[ARVADOS] updated: 1.1.4-707-ge8ebb2101

[Git user]

Summary of changes:
 doc/install/install-api-server.html.textile.liquid | 28 +++++++++++++++++++++-
 doc/user/cwl/cwl-style.html.textile.liquid         |  4 +++-
 sdk/cwl/arvados_cwl/__init__.py                    | 16 ++++++++++---
 3 files changed, 43 insertions(+), 5 deletions(-)

       via  e8ebb2101fa89294c91b404953cc2fbabb796e40 (commit)
       via  de76be07dcbb36d38f6714480570cddaeabe2194 (commit)
      from  c7cbb121dec3c356bf7d72087d601c7593410b8c (commit)

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not appeared on any other notification email; so we list those
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commit e8ebb2101fa89294c91b404953cc2fbabb796e40
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Tue Jul 31 13:26:14 2018 -0400

    13892: Make warning more obvious.
    
    Link to information about migrating for both users and admins.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/doc/user/cwl/cwl-style.html.textile.liquid b/doc/user/cwl/cwl-style.html.textile.liquid
index 6b5147ddc..07cb4aa90 100644
--- a/doc/user/cwl/cwl-style.html.textile.liquid
+++ b/doc/user/cwl/cwl-style.html.textile.liquid
@@ -176,7 +176,9 @@ steps:
           run: tool3.cwl
 </pre>
 
-* When migrating from crunch v1 API (--api=jobs) to the crunch v2 API (--api=containers) there are a few differences in behavior:
+h2(#migrate). Migrating running CWL on jobs API to containers API
+
+* When migrating from jobs API (--api=jobs) (sometimes referred to as "crunch v1") to the containers API (--api=containers) ("crunch v2") there are a few differences in behavior:
 ** The tool is limited to accessing only collections which are explicitly listed in the input, and further limited to only the subdirectories of collections listed in input.  For example, given an explicit file input @/dir/subdir/file1.txt@, a tool will not be able to implicitly access the file @/dir/file2.txt at .  Use @secondaryFiles@ or a @Directory@ input to describe trees of files.
 ** Files listed in @InitialWorkDirRequirement@ appear in the output directory as normal files (not symlinks) but cannot be moved, renamed or deleted.  These files will be added to the output collection but without any additional copies of the underlying data.
 ** Tools are disallowed network access by default.  Tools which require network access must include @arv:APIRequirement: {}@ in their @requirements@ section.
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 7e4142b10..8c3f0eade 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -136,9 +136,19 @@ class ArvCwlRunner(object):
                 raise Exception("Unsupported API '%s', expected one of %s" % (work_api, expected_api))
 
         if self.work_api == "jobs":
-            logger.warn("""Using the deprecated 'jobs' API.
-Suggest '--api=containers' or configure the cluster to disable the 'jobs' API as described at:
-http://doc.arvados.org/install/install-api-server.html#disable_api_methods""")
+            logger.warn("""
+*******************************
+Using the deprecated 'jobs' API.
+
+To get rid of this warning:
+
+Users: read about migrating at
+http://doc.arvados.org/user/cwl/cwl-style.html#migrate
+and use the option --api=containers
+
+Admins: configure the cluster to disable the 'jobs' API as described at:
+http://doc.arvados.org/install/install-api-server.html#disable_api_methods
+*******************************""")
 
         self.loadingContext = ArvLoadingContext(vars(arvargs))
         self.loadingContext.fetcher_constructor = self.fetcher_constructor

commit de76be07dcbb36d38f6714480570cddaeabe2194
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Tue Jul 31 11:40:28 2018 -0400

    13892: Update disable_api_methods with the full list
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/doc/install/install-api-server.html.textile.liquid b/doc/install/install-api-server.html.textile.liquid
index 1e762706f..51efe8dac 100644
--- a/doc/install/install-api-server.html.textile.liquid
+++ b/doc/install/install-api-server.html.textile.liquid
@@ -164,7 +164,33 @@ Set the @disable_api_methods@ configuration option to disable the deprecated @jo
 
 <notextile>
 <pre><code>
-  disable_api_methods: ["jobs.create", "pipeline_instances.create"]
+  disable_api_methods:
+    - jobs.create
+    - pipeline_instances.create
+    - pipeline_templates.create
+    - jobs.get
+    - pipeline_instances.get
+    - pipeline_templates.get
+    - jobs.list
+    - pipeline_instances.list
+    - pipeline_templates.list
+    - jobs.index
+    - pipeline_instances.index
+    - pipeline_templates.index
+    - jobs.update
+    - pipeline_instances.update
+    - pipeline_templates.update
+    - jobs.queue
+    - jobs.queue_size
+    - job_tasks.create
+    - job_tasks.get
+    - job_tasks.list
+    - job_tasks.index
+    - job_tasks.update
+    - jobs.show
+    - pipeline_instances.show
+    - pipeline_templates.show
+    - job_tasks.show
 </code></pre>
 </notextile>
 

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