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

[25.0] Dataset Display and Preferred Viz fixes

Author: mvdbeek

lib/galaxy/datatypes/images.py

@@ -20,6 +20,7 @@
 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 @@ def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
 
 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

@@ -516,22 +516,6 @@ def get_legacy_sites_by_build(self, site_type, build):
     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

@@ -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 @@ def view_visualization_mappings(
     "view_edam_formats",
     "view_edam_data",
     "view_visualization_mappings",
+    "get_preferred_visualization",
 )

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

@@ -18,13 +18,15 @@
 )
 
 from galaxy.datatypes.registry import Registry
+from galaxy.exceptions import ObjectNotFound
 from galaxy.managers.datatypes import (
     DatatypeConverterList,
     DatatypeDetails,
     DatatypesCombinedMap,
     DatatypesEDAMDetailsDict,
     DatatypesMap,
     DatatypeVisualizationMappingsList,
+    get_preferred_visualization,
     view_converters,
     view_edam_data,
     view_edam_formats,
@@ -33,8 +35,10 @@
     view_sniffers,
     view_visualization_mappings,
 )
+from galaxy.structured_app import StructuredApp
 from . import (
     depends,
+    DependsOnApp,
     Router,
 )
 
@@ -64,6 +68,7 @@
 @router.cbv
 class FastAPIDatatypes:
     datatypes_registry: Registry = depends(Registry)
+    app: StructuredApp = DependsOnApp
 
     @router.get(
         "/api/datatypes",
@@ -253,11 +258,24 @@ async def show(
         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:
-            result["preferred_visualization"] = {
-                "visualization": preferred_viz["visualization"],
-            }
+            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": 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