most mentioned changes

galaxyproject · Nov 6, 2024 · d19daa5 · d19daa5
1 parent 82e0606
commit d19daa5
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -975,6 +975,7 @@
     <datatype extension="gmsh.msh" type="galaxy.datatypes.constructive_solid_geometry:GmshMsh" display_in_upload="true"/>
     <datatype extension="gmsh.geo" type="galaxy.datatypes.constructive_solid_geometry:GmshGeo" display_in_upload="true"/>
     <datatype extension="zset.geof" type="galaxy.datatypes.constructive_solid_geometry:ZsetGeof" display_in_upload="true"/>
+    <datatype extension="vtu" type="galaxy.datatypes.constructive_solid_geometry:Vtu" display_in_upload="true"/>
     <datatype extension="stl" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" display_in_upload="true" description="STL is a file format native to the stereolithography CAD software created by 3D Systems."/>
     <!-- Povray script -->
     <datatype extension="pov" type="galaxy.datatypes.text:Text" subclass="true" display_in_upload="true"/>
@@ -1007,7 +1008,7 @@
     <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" 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>
+    </registration>
   <sniffers>
     <!--
     The order in which Galaxy attempts to determine data types is
@@ -1033,6 +1034,7 @@
     <sniffer type="galaxy.datatypes.mothur:Axes"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyAscii"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyBinary"/>
+    <sniffer type="galaxy.datatypes.constructive_solid_geometry:Vtu"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkAscii"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkBinary"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:NeperTess"/>

diff --git a/lib/galaxy/datatypes/constructive_solid_geometry.py b/lib/galaxy/datatypes/constructive_solid_geometry.py
@@ -191,9 +191,6 @@ class Vtk:
 
     Binary data must be placed into the file immediately after the newline
     ('\\n') character from the previous ASCII keyword and parameter sequence.
-
-    TODO: only legacy formats are currently supported and support for XML formats
-    should be added.
     """
 
     subtype = ""
@@ -817,7 +814,7 @@ def get_next_line(fh):
     return line.strip()
 
 class Vtu(GenericXml):
-    """Format for defining VTU (VTK Unstructured Grid) data https://docs.vtk.org/"""
+    """Format for defining VTU (VTK Unstructured Grid) data https://docs.vtk.org/en/latest/design_documents/VTKFileFormats.html"""
 
     edam_data = "edam:data_3671"
     edam_format = "edam:format_3621"