From d4aa9c47a429198c6511c9a7693b92f2d811bc12 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Thu, 2 May 2024 19:25:11 -0700
Subject: [PATCH] change extension to "ucsc.net" and improve description

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 4 ++--
 lib/galaxy/datatypes/chain.py                      | 4 ++--
 lib/galaxy/datatypes/test/{1.net => 1.ucsc.net}    | 0
 3 files changed, 4 insertions(+), 4 deletions(-)
 rename lib/galaxy/datatypes/test/{1.net => 1.ucsc.net} (100%)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 82ba36cac0cb..bd1577f4c00b 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -988,8 +988,8 @@
     <datatype extension="shp" type="galaxy.datatypes.gis:Shapefile" mimetype="application/octet-stream" display_in_upload="true" description="geospatial vector data format for geographic information system"/>
     <!-- Flexible Image Transport System (FITS) used in Astronomy https://fits.gsfc.nasa.gov/ https://fits.gsfc.nasa.gov/rfc4047.txt -->
     <datatype extension="fits" type="galaxy.datatypes.binary:FITS" mimetype="application/octet-stream" display_in_upload="true" description="Flexible Image Transport System (FITS) used in Astronomy"/>
-    <datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true"/>
-    <datatype extension="net" type="galaxy.datatypes.chain:Net" display_in_upload="true"/>
+    <datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/chain.html"/>
+    <datatype extension="ucsc.net" type="galaxy.datatypes.chain:Net" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/net.html"/>
   </registration>
   <sniffers>
     <!--
diff --git a/lib/galaxy/datatypes/chain.py b/lib/galaxy/datatypes/chain.py
index 0846715ffd7e..acf451ce85c8 100644
--- a/lib/galaxy/datatypes/chain.py
+++ b/lib/galaxy/datatypes/chain.py
@@ -133,7 +133,7 @@ class Net(data.Text):
     """Class describing a net format alignment file"""
 
     edam_format = "format_3983"
-    file_ext = "net"
+    file_ext = "ucsc.net"
 
     def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         """
@@ -153,7 +153,7 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         >>> fname = get_test_fname( '1.chain' )
         >>> Net().sniff( fname )
         False
-        >>> fname = get_test_fname( '1.net' )
+        >>> fname = get_test_fname( '1.ucsc.net' )
         >>> Net().sniff( fname )
         True
         >>>
diff --git a/lib/galaxy/datatypes/test/1.net b/lib/galaxy/datatypes/test/1.ucsc.net
similarity index 100%
rename from lib/galaxy/datatypes/test/1.net
rename to lib/galaxy/datatypes/test/1.ucsc.net