From 1a81f7590f10204cdfc9954ee0be6f8556910e32 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 30 Jan 2024 11:59:03 +0100
Subject: [PATCH 1/4] Update docs for webdav file source config

Include docs and settings to avoid loading entire files into memory.
---
 lib/galaxy/config/sample/file_sources_conf.yml.sample | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/lib/galaxy/config/sample/file_sources_conf.yml.sample b/lib/galaxy/config/sample/file_sources_conf.yml.sample
index f057b6e6b8a2..04156f44404d 100644
--- a/lib/galaxy/config/sample/file_sources_conf.yml.sample
+++ b/lib/galaxy/config/sample/file_sources_conf.yml.sample
@@ -12,6 +12,9 @@
   root: ${user.preferences['owncloud|root']}
   login: ${user.preferences['owncloud|username']}
   password: ${user.preferences['owncloud|password']}
+  # By default, the plugin will use temp files to avoid loading entire files into memory. 
+  # You can change the directory here or omit to use the default temp directory.
+  temp_path: /your/temp/path
 
 - type: posix
   root: '/data/5/galaxy_import/galaxy_user_data/covid-19/data/sequences/'

From ddf992cbfde9e6313f3e24b1abf61ab253992d86 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 30 Jan 2024 13:41:21 +0100
Subject: [PATCH 2/4] Add comment on writable for webdav file source

---
 lib/galaxy/config/sample/file_sources_conf.yml.sample | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/lib/galaxy/config/sample/file_sources_conf.yml.sample b/lib/galaxy/config/sample/file_sources_conf.yml.sample
index 04156f44404d..da81ba996959 100644
--- a/lib/galaxy/config/sample/file_sources_conf.yml.sample
+++ b/lib/galaxy/config/sample/file_sources_conf.yml.sample
@@ -15,6 +15,9 @@
   # By default, the plugin will use temp files to avoid loading entire files into memory. 
   # You can change the directory here or omit to use the default temp directory.
   temp_path: /your/temp/path
+  # Set writable to true if you have write access to this source
+  # and want to allow exporting files to it, by default is read only.
+  writable: false
 
 - type: posix
   root: '/data/5/galaxy_import/galaxy_user_data/covid-19/data/sequences/'

From 5153394f15cc4e106f19a4fb4e885d10129242c1 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 30 Jan 2024 13:43:09 +0100
Subject: [PATCH 3/4] Set webdav plugin to use temp files by default

it avoids the issue with loading the entire files into memory.
---
 lib/galaxy/files/sources/webdav.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/lib/galaxy/files/sources/webdav.py b/lib/galaxy/files/sources/webdav.py
index 86ed55483e70..60450dbb6c98 100644
--- a/lib/galaxy/files/sources/webdav.py
+++ b/lib/galaxy/files/sources/webdav.py
@@ -3,6 +3,7 @@
 except ImportError:
     WebDAVFS = None
 
+import tempfile
 from typing import (
     Optional,
     Union,
@@ -22,6 +23,11 @@ class WebDavFilesSource(PyFilesystem2FilesSource):
 
     def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None):
         props = self._serialization_props(user_context)
+        use_temp_files = props.pop("use_temp_files", None)
+        if use_temp_files is None:
+            # Default to True to avoid memory issues with large files.
+            props["use_temp_files"] = True
+            props["temp_path"] = props.get("temp_path", tempfile.gettempdir())
         extra_props: Union[FilesSourceProperties, dict] = opts.extra_props or {} if opts else {}
         handle = WebDAVFS(**{**props, **extra_props})
         return handle

From 7d27634879fe123822e5e4cb405e2af0ddd6cbc7 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 31 Jan 2024 11:25:46 +0100
Subject: [PATCH 4/4] Give webdav plugin a clean temp directory

Co-authored-by: mvdbeek <m.vandenbeek@gmail.com>
---
 lib/galaxy/files/sources/webdav.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/files/sources/webdav.py b/lib/galaxy/files/sources/webdav.py
index 60450dbb6c98..2e11a51d98b2 100644
--- a/lib/galaxy/files/sources/webdav.py
+++ b/lib/galaxy/files/sources/webdav.py
@@ -27,7 +27,7 @@ def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None)
         if use_temp_files is None:
             # Default to True to avoid memory issues with large files.
             props["use_temp_files"] = True
-            props["temp_path"] = props.get("temp_path", tempfile.gettempdir())
+            props["temp_path"] = props.get("temp_path", tempfile.TemporaryDirectory(prefix="webdav_"))
         extra_props: Union[FilesSourceProperties, dict] = opts.extra_props or {} if opts else {}
         handle = WebDAVFS(**{**props, **extra_props})
         return handle