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Source code for galaxy.managers.datatypes
from typing import (
Dict,
List,
Optional,
Union,
)
from pydantic.tools import parse_obj_as
from galaxy.datatypes._schema import (
DatatypeConverterList,
DatatypeDetails,
DatatypesCombinedMap,
DatatypesEDAMDetailsDict,
DatatypesMap,
DatatypeVisualizationMapping,
DatatypeVisualizationMappingsList,
)
from galaxy.datatypes.data import Data
from galaxy.datatypes.registry import Registry
[docs]
def view_index(
datatypes_registry: Registry, extension_only: Optional[bool] = True, upload_only: Optional[bool] = True
) -> Union[List[DatatypeDetails], List[str]]:
if extension_only:
if upload_only:
return datatypes_registry.upload_file_formats
else:
return list(datatypes_registry.datatypes_by_extension)
else:
rval = []
for datatype_info_dict in datatypes_registry.datatype_info_dicts:
if upload_only and not datatype_info_dict.get("display_in_upload"):
continue
rval.append(datatype_info_dict)
return rval
[docs]
def view_mapping(datatypes_registry: Registry) -> DatatypesMap:
ext_to_class_name: Dict[str, str] = {}
classes = []
for k, v in datatypes_registry.datatypes_by_extension.items():
c = v.__class__
ext_to_class_name[k] = f"{c.__module__}.{c.__name__}"
classes.append(c)
class_to_classes: Dict[str, Dict[str, bool]] = {}
def visit_bases(types, cls):
for base in cls.__bases__:
if issubclass(base, Data):
types.add(f"{base.__module__}.{base.__name__}")
visit_bases(types, base)
for c in classes:
n = f"{c.__module__}.{c.__name__}"
types = {n}
visit_bases(types, c)
class_to_classes[n] = dict.fromkeys(types, True)
return DatatypesMap(ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes)
[docs]
def view_types_and_mapping(
datatypes_registry: Registry, extension_only: Optional[bool] = True, upload_only: Optional[bool] = True
) -> DatatypesCombinedMap:
return DatatypesCombinedMap(
datatypes=view_index(datatypes_registry, extension_only, upload_only),
datatypes_mapping=view_mapping(datatypes_registry),
)
[docs]
def view_sniffers(datatypes_registry: Registry) -> List[str]:
rval: List[str] = []
for sniffer_elem in datatypes_registry.sniffer_elems:
datatype = sniffer_elem.get("type")
if datatype is not None:
rval.append(datatype)
return rval
[docs]
def view_converters(datatypes_registry: Registry) -> DatatypeConverterList:
converters = []
for source_type, targets in datatypes_registry.datatype_converters.items():
for target_type in targets:
converters.append(
{
"source": source_type,
"target": target_type,
"tool_id": targets[target_type].id,
}
)
return parse_obj_as(DatatypeConverterList, converters)
def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]) -> Dict[str, Dict]:
details_dict = {}
for format, edam_iri in edam_ids.items():
edam_details = datatypes_registry.edam.get(edam_iri, {})
details_dict[format] = {
"prefix_IRI": edam_iri,
"label": edam_details.get("label", None),
"definition": edam_details.get("definition", None),
}
return details_dict
[docs]
def view_edam_formats(
datatypes_registry: Registry, detailed: Optional[bool] = False
) -> Union[Dict[str, str], Dict[str, Dict[str, str]]]:
if detailed:
return _get_edam_details(datatypes_registry, datatypes_registry.edam_formats)
else:
return datatypes_registry.edam_formats
[docs]
def view_edam_data(
datatypes_registry: Registry, detailed: Optional[bool] = False
) -> Union[Dict[str, str], Dict[str, Dict[str, str]]]:
if detailed:
return _get_edam_details(datatypes_registry, datatypes_registry.edam_data)
else:
return datatypes_registry.edam_data
[docs]
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"],
}
)
elif not datatype:
for dt, mapping_info in all_mappings.items():
mappings.append(
{
"datatype": dt,
"visualization": mapping_info["visualization"],
}
)
return parse_obj_as(DatatypeVisualizationMappingsList, mappings)
[docs]
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",
"DatatypesCombinedMap",
"DatatypesEDAMDetailsDict",
"DatatypesMap",
"DatatypeVisualizationMapping",
"DatatypeVisualizationMappingsList",
"view_index",
"view_mapping",
"view_types_and_mapping",
"view_sniffers",
"view_converters",
"view_edam_formats",
"view_edam_data",
"view_visualization_mappings",
"get_preferred_visualization",
)