From ea3f48a5ec1220a1d1d0b614cbb66cbdeebaa79d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 4 Jul 2020 19:41:11 +0200
Subject: [PATCH] Document metadata_strategy

---
 doc/source/admin/galaxy_options.rst              | 16 ++++++++++++++++
 lib/galaxy/config/sample/galaxy.yml.sample       |  9 +++++++++
 .../config/sample/job_conf.xml.sample_advanced   | 11 +++++++++++
 lib/galaxy/webapps/galaxy/config_schema.yml      | 12 ++++++++++++
 4 files changed, 48 insertions(+)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 40defa60e8a..1682b35b062 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -3563,6 +3563,22 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~~~~~~
+``metadata_strategy``
+~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Determines how metadata will be set. Valid values are `directory`,
+    `extended` and `legacy`. In extended mode jobs will decide if a
+    tool run failed, the object stores  configuration is serialized
+    and made available to the job and is used for writing output
+    datasets to the  object store as part of the job and dynamic
+    output discovery (e.g. discovered datasets <discover_datasets>,
+    unpopulated collections, etc) happens as part of the job.
+:Default: ``directory``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``retry_metadata_internally``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 1fe69acef2a..c28ab6fab5b 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1741,6 +1741,15 @@ galaxy:
   # database.
   #enable_job_recovery: true
 
+  # Determines how metadata will be set. Valid values are `directory`,
+  # `extended` and `legacy`. In extended mode jobs will decide if a tool
+  # run failed, the object stores  configuration is serialized and made
+  # available to the job and is used for writing output datasets to the
+  # object store as part of the job and dynamic output discovery (e.g.
+  # discovered datasets <discover_datasets>, unpopulated collections,
+  # etc) happens as part of the job.
+  #metadata_strategy: directory
+
   # Although it is fairly reliable, setting metadata can occasionally
   # fail.  In these instances, you can choose to retry setting it
   # internally or leave it in a failed state (since retrying internally
diff --git a/lib/galaxy/config/sample/job_conf.xml.sample_advanced b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
index 53254618eba..f44a940a95e 100644
--- a/lib/galaxy/config/sample/job_conf.xml.sample_advanced
+++ b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
@@ -401,6 +401,17 @@
                try it early - it will slightly speed up local jobs by
                embedding metadata calculation in job script itself.
           -->
+          <param id="metadata_strategy">directory</param>
+          <!-- If set overwrites metadata_strategy (configurable in galaxy.yml).
+               Valid values are `directory` (default), `extended` and `legacy`.
+               Setting metadata_strategy to extended requires that all object stores
+               that can be written to store datasets by uuid. In extended mode jobs
+               will decide if a tool run failed, the object stores configuration
+               is serialized and made available to the job and is used for writing output
+               datasets to the object store as part of the job and dynamic output discovery
+               (e.g. discovered datasets <discover_datasets>, unpopulated collections, etc)
+               happens as part of the job.
+          -->
           <job_metrics />
           <!-- Above element demonstrates embedded job metrics definition - see
                job_metrics_conf.xml.sample for full documentation on possible nested
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 3e45d43fcbd..df648f396c3 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2638,6 +2638,18 @@ mapping:
           it can "recover" them when it starts).  This is not safe to use if you are
           running more than one Galaxy server using the same database.
 
+      metadata_strategy:
+        type: str
+        required: false
+        default: directory
+        desc: |
+          Determines how metadata will be set. Valid values are `directory`, `extended` and `legacy`.
+          In extended mode jobs will decide if a tool run failed, the object stores
+          configuration is serialized and made available to the job and is used for
+          writing output datasets to the  object store as part of the job and dynamic
+          output discovery (e.g. discovered datasets <discover_datasets>, unpopulated collections,
+          etc) happens as part of the job.
+
       retry_metadata_internally:
         type: bool
         default: true