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Merge pull request #446 from vladistan/convert-test-loaders-pydantic-to-pytest
Convert test_loaders_pydantic.py to pytest format
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‎CONTRIBUTING.md‎

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@@ -72,7 +72,7 @@ are correct and expected given the context of the PR.
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2. Install all the dependencies from your project, which are typically specified in a `uv.lock` file.
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```
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uv sync --all-extras --dev
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uv sync --all-extras --dev
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```
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3. Run any python scripts or CLI commands by prefixing with `uv run`.

‎tests/test_loaders_dumpers/input/book_series_lotr_json.yaml‎

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id: S001
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name: Lord of the Rings
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genres:
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- fantasy
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creator:
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name: JRR Tolkien
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from_country: England
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books:
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- id: S001.1
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name: Fellowship of the Ring
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summary: Hobbits
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price: 5.99
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- id: S001.2
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name: The Two Towers
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summary: More hobbits
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price: 5.99
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- id: S001.3
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name: Return of the King
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summary: Yet more hobbits
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price: 6.99

‎tests/test_loaders_dumpers/input/book_series_lotr_yaml.yaml‎

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id: S001
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name: Lord of the Rings
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genres:
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- fantasy
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creator:
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name: JRR Tolkien
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from_country: England
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books:
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- id: S001.1
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name: Fellowship of the Ring
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summary: Hobbits
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price: 5.99
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- id: S001.2
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name: The Two Towers
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summary: More hobbits
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price: 5.99
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- id: S001.3
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name: Return of the King
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summary: Yet more hobbits
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price: 6.99

‎tests/test_loaders_dumpers/input/kitchen_sink_normalized_inst_01_json.yaml‎

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persons:
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- id: P:001
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name: fred bloggs
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age_in_years: 33
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- id: P:002
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name: joe schmoe
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has_employment_history:
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- started_at_time: 2019-01-01
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is_current: true
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employed_at: ROR:1
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has_familial_relationships:
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- related_to: P:001
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type: SIBLING_OF
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has_medical_history:
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- started_at_time: 2019-01-01
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in_location: GEO:1234
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diagnosis:
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id: CODE:D0001
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name: headache
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in_code_system: DiseaseCodes
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procedure:
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id: CODE:P0001
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name: trepanation
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in_code_system: ProcedureCodes
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addresses:
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- street: 1 foo street
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city: foo city
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companies:
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- id: ROR:1
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name: foo
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activities:
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- id: A:1
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started_at_time: 2019-01-01
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was_associated_with: Agent:987
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code_systems:
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DiseaseCodes:
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id: DiseaseCodes
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name: disease codes
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ProcedureCodes:
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id: ProcedureCodes
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name: disease codes

‎tests/test_loaders_dumpers/input/kitchen_sink_normalized_inst_01_yaml.yaml‎

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persons:
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- id: P:001
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name: fred bloggs
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age_in_years: 33
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- id: P:002
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name: joe schmoe
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has_employment_history:
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- started_at_time: 2019-01-01
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is_current: true
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employed_at: ROR:1
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has_familial_relationships:
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- related_to: P:001
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type: SIBLING_OF
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has_medical_history:
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- started_at_time: 2019-01-01
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in_location: GEO:1234
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diagnosis:
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id: CODE:D0001
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name: headache
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in_code_system: DiseaseCodes
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procedure:
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id: CODE:P0001
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name: trepanation
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in_code_system: ProcedureCodes
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addresses:
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- street: 1 foo street
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city: foo city
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companies:
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- id: ROR:1
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name: foo
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activities:
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- id: A:1
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started_at_time: 2019-01-01
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was_associated_with: Agent:987
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code_systems:
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DiseaseCodes:
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id: DiseaseCodes
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name: disease codes
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ProcedureCodes:
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id: ProcedureCodes
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name: disease codes

‎tests/test_loaders_dumpers/test_loaders_pydantic.py‎

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import unittest
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from pathlib import Path
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import pytest
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from hbreader import FileInfo
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from pydantic import BaseModel
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from linkml_runtime.dumpers import yaml_dumper
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from linkml_runtime.loaders import json_loader, yaml_loader
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from tests.test_loaders_dumpers.environment import env
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from tests.test_loaders_dumpers.loaderdumpertestcase import LoaderDumperTestCase
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from tests.test_loaders_dumpers.models.books_normalized_pydantic import BookSeries
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from tests.test_loaders_dumpers.models.kitchen_sink_pydantic import Dataset
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class PydanticLoadersUnitTest(LoaderDumperTestCase):
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env = env
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def test_yaml_loader_single(self):
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"""Load obo_sample.yaml, emit obo_sample_yaml.yaml and compare to obo_sample_output.yaml"""
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self.loader_test("book_series_lotr.yaml", BookSeries, yaml_loader)
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def test_json_loader(self):
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"""Load obo_sample.json, emit obo_sample_json.yaml and check the results"""
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self.loader_test("book_series_lotr.json", BookSeries, json_loader)
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def test_yaml_loader_kitchen_sink(self):
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self.loader_test("kitchen_sink_normalized_inst_01.yaml", Dataset, yaml_loader)
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def test_json_loader_kitchen_sink(self):
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self.loader_test("kitchen_sink_normalized_inst_01.json", Dataset, json_loader)
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if __name__ == "__main__":
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unittest.main()
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@pytest.mark.parametrize(
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"filename,model,loader",
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[
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("book_series_lotr.yaml", BookSeries, yaml_loader),
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("book_series_lotr.json", BookSeries, json_loader),
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("kitchen_sink_normalized_inst_01.yaml", Dataset, yaml_loader),
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("kitchen_sink_normalized_inst_01.json", Dataset, json_loader),
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],
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)
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def test_loader_basemodel(filename, model, loader):
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name = Path(filename).stem
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type = Path(filename).suffix.lstrip(".")
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expected_yaml_file = env.input_path(f"{name}_{type}.yaml")
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metadata = FileInfo()
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python_obj: BaseModel = loader.load(filename, model, metadata=metadata, base_dir=env.indir)
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# Load expected output
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with open(expected_yaml_file) as expf:
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expected = expf.read()
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got = yaml_dumper.dumps(python_obj)
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expected_trimmed = expected.replace("\r\n", "\n").strip()
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got_trimmed = got.replace("\r\n", "\n").strip()
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assert expected_trimmed == got_trimmed

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