Unverified Commit 01209e17 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #20439 from dannon/preferred-viz-updates 

[25.0] Dataset Display and Preferred Viz fixes
parents 29b97b0a 8bd93063

lib/galaxy/datatypes/images.py

+6 −0
Original line number Diff line number Diff line
@@ -20,6 +20,7 @@ import mrcfile 
import numpy as np

import png

import tifffile

from typing_extensions import Literal



try:

    import PIL
@@ -65,6 +66,7 @@ class Image(data.Data): 
    edam_data = "data_2968"

    edam_format = "format_3547"

    file_ext = ""

    display_behavior: Literal["inline", "download"] = "inline"  # Most image formats can be displayed inline in browsers



    MetadataElement(

        name="axes",
@@ -419,18 +421,22 @@ class OMEZarr(data.ZarrDirectory): 


class Hamamatsu(Image):

    file_ext = "vms"

    display_behavior = "download"  # Proprietary microscopy format, not browser-displayable





class Mirax(Image):

    file_ext = "mrxs"

    display_behavior = "download"  # Proprietary microscopy format, not browser-displayable





class Sakura(Image):

    file_ext = "svslide"

    display_behavior = "download"  # Proprietary microscopy format, not browser-displayable





class Nrrd(Image):

    file_ext = "nrrd"

    display_behavior = "download"  # Medical imaging format, not browser-displayable





class Bmp(Image):

lib/galaxy/datatypes/registry.py

+0 −16
Original line number Diff line number Diff line
@@ -516,22 +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.



        Example configuration:

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

            <visualization plugin="igv" />

        </datatype>

        """

        return self.visualization_mappings.get(datatype_extension)



    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

+23 −5
Original line number Diff line number Diff line
@@ -18,6 +18,7 @@ from fastapi import ( 
)



from galaxy.datatypes.registry import Registry

from galaxy.exceptions import ObjectNotFound

from galaxy.managers.datatypes import (

    DatatypeConverterList,

    DatatypeDetails,
@@ -25,6 +26,7 @@ from galaxy.managers.datatypes import ( 
    DatatypesEDAMDetailsDict,

    DatatypesMap,

    DatatypeVisualizationMappingsList,

    get_preferred_visualization,

    view_converters,

    view_edam_data,

    view_edam_formats,
@@ -33,8 +35,10 @@ from galaxy.managers.datatypes import ( 
    view_sniffers,

    view_visualization_mappings,

)

from galaxy.structured_app import StructuredApp

from . import (

    depends,

    DependsOnApp,

    Router,

)
@@ -64,6 +68,7 @@ IdentifierOnly: Optional[bool] = Query( 
@router.cbv

class FastAPIDatatypes:

    datatypes_registry: Registry = depends(Registry)

    app: StructuredApp = DependsOnApp



    @router.get(

        "/api/datatypes",
@@ -253,11 +258,24 @@ class FastAPIDatatypes: 
        if converters:

            result["converters"] = list(converters.keys())



        # Add preferred visualization if any

        preferred_viz = self.datatypes_registry.get_preferred_visualization(datatype)

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

        preferred_viz = get_preferred_visualization(self.datatypes_registry, datatype)

        if preferred_viz:

            plugin_name = preferred_viz["visualization"]



            # Check if the visualization plugin is actually available

            try:

                if self.app.visualizations_registry:

                    self.app.visualizations_registry.get_plugin(plugin_name)

                    result["preferred_visualization"] = {

                "visualization": preferred_viz["visualization"],

                        "visualization": plugin_name,

                    }

                else:

                    log.warning(

                        f"Visualizations registry not available, skipping preferred visualization for '{datatype}'"

                    )

            except ObjectNotFound:

                # Plugin not available, don't include preferred_visualization

                log.warning(f"Preferred visualization '{plugin_name}' for datatype '{datatype}' is not available")



        return result