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working pydantic provider (at least superficially)

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sneakers-the-rat 2024-07-24 21:51:55 -07:00
parent 974058ce5f
commit 781b667952
Signed by untrusted user who does not match committer: jonny
GPG key ID: 6DCB96EF1E4D232D
8 changed files with 243 additions and 164 deletions
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5
docs/meta/todo.md
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@ -10,7 +10,7 @@ NWB schema translation
Cleanup Cleanup
- [ ] Update pydantic generator - [ ] Update pydantic generator
- [ ] Restore regresssions from stripping the generator - [ ] Restore regressions from stripping the generator
- [ ] Use the class rather than a string in _get_class_slot_range_origin: - [ ] Use the class rather than a string in _get_class_slot_range_origin:
``` ```
or inlined_as_list or inlined_as_list
@ -40,6 +40,9 @@ Important things that are not implemented yet!
- existing handler is fucked, for example, in `maps/hdmf` - existing handler is fucked, for example, in `maps/hdmf`
- [ ] Handle indirect indexing eg. https://pynwb.readthedocs.io/en/stable/tutorials/general/plot_timeintervals.html#accessing-referenced-timeseries - [ ] Handle indirect indexing eg. https://pynwb.readthedocs.io/en/stable/tutorials/general/plot_timeintervals.html#accessing-referenced-timeseries
Remove monkeypatches/overrides once PRs are closed
- [ ] https://github.com/linkml/linkml-runtime/pull/330
## Docs TODOs ## Docs TODOs
```{todolist} ```{todolist}

197
nwb_linkml/pdm.lock
View file

@ -630,7 +630,7 @@ files = [
[[package]] [[package]]
name = "importlib-metadata" name = "importlib-metadata"
version = "8.0.0" version = "8.2.0"
requires_python = ">=3.8" requires_python = ">=3.8"
summary = "Read metadata from Python packages" summary = "Read metadata from Python packages"
groups = ["default", "dev", "tests"] groups = ["default", "dev", "tests"]
@ -638,8 +638,8 @@ dependencies = [
"zipp>=0.5", "zipp>=0.5",
] ]
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[[package]] [[package]]
@ -842,7 +842,7 @@ version = "0.0.0"
requires_python = "<4.0.0,>=3.8.1" requires_python = "<4.0.0,>=3.8.1"
git = "https://github.com/sneakers-the-rat/linkml" git = "https://github.com/sneakers-the-rat/linkml"
ref = "nwb-linkml" ref = "nwb-linkml"
revision = "bf67a752618b0abdce8a802cce0da4e273b3a079" revision = "df8685eb9e99eaf9ec694db2e9cd59bab8892438"
summary = "Linked Open Data Modeling Language" summary = "Linked Open Data Modeling Language"
groups = ["default", "dev", "tests"] groups = ["default", "dev", "tests"]
dependencies = [ dependencies = [
@ -1181,7 +1181,7 @@ files = [
[[package]] [[package]]
name = "plotly" name = "plotly"
version = "5.22.0" version = "5.23.0"
requires_python = ">=3.8" requires_python = ">=3.8"
summary = "An open-source, interactive data visualization library for Python" summary = "An open-source, interactive data visualization library for Python"
groups = ["dev", "tests"] groups = ["dev", "tests"]
@ -1190,8 +1190,8 @@ dependencies = [
"tenacity>=6.2.0", "tenacity>=6.2.0",
] ]
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[[package]] [[package]]
@ -1730,84 +1730,75 @@ files = [
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name = "rpds-py" name = "rpds-py"
version = "0.19.0" version = "0.19.1"
requires_python = ">=3.8" requires_python = ">=3.8"
summary = "Python bindings to Rust's persistent data structures (rpds)" summary = "Python bindings to Rust's persistent data structures (rpds)"
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[[package]] [[package]]

4
nwb_linkml/pyproject.toml
View file

@ -73,6 +73,10 @@ addopts = [
"--ignore=src/nwb_linkml/models", "--ignore=src/nwb_linkml/models",
"--ignore=src/nwb_linkml/schema" "--ignore=src/nwb_linkml/schema"
] ]
markers = [
"dev: tests that are just for development rather than testing correctness",
"provider: tests for providers!"
]
testpaths = [ testpaths = [
"src/nwb_linkml", "src/nwb_linkml",
"tests", "tests",

1
nwb_linkml/src/nwb_linkml/adapters/dataset.py
View file

@ -1,7 +1,6 @@
""" """
Adapter for NWB datasets to linkml Classes Adapter for NWB datasets to linkml Classes
""" """
from abc import abstractmethod from abc import abstractmethod
from typing import ClassVar, Optional, Type from typing import ClassVar, Optional, Type

34
nwb_linkml/src/nwb_linkml/generators/pydantic.py
View file

@ -36,16 +36,11 @@ from copy import copy
from dataclasses import dataclass, field from dataclasses import dataclass, field
from pathlib import Path from pathlib import Path
from types import ModuleType from types import ModuleType
from typing import Dict, List, Optional, Tuple, Type, Union from typing import ClassVar, Dict, List, Optional, Tuple, Type, Union
from jinja2 import Template
from linkml.generators import PydanticGenerator from linkml.generators import PydanticGenerator
from linkml.generators.pydanticgen.build import SlotResult
from linkml.generators.pydanticgen.array import ArrayRepresentation from linkml.generators.pydanticgen.array import ArrayRepresentation
from linkml.generators.pydanticgen.black import format_black
from linkml.generators.common.type_designators import (
get_type_designator_value,
)
from linkml.utils.ifabsent_functions import ifabsent_value_declaration
from linkml_runtime.linkml_model.meta import ( from linkml_runtime.linkml_model.meta import (
Annotation, Annotation,
AnonymousSlotExpression, AnonymousSlotExpression,
@ -77,6 +72,8 @@ class NWBPydanticGenerator(PydanticGenerator):
'object_id: Optional[str] = Field(None, description="Unique UUID for each object")', 'object_id: Optional[str] = Field(None, description="Unique UUID for each object")',
) )
split: bool = True split: bool = True
schema_map: Optional[Dict[str, SchemaDefinition]] = None schema_map: Optional[Dict[str, SchemaDefinition]] = None
"""See :meth:`.LinkMLProvider.build` for usage - a list of specific versions to import from""" """See :meth:`.LinkMLProvider.build` for usage - a list of specific versions to import from"""
array_representations: List[ArrayRepresentation] = field( array_representations: List[ArrayRepresentation] = field(
@ -84,9 +81,12 @@ class NWBPydanticGenerator(PydanticGenerator):
) )
black: bool = True black: bool = True
inlined: bool = True inlined: bool = True
emit_metadata: bool = True, emit_metadata: bool = True
gen_classvars: bool = True, gen_classvars: bool = True
gen_slots: bool = True, gen_slots: bool = True
skip_meta: ClassVar[Tuple[str]] = ('domain_of',)
def _check_anyof( def _check_anyof(
self, s: SlotDefinition, sn: SlotDefinitionName, sv: SchemaView self, s: SlotDefinition, sn: SlotDefinitionName, sv: SchemaView
@ -111,6 +111,18 @@ class NWBPydanticGenerator(PydanticGenerator):
if not base_range_subsumes_any_of: if not base_range_subsumes_any_of:
raise ValueError("Slot cannot have both range and any_of defined") raise ValueError("Slot cannot have both range and any_of defined")
def before_generate_schema(self):
pass
def after_generate_slot(self, slot: SlotResult, sv: SchemaView) -> SlotResult:
"""
- strip unwanted metadata
"""
for key in self.skip_meta:
if key in slot.attribute.meta:
del slot.attribute.meta[key]
return slot
def compile_module( def compile_module(
self, module_path: Path = None, module_name: str = "test", **kwargs self, module_path: Path = None, module_name: str = "test", **kwargs
) -> ModuleType: # pragma: no cover - replaced with provider ) -> ModuleType: # pragma: no cover - replaced with provider
@ -131,6 +143,8 @@ class NWBPydanticGenerator(PydanticGenerator):
raise e raise e
def compile_python( def compile_python(
text_or_fn: str, package_path: Path = None, module_name: str = "test" text_or_fn: str, package_path: Path = None, module_name: str = "test"
) -> ModuleType: ) -> ModuleType:

129
nwb_linkml/src/nwb_linkml/providers/pydantic.py
View file

@ -3,6 +3,7 @@ Provider for pydantic models.
""" """
import importlib import importlib
import re
import sys import sys
from importlib.abc import MetaPathFinder from importlib.abc import MetaPathFinder
from importlib.machinery import ModuleSpec from importlib.machinery import ModuleSpec
@ -10,9 +11,10 @@ from pathlib import Path
from types import ModuleType from types import ModuleType
from typing import List, Optional, Type from typing import List, Optional, Type
from linkml_runtime.linkml_model.meta import SchemaDefinition
from linkml.generators.pydanticgen.pydanticgen import SplitMode, _import_to_path
from pydantic import BaseModel from pydantic import BaseModel
from nwb_linkml.io.yaml import yaml_peek
from nwb_linkml.generators.pydantic import NWBPydanticGenerator from nwb_linkml.generators.pydantic import NWBPydanticGenerator
from nwb_linkml.maps.naming import module_case, version_module_case from nwb_linkml.maps.naming import module_case, version_module_case
from nwb_linkml.providers import LinkMLProvider, Provider from nwb_linkml.providers import LinkMLProvider, Provider
@ -33,6 +35,20 @@ class PydanticProvider(Provider):
""" """
PROVIDES = "pydantic" PROVIDES = "pydantic"
SPLIT_PATTERN = (
"...{% if schema.annotations.namespace %}"
"{{ schema.annotations.namespace.value | replace('.', '_') }}"
"{% else %}unknown{% endif %}"
"."
"v{{ schema.version | replace('.', '_') }}"
"."
"{% if schema.annotations.is_namespace and schema.annotations.is_namespace.value %}"
"namespace"
"{% else %}"
"{{ schema.name | replace('.', '_') }}"
"{% endif %}"
)
"""See :attr:`~linkml.generators.PydanticGenerator.split_pattern"""
def __init__(self, path: Optional[Path] = None, verbose: bool = True): def __init__(self, path: Optional[Path] = None, verbose: bool = True):
super().__init__(path, verbose) super().__init__(path, verbose)
@ -45,7 +61,6 @@ class PydanticProvider(Provider):
def build( def build(
self, self,
namespace: str | Path, namespace: str | Path,
out_file: Optional[Path] = None,
version: Optional[str] = None, version: Optional[str] = None,
split: bool = True, split: bool = True,
dump: bool = True, dump: bool = True,
@ -66,8 +81,6 @@ class PydanticProvider(Provider):
:class:`.LinkMLProvider` to get the converted schema. If a path, :class:`.LinkMLProvider` to get the converted schema. If a path,
assume we have been given an explicit ``namespace.yaml`` from a converted assume we have been given an explicit ``namespace.yaml`` from a converted
NWB -> LinkML schema to load from. NWB -> LinkML schema to load from.
out_file (Optional[Path]): Optionally override the output file. If ``None``,
generate from namespace and version
split (bool): If ``False`` (default), generate a single ``namespace.py`` file, split (bool): If ``False`` (default), generate a single ``namespace.py`` file,
otherwise generate a python file for each schema in the namespace otherwise generate a python file for each schema in the namespace
in addition to a ``namespace.py`` that imports from them in addition to a ``namespace.py`` that imports from them
@ -85,32 +98,20 @@ class PydanticProvider(Provider):
namespace.endswith(".yaml") or namespace.endswith(".yml") namespace.endswith(".yaml") or namespace.endswith(".yml")
): ):
# we're given a name of a namespace to build # we're given a name of a namespace to build
name = namespace
path = ( path = (
LinkMLProvider(path=self.config.cache_dir).namespace_path(namespace, version) LinkMLProvider(path=self.config.cache_dir).namespace_path(namespace, version)
/ "namespace.yaml" / "namespace.yaml"
) )
if version is None:
# Get the most recently built version
version = LinkMLProvider(path=self.config.cache_dir).available_versions[name][-1]
fn = path.name
else: else:
# given a path to a namespace linkml yaml file # given a path to a namespace linkml yaml file
path = Path(namespace) path = Path(namespace)
name = yaml_peek('name', path)
version = yaml_peek('version', path)
fn = path.name
version = version_module_case(version)
if out_file is None:
fn = fn.removesuffix(".yaml")
fn = module_case(fn) + ".py"
out_file = self.path / name / version / fn
if split: if split:
result = self._build_split(path, dump, out_file, force, **kwargs) result = self._build_split(path, dump, force, **kwargs)
else: else:
result = self._build_unsplit(path, dump, out_file, force, **kwargs) result = self._build_unsplit(path, dump, force, **kwargs)
self.install_pathfinder() self.install_pathfinder()
return result return result
@ -119,16 +120,17 @@ class PydanticProvider(Provider):
self, self,
path: Path, path: Path,
dump: bool, dump: bool,
out_file: Path,
force: bool, force: bool,
**kwargs **kwargs
) -> Optional[str]: ) -> str:
generator = NWBPydanticGenerator(str(path), split=False, split_pattern=self.SPLIT_PATTERN, **kwargs)
out_module = generator.generate_module_import(generator.schemaview.schema)
out_file = (self.path / _import_to_path(out_module)).resolve()
if out_file.exists() and not force: if out_file.exists() and not force:
with open(out_file) as ofile: with open(out_file) as ofile:
serialized = ofile.read() serialized = ofile.read()
return serialized return serialized
generator = NWBPydanticGenerator(str(path), **kwargs)
serialized = generator.serialize() serialized = generator.serialize()
if dump: if dump:
out_file.parent.mkdir(parents=True, exist_ok=True) out_file.parent.mkdir(parents=True, exist_ok=True)
@ -143,35 +145,72 @@ class PydanticProvider(Provider):
self, self,
path: Path, path: Path,
dump: bool, dump: bool,
out_file: Path,
force: bool, force: bool,
**kwargs **kwargs
) -> List[str]: ) -> List[str]:
serialized = [] res = []
for schema_file in path.parent.glob("*.yaml"):
this_out = out_file.parent / (module_case(schema_file.stem) + ".py")
serialized.append(
self._build_unsplit(schema_file, default_kwargs, dump, this_out, force, **kwargs)
)
# If there are dependent versions that also need to be built, do that now! # first make the namespace file we were given
needed = [
(module_case(ns), version_module_case(version)) # remove any directory traversal at the head of the pattern for this,
for ns, version in versions.items() # we're making relative to the provider's path not the generated schema at first
if version_module_case(version) not in self.available_versions.get(ns, []) root_pattern = re.sub(r'^\.*', '', self.SPLIT_PATTERN)
] gen = NWBPydanticGenerator(schema=path, split=True, split_pattern=root_pattern, split_mode=SplitMode.FULL)
for needs in needed: mod_name = gen.generate_module_import(gen.schemaview.schema)
needed_path = path.parents[2] / needs[0] / needs[1] / "namespace.yaml" ns_file = (self.path / _import_to_path(mod_name)).resolve()
out_file_stem = out_file.parents[2] / needs[0] / needs[1]
for schema_file in needed_path.parent.glob("*.yaml"): # now replace the real import path so the generated module has it
this_out = out_file_stem / (module_case(schema_file.stem) + ".py") gen.split_pattern = self.SPLIT_PATTERN
serialized.append( # always render since we need to at least render to know what we're importing
self._build_unsplit( rendered = gen.render()
schema_file, versions, default_kwargs, dump, this_out, force
) if not ns_file.exists() or force:
ns_file.parent.mkdir(exist_ok=True, parents=True)
serialized = gen.serialize(rendered_module=rendered)
if dump:
with open(ns_file, 'w') as ofile:
ofile.write(serialized)
else:
with open(ns_file, 'r') as ofile:
serialized = ofile.read()
res.append(serialized)
# then each of the other schemas :)
imported_schema: dict[str, SchemaDefinition] = {
gen.generate_module_import(sch): sch for sch in gen.schemaview.schema_map.values()
}
for generated_import in [i for i in rendered.python_imports if i.schema]:
import_file = (ns_file.parent / _import_to_path(generated_import.module)).resolve()
if not import_file.exists() or force:
import_file.parent.mkdir(exist_ok=True, parents=True)
schema = imported_schema[generated_import.module]
is_namespace = False
ns_annotation = schema.annotations.get('is_namespace', None)
if ns_annotation:
is_namespace = ns_annotation.value
# fix schema source to absolute path so schemaview can find imports
schema.source_file = (Path(gen.schemaview.schema.source_file).parent / schema.source_file).resolve()
import_gen = NWBPydanticGenerator(
schema,
split=True,
split_pattern=self.SPLIT_PATTERN,
split_mode=SplitMode.FULL if is_namespace else SplitMode.AUTO
) )
serialized = import_gen.serialize()
if dump:
with open(import_file, 'w') as ofile:
ofile.write(serialized)
return serialized else:
with open(import_file, 'r') as ofile:
serialized = ofile.read()
res.append(serialized)
return res
def _make_inits(self, out_file: Path) -> None: def _make_inits(self, out_file: Path) -> None:
""" """

14
nwb_linkml/tests/conftest.py
View file

@ -1,5 +1,6 @@
import os import os
from pathlib import Path from pathlib import Path
from typing import List
import pytest import pytest
import requests_cache import requests_cache
@ -16,6 +17,18 @@ def pytest_addoption(parser):
parser.addoption( parser.addoption(
"--without-cache", action="store_true", help="Don't use a sqlite cache for network requests" "--without-cache", action="store_true", help="Don't use a sqlite cache for network requests"
) )
parser.addoption(
"--dev", action="store_true", help="run tests that are intended only for development use, eg. those that generate output for inspection"
)
def pytest_collection_modifyitems(config, items: List[pytest.Item]):
# remove dev tests from collection if we're not in dev mode!
if config.getoption('--dev'):
remove_tests = [t for t in items if not t.get_closest_marker('dev')]
else:
remove_tests = [t for t in items if t.get_closest_marker('dev')]
for t in remove_tests:
items.remove(t)
@pytest.fixture(autouse=True, scope="session") @pytest.fixture(autouse=True, scope="session")
@ -43,3 +56,4 @@ def patch_requests_cache(pytestconfig):
# delete cache file unless we have requested it to persist for inspection # delete cache file unless we have requested it to persist for inspection
if not pytestconfig.getoption("--with-output"): if not pytestconfig.getoption("--with-output"):
cache_file.unlink(missing_ok=True) cache_file.unlink(missing_ok=True)

23
nwb_linkml/tests/test_generate.py
View file

@ -16,13 +16,14 @@ from linkml_runtime.loaders.yaml_loader import YAMLLoader
from nwb_linkml.generators.pydantic import NWBPydanticGenerator from nwb_linkml.generators.pydantic import NWBPydanticGenerator
from nwb_linkml.lang_elements import NwbLangSchema from nwb_linkml.lang_elements import NwbLangSchema
from nwb_linkml.providers import LinkMLProvider, PydanticProvider
@pytest.mark.dev
def test_generate_nwblang(tmp_output_dir): def test_generate_nwblang(tmp_output_dir):
output_file = (tmp_output_dir / NwbLangSchema.name).with_suffix(".yml") output_file = (tmp_output_dir / NwbLangSchema.name).with_suffix(".yml")
yaml_dumper.dump(NwbLangSchema, output_file) yaml_dumper.dump(NwbLangSchema, output_file)
@pytest.mark.dev
def test_generate_core(nwb_core_fixture, tmp_output_dir): def test_generate_core(nwb_core_fixture, tmp_output_dir):
schemas = nwb_core_fixture.build().schemas schemas = nwb_core_fixture.build().schemas
@ -42,8 +43,7 @@ def load_schema_files(path: Path) -> Dict[str, SchemaDefinition]:
preloaded_schema[sch.name] = sch preloaded_schema[sch.name] = sch
return preloaded_schema return preloaded_schema
@pytest.mark.dev
@pytest.mark.xfail()
@pytest.mark.depends(on=["test_generate_core"]) @pytest.mark.depends(on=["test_generate_core"])
def test_generate_pydantic(tmp_output_dir): def test_generate_pydantic(tmp_output_dir):
@ -71,3 +71,18 @@ def test_generate_pydantic(tmp_output_dir):
# make __init__.py # make __init__.py
with open(tmp_output_dir / "models" / "__init__.py", "w") as initfile: with open(tmp_output_dir / "models" / "__init__.py", "w") as initfile:
initfile.write("# Autogenerated module indicator") initfile.write("# Autogenerated module indicator")
@pytest.mark.provider
@pytest.mark.dev
def test_generate_linkml_provider(tmp_output_dir, nwb_core_fixture):
provider = LinkMLProvider(path=tmp_output_dir, verbose=False)
result = provider.build(nwb_core_fixture)
@pytest.mark.provider
@pytest.mark.dev
def test_generate_pydantic_provider(tmp_output_dir):
provider = PydanticProvider(path=tmp_output_dir, verbose=False)
result = provider.build('core')