[ARVADOS] updated: 96fe9fc822c2270cb6e4212798d61e61481ec2e0
git at public.curoverse.com
git at public.curoverse.com
Tue Jul 1 16:38:59 EDT 2014
Summary of changes:
.../images/{ajax-loader.gif => spinner_32px.gif} | Bin
.../app/assets/javascripts/infinite_scroll.js | 21 ++-
.../app/assets/javascripts/select_modal.js | 2 +-
.../{loading.css => loading.css.scss.erb} | 21 +++
.../app/controllers/application_controller.rb | 195 +++++++++++----------
.../app/controllers/collections_controller.rb | 16 +-
apps/workbench/app/helpers/application_helper.rb | 2 +-
apps/workbench/app/models/arvados_api_client.rb | 83 ++++++---
apps/workbench/app/models/arvados_base.rb | 2 +-
apps/workbench/app/views/application/404.html.erb | 21 +++
.../application/{error.json.erb => 404.json.erb} | 0
.../workbench/app/views/application/_choose.js.erb | 2 +-
.../app/views/application/_content.html.erb | 2 +-
.../app/views/application/api_error.html.erb | 23 +++
.../{error.json.erb => api_error.json.erb} | 0
.../app/views/collections/_index_tbody.html.erb | 2 +-
.../app/views/collections/_show_recent.html.erb | 2 +-
apps/workbench/app/views/jobs/_show_log.html.erb | 22 +--
.../app/views/layouts/application.html.erb | 15 +-
.../views/pipeline_instances/_show_recent.html.erb | 4 +-
.../pipeline_templates/_show_components.html.erb | 18 +-
.../views/pipeline_templates/_show_recent.html.erb | 20 ++-
apps/workbench/app/views/users/_tables.html.erb | 10 +-
.../test/functional/application_controller_test.rb | 7 +
.../test/functional/collections_controller_test.rb | 7 +
.../test/functional/users_controller_test.rb | 2 +-
apps/workbench/test/integration/errors_test.rb | 61 ++++++-
.../test/integration/pipeline_instances_test.rb | 13 +-
doc/_config.yml | 5 +-
doc/_includes/_alert_docker.liquid | 4 +
doc/install/index.html.textile.liquid | 18 +-
doc/install/install-docker.html.textile.liquid | 112 ++++++++++++
docker/build_tools/Makefile | 6 +
docker/bwa-samtools/Dockerfile | 21 +++
sdk/cli/bin/arv | 20 ++-
sdk/cli/bin/crunch-job | 2 +
services/api/Gemfile | 2 +-
services/api/Gemfile.lock | 6 +-
.../api/app/controllers/application_controller.rb | 60 ++++---
.../v1/api_client_authorizations_controller.rb | 3 +-
.../app/controllers/arvados/v1/jobs_controller.rb | 5 +-
.../app/controllers/arvados/v1/links_controller.rb | 3 +-
services/api/app/models/user.rb | 6 +-
.../db/migrate/20140627210837_anonymous_group.rb | 17 ++
services/api/db/schema.rb | 2 +-
services/api/db/seeds.rb | 6 +-
services/api/lib/current_api_client.rb | 59 +++++++
services/api/script/crunch-dispatch.rb | 2 +-
services/api/script/get_anonymous_user_token.rb | 50 ++++++
.../test/fixtures/api_client_authorizations.yml | 14 ++
services/api/test/fixtures/groups.yml | 13 ++
services/api/test/fixtures/links.yml | 39 +++++
services/api/test/fixtures/users.yml | 8 +
.../test/functional/application_controller_test.rb | 49 ++++++
services/api/test/unit/user_test.rb | 3 +-
services/fuse/bin/arv-mount | 26 +--
56 files changed, 894 insertions(+), 240 deletions(-)
rename apps/workbench/app/assets/images/{ajax-loader.gif => spinner_32px.gif} (100%)
rename apps/workbench/app/assets/stylesheets/{loading.css => loading.css.scss.erb} (78%)
create mode 100644 apps/workbench/app/views/application/404.html.erb
copy apps/workbench/app/views/application/{error.json.erb => 404.json.erb} (100%)
create mode 100644 apps/workbench/app/views/application/api_error.html.erb
copy apps/workbench/app/views/application/{error.json.erb => api_error.json.erb} (100%)
create mode 100644 doc/_includes/_alert_docker.liquid
create mode 100644 doc/install/install-docker.html.textile.liquid
create mode 100644 docker/bwa-samtools/Dockerfile
create mode 100644 services/api/db/migrate/20140627210837_anonymous_group.rb
create mode 100755 services/api/script/get_anonymous_user_token.rb
create mode 100644 services/api/test/functional/application_controller_test.rb
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commit 96fe9fc822c2270cb6e4212798d61e61481ec2e0
Merge: 4b93172 c1966ec
Author: Ward Vandewege <ward at curoverse.com>
Date: Tue Jul 1 16:38:47 2014 -0400
Merge branch 'master' into 3118-docker-fixes
commit 4b9317289ef903fb74d681d3bf245d038be23514
Author: Ward Vandewege <ward at curoverse.com>
Date: Tue Jul 1 16:38:11 2014 -0400
Add documentation to doc.arvados.org for the local Docker install.
diff --git a/doc/_config.yml b/doc/_config.yml
index f3d34cb..bf19c95 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -115,8 +115,11 @@ navbar:
- admin/index.html.md.liquid
- admin/cheat_sheet.html.textile.liquid
installguide:
- - Install:
+ - Overview:
- install/index.html.textile.liquid
+ - Docker:
+ - install/install-docker.html.textile.liquid
+ - Manual installation:
- install/install-sso.html.textile.liquid
- install/install-api-server.html.textile.liquid
- install/install-workbench-app.html.textile.liquid
diff --git a/doc/_includes/_alert_docker.liquid b/doc/_includes/_alert_docker.liquid
new file mode 100644
index 0000000..c80af90
--- /dev/null
+++ b/doc/_includes/_alert_docker.liquid
@@ -0,0 +1,4 @@
+<div class="alert alert-block alert-info">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <p>The Docker installation is not feature complete. We do not have a Docker container yet for crunch-dispatch and the arvados compute nodes. This means that running pipelines from a Docker-based Arvados install is currently not supported without additional manual configuration. Without that manual configuration, it is possible to use arv-crunch-job to run a 'local' job against your Docker-based Arvados installation. To do this, please refer to the <a href="/user/topics/tutorial-job-debug.html">Debugging a Crunch script</a> page.</p>
+</div>
diff --git a/doc/install/index.html.textile.liquid b/doc/install/index.html.textile.liquid
index 5bf35f3..944a695 100644
--- a/doc/install/index.html.textile.liquid
+++ b/doc/install/index.html.textile.liquid
@@ -1,12 +1,24 @@
---
layout: default
navsection: installguide
-title: Overview
+title: Installation overview
...
-{% include 'alert_stub' %}
+Arvados can be installed in multiple ways. Arvados does not depend on any particular cloud operating stack. Arvados runs on one or more GNU/Linux system(s). Arvados is being developed on Debian and Ubuntu GNU/Linux.
+
+The simplest way to try out Arvados is to use the Docker-based installation, which installs Arvados in a series of Docker containers.
+
+For larger scale installations, a manual installation is more appropriate.
+
+h2. Docker
-h2. Installation Overview
+{% include 'alert_docker' %}
+
+"Installing with Docker":install-docker.html
+
+h2. Manual installation
+
+{% include 'alert_stub' %}
# Set up a cluster, or use Amazon
# Create and mount Keep volumes
diff --git a/doc/install/install-docker.html.textile.liquid b/doc/install/install-docker.html.textile.liquid
new file mode 100644
index 0000000..93629e9
--- /dev/null
+++ b/doc/install/install-docker.html.textile.liquid
@@ -0,0 +1,112 @@
+---
+layout: default
+navsection: installguide
+title: Installing with Docker
+...
+
+h2. Prerequisites:
+
+# A GNU/Linux (virtual) machine
+# A working Docker installation
+
+h2. Download the source tree
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd $HOME</span> # (or wherever you want to install)
+~$ <span class="userinput">git clone https://github.com/curoverse/arvados.git</span>
+</code></pre></notextile>
+
+See also: "Downloading the source code":https://arvados.org/projects/arvados/wiki/Download on the Arvados wiki.
+
+h2. Building the Arvados Docker containers
+
+First we need a suitable @config.yml@ file.
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd arvados/docker</span>
+~$ <span class="userinput">cp config.yml.example config.yml</span>
+</code></pre></notextile>
+
+Now it's time to edit the @config.yml@ file and fill in suitable values for at a minimum these parameters:
+
+<pre>
+PUBLIC_KEY_PATH
+API_HOSTNAME
+API_AUTO_ADMIN_USER
+</pre>
+
+h2. Running the Arvados Docker containers
+
+The @arvdock@ command can be used to start and stop the docker containers. It has a number of options:
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd arvados/docker</span>
+~$ <span class="userinput">./arvdock -h</span>
+
+usage: ./arvdock (start|stop|restart|test) [options]
+
+./arvdock start/stop/restart options:
+ -d [port], --doc[=port] Documentation server (default port 9898)
+ -w [port], --workbench[=port] Workbench server (default port 9899)
+ -s [port], --sso[=port] SSO server (default port 9901)
+ -a [port], --api[=port] API server (default port 9900)
+ -k, --keep Keep servers
+ --ssh Enable SSH access to server containers
+ -h, --help Display this help and exit
+
+ If no options are given, the action is applied to all servers.
+
+./arvdock test [testname] [testname] ...
+ By default, all tests are run.
+</code>
+</pre>
+</notextile>
+
+The @--ssh@ option can be useful to debug issues with the Docker containers; it allows you to ssh into the running containers as the @root@ user, provided you have access to the private key that matches the public key specified in @config.yml@'s PUBLIC_KEY_PATH variable.
+
+Start the docker containers:
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd arvados/docker</span>
+~$ <span class="userinput">./arvdock start</span>
+sso_server
+Starting container:
+ /usr/bin/docker.io run -d -i -t -p 9901:443 --name sso_server arvados/sso
+api_server
+Starting container:
+ /usr/bin/docker.io run -d -i -t -p 9900:443 --name api_server --link sso_server:sso arvados/api
+keep_server_0
+Starting container:
+ /usr/bin/docker.io run -d -i -t -p 25107:25107 --name keep_server_0 -v /tmp/tmp.aCSx8Pq6Wb:/dev/keep-0 --link api_server:api arvados/keep
+keep_server_1
+Starting container:
+ /usr/bin/docker.io run -d -i -t -p 25108:25107 --name keep_server_1 -v /tmp/tmp.m4OQ9WB73G:/dev/keep-0 --link api_server:api arvados/keep
+doc_server
+Starting container:
+ /usr/bin/docker.io run -d -i -t -p 9898:80 --name doc_server arvados/doc
+
+*****************************************************************
+You can access the Arvados documentation at http://localhost:9898
+*****************************************************************
+
+workbench_server
+Starting container:
+ /usr/bin/docker.io run -d -i -t -p 9899:80 --name workbench_server --link api_server:api arvados/workbench
+
+*****************************************************************
+You can access the Arvados workbench at http://localhost:9899
+*****************************************************************
+</code></pre></notextile>
+
+h2. Accessing workbench
+
+Point your browser to the Dockerized workbench:
+
+<notextile>
+<pre><code><span class="userinput">https://localhost:9899</span>
+</code></pre>
+</notextile>
+
+Now use the google account you specified as @API_AUTO_ADMIN_USER@ in @config.yml@ to log in. You will be prompted *twice* by your browser that you are accessing a site with an untrusted SSL certificate. This is normal; by default the Arvados Docker installation uses self-signed SSL certificates for the SSO and API servers, respectively.
+
+
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