[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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