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feat: update observed variable
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6 files changed

+207
-15
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6 files changed

+207
-15
lines changed

‎src/model/observed_variable.py‎

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@@ -21,14 +21,6 @@ class ObservedVariable(Variable):
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id: Mapped[UUID] = mapped_column(ForeignKey("variable_table.id"), primary_key=True, info=dto_field("read-only"))
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title: Mapped[str] = mapped_column(nullable=False)
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variable_reference_id: Mapped[UUID | None] = mapped_column(ForeignKey("vocabulary_table.id", ondelete="SET NULL"))
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variable_reference: Mapped[Optional["Vocabulary"]] = relationship(
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"Vocabulary",
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lazy=None,
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back_populates="variable_reference",
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info=dto_field("read-only"),
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foreign_keys=[variable_reference_id],
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)
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trait_reference_id: Mapped[UUID | None] = mapped_column(ForeignKey("vocabulary_table.id", ondelete="SET NULL"))
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trait_reference: Mapped[Optional["Vocabulary"]] = relationship(
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"Vocabulary",
@@ -42,5 +34,4 @@ class ObservedVariable(Variable):
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@dataclass(kw_only=True)
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class ObservedVariableDataclass(VariableDataclass):
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title: str
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variable_reference_id: UUID | None = field(default=None)
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trait_reference_id: UUID | None = field(default=None)

‎src/model/vocabulary.py‎

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@@ -82,12 +82,6 @@ class Vocabulary(Base):
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organism: Mapped[list["BiologicalMaterial"]] = relationship(
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back_populates="organism", lazy=None, info=dto_field("private")
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)
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variable_reference: Mapped[list["ObservedVariable"]] = relationship(
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lazy=None,
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back_populates="variable_reference",
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info=dto_field("read-only"),
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foreign_keys="[ObservedVariable.variable_reference_id]",
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)
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trait_reference: Mapped[list["ObservedVariable"]] = relationship(
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lazy=None,
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back_populates="trait_reference",

‎tests/conftest.py‎

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@@ -18,6 +18,7 @@
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InstitutionController,
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InvestigationController,
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MethodController,
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ObservedVariableController,
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StaffController,
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StudyController,
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UnitController,
@@ -38,6 +39,7 @@
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"tests.router.facility.fixture",
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"tests.router.experiment.fixture",
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"tests.router.biological_material.fixture",
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"tests.router.observed_variable.fixture",
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]
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@@ -61,6 +63,7 @@ async def test_client() -> AsyncGenerator[AsyncTestClient[Litestar], None]:
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FacilityController,
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ExperimentController,
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BiologicalMaterialController,
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ObservedVariableController,
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],
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dependencies={"transaction": provide_transaction},
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plugins=[SQLAlchemyPlugin(db_config)],

‎tests/router/observed_variable/__init__.py‎

Whitespace-only changes.

‎tests/router/observed_variable/fixture.py‎

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@@ -0,0 +1,123 @@
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from collections.abc import AsyncGenerator
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from dataclasses import dataclass
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from uuid import UUID
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import pytest
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from httpx import Response
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from litestar.testing import AsyncTestClient
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from src.model.observed_variable import ObservedVariable, ObservedVariableDataclass
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from src.model.vocabulary import Vocabulary
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from tests.helpers import delete_fixture, post_fixture, put_fixture
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from tests.router.study.fixture import AllStudyFixtureResponse
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@dataclass
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class ObservedVariableResponse:
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observed_variable_response: Response
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study_response: list[Response]
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@dataclass
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class AllObservedVariableFixtureResponse:
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projected_shoot_area: ObservedVariableResponse
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zn_concentration: ObservedVariableResponse
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@dataclass
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class VariableReferenceResponse:
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anthesis: Response
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@dataclass
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class VariableTraitResponse:
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anthesis: Response
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reproductive_growth_time: Response
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projected_shoot_area: Response
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zn_concentration: Response
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PATH = "observed_variable"
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ANTHESIS_TRAIT = Vocabulary(title="Anthesis time", accession_number="CO_322:0000030")
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REPRODUCTIVE_GROWTH_TIME_TRAIT = Vocabulary(title="Reproductive growth time", accession_number="TO:0000366")
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PROJECTED_SHOOT_AREA_TRAIT = Vocabulary(title="Projected shoot area")
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ZN_CONCENTRATION_TRAIT = Vocabulary(title="Zn concentration", accession_number="CDNO_0200170")
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ANTHESIS_VARIABLE = ObservedVariable(title="Ant_Cmp_Cday", description="Anthesis computed in growing degree days")
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PROJECTED_SHOOT_AREA_VARIABLE = ObservedVariable(title="PSA_img_kpixels")
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ZN_CONCENTRATION_VARIABLE = ObservedVariable(title="Zn_conc")
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async def get_observed_variable_fixture(
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data: ObservedVariable, studies: list[Response], test_client: AsyncTestClient, id: UUID | None = None
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) -> ObservedVariableResponse:
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study_id = [item.json()["id"] for item in studies]
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send_data = ObservedVariableDataclass(study_id=study_id, **data.to_dict())
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if id is None:
57+
send_data.updated_at = None
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response = await post_fixture(PATH, send_data, test_client)
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else:
60+
response = await put_fixture(PATH, send_data, test_client, id)
61+
return ObservedVariableResponse(study_response=studies, observed_variable_response=response)
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@pytest.fixture(scope="function")
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async def setup_observed_variable(
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setup_study: AllStudyFixtureResponse, test_client: AsyncTestClient
67+
) -> AsyncGenerator[AllObservedVariableFixtureResponse, None]:
68+
maize_study = setup_study.maize.study_response
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barley_study = setup_study.barley.study_response
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maize_sowing_density = await get_observed_variable_fixture(
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MAIZE_SOWING_DENSITY, [maize_study, barley_study], test_client
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)
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maize_rooting_medium = await get_observed_variable_fixture(MAIZE_ROOTING_MEDIUM, [maize_study], test_client)
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maize_ph = await get_observed_variable_fixture(MAIZE_PH, [maize_study], test_client)
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barley_sowing_density = await get_observed_variable_fixture(BARLEY_SOWING_DENSITY, [barley_study], test_client)
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barley_rooting_medium = await get_observed_variable_fixture(BARLEY_ROOTING_MEDIUM, [barley_study], test_client)
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barley_ferterlizer = await get_observed_variable_fixture(BARLEY_FERTILIZER, [barley_study], test_client)
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barley_watering_exposure = await get_observed_variable_fixture(
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BARLEY_WATERING_EXPOSURE, [barley_study], test_client
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)
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barley_light_intensity = await get_observed_variable_fixture(BARLEY_LIGHT_INTENSITY, [barley_study], test_client)
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barley_relative_humidity = await get_observed_variable_fixture(
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BARLEY_RELATIVE_HUMIDITY, [barley_study], test_client
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)
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barley_temperature = await get_observed_variable_fixture(BARLEY_TEMPERATURE, [barley_study], test_client)
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yield AllObservedVariableFixtureResponse(
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maize_sowing_density=maize_sowing_density,
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maize_rooting_medium=maize_rooting_medium,
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maize_ph=maize_ph,
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barley_sowing_density=barley_sowing_density,
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barley_rooting_medium=barley_rooting_medium,
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barley_fertilizer=barley_ferterlizer,
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barley_watering_exposure=barley_watering_exposure,
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barley_light_intensity=barley_light_intensity,
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barley_relative_humidity=barley_relative_humidity,
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barley_temperature=barley_temperature,
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study_response=setup_study,
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)
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await delete_fixture(PATH, maize_sowing_density.observed_variable_response.json()["id"], test_client)
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await delete_fixture(PATH, maize_rooting_medium.observed_variable_response.json()["id"], test_client)
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await delete_fixture(PATH, maize_ph.observed_variable_response.json()["id"], test_client)
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await delete_fixture(PATH, barley_sowing_density.observed_variable_response.json()["id"], test_client)
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await delete_fixture(PATH, barley_rooting_medium.observed_variable_response.json()["id"], test_client)
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await delete_fixture(PATH, barley_ferterlizer.observed_variable_response.json()["id"], test_client)
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await delete_fixture(PATH, barley_watering_exposure.observed_variable_response.json()["id"], test_client)
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await delete_fixture(PATH, barley_light_intensity.observed_variable_response.json()["id"], test_client)
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await delete_fixture(PATH, barley_relative_humidity.observed_variable_response.json()["id"], test_client)
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await delete_fixture(PATH, barley_temperature.observed_variable_response.json()["id"], test_client)
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@pytest.fixture(scope="function")
113+
async def update_observed_variable(
114+
setup_observed_variable: AllObservedVariableFixtureResponse, test_client: AsyncTestClient
115+
) -> AsyncGenerator[AllObservedVariableFixtureResponse, None]:
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all_responses = setup_observed_variable
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maize_study = all_responses.study_response.maize.study_response
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maize_sowing_density = all_responses.maize_sowing_density
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maize_sowing_density_response = await get_observed_variable_fixture(
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MAIZE_SOWING_DENSITY, [maize_study], test_client, maize_sowing_density.observed_variable_response.json()["id"]
121+
)
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all_responses.maize_sowing_density = maize_sowing_density_response
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yield all_responses

‎tests/router/observed_variable/test_observed_variable.py‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,81 @@
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from dataclasses import dataclass
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from uuid import UUID
3+
4+
from httpx import Response
5+
from litestar.testing import AsyncTestClient
6+
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from src.model.environment import Environment, EnvironmentDataclass
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from tests.helpers import validate_post, validate_put
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from tests.router.environment.fixture import (
10+
BARLEY_FERTILIZER,
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BARLEY_LIGHT_INTENSITY,
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BARLEY_RELATIVE_HUMIDITY,
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BARLEY_ROOTING_MEDIUM,
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BARLEY_SOWING_DENSITY,
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BARLEY_TEMPERATURE,
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BARLEY_WATERING_EXPOSURE,
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MAIZE_PH,
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MAIZE_ROOTING_MEDIUM,
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MAIZE_SOWING_DENSITY,
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PATH,
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AllEnvironmentFixtureResponse,
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EnvironmentResponse,
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)
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@dataclass
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class EnvironmentFixture:
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id: UUID
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response: Response
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data: EnvironmentDataclass
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study_id: list[UUID]
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def get_environment_fixture(response: EnvironmentResponse, data: Environment) -> EnvironmentFixture:
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environment_response = response.environment_response
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study_id = [item.json()["id"] for item in response.study_response]
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fixture = EnvironmentDataclass(study_id=study_id, **data.to_dict())
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return EnvironmentFixture(
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id=environment_response.json()["id"], response=environment_response, data=fixture, study_id=study_id
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)
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async def test_all_environments_created(
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setup_environment: AllEnvironmentFixtureResponse, test_client: AsyncTestClient
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) -> None:
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fixture = get_environment_fixture(setup_environment.maize_sowing_density, MAIZE_SOWING_DENSITY)
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await validate_post(PATH, fixture.data, test_client, fixture.response)
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fixture = get_environment_fixture(setup_environment.maize_rooting_medium, MAIZE_ROOTING_MEDIUM)
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await validate_post(PATH, fixture.data, test_client, fixture.response)
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fixture = get_environment_fixture(setup_environment.maize_ph, MAIZE_PH)
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await validate_post(PATH, fixture.data, test_client, fixture.response)
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fixture = get_environment_fixture(setup_environment.barley_fertilizer, BARLEY_FERTILIZER)
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await validate_post(PATH, fixture.data, test_client, fixture.response)
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fixture = get_environment_fixture(setup_environment.barley_light_intensity, BARLEY_LIGHT_INTENSITY)
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await validate_post(PATH, fixture.data, test_client, fixture.response)
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fixture = get_environment_fixture(setup_environment.barley_temperature, BARLEY_TEMPERATURE)
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await validate_post(PATH, fixture.data, test_client, fixture.response)
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fixture = get_environment_fixture(setup_environment.barley_watering_exposure, BARLEY_WATERING_EXPOSURE)
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await validate_post(PATH, fixture.data, test_client, fixture.response)
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fixture = get_environment_fixture(setup_environment.barley_sowing_density, BARLEY_SOWING_DENSITY)
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await validate_post(PATH, fixture.data, test_client, fixture.response)
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fixture = get_environment_fixture(setup_environment.barley_rooting_medium, BARLEY_ROOTING_MEDIUM)
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await validate_post(PATH, fixture.data, test_client, fixture.response)
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fixture = get_environment_fixture(setup_environment.barley_relative_humidity, BARLEY_RELATIVE_HUMIDITY)
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await validate_post(PATH, fixture.data, test_client, fixture.response)
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async def test_environment_file_updated(
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update_environment: AllEnvironmentFixtureResponse, test_client: AsyncTestClient
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) -> None:
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fixture = get_environment_fixture(update_environment.maize_sowing_density, MAIZE_SOWING_DENSITY)
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await validate_put(PATH, fixture.data, test_client, fixture.response)

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