""" Since NWB doesn't necessarily have a term for a single nwb schema file, we're going to call them "schema" objects """ from typing import Optional, List, TYPE_CHECKING from pathlib import Path from pydantic import Field from nwb_linkml.adapters.adapter import Adapter, BuildResult from nwb_linkml.adapters.classes import ClassAdapter if TYPE_CHECKING: from nwb_linkml.adapters.namespaces import NamespacesAdapter from nwb_schema_language import Group, Dataset from linkml_runtime.linkml_model import SchemaDefinition class SchemaAdapter(Adapter): """ An individual schema file in nwb_schema_language """ path: Path groups: List[Group] = Field(default_factory=list) datasets: List[Dataset] = Field(default_factory=list) imports: List['SchemaAdapter'] = Field(default_factory=list) namespace: Optional[str] = None """Populated by NamespacesAdapter""" @property def name(self) -> str: return '.'.join([self.namespace, self.path.with_suffix('').name]) def __repr__(self): out_str = '\n' + self.name + '\n' out_str += '-'*len(self.name) + '\n' if len(self.imports) > 0: out_str += "Imports:\n" out_str += " " + ', '.join([i.name for i in self.imports]) + '\n' out_str += 'Groups:\n' out_str += ' ' + ', '.join([g.neurodata_type_def for g in self.groups]) out_str += '\n' out_str += 'Datasets:\n' out_str += ' ' + ', '.join([d.neurodata_type_def for d in self.datasets]) out_str += "\n" return out_str def build(self) -> BuildResult: """ Make the LinkML representation for this schema file Things that will be populated later - `id` (but need to have a placeholder to instantiate) - `version` """ classes = [ClassAdapter(cls=dset) for dset in self.datasets] classes.extend(ClassAdapter(cls=group) for group in self.groups) built_results = None for cls in classes: if built_results is None: built_results = cls.build() else: built_results += cls.build() sch = SchemaDefinition( name = self.name, id = self.name, imports = [i.name for i in self.imports], classes=built_results.classes, slots=built_results.slots, types=built_results.types ) # every schema needs the language elements sch.imports.append('nwb.language') return BuildResult(schemas=[sch]) @property def created_classes(self) -> List[Group|Dataset]: classes = [t for t in self.walk_types([self.groups, self.datasets], (Group, Dataset)) if t.neurodata_type_def is not None] return classes @property def needed_imports(self) -> List[str]: """ Classes that need to be imported from other namespaces TODO: - Need to also check classes used in links/references """ type_incs = self.walk_fields(self, 'neurodata_type_inc') definitions = [c.neurodata_type_def for c in self.created_classes] need = [inc for inc in type_incs if inc not in definitions] return need