nwb-linkml/nwb_linkml/adapters/schema.py

"""
Since NWB doesn't necessarily have a term for a single nwb schema file, we're going
to call them "schema" objects
"""
import pdb
from typing import Optional, List, TYPE_CHECKING, Type
from pathlib import Path
from pydantic import Field, PrivateAttr

from nwb_linkml.adapters.adapter import Adapter, BuildResult
from nwb_linkml.adapters.dataset import DatasetAdapter
from nwb_linkml.adapters.group import GroupAdapter
if TYPE_CHECKING:
    from nwb_linkml.adapters.namespaces import NamespacesAdapter

from nwb_schema_language import Group, Dataset
from typing import NamedTuple

from linkml_runtime.linkml_model import SchemaDefinition


class SplitSchema(NamedTuple):
    main: BuildResult
    split: Optional[BuildResult]

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] = Field(
        None,
        description="""String of containing namespace. Populated by NamespacesAdapter""")
    split: bool = Field(
        True,
        description="Split anonymous subclasses into a separate schema file"
   )
    _created_classes: List[Type[Group | Dataset]] = PrivateAttr(default_factory=list)

    @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`


        """
        res = BuildResult()
        for dset in self.datasets:
            res += DatasetAdapter(cls=dset).build()
        for group in self.groups:
            res += GroupAdapter(cls=group).build()

        if len(res.slots) > 0:
            raise RuntimeError('Generated schema in this translation can only have classes, all slots should be attributes within a class')

        if self.split:
            sch_split = self.split_subclasses(res)
            return sch_split

        else:
            sch = SchemaDefinition(
                name = self.name,
                id = self.name,
                imports = [i.name for i in self.imports],
                classes=res.classes,
                slots=res.slots,
                types=res.types
            )
            # every schema needs the language elements
            sch.imports.append('nwb.language')
            return BuildResult(schemas=[sch])

    def split_subclasses(self, classes: BuildResult) -> BuildResult:
        """
        Split the generated classes into top-level "main" classes and
        nested/anonymous "split" classes.

        Args:
            classes (BuildResult): A Build result object containing the classes
                for the schema

        Returns:
            :class:`.SplitSchema`
        """
        # just split by the presence or absence of __
        main_classes = [c for c in classes.classes if '__' not in c.name]
        split_classes = [c for c in classes.classes if '__' in c.name]
        split_sch_name = '.'.join([self.name, 'include'])


        imports = [i.name for i in self.imports]
        imports.append('nwb.language')
        # need to mutually import the two schemas because the subclasses
        # could refer to the main classes
        main_imports = imports
        if len(split_classes)>0:
            main_imports.append(split_sch_name)
        imports.append(self.name)
        main_sch = SchemaDefinition(
            name=self.name,
            id=self.name,
            imports=main_imports,
            classes=main_classes,
            slots=classes.slots,
            types=classes.types
        )

        split_sch = SchemaDefinition(
            name=split_sch_name,
            id=split_sch_name,
            imports=imports,
            classes=split_classes,
            slots=classes.slots,
            types=classes.types
        )
        if len(split_classes) > 0:
            res = BuildResult(
                schemas=[main_sch, split_sch]
            )
        else:
            res = BuildResult(
                schemas=[main_sch]
            )
        return res



    @property
    def created_classes(self) -> List[Type[Group | Dataset]]:
        if len(self._created_classes) == 0:
            self._created_classes = [t for t in self.walk_types([self.groups, self.datasets], (Group, Dataset)) if t.neurodata_type_def is not None]
        return self._created_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', 'target_type'))

        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