[ARVADOS] updated: 7a260be18ddba67443a2be19d7f24406c7fe5131
git at public.curoverse.com
git at public.curoverse.com
Mon Sep 15 09:55:57 EDT 2014
Summary of changes:
apps/workbench/Gemfile | 2 +
apps/workbench/Gemfile.lock | 36 ++
.../app/assets/javascripts/select_modal.js | 16 +-
apps/workbench/app/assets/javascripts/selection.js | 35 +-
.../app/controllers/actions_controller.rb | 46 +-
.../app/controllers/application_controller.rb | 2 +
.../app/controllers/collections_controller.rb | 20 +-
.../app/controllers/projects_controller.rb | 29 +-
.../app/controllers/user_agreements_controller.rb | 2 +-
apps/workbench/app/helpers/collections_helper.rb | 22 +-
apps/workbench/app/models/arvados_base.rb | 4 +-
apps/workbench/app/models/collection.rb | 32 +-
.../app/views/application/_choose.html.erb | 24 +-
.../workbench/app/views/application/_choose.js.erb | 23 +-
.../app/views/collections/_show_files.html.erb | 47 +-
.../app/views/collections/_show_recent.html.erb | 21 +
.../collections/_show_source_summary.html.erb | 5 +-
.../app/views/collections/show_file_links.html.erb | 7 +-
.../app/views/projects/_show_tab_contents.html.erb | 57 ++-
apps/workbench/app/views/projects/show.html.erb | 2 +-
apps/workbench/config/application.default.yml | 3 +
apps/workbench/config/routes.rb | 2 +-
.../test/functional/actions_controller_test.rb | 30 ++
.../workbench/test/integration/collections_test.rb | 58 +++
.../test/integration/pipeline_instances_test.rb | 45 +-
apps/workbench/test/integration/projects_test.rb | 184 +++++++
crunch_scripts/arvados-bcbio-nextgen.py | 2 +
crunch_scripts/split-fastq.py | 7 +-
sdk/cli/Gemfile | 2 +-
sdk/cli/Gemfile.lock | 42 +-
sdk/cli/bin/arv | 6 +-
sdk/cli/bin/arv-run-pipeline-instance | 47 +-
sdk/cli/bin/crunch-job | 62 ++-
sdk/python/arvados/collection.py | 5 +-
sdk/python/arvados/commands/keepdocker.py | 149 +++++-
sdk/python/arvados/commands/put.py | 143 +++---
sdk/python/arvados/keep.py | 7 +-
sdk/python/arvados/stream.py | 7 +-
sdk/python/arvados/util.py | 18 +
sdk/python/tests/test_arv_put.py | 99 +---
sdk/python/tests/test_collections.py | 10 +-
sdk/python/tests/test_keep_client.py | 13 +
sdk/ruby/arvados.gemspec | 2 +-
sdk/ruby/lib/arvados/keep.rb | 189 +++++++
sdk/ruby/test/test_big_request.rb | 21 +-
sdk/ruby/test/test_keep_manifest.rb | 140 ++++++
services/api/.gitignore | 1 -
services/api/Gemfile | 3 +-
services/api/Gemfile.lock | 7 +-
.../api/app/assets/stylesheets/application.css | 2 +-
.../api/app/controllers/application_controller.rb | 42 +-
.../arvados/v1/collections_controller.rb | 14 +-
.../controllers/arvados/v1/schema_controller.rb | 28 +-
services/api/app/models/collection.rb | 99 +---
services/api/app/models/job.rb | 8 +
services/api/app/models/job_task.rb | 2 +
services/api/app/models/locator.rb | 104 ----
services/api/app/models/pipeline_instance.rb | 2 +
.../api/app/views/layouts/application.html.erb | 2 +-
services/api/app/views/static/intro.html.erb | 10 +-
.../api/app/views/static/login_failure.html.erb | 2 +-
.../migrate/20140828141043_job_priority_fixup.rb | 11 +
...add_start_finish_time_to_tasks_and_pipelines.rb | 15 +
services/api/db/structure.sql | 32 +-
services/api/test/fixtures/collections.yml | 12 +
services/api/test/fixtures/jobs.yml | 12 +-
services/api/test/fixtures/pipeline_templates.yml | 21 +
.../arvados/v1/collections_controller_test.rb | 70 +--
.../functional/arvados/v1/jobs_controller_test.rb | 1 +
services/crunchstat/crunchstat.go | 4 +-
services/fuse/arvados_fuse/__init__.py | 550 +++++++++++++++------
services/fuse/bin/arv-mount | 70 ++-
services/fuse/tests/test_mount.py | 272 +++++-----
73 files changed, 2119 insertions(+), 1002 deletions(-)
create mode 100644 sdk/ruby/lib/arvados/keep.rb
create mode 100644 sdk/ruby/test/test_keep_manifest.rb
delete mode 100644 services/api/app/models/locator.rb
create mode 100644 services/api/db/migrate/20140828141043_job_priority_fixup.rb
create mode 100644 services/api/db/migrate/20140909183946_add_start_finish_time_to_tasks_and_pipelines.rb
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commit 7a260be18ddba67443a2be19d7f24406c7fe5131
Merge: 4c4c295 f43a783
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Sep 15 09:55:22 2014 -0400
3550: Merge branch 'master' into 3550-local-pipeline
commit 4c4c295193379003fa6c94c9c06e3bdec574e265
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Sep 15 09:55:14 2014 -0400
3550: Clarify help message, mention that there are limitations.
diff --git a/sdk/cli/bin/arv-run-pipeline-instance b/sdk/cli/bin/arv-run-pipeline-instance
index 0f1f70e..3c7da7d 100755
--- a/sdk/cli/bin/arv-run-pipeline-instance
+++ b/sdk/cli/bin/arv-run-pipeline-instance
@@ -159,7 +159,7 @@ p = Trollop::Parser.new do
:short => :none,
:type => :boolean)
opt(:run_jobs_here,
- "Manage the pipeline instance in-process. Find/run/watch jobs until the pipeline finishes (or fails). Implies --run-pipeline-here.",
+ "Run jobs in the local terminal session instead of submitting them to Crunch. Implies --run-pipeline-here. Note: this results in a significantly different job execution environment, and some Crunch features are not supported. It can be necessary to modify a pipeline in order to make it run this way.",
:short => :none,
:type => :boolean)
opt(:run_here,
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