Add computed fields for requires_zarr and requires_plate

Author: TorecLuik

.github/workflows/test.yml

@@ -0,0 +1,15 @@
+name: Tests
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  test:
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/setup-pixi@v0.8.0
+        with:
+          pixi-version: latest
+      - run: pixi run test

pixi.lock

@@ -17,6 +17,12 @@ dependencies = [
     "pyyaml>=6.0.3"
 ]
 
+[project.optional-dependencies]
+test = ["pytest>=8.0.0"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
 [project.scripts]
 biomero-schema = "biomero_schema.cli:cli"
 
@@ -32,10 +38,12 @@ platforms = ["osx-64", "win-64"]
 
 [tool.pixi.pypi-dependencies]
 biomero-schema = { path = ".", editable = true }
+pytest = ">=8.0.0"
 
 [tool.pixi.tasks]
 json-schema = { cmd = ["biomero-schema", "schema"], description = "Print the json schema generated from pydantic model" }
 test-parse = { cmd = ["biomero-schema", "parse", "tests/example_workflow.json"], description = "Parse and run pydantic validation on test file" }
 test-pparse = { cmd = ["biomero-schema", "parse", "tests/example_workflow.json", "--pretty"], description = "Parse, validate, and show detailed info on test file" }
 test-jparse = { cmd = ["biomero-schema", "parse", "tests/example_workflow.json", "--json"], description = "Parse, validate, and show test file json contents" }
 test-validate = { cmd = ["biomero-schema", "validate", "tests/example_workflow.json"], description = "Run json schema validation on test file" }
+test = { cmd = ["pytest", "-v"], description = "Run all tests" }

pyproject.toml

@@ -1,6 +1,8 @@
 """Pydantic models for the workflow schema."""
 from typing import List, Optional, Union, Literal
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, computed_field, ConfigDict
+
+_ZARR_FORMATS = frozenset({'zarr', 'omezarr', 'ome.zarr', 'ome-zarr'})
 
 
 class Author(BaseModel):
@@ -133,6 +135,37 @@ class WorkflowSchema(BaseModel):
     outputs: List[OutputParameter] = Field([], description="List of output parameter descriptors")
     command_line: str = Field(..., alias="command-line", description="Command line template")
 
-    class Config:
-        populate_by_name = True
-        validate_by_name = True
+    @computed_field(alias="requires-zarr")
+    @property
+    def requires_zarr(self) -> bool:
+        """True when any image input uses a ZARR format or has plate subtype."""
+        for inp in self.inputs:
+            if inp.type != 'image':
+                continue
+            fmt = inp.format or []
+            if isinstance(fmt, str):
+                fmt = [fmt]
+            if any(f in _ZARR_FORMATS for f in fmt):
+                return True
+            sub = inp.sub_type or []
+            if isinstance(sub, str):
+                sub = [sub]
+            if 'plate' in sub:
+                return True
+        return False
+
+    @computed_field(alias="requires-plate")
+    @property
+    def requires_plate(self) -> bool:
+        """True when any image input has plate subtype."""
+        for inp in self.inputs:
+            if inp.type != 'image':
+                continue
+            sub = inp.sub_type or []
+            if isinstance(sub, str):
+                sub = [sub]
+            if 'plate' in sub:
+                return True
+        return False
+
+    model_config = ConfigDict(populate_by_name=True, validate_by_alias=True)

src/biomero_schema/models.py

@@ -0,0 +1,160 @@
+"""Tests for WorkflowSchema.requires_zarr and requires_plate computed fields."""
+import json
+import pytest
+from pathlib import Path
+from biomero_schema.models import WorkflowSchema
+
+
+TESTS_DIR = Path(__file__).parent
+
+
+def load_example() -> dict:
+    return json.loads((TESTS_DIR / "example_workflow.json").read_text())
+
+
+def make_schema(image_inputs: list) -> WorkflowSchema:
+    """Build a minimal WorkflowSchema with the given image input list."""
+    base = load_example()
+    base["inputs"] = image_inputs
+    return WorkflowSchema.model_validate(base)
+
+
+def image_input(fmt=None, subtype=None) -> dict:
+    inp = {
+        "id": "input_image",
+        "type": "image",
+        "name": "Input",
+        "value-key": "[INPUT_IMAGE]",
+        "command-line-flag": "--input",
+    }
+    if fmt is not None:
+        inp["format"] = fmt
+    if subtype is not None:
+        inp["sub-type"] = subtype
+    return inp
+
+
+# ---------------------------------------------------------------------------
+# requires_zarr
+# ---------------------------------------------------------------------------
+
+class TestRequiresZarr:
+    def test_false_for_tiff(self):
+        schema = make_schema([image_input(fmt="tif")])
+        assert schema.requires_zarr is False
+
+    def test_false_for_ometiff(self):
+        schema = make_schema([image_input(fmt="ometiff")])
+        assert schema.requires_zarr is False
+
+    def test_false_for_png(self):
+        schema = make_schema([image_input(fmt="png")])
+        assert schema.requires_zarr is False
+
+    def test_false_for_no_image_inputs(self):
+        base = load_example()
+        base["inputs"] = [
+            {"id": "x", "type": "float", "value-key": "[X]", "command-line-flag": "--x"}
+        ]
+        schema = WorkflowSchema.model_validate(base)
+        assert schema.requires_zarr is False
+
+    def test_true_for_zarr(self):
+        schema = make_schema([image_input(fmt="zarr")])
+        assert schema.requires_zarr is True
+
+    def test_true_for_omezarr(self):
+        schema = make_schema([image_input(fmt="omezarr")])
+        assert schema.requires_zarr is True
+
+    def test_true_for_ome_zarr_dot(self):
+        schema = make_schema([image_input(fmt="ome.zarr")])
+        assert schema.requires_zarr is True
+
+    def test_true_for_ome_zarr_dash(self):
+        schema = make_schema([image_input(fmt="ome-zarr")])
+        assert schema.requires_zarr is True
+
+    def test_true_for_format_list_containing_zarr(self):
+        schema = make_schema([image_input(fmt=["tif", "zarr"])])
+        assert schema.requires_zarr is True
+
+    def test_true_when_plate_subtype(self):
+        """Plate implies ZARR."""
+        schema = make_schema([image_input(fmt="omezarr", subtype="plate")])
+        assert schema.requires_zarr is True
+
+    def test_false_for_zarr_format_on_non_image_type(self):
+        """format field on a non-image input should not trigger zarr."""
+        base = load_example()
+        base["inputs"] = [
+            {"id": "x", "type": "file", "format": "zarr", "value-key": "[X]", "command-line-flag": "--x"}
+        ]
+        schema = WorkflowSchema.model_validate(base)
+        assert schema.requires_zarr is False
+
+
+# ---------------------------------------------------------------------------
+# requires_plate
+# ---------------------------------------------------------------------------
+
+class TestRequiresPlate:
+    def test_false_by_default(self):
+        schema = make_schema([image_input(fmt="tif", subtype="grayscale")])
+        assert schema.requires_plate is False
+
+    def test_false_for_no_subtype(self):
+        schema = make_schema([image_input(fmt="zarr")])
+        assert schema.requires_plate is False
+
+    def test_true_for_plate_subtype(self):
+        schema = make_schema([image_input(fmt="omezarr", subtype="plate")])
+        assert schema.requires_plate is True
+
+    def test_true_for_plate_in_subtype_list(self):
+        schema = make_schema([image_input(fmt="omezarr", subtype=["plate"])])
+        assert schema.requires_plate is True
+
+    def test_false_for_other_subtype(self):
+        schema = make_schema([image_input(fmt="tif", subtype="grayscale")])
+        assert schema.requires_plate is False
+
+    def test_plate_also_sets_zarr(self):
+        """Plate always implies requires_zarr too."""
+        schema = make_schema([image_input(fmt="omezarr", subtype="plate")])
+        assert schema.requires_zarr is True
+        assert schema.requires_plate is True
+
+
+# ---------------------------------------------------------------------------
+# Serialisation — flags appear in model_dump(by_alias=True)
+# ---------------------------------------------------------------------------
+
+class TestSerialisedOutput:
+    def test_keys_present_in_dump(self):
+        schema = make_schema([image_input(fmt="zarr", subtype="plate")])
+        data = schema.model_dump(by_alias=True)
+        assert "requires-zarr" in data
+        assert "requires-plate" in data
+
+    def test_values_correct_in_dump(self):
+        schema = make_schema([image_input(fmt="zarr", subtype="plate")])
+        data = schema.model_dump(by_alias=True)
+        assert data["requires-zarr"] is True
+        assert data["requires-plate"] is True
+
+    def test_false_values_in_dump(self):
+        schema = make_schema([image_input(fmt="tif")])
+        data = schema.model_dump(by_alias=True)
+        assert data["requires-zarr"] is False
+        assert data["requires-plate"] is False
+
+
+# ---------------------------------------------------------------------------
+# Round-trip through example_workflow.json (tiff input → both False)
+# ---------------------------------------------------------------------------
+
+def test_example_workflow_no_zarr():
+    schema = WorkflowSchema.model_validate(load_example())
+    assert schema.requires_zarr is False
+    assert schema.requires_plate is False