[ARVADOS] updated: 3ef580c47029ff0fbf959b044f29c183f41cb609
Git user
git at public.curoverse.com
Tue Apr 25 01:19:22 EDT 2017
Summary of changes:
.../app/assets/javascripts/edit_collection.js | 45 +++++++
.../app/assets/javascripts/selection.js.erb | 7 ++
.../app/assets/stylesheets/collections.css.scss | 6 +
.../app/controllers/keep_disks_controller.rb | 1 +
apps/workbench/app/controllers/users_controller.rb | 1 +
apps/workbench/app/helpers/application_helper.rb | 2 +
apps/workbench/app/models/arvados_base.rb | 4 +
apps/workbench/app/models/arvados_resource_list.rb | 8 ++
apps/workbench/app/models/job.rb | 2 +-
apps/workbench/app/models/pipeline_instance.rb | 7 +-
apps/workbench/app/models/proxy_work_unit.rb | 1 +
apps/workbench/app/models/workflow.rb | 8 ++
.../app/views/application/_content.html.erb | 2 +-
.../collections/_extra_tab_line_buttons.html.erb | 3 +
.../app/views/collections/_show_files.html.erb | 14 ++-
.../_extra_tab_line_buttons.html.erb | 2 +-
.../app/views/workflows/_show_recent.html.erb | 65 ++++++++++
.../test/integration/collection_upload_test.rb | 14 +++
.../workbench/test/integration/collections_test.rb | 67 +++++++++-
apps/workbench/test/integration/work_units_test.rb | 24 ++++
apps/workbench/test/integration_helper.rb | 15 +++
.../test/unit/arvados_resource_list_test.rb | 8 ++
apps/workbench/test/unit/link_test.rb | 3 +
apps/workbench/test/unit/pipeline_instance_test.rb | 3 +
apps/workbench/test/unit/work_unit_test.rb | 3 +
build/build.list | 2 +
build/run-build-packages-sso.sh | 3 +
build/run-build-packages.sh | 2 -
build/run-library.sh | 2 +
build/run-tests.sh | 2 +-
doc/_includes/_navbar_top.liquid | 2 +-
.../install-nodemanager.html.textile.liquid | 30 +++++
doc/user/cwl/cwl-extensions.html.textile.liquid | 17 +++
docker/migrate-docker19/build.sh | 2 +-
docker/migrate-docker19/dnd.sh | 2 +-
docker/migrate-docker19/migrate.sh | 62 +++++++--
sdk/cli/bin/crunch-job | 8 +-
sdk/cli/test/binstub_arv-mount/arv-mount | 1 +
.../test/binstub_clean_fail/{mount => arv-mount} | 0
sdk/cli/test/test_crunch-job.rb | 4 +-
sdk/cwl/arvados_cwl/__init__.py | 69 +++++------
sdk/cwl/arvados_cwl/arv-cwl-schema.yml | 31 +++++
sdk/cwl/arvados_cwl/arvcontainer.py | 12 +-
sdk/cwl/arvados_cwl/crunch_script.py | 15 ++-
sdk/cwl/arvados_cwl/fsaccess.py | 32 +++--
sdk/cwl/arvados_cwl/pathmapper.py | 87 +++++++------
sdk/cwl/arvados_cwl/runner.py | 2 +-
sdk/cwl/setup.py | 6 +-
sdk/cwl/test_with_arvbox.sh | 2 +
sdk/cwl/tests/arvados-tests.yml | 36 ++++++
sdk/cwl/tests/listing-job.yml | 3 +
sdk/cwl/tests/test_container.py | 81 +++++++++++-
sdk/cwl/tests/test_fsaccess.py | 28 +++++
sdk/cwl/tests/test_job.py | 9 +-
sdk/cwl/tests/test_pathmapper.py | 25 ++--
sdk/cwl/tests/test_submit.py | 25 ++--
.../cwl/tests/tmp1/tmp2/tmp3}/.gitkeep | 0
sdk/cwl/tests/wf/listing_deep.cwl | 15 +++
sdk/cwl/tests/wf/listing_none.cwl | 15 +++
sdk/cwl/tests/wf/listing_shallow.cwl | 15 +++
sdk/cwl/tests/wf/scatter2.cwl | 1 +
sdk/cwl/tests/wf/scatter2_subwf.cwl | 5 +-
sdk/go/crunchrunner/crunchrunner.go | 66 +++++-----
sdk/go/crunchrunner/crunchrunner_test.go | 51 ++++----
sdk/go/dispatch/throttle_test.go | 29 +++--
sdk/python/arvados/_ranges.py | 6 +-
sdk/python/arvados/arvfile.py | 83 ++++++++++---
sdk/python/arvados/commands/get.py | 16 ++-
sdk/python/arvados/commands/migrate19.py | 78 ++++++++++--
sdk/python/arvados/commands/put.py | 29 +++--
sdk/python/tests/test_arv_get.py | 49 ++++++--
sdk/python/tests/test_arvfile.py | 134 +++++++++++++++++++-
sdk/python/tests/test_stream.py | 7 +-
services/api/app/models/node.rb | 20 ++-
...1_add_created_by_job_task_index_to_job_tasks.rb | 5 +
...0170419173712_add_object_owner_index_to_logs.rb | 5 +
...esting_container_index_to_container_requests.rb | 5 +
services/api/db/structure.sql | 28 +++++
services/api/test/unit/node_test.rb | 12 ++
services/crunch-run/crunchrun.go | 138 +++++++++++++++++----
services/crunch-run/crunchrun_test.go | 136 +++++++++++++++++++-
services/keep-web/handler.go | 14 +++
services/keep-web/handler_test.go | 31 +++++
services/nodemanager/arvnodeman/config.py | 2 +
services/nodemanager/arvnodeman/daemon.py | 17 +++
services/nodemanager/arvnodeman/launcher.py | 3 +
services/nodemanager/arvnodeman/status.py | 65 ++++++++++
services/nodemanager/doc/azure.example.cfg | 10 ++
services/nodemanager/doc/ec2.example.cfg | 10 ++
services/nodemanager/doc/gce.example.cfg | 10 ++
services/nodemanager/doc/local.example.cfg | 4 +
services/nodemanager/setup.py | 22 ++--
services/nodemanager/tests/test_daemon.py | 8 ++
services/nodemanager/tests/test_status.py | 55 ++++++++
94 files changed, 1771 insertions(+), 345 deletions(-)
create mode 100644 apps/workbench/app/assets/javascripts/edit_collection.js
create mode 100644 apps/workbench/app/views/collections/_extra_tab_line_buttons.html.erb
create mode 100644 apps/workbench/app/views/workflows/_show_recent.html.erb
create mode 100755 sdk/cli/test/binstub_arv-mount/arv-mount
rename sdk/cli/test/binstub_clean_fail/{mount => arv-mount} (100%)
create mode 100644 sdk/cwl/tests/listing-job.yml
create mode 100644 sdk/cwl/tests/test_fsaccess.py
copy {services/api/vendor/plugins => sdk/cwl/tests/tmp1/tmp2/tmp3}/.gitkeep (100%)
create mode 100644 sdk/cwl/tests/wf/listing_deep.cwl
create mode 100644 sdk/cwl/tests/wf/listing_none.cwl
create mode 100644 sdk/cwl/tests/wf/listing_shallow.cwl
create mode 100644 services/api/db/migrate/20170419173031_add_created_by_job_task_index_to_job_tasks.rb
create mode 100644 services/api/db/migrate/20170419173712_add_object_owner_index_to_logs.rb
create mode 100644 services/api/db/migrate/20170419175801_add_requesting_container_index_to_container_requests.rb
create mode 100644 services/nodemanager/arvnodeman/status.py
create mode 100644 services/nodemanager/tests/test_status.py
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from de083a9fec0ca08afda5a9369c6cd32dbdcd0965 (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 3ef580c47029ff0fbf959b044f29c183f41cb609
Merge: de083a9 bf5d77b
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Apr 25 01:14:23 2017 -0400
7709: Merge branch 'master' into 7709-api-rails4
Conflicts:
services/api/db/structure.sql
diff --cc services/api/db/structure.sql
index 5c592a2,d672942..3e1fa3f
--- a/services/api/db/structure.sql
+++ b/services/api/db/structure.sql
@@@ -2757,3 -2778,9 +2778,10 @@@ INSERT INTO schema_migrations (version
INSERT INTO schema_migrations (version) VALUES ('20170328215436');
INSERT INTO schema_migrations (version) VALUES ('20170330012505');
+
+ INSERT INTO schema_migrations (version) VALUES ('20170419173031');
+
+ INSERT INTO schema_migrations (version) VALUES ('20170419173712');
+
-INSERT INTO schema_migrations (version) VALUES ('20170419175801');
++INSERT INTO schema_migrations (version) VALUES ('20170419175801');
++
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