[ARVADOS] updated: b23bcfdc041fa9459d2beb423eea35e3ad34e64a
git at public.curoverse.com
git at public.curoverse.com
Mon Sep 15 13:14:09 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 | 26 +-
.../app/controllers/actions_controller.rb | 38 +-
.../app/controllers/application_controller.rb | 2 +
.../app/controllers/collections_controller.rb | 20 +-
.../app/controllers/projects_controller.rb | 29 +-
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 +-
.../views/application/_report_issue_popup.html.erb | 2 +-
.../views/application/report_issue_popup.js.erb | 14 +
.../app/views/collections/_show_files.html.erb | 2 +-
.../app/views/collections/show_file_links.html.erb | 7 +-
.../app/views/projects/_show_tab_contents.html.erb | 45 +-
apps/workbench/app/views/projects/show.html.erb | 2 +-
apps/workbench/config/routes.rb | 1 -
apps/workbench/test/integration/errors_test.rb | 6 +-
.../test/integration/pipeline_instances_test.rb | 45 +-
apps/workbench/test/integration/projects_test.rb | 157 ++++++
.../test/integration/report_issue_test.rb | 6 +-
apps/workbench/test/integration/search_box_test.rb | 6 +-
crunch_scripts/arvados-bcbio-nextgen.py | 2 +
crunch_scripts/crunchutil/robust_put.py | 13 +-
crunch_scripts/crunchutil/subst.py | 39 +-
crunch_scripts/run-command | 35 +-
sdk/cli/Gemfile | 2 +-
sdk/cli/Gemfile.lock | 42 +-
sdk/cli/bin/arv | 6 +-
sdk/cli/bin/arv-run-pipeline-instance | 36 +-
sdk/cli/bin/crunch-job | 61 ++-
sdk/python/arvados/collection.py | 5 +-
sdk/python/arvados/commands/copy.py | 2 +
sdk/python/arvados/commands/keepdocker.py | 149 +++++-
sdk/python/arvados/commands/put.py | 149 +++---
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 | 106 +---
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/locator.rb | 104 ----
.../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 +
services/api/db/structure.sql | 22 +-
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 +++++-----
72 files changed, 1964 insertions(+), 1024 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
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commit b23bcfdc041fa9459d2beb423eea35e3ad34e64a
Author: Tim Pierce <twp at curoverse.com>
Date: Mon Sep 15 13:13:45 2014 -0400
3699: ensure unique names for new pipelines
diff --git a/sdk/python/arvados/commands/copy.py b/sdk/python/arvados/commands/copy.py
index b250119..a3ead8a 100755
--- a/sdk/python/arvados/commands/copy.py
+++ b/sdk/python/arvados/commands/copy.py
@@ -163,6 +163,7 @@ def copy_pipeline_instance(pi_uuid, src, dst, dst_git_repo, dst_project=None, re
# Create the new pipeline instance at the destination Arvados.
pi['properties']['copied_from_pipeline_instance_uuid'] = pi_uuid
del pi['uuid']
+ pi['ensure_unique_name'] = True
new_pi = dst.pipeline_instances().create(body=pi).execute()
return new_pi
@@ -188,6 +189,7 @@ def copy_pipeline_template(pt_uuid, src, dst, dst_git_repo, recursive=True):
copy_git_repos(pt, src, dst, dst_git_repo)
pt['name'] = pt['name'] + ' copy'
+ pt['ensure_unique_name'] = True
del pt['uuid']
del pt['owner_uuid']
commit bc59a822ddb8e55739fdbdb04e6fbd78d5116450
Merge: 6d84b6c 741bf44
Author: Tim Pierce <twp at curoverse.com>
Date: Mon Sep 15 13:11:21 2014 -0400
Merge branch 'master' into 3699-arv-copy
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