From def7c6b25c9356265ac5ca79d82849068b788ea4 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Wed, 8 Apr 2020 20:52:51 +0200
Subject: [PATCH 1/3] add xg,vg,protobuf datatypes

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 0480a651f4b..0b901b26b33 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -382,6 +382,10 @@
     </datatype>
     <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="odgi" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs self index used by odgi."/>
+    <datatype extension="vg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs."/>
+    <datatype extension="xg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs with vg index."/>
+    <datatype extension="protobuf2" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data."/>
+    <datatype extension="protobuf3" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data."/>
     <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">

From 524ea09f7cbc42f407a75030ca27b25942866d0f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 9 Apr 2020 09:29:20 +0200
Subject: [PATCH 2/3] add display_in_upload

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 0b901b26b33..9ebea36a237 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -381,9 +381,9 @@
       <display file="igb/wig.xml"/>
     </datatype>
     <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="true"/>
-    <datatype extension="odgi" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs self index used by odgi."/>
-    <datatype extension="vg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs."/>
-    <datatype extension="xg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs with vg index."/>
+    <datatype extension="odgi" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs self index used by odgi." display_in_upload="true"/>
+    <datatype extension="vg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs." display_in_upload="true"/>
+    <datatype extension="xg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs with vg index." display_in_upload="true"/>
     <datatype extension="protobuf2" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data."/>
     <datatype extension="protobuf3" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data."/>
     <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="true"/>

From 7bcd617c9f8558f5292ca369da596b329a4db306 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sat, 28 Mar 2020 14:38:38 -0400
Subject: [PATCH 3/3] Change session timeout redirect URL to login entrypoint.

---
 lib/galaxy/web/framework/webapp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py
index d77b230a275..179e6bd41f0 100644
--- a/lib/galaxy/web/framework/webapp.py
+++ b/lib/galaxy/web/framework/webapp.py
@@ -251,7 +251,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
                         self.user = None
                         self.galaxy_session = None
                     else:
-                        self.response.send_redirect(url_for(controller='user',
+                        self.response.send_redirect(url_for(controller='root',
                                                      action='login',
                                                      message="You have been logged out due to inactivity.  Please log in again to continue using Galaxy.",
                                                      status='info',