Adds checks for undefined fields in layers and contrasts (#160)

* Adds checks for undefined fields in layers and contrasts

* Addresses review comments

Author: DrPaulSharp

RATapi/inputs.py

@@ -151,11 +151,23 @@ def make_problem(project: RATapi.Project) -> ProblemDefinition:
         The problem input used in the compiled RAT code.
 
     """
-    hydrate_id = {"bulk in": 1, "bulk out": 2}
     prior_id = {"uniform": 1, "gaussian": 2, "jeffreys": 3}
 
-    # Ensure backgrounds and resolutions have a source defined
+    # Ensure all contrast fields are properly defined
     for contrast in project.contrasts:
+        contrast_fields = ["data", "background", "bulk_in", "bulk_out", "scalefactor", "resolution"]
+
+        if project.calculation == Calculations.Domains:
+            contrast_fields.append("domain_ratio")
+
+        for field in contrast_fields:
+            if getattr(contrast, field) == "":
+                raise ValueError(
+                    f'In the input project, the "{field}" field of contrast "{contrast.name}" does not have a '
+                    f"value defined. A value must be supplied before running the project."
+                )
+
+        # Ensure backgrounds and resolutions have a source defined
         background = project.backgrounds[contrast.background]
         resolution = project.resolutions[contrast.resolution]
         if background.source == "":
@@ -191,22 +203,7 @@ def make_problem(project: RATapi.Project) -> ProblemDefinition:
         contrast_custom_files = [project.custom_files.index(contrast.model[0], True) for contrast in project.contrasts]
 
     # Get details of defined layers
-    layer_details = []
-    for layer in project.layers:
-        if project.absorption:
-            layer_params = [
-                project.parameters.index(getattr(layer, attribute), True)
-                for attribute in list(RATapi.models.AbsorptionLayer.model_fields.keys())[1:-2]
-            ]
-        else:
-            layer_params = [
-                project.parameters.index(getattr(layer, attribute), True)
-                for attribute in list(RATapi.models.Layer.model_fields.keys())[1:-2]
-            ]
-        layer_params.append(project.parameters.index(layer.hydration, True) if layer.hydration else float("NaN"))
-        layer_params.append(hydrate_id[layer.hydrate_with])
-
-        layer_details.append(layer_params)
+    layer_details = get_layer_details(project)
 
     contrast_background_params = []
     contrast_background_types = []
@@ -387,6 +384,35 @@ def make_problem(project: RATapi.Project) -> ProblemDefinition:
     return problem
 
 
+def get_layer_details(project: RATapi.Project) -> list[int]:
+    """Get parameter indices for all layers defined in the project."""
+    hydrate_id = {"bulk in": 1, "bulk out": 2}
+    layer_details = []
+
+    # Get the thickness, SLD, roughness fields from the appropriate model
+    if project.absorption:
+        layer_fields = list(RATapi.models.AbsorptionLayer.model_fields.keys())[1:-2]
+    else:
+        layer_fields = list(RATapi.models.Layer.model_fields.keys())[1:-2]
+
+    for layer in project.layers:
+        for field in layer_fields:
+            if getattr(layer, field) == "":
+                raise ValueError(
+                    f'In the input project, the "{field}" field of layer {layer.name} does not have a value '
+                    f"defined. A value must be supplied before running the project."
+                )
+
+        layer_params = [project.parameters.index(getattr(layer, attribute), True) for attribute in list(layer_fields)]
+
+        layer_params.append(project.parameters.index(layer.hydration, True) if layer.hydration else float("NaN"))
+        layer_params.append(hydrate_id[layer.hydrate_with])
+
+        layer_details.append(layer_params)
+
+    return layer_details
+
+
 def make_resample(project: RATapi.Project) -> list[int]:
     """Construct the "resample" field of the problem input required for the compiled RAT code.
 

tests/test_inputs.py

@@ -572,6 +572,69 @@ def test_background_params_value_indices(self, test_problem, bad_value, request)
             check_indices(test_problem)
 
 
+@pytest.mark.parametrize("test_project", ["standard_layers_project", "custom_xy_project", "domains_project"])
+@pytest.mark.parametrize("field", ["data", "background", "bulk_in", "bulk_out", "scalefactor", "resolution"])
+def test_undefined_contrast_fields(test_project, field, request):
+    """If a field in a contrast is empty, we should raise an error."""
+    test_project = request.getfixturevalue(test_project)
+    setattr(test_project.contrasts[0], field, "")
+
+    with pytest.raises(
+        ValueError,
+        match=f'In the input project, the "{field}" field of contrast '
+        f'"{test_project.contrasts[0].name}" does not have a value defined. '
+        f"A value must be supplied before running the project.",
+    ):
+        make_problem(test_project)
+
+
+@pytest.mark.parametrize("test_project", ["standard_layers_project", "custom_xy_project", "domains_project"])
+def test_undefined_background(test_project, request):
+    """If the source field of a background defined in a contrast is empty, we should raise an error."""
+    test_project = request.getfixturevalue(test_project)
+    background = test_project.backgrounds[test_project.contrasts[0].background]
+    background.source = ""
+
+    with pytest.raises(
+        ValueError,
+        match=f"All backgrounds must have a source defined. For a {background.type} type "
+        f"background, the source must be defined in "
+        f'"{RATapi.project.values_defined_in[f"backgrounds.{background.type}.source"]}"',
+    ):
+        make_problem(test_project)
+
+
+@pytest.mark.parametrize("test_project", ["standard_layers_project", "custom_xy_project", "domains_project"])
+def test_undefined_resolution(test_project, request):
+    """If the source field of a resolution defined in a contrast is empty, we should raise an error."""
+    test_project = request.getfixturevalue(test_project)
+    resolution = test_project.resolutions[test_project.contrasts[0].resolution]
+    resolution.source = ""
+
+    with pytest.raises(
+        ValueError,
+        match=f"Constant resolutions must have a source defined. The source must be defined in "
+        f'"{RATapi.project.values_defined_in[f"resolutions.{resolution.type}.source"]}"',
+    ):
+        make_problem(test_project)
+
+
+@pytest.mark.parametrize("test_project", ["standard_layers_project", "domains_project"])
+@pytest.mark.parametrize("field", ["thickness", "SLD", "roughness"])
+def test_undefined_layers(test_project, field, request):
+    """If the thickness, SLD, or roughness fields of a layer defined in the project are empty, we should raise an
+    error."""
+    test_project = request.getfixturevalue(test_project)
+    setattr(test_project.layers[0], field, "")
+
+    with pytest.raises(
+        ValueError,
+        match=f'In the input project, the "{field}" field of layer {test_project.layers[0].name} '
+        f"does not have a value defined. A value must be supplied before running the project.",
+    ):
+        make_problem(test_project)
+
+
 def test_append_data_background():
     """Test that background data is correctly added to contrast data."""
     data = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])