[ARVADOS] updated: 4de2c25d6bd0974b456cbe1f5c2f0ff91a15f087
git at public.curoverse.com
git at public.curoverse.com
Fri Dec 20 18:38:54 EST 2013
Summary of changes:
apps/admin/setup-new-user.rb | 136 +
apps/workbench/public/favicon.ico | Bin 16958 -> 24838 bytes
doc/_includes/0-filter.py | 35 +
doc/_includes/parallel_hash_script.py | 90 +
doc/_includes/tutorial_hash_script.py | 63 +
doc/_layouts/default.html | 55 +-
doc/css/bootstrap-responsive.min.css | 20 +
doc/css/bootstrap.css | 6307 ++++++++++++++++++++
doc/examples/ruby/list-active-nodes.rb | 13 +
doc/images/favicon.ico | Bin 16958 -> 24838 bytes
doc/install/client.textile | 17 +-
doc/js/bootstrap.min.js | 7 +
doc/js/jquery.min.js | 5 +
doc/user/{ => examples}/crunch-examples.textile | 2 +-
doc/user/getting_started/check-environment.textile | 53 +
doc/user/{ => getting_started}/ssh-access.textile | 43 +-
doc/user/getting_started/workbench.textile | 17 +
doc/user/index.textile | 36 +-
doc/user/intro-git.md | 67 -
doc/user/intro-jobs.textile | 106 -
doc/user/{ => reference}/api-tokens.textile | 7 +-
.../crunch-utility-libraries.textile | 4 +-
doc/user/{ => reference}/sdk-cli.textile | 4 +-
doc/user/reference/sdk-python.textile | 127 +
doc/user/tutorial-firstscript.textile | 42 -
doc/user/tutorial-gatk-variantfiltration.textile | 125 -
doc/user/tutorial-job-debug.textile | 168 -
doc/user/tutorial-job1.textile | 252 -
doc/user/tutorial-keep.textile | 47 -
doc/user/tutorial-new-pipeline.textile | 358 --
doc/user/tutorial-trait-search.textile | 267 -
doc/user/tutorials/tutorial-firstscript.textile | 119 +
.../tutorial-gatk-variantfiltration.textile | 216 +
doc/user/tutorials/tutorial-job-debug.textile | 155 +
doc/user/tutorials/tutorial-job1.textile | 231 +
doc/user/tutorials/tutorial-keep.textile | 126 +
doc/user/tutorials/tutorial-new-pipeline.textile | 157 +
doc/user/tutorials/tutorial-parallel.textile | 80 +
doc/user/tutorials/tutorial-trait-search.textile | 273 +
docker/README.md | 33 +-
docker/config.yml.example | 5 +-
docker/run.sh | 1 -
sdk/cli/test/test_arv-put.rb | 75 +-
sdk/python/arvados/__init__.py | 87 +-
sdk/python/bin/arv-put | 20 +-
sdk/ruby/lib/arvados.rb | 38 +-
.../app/controllers/arvados/v1/jobs_controller.rb | 2 +-
services/api/public/favicon.ico | Bin 0 -> 24838 bytes
48 files changed, 8535 insertions(+), 1556 deletions(-)
create mode 100755 apps/admin/setup-new-user.rb
create mode 100644 doc/_includes/0-filter.py
create mode 100644 doc/_includes/parallel_hash_script.py
create mode 100644 doc/_includes/tutorial_hash_script.py
create mode 100644 doc/css/bootstrap-responsive.min.css
create mode 100644 doc/css/bootstrap.css
create mode 100755 doc/examples/ruby/list-active-nodes.rb
create mode 100644 doc/js/bootstrap.min.js
create mode 100644 doc/js/jquery.min.js
rename doc/user/{ => examples}/crunch-examples.textile (99%)
create mode 100644 doc/user/getting_started/check-environment.textile
rename doc/user/{ => getting_started}/ssh-access.textile (88%)
create mode 100644 doc/user/getting_started/workbench.textile
delete mode 100644 doc/user/intro-git.md
delete mode 100644 doc/user/intro-jobs.textile
rename doc/user/{ => reference}/api-tokens.textile (88%)
rename doc/user/{ => reference}/crunch-utility-libraries.textile (98%)
rename doc/user/{ => reference}/sdk-cli.textile (97%)
create mode 100644 doc/user/reference/sdk-python.textile
delete mode 100644 doc/user/tutorial-firstscript.textile
delete mode 100644 doc/user/tutorial-gatk-variantfiltration.textile
delete mode 100644 doc/user/tutorial-job-debug.textile
delete mode 100644 doc/user/tutorial-job1.textile
delete mode 100644 doc/user/tutorial-keep.textile
delete mode 100644 doc/user/tutorial-new-pipeline.textile
delete mode 100644 doc/user/tutorial-trait-search.textile
create mode 100644 doc/user/tutorials/tutorial-firstscript.textile
create mode 100644 doc/user/tutorials/tutorial-gatk-variantfiltration.textile
create mode 100644 doc/user/tutorials/tutorial-job-debug.textile
create mode 100644 doc/user/tutorials/tutorial-job1.textile
create mode 100644 doc/user/tutorials/tutorial-keep.textile
create mode 100644 doc/user/tutorials/tutorial-new-pipeline.textile
create mode 100644 doc/user/tutorials/tutorial-parallel.textile
create mode 100644 doc/user/tutorials/tutorial-trait-search.textile
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commit 4de2c25d6bd0974b456cbe1f5c2f0ff91a15f087
Merge: 69c51db 2e95340
Author: Tim Pierce <twp at clinicalfuture.com>
Date: Fri Dec 20 18:38:34 2013 -0500
Merge branch '1608-api-documentation' of git.clinicalfuture.com:arvados into 1608-api-documentation
commit 69c51db395b69d53ac92463035aa8ab743740334
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 fc3b1834a6ffe0d91de0c9305c7e58453a54a870
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 a9e367e052468a6727bbda0de9dc0311d2307a4a
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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