mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-09-19 15:34:28 +00:00
assorted cleanings but i am tired
This commit is contained in:
parent
43187bfa3e
commit
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GPG key ID:
6DCB96EF1E4D232D
9 changed files with 67 additions and 106 deletions
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@ -405,7 +405,7 @@ files = [
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[[package]]
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name = "dask"
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version = "2024.7.0"
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version = "2024.7.1"
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requires_python = ">=3.9"
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summary = "Parallel PyData with Task Scheduling"
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groups = ["default", "dev", "tests"]
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@ -420,8 +420,8 @@ dependencies = [
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"toolz>=0.10.0",
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]
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files = [
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{file = "dask-2024.7.0-py3-none-any.whl", hash = "sha256:0f30f218a1fe1c8e9a6ba8add1207088ba9ff049098d4ea4ce045fd5ff7ca914"},
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{file = "dask-2024.7.0.tar.gz", hash = "sha256:0060bae9a58b5b3ce7e0d97040e903b4d3db09ba49222101cfc40f9834a8a6bc"},
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{file = "dask-2024.7.1-py3-none-any.whl", hash = "sha256:dd046840050376c317de90629db5c6197adda820176cf3e2df10c3219d11951f"},
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{file = "dask-2024.7.1.tar.gz", hash = "sha256:dbaef2d50efee841a9d981a218cfeb50392fc9a95e0403b6d680450e4f50d531"},
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]
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[[package]]
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@ -1234,7 +1234,7 @@ files = [
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[[package]]
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name = "prefixmaps"
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version = "0.2.4"
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version = "0.2.5"
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requires_python = "<4.0,>=3.8"
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summary = "A python library for retrieving semantic prefix maps"
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groups = ["default", "dev", "tests"]
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@ -1243,8 +1243,8 @@ dependencies = [
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"pyyaml>=5.3.1",
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]
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files = [
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{file = "prefixmaps-0.2.4-py3-none-any.whl", hash = "sha256:89bf0e6fb08c276f754f9624c42adf2e87c64ee92a3dde1f7eff01f22d85b512"},
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{file = "prefixmaps-0.2.4.tar.gz", hash = "sha256:ae86a1b31189d0516d199756d5808f75f44b39e86546c356cc78c0fe8d2078af"},
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{file = "prefixmaps-0.2.5-py3-none-any.whl", hash = "sha256:68caa04b3a6a8e058aa1c55affe32c62e44b564d031d63f768e267b796a1f3ee"},
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{file = "prefixmaps-0.2.5.tar.gz", hash = "sha256:aaccd2425ade2ea97a502c58be49fe8f3536e3d5e919712ae0358a39fc800799"},
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]
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[[package]]
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@ -1861,40 +1861,40 @@ files = [
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[[package]]
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name = "ruff"
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version = "0.5.2"
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version = "0.5.3"
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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-0.5.2-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:1aa7acad382ada0189dbe76095cf0a36cd0036779607c397ffdea16517f535b1"},
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{file = "ruff-0.5.2-py3-none-macosx_11_0_arm64.whl", hash = "sha256:aec618d5a0cdba5592c60c2dee7d9c865180627f1a4a691257dea14ac1aa264d"},
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{file = "ruff-0.5.2-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a0b62adc5ce81780ff04077e88bac0986363e4a3260ad3ef11ae9c14aa0e67ef"},
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{file = "ruff-0.5.2-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:dc42ebf56ede83cb080a50eba35a06e636775649a1ffd03dc986533f878702a3"},
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{file = "ruff-0.5.2-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:c15c6e9f88c67ffa442681365d11df38afb11059fc44238e71a9d9f1fd51de70"},
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{file = "ruff-0.5.2-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:d3de9a5960f72c335ef00763d861fc5005ef0644cb260ba1b5a115a102157251"},
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{file = "ruff-0.5.2-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:a04f54a9018f75615ae52f36ea1c5515e356e5d5e214b22609ddb546baef7132"},
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{file = "ruff-0.5.2-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:1ed02fb52e3741f0738db5f93e10ae0fb5c71eb33a4f2ba87c9a2fa97462a649"},
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{file = "ruff-0.5.2-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:3cf8fe659f6362530435d97d738eb413e9f090e7e993f88711b0377fbdc99f60"},
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{file = "ruff-0.5.2-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:237a37e673e9f3cbfff0d2243e797c4862a44c93d2f52a52021c1a1b0899f846"},
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{file = "ruff-0.5.2-py3-none-musllinux_1_2_i686.whl", hash = "sha256:2a2949ce7c1cbd8317432ada80fe32156df825b2fd611688814c8557824ef060"},
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{file = "ruff-0.5.2-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:481af57c8e99da92ad168924fd82220266043c8255942a1cb87958b108ac9335"},
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{file = "ruff-0.5.2-py3-none-win32.whl", hash = "sha256:f1aea290c56d913e363066d83d3fc26848814a1fed3d72144ff9c930e8c7c718"},
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{file = "ruff-0.5.2-py3-none-win_amd64.whl", hash = "sha256:8532660b72b5d94d2a0a7a27ae7b9b40053662d00357bb2a6864dd7e38819084"},
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{file = "ruff-0.5.2-py3-none-win_arm64.whl", hash = "sha256:73439805c5cb68f364d826a5c5c4b6c798ded6b7ebaa4011f01ce6c94e4d5583"},
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{file = "ruff-0.5.2.tar.gz", hash = "sha256:2c0df2d2de685433794a14d8d2e240df619b748fbe3367346baa519d8e6f1ca2"},
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{file = "ruff-0.5.3-py3-none-linux_armv6l.whl", hash = "sha256:b12424d9db7347fa63c5ed9af010003338c63c629fb9c9c6adb2aa4f5699729b"},
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{file = "ruff-0.5.3-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:b8d72c5684bbd4ed304a9a955ee2e67f57b35f6193222ade910cca8a805490e3"},
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{file = "ruff-0.5.3-py3-none-macosx_11_0_arm64.whl", hash = "sha256:d2fc2cdb85ccac1e816cc9d5d8cedefd93661bd957756d902543af32a6b04a71"},
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{file = "ruff-0.5.3-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:cf4bc751240b2fab5d19254571bcacb315c7b0b00bf3c912d52226a82bbec073"},
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{file = "ruff-0.5.3-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:bc697ec874fdd7c7ba0a85ec76ab38f8595224868d67f097c5ffc21136e72fcd"},
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{file = "ruff-0.5.3-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:e791d34d3557a3819b3704bc1f087293c821083fa206812842fa363f6018a192"},
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{file = "ruff-0.5.3-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:76bb5a87fd397520b91a83eae8a2f7985236d42dd9459f09eef58e7f5c1d8316"},
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{file = "ruff-0.5.3-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:a8cfc7a26422c78e94f1ec78ec02501bbad2df5834907e75afe474cc6b83a8c1"},
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{file = "ruff-0.5.3-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:96066c4328a49fce2dd40e80f7117987369feec30ab771516cf95f1cc2db923c"},
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{file = "ruff-0.5.3-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:03bfe9ab5bdc0b08470c3b261643ad54ea86edc32b64d1e080892d7953add3ad"},
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{file = "ruff-0.5.3-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:7704582a026fa02cca83efd76671a98ee6eb412c4230209efe5e2a006c06db62"},
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{file = "ruff-0.5.3-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:08058d077e21b856d32ebf483443390e29dc44d927608dc8f092ff6776519da9"},
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{file = "ruff-0.5.3-py3-none-musllinux_1_2_i686.whl", hash = "sha256:77d49484429ed7c7e6e2e75a753f153b7b58f875bdb4158ad85af166a1ec1822"},
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{file = "ruff-0.5.3-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:642cbff6cbfa38d2566d8db086508d6f472edb136cbfcc4ea65997745368c29e"},
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{file = "ruff-0.5.3-py3-none-win32.whl", hash = "sha256:eafc45dd8bdc37a00b28e68cc038daf3ca8c233d73fea276dcd09defb1352841"},
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{file = "ruff-0.5.3-py3-none-win_amd64.whl", hash = "sha256:cbaec2ddf4f78e5e9ecf5456ea0f496991358a1d883862ed0b9e947e2b6aea93"},
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{file = "ruff-0.5.3-py3-none-win_arm64.whl", hash = "sha256:05fbd2cb404775d6cd7f2ff49504e2d20e13ef95fa203bd1ab22413af70d420b"},
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{file = "ruff-0.5.3.tar.gz", hash = "sha256:2a3eb4f1841771fa5b67a56be9c2d16fd3cc88e378bd86aaeaec2f7e6bcdd0a2"},
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]
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[[package]]
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name = "setuptools"
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version = "71.0.1"
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version = "71.0.4"
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requires_python = ">=3.8"
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summary = "Easily download, build, install, upgrade, and uninstall Python packages"
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groups = ["dev", "tests"]
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files = [
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{file = "setuptools-71.0.1-py3-none-any.whl", hash = "sha256:1eb8ef012efae7f6acbc53ec0abde4bc6746c43087fd215ee09e1df48998711f"},
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{file = "setuptools-71.0.1.tar.gz", hash = "sha256:c51d7fd29843aa18dad362d4b4ecd917022131425438251f4e3d766c964dd1ad"},
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{file = "setuptools-71.0.4-py3-none-any.whl", hash = "sha256:ed2feca703be3bdbd94e6bb17365d91c6935c6b2a8d0bb09b66a2c435ba0b1a5"},
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{file = "setuptools-71.0.4.tar.gz", hash = "sha256:48297e5d393a62b7cb2a10b8f76c63a73af933bd809c9e0d0d6352a1a0135dd8"},
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]
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[[package]]
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@ -38,7 +38,7 @@ class ClassAdapter(Adapter):
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Cast from YAML string to desired class
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"""
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if isinstance(value, str):
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from nwb_linkml.io.schema import load_yaml
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from nwb_linkml.io.yaml import load_yaml
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value = load_yaml(value)
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value = cls.TYPE(**value)
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@ -83,6 +83,10 @@ class NWBPydanticGenerator(PydanticGenerator):
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default_factory=lambda: [ArrayRepresentation.NUMPYDANTIC]
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)
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black: bool = True
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inlined: bool = True
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emit_metadata: bool = True,
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gen_classvars: bool = True,
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gen_slots: bool = True,
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def _check_anyof(
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self, s: SlotDefinition, sn: SlotDefinitionName, sv: SchemaView
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@ -6,38 +6,16 @@ from pathlib import Path
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from pprint import pprint
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from typing import Optional
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import yaml
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from linkml_runtime.loaders import yaml_loader
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from nwb_linkml.adapters.namespaces import NamespacesAdapter
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from nwb_linkml.adapters.schema import SchemaAdapter
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from nwb_linkml.io.yaml import load_yaml
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from nwb_linkml.maps.postload import apply_postload
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from nwb_linkml.providers.git import HDMF_COMMON_REPO, NWB_CORE_REPO, NamespaceRepo
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from nwb_schema_language import Dataset, Group, Namespaces
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def load_yaml(path: Path | str) -> dict:
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"""
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Load yaml file from file, applying postload modifications
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"""
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is_file = False
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try:
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a_path = Path(path)
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if a_path.exists():
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is_file = True
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except OSError:
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# long strings can't be made into paths!
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pass
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if not is_file:
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ns_dict = yaml.safe_load(path)
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else:
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with open(path) as file:
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ns_dict = yaml.safe_load(file)
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ns_dict = apply_postload(ns_dict)
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return ns_dict
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def load_namespaces(path: Path | NamespaceRepo) -> Namespaces:
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"""Loads the NWB SCHEMA LANGUAGE namespaces (not the namespacesadapter)"""
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if isinstance(path, NamespaceRepo):
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@ -7,6 +7,10 @@ import re
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from pathlib import Path
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from typing import Literal, List, Union, overload
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import yaml
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from nwb_linkml.maps.postload import apply_postload
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@overload
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def yaml_peek(key: str, path: Union[str, Path], root:bool = True, first:Literal[True]=True) -> str: ...
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@ -61,3 +65,24 @@ def yaml_peek(key: str, path: Union[str, Path], root:bool = True, first:bool=Tru
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raise KeyError(f'Key {key} not found in {path}')
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def load_yaml(path: Path | str) -> dict:
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"""
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Load yaml file from file, applying postload modifications
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"""
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is_file = False
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try:
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a_path = Path(path)
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if a_path.exists():
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is_file = True
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except OSError:
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# long strings can't be made into paths!
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pass
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if not is_file:
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ns_dict = yaml.safe_load(path)
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else:
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with open(path) as file:
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ns_dict = yaml.safe_load(file)
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ns_dict = apply_postload(ns_dict)
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return ns_dict
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@ -12,7 +12,6 @@ from typing import List, Optional, Type
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from pydantic import BaseModel
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from nwb_linkml import io
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from nwb_linkml.io.yaml import yaml_peek
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from nwb_linkml.generators.pydantic import NWBPydanticGenerator
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from nwb_linkml.maps.naming import module_case, version_module_case
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@ -69,9 +68,6 @@ class PydanticProvider(Provider):
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NWB -> LinkML schema to load from.
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out_file (Optional[Path]): Optionally override the output file. If ``None``,
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generate from namespace and version
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version (Optional[str]): The version of the schema to build, if present.
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Works similarly to ``version`` in :class:`.LinkMLProvider`.
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Ignored if ``namespace`` is a Path.
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split (bool): If ``False`` (default), generate a single ``namespace.py`` file,
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otherwise generate a python file for each schema in the namespace
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in addition to a ``namespace.py`` that imports from them
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@ -111,23 +107,10 @@ class PydanticProvider(Provider):
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fn = module_case(fn) + ".py"
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out_file = self.path / name / version / fn
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default_kwargs = {
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"split": split,
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"emit_metadata": True,
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"gen_slots": True,
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"pydantic_version": "2",
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}
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default_kwargs.update(kwargs)
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# if we weren't given explicit versions to load, figure them out from the namespace
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if versions is None:
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versions = self._get_dependent_versions(path)
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if split:
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result = self._build_split(path, versions, default_kwargs, dump, out_file, force)
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result = self._build_split(path, dump, out_file, force, **kwargs)
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else:
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result = self._build_unsplit(path, versions, default_kwargs, dump, out_file, force)
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result = self._build_unsplit(path, dump, out_file, force, **kwargs)
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self.install_pathfinder()
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return result
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@ -135,18 +118,17 @@ class PydanticProvider(Provider):
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def _build_unsplit(
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self,
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path: Path,
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versions: dict,
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default_kwargs: dict,
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dump: bool,
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out_file: Path,
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force: bool,
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**kwargs
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) -> Optional[str]:
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if out_file.exists() and not force:
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with open(out_file) as ofile:
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serialized = ofile.read()
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return serialized
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generator = NWBPydanticGenerator(str(path), versions=versions, **default_kwargs)
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generator = NWBPydanticGenerator(str(path), **kwargs)
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serialized = generator.serialize()
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if dump:
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out_file.parent.mkdir(parents=True, exist_ok=True)
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@ -160,17 +142,16 @@ class PydanticProvider(Provider):
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def _build_split(
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self,
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path: Path,
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versions: dict,
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default_kwargs: dict,
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dump: bool,
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out_file: Path,
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force: bool,
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**kwargs
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) -> List[str]:
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serialized = []
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for schema_file in path.parent.glob("*.yaml"):
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this_out = out_file.parent / (module_case(schema_file.stem) + ".py")
|
||||
serialized.append(
|
||||
self._build_unsplit(schema_file, versions, default_kwargs, dump, this_out, force)
|
||||
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!
|
||||
|
|
@ -204,28 +185,6 @@ class PydanticProvider(Provider):
|
|||
with open(ifile, "w") as ifile_open:
|
||||
ifile_open.write(" ")
|
||||
|
||||
def _get_dependent_versions(self, path: Path) -> dict[str, str]:
|
||||
"""
|
||||
For a given namespace schema file, get the versions of any other schemas it imports
|
||||
|
||||
Namespace imports will be in the importing schema like:
|
||||
|
||||
imports:
|
||||
-../../hdmf_common/v1_8_0/namespace
|
||||
-../../hdmf_experimental/v0_5_0/namespace
|
||||
|
||||
Returns:
|
||||
dict[str,str]: A dictionary mapping a namespace to a version number
|
||||
"""
|
||||
schema = io.schema.load_yaml(path)
|
||||
versions = {}
|
||||
for i in schema["imports"]:
|
||||
if i.startswith(".."):
|
||||
import_path = (Path(path).parent / Path(i + ".yaml")).resolve()
|
||||
imported_schema = io.schema.load_yaml(import_path)
|
||||
versions[imported_schema["name"]] = imported_schema["version"]
|
||||
return versions
|
||||
|
||||
@classmethod
|
||||
def module_name(self, namespace: str, version: str) -> str:
|
||||
"""Module name for the built module
|
||||
|
|
|
|||
|
|
@ -61,10 +61,6 @@ def test_generate_pydantic(tmp_output_dir):
|
|||
|
||||
generator = NWBPydanticGenerator(
|
||||
str(schema_path),
|
||||
pydantic_version="2",
|
||||
emit_metadata=True,
|
||||
gen_classvars=True,
|
||||
gen_slots=True,
|
||||
schema_map=preloaded_schema,
|
||||
)
|
||||
gen_pydantic = generator.serialize()
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@ from pathlib import Path
|
|||
import yaml
|
||||
from yaml import CDumper as Dumper
|
||||
|
||||
from nwb_linkml.io.schema import load_yaml
|
||||
from nwb_linkml.io.yaml import load_yaml
|
||||
|
||||
|
||||
def test_preload_maps():
|
||||
|
|
|
|||
|
|
@ -64,8 +64,7 @@ def test_linkml_build_from_yaml(tmp_output_dir):
|
|||
res = provider.build_from_yaml(ns_file)
|
||||
|
||||
|
||||
@pytest.mark.skip()
|
||||
@pytest.mark.depends(on=["test_linkml_provider"])
|
||||
# @pytest.mark.depends(on=["test_linkml_provider"])
|
||||
@pytest.mark.parametrize(
|
||||
["class_name", "test_fields"],
|
||||
[
|
||||
|
|
|
|||
Loading…
Reference in a new issue