From dfc194ddc5be542acb2925211c856d1dcbcea89f Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 2 Oct 2024 10:31:15 -0400
Subject: [PATCH] Rebuild schema...

---
 doc/source/admin/galaxy_options.rst        | 56 ++++++++++++++++++++++
 lib/galaxy/config/sample/galaxy.yml.sample | 26 ++++++++++
 2 files changed, 82 insertions(+)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 8f4aef21d667..aa7f4cd37708 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -5115,6 +5115,26 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``workflow_scheduling_separate_materialization_iteration``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Workflows launched with URI/URL inputs that are not marked as
+    'deferred' are "materialized" (or undeferred) by the workflow
+    scheduler. This might be a lengthy process. Setting this to 'True'
+    will place the invocation back in the queue after materialization
+    before scheduling the workflow so it is less  likely to starve
+    other workflow scheduling. Ideally, Galaxy would allow more fine
+    grain control of handlers but until then, this provides a way to
+    tip the balance between "doing more work" and "being more fair".
+    The default here is pretty arbitrary - it has been to False to
+    optimize Galaxy for automated, single user applications where
+    "fairness" is mostly irrelevant.
+:Default: ``false``
+:Type: bool
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~
 ``cache_user_job_count``
 ~~~~~~~~~~~~~~~~~~~~~~~~
@@ -5602,3 +5622,39 @@
     This requires the help_forum_api_url to be set.
 :Default: ``false``
 :Type: bool
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~
+``file_source_temp_dir``
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Directory to store temporary files for file sources. This defaults
+    to new_file_path if not set.
+:Default: ``None``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``file_source_webdav_use_temp_files``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Default value for use_temp_files for webdav plugins that don't
+    explicitly declare this.
+:Default: ``true``
+:Type: bool
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``file_source_listings_expiry_time``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Default value for listings_expiry_time for s3fs file source
+    plugins that don't explicitly declare this.
+:Default: ``60``
+:Type: int
+
+
+
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 7c3e326a0a0c..9edf7b49a6e7 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -2748,6 +2748,19 @@ galaxy:
   # <config_dir>.
   #workflow_schedulers_config_file: workflow_schedulers_conf.xml
 
+  # Workflows launched with URI/URL inputs that are not marked as
+  # 'deferred' are "materialized" (or undeferred) by the workflow
+  # scheduler. This might be a lengthy process. Setting this to 'True'
+  # will place the invocation back in the queue after materialization
+  # before scheduling the workflow so it is less  likely to starve other
+  # workflow scheduling. Ideally, Galaxy would allow more fine grain
+  # control of handlers but until then, this provides a way to tip the
+  # balance between "doing more work" and "being more fair". The default
+  # here is pretty arbitrary - it has been to False to optimize Galaxy
+  # for automated, single user applications where "fairness" is mostly
+  # irrelevant.
+  #workflow_scheduling_separate_materialization_iteration: false
+
   # If using job concurrency limits (configured in job_config_file),
   # several extra database queries must be performed to determine the
   # number of jobs a user has dispatched to a given destination.  By
@@ -2978,3 +2991,16 @@ galaxy:
   # Enable the integration of the Galaxy Help Forum in the tool panel.
   # This requires the help_forum_api_url to be set.
   #enable_help_forum_tool_panel_integration: false
+
+  # Directory to store temporary files for file sources. This defaults
+  # to new_file_path if not set.
+  #file_source_temp_dir: null
+
+  # Default value for use_temp_files for webdav plugins that don't
+  # explicitly declare this.
+  #file_source_webdav_use_temp_files: true
+
+  # Default value for listings_expiry_time for s3fs file source plugins
+  # that don't explicitly declare this.
+  #file_source_listings_expiry_time: 60
+