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Source code for galaxy.managers.datatypes

from typing import (

from pydantic.tools import parse_obj_as

from galaxy.datatypes._schema import (
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