[ARVADOS] updated: 26678170e7a981461f1676855358e52bf1d6bf72
git at public.curoverse.com
git at public.curoverse.com
Wed Jul 30 16:03:21 EDT 2014
Summary of changes:
apps/workbench/Gemfile | 1 +
apps/workbench/Gemfile.lock | 2 +
.../app/assets/javascripts/application.js | 34 ++++-
.../workbench/app/assets/javascripts/filterable.js | 11 ++
.../app/assets/javascripts/infinite_scroll.js | 84 ++++++++---
.../app/assets/javascripts/select_modal.js | 34 ++++-
.../app/assets/stylesheets/application.css.scss | 4 +
.../app/assets/stylesheets/select_modal.css.scss | 3 +
.../app/controllers/actions_controller.rb | 11 ++
.../app/controllers/application_controller.rb | 43 ++++--
.../app/controllers/collections_controller.rb | 14 +-
.../workbench/app/controllers/search_controller.rb | 10 ++
apps/workbench/app/helpers/application_helper.rb | 9 ++
apps/workbench/app/models/group.rb | 9 ++
.../app/views/application/_choose.html.erb | 68 +++++----
.../workbench/app/views/application/_choose.js.erb | 22 +--
.../views/application/_projects_tree_menu.html.erb | 17 +--
.../app/views/collections/_choose_rows.html.erb | 4 +-
.../app/views/groups/_choose_rows.html.erb | 2 +-
.../app/views/layouts/application.html.erb | 167 +--------------------
.../{application.html.erb => body.html.erb} | 87 +++++------
.../views/pipeline_templates/_choose_rows.html.erb | 2 +-
.../app/views/search/_choose_rows.html.erb | 22 +++
.../app/views/users/_choose_rows.html.erb | 2 +-
apps/workbench/config/routes.rb | 4 +
.../search_controller_test.rb} | 2 +-
apps/workbench/test/helpers/search_helper_test.rb | 4 +
apps/workbench/test/integration/smoke_test.rb | 3 +
doc/_config.yml | 1 +
doc/_includes/_alert_docker.liquid | 4 -
doc/install/index.html.textile.liquid | 2 -
doc/install/install-docker.html.textile.liquid | 94 ++++++------
.../check-environment.html.textile.liquid | 2 +-
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/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 | 120 ++++++++++++---
docker/base/Dockerfile | 4 +
docker/base/apt.arvados.org.list | 2 +
docker/build.sh | 32 +++-
docker/build_tools/Makefile | 143 ++++++++++++++++--
docker/build_tools/build.rb | 28 +++-
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 | 4 +
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 | 3 +
sdk/cli/bin/crunch-job | 11 +-
sdk/python/arvados/commands/put.py | 21 +--
sdk/python/arvados/keep.py | 139 ++++++++++-------
sdk/python/bin/arv-get | 2 +-
sdk/python/bin/arv-ls | 2 +-
.../api/app/controllers/application_controller.rb | 1 +
.../controllers/arvados/v1/groups_controller.rb | 88 +++++++----
services/api/app/models/user.rb | 2 +-
services/api/config/application.default.yml | 11 ++
services/api/config/application.yml.example | 26 +---
services/api/config/routes.rb | 1 +
services/api/test/fixtures/groups.yml | 2 +-
.../arvados/v1/groups_controller_test.rb | 27 ++++
services/fuse/arvados_fuse/__init__.py | 3 +-
83 files changed, 1694 insertions(+), 559 deletions(-)
create mode 100644 apps/workbench/app/controllers/search_controller.rb
copy apps/workbench/app/views/layouts/{application.html.erb => body.html.erb} (80%)
create mode 100644 apps/workbench/app/views/search/_choose_rows.html.erb
copy apps/workbench/test/{unit/job_test.rb => controllers/search_controller_test.rb} (57%)
create mode 100644 apps/workbench/test/helpers/search_helper_test.rb
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/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
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commit 26678170e7a981461f1676855358e52bf1d6bf72
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Jul 30 16:03:19 2014 -0400
3349: More example/default config cleanup.
diff --git a/services/api/config/application.default.yml b/services/api/config/application.default.yml
index 0d26804..5436f02 100644
--- a/services/api/config/application.default.yml
+++ b/services/api/config/application.default.yml
@@ -40,6 +40,8 @@ test:
active_support.deprecation: :stderr
active_record.mass_assignment_sanitizer: :strict
uuid_prefix: zzzzz
+ secret_token: <%= rand(2**512).to_s(36) %>
+ blob_signing_key: <%= rand(2**512).to_s(36) %>
common:
uuid_prefix: <%= Digest::MD5.hexdigest(`hostname`).to_i(16).to_s(36)[0..4] %>
@@ -92,6 +94,15 @@ common:
- 192.168.1.1
compute_node_ec2_tag_enable: false
+ # The version below is suitable for AWS.
+ # To use it, copy it to your application.yml, uncomment, and change <%# to <%=
+ # compute_node_nameservers: <%#
+ # require 'net/http'
+ # ['local', 'public'].collect do |iface|
+ # Net::HTTP.get(URI("http://169.254.169.254/latest/meta-data/#{iface}-ipv4")).match(/^[\d\.]+$/)[0]
+ # end << '172.16.0.23'
+ # %>
+
accept_api_token: {}
new_users_are_active: false
diff --git a/services/api/config/application.yml.example b/services/api/config/application.yml.example
index 09dd78c..d6de1ff 100644
--- a/services/api/config/application.yml.example
+++ b/services/api/config/application.yml.example
@@ -19,29 +19,13 @@ production:
# Mandatory site secrets. See application.default.yml for more info.
secret_token: ~
blob_signing_key: ~
-
uuid_prefix: bogus
- # compute_node_domain: example.org
- # compute_node_nameservers:
- # - 127.0.0.1
- # - 192.168.1.1
- #
- # The version below is suitable for AWS.
- # Uncomment and change <%# to <%= to use it.
- # compute_node_nameservers: <%#
- # require 'net/http'
- # ['local', 'public'].collect do |iface|
- # Net::HTTP.get(URI("http://169.254.169.254/latest/meta-data/#{iface}-ipv4")).match(/^[\d\.]+$/)[0]
- # end << '172.16.0.23'
- # %>
-
test:
- uuid_prefix: zzzzz
- secret_token: <%= rand(2**512).to_s(36) %>
- blob_signing_key: <%= rand(2**512).to_s(36) %>
+ # Tests should be able to run without further configuration, but if you do
+ # want to change your local test configuration, this is where to do it.
common:
- #git_repositories_dir: /var/cache/git
- #git_internal_dir: /var/cache/arvados/internal.git
-
+ # Settings in this section will be used in all environments
+ # (development, production, test) except when overridden in the
+ # environment-specific sections above.
commit b3eb8176f8d060b0e4652cae8e041c6bf2b7103e
Merge: 062a8bf 20f944b
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Jul 30 15:56:46 2014 -0400
3349: Merge branch 'master' into 3349-install-docs
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