mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-11-13 02:04:29 +00:00
96 lines
2.8 KiB
Python
96 lines
2.8 KiB
Python
|
"""
|
||
|
|
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
|
||
|
|
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) -> SchemaDefinition:
|
||
|
|
"""
|
||
|
|
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_classes = [c.build() for c in classes]
|
||
|
|
|
||
|
|
|
||
|
|
sch = SchemaDefinition(
|
||
|
|
name = self.name,
|
||
|
|
id = self.name,
|
||
|
|
imports = [i.name for i in self.imports],
|
||
|
|
classes=built_classes
|
||
|
|
)
|
||
|
|
return 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
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
|