01 12:00:00
+ portable_data_hash: 3399cbb0953a7823618f3e288a85ee26+81
+ manifest_text: ". b9f7e25b33844d816d8531686f8bf360+195 0:195:zzzzz-8i9sb-abcdefghijklmno.log.txt\n"
+ name: real_log_collection
++
+ collection_in_home_project_with_same_name_as_in_aproject:
+ uuid: zzzzz-4zz18-12342x4u7ftabcd
+ portable_data_hash: ea10d51bcf88862dbcc36eb292017dfd+45
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz\n"
+ name: collection_with_same_name_in_aproject_and_home_project
+
+ collection_in_aproject_with_same_name_as_in_home_project:
+ uuid: zzzzz-4zz18-56782x4u7ftefgh
+ portable_data_hash: ea10d51bcf88862dbcc36eb292017dfd+45
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz\n"
+ name: collection_with_same_name_in_aproject_and_home_project
diff --cc services/api/test/fixtures/jobs.yml
index 7c375bc,b84922d..b46cd06
--- a/services/api/test/fixtures/jobs.yml
+++ b/services/api/test/fixtures/jobs.yml
@@@ -212,11 -222,4 +222,12 @@@ queued
is_locked_by_uuid: ~
tasks_summary: {}
runtime_constraints: {}
+ state: Queued
+
+# A job with a log collection that can be parsed by the log viewer.
+job_with_real_log:
+ uuid: zzzzz-8i9sb-0vsrcqi7whchuil
+ created_at: 2014-09-01 12:00:00
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ log: 3399cbb0953a7823618f3e288a85ee26+81
+ script_version: 7def43a4d3f20789dda4700f703b5514cc3ed250
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