[ARVADOS] updated: 95d1231a25637c5ba0fd07b116876b17711ec201
git at public.curoverse.com
git at public.curoverse.com
Tue Nov 4 23:31:51 EST 2014
Summary of changes:
.../app/assets/javascripts/application.js | 4 +
.../workbench/app/assets/javascripts/filterable.js | 51 ++++
.../app/assets/javascripts/infinite_scroll.js | 75 +++++
.../app/assets/stylesheets/application.css.scss | 4 +
.../app/controllers/application_controller.rb | 22 +-
apps/workbench/app/controllers/jobs_controller.rb | 20 +-
.../controllers/pipeline_instances_controller.rb | 73 +++--
.../app/controllers/projects_controller.rb | 29 +-
apps/workbench/app/helpers/provenance_helper.rb | 305 ++++++++++-----------
apps/workbench/app/models/arvados_api_client.rb | 2 +-
apps/workbench/app/models/pipeline_instance.rb | 6 +-
.../app/views/collections/_show_files.html.erb | 33 ++-
.../pipeline_instances/_running_component.html.erb | 2 +-
.../views/projects/_show_data_collections.html.erb | 3 +-
.../projects/_show_jobs_and_pipelines.html.erb | 4 +-
.../views/projects/_show_other_objects.html.erb | 3 +-
.../projects/_show_pipeline_templates.html.erb | 3 +-
.../app/views/projects/_show_subprojects.html.erb | 3 +-
.../app/views/projects/_show_tab_contents.html.erb | 17 +-
apps/workbench/config/application.yml.example | 9 +
.../config/environments/production.rb.example | 2 +-
.../controllers/collections_controller_test.rb | 69 +++++
.../pipeline_instances_controller_test.rb | 169 ++++++++++++
.../workbench/test/integration/collections_test.rb | 39 +++
.../test/integration/pipeline_instances_test.rb | 6 +-
apps/workbench/test/integration/projects_test.rb | 204 +++++++-------
apps/workbench/test/test_helper.rb | 15 +
apps/workbench/test/unit/pipeline_instance_test.rb | 42 ++-
doc/_config.yml | 11 +-
.../create-standard-objects.html.textile.liquid | 62 ++---
doc/install/index.html.textile.liquid | 21 +-
doc/install/install-api-server.html.textile.liquid | 142 +++++-----
.../install-crunch-dispatch.html.textile.liquid | 8 +-
doc/install/install-keep.html.textile.liquid | 54 ----
doc/install/install-keepproxy.html.textile.liquid | 84 ++++++
doc/install/install-keepstore.html.textile.liquid | 90 ++++++
.../install-manual-overview.html.textile.liquid | 16 ++
...l-manual-prerequisites-ruby.html.textile.liquid | 31 +++
...nstall-manual-prerequisites.html.textile.liquid | 46 ++++
.../install-shell-server.html.textile.liquid | 17 ++
doc/install/install-sso.html.textile.liquid | 9 +-
.../install-workbench-app.html.textile.liquid | 106 ++++---
docker/api/Dockerfile | 9 +-
docker/api/application.yml.in | 2 +
docker/arvdock | 18 +-
docker/base/Dockerfile | 15 +-
docker/compute/Dockerfile | 11 +-
docker/compute/supervisor.conf | 5 +
docker/doc/Dockerfile | 4 +-
docker/java-bwa-samtools/Dockerfile | 4 +-
docker/passenger/Dockerfile | 13 +-
docker/shell/Dockerfile | 7 +-
docker/slurm/Dockerfile | 3 +-
docker/workbench/Dockerfile | 3 +-
sdk/cli/arvados-cli.gemspec | 2 +-
sdk/cli/bin/arv | 4 +-
sdk/cli/bin/arv-tag | 4 +-
sdk/cli/bin/crunch-job | 99 ++++---
sdk/python/arvados/collection.py | 208 ++++++++------
sdk/python/arvados/commands/put.py | 49 ++--
sdk/python/arvados/config.py | 2 +-
sdk/python/arvados/keep.py | 2 +-
sdk/python/arvados/stream.py | 4 +-
sdk/python/arvados/util.py | 29 +-
sdk/python/bin/arv-get | 2 +
sdk/python/bin/arv-normalize | 1 +
sdk/python/tests/run_test_server.py | 8 +-
sdk/python/tests/test_collections.py | 162 ++++++++---
sdk/ruby/arvados.gemspec | 2 +-
sdk/ruby/lib/arvados.rb | 2 +-
sdk/ruby/lib/arvados/keep.rb | 1 +
sdk/ruby/test/test_keep_manifest.rb | 22 +-
.../arvados/v1/collections_controller.rb | 53 +++-
.../controllers/arvados/v1/groups_controller.rb | 14 +-
services/api/app/models/user.rb | 2 +
services/api/config/application.yml.example | 1 +
services/api/lib/load_param.rb | 16 +-
.../test/fixtures/api_client_authorizations.yml | 7 +
services/api/test/fixtures/collections.yml | 61 ++++-
services/api/test/fixtures/groups.yml | 16 +-
services/api/test/fixtures/jobs.yml | 45 ++-
services/api/test/fixtures/links.yml | 15 +
services/api/test/fixtures/pipeline_instances.yml | 51 +++-
services/api/test/fixtures/pipeline_templates.yml | 21 ++
services/api/test/fixtures/users.yml | 14 +
.../arvados/v1/groups_controller_test.rb | 32 +++
services/fuse/arvados_fuse/__init__.py | 1 +
services/fuse/setup.py | 2 +-
services/fuse/tests/test_mount.py | 67 ++---
services/nodemanager/tests/test_computenode.py | 3 +-
90 files changed, 2178 insertions(+), 851 deletions(-)
create mode 100644 apps/workbench/test/controllers/collections_controller_test.rb
delete mode 100644 doc/install/install-keep.html.textile.liquid
create mode 100644 doc/install/install-keepproxy.html.textile.liquid
create mode 100644 doc/install/install-keepstore.html.textile.liquid
create mode 100644 doc/install/install-manual-overview.html.textile.liquid
create mode 100644 doc/install/install-manual-prerequisites-ruby.html.textile.liquid
create mode 100644 doc/install/install-manual-prerequisites.html.textile.liquid
create mode 100644 doc/install/install-shell-server.html.textile.liquid
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Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
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commit 95d1231a25637c5ba0fd07b116876b17711ec201
Merge: f075cec d5cf000
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Nov 4 23:28:22 2014 -0500
4084: Merge branch 'master' into 4084-log-pane-refresh-TC
Conflicts:
services/api/test/fixtures/jobs.yml
diff --cc apps/workbench/test/test_helper.rb
index d1d63e2,49b9c7f..ab2ac39
--- a/apps/workbench/test/test_helper.rb
+++ b/apps/workbench/test/test_helper.rb
@@@ -204,7 -190,21 +204,22 @@@ class ActionController::TestCas
end
end
+ # If it quacks like a duck, it must be a HTTP request object.
+ class RequestDuck
+ def self.host
+ "localhost"
+ end
+
+ def self.port
+ 8080
+ end
+
+ def self.protocol
+ "http"
+ end
+ end
+
if ENV["RAILS_ENV"].eql? 'test'
- ApiServerForTests.run
+ ApiServerForTests.new.run
+ ApiServerForTests.new.run ["--websockets"]
end
diff --cc services/api/test/fixtures/jobs.yml
index 9026e59,ebcecf4..65b40d7
--- a/services/api/test/fixtures/jobs.yml
+++ b/services/api/test/fixtures/jobs.yml
@@@ -295,30 -297,39 +297,63 @@@ job_in_subproject
script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
state: Complete
+running_will_be_completed:
+ uuid: zzzzz-8i9sb-pshmckwoma9plh8
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ created_at: <%= 3.minute.ago.to_s(:db) %>
+ started_at: <%= 3.minute.ago.to_s(:db) %>
+ finished_at: ~
+ script_version: 1de84a854e2b440dc53bf42f8548afa4c17da332
+ running: true
+ success: ~
+ output: ~
+ priority: 0
+ log: ~
+ is_locked_by_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ tasks_summary:
+ failed: 0
+ todo: 3
+ running: 1
+ done: 1
+ runtime_constraints: {}
+ state: Running
+
+ graph_stage1:
+ uuid: zzzzz-8i9sb-graphstage10000
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ repository: foo
+ script: hash
+ script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
+ state: Complete
+ output: fa7aeb5140e2848d39b416daeef4ffc5+45
+
+ graph_stage2:
+ uuid: zzzzz-8i9sb-graphstage20000
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ repository: foo
+ script: hash2
+ script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
+ state: Complete
+ script_parameters:
+ input: fa7aeb5140e2848d39b416daeef4ffc5+45
+ input2: "stuff"
+ output: 65b17c95fdbc9800fc48acda4e9dcd0b+93
+
+ graph_stage3:
+ uuid: zzzzz-8i9sb-graphstage30000
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ repository: foo
+ script: hash2
+ script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
+ state: Complete
+ script_parameters:
+ input: fa7aeb5140e2848d39b416daeef4ffc5+45
+ input2: "stuff2"
+ output: ea10d51bcf88862dbcc36eb292017dfd+45
+
# Test Helper trims the rest of the file
-----------------------------------------------------------------------
hooks/post-receive
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