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https://github.com/p2p-ld/nwb-linkml.git
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remove translate
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parent
42e64dce75
commit
f071705ac8
2 changed files with 3 additions and 156 deletions
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@ -21,12 +21,12 @@ class DatasetMap(Map):
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@classmethod
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@abstractmethod
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def check(c, cls:Dataset) -> bool:
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pass
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pass # pragma: no cover
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@classmethod
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@abstractmethod
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def apply(c, res: BuildResult, cls:Dataset, name:Optional[str] = None) -> BuildResult:
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pass
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pass # pragma: no cover
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class MapScalar(DatasetMap):
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"""
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@ -355,7 +355,7 @@ class DatasetAdapter(ClassAdapter):
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# find a map to use
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matches = [m for m in DatasetMap.__subclasses__() if m.check(self.cls)]
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if len(matches) > 1:
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if len(matches) > 1: # pragma: no cover
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raise RuntimeError(f"Only one map should apply to a dataset, you need to refactor the maps! Got maps: {matches}")
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# apply matching maps
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@ -1,153 +0,0 @@
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"""
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Convenience functions for translating NWB schema
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This module will be deprecated and removed in favor of :mod:`.providers`
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"""
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import tempfile
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from typing import List, Optional, Dict
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from types import ModuleType
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from pathlib import Path
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import json
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import h5py
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from linkml_runtime.dumpers import yaml_dumper
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from nwb_schema_language import Namespaces
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from nwb_linkml.io.schema import load_schema_file
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from nwb_linkml.generators.pydantic import NWBPydanticGenerator
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from nwb_linkml.maps.postload import apply_preload
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from nwb_linkml.adapters import SchemaAdapter, NamespacesAdapter
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#from nwb_linkml.models import core, hdmf_common
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def make_namespace_adapter(schema: dict) -> NamespacesAdapter:
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"""
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Create a :class:`.NamespacesAdapter` from a dictionary of loaded schema + namespace as are commonly
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serialized in nwbfiles under /specifications
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Args:
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schema:
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Returns:
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"""
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namespace = Namespaces(**schema['namespace'])
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schema_adapters = [] # type: List[SchemaAdapter]
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for schema_name, schema_dict in schema.items():
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if schema_name == 'namespace':
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continue
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path = Path(schema_name + '.yaml')
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schema_adapters.append(load_schema_file(path, schema_dict))
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ns_adapter = NamespacesAdapter(
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namespaces=namespace,
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schemas=schema_adapters
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)
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return ns_adapter
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def populate_namespaces_imports(namespaces: List[NamespacesAdapter]) -> List[NamespacesAdapter]:
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"""
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Given a set of :class:`.NamespacesAdapter`s, populate their imports with the other namespaces, if necessary
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"""
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for ns in namespaces:
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needed_imports = []
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for imported_ns in ns.namespaces.namespaces:
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for imported_sch in imported_ns.schema_:
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if imported_sch.namespace and not imported_sch.source:
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needed_imports.append(imported_sch.namespace)
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# find the import among the namespaces we have
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for other_ns in namespaces:
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if any([imported_ns.name in needed_imports for imported_ns in other_ns.namespaces.namespaces]):
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ns.imported.append(other_ns)
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return namespaces
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def translate_namespaces(namespaces: NamespacesAdapter, base_dir: Path) -> List[Path]:
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"""
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Write translated namespaces to disk
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"""
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built_schemas = namespaces.build().schemas
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base_dir = Path(base_dir)
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paths = []
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for schema in built_schemas:
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output_file = base_dir / (schema.name + '.yaml')
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paths.append(output_file)
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yaml_dumper.dump(schema, output_file)
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return paths
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def generate_pydantic(
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namespaces: NamespacesAdapter,
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schema_dir:Optional[Path]=None,
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pydantic_dir:Optional[Path]=None
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) -> ModuleType:
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if schema_dir is None:
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temp_schema_dir = tempfile.TemporaryDirectory()
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schema_dir = Path(temp_schema_dir.name)
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if pydantic_dir is None:
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temp_pydantic_dir = tempfile.TemporaryDirectory()
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pydantic_dir = Path(temp_pydantic_dir.name)
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if any(schema_dir.glob('*.yaml')):
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# read already generated schema, do nothing here
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schema_paths = list(schema_dir.glob('*.yaml'))
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else:
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# generate schema files
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schema_paths = translate_namespaces(namespaces, base_dir=schema_dir)
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# just generate the namespace file, which should import everything
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ns_file = [s_path for s_path in schema_paths if s_path.stem == namespaces.namespaces.namespaces[0].name]
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if len(ns_file) == 0:
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raise ValueError("Could not find main namespace file")
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ns_file = ns_file[0]
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generator = NWBPydanticGenerator(
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str(ns_file),
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split=False,
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emit_metadata=True,
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gen_classvars=True,
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gen_slots=True,
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pydantic_version='2'
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)
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serialized = generator.serialize()
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with open(pydantic_dir / 'models.py', 'w') as mfile:
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mfile.write(serialized)
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module = generator.compile_module(pydantic_dir)
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return module
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def generate_from_nwbfile(path:Path) -> Dict[str, ModuleType]:
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namespaces = []
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h5f = h5py.File(path, 'r')
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for ns_name, ns in h5f['specifications'].items():
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#if ns_name in ('core', 'hdmf-common'):
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# continue
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ns_schema = {}
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for version in ns.values():
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for schema_name, schema in version.items():
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# read the source json binary string
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sch_str = schema[()]
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sch_dict = json.loads(sch_str)
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ns_schema[schema_name] = apply_preload(sch_dict)
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namespaces.append(ns_schema)
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adapters = [make_namespace_adapter(sch) for sch in namespaces]
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adapters = populate_namespaces_imports(adapters)
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pydantic_modules = {
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adapter.namespaces.namespaces[0].name: generate_pydantic(adapter)
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for adapter in adapters
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}
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#pydantic_modules.update({'core': core, 'hdmf-common': hdmf_common})
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return pydantic_modules
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