[ARVADOS] updated: ddeef8adc0cb7cdb55be644b9335ea51919ed513
Git user
git at public.curoverse.com
Thu Nov 10 22:44:59 EST 2016
Summary of changes:
doc/api/crunch-scripts.html.textile.liquid | 5 ++---
doc/api/execution.html.textile.liquid | 2 +-
doc/api/methods/jobs.html.textile.liquid | 2 +-
doc/api/methods/pipeline_instances.html.textile.liquid | 2 +-
doc/sdk/python/events.html.textile.liquid | 2 +-
doc/user/reference/job-pipeline-ref.html.textile.liquid | 2 +-
doc/user/tutorials/running-external-program.html.textile.liquid | 4 ++--
doc/user/tutorials/tutorial-submit-job.html.textile.liquid | 4 ++--
8 files changed, 11 insertions(+), 12 deletions(-)
via ddeef8adc0cb7cdb55be644b9335ea51919ed513 (commit)
from c198274863bb5d72ef34dfc311c62bf50d6bd4f4 (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 ddeef8adc0cb7cdb55be644b9335ea51919ed513
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Nov 10 22:44:55 2016 -0500
10346: Fix cross references
diff --git a/doc/api/crunch-scripts.html.textile.liquid b/doc/api/crunch-scripts.html.textile.liquid
index 98634cd..4642ed5 100644
--- a/doc/api/crunch-scripts.html.textile.liquid
+++ b/doc/api/crunch-scripts.html.textile.liquid
@@ -20,8 +20,8 @@ A task's context is provided in environment variables.
table(table table-bordered table-condensed).
|Environment variable|Description|
-|@JOB_UUID@|UUID of the current "Job":schema/Job.html|
-|@TASK_UUID@|UUID of the current "JobTask":schema/JobTask.html|
+|@JOB_UUID@|UUID of the current "Job":methods/jobs.html|
+|@TASK_UUID@|UUID of the current "JobTask":methods/job_tasks.html|
|@ARVADOS_API_HOST@|Hostname and port number of API server|
|@ARVADOS_API_TOKEN@|Authentication token to use with API calls made by the current task|
@@ -43,4 +43,3 @@ task = arvados.api().job_tasks().get(uuid=os.environ['TASK_UUID']).execute()
$sys.stderr.write("current task sequence number is %d"
% task['sequence'])
</pre>
-
diff --git a/doc/api/execution.html.textile.liquid b/doc/api/execution.html.textile.liquid
index 3476879..fb03b01 100644
--- a/doc/api/execution.html.textile.liquid
+++ b/doc/api/execution.html.textile.liquid
@@ -19,7 +19,7 @@ Note: although the preferred API for Aravdos going forward, the Container API ma
h2. Job API (deprecated)
-# To submit work, create a "job":{{site.baseurl}}/api/methods/job.html . If the same job has been submitted in the past, it will return an existing job in @Completed@ state.
+# To submit work, create a "job":{{site.baseurl}}/api/methods/jobs.html . If the same job has been submitted in the past, it will return an existing job in @Completed@ state.
# The dispatcher process will notice a new job in @Queued@ state and attempt to allocate nodes to run the job.
# The job executes.
# Retrieve the @output@ field with the portable data hash of the collection with the output files of the job.
diff --git a/doc/api/methods/jobs.html.textile.liquid b/doc/api/methods/jobs.html.textile.liquid
index cd14f0f..89c79ab 100644
--- a/doc/api/methods/jobs.html.textile.liquid
+++ b/doc/api/methods/jobs.html.textile.liquid
@@ -102,7 +102,7 @@ table(table table-bordered table-condensed).
When a job is submitted to the queue using the **create** method, the @script_version@ attribute is updated to a full 40-character Git commit hash based on the current content of the specified repository. If @script_version@ cannot be resolved, the job submission is rejected.
-fn1. See the "note about specifying Git commits on the Job resource page":{{site.baseurl}}/api/schema/Job.html#script_version for more detail.
+fn1. See the "note about specifying Git commits":#script_version for more detail.
h4. Specialized filters
diff --git a/doc/api/methods/pipeline_instances.html.textile.liquid b/doc/api/methods/pipeline_instances.html.textile.liquid
index 647fafe..3be3a7a 100644
--- a/doc/api/methods/pipeline_instances.html.textile.liquid
+++ b/doc/api/methods/pipeline_instances.html.textile.liquid
@@ -20,7 +20,7 @@ Each PipelineInstance has, in addition to the "Common resource fields":{{site.ba
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
-|pipeline_template_uuid|string|The "pipeline template":pipeline_template.html that this instance was created from.||
+|pipeline_template_uuid|string|The "pipeline template":pipeline_templates.html that this instance was created from.||
|name|string|||
|components|hash|||
|success|boolean|||
diff --git a/doc/sdk/python/events.html.textile.liquid b/doc/sdk/python/events.html.textile.liquid
index 6afb9b5..0988a7c 100644
--- a/doc/sdk/python/events.html.textile.liquid
+++ b/doc/sdk/python/events.html.textile.liquid
@@ -5,7 +5,7 @@ navmenu: Python
title: Subscribing to events
...
-Arvados applications can subscribe to a live event stream from the database. Events are described in the "Log record schema.":{{site.baseurl}}/api/schema/Log.html
+Arvados applications can subscribe to a live event stream from the database. Events are described in the "Log resource.":{{site.baseurl}}/api/methods/logs.html
<notextile>
{% code 'events_py' as python %}
diff --git a/doc/user/reference/job-pipeline-ref.html.textile.liquid b/doc/user/reference/job-pipeline-ref.html.textile.liquid
index f8f749c..643e6bb 100644
--- a/doc/user/reference/job-pipeline-ref.html.textile.liquid
+++ b/doc/user/reference/job-pipeline-ref.html.textile.liquid
@@ -4,4 +4,4 @@ navsection: userguide
title: "Pipeline template reference"
...
-Pipeline template options are described on the "pipeline template schema page.":{{site.baseurl}}/api/schema/PipelineTemplate.html
+Pipeline template options are described on the "pipeline template schema page.":{{site.baseurl}}/api/methods/pipeline_templates.html
diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index ef4634e..a768259 100644
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -22,7 +22,7 @@ This will open the template record in an interactive text editor (as specified b
* @"name"@ is a human-readable name for the pipeline.
* @"components"@ is a set of scripts or commands that make up the pipeline. Each component is given an identifier (@"bwa-mem"@ and @"SortSam"@) in this example).
-** Each entry in components @"components"@ is an Arvados job submission. For more information about individual jobs, see the "job object reference":{{site.baseurl}}/api/schema/Job.html and "job create method.":{{site.baseurl}}/api/methods/jobs.html#create
+** Each entry in components @"components"@ is an Arvados job submission. For more information about individual jobs, see the "job resource reference.":{{site.baseurl}}/api/methods/jobs.html
* @"repository"@, @"script_version"@, and @"script"@ indicate that we intend to use the external @"run-command"@ tool wrapper that is part of the Arvados. These parameters are described in more detail in "Writing a script":tutorial-firstscript.html.
* @"runtime_constraints"@ describes runtime resource requirements for the component.
** @"docker_image"@ specifies the "Docker":https://www.docker.com/ runtime environment in which to run the job. The Docker image @"bcosc/arv-base-java"@ supplied here has the Java runtime environment, bwa, and samtools installed.
@@ -62,7 +62,7 @@ Test data is available in the "Arvados Tutorial":{{site.arvados_workbench_host}}
* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":{{site.arvados_workbench_host}}/collections/2463fa9efeb75e099685528b3b9071e0+438 for the "reference_collection" parameter
* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":{{site.arvados_workbench_host}}/collections/3229739b505d2b878b62aed09895a55a+142 for the "sample" parameter
-For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
+For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/methods/pipeline_templates.html
h2. Re-using your pipeline run
diff --git a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
index 47e8dc7..d1556cf 100644
--- a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
@@ -81,10 +81,10 @@ In the editor, enter the following template:
* @"repository"@ is the name of a git repository to search for the script version. You can access a list of available git repositories on the Arvados Workbench in the *Repositories* page using the <span class="fa fa-lg fa-user"></span> <span class="caret"></span> top navigation menu icon.
* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit Git revision hash, a tag, or a branch (in which case it will use the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
* @"script"@ specifies the filename of the script to run. Crunch expects to find this in the @crunch_scripts/@ subdirectory of the Git repository.
-* @"runtime_constraints"@ describes the runtime environment required to run the job. These are described in the "job record schema":{{site.baseurl}}/api/schema/Job.html
+* @"runtime_constraints"@ describes the runtime environment required to run the job. These are described in the "job record schema":{{site.baseurl}}/api/methods/jobs.html
h2. Running your pipeline
Your new pipeline template should appear at the top of the Workbench "pipeline templates":{{site.arvados_workbench_host}}/pipeline_templates page. You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html
-For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
+For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/methods/pipeline_templates.html
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list