Commit d0b9ef67 authored by Dannon Baker's avatar Dannon Baker
Browse files

Refactor preferred visualization logic 

 to eliminate circular import between datatypes registry and managers.
 Move get_preferred_visualization from registry to datatypes manager
 module where the class hierarchy mapping logic already exists.
parent 5fb725a1

lib/galaxy/datatypes/registry.py

+0 −50
Original line number Diff line number Diff line
@@ -516,56 +516,6 @@ class Registry: 
    def get_display_sites(self, site_type):

        return self.display_sites.get(site_type, [])



    def get_preferred_visualization(self, datatype_extension):

        """

        Get the preferred visualization mapping for a specific datatype extension.

        Returns a dictionary with 'visualization' and 'default_params' keys, or None if no mapping exists.



        Preferred visualizations are defined inline within each datatype definition in the

        datatypes_conf.xml configuration file. These mappings determine which visualization plugin

        should be used by default when viewing datasets of a specific type.



        If no direct mapping exists for the extension, this method will walk up the inheritance

        chain to find a preferred visualization from a parent datatype class.



        Example configuration:

        <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true">

            <visualization plugin="igv" />

        </datatype>

        """

        direct_mapping = self.visualization_mappings.get(datatype_extension)

        if direct_mapping:

            return direct_mapping



        current_datatype = self.get_datatype_by_extension(datatype_extension)

        if not current_datatype:

            return None



        # Use the same mapping approach as the datatypes API for consistency

        from galaxy.managers.datatypes import view_mapping



        mapping_data = view_mapping(self)



        current_class_name = mapping_data.ext_to_class_name.get(datatype_extension)

        if not current_class_name:

            return None



        current_class_mappings = mapping_data.class_to_classes.get(current_class_name, {})



        # Find parent extensions that have preferred visualizations

        for ext, visualization_mapping in self.visualization_mappings.items():

            if ext == datatype_extension:

                continue



            parent_class_name = mapping_data.ext_to_class_name.get(ext)

            if parent_class_name and parent_class_name in current_class_mappings:

                self.log.debug(

                    f"Found inherited preferred visualization '{visualization_mapping['visualization']}' for datatype '{datatype_extension}' from parent '{ext}'"

                )

                return visualization_mapping



        return None



    def get_all_visualization_mappings(self):

        """

        Get all datatype to visualization mappings.

lib/galaxy/managers/datatypes.py

+46 −0
Original line number Diff line number Diff line
@@ -163,6 +163,51 @@ def view_visualization_mappings( 
    return parse_obj_as(DatatypeVisualizationMappingsList, mappings)





def get_preferred_visualization(datatypes_registry: Registry, datatype_extension: str) -> Optional[Dict[str, str]]:

    """

    Get the preferred visualization mapping for a specific datatype extension.

    Returns a dictionary with 'visualization' and 'default_params' keys, or None if no mapping exists.



    Preferred visualizations are defined inline within each datatype definition in the

    datatypes_conf.xml configuration file. These mappings determine which visualization plugin

    should be used by default when viewing datasets of a specific type.



    If no direct mapping exists for the extension, this method will walk up the inheritance

    chain to find a preferred visualization from a parent datatype class.



    Example configuration:

    <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true">

        <visualization plugin="igv" />

    </datatype>

    """

    direct_mapping = datatypes_registry.visualization_mappings.get(datatype_extension)

    if direct_mapping:

        return direct_mapping



    current_datatype = datatypes_registry.get_datatype_by_extension(datatype_extension)

    if not current_datatype:

        return None



    # Use the same mapping approach as the datatypes API for consistency

    mapping_data = view_mapping(datatypes_registry)



    current_class_name = mapping_data.ext_to_class_name.get(datatype_extension)

    if not current_class_name:

        return None



    current_class_mappings = mapping_data.class_to_classes.get(current_class_name, {})



    for ext, visualization_mapping in datatypes_registry.visualization_mappings.items():

        if ext == datatype_extension:

            continue



        parent_class_name = mapping_data.ext_to_class_name.get(ext)

        if parent_class_name and parent_class_name in current_class_mappings:

            return visualization_mapping



    return None





__all__ = (

    "DatatypeConverterList",

    "DatatypeDetails",
@@ -179,4 +224,5 @@ __all__ = ( 
    "view_edam_formats",

    "view_edam_data",

    "view_visualization_mappings",

    "get_preferred_visualization",

)

lib/galaxy/webapps/galaxy/api/datatypes.py

+2 −1
Original line number Diff line number Diff line
@@ -26,6 +26,7 @@ from galaxy.managers.datatypes import ( 
    DatatypesEDAMDetailsDict,

    DatatypesMap,

    DatatypeVisualizationMappingsList,

    get_preferred_visualization,

    view_converters,

    view_edam_data,

    view_edam_formats,
@@ -258,7 +259,7 @@ class FastAPIDatatypes: 
            result["converters"] = list(converters.keys())



        # Add preferred visualization if any and if the plugin is available

        preferred_viz = self.datatypes_registry.get_preferred_visualization(datatype)

        preferred_viz = get_preferred_visualization(self.datatypes_registry, datatype)

        if preferred_viz:

            plugin_name = preferred_viz["visualization"]