[ARVADOS] updated: aed823dfc63b6d6876c2736ac3b7e11b312378d5
git at public.curoverse.com
git at public.curoverse.com
Thu Dec 26 12:56:39 EST 2013
Summary of changes:
apps/admin/setup-new-user.rb | 2 +-
crunch_scripts/pgp-survey-import | 18 +++++++++---------
doc/examples/ruby/list-active-nodes.rb | 2 +-
doc/user/tutorials/tutorial-trait-search.textile | 12 ++++++------
docker/Makefile | 14 +++++++-------
docker/api/Dockerfile | 12 +++++++++---
sdk/cli/bin/crunch-job | 2 +-
sdk/python/test_pipeline_template.py | 10 +++++-----
services/keep/keep.rb | 2 +-
9 files changed, 40 insertions(+), 34 deletions(-)
via aed823dfc63b6d6876c2736ac3b7e11b312378d5 (commit)
via 0f55cc56432a2d494ec239daa9cfa2a3b43ea997 (commit)
via 9cf4008391992b103d178eccc061a4485db46445 (commit)
via 395f0a8f02b335dd970a38584da5ae674440b972 (commit)
via 7b475aea175a7e9ffc35a66cf1748ae95ceca8af (commit)
via c5b49509ce831b3ebbf9f1c4129269ea169bbaab (commit)
via ae8f0b4ba5d446de5fbddde8f314d4a69b7cf86e (commit)
via 012a0e4d585b078de136328496acdc35b40971cb (commit)
via 416de5990f82edf4e065438cd56e04c06ba4171c (commit)
via 0e5acaae2070c991628dd5f658aa1ce77125a981 (commit)
via 15f2a2c449095c4be2d41d2cd6915ca07ae07644 (commit)
via eff9d0deac0e06f7310ba1463aab89b342e71aa9 (commit)
via b6f6708ada5dd029f90022f7b1b82fccc4868dcc (commit)
via 44b3e4df6236f40eb4c41663b91e6bde1a3c3d17 (commit)
from 09f20203faabdd65367c7db1f84fd63527101903 (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 aed823dfc63b6d6876c2736ac3b7e11b312378d5
Merge: 0f55cc5 09f2020
Author: Tim Pierce <twp at clinicalfuture.com>
Date: Thu Dec 26 12:56:35 2013 -0500
Merge branch '1608-api-documentation' of git.clinicalfuture.com:arvados into 1608-api-documentation
commit 0f55cc56432a2d494ec239daa9cfa2a3b43ea997
Author: Tim Pierce <twp at clinicalfuture.com>
Date: Mon Dec 23 15:51:54 2013 -0500
Fix bug in default argument types.
diff --git a/services/api/app/controllers/arvados/v1/schema_controller.rb b/services/api/app/controllers/arvados/v1/schema_controller.rb
index 80b2cb6..1d50daa 100644
--- a/services/api/app/controllers/arvados/v1/schema_controller.rb
+++ b/services/api/app/controllers/arvados/v1/schema_controller.rb
@@ -193,9 +193,9 @@ class Arvados::V1::SchemaController < ApplicationController
limit: {
type: "integer",
description: "Maximum number of #{k.to_s.underscore.pluralize} to return.",
- default: "100",
+ default: 100,
format: "int32",
- minimum: "0",
+ minimum: 0,
location: "query"
},
pageToken: {
commit 9cf4008391992b103d178eccc061a4485db46445
Author: Tim Pierce <twp at clinicalfuture.com>
Date: Mon Dec 23 15:13:19 2013 -0500
Reorganizing API documentation to support new navbar (refs #1651).
Add site.navbar.api to _config.yml, and add matching "navmenu" fields to API documentation pages.
diff --git a/doc/_config.yml b/doc/_config.yml
index d214f84..a4fed53 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -2,7 +2,11 @@ baseurl: /doc
arvados_api_host: qr1hi.arvadosapi.com
navbar:
userguide:
- - Getting Started
- - Tutorials
- - Examples
- - Reference
+ - Getting Started
+ - Tutorials
+ - Examples
+ - Reference
+ api:
+ - Concepts
+ - API Methods
+ - Schema
diff --git a/doc/_includes/navbar_left.html b/doc/_includes/navbar_left.html
index 81e94b7..d593ff3 100644
--- a/doc/_includes/navbar_left.html
+++ b/doc/_includes/navbar_left.html
@@ -1,14 +1,14 @@
<div class="span3">
<div class="affix-top">
<div class="well sidebar-nav">
- {% if page.navsection == 'userguide' %}
+ {% if page.navsection == 'userguide' or page.navsection == 'api' %}
<ol class="nav nav-list">
- {% for menu_item in site.navbar.userguide %}
+ {% for menu_item in site.navbar[page.navsection] %}
<li>{{ menu_item }}
<ol class="nav nav-list">
{% for navorder in (0..99) %}
{% for p in site.pages %}
- {% if p.navmenu == menu_item and p.navorder == navorder %}
+ {% if p.navsection == page.navsection and p.navmenu == menu_item and p.navorder == navorder %}
<li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}><a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
{% endif %}{% endfor %}{% endfor %}
</ol>
diff --git a/doc/api/ApiClientAuthorization.textile b/doc/api/ApiClientAuthorization.textile
index 133b9cb..cb8a8e6 100644
--- a/doc/api/ApiClientAuthorization.textile
+++ b/doc/api/ApiClientAuthorization.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: ApiClientAuthorization"
navorder: 101
---
diff --git a/doc/api/ApiClients.textile b/doc/api/ApiClients.textile
index b4bc5d1..7acfcf0 100644
--- a/doc/api/ApiClients.textile
+++ b/doc/api/ApiClients.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: ApiClient"
navorder: 101
---
diff --git a/doc/api/AuthorizedKey.textile b/doc/api/AuthorizedKey.textile
index 6450807..28b7769 100644
--- a/doc/api/AuthorizedKey.textile
+++ b/doc/api/AuthorizedKey.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: AuthorizedKey"
navorder: 101
---
diff --git a/doc/api/Collections.textile b/doc/api/Collections.textile
index 428cddd..90dcf2e 100644
--- a/doc/api/Collections.textile
+++ b/doc/api/Collections.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: Collections"
navorder: 13
---
diff --git a/doc/api/Commit.textile b/doc/api/Commit.textile
index 9bb8dbf..dddb61e 100644
--- a/doc/api/Commit.textile
+++ b/doc/api/Commit.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: Commit"
navorder: 101
---
diff --git a/doc/api/CommitAncestor.textile b/doc/api/CommitAncestor.textile
index d8921c3..ae444ea 100644
--- a/doc/api/CommitAncestor.textile
+++ b/doc/api/CommitAncestor.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: CommitAncestor"
navorder: 101
---
diff --git a/doc/api/Group.textile b/doc/api/Group.textile
index 5b4fae8..853d052 100644
--- a/doc/api/Group.textile
+++ b/doc/api/Group.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: Group"
navorder: 101
---
diff --git a/doc/api/Human.textile b/doc/api/Human.textile
index 15718f3..11a1dde 100644
--- a/doc/api/Human.textile
+++ b/doc/api/Human.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: Human"
navorder: 101
---
diff --git a/doc/api/JobTasks.textile b/doc/api/JobTasks.textile
index 7cb3ea3..656ca1d 100644
--- a/doc/api/JobTasks.textile
+++ b/doc/api/JobTasks.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: JobTasks"
navorder: 16
---
diff --git a/doc/api/Jobs.textile b/doc/api/Jobs.textile
index d238c13..b837b3e 100644
--- a/doc/api/Jobs.textile
+++ b/doc/api/Jobs.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: Jobs"
navorder: 15
---
diff --git a/doc/api/KeepDisk.textile b/doc/api/KeepDisk.textile
index 6873e8b..b013ede 100644
--- a/doc/api/KeepDisk.textile
+++ b/doc/api/KeepDisk.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: KeepDisk"
navorder: 101
---
diff --git a/doc/api/Link.textile b/doc/api/Link.textile
index 95ddeb5..1bffc1f 100644
--- a/doc/api/Link.textile
+++ b/doc/api/Link.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: Link"
navorder: 101
---
diff --git a/doc/api/Links.textile b/doc/api/Links.textile
index be3c089..5faa9b0 100644
--- a/doc/api/Links.textile
+++ b/doc/api/Links.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: Links"
navorder: 17
---
diff --git a/doc/api/Log.textile b/doc/api/Log.textile
index adeb166..34ec27f 100644
--- a/doc/api/Log.textile
+++ b/doc/api/Log.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: Log"
navorder: 101
---
diff --git a/doc/api/Node.textile b/doc/api/Node.textile
index 9c4c426..c2f0ee9 100644
--- a/doc/api/Node.textile
+++ b/doc/api/Node.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: Node"
navorder: 101
---
diff --git a/doc/api/PipelineInstance.textile b/doc/api/PipelineInstance.textile
index 9b4c9a3..2a646c9 100644
--- a/doc/api/PipelineInstance.textile
+++ b/doc/api/PipelineInstance.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: PipelineInstance"
navorder: 101
---
diff --git a/doc/api/PipelineTemplate.textile b/doc/api/PipelineTemplate.textile
index 84e0128..c316ac4 100644
--- a/doc/api/PipelineTemplate.textile
+++ b/doc/api/PipelineTemplate.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: PipelineTemplate"
navorder: 101
---
diff --git a/doc/api/Repository.textile b/doc/api/Repository.textile
index ad95479..f014b48 100644
--- a/doc/api/Repository.textile
+++ b/doc/api/Repository.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: Repository"
navorder: 101
---
diff --git a/doc/api/Specimen.textile b/doc/api/Specimen.textile
index 90216aa..dcb4326 100644
--- a/doc/api/Specimen.textile
+++ b/doc/api/Specimen.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: Specimen"
navorder: 101
---
diff --git a/doc/api/Trait.textile b/doc/api/Trait.textile
index d2e625d..49c444e 100644
--- a/doc/api/Trait.textile
+++ b/doc/api/Trait.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: Trait"
navorder: 101
---
diff --git a/doc/api/User.textile b/doc/api/User.textile
index d5fce1a..5d9d90d 100644
--- a/doc/api/User.textile
+++ b/doc/api/User.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: User"
navorder: 101
---
diff --git a/doc/api/VirtualMachine.textile b/doc/api/VirtualMachine.textile
index 964df01..241f4c7 100644
--- a/doc/api/VirtualMachine.textile
+++ b/doc/api/VirtualMachine.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Schema
title: "Resource: VirtualMachine"
navorder: 101
---
diff --git a/doc/api/authentication.textile b/doc/api/authentication.textile
index e48be7d..d02f834 100644
--- a/doc/api/authentication.textile
+++ b/doc/api/authentication.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Concepts
title: Authentication
navorder: 2
---
diff --git a/doc/api/crunch-scripts.textile b/doc/api/crunch-scripts.textile
index 859e5a7..10f0c65 100644
--- a/doc/api/crunch-scripts.textile
+++ b/doc/api/crunch-scripts.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Concepts
title: Crunch scripts
navorder: 5
---
diff --git a/doc/api/methods.textile b/doc/api/methods.textile
index 5b47d3f..fd11ddb 100644
--- a/doc/api/methods.textile
+++ b/doc/api/methods.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Concepts
title: REST methods
navorder: 3
---
diff --git a/doc/api/permission-model.textile b/doc/api/permission-model.textile
index 78b8384..843ab25 100644
--- a/doc/api/permission-model.textile
+++ b/doc/api/permission-model.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Concepts
title: "Permission model"
navorder: 6
---
diff --git a/doc/api/resources.textile b/doc/api/resources.textile
index e6ab62e..f7c1e69 100644
--- a/doc/api/resources.textile
+++ b/doc/api/resources.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: api
+navmenu: Concepts
title: Resources
navorder: 4
---
commit 395f0a8f02b335dd970a38584da5ae674440b972
Author: Tim Pierce <twp at clinicalfuture.com>
Date: Mon Dec 23 13:54:39 2013 -0500
Reorganize navbars.
Move top and left-side navbars to their own _include pages.
Define navbar sections in _config.yml.
diff --git a/doc/_config.yml b/doc/_config.yml
index e6cc670..d214f84 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -1,2 +1,8 @@
baseurl: /doc
arvados_api_host: qr1hi.arvadosapi.com
+navbar:
+ userguide:
+ - Getting Started
+ - Tutorials
+ - Examples
+ - Reference
diff --git a/doc/_includes/navbar_left.html b/doc/_includes/navbar_left.html
new file mode 100644
index 0000000..81e94b7
--- /dev/null
+++ b/doc/_includes/navbar_left.html
@@ -0,0 +1,27 @@
+ <div class="span3">
+ <div class="affix-top">
+ <div class="well sidebar-nav">
+ {% if page.navsection == 'userguide' %}
+ <ol class="nav nav-list">
+ {% for menu_item in site.navbar.userguide %}
+ <li>{{ menu_item }}
+ <ol class="nav nav-list">
+ {% for navorder in (0..99) %}
+ {% for p in site.pages %}
+ {% if p.navmenu == menu_item and p.navorder == navorder %}
+ <li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}><a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
+ {% endif %}{% endfor %}{% endfor %}
+ </ol>
+ </li>
+ {% endfor %}
+ </ol>
+ {% else %}
+ <ol class="nav nav-list">
+ {% for navorder in (0..99) %}{% for p in site.pages %}{% if p.navsection == page.navsection and p.navorder == navorder %}
+ <li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}><a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
+ {% endif %}{% endfor %}{% endfor %}
+ </ol>
+ {% endif %}
+ </div>
+ </div>
+ </div>
diff --git a/doc/_includes/navbar_top.html b/doc/_includes/navbar_top.html
new file mode 100644
index 0000000..fc2098d
--- /dev/null
+++ b/doc/_includes/navbar_top.html
@@ -0,0 +1,22 @@
+ <div class="navbar navbar-inverse navbar-fixed-top" style="margin-bottom:0;">
+ <div class="navbar-inner">
+ <div class="container">
+ <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="brand" href="{{ site.baseurl }}/">Arvados Docs</a>
+ <div class="nav-collapse collapse">
+ <ul class="nav">
+ <li {% if page.navsection == 'userguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/user/">User Guide</a></li>
+ <li {% if page.navsection == 'api' %} class="active" {% endif %}><a href="{{ site.baseurl }}/api/">API Reference</a></li>
+ <li {% if page.navsection == 'adminguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/admin/">Admin Guide</a></li>
+ <li {% if page.navsection == 'installguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/install/">Install Guide</a></li>
+ <li><a></a></li>
+ <li><a href="https://arvados.org/">arvados.org »</a></li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div>
+ </div>
+ </div>
diff --git a/doc/_layouts/default.html b/doc/_layouts/default.html
index 75b64e5..380d5f6 100644
--- a/doc/_layouts/default.html
+++ b/doc/_layouts/default.html
@@ -67,28 +67,7 @@
<![endif]-->
</head>
<body class="nopad">
- <div class="navbar navbar-inverse navbar-fixed-top" style="margin-bottom:0;">
- <div class="navbar-inner">
- <div class="container">
- <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
- <span class="icon-bar"></span>
- <span class="icon-bar"></span>
- <span class="icon-bar"></span>
- </button>
- <a class="brand" href="{{ site.baseurl }}/">Arvados Docs</a>
- <div class="nav-collapse collapse">
- <ul class="nav">
- <li {% if page.navsection == 'userguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/user/">User Guide</a></li>
- <li {% if page.navsection == 'api' %} class="active" {% endif %}><a href="{{ site.baseurl }}/api/">API Reference</a></li>
- <li {% if page.navsection == 'adminguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/admin/">Admin Guide</a></li>
- <li {% if page.navsection == 'installguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/install/">Install Guide</a></li>
- <li><a></a></li>
- <li><a href="https://arvados.org/">arvados.org »</a></li>
- </ul>
- </div><!--/.nav-collapse -->
- </div>
- </div>
- </div>
+ {% include navbar_top.html %}
{% if page.navsection == 'top' %}
{{ content }}
@@ -98,50 +77,7 @@
<div class="container-fluid">
<div class="row-fluid">
- <div class="span3">
- <div class="affix-top">
- <div class="well sidebar-nav">
- {% if page.navsection == 'userguide' %}
- <ol class="nav nav-list">
- <li>Getting Started
- <ol class="nav nav-list">
- {% for navorder in (0..99) %}{% for p in site.pages %}{% if p.navsection == page.navsection and p.navorder == navorder %}
- <li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}><a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
- {% endif %}{% endfor %}{% endfor %}
- </ol>
- </li>
- <li>Tutorials
- <ol class="nav nav-list">
- {% for navorder in (100..199) %}{% for p in site.pages %}{% if p.navsection == page.navsection and p.navorder == navorder %}
- <li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}><a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
- {% endif %}{% endfor %}{% endfor %}
- </ol>
- </li>
- <li>Examples
- <ol class="nav nav-list">
- {% for navorder in (200..299) %}{% for p in site.pages %}{% if p.navsection == page.navsection and p.navorder == navorder %}
- <li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}><a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
- {% endif %}{% endfor %}{% endfor %}
- </ol>
- </li>
- <li>Reference
- <ol class="nav nav-list">
- {% for navorder in (300..399) %}{% for p in site.pages %}{% if p.navsection == page.navsection and p.navorder == navorder %}
- <li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}><a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
- {% endif %}{% endfor %}{% endfor %}
- </ol>
- </li>
- </ol>
- {% else %}
- <ol class="nav nav-list">
- {% for navorder in (0..99) %}{% for p in site.pages %}{% if p.navsection == page.navsection and p.navorder == navorder %}
- <li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}><a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
- {% endif %}{% endfor %}{% endfor %}
- </ol>
- {% endif %}
- </div>
- </div>
- </div>
+ {% include navbar_left.html %}
<div class="span9"><div style="padding-left: 2em;">
{{ content }}
</div></div>
diff --git a/doc/user/examples/crunch-examples.textile b/doc/user/examples/crunch-examples.textile
index 2140c8e..6fc9dc0 100644
--- a/doc/user/examples/crunch-examples.textile
+++ b/doc/user/examples/crunch-examples.textile
@@ -1,8 +1,9 @@
---
layout: default
navsection: userguide
+navmenu: Examples
title: "Crunch examples"
-navorder: 230
+navorder: 30
---
h1. Crunch examples
diff --git a/doc/user/getting_started/check-environment.textile b/doc/user/getting_started/check-environment.textile
index c199db9..298f188 100644
--- a/doc/user/getting_started/check-environment.textile
+++ b/doc/user/getting_started/check-environment.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: userguide
+navmenu: Getting Started
title: "Checking your environment"
navorder: 10
---
diff --git a/doc/user/getting_started/ssh-access.textile b/doc/user/getting_started/ssh-access.textile
index 4c8019c..5cd73c9 100644
--- a/doc/user/getting_started/ssh-access.textile
+++ b/doc/user/getting_started/ssh-access.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: userguide
+navmenu: Getting Started
title: Accessing an Arvados VM over ssh
navorder: 2
---
diff --git a/doc/user/getting_started/workbench.textile b/doc/user/getting_started/workbench.textile
index c463cfd..f4f8f08 100644
--- a/doc/user/getting_started/workbench.textile
+++ b/doc/user/getting_started/workbench.textile
@@ -1,6 +1,7 @@
---
layout: default
navsection: userguide
+navmenu: Getting Started
title: Accessing Arvados Workbench
navorder: 1
---
diff --git a/doc/user/reference/api-tokens.textile b/doc/user/reference/api-tokens.textile
index 49fd9a4..928ba26 100644
--- a/doc/user/reference/api-tokens.textile
+++ b/doc/user/reference/api-tokens.textile
@@ -1,8 +1,9 @@
---
layout: default
navsection: userguide
+navmenu: Reference
title: "Getting an API token"
-navorder: 301
+navorder: 01
---
h1. Reference: Getting an API token
diff --git a/doc/user/reference/crunch-utility-libraries.textile b/doc/user/reference/crunch-utility-libraries.textile
index 8233791..524040f 100644
--- a/doc/user/reference/crunch-utility-libraries.textile
+++ b/doc/user/reference/crunch-utility-libraries.textile
@@ -1,8 +1,9 @@
---
layout: default
navsection: userguide
+navmenu: Reference
title: "Crunch utility libraries"
-navorder: 331
+navorder: 31
---
h1. Crunch utility libraries
diff --git a/doc/user/reference/sdk-cli.textile b/doc/user/reference/sdk-cli.textile
index e909a8b..706fe93 100644
--- a/doc/user/reference/sdk-cli.textile
+++ b/doc/user/reference/sdk-cli.textile
@@ -1,8 +1,9 @@
---
layout: default
navsection: userguide
+navmenu: Reference
title: "Command line SDK"
-navorder: 322
+navorder: 22
---
h1. Reference: Command line SDK
diff --git a/doc/user/reference/sdk-python.textile b/doc/user/reference/sdk-python.textile
index fe824ac..29212c1 100644
--- a/doc/user/reference/sdk-python.textile
+++ b/doc/user/reference/sdk-python.textile
@@ -1,8 +1,9 @@
---
layout: default
navsection: userguide
+navmenu: Reference
title: "Python SDK"
-navorder: 323
+navorder: 23
---
h1. Reference: Python SDK
diff --git a/doc/user/tutorials/tutorial-firstscript.textile b/doc/user/tutorials/tutorial-firstscript.textile
index 3b557ae..bfde02c 100644
--- a/doc/user/tutorials/tutorial-firstscript.textile
+++ b/doc/user/tutorials/tutorial-firstscript.textile
@@ -1,8 +1,9 @@
---
layout: default
navsection: userguide
+navmenu: Tutorials
title: "Writing a Crunch script"
-navorder: 113
+navorder: 13
---
h1. Tutorial: Writing a Crunch script
diff --git a/doc/user/tutorials/tutorial-gatk-variantfiltration.textile b/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
index c1cdf05..77306d0 100644
--- a/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
+++ b/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
@@ -1,8 +1,9 @@
---
layout: default
navsection: userguide
+navmenu: Tutorials
title: "Using GATK with Arvados"
-navorder: 116
+navorder: 16
---
h1. Tutorial: Using GATK with Arvados
diff --git a/doc/user/tutorials/tutorial-job-debug.textile b/doc/user/tutorials/tutorial-job-debug.textile
index 3b68929..9ea454c 100644
--- a/doc/user/tutorials/tutorial-job-debug.textile
+++ b/doc/user/tutorials/tutorial-job-debug.textile
@@ -1,8 +1,9 @@
---
layout: default
navsection: userguide
+navmenu: Tutorials
title: "Debugging a Crunch script"
-navorder: 114
+navorder: 14
---
h1. Tutorial: Debugging a Crunch script
diff --git a/doc/user/tutorials/tutorial-job1.textile b/doc/user/tutorials/tutorial-job1.textile
index 176b087..253c4bd 100644
--- a/doc/user/tutorials/tutorial-job1.textile
+++ b/doc/user/tutorials/tutorial-job1.textile
@@ -1,8 +1,9 @@
---
layout: default
navsection: userguide
+navmenu: Tutorials
title: "Running a Crunch job"
-navorder: 112
+navorder: 12
---
h1. Tutorial: Running a crunch job
diff --git a/doc/user/tutorials/tutorial-keep.textile b/doc/user/tutorials/tutorial-keep.textile
index d156e0a..8255440 100644
--- a/doc/user/tutorials/tutorial-keep.textile
+++ b/doc/user/tutorials/tutorial-keep.textile
@@ -1,8 +1,9 @@
---
layout: default
navsection: userguide
+navmenu: Tutorials
title: "Storing and Retrieving data using Arvados Keep"
-navorder: 111
+navorder: 11
---
h1. Tutorial: Storing and Retrieving data using Arvados Keep
diff --git a/doc/user/tutorials/tutorial-new-pipeline.textile b/doc/user/tutorials/tutorial-new-pipeline.textile
index 9a127bd..5277bfc 100644
--- a/doc/user/tutorials/tutorial-new-pipeline.textile
+++ b/doc/user/tutorials/tutorial-new-pipeline.textile
@@ -1,8 +1,9 @@
---
layout: default
navsection: userguide
+navmenu: Tutorials
title: "Constructing a Crunch pipeline"
-navorder: 115
+navorder: 15
---
h1. Tutorial: Constructing a Crunch pipeline
diff --git a/doc/user/tutorials/tutorial-parallel.textile b/doc/user/tutorials/tutorial-parallel.textile
index b6e0b68..149da77 100644
--- a/doc/user/tutorials/tutorial-parallel.textile
+++ b/doc/user/tutorials/tutorial-parallel.textile
@@ -1,8 +1,9 @@
---
layout: default
navsection: userguide
+navmenu: Tutorials
title: "Parallel Crunch tasks"
-navorder: 115
+navorder: 15
---
h1. Tutorial: Parallel Crunch tasks
diff --git a/doc/user/tutorials/tutorial-trait-search.textile b/doc/user/tutorials/tutorial-trait-search.textile
index 0908c1f..4f4ec9c 100644
--- a/doc/user/tutorials/tutorial-trait-search.textile
+++ b/doc/user/tutorials/tutorial-trait-search.textile
@@ -1,8 +1,9 @@
---
layout: default
navsection: userguide
+navmenu: Tutorials
title: "Querying the Metadata Database"
-navorder: 116
+navorder: 16
---
h1. Tutorial: Querying the Metadata Database
commit 7b475aea175a7e9ffc35a66cf1748ae95ceca8af
Author: Tim Pierce <twp at unchi.org>
Date: Wed Dec 18 17:55:32 2013 -0500
Updated table headings, removed redundant fields.
diff --git a/doc/api/ApiClientAuthorization.textile b/doc/api/ApiClientAuthorization.textile
index 254ee4d..133b9cb 100644
--- a/doc/api/ApiClientAuthorization.textile
+++ b/doc/api/ApiClientAuthorization.textile
@@ -30,8 +30,7 @@ h2. Resources
An ApiClientAuthorization is not a generic Arvados resource. The full list of properties that belong to an ApiClientAuthorization is:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
+|*Attribute*|*Type*|*Description*|*Example*|
|api_token|string|||
|api_client_id|integer|||
|user_id|integer|||
@@ -39,7 +38,6 @@ table(table table-bordered table-condensed).
|last_used_by_ip_address|string|||
|last_used_at|datetime|||
|expires_at|datetime|||
-|created_at|datetime|||
|updated_at|datetime|||
|default_owner_uuid|string|||
|scopes|Array|||
diff --git a/doc/api/ApiClients.textile b/doc/api/ApiClients.textile
index 791c652..b4bc5d1 100644
--- a/doc/api/ApiClients.textile
+++ b/doc/api/ApiClients.textile
@@ -31,7 +31,7 @@ h2. Resources
Each ApiClient has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
+|*Attribute*|*Type*|*Description*|*Example*|
|name|string|||
|url_prefix|string|||
|is_trusted|boolean|||
diff --git a/doc/api/AuthorizedKey.textile b/doc/api/AuthorizedKey.textile
index fc15c54..6450807 100644
--- a/doc/api/AuthorizedKey.textile
+++ b/doc/api/AuthorizedKey.textile
@@ -30,17 +30,10 @@ h2. Resources
Each AuthorizedKey has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|name|string|||
|key_type|string|||
|authorized_user_uuid|string|||
|public_key|text|||
|expires_at|datetime|||
-|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/Collections.textile b/doc/api/Collections.textile
index 38002fe..428cddd 100644
--- a/doc/api/Collections.textile
+++ b/doc/api/Collections.textile
@@ -33,7 +33,7 @@ h2. Resource
Each collection has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
+|*Attribute*|*Type*|*Description*|*Example*|
|locator|string|||
|portable_data_hash|string|||
|name|string|||
diff --git a/doc/api/Commit.textile b/doc/api/Commit.textile
index 2dab839..9bb8dbf 100644
--- a/doc/api/Commit.textile
+++ b/doc/api/Commit.textile
@@ -30,10 +30,8 @@ h2. Resources
Each Commit has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
+|*Attribute*|*Type*|*Description*|*Example*|
|repository_name|string|||
|sha1|string|||
|message|string|||
-|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/CommitAncestor.textile b/doc/api/CommitAncestor.textile
index 675b5dc..d8921c3 100644
--- a/doc/api/CommitAncestor.textile
+++ b/doc/api/CommitAncestor.textile
@@ -30,11 +30,9 @@ h2. Resources
Each CommitAncestor has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
+|*Attribute*|*Type*|*Description*|*Example*|
|repository_name|string|||
|descendant|string|||
|ancestor|string|||
|is|boolean|||
-|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/Group.textile b/doc/api/Group.textile
index 49b6851..5b4fae8 100644
--- a/doc/api/Group.textile
+++ b/doc/api/Group.textile
@@ -30,14 +30,7 @@ h2. Resources
Each Group has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|name|string|||
|description|text|||
|updated_at|datetime|||
diff --git a/doc/api/Human.textile b/doc/api/Human.textile
index 0cd53cd..15718f3 100644
--- a/doc/api/Human.textile
+++ b/doc/api/Human.textile
@@ -30,13 +30,6 @@ h2. Resources
Each Human has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|properties|Hash|||
-|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/Job.textile b/doc/api/Job.textile
deleted file mode 100644
index cfce311..0000000
--- a/doc/api/Job.textile
+++ /dev/null
@@ -1,58 +0,0 @@
----
-layout: default
-navsection: api
-title: "Resource: Job"
-navorder: 101
----
-
-h1. Job
-
-A **Job** represents...
-
-h2. Methods
-
-See "REST methods for working with Arvados resources":methods.html
-
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/job@
-
-h2. Creation
-
-h3. Prerequisites
-
-Prerequisites for creating a Job.
-
-h3. Side effects
-
-Side effects of creating a Job.
-
-h2. Resources
-
-Each Job has, in addition to the usual "attributes of Arvados resources":resources.html:
-
-table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
-|submit_id|string|||
-|script|string|||
-|script_version|string|||
-|script_parameters|Hash|||
-|cancelled_by_client_uuid|string|||
-|cancelled_by_user_uuid|string|||
-|cancelled_at|datetime|||
-|started_at|datetime|||
-|finished_at|datetime|||
-|running|boolean|||
-|success|boolean|||
-|output|string|||
-|created_at|datetime|||
-|updated_at|datetime|||
-|priority|string|||
-|is_locked_by_uuid|string|||
-|log|string|||
-|tasks_summary|Hash|||
-|runtime_constraints|Hash|||
diff --git a/doc/api/JobTask.textile b/doc/api/JobTask.textile
deleted file mode 100644
index 7ff4605..0000000
--- a/doc/api/JobTask.textile
+++ /dev/null
@@ -1,49 +0,0 @@
----
-layout: default
-navsection: api
-title: "Resource: JobTask"
-navorder: 101
----
-
-h1. JobTask
-
-A **JobTask** represents...
-
-h2. Methods
-
-See "REST methods for working with Arvados resources":methods.html
-
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/job_task@
-
-h2. Creation
-
-h3. Prerequisites
-
-Prerequisites for creating a JobTask.
-
-h3. Side effects
-
-Side effects of creating a JobTask.
-
-h2. Resources
-
-Each JobTask has, in addition to the usual "attributes of Arvados resources":resources.html:
-
-table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
-|job_uuid|string|||
-|sequence|integer|||
-|parameters|Hash|||
-|output|text|||
-|progress|float|||
-|success|boolean|||
-|created_at|datetime|||
-|updated_at|datetime|||
-|created_by_job_task_uuid|string|||
-|qsequence|integer|||
diff --git a/doc/api/KeepDisk.textile b/doc/api/KeepDisk.textile
index 4a1b768..6873e8b 100644
--- a/doc/api/KeepDisk.textile
+++ b/doc/api/KeepDisk.textile
@@ -30,13 +30,7 @@ h2. Resources
Each KeepDisk has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|ping_secret|string|||
|node_uuid|string|||
|filesystem_uuid|string|||
@@ -47,7 +41,6 @@ table(table table-bordered table-condensed).
|last_read_at|datetime|||
|last_write_at|datetime|||
|last_ping_at|datetime|||
-|created_at|datetime|||
|updated_at|datetime|||
|service_host|string|||
|service_port|integer|||
diff --git a/doc/api/Link.textile b/doc/api/Link.textile
index b840798..95ddeb5 100644
--- a/doc/api/Link.textile
+++ b/doc/api/Link.textile
@@ -30,14 +30,7 @@ h2. Resources
Each Link has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|tail_uuid|string|||
|tail_kind|string|||
|link_class|string|||
diff --git a/doc/api/Log.textile b/doc/api/Log.textile
index 033ff3a..adeb166 100644
--- a/doc/api/Log.textile
+++ b/doc/api/Log.textile
@@ -30,18 +30,11 @@ h2. Resources
Each Log has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
+|*Attribute*|*Type*|*Description*|*Example*|
|object_kind|string|||
|object_uuid|string|||
|event_at|datetime|||
|event_type|string|||
|summary|text|||
|info|Hash|||
-|created_at|datetime|||
|updated_at|datetime|||
-|modified_at|datetime|||
diff --git a/doc/api/Node.textile b/doc/api/Node.textile
index e64730f..9c4c426 100644
--- a/doc/api/Node.textile
+++ b/doc/api/Node.textile
@@ -30,14 +30,7 @@ h2. Resources
Each Node has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|slot_number|integer|||
|hostname|string|||
|domain|string|||
diff --git a/doc/api/PipelineInstance.textile b/doc/api/PipelineInstance.textile
index eca4026..9b4c9a3 100644
--- a/doc/api/PipelineInstance.textile
+++ b/doc/api/PipelineInstance.textile
@@ -30,14 +30,7 @@ h2. Resources
Each PipelineInstance has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|pipeline_template_uuid|string|||
|name|string|||
|components|Hash|||
diff --git a/doc/api/PipelineTemplate.textile b/doc/api/PipelineTemplate.textile
index 876200f..84e0128 100644
--- a/doc/api/PipelineTemplate.textile
+++ b/doc/api/PipelineTemplate.textile
@@ -30,14 +30,7 @@ h2. Resources
Each PipelineTemplate has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|name|string|||
|components|Hash|||
|updated_at|datetime|||
diff --git a/doc/api/Repository.textile b/doc/api/Repository.textile
index f26efc3..ad95479 100644
--- a/doc/api/Repository.textile
+++ b/doc/api/Repository.textile
@@ -30,15 +30,8 @@ h2. Resources
Each Repository has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|name|string|||
|fetch_url|string|||
|push_url|string|||
-|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/Specimen.textile b/doc/api/Specimen.textile
index 0110682..90216aa 100644
--- a/doc/api/Specimen.textile
+++ b/doc/api/Specimen.textile
@@ -30,14 +30,7 @@ h2. Resources
Each Specimen has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|material|string|||
|updated_at|datetime|||
|properties|Hash|||
diff --git a/doc/api/Trait.textile b/doc/api/Trait.textile
index 2cac6a5..d2e625d 100644
--- a/doc/api/Trait.textile
+++ b/doc/api/Trait.textile
@@ -30,14 +30,7 @@ h2. Resources
Each Trait has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|name|string|||
|properties|Hash|||
-|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/User.textile b/doc/api/User.textile
index b3022e4..d5fce1a 100644
--- a/doc/api/User.textile
+++ b/doc/api/User.textile
@@ -30,14 +30,7 @@ h2. Resources
Each User has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|email|string|||
|first_name|string|||
|last_name|string|||
diff --git a/doc/api/VirtualMachine.textile b/doc/api/VirtualMachine.textile
index 5cabc54..964df01 100644
--- a/doc/api/VirtualMachine.textile
+++ b/doc/api/VirtualMachine.textile
@@ -30,13 +30,6 @@ h2. Resources
Each VirtualMachine has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|hostname|string|||
-|created_at|datetime|||
|updated_at|datetime|||
commit c5b49509ce831b3ebbf9f1c4129269ea169bbaab
Author: Tim Pierce <twp at clinicalfuture.com>
Date: Mon Dec 16 20:06:51 2013 -0500
Linking all generated doc pages to index. (refs #1608)
diff --git a/doc/api/ApiClient.textile b/doc/api/ApiClient.textile
deleted file mode 100644
index 60301b3..0000000
--- a/doc/api/ApiClient.textile
+++ /dev/null
@@ -1,44 +0,0 @@
----
-layout: default
-navsection: api
-title: "Resource: ApiClient"
-navorder: 101
----
-
-h1. ApiClient
-
-A **ApiClient** represents...
-
-h2. Methods
-
-See "REST methods for working with Arvados resources":methods.html
-
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_client@
-
-h2. Creation
-
-h3. Prerequisites
-
-Prerequisites for creating a ApiClient.
-
-h3. Side effects
-
-Side effects of creating a ApiClient.
-
-h2. Resources
-
-Each ApiClient has, in addition to the usual "attributes of Arvados resources":resources.html:
-
-table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
-|name|string|||
-|url_prefix|string|||
-|created_at|datetime|||
-|updated_at|datetime|||
-|is_trusted|boolean|||
diff --git a/doc/api/ApiClientAuthorization.textile b/doc/api/ApiClientAuthorization.textile
index b633c53..254ee4d 100644
--- a/doc/api/ApiClientAuthorization.textile
+++ b/doc/api/ApiClientAuthorization.textile
@@ -7,7 +7,7 @@ navorder: 101
h1. ApiClientAuthorization
-A **ApiClientAuthorization** represents...
+A **ApiClientAuthorization** represents the API authorization token that has been issued to each "ApiClient":ApiClient.html known to this Arvados instance.
h2. Methods
@@ -27,7 +27,7 @@ Side effects of creating a ApiClientAuthorization.
h2. Resources
-Each ApiClientAuthorization has, in addition to the usual "attributes of Arvados resources":resources.html:
+An ApiClientAuthorization is not a generic Arvados resource. The full list of properties that belong to an ApiClientAuthorization is:
table(table table-bordered table-condensed).
|*Property name*|*Value*|*Description*|*Example*|
diff --git a/doc/api/Collection.textile b/doc/api/Collection.textile
deleted file mode 100644
index 8672b2b..0000000
--- a/doc/api/Collection.textile
+++ /dev/null
@@ -1,49 +0,0 @@
----
-layout: default
-navsection: api
-title: "Resource: Collection"
-navorder: 101
----
-
-h1. Collection
-
-A **Collection** represents...
-
-h2. Methods
-
-See "REST methods for working with Arvados resources":methods.html
-
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/collection@
-
-h2. Creation
-
-h3. Prerequisites
-
-Prerequisites for creating a Collection.
-
-h3. Side effects
-
-Side effects of creating a Collection.
-
-h2. Resources
-
-Each Collection has, in addition to the usual "attributes of Arvados resources":resources.html:
-
-table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|locator|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
-|portable_data_hash|string|||
-|name|string|||
-|redundancy|integer|||
-|redundancy_confirmed_by_client_uuid|string|||
-|redundancy_confirmed_at|datetime|||
-|redundancy_confirmed_as|integer|||
-|updated_at|datetime|||
-|uuid|string|||
-|manifest_text|text|||
commit ae8f0b4ba5d446de5fbddde8f314d4a69b7cf86e
Author: Tim Pierce <twp at clinicalfuture.com>
Date: Fri Dec 13 18:11:14 2013 -0500
Added skeleton doc files for all API resources.
diff --git a/doc/api/ApiClients.textile b/doc/api/ApiClient.textile
similarity index 56%
copy from doc/api/ApiClients.textile
copy to doc/api/ApiClient.textile
index b4bc5d1..60301b3 100644
--- a/doc/api/ApiClients.textile
+++ b/doc/api/ApiClient.textile
@@ -5,33 +5,40 @@ title: "Resource: ApiClient"
navorder: 101
---
-h1. ApiClients
-
-An **ApiClient** represents a client program that has issued a request to the API server.
+h1. ApiClient
+A **ApiClient** represents...
h2. Methods
See "REST methods for working with Arvados resources":methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_clients@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_client@
h2. Creation
h3. Prerequisites
-Prerequisites for creating an ApiClient.
+Prerequisites for creating a ApiClient.
h3. Side effects
-Side effects of creating an ApiClient.
+Side effects of creating a ApiClient.
h2. Resources
Each ApiClient has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|name|string|||
|url_prefix|string|||
+|created_at|datetime|||
+|updated_at|datetime|||
|is_trusted|boolean|||
diff --git a/doc/api/ApiClientAuthorization.textile b/doc/api/ApiClientAuthorization.textile
index 133b9cb..b633c53 100644
--- a/doc/api/ApiClientAuthorization.textile
+++ b/doc/api/ApiClientAuthorization.textile
@@ -7,7 +7,7 @@ navorder: 101
h1. ApiClientAuthorization
-A **ApiClientAuthorization** represents the API authorization token that has been issued to each "ApiClient":ApiClient.html known to this Arvados instance.
+A **ApiClientAuthorization** represents...
h2. Methods
@@ -27,10 +27,11 @@ Side effects of creating a ApiClientAuthorization.
h2. Resources
-An ApiClientAuthorization is not a generic Arvados resource. The full list of properties that belong to an ApiClientAuthorization is:
+Each ApiClientAuthorization has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
|api_token|string|||
|api_client_id|integer|||
|user_id|integer|||
@@ -38,6 +39,7 @@ table(table table-bordered table-condensed).
|last_used_by_ip_address|string|||
|last_used_at|datetime|||
|expires_at|datetime|||
+|created_at|datetime|||
|updated_at|datetime|||
|default_owner_uuid|string|||
|scopes|Array|||
diff --git a/doc/api/ApiClients.textile b/doc/api/ApiClients.textile
index b4bc5d1..791c652 100644
--- a/doc/api/ApiClients.textile
+++ b/doc/api/ApiClients.textile
@@ -31,7 +31,7 @@ h2. Resources
Each ApiClient has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
|name|string|||
|url_prefix|string|||
|is_trusted|boolean|||
diff --git a/doc/api/AuthorizedKey.textile b/doc/api/AuthorizedKey.textile
index 6450807..fc15c54 100644
--- a/doc/api/AuthorizedKey.textile
+++ b/doc/api/AuthorizedKey.textile
@@ -30,10 +30,17 @@ h2. Resources
Each AuthorizedKey has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|name|string|||
|key_type|string|||
|authorized_user_uuid|string|||
|public_key|text|||
|expires_at|datetime|||
+|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/Collection.textile b/doc/api/Collection.textile
new file mode 100644
index 0000000..8672b2b
--- /dev/null
+++ b/doc/api/Collection.textile
@@ -0,0 +1,49 @@
+---
+layout: default
+navsection: api
+title: "Resource: Collection"
+navorder: 101
+---
+
+h1. Collection
+
+A **Collection** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/collection@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a Collection.
+
+h3. Side effects
+
+Side effects of creating a Collection.
+
+h2. Resources
+
+Each Collection has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|locator|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|portable_data_hash|string|||
+|name|string|||
+|redundancy|integer|||
+|redundancy_confirmed_by_client_uuid|string|||
+|redundancy_confirmed_at|datetime|||
+|redundancy_confirmed_as|integer|||
+|updated_at|datetime|||
+|uuid|string|||
+|manifest_text|text|||
diff --git a/doc/api/Collections.textile b/doc/api/Collections.textile
index 428cddd..38002fe 100644
--- a/doc/api/Collections.textile
+++ b/doc/api/Collections.textile
@@ -33,7 +33,7 @@ h2. Resource
Each collection has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
|locator|string|||
|portable_data_hash|string|||
|name|string|||
diff --git a/doc/api/Commit.textile b/doc/api/Commit.textile
index 9bb8dbf..2dab839 100644
--- a/doc/api/Commit.textile
+++ b/doc/api/Commit.textile
@@ -30,8 +30,10 @@ h2. Resources
Each Commit has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
|repository_name|string|||
|sha1|string|||
|message|string|||
+|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/CommitAncestor.textile b/doc/api/CommitAncestor.textile
index d8921c3..675b5dc 100644
--- a/doc/api/CommitAncestor.textile
+++ b/doc/api/CommitAncestor.textile
@@ -30,9 +30,11 @@ h2. Resources
Each CommitAncestor has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
|repository_name|string|||
|descendant|string|||
|ancestor|string|||
|is|boolean|||
+|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/Group.textile b/doc/api/Group.textile
index 5b4fae8..49b6851 100644
--- a/doc/api/Group.textile
+++ b/doc/api/Group.textile
@@ -30,7 +30,14 @@ h2. Resources
Each Group has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|name|string|||
|description|text|||
|updated_at|datetime|||
diff --git a/doc/api/Human.textile b/doc/api/Human.textile
index 15718f3..0cd53cd 100644
--- a/doc/api/Human.textile
+++ b/doc/api/Human.textile
@@ -30,6 +30,13 @@ h2. Resources
Each Human has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|properties|Hash|||
+|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/Job.textile b/doc/api/Job.textile
new file mode 100644
index 0000000..cfce311
--- /dev/null
+++ b/doc/api/Job.textile
@@ -0,0 +1,58 @@
+---
+layout: default
+navsection: api
+title: "Resource: Job"
+navorder: 101
+---
+
+h1. Job
+
+A **Job** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/job@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a Job.
+
+h3. Side effects
+
+Side effects of creating a Job.
+
+h2. Resources
+
+Each Job has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|submit_id|string|||
+|script|string|||
+|script_version|string|||
+|script_parameters|Hash|||
+|cancelled_by_client_uuid|string|||
+|cancelled_by_user_uuid|string|||
+|cancelled_at|datetime|||
+|started_at|datetime|||
+|finished_at|datetime|||
+|running|boolean|||
+|success|boolean|||
+|output|string|||
+|created_at|datetime|||
+|updated_at|datetime|||
+|priority|string|||
+|is_locked_by_uuid|string|||
+|log|string|||
+|tasks_summary|Hash|||
+|runtime_constraints|Hash|||
diff --git a/doc/api/JobTask.textile b/doc/api/JobTask.textile
new file mode 100644
index 0000000..7ff4605
--- /dev/null
+++ b/doc/api/JobTask.textile
@@ -0,0 +1,49 @@
+---
+layout: default
+navsection: api
+title: "Resource: JobTask"
+navorder: 101
+---
+
+h1. JobTask
+
+A **JobTask** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/job_task@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a JobTask.
+
+h3. Side effects
+
+Side effects of creating a JobTask.
+
+h2. Resources
+
+Each JobTask has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|job_uuid|string|||
+|sequence|integer|||
+|parameters|Hash|||
+|output|text|||
+|progress|float|||
+|success|boolean|||
+|created_at|datetime|||
+|updated_at|datetime|||
+|created_by_job_task_uuid|string|||
+|qsequence|integer|||
diff --git a/doc/api/KeepDisk.textile b/doc/api/KeepDisk.textile
index 6873e8b..4a1b768 100644
--- a/doc/api/KeepDisk.textile
+++ b/doc/api/KeepDisk.textile
@@ -30,7 +30,13 @@ h2. Resources
Each KeepDisk has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|ping_secret|string|||
|node_uuid|string|||
|filesystem_uuid|string|||
@@ -41,6 +47,7 @@ table(table table-bordered table-condensed).
|last_read_at|datetime|||
|last_write_at|datetime|||
|last_ping_at|datetime|||
+|created_at|datetime|||
|updated_at|datetime|||
|service_host|string|||
|service_port|integer|||
diff --git a/doc/api/Link.textile b/doc/api/Link.textile
index 95ddeb5..b840798 100644
--- a/doc/api/Link.textile
+++ b/doc/api/Link.textile
@@ -30,7 +30,14 @@ h2. Resources
Each Link has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|tail_uuid|string|||
|tail_kind|string|||
|link_class|string|||
diff --git a/doc/api/Log.textile b/doc/api/Log.textile
index adeb166..033ff3a 100644
--- a/doc/api/Log.textile
+++ b/doc/api/Log.textile
@@ -30,11 +30,18 @@ h2. Resources
Each Log has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
|object_kind|string|||
|object_uuid|string|||
|event_at|datetime|||
|event_type|string|||
|summary|text|||
|info|Hash|||
+|created_at|datetime|||
|updated_at|datetime|||
+|modified_at|datetime|||
diff --git a/doc/api/Node.textile b/doc/api/Node.textile
index 9c4c426..e64730f 100644
--- a/doc/api/Node.textile
+++ b/doc/api/Node.textile
@@ -30,7 +30,14 @@ h2. Resources
Each Node has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|slot_number|integer|||
|hostname|string|||
|domain|string|||
diff --git a/doc/api/PipelineInstance.textile b/doc/api/PipelineInstance.textile
index 9b4c9a3..eca4026 100644
--- a/doc/api/PipelineInstance.textile
+++ b/doc/api/PipelineInstance.textile
@@ -30,7 +30,14 @@ h2. Resources
Each PipelineInstance has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|pipeline_template_uuid|string|||
|name|string|||
|components|Hash|||
diff --git a/doc/api/PipelineTemplate.textile b/doc/api/PipelineTemplate.textile
index 84e0128..876200f 100644
--- a/doc/api/PipelineTemplate.textile
+++ b/doc/api/PipelineTemplate.textile
@@ -30,7 +30,14 @@ h2. Resources
Each PipelineTemplate has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|name|string|||
|components|Hash|||
|updated_at|datetime|||
diff --git a/doc/api/Repository.textile b/doc/api/Repository.textile
index ad95479..f26efc3 100644
--- a/doc/api/Repository.textile
+++ b/doc/api/Repository.textile
@@ -30,8 +30,15 @@ h2. Resources
Each Repository has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|name|string|||
|fetch_url|string|||
|push_url|string|||
+|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/Specimen.textile b/doc/api/Specimen.textile
index 90216aa..0110682 100644
--- a/doc/api/Specimen.textile
+++ b/doc/api/Specimen.textile
@@ -30,7 +30,14 @@ h2. Resources
Each Specimen has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|material|string|||
|updated_at|datetime|||
|properties|Hash|||
diff --git a/doc/api/Trait.textile b/doc/api/Trait.textile
index d2e625d..2cac6a5 100644
--- a/doc/api/Trait.textile
+++ b/doc/api/Trait.textile
@@ -30,7 +30,14 @@ h2. Resources
Each Trait has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|name|string|||
|properties|Hash|||
+|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/User.textile b/doc/api/User.textile
index d5fce1a..b3022e4 100644
--- a/doc/api/User.textile
+++ b/doc/api/User.textile
@@ -30,7 +30,14 @@ h2. Resources
Each User has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|email|string|||
|first_name|string|||
|last_name|string|||
diff --git a/doc/api/VirtualMachine.textile b/doc/api/VirtualMachine.textile
index 964df01..5cabc54 100644
--- a/doc/api/VirtualMachine.textile
+++ b/doc/api/VirtualMachine.textile
@@ -30,6 +30,13 @@ h2. Resources
Each VirtualMachine has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|*Example*|
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
|hostname|string|||
+|created_at|datetime|||
|updated_at|datetime|||
commit 012a0e4d585b078de136328496acdc35b40971cb
Author: Tim Pierce <twp at unchi.org>
Date: Wed Dec 18 17:55:32 2013 -0500
Updated table headings, removed redundant fields.
diff --git a/doc/api/ApiClientAuthorization.textile b/doc/api/ApiClientAuthorization.textile
index 254ee4d..133b9cb 100644
--- a/doc/api/ApiClientAuthorization.textile
+++ b/doc/api/ApiClientAuthorization.textile
@@ -30,8 +30,7 @@ h2. Resources
An ApiClientAuthorization is not a generic Arvados resource. The full list of properties that belong to an ApiClientAuthorization is:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
+|*Attribute*|*Type*|*Description*|*Example*|
|api_token|string|||
|api_client_id|integer|||
|user_id|integer|||
@@ -39,7 +38,6 @@ table(table table-bordered table-condensed).
|last_used_by_ip_address|string|||
|last_used_at|datetime|||
|expires_at|datetime|||
-|created_at|datetime|||
|updated_at|datetime|||
|default_owner_uuid|string|||
|scopes|Array|||
diff --git a/doc/api/ApiClients.textile b/doc/api/ApiClients.textile
index 791c652..b4bc5d1 100644
--- a/doc/api/ApiClients.textile
+++ b/doc/api/ApiClients.textile
@@ -31,7 +31,7 @@ h2. Resources
Each ApiClient has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
+|*Attribute*|*Type*|*Description*|*Example*|
|name|string|||
|url_prefix|string|||
|is_trusted|boolean|||
diff --git a/doc/api/AuthorizedKey.textile b/doc/api/AuthorizedKey.textile
index fc15c54..6450807 100644
--- a/doc/api/AuthorizedKey.textile
+++ b/doc/api/AuthorizedKey.textile
@@ -30,17 +30,10 @@ h2. Resources
Each AuthorizedKey has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|name|string|||
|key_type|string|||
|authorized_user_uuid|string|||
|public_key|text|||
|expires_at|datetime|||
-|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/Collections.textile b/doc/api/Collections.textile
index 38002fe..428cddd 100644
--- a/doc/api/Collections.textile
+++ b/doc/api/Collections.textile
@@ -33,7 +33,7 @@ h2. Resource
Each collection has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
+|*Attribute*|*Type*|*Description*|*Example*|
|locator|string|||
|portable_data_hash|string|||
|name|string|||
diff --git a/doc/api/Commit.textile b/doc/api/Commit.textile
index 2dab839..9bb8dbf 100644
--- a/doc/api/Commit.textile
+++ b/doc/api/Commit.textile
@@ -30,10 +30,8 @@ h2. Resources
Each Commit has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
+|*Attribute*|*Type*|*Description*|*Example*|
|repository_name|string|||
|sha1|string|||
|message|string|||
-|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/CommitAncestor.textile b/doc/api/CommitAncestor.textile
index 675b5dc..d8921c3 100644
--- a/doc/api/CommitAncestor.textile
+++ b/doc/api/CommitAncestor.textile
@@ -30,11 +30,9 @@ h2. Resources
Each CommitAncestor has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
+|*Attribute*|*Type*|*Description*|*Example*|
|repository_name|string|||
|descendant|string|||
|ancestor|string|||
|is|boolean|||
-|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/Group.textile b/doc/api/Group.textile
index 49b6851..5b4fae8 100644
--- a/doc/api/Group.textile
+++ b/doc/api/Group.textile
@@ -30,14 +30,7 @@ h2. Resources
Each Group has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|name|string|||
|description|text|||
|updated_at|datetime|||
diff --git a/doc/api/Human.textile b/doc/api/Human.textile
index 0cd53cd..15718f3 100644
--- a/doc/api/Human.textile
+++ b/doc/api/Human.textile
@@ -30,13 +30,6 @@ h2. Resources
Each Human has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|properties|Hash|||
-|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/Job.textile b/doc/api/Job.textile
deleted file mode 100644
index cfce311..0000000
--- a/doc/api/Job.textile
+++ /dev/null
@@ -1,58 +0,0 @@
----
-layout: default
-navsection: api
-title: "Resource: Job"
-navorder: 101
----
-
-h1. Job
-
-A **Job** represents...
-
-h2. Methods
-
-See "REST methods for working with Arvados resources":methods.html
-
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/job@
-
-h2. Creation
-
-h3. Prerequisites
-
-Prerequisites for creating a Job.
-
-h3. Side effects
-
-Side effects of creating a Job.
-
-h2. Resources
-
-Each Job has, in addition to the usual "attributes of Arvados resources":resources.html:
-
-table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
-|submit_id|string|||
-|script|string|||
-|script_version|string|||
-|script_parameters|Hash|||
-|cancelled_by_client_uuid|string|||
-|cancelled_by_user_uuid|string|||
-|cancelled_at|datetime|||
-|started_at|datetime|||
-|finished_at|datetime|||
-|running|boolean|||
-|success|boolean|||
-|output|string|||
-|created_at|datetime|||
-|updated_at|datetime|||
-|priority|string|||
-|is_locked_by_uuid|string|||
-|log|string|||
-|tasks_summary|Hash|||
-|runtime_constraints|Hash|||
diff --git a/doc/api/JobTask.textile b/doc/api/JobTask.textile
deleted file mode 100644
index 7ff4605..0000000
--- a/doc/api/JobTask.textile
+++ /dev/null
@@ -1,49 +0,0 @@
----
-layout: default
-navsection: api
-title: "Resource: JobTask"
-navorder: 101
----
-
-h1. JobTask
-
-A **JobTask** represents...
-
-h2. Methods
-
-See "REST methods for working with Arvados resources":methods.html
-
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/job_task@
-
-h2. Creation
-
-h3. Prerequisites
-
-Prerequisites for creating a JobTask.
-
-h3. Side effects
-
-Side effects of creating a JobTask.
-
-h2. Resources
-
-Each JobTask has, in addition to the usual "attributes of Arvados resources":resources.html:
-
-table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
-|job_uuid|string|||
-|sequence|integer|||
-|parameters|Hash|||
-|output|text|||
-|progress|float|||
-|success|boolean|||
-|created_at|datetime|||
-|updated_at|datetime|||
-|created_by_job_task_uuid|string|||
-|qsequence|integer|||
diff --git a/doc/api/JobTasks.textile b/doc/api/JobTasks.textile
index 2d9e00f..7cb3ea3 100644
--- a/doc/api/JobTasks.textile
+++ b/doc/api/JobTasks.textile
@@ -25,38 +25,26 @@ See "REST methods for working with Arvados resources":methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/job_tasks@
-h2. Resource
+h2. Resources
-Each job has, in addition to the usual "attributes of Arvados resources":resources.html:
+Each JobTask has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Attribute*|*Type*|*Description*|
+|*Attribute*|*Type*|*Description*|*Example*|
|sequence|integer|Execution sequence.
A step cannot be run until all steps with lower sequence numbers have completed.
-Job steps with the same sequence number can be run in any order.|
-|parameters{}|list||
-|runtime_constraints{}|list|Constraints that must be satisfied by the job/task scheduler in order to run the task (see "Jobs":Jobs.html).|
-|output|string||
-|progress|float||
-|success|boolean|Is null if the task has neither completed successfully nor failed permanently.|
+Job steps with the same sequence number can be run in any order.||
+|parameters{}|list|||
+|output|text|||
+|progress|float|||
+|success|boolean|Is null if the task has neither completed successfully nor failed permanently.||
The following attributes should not be updated by anyone other than the job manager:
table(table table-bordered table-condensed).
|*Attribute*|*Type*|*Description*|*Notes*|
|qsequence|integer|Order of arrival|0-based|
-|failed_count|number|Times this step has failed||
-|failed_at|number|Time of last failure|Is null if failed_count=0|
-|failed_log|string|stderr from last failure|Is null if failed_count=0|
-|log|string|stderr||
+|job_uuid|string|||
+|created_by_job_task_uuid|string|||
-h3. Resource limits
-
-table(table table-bordered table-condensed).
-|*Key*|*Type*|*Description*|*Implemented*|
-|min_nodes|integer|||
-|max_nodes|integer|||
-|max_tasks_per_node|integer|Maximum simultaneous tasks on a single node|✓|
-|min_ram_per_task|integer|Minimum real memory (KiB) per task||
-|min_ram_per_node|integer|Minimum real memory (KiB) per node||
diff --git a/doc/api/Jobs.textile b/doc/api/Jobs.textile
index 44796f3..d238c13 100644
--- a/doc/api/Jobs.textile
+++ b/doc/api/Jobs.textile
@@ -43,7 +43,7 @@ h2. Resource
Each job has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Type*|*Description*|*Notes*|
+|*Attribute*|*Type*|*Description*|*Notes*|
|submit_id|string|Unique ID provided by client when job was submitted|Optional. Can be used by client to ensure idempotence|
|priority|string|||
|runtime_constraints{}|list|Constraints that must be satisfied by the job/task scheduler in order to run the job.|See below.|
@@ -52,12 +52,15 @@ table(table table-bordered table-condensed).
|script_version|string|git commit/tree used when running the job|This can be submitted as an unambiguous prefix of a commit sha1, "repository:tag", or "repository:branch". Before the job starts, Arvados will resolve it to a full 40-character git commit sha1.|
|cancelled_by_client_uuid|string|API client ID|Is null if job has not been cancelled|
|cancelled_by_user_uuid|string|Authenticated user ID|Is null if job has not been cancelled|
-|cancelled_at|string|When job was cancelled|Is null if job has not been cancelled|
+|cancelled_at|datetime|When job was cancelled|Is null if job has not been cancelled|
|started_at|datetime|When job started running|Is null if job has not [yet] started|
|finished_at|datetime|When job finished running|Is null if job has not [yet] finished|
|running|boolean|Whether the job is running||
|success|boolean|Whether the job indicated successful completion|Is null if job has not finished|
|is_locked_by_uuid|string|UUID of the user who has locked this job|Is null if job is not locked. The system user locks the job when starting the job, in order to prevent job attributes from being altered.|
+|log|string|||
+|tasks_summary|Hash|||
+|output|string|||
h3. Runtime constraints
@@ -76,4 +79,4 @@ table(table table-bordered table-condensed).
|max_nodes|integer|||
|max_tasks_per_node|integer|Maximum simultaneous tasks on a single node|✓|
|min_ram_per_task|integer|Minimum real memory (KiB) per task||
-|min_ram_per_node|integer|Minimum real memory (KiB) per node||
\ No newline at end of file
+|min_ram_per_node|integer|Minimum real memory (KiB) per node||
diff --git a/doc/api/KeepDisk.textile b/doc/api/KeepDisk.textile
index 4a1b768..6873e8b 100644
--- a/doc/api/KeepDisk.textile
+++ b/doc/api/KeepDisk.textile
@@ -30,13 +30,7 @@ h2. Resources
Each KeepDisk has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|ping_secret|string|||
|node_uuid|string|||
|filesystem_uuid|string|||
@@ -47,7 +41,6 @@ table(table table-bordered table-condensed).
|last_read_at|datetime|||
|last_write_at|datetime|||
|last_ping_at|datetime|||
-|created_at|datetime|||
|updated_at|datetime|||
|service_host|string|||
|service_port|integer|||
diff --git a/doc/api/Link.textile b/doc/api/Link.textile
index b840798..95ddeb5 100644
--- a/doc/api/Link.textile
+++ b/doc/api/Link.textile
@@ -30,14 +30,7 @@ h2. Resources
Each Link has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|tail_uuid|string|||
|tail_kind|string|||
|link_class|string|||
diff --git a/doc/api/Log.textile b/doc/api/Log.textile
index 033ff3a..adeb166 100644
--- a/doc/api/Log.textile
+++ b/doc/api/Log.textile
@@ -30,18 +30,11 @@ h2. Resources
Each Log has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
+|*Attribute*|*Type*|*Description*|*Example*|
|object_kind|string|||
|object_uuid|string|||
|event_at|datetime|||
|event_type|string|||
|summary|text|||
|info|Hash|||
-|created_at|datetime|||
|updated_at|datetime|||
-|modified_at|datetime|||
diff --git a/doc/api/Node.textile b/doc/api/Node.textile
index e64730f..9c4c426 100644
--- a/doc/api/Node.textile
+++ b/doc/api/Node.textile
@@ -30,14 +30,7 @@ h2. Resources
Each Node has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|slot_number|integer|||
|hostname|string|||
|domain|string|||
diff --git a/doc/api/PipelineInstance.textile b/doc/api/PipelineInstance.textile
index eca4026..9b4c9a3 100644
--- a/doc/api/PipelineInstance.textile
+++ b/doc/api/PipelineInstance.textile
@@ -30,14 +30,7 @@ h2. Resources
Each PipelineInstance has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|pipeline_template_uuid|string|||
|name|string|||
|components|Hash|||
diff --git a/doc/api/PipelineTemplate.textile b/doc/api/PipelineTemplate.textile
index 876200f..84e0128 100644
--- a/doc/api/PipelineTemplate.textile
+++ b/doc/api/PipelineTemplate.textile
@@ -30,14 +30,7 @@ h2. Resources
Each PipelineTemplate has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|name|string|||
|components|Hash|||
|updated_at|datetime|||
diff --git a/doc/api/Repository.textile b/doc/api/Repository.textile
index f26efc3..ad95479 100644
--- a/doc/api/Repository.textile
+++ b/doc/api/Repository.textile
@@ -30,15 +30,8 @@ h2. Resources
Each Repository has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|name|string|||
|fetch_url|string|||
|push_url|string|||
-|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/Specimen.textile b/doc/api/Specimen.textile
index 0110682..90216aa 100644
--- a/doc/api/Specimen.textile
+++ b/doc/api/Specimen.textile
@@ -30,14 +30,7 @@ h2. Resources
Each Specimen has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|material|string|||
|updated_at|datetime|||
|properties|Hash|||
diff --git a/doc/api/Trait.textile b/doc/api/Trait.textile
index 2cac6a5..d2e625d 100644
--- a/doc/api/Trait.textile
+++ b/doc/api/Trait.textile
@@ -30,14 +30,7 @@ h2. Resources
Each Trait has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|name|string|||
|properties|Hash|||
-|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/User.textile b/doc/api/User.textile
index b3022e4..d5fce1a 100644
--- a/doc/api/User.textile
+++ b/doc/api/User.textile
@@ -30,14 +30,7 @@ h2. Resources
Each User has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|email|string|||
|first_name|string|||
|last_name|string|||
diff --git a/doc/api/VirtualMachine.textile b/doc/api/VirtualMachine.textile
index 5cabc54..964df01 100644
--- a/doc/api/VirtualMachine.textile
+++ b/doc/api/VirtualMachine.textile
@@ -30,13 +30,6 @@ h2. Resources
Each VirtualMachine has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
+|*Attribute*|*Type*|*Description*|*Example*|
|hostname|string|||
-|created_at|datetime|||
|updated_at|datetime|||
diff --git a/doc/api/resources.textile b/doc/api/resources.textile
index 905fb5a..e6ab62e 100644
--- a/doc/api/resources.textile
+++ b/doc/api/resources.textile
@@ -18,7 +18,7 @@ Object IDs are alphanumeric strings, unique across all installations (each insta
h2. Attributes of resources
table(table table-bordered table-condensed).
-|*Attribute name*|*Value*|*Description*|*Example*|
+|*Attribute*|*Type*|*Description*|*Example*|
|uuid|string|universally unique object identifier|@mk2qn-4zz18-w3anr2hk2wgfpuo@|
|href|string|a URL that can be used to address this resource||
|kind|string|@arvados#{resource_type}@|@arvados#collection@|
@@ -33,7 +33,7 @@ table(table table-bordered table-condensed).
h2. Attributes of resource lists
table(table table-bordered table-condensed).
-|*Attribute name*|*Value*|*Description*|*Example*|
+|*Attribute*|*Type*|*Description*|*Example*|
|kind|string|@arvados#{resource_type}_list@|@arvados#project_list@|
|etag|string|The ETag[1] of the resource list|@cd3o1wi9sf934saajykawrz2e@|
|self_link|string|||
commit 416de5990f82edf4e065438cd56e04c06ba4171c
Author: Tim Pierce <twp at clinicalfuture.com>
Date: Mon Dec 16 20:06:51 2013 -0500
Linking all generated doc pages to index. (refs #1608)
diff --git a/doc/api/ApiClient.textile b/doc/api/ApiClient.textile
deleted file mode 100644
index 60301b3..0000000
--- a/doc/api/ApiClient.textile
+++ /dev/null
@@ -1,44 +0,0 @@
----
-layout: default
-navsection: api
-title: "Resource: ApiClient"
-navorder: 101
----
-
-h1. ApiClient
-
-A **ApiClient** represents...
-
-h2. Methods
-
-See "REST methods for working with Arvados resources":methods.html
-
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_client@
-
-h2. Creation
-
-h3. Prerequisites
-
-Prerequisites for creating a ApiClient.
-
-h3. Side effects
-
-Side effects of creating a ApiClient.
-
-h2. Resources
-
-Each ApiClient has, in addition to the usual "attributes of Arvados resources":resources.html:
-
-table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|uuid|string|||
-|owner_uuid|string|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
-|name|string|||
-|url_prefix|string|||
-|created_at|datetime|||
-|updated_at|datetime|||
-|is_trusted|boolean|||
diff --git a/doc/api/ApiClientAuthorization.textile b/doc/api/ApiClientAuthorization.textile
index b633c53..254ee4d 100644
--- a/doc/api/ApiClientAuthorization.textile
+++ b/doc/api/ApiClientAuthorization.textile
@@ -7,7 +7,7 @@ navorder: 101
h1. ApiClientAuthorization
-A **ApiClientAuthorization** represents...
+A **ApiClientAuthorization** represents the API authorization token that has been issued to each "ApiClient":ApiClient.html known to this Arvados instance.
h2. Methods
@@ -27,7 +27,7 @@ Side effects of creating a ApiClientAuthorization.
h2. Resources
-Each ApiClientAuthorization has, in addition to the usual "attributes of Arvados resources":resources.html:
+An ApiClientAuthorization is not a generic Arvados resource. The full list of properties that belong to an ApiClientAuthorization is:
table(table table-bordered table-condensed).
|*Property name*|*Value*|*Description*|*Example*|
diff --git a/doc/api/Collection.textile b/doc/api/Collection.textile
deleted file mode 100644
index 8672b2b..0000000
--- a/doc/api/Collection.textile
+++ /dev/null
@@ -1,49 +0,0 @@
----
-layout: default
-navsection: api
-title: "Resource: Collection"
-navorder: 101
----
-
-h1. Collection
-
-A **Collection** represents...
-
-h2. Methods
-
-See "REST methods for working with Arvados resources":methods.html
-
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/collection@
-
-h2. Creation
-
-h3. Prerequisites
-
-Prerequisites for creating a Collection.
-
-h3. Side effects
-
-Side effects of creating a Collection.
-
-h2. Resources
-
-Each Collection has, in addition to the usual "attributes of Arvados resources":resources.html:
-
-table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|*Example*|
-|id|integer|||
-|locator|string|||
-|owner_uuid|string|||
-|created_at|datetime|||
-|modified_by_client_uuid|string|||
-|modified_by_user_uuid|string|||
-|modified_at|datetime|||
-|portable_data_hash|string|||
-|name|string|||
-|redundancy|integer|||
-|redundancy_confirmed_by_client_uuid|string|||
-|redundancy_confirmed_at|datetime|||
-|redundancy_confirmed_as|integer|||
-|updated_at|datetime|||
-|uuid|string|||
-|manifest_text|text|||
diff --git a/doc/api/index.md b/doc/api/index.md
deleted file mode 100644
index 31c0d18..0000000
--- a/doc/api/index.md
+++ /dev/null
@@ -1,37 +0,0 @@
----
-layout: default
-navsection: api
-title: API Reference
-navorder: 0
----
-
-# API Reference
-
-### Concepts
-
-* Each API uses the same [authentication mechanism](authentication.html).
-* Resources in requests and responses adhere to a [common structure](resources.html).
-* API transactions use common [REST methods](methods.html).
-* API transactions are subject to a [permission model](permission-model.html).
-* [Job tasks](job-task.html) use some special API features.
-
-### Resources
-
-* ApiClients
-* ApiClientAuthorizations
-* [Collections](Collections.html)
-* Files
-* [Jobs](Jobs.html)
-* [JobTasks](JobTasks.html)
-* [Links](Links.html)
-* Logs
-* People
-* PipelineTemplates
-* PipelineInstances
-* Groups
-* Specimens
-* Traits
-* Users
-* Variants
-* VariantAnnotations
-* VariantCalls
diff --git a/doc/api/index.textile b/doc/api/index.textile
new file mode 100644
index 0000000..5582fb0
--- /dev/null
+++ b/doc/api/index.textile
@@ -0,0 +1,52 @@
+---
+layout: default
+navsection: api
+title: API Reference
+navorder: 0
+---
+
+h1. API Reference
+
+h2. Concepts
+
+* Each API uses the same "authentication mechanism":authentication.html.
+* Resources in requests and responses adhere to a "common structure":resources.html.
+* API transactions use common "REST methods":methods.html.
+* API transactions are subject to a "permission model":permission-model.html.
+* "Job tasks":job-task.html use some special API features.
+
+h2. Resources
+
+h3. Generic Resources
+
+* "Collections":Collections.html
+* "Jobs":Jobs.html
+* "JobTasks":JobTasks.html
+* "Links":Links.html
+* "Log":Log.html
+* "PipelineTemplate":PipelineTemplate.html
+* "PipelineInstance":PipelineInstance.html
+* "Group":Group.html
+* "Human":Human.html
+* "Specimen":Specimen.html
+* "Trait":Trait.html
+* "User":User.html
+
+h3. Authentication
+
+These Arvados resources govern authorization and "authentication":authentication.html:
+
+* "ApiClients":ApiClients.html
+* "ApiClientAuthorization":ApiClientAuthorization.html
+* "AuthorizedKey":AuthorizedKey.html
+
+h3. Arvados Infrastructure
+
+These resources govern the Arvados infrastructure itself: Git repositories, Keep disks, active nodes, etc.
+
+* "CommitAncestor":CommitAncestor.html
+* "Commit":Commit.html
+* "KeepDisk":KeepDisk.html
+* "Node":Node.html
+* "Repository":Repository.html
+* "VirtualMachine":VirtualMachine.html
commit 0e5acaae2070c991628dd5f658aa1ce77125a981
Author: Tim Pierce <twp at clinicalfuture.com>
Date: Fri Dec 13 18:11:14 2013 -0500
Added skeleton doc files for all API resources.
diff --git a/doc/api/ApiClient.textile b/doc/api/ApiClient.textile
new file mode 100644
index 0000000..60301b3
--- /dev/null
+++ b/doc/api/ApiClient.textile
@@ -0,0 +1,44 @@
+---
+layout: default
+navsection: api
+title: "Resource: ApiClient"
+navorder: 101
+---
+
+h1. ApiClient
+
+A **ApiClient** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_client@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a ApiClient.
+
+h3. Side effects
+
+Side effects of creating a ApiClient.
+
+h2. Resources
+
+Each ApiClient has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|name|string|||
+|url_prefix|string|||
+|created_at|datetime|||
+|updated_at|datetime|||
+|is_trusted|boolean|||
diff --git a/doc/api/ApiClientAuthorization.textile b/doc/api/ApiClientAuthorization.textile
new file mode 100644
index 0000000..b633c53
--- /dev/null
+++ b/doc/api/ApiClientAuthorization.textile
@@ -0,0 +1,45 @@
+---
+layout: default
+navsection: api
+title: "Resource: ApiClientAuthorization"
+navorder: 101
+---
+
+h1. ApiClientAuthorization
+
+A **ApiClientAuthorization** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_client_authorization@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a ApiClientAuthorization.
+
+h3. Side effects
+
+Side effects of creating a ApiClientAuthorization.
+
+h2. Resources
+
+Each ApiClientAuthorization has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|api_token|string|||
+|api_client_id|integer|||
+|user_id|integer|||
+|created_by_ip_address|string|||
+|last_used_by_ip_address|string|||
+|last_used_at|datetime|||
+|expires_at|datetime|||
+|created_at|datetime|||
+|updated_at|datetime|||
+|default_owner_uuid|string|||
+|scopes|Array|||
diff --git a/doc/api/ApiClients.textile b/doc/api/ApiClients.textile
new file mode 100644
index 0000000..791c652
--- /dev/null
+++ b/doc/api/ApiClients.textile
@@ -0,0 +1,37 @@
+---
+layout: default
+navsection: api
+title: "Resource: ApiClient"
+navorder: 101
+---
+
+h1. ApiClients
+
+An **ApiClient** represents a client program that has issued a request to the API server.
+
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_clients@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating an ApiClient.
+
+h3. Side effects
+
+Side effects of creating an ApiClient.
+
+h2. Resources
+
+Each ApiClient has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|name|string|||
+|url_prefix|string|||
+|is_trusted|boolean|||
diff --git a/doc/api/AuthorizedKey.textile b/doc/api/AuthorizedKey.textile
new file mode 100644
index 0000000..fc15c54
--- /dev/null
+++ b/doc/api/AuthorizedKey.textile
@@ -0,0 +1,46 @@
+---
+layout: default
+navsection: api
+title: "Resource: AuthorizedKey"
+navorder: 101
+---
+
+h1. AuthorizedKey
+
+A **AuthorizedKey** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/authorized_key@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a AuthorizedKey.
+
+h3. Side effects
+
+Side effects of creating a AuthorizedKey.
+
+h2. Resources
+
+Each AuthorizedKey has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|name|string|||
+|key_type|string|||
+|authorized_user_uuid|string|||
+|public_key|text|||
+|expires_at|datetime|||
+|created_at|datetime|||
+|updated_at|datetime|||
diff --git a/doc/api/Collection.textile b/doc/api/Collection.textile
new file mode 100644
index 0000000..8672b2b
--- /dev/null
+++ b/doc/api/Collection.textile
@@ -0,0 +1,49 @@
+---
+layout: default
+navsection: api
+title: "Resource: Collection"
+navorder: 101
+---
+
+h1. Collection
+
+A **Collection** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/collection@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a Collection.
+
+h3. Side effects
+
+Side effects of creating a Collection.
+
+h2. Resources
+
+Each Collection has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|locator|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|portable_data_hash|string|||
+|name|string|||
+|redundancy|integer|||
+|redundancy_confirmed_by_client_uuid|string|||
+|redundancy_confirmed_at|datetime|||
+|redundancy_confirmed_as|integer|||
+|updated_at|datetime|||
+|uuid|string|||
+|manifest_text|text|||
diff --git a/doc/api/Collections.textile b/doc/api/Collections.textile
index 9a84b6e..38002fe 100644
--- a/doc/api/Collections.textile
+++ b/doc/api/Collections.textile
@@ -33,9 +33,12 @@ h2. Resource
Each collection has, in addition to the usual "attributes of Arvados resources":resources.html:
table(table table-bordered table-condensed).
-|*Property name*|*Value*|*Description*|
-|portable_data_hash|string||
-|redundancy|number||
-|redundancy_confirmed_by_client_uuid|string|API client|
-|redundancy_confirmed_at|datetime||
-|redundancy_confirmed_as|number||
+|*Property name*|*Value*|*Description*|*Example*|
+|locator|string|||
+|portable_data_hash|string|||
+|name|string|||
+|redundancy|number|||
+|redundancy_confirmed_by_client_uuid|string|API client||
+|redundancy_confirmed_at|datetime|||
+|redundancy_confirmed_as|number|||
+|manifest_text|text|||
diff --git a/doc/api/Commit.textile b/doc/api/Commit.textile
new file mode 100644
index 0000000..2dab839
--- /dev/null
+++ b/doc/api/Commit.textile
@@ -0,0 +1,39 @@
+---
+layout: default
+navsection: api
+title: "Resource: Commit"
+navorder: 101
+---
+
+h1. Commit
+
+A **Commit** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/commit@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a Commit.
+
+h3. Side effects
+
+Side effects of creating a Commit.
+
+h2. Resources
+
+Each Commit has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|repository_name|string|||
+|sha1|string|||
+|message|string|||
+|created_at|datetime|||
+|updated_at|datetime|||
diff --git a/doc/api/CommitAncestor.textile b/doc/api/CommitAncestor.textile
new file mode 100644
index 0000000..675b5dc
--- /dev/null
+++ b/doc/api/CommitAncestor.textile
@@ -0,0 +1,40 @@
+---
+layout: default
+navsection: api
+title: "Resource: CommitAncestor"
+navorder: 101
+---
+
+h1. CommitAncestor
+
+A **CommitAncestor** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/commit_ancestor@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a CommitAncestor.
+
+h3. Side effects
+
+Side effects of creating a CommitAncestor.
+
+h2. Resources
+
+Each CommitAncestor has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|repository_name|string|||
+|descendant|string|||
+|ancestor|string|||
+|is|boolean|||
+|created_at|datetime|||
+|updated_at|datetime|||
diff --git a/doc/api/Group.textile b/doc/api/Group.textile
new file mode 100644
index 0000000..49b6851
--- /dev/null
+++ b/doc/api/Group.textile
@@ -0,0 +1,43 @@
+---
+layout: default
+navsection: api
+title: "Resource: Group"
+navorder: 101
+---
+
+h1. Group
+
+A **Group** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/group@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a Group.
+
+h3. Side effects
+
+Side effects of creating a Group.
+
+h2. Resources
+
+Each Group has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|name|string|||
+|description|text|||
+|updated_at|datetime|||
diff --git a/doc/api/Human.textile b/doc/api/Human.textile
new file mode 100644
index 0000000..0cd53cd
--- /dev/null
+++ b/doc/api/Human.textile
@@ -0,0 +1,42 @@
+---
+layout: default
+navsection: api
+title: "Resource: Human"
+navorder: 101
+---
+
+h1. Human
+
+A **Human** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/human@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a Human.
+
+h3. Side effects
+
+Side effects of creating a Human.
+
+h2. Resources
+
+Each Human has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|properties|Hash|||
+|created_at|datetime|||
+|updated_at|datetime|||
diff --git a/doc/api/Job.textile b/doc/api/Job.textile
new file mode 100644
index 0000000..cfce311
--- /dev/null
+++ b/doc/api/Job.textile
@@ -0,0 +1,58 @@
+---
+layout: default
+navsection: api
+title: "Resource: Job"
+navorder: 101
+---
+
+h1. Job
+
+A **Job** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/job@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a Job.
+
+h3. Side effects
+
+Side effects of creating a Job.
+
+h2. Resources
+
+Each Job has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|submit_id|string|||
+|script|string|||
+|script_version|string|||
+|script_parameters|Hash|||
+|cancelled_by_client_uuid|string|||
+|cancelled_by_user_uuid|string|||
+|cancelled_at|datetime|||
+|started_at|datetime|||
+|finished_at|datetime|||
+|running|boolean|||
+|success|boolean|||
+|output|string|||
+|created_at|datetime|||
+|updated_at|datetime|||
+|priority|string|||
+|is_locked_by_uuid|string|||
+|log|string|||
+|tasks_summary|Hash|||
+|runtime_constraints|Hash|||
diff --git a/doc/api/JobTask.textile b/doc/api/JobTask.textile
new file mode 100644
index 0000000..7ff4605
--- /dev/null
+++ b/doc/api/JobTask.textile
@@ -0,0 +1,49 @@
+---
+layout: default
+navsection: api
+title: "Resource: JobTask"
+navorder: 101
+---
+
+h1. JobTask
+
+A **JobTask** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/job_task@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a JobTask.
+
+h3. Side effects
+
+Side effects of creating a JobTask.
+
+h2. Resources
+
+Each JobTask has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|job_uuid|string|||
+|sequence|integer|||
+|parameters|Hash|||
+|output|text|||
+|progress|float|||
+|success|boolean|||
+|created_at|datetime|||
+|updated_at|datetime|||
+|created_by_job_task_uuid|string|||
+|qsequence|integer|||
diff --git a/doc/api/KeepDisk.textile b/doc/api/KeepDisk.textile
new file mode 100644
index 0000000..4a1b768
--- /dev/null
+++ b/doc/api/KeepDisk.textile
@@ -0,0 +1,54 @@
+---
+layout: default
+navsection: api
+title: "Resource: KeepDisk"
+navorder: 101
+---
+
+h1. KeepDisk
+
+A **KeepDisk** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/keep_disk@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a KeepDisk.
+
+h3. Side effects
+
+Side effects of creating a KeepDisk.
+
+h2. Resources
+
+Each KeepDisk has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|ping_secret|string|||
+|node_uuid|string|||
+|filesystem_uuid|string|||
+|bytes_total|integer|||
+|bytes_free|integer|||
+|is_readable|boolean|||
+|is_writable|boolean|||
+|last_read_at|datetime|||
+|last_write_at|datetime|||
+|last_ping_at|datetime|||
+|created_at|datetime|||
+|updated_at|datetime|||
+|service_host|string|||
+|service_port|integer|||
+|service_ssl_flag|boolean|||
diff --git a/doc/api/Link.textile b/doc/api/Link.textile
new file mode 100644
index 0000000..b840798
--- /dev/null
+++ b/doc/api/Link.textile
@@ -0,0 +1,48 @@
+---
+layout: default
+navsection: api
+title: "Resource: Link"
+navorder: 101
+---
+
+h1. Link
+
+A **Link** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/link@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a Link.
+
+h3. Side effects
+
+Side effects of creating a Link.
+
+h2. Resources
+
+Each Link has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|tail_uuid|string|||
+|tail_kind|string|||
+|link_class|string|||
+|name|string|||
+|head_uuid|string|||
+|properties|Hash|||
+|updated_at|datetime|||
+|head_kind|string|||
diff --git a/doc/api/Log.textile b/doc/api/Log.textile
new file mode 100644
index 0000000..033ff3a
--- /dev/null
+++ b/doc/api/Log.textile
@@ -0,0 +1,47 @@
+---
+layout: default
+navsection: api
+title: "Resource: Log"
+navorder: 101
+---
+
+h1. Log
+
+A **Log** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/log@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a Log.
+
+h3. Side effects
+
+Side effects of creating a Log.
+
+h2. Resources
+
+Each Log has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|object_kind|string|||
+|object_uuid|string|||
+|event_at|datetime|||
+|event_type|string|||
+|summary|text|||
+|info|Hash|||
+|created_at|datetime|||
+|updated_at|datetime|||
+|modified_at|datetime|||
diff --git a/doc/api/Node.textile b/doc/api/Node.textile
new file mode 100644
index 0000000..e64730f
--- /dev/null
+++ b/doc/api/Node.textile
@@ -0,0 +1,48 @@
+---
+layout: default
+navsection: api
+title: "Resource: Node"
+navorder: 101
+---
+
+h1. Node
+
+A **Node** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/node@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a Node.
+
+h3. Side effects
+
+Side effects of creating a Node.
+
+h2. Resources
+
+Each Node has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|slot_number|integer|||
+|hostname|string|||
+|domain|string|||
+|ip_address|string|||
+|first_ping_at|datetime|||
+|last_ping_at|datetime|||
+|info|Hash|||
+|updated_at|datetime|||
diff --git a/doc/api/PipelineInstance.textile b/doc/api/PipelineInstance.textile
new file mode 100644
index 0000000..eca4026
--- /dev/null
+++ b/doc/api/PipelineInstance.textile
@@ -0,0 +1,47 @@
+---
+layout: default
+navsection: api
+title: "Resource: PipelineInstance"
+navorder: 101
+---
+
+h1. PipelineInstance
+
+A **PipelineInstance** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_instance@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a PipelineInstance.
+
+h3. Side effects
+
+Side effects of creating a PipelineInstance.
+
+h2. Resources
+
+Each PipelineInstance has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|pipeline_template_uuid|string|||
+|name|string|||
+|components|Hash|||
+|success|boolean|||
+|active|boolean|||
+|updated_at|datetime|||
+|properties|Hash|||
diff --git a/doc/api/PipelineTemplate.textile b/doc/api/PipelineTemplate.textile
new file mode 100644
index 0000000..876200f
--- /dev/null
+++ b/doc/api/PipelineTemplate.textile
@@ -0,0 +1,43 @@
+---
+layout: default
+navsection: api
+title: "Resource: PipelineTemplate"
+navorder: 101
+---
+
+h1. PipelineTemplate
+
+A **PipelineTemplate** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_template@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a PipelineTemplate.
+
+h3. Side effects
+
+Side effects of creating a PipelineTemplate.
+
+h2. Resources
+
+Each PipelineTemplate has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|name|string|||
+|components|Hash|||
+|updated_at|datetime|||
diff --git a/doc/api/Repository.textile b/doc/api/Repository.textile
new file mode 100644
index 0000000..f26efc3
--- /dev/null
+++ b/doc/api/Repository.textile
@@ -0,0 +1,44 @@
+---
+layout: default
+navsection: api
+title: "Resource: Repository"
+navorder: 101
+---
+
+h1. Repository
+
+A **Repository** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/repository@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a Repository.
+
+h3. Side effects
+
+Side effects of creating a Repository.
+
+h2. Resources
+
+Each Repository has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|name|string|||
+|fetch_url|string|||
+|push_url|string|||
+|created_at|datetime|||
+|updated_at|datetime|||
diff --git a/doc/api/Specimen.textile b/doc/api/Specimen.textile
new file mode 100644
index 0000000..0110682
--- /dev/null
+++ b/doc/api/Specimen.textile
@@ -0,0 +1,43 @@
+---
+layout: default
+navsection: api
+title: "Resource: Specimen"
+navorder: 101
+---
+
+h1. Specimen
+
+A **Specimen** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/specimen@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a Specimen.
+
+h3. Side effects
+
+Side effects of creating a Specimen.
+
+h2. Resources
+
+Each Specimen has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|material|string|||
+|updated_at|datetime|||
+|properties|Hash|||
diff --git a/doc/api/Trait.textile b/doc/api/Trait.textile
new file mode 100644
index 0000000..2cac6a5
--- /dev/null
+++ b/doc/api/Trait.textile
@@ -0,0 +1,43 @@
+---
+layout: default
+navsection: api
+title: "Resource: Trait"
+navorder: 101
+---
+
+h1. Trait
+
+A **Trait** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/trait@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a Trait.
+
+h3. Side effects
+
+Side effects of creating a Trait.
+
+h2. Resources
+
+Each Trait has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|name|string|||
+|properties|Hash|||
+|created_at|datetime|||
+|updated_at|datetime|||
diff --git a/doc/api/User.textile b/doc/api/User.textile
new file mode 100644
index 0000000..b3022e4
--- /dev/null
+++ b/doc/api/User.textile
@@ -0,0 +1,49 @@
+---
+layout: default
+navsection: api
+title: "Resource: User"
+navorder: 101
+---
+
+h1. User
+
+A **User** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/user@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a User.
+
+h3. Side effects
+
+Side effects of creating a User.
+
+h2. Resources
+
+Each User has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|created_at|datetime|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|email|string|||
+|first_name|string|||
+|last_name|string|||
+|identity_url|string|||
+|is_admin|boolean|||
+|prefs|Hash|||
+|updated_at|datetime|||
+|default_owner_uuid|string|||
+|is_active|boolean|||
diff --git a/doc/api/VirtualMachine.textile b/doc/api/VirtualMachine.textile
new file mode 100644
index 0000000..5cabc54
--- /dev/null
+++ b/doc/api/VirtualMachine.textile
@@ -0,0 +1,42 @@
+---
+layout: default
+navsection: api
+title: "Resource: VirtualMachine"
+navorder: 101
+---
+
+h1. VirtualMachine
+
+A **VirtualMachine** represents...
+
+h2. Methods
+
+See "REST methods for working with Arvados resources":methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/virtual_machine@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a VirtualMachine.
+
+h3. Side effects
+
+Side effects of creating a VirtualMachine.
+
+h2. Resources
+
+Each VirtualMachine has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|*Property name*|*Value*|*Description*|*Example*|
+|id|integer|||
+|uuid|string|||
+|owner_uuid|string|||
+|modified_by_client_uuid|string|||
+|modified_by_user_uuid|string|||
+|modified_at|datetime|||
+|hostname|string|||
+|created_at|datetime|||
+|updated_at|datetime|||
diff --git a/doc/api/resources.textile b/doc/api/resources.textile
index 038ce9d..905fb5a 100644
--- a/doc/api/resources.textile
+++ b/doc/api/resources.textile
@@ -20,6 +20,7 @@ h2. Attributes of resources
table(table table-bordered table-condensed).
|*Attribute name*|*Value*|*Description*|*Example*|
|uuid|string|universally unique object identifier|@mk2qn-4zz18-w3anr2hk2wgfpuo@|
+|href|string|a URL that can be used to address this resource||
|kind|string|@arvados#{resource_type}@|@arvados#collection@|
|etag|string|The ETag[1] of the resource|@1xlmizzjq7wro3dlb2dirf505@|
|self_link|string|||
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