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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,
DatatypesMap,
)
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 [ext for ext in 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] = {t: True for t in types}
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)
[docs]def view_edam_formats(datatypes_registry: Registry) -> Dict[str, str]:
return datatypes_registry.edam_formats
[docs]def view_edam_data(datatypes_registry: Registry) -> Dict[str, str]:
return datatypes_registry.edam_data