Merge pull request #61 from BioImageTools/de-dupe-example-tests

De-duplicate example JSON testing

tests/v04/conftest.py

@@ -1,5 +1,6 @@
 from collections.abc import Sequence
-from typing import Any, Literal
+from pathlib import Path
+from typing import Any, Literal, TypeVar
 
 import numcodecs
 import numpy as np
@@ -8,13 +9,21 @@
 from pydantic_zarr.v2 import ArraySpec, GroupSpec
 from zarr.util import guess_chunks
 
+from ome_zarr_models.base import Base
 from ome_zarr_models.v04.axes import Axis
 from ome_zarr_models.v04.image import Image, ImageAttrs
 from ome_zarr_models.v04.multiscales import (
     Dataset,
     Multiscale,
 )
 
+T = TypeVar("T", bound=Base)
+
+
+def read_in_json(*, json_fname: str, model_cls: type[T]) -> T:
+    with open(Path(__file__).parent / "data" / json_fname) as f:
+        return model_cls.model_validate_json(f.read())
+
 
 def normalize_chunks(
     chunks: Any,

tests/v04/data/well_example_1.json

@@ -1,23 +1,21 @@
 {
-  "well": {
-    "images": [
-      {
-        "acquisition": 1,
-        "path": "0"
-      },
-      {
-        "acquisition": 1,
-        "path": "1"
-      },
-      {
-        "acquisition": 2,
-        "path": "2"
-      },
-      {
-        "acquisition": 2,
-        "path": "3"
-      }
-    ],
-    "version": "0.4"
-  }
+  "images": [
+    {
+      "acquisition": 1,
+      "path": "0"
+    },
+    {
+      "acquisition": 1,
+      "path": "1"
+    },
+    {
+      "acquisition": 2,
+      "path": "2"
+    },
+    {
+      "acquisition": 2,
+      "path": "3"
+    }
+  ],
+  "version": "0.4"
 }

tests/v04/data/well_example_2.json

@@ -1,15 +1,13 @@
 {
-  "well": {
-    "images": [
-      {
-        "acquisition": 0,
-        "path": "0"
-      },
-      {
-        "acquisition": 3,
-        "path": "1"
-      }
-    ],
-    "version": "0.4"
-  }
+  "images": [
+    {
+      "acquisition": 0,
+      "path": "0"
+    },
+    {
+      "acquisition": 3,
+      "path": "1"
+    }
+  ],
+  "version": "0.4"
 }

tests/v04/test_bioformats2raw.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+from tests.v04.conftest import read_in_json
 
 from ome_zarr_models.v04.bioformats2raw import BioFormats2RawAttrs
 from ome_zarr_models.v04.plate import (
@@ -10,9 +10,10 @@
 )
 
 
-def test_bioformats2raw_exmaple_json():
-    with open(Path(__file__).parent / "data" / "bioformats2raw_example.json") as f:
-        model = BioFormats2RawAttrs.model_validate_json(f.read())
+def test_bioformats2raw_exmaple_json() -> None:
+    model = read_in_json(
+        json_fname="bioformats2raw_example.json", model_cls=BioFormats2RawAttrs
+    )
 
     assert model == BioFormats2RawAttrs(
         bioformats2raw_layout=3,

tests/v04/test_omero.py

@@ -1,14 +1,12 @@
-import json
-from pathlib import Path
+from tests.v04.conftest import read_in_json
 
 from ome_zarr_models.v04.omero import Channel, Omero, Window
 
 
-def test_load_example_json():
-    with open(Path(__file__).parent / "data" / "omero_example.json") as f:
-        data = json.load(f)
+def test_load_example_json() -> None:
+    model = read_in_json(json_fname="omero_example.json", model_cls=Omero)
 
-    assert Omero(**data) == Omero(
+    assert model == Omero(
         channels=[
             Channel(
                 color="0000FF",

tests/v04/test_well.py

@@ -3,6 +3,7 @@
 
 import pytest
 from pydantic import BaseModel
+from tests.v04.conftest import read_in_json
 
 from ome_zarr_models.v04.well import Well, WellImage
 
@@ -15,7 +16,7 @@ def check_against_json(json_path: Path, expected_model: BaseModel) -> None:
 
 
 @pytest.mark.parametrize(
-    ("filename", "model"),
+    ("filename", "model_expected"),
     [
         (
             "well_example_1.json",
@@ -41,11 +42,9 @@ def check_against_json(json_path: Path, expected_model: BaseModel) -> None:
         ),
     ],
 )
-def test_examples_valid(filename: str, model: Well):
-    with open(Path(__file__).parent / "data" / filename) as f:
-        data = json.load(f)
-
-    assert Well(**data["well"]) == model
+def test_examples_valid(filename: str, model_expected: Well) -> None:
+    model = read_in_json(json_fname=filename, model_cls=Well)
+    assert model == model_expected
 
 
 def test_get_paths():