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remove outdated generator tests, unskip module

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sneakers-the-rat 2024-09-30 22:51:56 -07:00
parent ae37db3a41
commit dfeac9e808
Signed by untrusted user who does not match committer: jonny
GPG key ID: 6DCB96EF1E4D232D
3 changed files with 52 additions and 210 deletions
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31
nwb_linkml/src/nwb_linkml/generators/pydantic.py
View file

@ -7,8 +7,6 @@ See class and module docstrings for details :)
import re import re
from dataclasses import dataclass, field from dataclasses import dataclass, field
from pathlib import Path
from types import ModuleType
from typing import Callable, ClassVar, Dict, List, Optional, Tuple from typing import Callable, ClassVar, Dict, List, Optional, Tuple
from linkml.generators import PydanticGenerator from linkml.generators import PydanticGenerator
@ -146,7 +144,6 @@ class NWBPydanticGenerator(PydanticGenerator):
cls = AfterGenerateClass.inject_dynamictable(cls) cls = AfterGenerateClass.inject_dynamictable(cls)
cls = AfterGenerateClass.wrap_dynamictable_columns(cls, sv) cls = AfterGenerateClass.wrap_dynamictable_columns(cls, sv)
cls = AfterGenerateClass.inject_dynamictable_imports(cls, sv, self._get_element_import) cls = AfterGenerateClass.inject_dynamictable_imports(cls, sv, self._get_element_import)
cls = AfterGenerateClass.strip_vector_data_slots(cls, sv)
return cls return cls
def before_render_template(self, template: PydanticModule, sv: SchemaView) -> PydanticModule: def before_render_template(self, template: PydanticModule, sv: SchemaView) -> PydanticModule:
@ -157,25 +154,6 @@ class NWBPydanticGenerator(PydanticGenerator):
del template.meta["source_file"] del template.meta["source_file"]
return template return template
def compile_module(
self, module_path: Path = None, module_name: str = "test", **kwargs
) -> ModuleType: # pragma: no cover - replaced with provider
"""
Compiles generated python code to a module
:return:
"""
pycode = self.serialize(**kwargs)
if module_path is not None:
module_path = Path(module_path)
init_file = module_path / "__init__.py"
with open(init_file, "w") as ifile:
ifile.write(" ")
try:
return compile_python(pycode, module_path, module_name)
except NameError as e:
raise e
class AfterGenerateSlot: class AfterGenerateSlot:
""" """
@ -373,15 +351,6 @@ class AfterGenerateClass:
cls.imports += imp cls.imports += imp
return cls return cls
@staticmethod
def strip_vector_data_slots(cls: ClassResult, sv: SchemaView) -> ClassResult:
"""
Remove spurious ``vector_data`` slots from DynamicTables
"""
if "vector_data" in cls.cls.attributes:
del cls.cls.attributes["vector_data"]
return cls
def wrap_preserving_optional(annotation: str, wrap: str) -> str: def wrap_preserving_optional(annotation: str, wrap: str) -> str:
""" """

63
nwb_linkml/tests/fixtures/schema.py vendored
View file

@ -5,8 +5,10 @@ from typing import Dict, Optional
import pytest import pytest
from linkml_runtime.dumpers import yaml_dumper from linkml_runtime.dumpers import yaml_dumper
from linkml_runtime.linkml_model import ( from linkml_runtime.linkml_model.meta import (
ArrayExpression,
ClassDefinition, ClassDefinition,
DimensionExpression,
Prefix, Prefix,
SchemaDefinition, SchemaDefinition,
SlotDefinition, SlotDefinition,
@ -88,10 +90,6 @@ def linkml_schema_bare() -> TestSchemas:
equals_string="toplevel", equals_string="toplevel",
identifier=True, identifier=True,
), ),
SlotDefinition(name="array", range="MainTopLevel__Array"),
SlotDefinition(
name="SkippableSlot", description="A slot that was meant to be skipped!"
),
SlotDefinition( SlotDefinition(
name="inline_dict", name="inline_dict",
description=( description=(
@ -103,35 +101,42 @@ def linkml_schema_bare() -> TestSchemas:
inlined_as_list=False, inlined_as_list=False,
any_of=[{"range": "OtherClass"}, {"range": "StillAnotherClass"}], any_of=[{"range": "OtherClass"}, {"range": "StillAnotherClass"}],
), ),
],
),
ClassDefinition(
name="MainTopLevel__Array",
description="Main class's array",
is_a="Arraylike",
attributes=[
SlotDefinition(name="x", range="numeric", required=True),
SlotDefinition(name="y", range="numeric", required=True),
SlotDefinition( SlotDefinition(
name="z", name="value",
description="Main class's array",
range="numeric", range="numeric",
required=False, any_of=[
maximum_cardinality=3, {
minimum_cardinality=3, "array": ArrayExpression(
), dimensions=[
SlotDefinition( DimensionExpression(alias="x"),
name="a", DimensionExpression(alias="y"),
range="numeric", ]
required=False, )
minimum_cardinality=4, },
maximum_cardinality=4, {
"array": ArrayExpression(
dimensions=[
DimensionExpression(alias="x"),
DimensionExpression(alias="y"),
DimensionExpression(alias="z", exact_cardinality=3),
]
)
},
{
"array": ArrayExpression(
dimensions=[
DimensionExpression(alias="x"),
DimensionExpression(alias="y"),
DimensionExpression(alias="z", exact_cardinality=3),
DimensionExpression(alias="a", exact_cardinality=4),
]
)
},
],
), ),
], ],
), ),
ClassDefinition(
name="skippable",
description="A class that lives to be skipped!",
),
ClassDefinition( ClassDefinition(
name="OtherClass", name="OtherClass",
description="Another class yno!", description="Another class yno!",

168
nwb_linkml/tests/test_generators/test_generator_pydantic.py
View file

@ -7,7 +7,6 @@ because it's tested in the base linkml package.
# ruff: noqa: F821 - until the tests here settle down # ruff: noqa: F821 - until the tests here settle down
import re
import sys import sys
import typing import typing
from types import ModuleType from types import ModuleType
@ -16,8 +15,9 @@ from typing import Optional, TypedDict
import numpy as np import numpy as np
import pytest import pytest
from numpydantic.ndarray import NDArrayMeta from numpydantic.ndarray import NDArrayMeta
from pydantic import BaseModel from numpydantic.dtype import Float
from linkml_runtime.utils.compile_python import compile_python
from nwb_linkml.generators.pydantic import NWBPydanticGenerator from nwb_linkml.generators.pydantic import NWBPydanticGenerator
from ..fixtures import ( from ..fixtures import (
@ -35,7 +35,6 @@ class TestModules(TypedDict):
TestModules.__test__ = False TestModules.__test__ = False
@pytest.mark.xfail()
def generate_and_import( def generate_and_import(
linkml_schema: TestSchemas, split: bool, generator_kwargs: Optional[dict] = None linkml_schema: TestSchemas, split: bool, generator_kwargs: Optional[dict] = None
) -> TestModules: ) -> TestModules:
@ -45,7 +44,6 @@ def generate_and_import(
"split": split, "split": split,
"emit_metadata": True, "emit_metadata": True,
"gen_slots": True, "gen_slots": True,
"pydantic_version": "2",
**generator_kwargs, **generator_kwargs,
} }
@ -68,20 +66,13 @@ def generate_and_import(
sys.path.append(str(linkml_schema.core_path.parents[1])) sys.path.append(str(linkml_schema.core_path.parents[1]))
core = compile_python( core = compile_python(str(linkml_schema.core_path.with_suffix(".py")))
str(linkml_schema.core_path.with_suffix(".py")), module_name="test_schema.core" imported = compile_python(str(linkml_schema.imported_path.with_suffix(".py")))
) namespace = compile_python(str(linkml_schema.namespace_path.with_suffix(".py")))
imported = compile_python(
str(linkml_schema.imported_path.with_suffix(".py")), module_name="test_schema.imported"
)
namespace = compile_python(
str(linkml_schema.namespace_path.with_suffix(".py")), module_name="test_schema.namespace"
)
return TestModules(core=core, imported=imported, namespace=namespace, split=split) return TestModules(core=core, imported=imported, namespace=namespace, split=split)
@pytest.mark.xfail()
@pytest.fixture(scope="module", params=["split", "unsplit"]) @pytest.fixture(scope="module", params=["split", "unsplit"])
def imported_schema(linkml_schema, request) -> TestModules: def imported_schema(linkml_schema, request) -> TestModules:
""" """
@ -90,97 +81,10 @@ def imported_schema(linkml_schema, request) -> TestModules:
""" """
split = request.param == "split" split = request.param == "split"
yield generate_and_import(linkml_schema, split) return generate_and_import(linkml_schema, split)
del sys.modules["test_schema.core"]
del sys.modules["test_schema.imported"]
del sys.modules["test_schema.namespace"]
def _model_correctness(modules: TestModules): def test_array(imported_schema):
"""
Shared assertions for model correctness.
Only tests very basic things like type and existence,
more specific tests are in their own test functions!
"""
assert issubclass(modules["core"].MainTopLevel, BaseModel)
assert issubclass(modules["core"].Skippable, BaseModel)
assert issubclass(modules["core"].OtherClass, BaseModel)
assert issubclass(modules["core"].StillAnotherClass, BaseModel)
assert issubclass(modules["imported"].MainThing, BaseModel)
@pytest.mark.xfail()
def test_generate(linkml_schema):
"""
Base case, we can generate pydantic models from linkml schema
Tests basic functionality of serializer including
- serialization
- compilation (loading as a python model)
- existence and correctness of attributes
"""
modules = generate_and_import(linkml_schema, split=False)
assert isinstance(modules["core"], ModuleType)
assert isinstance(modules["imported"], ModuleType)
assert isinstance(modules["namespace"], ModuleType)
_model_correctness(modules)
# unsplit modules should have all the classes present, even if they aren't defined in it
assert modules["core"].MainThing.__module__ == "test_schema.core"
assert issubclass(modules["core"].MainTopLevel, modules["core"].MainThing)
del sys.modules["test_schema.core"]
del sys.modules["test_schema.imported"]
del sys.modules["test_schema.namespace"]
@pytest.mark.xfail()
def test_generate_split(linkml_schema):
"""
We can generate schema split into separate files
"""
modules = generate_and_import(linkml_schema, split=True)
assert isinstance(modules["core"], ModuleType)
assert isinstance(modules["imported"], ModuleType)
assert isinstance(modules["namespace"], ModuleType)
_model_correctness(modules)
# split modules have classes defined once and imported
assert modules["core"].MainThing.__module__ == "test_schema.imported"
# can't assert subclass here because of the weird way relative imports work
# when we don't actually import using normal python import machinery
assert modules["core"].MainTopLevel.__mro__[1].__module__ == "test_schema.imported"
del sys.modules["test_schema.core"]
del sys.modules["test_schema.imported"]
del sys.modules["test_schema.namespace"]
@pytest.mark.xfail()
def test_versions(linkml_schema):
"""
We can use explicit versions that import from relative paths generated by
SchemaProvider
"""
# here all we do is check that we have the correct relative import, since we test
# the actual generation of these path structures elsewhere in the provider tests
core_str = NWBPydanticGenerator(
str(linkml_schema.core_path), versions={"imported": "v4.2.0"}, split=True
).serialize()
# the import should be like
# from ...imported.v4_2_0.imported import (
# MainThing
# )
match = re.findall(r"from \.\.\.imported\.v4_2_0.*?MainThing.*?\)", core_str, flags=re.DOTALL)
assert len(match) == 1
@pytest.mark.xfail()
def test_arraylike(imported_schema):
""" """
Arraylike classes are converted to slots that specify nptyping arrays Arraylike classes are converted to slots that specify nptyping arrays
@ -191,19 +95,18 @@ def test_arraylike(imported_schema):
]] = Field(None) ]] = Field(None)
""" """
# check that we have gotten an NDArray annotation and its shape is correct # check that we have gotten an NDArray annotation and its shape is correct
array = imported_schema["core"].MainTopLevel.model_fields["array"].annotation array = imported_schema["core"].MainTopLevel.model_fields["value"].annotation
args = typing.get_args(array) args = typing.get_args(array)
for i, _ in enumerate(("* x, * y", "* x, * y, 3 z", "* x, * y, 3 z, 4 a")): for i, shape in enumerate(("* x, * y", "* x, * y, 3 z", "* x, * y, 3 z, 4 a")):
assert isinstance(args[i], NDArrayMeta) assert isinstance(args[i], NDArrayMeta)
assert args[i].__args__[0].__args__ assert args[i].__args__[0].__args__[0] == shape
assert args[i].__args__[1] == np.number assert args[i].__args__[1] == Float
# we shouldn't have an actual class for the array # we shouldn't have an actual class for the array
assert not hasattr(imported_schema["core"], "MainTopLevel__Array") assert not hasattr(imported_schema["core"], "MainTopLevel__Array")
assert not hasattr(imported_schema["core"], "MainTopLevelArray") assert not hasattr(imported_schema["core"], "MainTopLevelArray")
@pytest.mark.xfail()
def test_inject_fields(imported_schema): def test_inject_fields(imported_schema):
""" """
Our root model should have the special fields we injected Our root model should have the special fields we injected
@ -213,35 +116,6 @@ def test_inject_fields(imported_schema):
assert "object_id" in base.model_fields assert "object_id" in base.model_fields
@pytest.mark.xfail()
def test_linkml_meta(imported_schema):
"""
We should be able to store some linkml metadata with our classes
"""
meta = imported_schema["core"].LinkML_Meta
assert "tree_root" in meta.model_fields
assert imported_schema["core"].MainTopLevel.linkml_meta.default.tree_root
assert not imported_schema["core"].OtherClass.linkml_meta.default.tree_root
@pytest.mark.xfail()
def test_skip(linkml_schema):
"""
We can skip slots and classes
"""
modules = generate_and_import(
linkml_schema,
split=False,
generator_kwargs={
"SKIP_SLOTS": ("SkippableSlot",),
"SKIP_CLASSES": ("Skippable", "skippable"),
},
)
assert not hasattr(modules["core"], "Skippable")
assert "SkippableSlot" not in modules["core"].MainTopLevel.model_fields
@pytest.mark.xfail()
def test_inline_with_identifier(imported_schema): def test_inline_with_identifier(imported_schema):
""" """
By default, if a class has an identifier attribute, it is inlined By default, if a class has an identifier attribute, it is inlined
@ -256,7 +130,6 @@ def test_inline_with_identifier(imported_schema):
assert stillanother is imported_schema["core"].StillAnotherClass assert stillanother is imported_schema["core"].StillAnotherClass
@pytest.mark.xfail()
def test_namespace(imported_schema): def test_namespace(imported_schema):
""" """
Namespace schema import all classes from the other schema Namespace schema import all classes from the other schema
@ -269,23 +142,18 @@ def test_namespace(imported_schema):
("MainThing", "test_schema.imported"), ("MainThing", "test_schema.imported"),
("Arraylike", "test_schema.imported"), ("Arraylike", "test_schema.imported"),
("MainTopLevel", "test_schema.core"), ("MainTopLevel", "test_schema.core"),
("Skippable", "test_schema.core"),
("OtherClass", "test_schema.core"), ("OtherClass", "test_schema.core"),
("StillAnotherClass", "test_schema.core"), ("StillAnotherClass", "test_schema.core"),
): ):
assert hasattr(ns, classname) assert hasattr(ns, classname)
if imported_schema["split"]: if imported_schema["split"]:
assert getattr(ns, classname).__module__ == modname module_end_name = ".".join(getattr(ns, classname).__module__.split(".")[-2:])
assert module_end_name == modname
@pytest.mark.xfail() def test_get_item(imported_schema):
def test_get_set_item(imported_schema): """We can get without explicitly addressing array"""
"""We can get and set without explicitly addressing array""" cls = imported_schema["core"].MainTopLevel(value=np.array([[1, 2, 3], [4, 5, 6]], dtype=float))
cls = imported_schema["core"].MainTopLevel(array=np.array([[1, 2, 3], [4, 5, 6]])) assert np.array_equal(cls[0], np.array([1, 2, 3], dtype=float))
cls[0] = 50
assert (cls[0] == 50).all()
assert (cls.array[0] == 50).all()
cls[1, 1] = 100
assert cls[1, 1] == 100
assert cls.array[1, 1] == 100