[ARVADOS] updated: fdd0351cfcf54dd64423c9df16902fe83b512619
git at public.curoverse.com
git at public.curoverse.com
Mon Aug 4 16:42:23 EDT 2014
Summary of changes:
apps/workbench/Gemfile | 1 +
apps/workbench/Gemfile.lock | 2 +
.../workbench/app/assets/javascripts/filterable.js | 4 +-
.../app/assets/javascripts/select_modal.js | 51 +++++-
.../app/controllers/actions_controller.rb | 6 +-
.../app/controllers/application_controller.rb | 4 +-
.../app/controllers/projects_controller.rb | 26 +++
.../workbench/app/controllers/search_controller.rb | 13 +-
apps/workbench/app/controllers/users_controller.rb | 67 +++++++
apps/workbench/app/helpers/application_helper.rb | 1 +
apps/workbench/app/views/application/404.html.erb | 7 +-
.../app/views/application/_choose.html.erb | 2 +-
.../workbench/app/views/application/_choose.js.erb | 2 +-
.../workbench/app/views/application/index.html.erb | 2 +
apps/workbench/app/views/layouts/body.html.erb | 53 +++---
.../app/views/projects/_show_tab_contents.html.erb | 13 ++
.../app/views/search/_choose_rows.html.erb | 8 +-
.../app/views/users/_add_ssh_key_popup.html.erb | 38 ++++
.../app/views/users/_manage_account.html.erb | 52 ++++++
.../app/views/users/_manage_current_token.html.erb | 13 ++
.../app/views/users/_manage_repositories.html.erb | 40 ++++
.../app/views/users/_manage_ssh_keys.html.erb | 55 ++++++
.../views/users/_manage_virtual_machines.html.erb | 50 +++++
.../app/views/users/_setup_popup.html.erb | 2 +-
apps/workbench/app/views/users/add_ssh_key.js.erb | 2 +
.../app/views/users/add_ssh_key_popup.js.erb | 8 +
.../app/views/users/manage_account.html.erb | 1 +
apps/workbench/config/application.yml.example | 2 +-
apps/workbench/config/routes.rb | 4 +
crunch_scripts/run-command | 4 +-
doc/_config.yml | 1 +
doc/_includes/_alert_docker.liquid | 4 -
doc/_includes/_ssh_addkey.liquid | 10 +-
.../schema/PipelineTemplate.html.textile.liquid | 6 +-
doc/images/ssh-adding-public-key.png | Bin 17463 -> 15117 bytes
doc/install/index.html.textile.liquid | 2 -
doc/install/install-api-server.html.textile.liquid | 6 +-
doc/install/install-docker.html.textile.liquid | 141 ++++++++------
.../check-environment.html.textile.liquid | 2 +-
doc/user/reference/api-tokens.html.textile.liquid | 39 +---
docker/api/Dockerfile | 37 +++-
docker/api/application.yml.in | 5 +
docker/api/apt.arvados.org.list | 2 +
docker/api/arvados-clients.yml.in | 5 +
docker/api/crunch-dispatch-run.sh | 24 +++
docker/api/keep_server_0.json | 6 +
docker/api/keep_server_1.json | 7 +
docker/api/munge.key | Bin 0 -> 1024 bytes
docker/api/omniauth.rb.in | 6 +-
docker/api/setup-gitolite.sh.in | 77 ++++++++
docker/api/setup.sh.in | 62 +++++++
docker/api/slurm.conf.in | 60 ++++++
docker/api/supervisor.conf | 29 +++
docker/api/update-gitolite.rb | 162 ++++++++++++++++
docker/arvdock | 128 ++++++++++---
docker/base/Dockerfile | 4 +
docker/base/apt.arvados.org.list | 2 +
docker/build.sh | 41 ++++-
docker/build_tools/Makefile | 203 ++++++++++++++-------
docker/build_tools/build.rb | 36 +++-
docker/build_tools/config.rb | 20 +-
docker/compute/Dockerfile | 28 +++
docker/compute/fuse.conf | 10 +
docker/compute/setup.sh.in | 20 ++
docker/{api => compute}/ssh.sh | 0
docker/compute/supervisor.conf | 29 +++
docker/compute/wrapdocker | 90 +++++++++
docker/config.yml.example | 19 +-
docker/keep/Dockerfile | 9 +-
docker/keep/keep_signing_secret.in | 1 +
docker/keep/run-keep.in | 11 ++
docker/shell/Dockerfile | 19 ++
docker/shell/fuse.conf | 10 +
docker/shell/setup.sh.in | 21 +++
docker/{api => shell}/superuser_token.in | 0
docker/shell/supervisor.conf | 15 ++
docker/slurm/Dockerfile | 11 ++
docker/slurm/munge.key | Bin 0 -> 1024 bytes
docker/slurm/slurm.conf.in | 60 ++++++
docker/slurm/supervisor.conf | 14 ++
docker/workbench/Dockerfile | 15 +-
docker/workbench/workbench_rails_env.in | 1 +
sdk/cli/bin/crunch-job | 15 +-
sdk/python/arvados/stream.py | 2 +-
sdk/python/tests/test_collections.py | 20 ++
services/api/Gemfile | 1 +
services/api/Gemfile.lock | 2 +
.../api/app/controllers/application_controller.rb | 1 +
.../controllers/arvados/v1/groups_controller.rb | 28 +--
.../app/controllers/arvados/v1/jobs_controller.rb | 20 +-
services/api/app/models/arvados_model.rb | 6 +
services/api/app/models/authorized_key.rb | 9 +-
services/api/config/application.default.yml | 24 ++-
services/api/config/application.yml.example | 39 +---
... => 20140607150616_rename_folder_to_project.rb} | 0
.../db/migrate/20140714184006_empty_collection.rb | 4 +-
services/api/db/structure.sql | 2 +
services/api/lib/current_api_client.rb | 2 +-
.../test/fixtures/api_client_authorizations.yml | 6 +
services/api/test/fixtures/links.yml | 46 +++++
services/api/test/fixtures/users.yml | 11 ++
.../arvados/v1/groups_controller_test.rb | 33 ++++
.../arvados/v1/job_reuse_controller_test.rb | 21 +++
services/fuse/tests/test_mount.py | 1 +
104 files changed, 1991 insertions(+), 345 deletions(-)
create mode 100644 apps/workbench/app/views/users/_add_ssh_key_popup.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_account.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_current_token.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_repositories.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_ssh_keys.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_virtual_machines.html.erb
create mode 100644 apps/workbench/app/views/users/add_ssh_key.js.erb
create mode 100644 apps/workbench/app/views/users/add_ssh_key_popup.js.erb
create mode 100644 apps/workbench/app/views/users/manage_account.html.erb
delete mode 100644 doc/_includes/_alert_docker.liquid
create mode 100644 docker/api/apt.arvados.org.list
create mode 100644 docker/api/arvados-clients.yml.in
create mode 100755 docker/api/crunch-dispatch-run.sh
create mode 100644 docker/api/keep_server_0.json
create mode 100644 docker/api/keep_server_1.json
create mode 100644 docker/api/munge.key
create mode 100755 docker/api/setup-gitolite.sh.in
create mode 100755 docker/api/setup.sh.in
create mode 100644 docker/api/slurm.conf.in
create mode 100755 docker/api/update-gitolite.rb
create mode 100644 docker/base/apt.arvados.org.list
create mode 100644 docker/compute/Dockerfile
create mode 100644 docker/compute/fuse.conf
create mode 100755 docker/compute/setup.sh.in
copy docker/{api => compute}/ssh.sh (100%)
create mode 100644 docker/compute/supervisor.conf
create mode 100755 docker/compute/wrapdocker
create mode 100644 docker/keep/keep_signing_secret.in
create mode 100755 docker/keep/run-keep.in
create mode 100644 docker/shell/Dockerfile
create mode 100644 docker/shell/fuse.conf
create mode 100755 docker/shell/setup.sh.in
copy docker/{api => shell}/superuser_token.in (100%)
create mode 100644 docker/shell/supervisor.conf
create mode 100644 docker/slurm/Dockerfile
create mode 100644 docker/slurm/munge.key
create mode 100644 docker/slurm/slurm.conf.in
create mode 100644 docker/slurm/supervisor.conf
create mode 100644 docker/workbench/workbench_rails_env.in
rename services/api/db/migrate/{20140607150616_rename_folder_to_project.rb_deferred => 20140607150616_rename_folder_to_project.rb} (100%)
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commit fdd0351cfcf54dd64423c9df16902fe83b512619
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Aug 4 16:42:04 2014 -0400
$(link ...) now expects complete path.
diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command
index 0d20748..253e66e 100755
--- a/crunch_scripts/run-command
+++ b/crunch_scripts/run-command
@@ -38,8 +38,8 @@ if len(arvados.current_task()['parameters']) > 0:
links = []
def sub_link(v):
- r = os.path.basename(v)
- os.symlink(os.path.join(os.environ['TASK_KEEPMOUNT'], v) , r)
+ r = os.path.join(outdir, os.path.basename(v))
+ os.symlink(v, r)
links.append(r)
return r
commit c96db8766d22832ac19d260377d0fa747a657dd1
Merge: e9509c5 583e9e1
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Aug 4 15:41:10 2014 -0400
Merge branch 'master' into 3373-improve-gatk3-snv-pipeline
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