From 5b796aa40288ff6b295df2f94e180d73cf5cc71a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 16 Jun 2025 09:36:31 +0200
Subject: [PATCH] Rename vitessce_json file_ext to vitessce.json

Pretty sure this hasn't been used yet, added in
https://github.com/galaxyproject/galaxy/pull/20027/files. A proper json
extension allows json tooling to work with this file.
---
 .../plugins/visualizations/vitessce/config/vitessce.xml  | 2 +-
 lib/galaxy/config/sample/datatypes_conf.xml.sample       | 8 ++++----
 .../datatypes/test/{1.vitesscejson => 1.vitessce.json}   | 1 -
 lib/galaxy/datatypes/text.py                             | 9 ++-------
 4 files changed, 7 insertions(+), 13 deletions(-)
 rename lib/galaxy/datatypes/test/{1.vitesscejson => 1.vitessce.json} (99%)

diff --git a/config/plugins/visualizations/vitessce/config/vitessce.xml b/config/plugins/visualizations/vitessce/config/vitessce.xml
index aa6dc661eaf..544abf50ee2 100644
--- a/config/plugins/visualizations/vitessce/config/vitessce.xml
+++ b/config/plugins/visualizations/vitessce/config/vitessce.xml
@@ -5,7 +5,7 @@
     <data_sources>
         <data_source>
             <model_class>HistoryDatasetAssociation</model_class>
-            <test test_attr="ext">vitesscejson</test>
+            <test test_attr="ext">vitessce.json</test>
         </data_source>
     </data_sources>
     <params>
diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 2e3039c0dfd..a9c697aaafd 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -145,7 +145,7 @@
     <datatype extension="geojson" type="galaxy.datatypes.text:GeoJson" mimetype="application/json" display_in_upload="True">
       <visualization plugin="openlayers" />
     </datatype>
-    <datatype extension="vitesscejson" type="galaxy.datatypes.text:VitessceJson" mimetype="application/json" display_in_upload="True">
+    <datatype extension="vitessce.json" type="galaxy.datatypes.text:VitessceJson" mimetype="application/json" display_in_upload="True">
       <visualization plugin="vitessce" />
     </datatype>
     <datatype extension="data_manager_json" type="galaxy.datatypes.text:DataManagerJson" mimetype="application/json" subclass="true" display_in_upload="false"/>
@@ -611,11 +611,11 @@
     </datatype>
     <datatype extension="nhx" type="galaxy.datatypes.data:Newick" subclass="true" display_in_upload="true" description="The New Hampshire X (NHX) format is an extension to Newick that adds key-value data to Newick nodes.">
         <infer_from suffix="nhx" />
-    </datatype>    
+    </datatype>
     <datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true"/>
     <datatype extension="iqtree" type="galaxy.datatypes.text:IQTree">
         <infer_from suffix="iqtree" />
-    </datatype>  
+    </datatype>
     <datatype extension="mldist" type="galaxy.datatypes.mothur:SquareDistanceMatrix"/>
     <!-- Start RGenetics Datatypes -->
     <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/>
@@ -655,7 +655,7 @@
     <!-- deprecated, should use excel.xls -->
     <datatype extension="xls" type="galaxy.datatypes.binary:ExcelXls">
         <infer_from suffix="xls" />
-    </datatype>  
+    </datatype>
     <!-- End RGenetics Datatypes -->
     <datatype extension="ipynb" type="galaxy.datatypes.text:Ipynb" display_in_upload="true">
         <infer_from suffix="ipynb" />
diff --git a/lib/galaxy/datatypes/test/1.vitesscejson b/lib/galaxy/datatypes/test/1.vitessce.json
similarity index 99%
rename from lib/galaxy/datatypes/test/1.vitesscejson
rename to lib/galaxy/datatypes/test/1.vitessce.json
index b99594f654d..89efeef05db 100644
--- a/lib/galaxy/datatypes/test/1.vitesscejson
+++ b/lib/galaxy/datatypes/test/1.vitessce.json
@@ -18,4 +18,3 @@
         }
     ]
 }
-  
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
index bf4f51e4753..11f3a7fc228 100644
--- a/lib/galaxy/datatypes/text.py
+++ b/lib/galaxy/datatypes/text.py
@@ -662,12 +662,7 @@ class VitessceJson(Json):
     https://www.npmjs.com/package/@vitessce/json-schema
     """
 
-    file_ext = "vitesscejson"
-
-    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
-        super().set_peek(dataset)
-        if not dataset.dataset.purged:
-            dataset.blurb = "VitessceJSON"
+    file_ext = "vitessce.json"
 
     def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         """
@@ -677,7 +672,7 @@ class VitessceJson(Json):
         >>> fname = get_test_fname( '1.json' )
         >>> VitessceJson().sniff( fname )
         False
-        >>> fname = get_test_fname( '1.vitesscejson' )
+        >>> fname = get_test_fname( '1.vitessce.json' )
         >>> VitessceJson().sniff( fname )
         True
         """