mirror of
https://github.com/p2p-ld/nwb-linkml.git
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working pydantic provider (at least superficially)
This commit is contained in:
parent
974058ce5f
commit
781b667952
GPG key ID:
6DCB96EF1E4D232D
8 changed files with 243 additions and 164 deletions
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@ -10,7 +10,7 @@ NWB schema translation
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Cleanup
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- [ ] Update pydantic generator
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- [ ] Restore regresssions from stripping the generator
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- [ ] Restore regressions from stripping the generator
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- [ ] Use the class rather than a string in _get_class_slot_range_origin:
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```
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or inlined_as_list
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@ -40,6 +40,9 @@ Important things that are not implemented yet!
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- existing handler is fucked, for example, in `maps/hdmf`
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- [ ] Handle indirect indexing eg. https://pynwb.readthedocs.io/en/stable/tutorials/general/plot_timeintervals.html#accessing-referenced-timeseries
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Remove monkeypatches/overrides once PRs are closed
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- [ ] https://github.com/linkml/linkml-runtime/pull/330
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## Docs TODOs
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```{todolist}
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@ -630,7 +630,7 @@ files = [
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[[package]]
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name = "importlib-metadata"
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version = "8.0.0"
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version = "8.2.0"
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requires_python = ">=3.8"
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summary = "Read metadata from Python packages"
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groups = ["default", "dev", "tests"]
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@ -638,8 +638,8 @@ dependencies = [
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"zipp>=0.5",
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]
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files = [
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{file = "importlib_metadata-8.0.0-py3-none-any.whl", hash = "sha256:15584cf2b1bf449d98ff8a6ff1abef57bf20f3ac6454f431736cd3e660921b2f"},
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{file = "importlib_metadata-8.0.0.tar.gz", hash = "sha256:188bd24e4c346d3f0a933f275c2fec67050326a856b9a359881d7c2a697e8812"},
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{file = "importlib_metadata-8.2.0-py3-none-any.whl", hash = "sha256:11901fa0c2f97919b288679932bb64febaeacf289d18ac84dd68cb2e74213369"},
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{file = "importlib_metadata-8.2.0.tar.gz", hash = "sha256:72e8d4399996132204f9a16dcc751af254a48f8d1b20b9ff0f98d4a8f901e73d"},
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]
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[[package]]
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@ -842,7 +842,7 @@ version = "0.0.0"
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requires_python = "<4.0.0,>=3.8.1"
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git = "https://github.com/sneakers-the-rat/linkml"
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ref = "nwb-linkml"
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revision = "bf67a752618b0abdce8a802cce0da4e273b3a079"
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revision = "df8685eb9e99eaf9ec694db2e9cd59bab8892438"
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summary = "Linked Open Data Modeling Language"
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groups = ["default", "dev", "tests"]
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dependencies = [
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@ -1181,7 +1181,7 @@ files = [
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[[package]]
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name = "plotly"
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version = "5.22.0"
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version = "5.23.0"
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requires_python = ">=3.8"
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summary = "An open-source, interactive data visualization library for Python"
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groups = ["dev", "tests"]
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@ -1190,8 +1190,8 @@ dependencies = [
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"tenacity>=6.2.0",
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]
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files = [
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{file = "plotly-5.22.0-py3-none-any.whl", hash = "sha256:68fc1901f098daeb233cc3dd44ec9dc31fb3ca4f4e53189344199c43496ed006"},
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{file = "plotly-5.22.0.tar.gz", hash = "sha256:859fdadbd86b5770ae2466e542b761b247d1c6b49daed765b95bb8c7063e7469"},
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{file = "plotly-5.23.0-py3-none-any.whl", hash = "sha256:76cbe78f75eddc10c56f5a4ee3e7ccaade7c0a57465546f02098c0caed6c2d1a"},
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{file = "plotly-5.23.0.tar.gz", hash = "sha256:89e57d003a116303a34de6700862391367dd564222ab71f8531df70279fc0193"},
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]
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[[package]]
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@ -1730,84 +1730,75 @@ files = [
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[[package]]
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name = "rpds-py"
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version = "0.19.0"
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version = "0.19.1"
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requires_python = ">=3.8"
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summary = "Python bindings to Rust's persistent data structures (rpds)"
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groups = ["default", "dev", "tests"]
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[[package]]
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||||
|
|
@ -1861,40 +1852,40 @@ files = [
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||||
[[package]]
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||||
name = "ruff"
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||||
version = "0.5.3"
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||||
version = "0.5.4"
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requires_python = ">=3.7"
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summary = "An extremely fast Python linter and code formatter, written in Rust."
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groups = ["dev"]
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files = [
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||||
{file = "ruff-0.5.3-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:08058d077e21b856d32ebf483443390e29dc44d927608dc8f092ff6776519da9"},
|
||||
{file = "ruff-0.5.3-py3-none-musllinux_1_2_i686.whl", hash = "sha256:77d49484429ed7c7e6e2e75a753f153b7b58f875bdb4158ad85af166a1ec1822"},
|
||||
{file = "ruff-0.5.3-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:642cbff6cbfa38d2566d8db086508d6f472edb136cbfcc4ea65997745368c29e"},
|
||||
{file = "ruff-0.5.3-py3-none-win32.whl", hash = "sha256:eafc45dd8bdc37a00b28e68cc038daf3ca8c233d73fea276dcd09defb1352841"},
|
||||
{file = "ruff-0.5.3-py3-none-win_amd64.whl", hash = "sha256:cbaec2ddf4f78e5e9ecf5456ea0f496991358a1d883862ed0b9e947e2b6aea93"},
|
||||
{file = "ruff-0.5.3-py3-none-win_arm64.whl", hash = "sha256:05fbd2cb404775d6cd7f2ff49504e2d20e13ef95fa203bd1ab22413af70d420b"},
|
||||
{file = "ruff-0.5.3.tar.gz", hash = "sha256:2a3eb4f1841771fa5b67a56be9c2d16fd3cc88e378bd86aaeaec2f7e6bcdd0a2"},
|
||||
{file = "ruff-0.5.4-py3-none-linux_armv6l.whl", hash = "sha256:82acef724fc639699b4d3177ed5cc14c2a5aacd92edd578a9e846d5b5ec18ddf"},
|
||||
{file = "ruff-0.5.4-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:da62e87637c8838b325e65beee485f71eb36202ce8e3cdbc24b9fcb8b99a37be"},
|
||||
{file = "ruff-0.5.4-py3-none-macosx_11_0_arm64.whl", hash = "sha256:e98ad088edfe2f3b85a925ee96da652028f093d6b9b56b76fc242d8abb8e2059"},
|
||||
{file = "ruff-0.5.4-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4c55efbecc3152d614cfe6c2247a3054cfe358cefbf794f8c79c8575456efe19"},
|
||||
{file = "ruff-0.5.4-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:f9b85eaa1f653abd0a70603b8b7008d9e00c9fa1bbd0bf40dad3f0c0bdd06793"},
|
||||
{file = "ruff-0.5.4-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:0cf497a47751be8c883059c4613ba2f50dd06ec672692de2811f039432875278"},
|
||||
{file = "ruff-0.5.4-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:09c14ed6a72af9ccc8d2e313d7acf7037f0faff43cde4b507e66f14e812e37f7"},
|
||||
{file = "ruff-0.5.4-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:628f6b8f97b8bad2490240aa84f3e68f390e13fabc9af5c0d3b96b485921cd60"},
|
||||
{file = "ruff-0.5.4-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:3520a00c0563d7a7a7c324ad7e2cde2355733dafa9592c671fb2e9e3cd8194c1"},
|
||||
{file = "ruff-0.5.4-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:93789f14ca2244fb91ed481456f6d0bb8af1f75a330e133b67d08f06ad85b516"},
|
||||
{file = "ruff-0.5.4-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:029454e2824eafa25b9df46882f7f7844d36fd8ce51c1b7f6d97e2615a57bbcc"},
|
||||
{file = "ruff-0.5.4-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:9492320eed573a13a0bc09a2957f17aa733fff9ce5bf00e66e6d4a88ec33813f"},
|
||||
{file = "ruff-0.5.4-py3-none-musllinux_1_2_i686.whl", hash = "sha256:a6e1f62a92c645e2919b65c02e79d1f61e78a58eddaebca6c23659e7c7cb4ac7"},
|
||||
{file = "ruff-0.5.4-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:768fa9208df2bec4b2ce61dbc7c2ddd6b1be9fb48f1f8d3b78b3332c7d71c1ff"},
|
||||
{file = "ruff-0.5.4-py3-none-win32.whl", hash = "sha256:e1e7393e9c56128e870b233c82ceb42164966f25b30f68acbb24ed69ce9c3a4e"},
|
||||
{file = "ruff-0.5.4-py3-none-win_amd64.whl", hash = "sha256:58b54459221fd3f661a7329f177f091eb35cf7a603f01d9eb3eb11cc348d38c4"},
|
||||
{file = "ruff-0.5.4-py3-none-win_arm64.whl", hash = "sha256:bd53da65f1085fb5b307c38fd3c0829e76acf7b2a912d8d79cadcdb4875c1eb7"},
|
||||
{file = "ruff-0.5.4.tar.gz", hash = "sha256:2795726d5f71c4f4e70653273d1c23a8182f07dd8e48c12de5d867bfb7557eed"},
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "setuptools"
|
||||
version = "71.0.4"
|
||||
version = "71.1.0"
|
||||
requires_python = ">=3.8"
|
||||
summary = "Easily download, build, install, upgrade, and uninstall Python packages"
|
||||
groups = ["dev", "tests"]
|
||||
files = [
|
||||
{file = "setuptools-71.0.4-py3-none-any.whl", hash = "sha256:ed2feca703be3bdbd94e6bb17365d91c6935c6b2a8d0bb09b66a2c435ba0b1a5"},
|
||||
{file = "setuptools-71.0.4.tar.gz", hash = "sha256:48297e5d393a62b7cb2a10b8f76c63a73af933bd809c9e0d0d6352a1a0135dd8"},
|
||||
{file = "setuptools-71.1.0-py3-none-any.whl", hash = "sha256:33874fdc59b3188304b2e7c80d9029097ea31627180896fb549c578ceb8a0855"},
|
||||
{file = "setuptools-71.1.0.tar.gz", hash = "sha256:032d42ee9fb536e33087fb66cac5f840eb9391ed05637b3f2a76a7c8fb477936"},
|
||||
]
|
||||
|
||||
[[package]]
|
||||
|
|
|
|||
|
|
@ -73,6 +73,10 @@ addopts = [
|
|||
"--ignore=src/nwb_linkml/models",
|
||||
"--ignore=src/nwb_linkml/schema"
|
||||
]
|
||||
markers = [
|
||||
"dev: tests that are just for development rather than testing correctness",
|
||||
"provider: tests for providers!"
|
||||
]
|
||||
testpaths = [
|
||||
"src/nwb_linkml",
|
||||
"tests",
|
||||
|
|
|
|||
|
|
@ -1,7 +1,6 @@
|
|||
"""
|
||||
Adapter for NWB datasets to linkml Classes
|
||||
"""
|
||||
|
||||
from abc import abstractmethod
|
||||
from typing import ClassVar, Optional, Type
|
||||
|
||||
|
|
|
|||
|
|
@ -36,16 +36,11 @@ from copy import copy
|
|||
from dataclasses import dataclass, field
|
||||
from pathlib import Path
|
||||
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.pydanticgen.build import SlotResult
|
||||
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 (
|
||||
Annotation,
|
||||
AnonymousSlotExpression,
|
||||
|
|
@ -77,6 +72,8 @@ class NWBPydanticGenerator(PydanticGenerator):
|
|||
'object_id: Optional[str] = Field(None, description="Unique UUID for each object")',
|
||||
)
|
||||
split: bool = True
|
||||
|
||||
|
||||
schema_map: Optional[Dict[str, SchemaDefinition]] = None
|
||||
"""See :meth:`.LinkMLProvider.build` for usage - a list of specific versions to import from"""
|
||||
array_representations: List[ArrayRepresentation] = field(
|
||||
|
|
@ -84,9 +81,12 @@ class NWBPydanticGenerator(PydanticGenerator):
|
|||
)
|
||||
black: bool = True
|
||||
inlined: bool = True
|
||||
emit_metadata: bool = True,
|
||||
gen_classvars: bool = True,
|
||||
gen_slots: bool = True,
|
||||
emit_metadata: bool = True
|
||||
gen_classvars: bool = True
|
||||
gen_slots: bool = True
|
||||
|
||||
|
||||
skip_meta: ClassVar[Tuple[str]] = ('domain_of',)
|
||||
|
||||
def _check_anyof(
|
||||
self, s: SlotDefinition, sn: SlotDefinitionName, sv: SchemaView
|
||||
|
|
@ -111,6 +111,18 @@ class NWBPydanticGenerator(PydanticGenerator):
|
|||
if not base_range_subsumes_any_of:
|
||||
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(
|
||||
self, module_path: Path = None, module_name: str = "test", **kwargs
|
||||
) -> ModuleType: # pragma: no cover - replaced with provider
|
||||
|
|
@ -131,6 +143,8 @@ class NWBPydanticGenerator(PydanticGenerator):
|
|||
raise e
|
||||
|
||||
|
||||
|
||||
|
||||
def compile_python(
|
||||
text_or_fn: str, package_path: Path = None, module_name: str = "test"
|
||||
) -> ModuleType:
|
||||
|
|
|
|||
|
|
@ -3,6 +3,7 @@ Provider for pydantic models.
|
|||
"""
|
||||
|
||||
import importlib
|
||||
import re
|
||||
import sys
|
||||
from importlib.abc import MetaPathFinder
|
||||
from importlib.machinery import ModuleSpec
|
||||
|
|
@ -10,9 +11,10 @@ from pathlib import Path
|
|||
from types import ModuleType
|
||||
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 nwb_linkml.io.yaml import yaml_peek
|
||||
from nwb_linkml.generators.pydantic import NWBPydanticGenerator
|
||||
from nwb_linkml.maps.naming import module_case, version_module_case
|
||||
from nwb_linkml.providers import LinkMLProvider, Provider
|
||||
|
|
@ -33,6 +35,20 @@ class PydanticProvider(Provider):
|
|||
"""
|
||||
|
||||
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):
|
||||
super().__init__(path, verbose)
|
||||
|
|
@ -45,7 +61,6 @@ class PydanticProvider(Provider):
|
|||
def build(
|
||||
self,
|
||||
namespace: str | Path,
|
||||
out_file: Optional[Path] = None,
|
||||
version: Optional[str] = None,
|
||||
split: bool = True,
|
||||
dump: bool = True,
|
||||
|
|
@ -66,8 +81,6 @@ class PydanticProvider(Provider):
|
|||
:class:`.LinkMLProvider` to get the converted schema. If a path,
|
||||
assume we have been given an explicit ``namespace.yaml`` from a converted
|
||||
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,
|
||||
otherwise generate a python file for each schema in the namespace
|
||||
in addition to a ``namespace.py`` that imports from them
|
||||
|
|
@ -85,32 +98,20 @@ class PydanticProvider(Provider):
|
|||
namespace.endswith(".yaml") or namespace.endswith(".yml")
|
||||
):
|
||||
# we're given a name of a namespace to build
|
||||
name = namespace
|
||||
path = (
|
||||
LinkMLProvider(path=self.config.cache_dir).namespace_path(namespace, version)
|
||||
/ "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:
|
||||
# given a path to a namespace linkml yaml file
|
||||
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:
|
||||
result = self._build_split(path, dump, out_file, force, **kwargs)
|
||||
result = self._build_split(path, dump, force, **kwargs)
|
||||
else:
|
||||
result = self._build_unsplit(path, dump, out_file, force, **kwargs)
|
||||
result = self._build_unsplit(path, dump, force, **kwargs)
|
||||
|
||||
self.install_pathfinder()
|
||||
return result
|
||||
|
|
@ -119,16 +120,17 @@ class PydanticProvider(Provider):
|
|||
self,
|
||||
path: Path,
|
||||
dump: bool,
|
||||
out_file: Path,
|
||||
force: bool,
|
||||
**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:
|
||||
with open(out_file) as ofile:
|
||||
serialized = ofile.read()
|
||||
return serialized
|
||||
|
||||
generator = NWBPydanticGenerator(str(path), **kwargs)
|
||||
serialized = generator.serialize()
|
||||
if dump:
|
||||
out_file.parent.mkdir(parents=True, exist_ok=True)
|
||||
|
|
@ -143,35 +145,72 @@ class PydanticProvider(Provider):
|
|||
self,
|
||||
path: Path,
|
||||
dump: bool,
|
||||
out_file: Path,
|
||||
force: bool,
|
||||
**kwargs
|
||||
) -> List[str]:
|
||||
serialized = []
|
||||
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)
|
||||
)
|
||||
res = []
|
||||
|
||||
# If there are dependent versions that also need to be built, do that now!
|
||||
needed = [
|
||||
(module_case(ns), version_module_case(version))
|
||||
for ns, version in versions.items()
|
||||
if version_module_case(version) not in self.available_versions.get(ns, [])
|
||||
]
|
||||
for needs in needed:
|
||||
needed_path = path.parents[2] / needs[0] / needs[1] / "namespace.yaml"
|
||||
out_file_stem = out_file.parents[2] / needs[0] / needs[1]
|
||||
for schema_file in needed_path.parent.glob("*.yaml"):
|
||||
this_out = out_file_stem / (module_case(schema_file.stem) + ".py")
|
||||
serialized.append(
|
||||
self._build_unsplit(
|
||||
schema_file, versions, default_kwargs, dump, this_out, force
|
||||
)
|
||||
# first make the namespace file we were given
|
||||
|
||||
# remove any directory traversal at the head of the pattern for this,
|
||||
# we're making relative to the provider's path not the generated schema at first
|
||||
root_pattern = re.sub(r'^\.*', '', self.SPLIT_PATTERN)
|
||||
gen = NWBPydanticGenerator(schema=path, split=True, split_pattern=root_pattern, split_mode=SplitMode.FULL)
|
||||
mod_name = gen.generate_module_import(gen.schemaview.schema)
|
||||
ns_file = (self.path / _import_to_path(mod_name)).resolve()
|
||||
|
||||
# now replace the real import path so the generated module has it
|
||||
gen.split_pattern = self.SPLIT_PATTERN
|
||||
# always render since we need to at least render to know what we're importing
|
||||
rendered = gen.render()
|
||||
|
||||
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:
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -1,5 +1,6 @@
|
|||
import os
|
||||
from pathlib import Path
|
||||
from typing import List
|
||||
|
||||
import pytest
|
||||
import requests_cache
|
||||
|
|
@ -16,6 +17,18 @@ def pytest_addoption(parser):
|
|||
parser.addoption(
|
||||
"--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")
|
||||
|
|
@ -43,3 +56,4 @@ def patch_requests_cache(pytestconfig):
|
|||
# delete cache file unless we have requested it to persist for inspection
|
||||
if not pytestconfig.getoption("--with-output"):
|
||||
cache_file.unlink(missing_ok=True)
|
||||
|
||||
|
|
|
|||
|
|
@ -16,13 +16,14 @@ from linkml_runtime.loaders.yaml_loader import YAMLLoader
|
|||
|
||||
from nwb_linkml.generators.pydantic import NWBPydanticGenerator
|
||||
from nwb_linkml.lang_elements import NwbLangSchema
|
||||
from nwb_linkml.providers import LinkMLProvider, PydanticProvider
|
||||
|
||||
|
||||
@pytest.mark.dev
|
||||
def test_generate_nwblang(tmp_output_dir):
|
||||
output_file = (tmp_output_dir / NwbLangSchema.name).with_suffix(".yml")
|
||||
yaml_dumper.dump(NwbLangSchema, output_file)
|
||||
|
||||
|
||||
@pytest.mark.dev
|
||||
def test_generate_core(nwb_core_fixture, tmp_output_dir):
|
||||
schemas = nwb_core_fixture.build().schemas
|
||||
|
||||
|
|
@ -42,8 +43,7 @@ def load_schema_files(path: Path) -> Dict[str, SchemaDefinition]:
|
|||
preloaded_schema[sch.name] = sch
|
||||
return preloaded_schema
|
||||
|
||||
|
||||
@pytest.mark.xfail()
|
||||
@pytest.mark.dev
|
||||
@pytest.mark.depends(on=["test_generate_core"])
|
||||
def test_generate_pydantic(tmp_output_dir):
|
||||
|
||||
|
|
@ -71,3 +71,18 @@ def test_generate_pydantic(tmp_output_dir):
|
|||
# make __init__.py
|
||||
with open(tmp_output_dir / "models" / "__init__.py", "w") as initfile:
|
||||
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')
|
||||
Loading…
Reference in a new issue