[ARVADOS] updated: 869e3d2572ec2ede29cc0f14b09db80855aca333
git at public.curoverse.com
git at public.curoverse.com
Tue Mar 25 18:50:40 EDT 2014
Summary of changes:
COPYING | 11 +
LICENSE-2.0.txt | 202 ++++++
README | 21 +
agpl-3.0.txt | 661 +++++++++++++++++++
apps/workbench/Gemfile | 9 +-
apps/workbench/Gemfile.lock | 31 +
apps/workbench/README.rdoc | 261 --------
apps/workbench/README.textile | 19 +
apps/workbench/app/assets/javascripts/editable.js | 9 +
.../api_client_authorizations_controller.rb | 9 +-
.../app/controllers/application_controller.rb | 33 +-
.../app/controllers/collections_controller.rb | 16 +-
.../controllers/pipeline_templates_controller.rb | 5 +-
apps/workbench/app/controllers/users_controller.rb | 63 ++-
apps/workbench/app/helpers/application_helper.rb | 14 +-
apps/workbench/app/helpers/provenance_helper.rb | 32 +-
apps/workbench/app/models/arvados_api_client.rb | 26 +-
apps/workbench/app/models/arvados_base.rb | 31 +-
apps/workbench/app/models/arvados_resource_list.rb | 26 +
.../app/views/application/_paging.html.erb | 126 ++++
.../app/views/application/_show_recent.html.erb | 4 +
.../app/views/collections/_show_recent.html.erb | 6 +-
.../app/views/groups/_show_recent.html.erb | 4 +
.../app/views/layouts/application.html.erb | 6 +-
.../notifications/_pipelines_notification.html.erb | 2 +-
.../views/pipeline_instances/_show_recent.html.erb | 4 +
.../views/pipeline_templates/_show_recent.html.erb | 4 +
.../app/views/users/_show_activity.html.erb | 4 +
apps/workbench/app/views/users/activity.html.erb | 72 ++
apps/workbench/config/application.default.yml | 12 +-
.../config/environments/development.rb.example | 20 -
.../config/environments/production.rb.example | 19 -
apps/workbench/config/environments/test.rb.example | 19 -
apps/workbench/config/routes.rb | 7 +-
apps/workbench/lib/tasks/config_check.rake | 13 +-
apps/workbench/test/integration/logins_test.rb | 14 +
apps/workbench/test/integration/smoke_test.rb | 39 ++
.../test/integration/virtual_machines_test.rb | 17 +
apps/workbench/test/integration_helper.rb | 77 +++
by-sa-3.0.txt | 297 +++++++++
doc/Gemfile | 2 +-
doc/README.textile | 52 ++
doc/Rakefile | 9 +
doc/_config.yml | 34 +-
doc/_includes/_run_md5sum_py.liquid | 33 +-
doc/_includes/_tutorial_hash_script_py.liquid | 72 +--
doc/_includes/_webring.liquid | 29 +
doc/_layouts/default.html.liquid | 18 +-
doc/admin/cheat_sheet.html.textile.liquid | 2 +-
doc/api/authentication.html.textile.liquid | 2 +-
doc/api/index.html.textile.liquid | 2 +-
doc/api/methods.html.textile.liquid | 2 +-
.../api_client_authorizations.html.textile.liquid | 2 +-
doc/api/methods/api_clients.html.textile.liquid | 2 +-
.../methods/authorized_keys.html.textile.liquid | 2 +-
doc/api/methods/collections.html.textile.liquid | 2 +-
doc/api/methods/groups.html.textile.liquid | 2 +-
doc/api/methods/humans.html.textile.liquid | 2 +-
doc/api/methods/job_tasks.html.textile.liquid | 2 +-
doc/api/methods/jobs.html.textile.liquid | 2 +-
doc/api/methods/keep_disks.html.textile.liquid | 2 +-
doc/api/methods/links.html.textile.liquid | 2 +-
doc/api/methods/logs.html.textile.liquid | 2 +-
doc/api/methods/nodes.html.textile.liquid | 2 +-
.../methods/pipeline_instances.html.textile.liquid | 2 +-
.../methods/pipeline_templates.html.textile.liquid | 2 +-
doc/api/methods/repositories.html.textile.liquid | 2 +-
doc/api/methods/specimens.html.textile.liquid | 2 +-
doc/api/methods/traits.html.textile.liquid | 2 +-
doc/api/methods/users.html.textile.liquid | 2 +-
.../methods/virtual_machines.html.textile.liquid | 2 +-
doc/api/permission-model.html.textile.liquid | 2 +-
doc/api/resources.html.textile.liquid | 2 +-
doc/api/schema/ApiClient.html.textile.liquid | 2 +-
.../ApiClientAuthorization.html.textile.liquid | 2 +-
doc/api/schema/AuthorizedKey.html.textile.liquid | 2 +-
doc/api/schema/Collection.html.textile.liquid | 2 +-
doc/api/schema/Commit.html.textile.liquid | 2 +-
doc/api/schema/CommitAncestor.html.textile.liquid | 2 +-
doc/api/schema/Group.html.textile.liquid | 2 +-
doc/api/schema/Human.html.textile.liquid | 2 +-
doc/api/schema/Job.html.textile.liquid | 2 +-
doc/api/schema/JobTask.html.textile.liquid | 2 +-
doc/api/schema/KeepDisk.html.textile.liquid | 2 +-
doc/api/schema/Link.html.textile.liquid | 2 +-
doc/api/schema/Log.html.textile.liquid | 2 +-
doc/api/schema/Node.html.textile.liquid | 2 +-
.../schema/PipelineInstance.html.textile.liquid | 2 +-
.../schema/PipelineTemplate.html.textile.liquid | 2 +-
doc/api/schema/Repository.html.textile.liquid | 2 +-
doc/api/schema/Specimen.html.textile.liquid | 2 +-
doc/api/schema/Trait.html.textile.liquid | 2 +-
doc/api/schema/User.html.textile.liquid | 2 +-
doc/api/schema/VirtualMachine.html.textile.liquid | 2 +-
doc/css/code.css | 27 +
doc/css/nav-list.css | 4 +
.../pipeline_templates/gatk-exome-fq-snp.json | 85 ++-
doc/index.html.liquid | 10 +-
doc/install/client.html.textile.liquid | 2 +-
.../create-standard-objects.html.textile.liquid | 2 +-
doc/install/index.html.md.liquid | 1 +
doc/install/install-api-server.html.md.liquid | 115 ----
doc/install/install-api-server.html.textile.liquid | 128 ++++
.../install-crunch-dispatch.html.textile.liquid | 2 +-
doc/install/install-sso.html.textile.liquid | 24 +
doc/install/install-workbench-app.html.md.liquid | 63 --
.../install-workbench-app.html.textile.liquid | 52 ++
doc/sdk/cli/index.html.textile.liquid | 2 -
doc/sdk/index.html.textile.liquid | 17 +-
doc/sdk/perl/index.html.textile.liquid | 2 -
.../crunch-utility-libraries.html.textile.liquid | 2 -
doc/sdk/python/sdk-python.html.textile.liquid | 12 +-
doc/sdk/ruby/index.html.textile.liquid | 125 ++++
doc/user/copying/LICENSE-2.0.html | 182 ++++++
doc/user/copying/agpl-3.0.html | 684 ++++++++++++++++++++
doc/user/copying/by-sa-3.0.html | 418 ++++++++++++
doc/user/copying/copying.html.textile.liquid | 11 +
.../examples/crunch-examples.html.textile.liquid | 4 -
.../check-environment.html.textile.liquid | 6 -
.../getting_started/community.html.textile.liquid | 4 -
.../getting_started/ssh-access.html.textile.liquid | 9 +-
.../getting_started/workbench.html.textile.liquid | 7 +-
doc/user/index.html.textile.liquid | 18 +-
doc/user/reference/api-tokens.html.textile.liquid | 6 +-
doc/user/reference/sdk-cli.html.textile.liquid | 3 -
doc/user/topics/keep.html.textile.liquid | 48 ++
...nning-pipeline-command-line.html.textile.liquid | 119 ++++
...rial-gatk-variantfiltration.html.textile.liquid | 6 +-
.../tutorial-job-debug.html.textile.liquid | 17 +-
.../tutorial-job1.html.textile.liquid | 46 +-
.../tutorial-parallel.html.textile.liquid | 19 +-
.../tutorial-trait-search.html.textile.liquid | 4 -
.../tutorials/intro-crunch.html.textile.liquid | 17 +
.../running-external-program.html.textile.liquid | 46 +-
.../tutorial-firstscript.html.textile.liquid | 72 ++-
.../tutorials/tutorial-keep.html.textile.liquid | 95 ++-
.../tutorial-new-pipeline.html.textile.liquid | 129 +---
...tutorial-pipeline-workbench.html.textile.liquid | 25 +
doc/zenweb-liquid.rb | 33 +-
docker/README.md | 27 +-
sdk/cli/bin/arv | 21 +-
sdk/cli/bin/arv-run-pipeline-instance | 7 +-
sdk/cli/bin/crunch-job | 69 ++-
sdk/python/arvados/collection.py | 1 +
sdk/python/bin/arv-mount | 8 +-
services/api/Gemfile | 10 +-
services/api/Gemfile.lock | 12 +
.../api/app/controllers/application_controller.rb | 107 +++-
.../app/controllers/arvados/v1/jobs_controller.rb | 4 +-
.../controllers/arvados/v1/schema_controller.rb | 41 +-
.../app/controllers/arvados/v1/users_controller.rb | 49 ++-
.../app/controllers/user_sessions_controller.rb | 3 +-
services/api/app/models/arvados_model.rb | 6 +-
services/api/app/models/job.rb | 7 +-
services/api/app/models/user.rb | 154 +++++-
services/api/config/application.default.yml | 19 +-
services/api/config/application.rb | 26 -
services/api/config/application.yml.example | 27 +-
services/api/config/database.yml.sample | 8 +-
.../api/config/environments/development.rb.example | 39 --
.../api/config/environments/production.rb.example | 42 --
services/api/config/environments/test.rb.example | 40 --
.../api/config/initializers/omniauth.rb.example | 2 +-
services/api/config/routes.rb | 4 +-
services/api/lib/tasks/config_check.rake | 13 +-
services/api/script/crunch-dispatch.rb | 12 +-
services/api/script/rails | 4 -
services/api/script/setup-new-user.rb | 66 ++
.../arvados/v1/collections_controller_test.rb | 22 +
.../functional/arvados/v1/jobs_controller_test.rb | 123 ++++
.../arvados/v1/keep_disks_controller_test.rb | 28 +
.../arvados/v1/schema_controller_test.rb | 2 +-
.../functional/arvados/v1/users_controller_test.rb | 645 ++++++++++++++++++
.../api/test/integration/collections_api_test.rb | 12 +
services/api/test/integration/permissions_test.rb | 244 +++++++
services/api/test/unit/user_test.rb | 280 ++++++++-
176 files changed, 6124 insertions(+), 1349 deletions(-)
create mode 100644 COPYING
create mode 100644 LICENSE-2.0.txt
create mode 100644 README
create mode 100644 agpl-3.0.txt
delete mode 100644 apps/workbench/README.rdoc
create mode 100644 apps/workbench/README.textile
create mode 100644 apps/workbench/app/views/application/_paging.html.erb
create mode 100644 apps/workbench/app/views/users/_show_activity.html.erb
create mode 100644 apps/workbench/app/views/users/activity.html.erb
create mode 100644 apps/workbench/test/integration/logins_test.rb
create mode 100644 apps/workbench/test/integration/smoke_test.rb
create mode 100644 apps/workbench/test/integration/virtual_machines_test.rb
create mode 100644 apps/workbench/test/integration_helper.rb
create mode 100644 by-sa-3.0.txt
create mode 100644 doc/README.textile
create mode 100644 doc/_includes/_webring.liquid
create mode 100644 doc/css/code.css
delete mode 100644 doc/install/install-api-server.html.md.liquid
create mode 100644 doc/install/install-api-server.html.textile.liquid
create mode 100644 doc/install/install-sso.html.textile.liquid
delete mode 100644 doc/install/install-workbench-app.html.md.liquid
create mode 100644 doc/install/install-workbench-app.html.textile.liquid
create mode 100644 doc/sdk/ruby/index.html.textile.liquid
create mode 100644 doc/user/copying/LICENSE-2.0.html
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create mode 100644 doc/user/copying/by-sa-3.0.html
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create mode 100644 doc/user/topics/keep.html.textile.liquid
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rename doc/user/{tutorials => topics}/tutorial-job1.html.textile.liquid (74%)
rename doc/user/{tutorials => topics}/tutorial-parallel.html.textile.liquid (71%)
rename doc/user/{tutorials => topics}/tutorial-trait-search.html.textile.liquid (99%)
create mode 100644 doc/user/tutorials/intro-crunch.html.textile.liquid
create mode 100644 doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
create mode 100755 services/api/script/setup-new-user.rb
create mode 100644 services/api/test/integration/permissions_test.rb
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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 869e3d2572ec2ede29cc0f14b09db80855aca333
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Mar 25 18:50:31 2014 -0400
Add list of in-progress/planned SDKs.
diff --git a/doc/sdk/index.html.textile.liquid b/doc/sdk/index.html.textile.liquid
index 10423fe..061e964 100644
--- a/doc/sdk/index.html.textile.liquid
+++ b/doc/sdk/index.html.textile.liquid
@@ -10,3 +10,8 @@ This section documents how to access the Arvados API and Keep using various prog
* "Perl SDK":{{site.baseurl}}/sdk/perl/index.html
* "Ruby SDK":{{site.baseurl}}/sdk/ruby/index.html
* "Command line SDK":{{site.baseurl}}/sdk/cli/index.html ("arv")
+
+SDKs not yet implemented:
+
+* Rails SDK: Workbench uses an ActiveRecord-like interface to Arvados. This hasn't yet been extracted from Workbench and packaged as a gem.
+* R and Java: We plan to support these, but they have not been implemented yet.
commit d2851b52b83aaea56bfabefeaf4f3ae47df24ca9
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Mar 25 18:36:17 2014 -0400
Add Ruby SDK page.
diff --git a/doc/_config.yml b/doc/_config.yml
index c75b0a4..167188a 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -54,6 +54,8 @@ navbar:
- sdk/python/crunch-utility-libraries.html.textile.liquid
- Perl:
- sdk/perl/index.html.textile.liquid
+ - Ruby:
+ - sdk/ruby/index.html.textile.liquid
- CLI:
- sdk/cli/index.html.textile.liquid
api:
diff --git a/doc/sdk/index.html.textile.liquid b/doc/sdk/index.html.textile.liquid
index cea3ab0..10423fe 100644
--- a/doc/sdk/index.html.textile.liquid
+++ b/doc/sdk/index.html.textile.liquid
@@ -8,4 +8,5 @@ This section documents how to access the Arvados API and Keep using various prog
* "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html
* "Perl SDK":{{site.baseurl}}/sdk/perl/index.html
+* "Ruby SDK":{{site.baseurl}}/sdk/ruby/index.html
* "Command line SDK":{{site.baseurl}}/sdk/cli/index.html ("arv")
diff --git a/doc/sdk/ruby/index.html.textile.liquid b/doc/sdk/ruby/index.html.textile.liquid
new file mode 100644
index 0000000..1a455b1
--- /dev/null
+++ b/doc/sdk/ruby/index.html.textile.liquid
@@ -0,0 +1,125 @@
+---
+layout: default
+navsection: sdk
+navmenu: Ruby
+title: "Ruby SDK"
+
+...
+
+The Ruby SDK provides a generic set of wrappers so you can make API calls easily.
+
+h3. Installation
+
+If you are logged in to an Arvados VM, the Ruby SDK should be installed.
+
+To use it elsewhere, you can either install the @arvados@ gem via RubyGems or build and install the package using the arvados source tree.
+
+h4. Prerequisites: Ruby >= 2.0.0
+
+You can use "RVM":http://rvm.io/rvm/install to install and manage Ruby versions.
+
+h4. Option 1: install with RubyGems
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo gem install arvados</code>
+</pre>
+</notextile>
+
+h4. Option 2: build and install from source
+
+<notextile>
+<pre>
+$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+$ <code class="userinput">cd arvados/sdk/cli</code>
+$ <code class="userinput">gem build arvados.gemspec</code>
+$ <code class="userinput">sudo gem install arvados-*.gem</code>
+</pre>
+</notextile>
+
+h4. Test installation
+
+If the SDK is installed, @ruby -r arvados -e 'puts "OK!"'@ should produce no errors.
+
+If your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ environment variables are set up correctly (see "api-tokens":{{site.baseurl}}/user/reference/api-tokens.html for details), the following test script should work:
+
+<notextile>
+<pre>$ <code class="userinput">ruby -r arvados <<'EOF'
+arv = Arvados.new api_version: 'v1'
+my_full_name = arv.user.current[:full_name]
+puts "arvados.v1.users.current.full_name = '#{my_full_name}'"
+EOF</code>
+arvados.v1.users.current.full_name = 'Your Name'
+</pre>
+</notextile>
+
+h3. Examples
+
+Import the module (we skipped this step above by using "ruby -r arvados"):
+
+<notextile>
+<pre><code class="userinput">require 'arvados'
+</code></pre>
+</notextile>
+
+Set up an API client user agent:
+
+<notextile>
+<pre><code class="userinput">arv = Arvados.new(apiVersion: 'v1')
+</code></pre>
+</notextile>
+
+Get the User object for the current user:
+
+<notextile>
+<pre><code class="userinput">current_user = arv.user.current
+</code></pre>
+</notextile>
+
+Get the UUID of an object that was retrieved using the SDK:
+
+<notextile>
+<pre><code class="userinput">current_user_uuid = current_user[:uuid]
+</code></pre>
+</notextile>
+
+Retrieve an object by ID:
+
+<notextile>
+<pre><code class="userinput">some_user = arv.user.get(uuid: current_user_uuid)
+</code></pre>
+</notextile>
+
+Create an object:
+
+<notextile>
+<pre><code class="userinput">new_link = arv.link.create(link: {link_class: 'test', name: 'test'})
+</code></pre>
+</notextile>
+
+Update an object:
+
+<notextile>
+<pre><code class="userinput">updated_link = arv.link.update(uuid: new_link[:uuid],
+ link: {properties: {foo: 'bar'}})
+</code></pre>
+</notextile>
+
+Delete an object:
+
+<notextile>
+<pre><code class="userinput">arv.link.delete(uuid: new_link[:uuid])
+</code></pre>
+</notextile>
+
+Get a list of objects:
+
+<notextile>
+<pre><code class="userinput">repos = arv.repository.list
+first_repo = repos[:items][0]
+puts "UUID of first repo returned is #{first_repo[:uuid]}"</code>
+UUID of first repo returned is qr1hi-s0uqq-b1bnybpx3u5temz
+</pre>
+</notextile>
+
+The SDK retrieves the list of API methods from the server at run time. Therefore, the set of available methods is determined by the server version rather than the SDK version.
commit 74e9c46eeba14471209ebeed36fe8899a4e23663
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Mar 25 17:38:02 2014 -0400
Fix broken links and duplicate titles.
diff --git a/doc/sdk/cli/index.html.textile.liquid b/doc/sdk/cli/index.html.textile.liquid
index ab5a41d..3b63079 100644
--- a/doc/sdk/cli/index.html.textile.liquid
+++ b/doc/sdk/cli/index.html.textile.liquid
@@ -6,8 +6,6 @@ title: "Command line SDK"
...
-h1. Command line SDK
-
The @arv@ CLI tool provides a generic set of wrappers so you can make API calls easily. It performs some validation before connecting to the API server: for example, it refuses to do an API call if a required parameter is missing.
It also provides access to Keep storage services with the @arv keep@ subcommand.
diff --git a/doc/sdk/index.html.textile.liquid b/doc/sdk/index.html.textile.liquid
index 7a81f1d..cea3ab0 100644
--- a/doc/sdk/index.html.textile.liquid
+++ b/doc/sdk/index.html.textile.liquid
@@ -6,6 +6,6 @@ title: "Arvados SDK Reference"
This section documents how to access the Arvados API and Keep using various programming languages.
-* "Python SDK":python/sdk-python.html
-* "Perl SDK":perl/index.html
-* "Command line SDK":cli/index.html ("arv")
+* "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html
+* "Perl SDK":{{site.baseurl}}/sdk/perl/index.html
+* "Command line SDK":{{site.baseurl}}/sdk/cli/index.html ("arv")
diff --git a/doc/sdk/perl/index.html.textile.liquid b/doc/sdk/perl/index.html.textile.liquid
index c164d60..288bc31 100644
--- a/doc/sdk/perl/index.html.textile.liquid
+++ b/doc/sdk/perl/index.html.textile.liquid
@@ -6,8 +6,6 @@ title: "Perl SDK"
...
-h1. Perl SDK
-
The Perl SDK provides a generic set of wrappers so you can make API calls easily.
It should be treated as alpha/experimental. Currently, limitations include:
commit 6fb5d2bd10901a1e0ced4ea8849419145d47a0b5
Merge: e287d16 921c13a
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Mar 25 17:30:37 2014 -0400
Merge branch 'master' into 2244-sdk-docs
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