[ARVADOS] updated: 26e1c10f963a586e40ea9dcb46a87b0107c97b7c

Git user git at public.curoverse.com
Thu Nov 3 16:00:51 EDT 2016 

Summary of changes:
 doc/_config.yml                                        |  1 +
 doc/api/index.html.textile.liquid                      |  4 ++++
 doc/api/methods/api_clients.html.textile.liquid        |  2 +-
 doc/api/methods/authorized_keys.html.textile.liquid    |  2 ++
 doc/api/methods/collections.html.textile.liquid        |  2 ++
 doc/api/methods/container_requests.html.textile.liquid |  2 ++
 doc/api/methods/containers.html.textile.liquid         |  2 ++
 doc/api/methods/groups.html.textile.liquid             |  3 ++-
 doc/api/methods/humans.html.textile.liquid             |  2 ++
 doc/api/methods/job_tasks.html.textile.liquid          |  4 ++++
 doc/api/methods/jobs.html.textile.liquid               |  4 ++++
 doc/api/methods/keep_disks.html.textile.liquid         |  4 ++--
 doc/api/methods/keep_services.html.textile.liquid      |  2 ++
 doc/api/methods/links.html.textile.liquid              |  2 ++
 doc/api/methods/logs.html.textile.liquid               | 16 ++++++++--------
 doc/api/methods/nodes.html.textile.liquid              |  2 ++
 doc/api/methods/pipeline_instances.html.textile.liquid |  2 ++
 doc/api/methods/pipeline_templates.html.textile.liquid |  2 ++
 doc/api/methods/repositories.html.textile.liquid       |  2 ++
 doc/api/methods/specimens.html.textile.liquid          |  2 ++
 doc/api/methods/traits.html.textile.liquid             |  2 ++
 doc/api/methods/users.html.textile.liquid              |  2 ++
 doc/api/methods/virtual_machines.html.textile.liquid   |  2 ++
 doc/api/methods/workflows.html.textile.liquid          |  2 ++
 doc/api/storage.html.textile.liquid                    |  4 ++--
 doc/api/tokens.html.textile.liquid                     |  2 +-
 26 files changed, 61 insertions(+), 15 deletions(-)

       via  26e1c10f963a586e40ea9dcb46a87b0107c97b7c (commit)
       via  7e52fd153f2d16f94061ef1eabfe653d4a83852a (commit)
      from  b8610f34c21f1cf44b938802f37971b06af4361c (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 26e1c10f963a586e40ea9dcb46a87b0107c97b7c
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Nov 3 16:00:46 2016 -0400

    10346: Add storage to sidebar.  Tweak headings.

diff --git a/doc/_config.yml b/doc/_config.yml
index 2f66fcd..96aea34 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -107,6 +107,7 @@ navbar:
       - api/methods.html.textile.liquid
       - api/resources.html.textile.liquid
       - api/permission-model.html.textile.liquid
+      - api/storage.html.textile.liquid
       - api/execution.html.textile.liquid
     - Permission and authentication:
       - api/methods/api_client_authorizations.html.textile.liquid
diff --git a/doc/api/index.html.textile.liquid b/doc/api/index.html.textile.liquid
index 9eff786..d90a35e 100644
--- a/doc/api/index.html.textile.liquid
+++ b/doc/api/index.html.textile.liquid
@@ -7,6 +7,10 @@ title: API Reference
 
 This reference describes the semantics of Arvados resources and how to programatically access Arvados via its REST API.  Each resource listed in this section is exposed on the Arvados API server under the @/arvados/v1/@ path prefix, for example, @https://{{ site.arvados_api_host }}/arvados/v1/collections at .
 
+h2. Discovery document
+
 The API server publishes a machine-readable description of its endpoints and some additional site configuration values via a JSON-formatted discovery document.  This is available at @/discovery/v1/apis/arvados/v1/rest@, for example @https://{{ site.arvados_api_host }}/discovery/v1/apis/arvados/v1/rest at .  Some Arvados SDKs use the discovery document to generate language bindings.
 
+h2. Workbench examples
+
 Many Arvados Workbench pages, under the the *Advanced* tab, provide examples of API and SDK use for accessing the current resource .
diff --git a/doc/api/storage.html.textile.liquid b/doc/api/storage.html.textile.liquid
index f70ecc2..c03a456 100644
--- a/doc/api/storage.html.textile.liquid
+++ b/doc/api/storage.html.textile.liquid
@@ -29,11 +29,11 @@ h2. Keep server API
 
 The Keep server is accessed via a simple HTTP REST API.
 
-*GET /blockidentifier+size+A at token*
+*GET /blocklocator+size+A at token*
 
 Fetch the data block, if the token is valid.
 
-*PUT /blockidentifier*
+*PUT /blocklocator*
 
 Returns the md5 sum of the data along with the signed token.
 

commit 7e52fd153f2d16f94061ef1eabfe653d4a83852a
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Nov 3 15:53:17 2016 -0400

    10346: Add a brief description about each resource.

diff --git a/doc/api/methods/api_clients.html.textile.liquid b/doc/api/methods/api_clients.html.textile.liquid
index d7c834e..bc5d9e4 100644
--- a/doc/api/methods/api_clients.html.textile.liquid
+++ b/doc/api/methods/api_clients.html.textile.liquid
@@ -16,7 +16,7 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
-which are permitted to access the API server.  Applications must provide
+The "api_clients" resource determines if web applications that have gone through the browser login flow may create or list API tokens.
 
 Each ApiClient has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
diff --git a/doc/api/methods/authorized_keys.html.textile.liquid b/doc/api/methods/authorized_keys.html.textile.liquid
index 079d150..897c849 100644
--- a/doc/api/methods/authorized_keys.html.textile.liquid
+++ b/doc/api/methods/authorized_keys.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+The authorized_keys resource stores SSH public keys which grant access to virtual machines or git repositories on the Arvados cluster as the user in @authorized_user_uuid at .
+
 Each AuthorizedKey has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/collections.html.textile.liquid b/doc/api/methods/collections.html.textile.liquid
index 4379f72..594c501 100644
--- a/doc/api/methods/collections.html.textile.liquid
+++ b/doc/api/methods/collections.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+Collections describe sets of files in terms of data blocks stored in Keep.  See "storage in Keep":{{site.baseurl}}/api/execution.html for details.
+
 Each collection has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/container_requests.html.textile.liquid b/doc/api/methods/container_requests.html.textile.liquid
index a024527..f39262c 100644
--- a/doc/api/methods/container_requests.html.textile.liquid
+++ b/doc/api/methods/container_requests.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+A container request is a request for the Arvados cluster to perform some computational work.  See "computing with Crunch":{{site.baseurl}}/api/execution.html for details.
+
 Each ContainerRequest offers the following attributes, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 All attributes are optional, unless otherwise marked as required.
diff --git a/doc/api/methods/containers.html.textile.liquid b/doc/api/methods/containers.html.textile.liquid
index 145b1d6..31922ff 100644
--- a/doc/api/methods/containers.html.textile.liquid
+++ b/doc/api/methods/containers.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+A container is work order to be dispatched to an Arvados cluster to perform some computational work.  A container is created in response to a container request.  See "computing with Crunch":{{site.baseurl}}/api/execution.html for details.
+
 Each Container offers the following attributes, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/groups.html.textile.liquid b/doc/api/methods/groups.html.textile.liquid
index 3e4a252..2590dfc 100644
--- a/doc/api/methods/groups.html.textile.liquid
+++ b/doc/api/methods/groups.html.textile.liquid
@@ -3,7 +3,6 @@ layout: default
 navsection: api
 navmenu: API Methods
 title: "groups"
-
 ...
 
 
@@ -17,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+Groups provides a way to apply the same permissions to a set of Arvados objects.  See "permission model":{{site.baseurl}}/api/permission-model.html for details.
+
 Each Group has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/humans.html.textile.liquid b/doc/api/methods/humans.html.textile.liquid
index 0d4b2cc..abd4a96 100644
--- a/doc/api/methods/humans.html.textile.liquid
+++ b/doc/api/methods/humans.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+A metadata record that may be used to represent a human subject.
+
 Each Human has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/job_tasks.html.textile.liquid b/doc/api/methods/job_tasks.html.textile.liquid
index 6d031c9..778a454 100644
--- a/doc/api/methods/job_tasks.html.textile.liquid
+++ b/doc/api/methods/job_tasks.html.textile.liquid
@@ -16,6 +16,10 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+Deprecated.
+
+A job task is a individually scheduled and task executed as part of an overall job.
+
 Each JobTask has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/jobs.html.textile.liquid b/doc/api/methods/jobs.html.textile.liquid
index 4779fb9..edf2e16 100644
--- a/doc/api/methods/jobs.html.textile.liquid
+++ b/doc/api/methods/jobs.html.textile.liquid
@@ -16,6 +16,10 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+Deprecated.
+
+A job describes a work order to be executed by the Arvados cluster.
+
 Each job has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/keep_disks.html.textile.liquid b/doc/api/methods/keep_disks.html.textile.liquid
index 7cec243..dd4d740 100644
--- a/doc/api/methods/keep_disks.html.textile.liquid
+++ b/doc/api/methods/keep_disks.html.textile.liquid
@@ -14,10 +14,10 @@ UUID type: @penuu@
 
 Required arguments are displayed in %{background:#ccffcc}green%.
 
-Obsoleted by "keep_services":{{site.baseurl}}/api/methods/keep_services.html
-
 h2. Resource
 
+Obsoleted by "keep_services":{{site.baseurl}}/api/methods/keep_services.html
+
 Each KeepDisk has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/keep_services.html.textile.liquid b/doc/api/methods/keep_services.html.textile.liquid
index 97ed7d8..d433568 100644
--- a/doc/api/methods/keep_services.html.textile.liquid
+++ b/doc/api/methods/keep_services.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+The keep_services resource storage servers and proxies available on the cluster for persistent storage and retrieval of keep blocks.
+
 Each KeepService has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/links.html.textile.liquid b/doc/api/methods/links.html.textile.liquid
index 99205be..96e25a4 100644
--- a/doc/api/methods/links.html.textile.liquid
+++ b/doc/api/methods/links.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+Links are an extensible way to describe relationships between Arvados objects and metadata about individual objects.
+
 Each link has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/logs.html.textile.liquid b/doc/api/methods/logs.html.textile.liquid
index e878071..574c8ed 100644
--- a/doc/api/methods/logs.html.textile.liquid
+++ b/doc/api/methods/logs.html.textile.liquid
@@ -14,14 +14,6 @@ UUID type: @57u5n@
 
 Required arguments are displayed in %{background:#ccffcc}green%.
 
-h2. Creation
-
-Any user may create Log entries for any event they find useful. User-generated Logs have no intrinsic meaning to other users or to the Arvados system itself; it is up to each user to choose appropriate log event types and summaries for their project.
-
-h3. System Logs
-
-Arvados uses Logs to record creation, deletion, and updates of other Arvados resources.
-
 h2. Resource
 
 Each Log has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
@@ -34,6 +26,14 @@ table(table table-bordered table-condensed).
 |summary|text|||
 |properties|hash|||
 
+h3. Creation
+
+Any user may create Log entries for any event they find useful. User-generated Logs have no intrinsic meaning to other users or to the Arvados system itself; it is up to each user to choose appropriate log event types and summaries for their project.
+
+h3. System Logs
+
+Arvados uses Logs to record creation, deletion, and updates of other Arvados resources.
+
 h2. Methods
 
 h3. create
diff --git a/doc/api/methods/nodes.html.textile.liquid b/doc/api/methods/nodes.html.textile.liquid
index e5cb80a..794755d 100644
--- a/doc/api/methods/nodes.html.textile.liquid
+++ b/doc/api/methods/nodes.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+Node resources list compute nodes on which Crunch may schedule work.
+
 Each Node has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/pipeline_instances.html.textile.liquid b/doc/api/methods/pipeline_instances.html.textile.liquid
index cacdaca..33f927f 100644
--- a/doc/api/methods/pipeline_instances.html.textile.liquid
+++ b/doc/api/methods/pipeline_instances.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+Deprecated.  A pipeline instance is a collection of jobs managed by @aravdos-run-pipeline-instance at .
+
 Each PipelineInstance has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/pipeline_templates.html.textile.liquid b/doc/api/methods/pipeline_templates.html.textile.liquid
index 672b274..80ab400 100644
--- a/doc/api/methods/pipeline_templates.html.textile.liquid
+++ b/doc/api/methods/pipeline_templates.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+Deprecated.  A pipeline template is a collection of jobs that can be instantiated as a pipeline_instance.
+
 Each PipelineTemplate has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/repositories.html.textile.liquid b/doc/api/methods/repositories.html.textile.liquid
index d745703..27c98ea 100644
--- a/doc/api/methods/repositories.html.textile.liquid
+++ b/doc/api/methods/repositories.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+The repositories resource lists git repositories managed by Arvados.
+
 Each Repository has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/specimens.html.textile.liquid b/doc/api/methods/specimens.html.textile.liquid
index 55a7b0c..316e115 100644
--- a/doc/api/methods/specimens.html.textile.liquid
+++ b/doc/api/methods/specimens.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+A metadata record that may be used to represent a biological specimen.
+
 Each Specimen has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/traits.html.textile.liquid b/doc/api/methods/traits.html.textile.liquid
index 9ed0df2..01ab677 100644
--- a/doc/api/methods/traits.html.textile.liquid
+++ b/doc/api/methods/traits.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+A metadata record that may be used to represent a genotype or phenotype trait.
+
 Each Trait has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/users.html.textile.liquid b/doc/api/methods/users.html.textile.liquid
index 25eac28..ab89435 100644
--- a/doc/api/methods/users.html.textile.liquid
+++ b/doc/api/methods/users.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+Users represent individuals with access to the Arvados cluster.
+
 Each User has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/virtual_machines.html.textile.liquid b/doc/api/methods/virtual_machines.html.textile.liquid
index b353325..1fc83a8 100644
--- a/doc/api/methods/virtual_machines.html.textile.liquid
+++ b/doc/api/methods/virtual_machines.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+The virtual_machines resource lists nodes in the Arvados cluster to which a user may log in to get an interactive shell (via ssh or webshell).
+
 Each VirtualMachine has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/methods/workflows.html.textile.liquid b/doc/api/methods/workflows.html.textile.liquid
index 17fb351..bde0ee4 100644
--- a/doc/api/methods/workflows.html.textile.liquid
+++ b/doc/api/methods/workflows.html.textile.liquid
@@ -16,6 +16,8 @@ Required arguments are displayed in %{background:#ccffcc}green%.
 
 h2. Resource
 
+Stores a "Common Workflow Language":http://commonwl.org (CWL) computational workflow that can be searched for, browsed and executed (submitted to Crunch) from the workbench.
+
 Each Workflow offers the following optional attributes, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
 
 table(table table-bordered table-condensed).
diff --git a/doc/api/tokens.html.textile.liquid b/doc/api/tokens.html.textile.liquid
index 83b0858..c8dafd9 100644
--- a/doc/api/tokens.html.textile.liquid
+++ b/doc/api/tokens.html.textile.liquid
@@ -22,7 +22,7 @@ Use the @create@ method of the "API client authorizations":{{site.baseurl}}/api/
 
 h2. Trusted API clients
 
-The "api_clients" resource applies access restrictions to web applications that have gone through the browser login flow.
+The "api_clients" resource determines if web applications that have gone through the browser login flow may create or list or API tokens.
 
 After the user has authenticated, but before an authorization token is issued and browser redirect sent (sending the browser back to the @return_to@ login page bearing @api_token@), the server strips the path and query portion from @return_to@ to get @url_prefix@ finds or creates an ApiClient object.  The newly issued API client authorization (API token) is associated with this ApiClient object.
 

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