mirror of
https://github.com/p2p-ld/nwb-linkml.git
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patch pydantic code generation, use anytype for dims because modeling lists of lists is not possible
This commit is contained in:
parent
63ccd800b3
commit
fe44c1c657
8 changed files with 149 additions and 151 deletions
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@ -108,6 +108,7 @@ gen-project: $(PYMODEL)
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gen-pydantic: $(PYMODEL)
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$(RUN) gen-pydantic $(SOURCE_SCHEMA_PATH) --pydantic_version 1 > $(PYMODEL)/nwb_schema_pydantic.py
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$(RUN) run_patches --phase post_generation
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test: test-schema test-python test-examples
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175
nwb-schema-language/poetry.lock
generated
175
nwb-schema-language/poetry.lock
generated
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@ -1,16 +1,5 @@
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# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
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[[package]]
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name = "annotated-types"
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version = "0.5.0"
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description = "Reusable constraint types to use with typing.Annotated"
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optional = false
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python-versions = ">=3.7"
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files = [
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{file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"},
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{file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"},
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]
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[[package]]
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name = "antlr4-python3-runtime"
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version = "4.9.3"
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@ -1362,135 +1351,55 @@ pyasn1 = ">=0.4.6,<0.6.0"
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[[package]]
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name = "pydantic"
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version = "2.1.1"
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description = "Data validation using Python type hints"
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version = "1.10.12"
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description = "Data validation and settings management using python type hints"
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optional = false
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python-versions = ">=3.7"
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[package.dependencies]
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annotated-types = ">=0.4.0"
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pydantic-core = "2.4.0"
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typing-extensions = ">=4.6.1"
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typing-extensions = ">=4.2.0"
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[package.extras]
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email = ["email-validator (>=2.0.0)"]
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[[package]]
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name = "pydantic-core"
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version = "2.4.0"
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description = ""
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optional = false
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{file = "pydantic_core-2.4.0-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:04922fea7b13cd480586fa106345fe06e43220b8327358873c22d8dfa7a711c7"},
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{file = "pydantic_core-2.4.0-pp37-pypy37_pp73-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:17156abac20a9feed10feec867fddd91a80819a485b0107fe61f09f2117fe5f3"},
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{file = "pydantic_core-2.4.0-pp37-pypy37_pp73-musllinux_1_1_aarch64.whl", hash = "sha256:4e562cc63b04636cde361fd47569162f1daa94c759220ff202a8129902229114"},
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{file = "pydantic_core-2.4.0-pp37-pypy37_pp73-musllinux_1_1_x86_64.whl", hash = "sha256:90f3785146f701e053bb6b9e8f53acce2c919aca91df88bd4975be0cb926eb41"},
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{file = "pydantic_core-2.4.0-pp37-pypy37_pp73-win_amd64.whl", hash = "sha256:e40b1e97edd3dc127aa53d8a5e539a3d0c227d71574d3f9ac1af02d58218a122"},
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{file = "pydantic_core-2.4.0-pp38-pypy38_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:be86c2eb12fb0f846262ace9d8f032dc6978b8cb26a058920ecb723dbcb87d05"},
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{file = "pydantic_core-2.4.0-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4665f7ed345012a8d2eddf4203ef145f5f56a291d010382d235b94e91813f88a"},
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{file = "pydantic_core-2.4.0-pp38-pypy38_pp73-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:79262be5a292d1df060f29b9a7cdd66934801f987a817632d7552534a172709a"},
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{file = "pydantic_core-2.4.0-pp38-pypy38_pp73-musllinux_1_1_aarch64.whl", hash = "sha256:5fd905a69ac74eaba5041e21a1e8b1a479dab2b41c93bdcc4c1cede3c12a8d86"},
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{file = "pydantic_core-2.4.0-pp38-pypy38_pp73-musllinux_1_1_x86_64.whl", hash = "sha256:2ad538b7e07343001934417cdc8584623b4d8823c5b8b258e75ec8d327cec969"},
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{file = "pydantic_core-2.4.0-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:dd2429f7635ad4857b5881503f9c310be7761dc681c467a9d27787b674d1250a"},
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{file = "pydantic_core-2.4.0-pp39-pypy39_pp73-macosx_10_7_x86_64.whl", hash = "sha256:efff8b6761a1f6e45cebd1b7a6406eb2723d2d5710ff0d1b624fe11313693989"},
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{file = "pydantic_core-2.4.0-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:32a1e0352558cd7ccc014ffe818c7d87b15ec6145875e2cc5fa4bb7351a1033d"},
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{file = "pydantic_core-2.4.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a027f41c5008571314861744d83aff75a34cf3a07022e0be32b214a5bc93f7f1"},
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{file = "pydantic_core-2.4.0-pp39-pypy39_pp73-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:1927f0e15d190f11f0b8344373731e28fd774c6d676d8a6cfadc95c77214a48b"},
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{file = "pydantic_core-2.4.0-pp39-pypy39_pp73-musllinux_1_1_aarch64.whl", hash = "sha256:7aa82d483d5fb867d4fb10a138ffd57b0f1644e99f2f4f336e48790ada9ada5e"},
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||||
{file = "pydantic_core-2.4.0-pp39-pypy39_pp73-musllinux_1_1_x86_64.whl", hash = "sha256:b85778308bf945e9b33ac604e6793df9b07933108d20bdf53811bc7c2798a4af"},
|
||||
{file = "pydantic_core-2.4.0-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:3ded19dcaefe2f6706d81e0db787b59095f4ad0fbadce1edffdf092294c8a23f"},
|
||||
{file = "pydantic_core-2.4.0.tar.gz", hash = "sha256:ec3473c9789cc00c7260d840c3db2c16dbfc816ca70ec87a00cddfa3e1a1cdd5"},
|
||||
]
|
||||
|
||||
[package.dependencies]
|
||||
typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
|
||||
dotenv = ["python-dotenv (>=0.10.4)"]
|
||||
email = ["email-validator (>=1.0.3)"]
|
||||
|
||||
[[package]]
|
||||
name = "pygments"
|
||||
|
|
@ -2518,4 +2427,4 @@ docs = []
|
|||
[metadata]
|
||||
lock-version = "2.0"
|
||||
python-versions = "^3.9"
|
||||
content-hash = "45ab0641686b3572e070cc39ae4a66ac504af0e079ac7e36c12fdaee200a1f11"
|
||||
content-hash = "7f1c4bbcfac50aaa741976f74d8ceac46ba630ea5ed649b90184f9698c05d536"
|
||||
|
|
|
|||
|
|
@ -13,6 +13,7 @@ include = ["README.md", "src/nwb_schema_language/schema", "project"]
|
|||
[tool.poetry.dependencies]
|
||||
python = "^3.9"
|
||||
linkml-runtime = "^1.1.24"
|
||||
pydantic = "<2"
|
||||
|
||||
[tool.poetry-dynamic-versioning]
|
||||
enable = true
|
||||
|
|
@ -25,6 +26,9 @@ mkdocs-material = "^8.2.8"
|
|||
mkdocs-mermaid2-plugin = "^0.6.0"
|
||||
schemasheets = "^0.1.14"
|
||||
|
||||
[tool.poetry.scripts]
|
||||
run_patches = 'nwb_schema_language.patches:main'
|
||||
|
||||
[build-system]
|
||||
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
|
||||
build-backend = "poetry_dynamic_versioning.backend"
|
||||
|
|
|
|||
|
|
@ -1,9 +1,13 @@
|
|||
from .datamodel.nwb_schema_pydantic import Namespace, \
|
||||
Namespaces, \
|
||||
Schema, \
|
||||
Group, \
|
||||
Attribute, \
|
||||
Link, \
|
||||
Dataset, \
|
||||
ReferenceDtype, \
|
||||
CompoundDtype
|
||||
import warnings
|
||||
try:
|
||||
from .datamodel.nwb_schema_pydantic import Namespace, \
|
||||
Namespaces, \
|
||||
Schema, \
|
||||
Group, \
|
||||
Attribute, \
|
||||
Link, \
|
||||
Dataset, \
|
||||
ReferenceDtype, \
|
||||
CompoundDtype
|
||||
except NameError:
|
||||
warnings.warn('Error importing pydantic classes, passing because we might be in the process of patching them, but it is likely they are broken and you will be unable to use them!')
|
||||
|
|
@ -174,8 +174,8 @@ class DtypeMixin(ConfiguredBaseModel):
|
|||
class Attribute(DtypeMixin):
|
||||
|
||||
name: str = Field(...)
|
||||
dims: Optional[List[str]] = Field(default_factory=list)
|
||||
shape: Optional[List[str]] = Field(default_factory=list)
|
||||
dims: Optional[List[Union[Any, str]]] = Field(default_factory=list)
|
||||
shape: Optional[List[Union[Any, int, str]]] = Field(default_factory=list)
|
||||
value: Optional[Any] = Field(None, description="""Optional constant, fixed value for the attribute.""")
|
||||
default_value: Optional[Any] = Field(None, description="""Optional default value for variable-valued attributes.""")
|
||||
doc: str = Field(..., description="""Description of corresponding object.""")
|
||||
|
|
@ -211,8 +211,8 @@ class Dataset(NamingMixin, DtypeMixin):
|
|||
neurodata_type_inc: Optional[str] = Field(None)
|
||||
name: Optional[str] = Field(None)
|
||||
default_name: Optional[str] = Field(None)
|
||||
dims: Optional[List[str]] = Field(default_factory=list)
|
||||
shape: Optional[List[str]] = Field(default_factory=list)
|
||||
dims: Optional[List[Union[Any, str]]] = Field(default_factory=list)
|
||||
shape: Optional[List[Union[Any, int, str]]] = Field(default_factory=list)
|
||||
value: Optional[Any] = Field(None, description="""Optional constant, fixed value for the attribute.""")
|
||||
default_value: Optional[Any] = Field(None, description="""Optional default value for variable-valued attributes.""")
|
||||
doc: str = Field(..., description="""Description of corresponding object.""")
|
||||
|
|
|
|||
68
nwb-schema-language/src/nwb_schema_language/patches.py
Normal file
68
nwb-schema-language/src/nwb_schema_language/patches.py
Normal file
|
|
@ -0,0 +1,68 @@
|
|||
"""
|
||||
Patching the source code at different stages of the code generation process
|
||||
"""
|
||||
|
||||
from dataclasses import dataclass
|
||||
from enum import StrEnum
|
||||
from pathlib import Path
|
||||
from typing import ClassVar, List
|
||||
import re
|
||||
import argparse
|
||||
import pprint
|
||||
|
||||
class Phases(StrEnum):
|
||||
post_generation = "post_generation"
|
||||
|
||||
@dataclass
|
||||
class Patch:
|
||||
phase: Phases
|
||||
path: Path
|
||||
"""Path relative to repository root"""
|
||||
match: str
|
||||
"""Regex to match the thing to be replaced"""
|
||||
replacement: str
|
||||
"""Regex to replace with (eg. can use capturing groups in match)"""
|
||||
|
||||
instances: ClassVar[List['Patch']] = []
|
||||
"""
|
||||
List of patches!
|
||||
"""
|
||||
|
||||
def __post_init__(self):
|
||||
self.instances.append(self)
|
||||
|
||||
|
||||
### Patches
|
||||
|
||||
patch_schema_slot = Patch(
|
||||
phase=Phases.post_generation,
|
||||
path=Path('src/nwb_schema_language/datamodel/nwb_schema_pydantic.py'),
|
||||
match=r"\n\s*(schema)(.*Field\()(.*)",
|
||||
replacement=r'\n schema_\2alias="schema", \3',
|
||||
)
|
||||
|
||||
def run_patches(phase:Phases, verbose:bool=False):
|
||||
patches = [p for p in Patch.instances if p.phase == phase]
|
||||
for patch in patches:
|
||||
print('Patching:')
|
||||
pprint.pprint(patch)
|
||||
with open(patch.path, 'r') as pfile:
|
||||
string = pfile.read()
|
||||
string = re.sub(patch.match, patch.replacement, string)
|
||||
with open(patch.path, 'w') as pfile:
|
||||
pfile.write(string)
|
||||
|
||||
|
||||
def main():
|
||||
parser = argparse.ArgumentParser(
|
||||
description="Run patches for a given phase of code generation"
|
||||
)
|
||||
parser.add_argument("--phase",
|
||||
choices=list(Phases.__members__.keys()),
|
||||
type=Phases)
|
||||
args = parser.parse_args()
|
||||
run_patches(args.phase, verbose=True)
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
@ -216,6 +216,7 @@ slots:
|
|||
range: Schema
|
||||
description: List of the schema to be included in this namespace.
|
||||
inlined_as_list: true
|
||||
alias: schema_
|
||||
|
||||
# schema
|
||||
source:
|
||||
|
|
@ -285,17 +286,21 @@ slots:
|
|||
multivalued: true
|
||||
dims:
|
||||
multivalued: true
|
||||
range: string
|
||||
any_of:
|
||||
- range: string
|
||||
- range: AnyType
|
||||
todos:
|
||||
- Can't quite figure out how to allow an array of arrays
|
||||
- Can't quite figure out how to allow an array of arrays - see https://github.com/linkml/linkml/issues/895
|
||||
shape:
|
||||
multivalued: true
|
||||
exactly_one_of:
|
||||
any_of:
|
||||
- range: integer
|
||||
minimum_value: 1
|
||||
- equals_string: "null"
|
||||
range: string
|
||||
- range: AnyType
|
||||
todos:
|
||||
- Can't quite figure out how to allow an array of arrays
|
||||
- Can't quite figure out how to allow an array of arrays - see https://github.com/linkml/linkml/issues/895
|
||||
value:
|
||||
range: AnyType
|
||||
description: Optional constant, fixed value for the attribute.
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ from linkml_runtime.loaders import yaml_loader
|
|||
import yaml
|
||||
|
||||
from nwb_schema_language import Namespaces, Group, Dataset
|
||||
from nwb_linkml.namespaces import GitRepo, NamespaceRepo
|
||||
from nwb_linkml.namespaces import GitRepo, NamespaceRepo, NWB_CORE_REPO
|
||||
|
||||
|
||||
|
||||
|
|
@ -41,6 +41,13 @@ def load_schema_file(path:Path) -> List[Dataset | Group]:
|
|||
#schema.extend([Group(**group) for group in source.get('groups', [])])
|
||||
return schema
|
||||
|
||||
def load_nwb_core():
|
||||
namespace_file = NWB_CORE_REPO.provide_from_git()
|
||||
ns = load_namespaces(namespace_file)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Reference in a new issue