opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 02:04:04 +08:00
Code Issues Packages Projects Releases Wiki Activity

Adjust datatypes preferred viz API /datatypes/{type}/visualizations

Browse Source
This commit is contained in:
Dannon Baker
2025-05-14 08:50:33 -04:00
parent a1ce48a282
commit 47ca870ae4
4 changed files with 56 additions and 73 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/src/api/datatypeVisualizations.ts
+1 -23
View File
@@ -24,35 +24,13 @@ export async function fetchDatatypeVisualizations(): Promise<DatatypeVisualizati
}
}
/**
* Updates a datatype visualization mapping
*/
export async function updateDatatypeVisualization(mapping: DatatypeVisualization): Promise<DatatypeVisualization> {
try {
const { data } = await axios.put(withPrefix(`/api/datatypes/visualizations/${mapping.datatype}`), mapping);
return data;
} catch (error) {
rethrowSimple(error);
}
}
/**
* Deletes a datatype visualization mapping
*/
export async function deleteDatatypeVisualization(datatype: string): Promise<void> {
try {
await axios.delete(withPrefix(`/api/datatypes/visualizations/${datatype}`));
} catch (error) {
rethrowSimple(error);
}
}
/**
* Gets the preferred visualization for a specific datatype
*/
export async function getPreferredVisualization(datatype: string): Promise<DatatypeVisualization | null> {
try {
const url = withPrefix(`/api/datatypes/visualizations/${datatype}`);
const url = withPrefix(`/api/datatypes/${datatype}/visualizations`);
const { data } = await axios.get(url);
// If the API returns an array with one item, return that item
lib/galaxy/datatypes/registry.py
+24 -26
View File
@@ -419,7 +419,7 @@ class Registry:
# Load build sites
if use_build_sites:
self._load_build_sites(root)
# Load visualization mappings
self._load_visualization_mappings(root)
self.set_default_values()
@@ -444,57 +444,55 @@ class Registry:
def _load_visualization_mappings(self, root):
"""
Load datatype to visualization mappings from the datatypes_conf.xml file.
Administrators can define preferred visualizations for datatypes in the
Administrators can define preferred visualizations for datatypes in the
datatypes_conf.xml configuration file using the visualization_mappings section.
For example:
<visualization_mappings>
<visualization_mapping datatype="bam" visualization="igv" />
<visualization_mapping datatype="vcf" visualization="jbrowse" />
<visualization_mapping datatype="h5" visualization="vitessce" default_params='{"layer":"primary"}' />
</visualization_mappings>
These mappings are read-only and must be manually edited in the configuration file.
"""
# Clear existing mappings
self.visualization_mappings = {}
# Find the visualization_mappings element
mappings_elem = root.find("visualization_mappings")
if mappings_elem is None:
# No mappings defined, that's okay
return
for mapping_elem in mappings_elem.findall("visualization_mapping"):
datatype = mapping_elem.get("datatype", None)
visualization = mapping_elem.get("visualization", None)
default_params_str = mapping_elem.get("default_params", None)
# Skip incomplete mappings
if not datatype or not visualization:
self.log.warning("Incomplete visualization mapping (missing datatype or visualization)")
continue
# Parse default parameters if provided
default_params = None
if default_params_str:
try:
default_params = galaxy.util.safe_loads(default_params_str)
except Exception:
self.log.exception("Error parsing default_params for visualization mapping: %s -> %s",
datatype, visualization)
self.log.exception(
"Error parsing default_params for visualization mapping: %s -> %s", datatype, visualization
)
continue
# Store the mapping
self.visualization_mappings[datatype] = {
"visualization": visualization,
"default_params": default_params
}
self.visualization_mappings[datatype] = {"visualization": visualization, "default_params": default_params}
self.log.debug("Loaded visualization mapping: %s -> %s", datatype, visualization)
def _load_build_sites(self, root):
def load_build_site(build_site_config):
# Take in either an XML element or simple dictionary from YAML and add build site for this.
@@ -548,28 +546,28 @@ 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 in the datatypes_conf.xml configuration file using
the visualization_mappings section. These mappings determine which visualization plugin
Preferred visualizations are defined in the datatypes_conf.xml configuration file using
the visualization_mappings section. These mappings determine which visualization plugin
should be used by default when viewing datasets of a specific type.
Example configuration:
<visualization_mappings>
<visualization_mapping datatype="bam" visualization="igv" />
</visualization_mappings>
"""
return self.visualization_mappings.get(datatype_extension)
def get_all_visualization_mappings(self):
"""
Get all datatype to visualization mappings.
Returns a dictionary where keys are datatype extensions and values are mapping configurations.
Mappings are defined in the datatypes_conf.xml configuration file and are read-only.
"""
return self.visualization_mappings
lib/galaxy/managers/datatypes.py
+23 -19
View File
@@ -11,7 +11,7 @@ from galaxy.datatypes._schema import (
DatatypeConverterList,
DatatypeDetails,
DatatypesCombinedMap,
DatatypesEDAMDetailsDict,
DatatypesEDAMDetailsDict,
DatatypesMap,
DatatypeVisualizationMapping,
DatatypeVisualizationMappingsList,
@@ -124,43 +124,47 @@ def view_edam_data(
return datatypes_registry.edam_data
def view_visualization_mappings(datatypes_registry: Registry, datatype: Optional[str] = None) -> DatatypeVisualizationMappingsList:
def view_visualization_mappings(
datatypes_registry: Registry, datatype: Optional[str] = None
) -> DatatypeVisualizationMappingsList:
"""
Get datatype visualization mappings from the registry.
Args:
datatypes_registry: The datatypes registry
datatype: If provided, return only the mapping for this datatype extension
Returns:
A list of datatype visualization mappings
"""
mappings = []
# Get all mappings
all_mappings = datatypes_registry.get_all_visualization_mappings()
# Filter for a specific datatype if requested
if datatype and datatype in all_mappings:
mapping_info = all_mappings[datatype]
mappings.append({
"datatype": datatype,
"visualization": mapping_info["visualization"],
"default_params": mapping_info.get("default_params")
})
mappings.append(
{
"datatype": datatype,
"visualization": mapping_info["visualization"],
"default_params": mapping_info.get("default_params"),
}
)
elif not datatype:
for dt, mapping_info in all_mappings.items():
mappings.append({
"datatype": dt,
"visualization": mapping_info["visualization"],
"default_params": mapping_info.get("default_params")
})
mappings.append(
{
"datatype": dt,
"visualization": mapping_info["visualization"],
"default_params": mapping_info.get("default_params"),
}
)
return parse_obj_as(DatatypeVisualizationMappingsList, mappings)
__all__ = (
"DatatypeConverterList",
"DatatypeDetails",
lib/galaxy/webapps/galaxy/api/datatypes.py
+8 -5
View File
@@ -11,7 +11,10 @@ from typing import (
Union,
)
from fastapi import Path, Query
from fastapi import (
Path,
Query,
)
from galaxy.datatypes.registry import Registry
from galaxy.managers.datatypes import (
@@ -168,7 +171,7 @@ class FastAPIDatatypes:
"""Gets a map of datatypes and their corresponding EDAM data.
EDAM data contains the EDAM iri, label, and definition."""
return view_edam_data(self.datatypes_registry, True)
@router.get(
"/api/datatypes/visualizations",
public=True,
@@ -179,9 +182,9 @@ class FastAPIDatatypes:
async def visualizations(self) -> DatatypeVisualizationMappingsList:
"""Gets a list of all datatype visualization mappings."""
return view_visualization_mappings(self.datatypes_registry)
@router.get(
"/api/datatypes/visualizations/{datatype}",
"/api/datatypes/{datatype}/visualizations",
public=True,
summary="Returns the visualization mapping for a specific datatype",
response_description="Visualization mapping for the specified datatype",
@@ -197,7 +200,7 @@ class FastAPIDatatypes:
),
) -> DatatypeVisualizationMappingsList:
"""Gets the visualization mapping for a specific datatype.
Mappings are defined in the datatypes_conf.xml configuration file.
"""
return view_visualization_mappings(self.datatypes_registry, datatype)