From 073066f7cc5631af34d7228cb31dcdc9b79b39e6 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 27 Feb 2024 16:39:26 +0100
Subject: [PATCH 1/3] Move Tiff offsets metadata to base class

---
 lib/galaxy/datatypes/images.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/datatypes/images.py b/lib/galaxy/datatypes/images.py
index 3420b1be183a..e61efeaca05a 100644
--- a/lib/galaxy/datatypes/images.py
+++ b/lib/galaxy/datatypes/images.py
@@ -91,10 +91,6 @@ class Png(Image):
 class Tiff(Image):
     edam_format = "format_3591"
     file_ext = "tiff"
-
-
-class OMETiff(Tiff):
-    file_ext = "ome.tiff"
     MetadataElement(
         name="offsets",
         desc="Offsets File",
@@ -120,6 +116,10 @@ def set_meta(
             json.dump(offsets, f)
         dataset.metadata.offsets = offsets_file
 
+
+class OMETiff(Tiff):
+    file_ext = "ome.tiff"
+
     def sniff(self, filename: str) -> bool:
         with tifffile.TiffFile(filename) as tif:
             if tif.is_ome:

From 931b39e5d7c764af24db7ac31c3af1dbd878c228 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 27 Feb 2024 16:40:03 +0100
Subject: [PATCH 2/3] Allow Avivator display application for regular Tiffs

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 1ecd25ee5761..86ad796485c9 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -239,7 +239,9 @@
     <datatype extension="cnr" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
     <datatype extension="hhr" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
     <datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/>
-    <datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff" display_in_upload="true"/>
+    <datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff" display_in_upload="true">
+      <display file="image/avivator.xml"/>
+    </datatype>
     <datatype extension="tf2" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
     <datatype extension="tf8" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
     <datatype extension="btf" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>

From 110f46fcd670d2c181077a35a302ad5bcc3e789c Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 27 Feb 2024 16:40:40 +0100
Subject: [PATCH 3/3] Use correct extension when passing image to Avivator

---
 .../datatypes/display_applications/configs/image/avivator.xml   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/display_applications/configs/image/avivator.xml b/lib/galaxy/datatypes/display_applications/configs/image/avivator.xml
index b1c54b8a89d3..4d731b4f9bfa 100644
--- a/lib/galaxy/datatypes/display_applications/configs/image/avivator.xml
+++ b/lib/galaxy/datatypes/display_applications/configs/image/avivator.xml
@@ -1,7 +1,7 @@
 <display id="avivator" version="1.0.0" name="display at">
     <link id="main" name="Avivator">
         <url>http://avivator.gehlenborglab.org/?image_url=${qp($tiff_file.url)}</url>
-        <param type="data" name="tiff_file" url="galaxy_${DATASET_HASH}.ome.tiff" allow_cors="true"/>
+        <param type="data" name="tiff_file" url="galaxy_${DATASET_HASH}.${dataset.extension}" allow_cors="true"/>
         <param type="data" name="offsets_file" url="galaxy_${DATASET_HASH}.offsets.json" metadata="offsets" allow_cors="true"/>
     </link>
 </display>