Validate modelId in measurements (PEtab-dev#426)

Check that we have a valid model ID. Related to PEtab-dev#392.

Author: dweindl

petab/v1/models/sbml_model.py

@@ -130,16 +130,18 @@ def from_string(sbml_string, model_id: str = None) -> SbmlModel:
         )
 
     @staticmethod
-    def from_antimony(ant_model: str | Path) -> SbmlModel:
+    def from_antimony(ant_model: str | Path, **kwargs) -> SbmlModel:
         """Create SBML model from an Antimony model.
 
         Requires the `antimony` package (https://github.com/sys-bio/antimony).
 
         :param ant_model: Antimony model as string or path to file.
             Strings are interpreted as Antimony model strings.
+        :param kwargs: Additional keyword arguments passed to
+            :meth:`SbmlModel.from_string`.
         """
         sbml_str = antimony2sbml(ant_model)
-        return SbmlModel.from_string(sbml_str)
+        return SbmlModel.from_string(sbml_str, **kwargs)
 
     def to_antimony(self) -> str:
         """Convert the SBML model to an Antimony string."""

petab/v2/lint.py

@@ -27,6 +27,10 @@
     "ValidationTask",
     "CheckModel",
     "CheckProblemConfig",
+    "CheckMeasuredObservablesDefined",
+    "CheckOverridesMatchPlaceholders",
+    "CheckMeasuredExperimentsDefined",
+    "CheckMeasurementModelId",
     "CheckPosLogMeasurements",
     "CheckValidConditionTargets",
     "CheckUniquePrimaryKeys",
@@ -769,8 +773,39 @@ def run(self, problem: Problem) -> ValidationIssue | None:
         return None
 
 
-# TODO: check that Measurements model IDs match the available ones
-#  https://github.com/PEtab-dev/libpetab-python/issues/392
+class CheckMeasurementModelId(ValidationTask):
+    """Validate model IDs of measurements."""
+
+    def run(self, problem: Problem) -> ValidationIssue | None:
+        messages = []
+        available_models = {m.model_id for m in problem.models}
+
+        for measurement in problem.measurements:
+            if not measurement.model_id:
+                if len(available_models) < 2:
+                    # If there is only one model, it is not required to specify
+                    # the model ID in the measurement table.
+                    continue
+
+                messages.append(
+                    f"Measurement `{measurement}' does not have a model ID, "
+                    "but there are multiple models available. "
+                    "Please specify the model ID in the measurement table."
+                )
+                continue
+
+            if measurement.model_id not in available_models:
+                messages.append(
+                    f"Measurement `{measurement}' has model ID "
+                    f"`{measurement.model_id}' which does not match "
+                    "any of the available models: "
+                    f"{available_models}."
+                )
+
+        if messages:
+            return ValidationError("\n".join(messages))
+
+        return None
 
 
 def get_valid_parameters_for_parameter_table(
@@ -1011,6 +1046,7 @@ def get_placeholders(
     CheckProblemConfig(),
     CheckModel(),
     CheckUniquePrimaryKeys(),
+    CheckMeasurementModelId(),
     CheckMeasuredObservablesDefined(),
     CheckPosLogMeasurements(),
     CheckOverridesMatchPlaceholders(),

tests/v2/test_lint.py

@@ -37,3 +37,30 @@ def test_check_incompatible_targets():
     problem["e1"].periods[0].condition_ids.append("c2")
     assert (error := check.run(problem)) is not None
     assert "overlapping targets {'p1'}" in error.message
+
+
+def test_invalid_model_id_in_measurements():
+    """Test that measurements with an invalid model ID are caught."""
+    problem = Problem()
+    problem.models.append(SbmlModel.from_antimony("p1 = 1", model_id="model1"))
+    problem.add_observable("obs1", "A")
+    problem.add_measurement("obs1", experiment_id="e1", time=0, measurement=1)
+
+    check = CheckMeasurementModelId()
+
+    # Single model -> model ID is optional
+    assert (error := check.run(problem)) is None, error
+
+    # Two models -> model ID must be set
+    problem.models.append(SbmlModel.from_antimony("p2 = 2", model_id="model2"))
+    assert (error := check.run(problem)) is not None
+    assert "multiple models" in error.message
+
+    # Set model ID to a non-existing model ID
+    problem.measurements[0].model_id = "invalid_model_id"
+    assert (error := check.run(problem)) is not None
+    assert "does not match" in error.message
+
+    # Use a valid model ID
+    problem.measurements[0].model_id = "model1"
+    assert (error := check.run(problem)) is None, error