Lint mapping table

petab/v2/core.py

@@ -19,6 +19,7 @@
     Annotated,
     Any,
     Generic,
+    Literal,
     Self,
     TypeVar,
     get_args,
@@ -318,9 +319,9 @@ class Observable(BaseModel):
     #: Observable name.
     name: str | None = Field(alias=C.OBSERVABLE_NAME, default=None)
     #: Observable formula.
-    formula: sp.Basic | None = Field(alias=C.OBSERVABLE_FORMULA, default=None)
+    formula: sp.Basic = Field(alias=C.OBSERVABLE_FORMULA)
     #: Noise formula.
-    noise_formula: sp.Basic | None = Field(alias=C.NOISE_FORMULA, default=None)
+    noise_formula: sp.Basic = Field(alias=C.NOISE_FORMULA)
     #: Noise distribution.
     noise_distribution: NoiseDistribution = Field(
         alias=C.NOISE_DISTRIBUTION, default=NoiseDistribution.NORMAL
@@ -926,7 +927,7 @@ class Parameter(BaseModel):
     )
     #: Nominal value.
     nominal_value: Annotated[
-        float | None, BeforeValidator(_convert_nan_to_none)
+        float | Literal["array"] | None, BeforeValidator(_convert_nan_to_none)
     ] = Field(alias=C.NOMINAL_VALUE, default=None)
     #: Is the parameter to be estimated?
     estimate: bool = Field(alias=C.ESTIMATE, default=True)

petab/v2/lint.py

@@ -44,6 +44,7 @@
     "CheckPriorDistribution",
     "CheckUndefinedExperiments",
     "CheckInitialChangeSymbols",
+    "CheckMappingTable",
     "lint_problem",
     "default_validation_tasks",
 ]
@@ -445,31 +446,31 @@ def run(self, problem: Problem) -> ValidationIssue | None:
 
         # check for uniqueness of all primary keys
         counter = Counter(c.id for c in problem.conditions)
-        duplicates = {id_ for id_, count in counter.items() if count > 1}
+        duplicates = sorted(id_ for id_, count in counter.items() if count > 1)
 
         if duplicates:
             return ValidationError(
                 f"Condition table contains duplicate IDs: {duplicates}"
             )
 
         counter = Counter(o.id for o in problem.observables)
-        duplicates = {id_ for id_, count in counter.items() if count > 1}
+        duplicates = sorted(id_ for id_, count in counter.items() if count > 1)
 
         if duplicates:
             return ValidationError(
                 f"Observable table contains duplicate IDs: {duplicates}"
             )
 
         counter = Counter(e.id for e in problem.experiments)
-        duplicates = {id_ for id_, count in counter.items() if count > 1}
+        duplicates = sorted(id_ for id_, count in counter.items() if count > 1)
 
         if duplicates:
             return ValidationError(
                 f"Experiment table contains duplicate IDs: {duplicates}"
             )
 
         counter = Counter(p.id for p in problem.parameters)
-        duplicates = {id_ for id_, count in counter.items() if count > 1}
+        duplicates = sorted(id_ for id_, count in counter.items() if count > 1)
 
         if duplicates:
             return ValidationError(
@@ -508,7 +509,9 @@ def run(self, problem: Problem) -> ValidationIssue | None:
         for experiment in problem.experiments:
             # Check that there are no duplicate timepoints
             counter = Counter(period.time for period in experiment.periods)
-            duplicates = {time for time, count in counter.items() if count > 1}
+            duplicates = sorted(
+                time for time, count in counter.items() if count > 1
+            )
             if duplicates:
                 messages.append(
                     f"Experiment {experiment.id} contains duplicate "
@@ -551,7 +554,8 @@ def run(self, problem: Problem) -> ValidationIssue | None:
 
 class CheckAllParametersPresentInParameterTable(ValidationTask):
     """Ensure all required parameters are contained in the parameter table
-    with no additional ones."""
+    with no additional ones. This also ensures that the mapping table petab ids
+    are used in the PEtab problem."""
 
     def run(self, problem: Problem) -> ValidationIssue | None:
         if problem.model is None:
@@ -825,17 +829,17 @@ def run(self, problem: Problem) -> ValidationIssue | None:
 
             if parameter.prior_distribution not in PRIOR_DISTRIBUTIONS:
                 messages.append(
-                    f"Prior distribution `{parameter.prior_distribution}' "
-                    f"for parameter `{parameter.id}' is not valid."
+                    f"Prior distribution `{parameter.prior_distribution}` "
+                    f"for parameter `{parameter.id}` is not valid."
                 )
                 continue
 
             if (
                 exp_num_par := self._num_pars[parameter.prior_distribution]
             ) != len(parameter.prior_parameters):
                 messages.append(
-                    f"Prior distribution `{parameter.prior_distribution}' "
-                    f"for parameter `{parameter.id}' requires "
+                    f"Prior distribution `{parameter.prior_distribution}` "
+                    f"for parameter `{parameter.id}` requires "
                     f"{exp_num_par} parameters, but got "
                     f"{len(parameter.prior_parameters)} "
                     f"({parameter.prior_parameters})."
@@ -848,8 +852,8 @@ def run(self, problem: Problem) -> ValidationIssue | None:
                     _ = parameter.prior_dist.sample(1)
             except Exception as e:
                 messages.append(
-                    f"Prior parameters `{parameter.prior_parameters}' "
-                    f"for parameter `{parameter.id}' are invalid "
+                    f"Prior parameters `{parameter.prior_parameters}` "
+                    f"for parameter `{parameter.id}` are invalid "
                     f"(hint: {e})."
                 )
 
@@ -874,16 +878,16 @@ def run(self, problem: Problem) -> ValidationIssue | None:
                     continue
 
                 messages.append(
-                    f"Measurement `{measurement}' does not have a model ID, "
+                    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 "
+                    f"Measurement `{measurement}` has model ID "
+                    f"`{measurement.model_id}` which does not match "
                     "any of the available models: "
                     f"{available_models}."
                 )
@@ -894,6 +898,78 @@ def run(self, problem: Problem) -> ValidationIssue | None:
         return None
 
 
+class CheckMappingTable(ValidationTask):
+    """Validate the mapping table."""
+
+    def run(self, problem: Problem) -> ValidationIssue | None:
+        messages = []
+
+        # Mapping table is optional
+        if problem.mappings:
+            # Check that each id, across both the petabEntityId and
+            # modelEntityId columns, occurs only once
+            must_be_unique_ids = []
+            for mapping in problem.mappings:
+                petab_id = getattr(mapping, "petab_id", None)
+                model_id = getattr(mapping, "model_id", None)
+
+                if petab_id:
+                    must_be_unique_ids.append(petab_id)
+                # Duplicates for annotation-only rows (identity mappings)
+                # are permitted.
+                if petab_id == model_id:
+                    continue
+                if model_id:
+                    must_be_unique_ids.append(model_id)
+
+            non_unique_ids = sorted(
+                id_
+                for id_, count in Counter(must_be_unique_ids).items()
+                if count > 1
+            )
+            if non_unique_ids:
+                return ValidationError(
+                    f"Mapping table contains non-unique IDs: {non_unique_ids}."
+                )
+
+            # petabEntityId is not defined elsewhere in the PEtab problem
+            new_petab_ids = {
+                m.petab_id
+                for m in problem.mappings
+                # Ignore identity mappings used for annotation
+                if m.petab_id != m.model_id
+            }
+            old_petab_ids = (
+                {c.id for c in problem.conditions}
+                | {e.id for e in problem.experiments}
+                | {o.id for o in problem.observables}
+            )
+            if overdefined_ids := sorted(new_petab_ids & old_petab_ids):
+                messages.append(
+                    f"PEtab IDs `{overdefined_ids}` are "
+                    "defined in the mapping table but also defined through "
+                    "other PEtab tables."
+                )
+
+            for mapping in problem.mappings:
+                # petabEntityId not referenced in any model, if alias
+                for model in problem.models:
+                    if (
+                        mapping.petab_id != mapping.model_id
+                        and model.has_entity_with_id(mapping.petab_id)
+                    ):
+                        messages.append(
+                            f"`{mapping.petab_id}` is used in the mapping "
+                            "table and referenced directly in the model "
+                            f"`{model.model_id}`."
+                        )
+
+        if messages:
+            return ValidationError("\n".join(messages))
+
+        return None
+
+
 def get_valid_parameters_for_parameter_table(
     problem: Problem,
 ) -> set[str]:
@@ -933,9 +1009,20 @@ def get_valid_parameters_for_parameter_table(
         if p not in invalid
     )
 
+    # Add petab ids from mapping table if they are used for aliasing
+    # FIXME only add mapping.petab_id to allowed parameter IDs list if it
+    #       aliases an invalid PEtab ID? See
+    #       https://github.com/PEtab-dev/libpetab-python/pull/482#discussion_r3420762034
     for mapping in problem.mappings:
-        if mapping.model_id and mapping.model_id in parameter_ids.keys():
+        if mapping.petab_id not in invalid:
             parameter_ids[mapping.petab_id] = None
+        # An aliased model id is not a valid parameter id
+        if (
+            mapping.model_id
+            and mapping.model_id != mapping.petab_id
+            and mapping.model_id in parameter_ids
+        ):
+            del parameter_ids[mapping.model_id]
 
     # add output parameters from observable table
     output_parameters = problem.get_output_parameters()
@@ -977,20 +1064,13 @@ def get_required_parameters_for_parameter_table(
         measurement table as well as all parametric condition table overrides
         that are not defined in the model.
     """
-    parameter_ids = set()
-    condition_targets = {
-        change.target_id
-        for cond in problem.conditions
-        for change in cond.changes
-    }
+    # Start with mapping table petab ids
+    parameter_ids = {m.petab_id for m in problem.mappings}
 
     # Add parameters from measurement table, unless they are fixed parameters
     def append_overrides(overrides):
         parameter_ids.update(
-            str_p
-            for p in overrides
-            if isinstance(p, sp.Symbol)
-            and (str_p := str(p)) not in condition_targets
+            str(p) for p in overrides if isinstance(p, sp.Symbol)
         )
 
     for m in problem.measurements:
@@ -1033,7 +1113,12 @@ def append_overrides(overrides):
         if not problem.model.has_entity_with_id(str(p))
     )
 
-    # parameters that are overridden via the condition table are not allowed
+    # Parameters that are overridden via the condition table are not allowed
+    condition_targets = {
+        change.target_id
+        for cond in problem.conditions
+        for change in cond.changes
+    }
     parameter_ids -= condition_targets
 
     return parameter_ids
@@ -1090,5 +1175,5 @@ def get_placeholders(
     CheckUnusedConditions(),
     CheckPriorDistribution(),
     CheckInitialChangeSymbols(),
-    # TODO validate mapping table
+    CheckMappingTable(),
 ]

tests/v2/test_core.py

@@ -181,7 +181,7 @@ def test_measurments():
 
 
 def test_observable():
-    Observable(id="obs1", formula=x + y)
+    Observable(id="obs1", formula=x + y, noiseFormula=1)
     Observable(id="obs1", formula="x + y", noise_formula="x + y")
     Observable(id="obs1", formula=1, noise_formula=2)
     Observable(
@@ -198,9 +198,17 @@ def test_observable():
         observable_parameters=[sp.Symbol("p1")],
         noise_parameters=[sp.Symbol("n1")],
     )
-    assert Observable(id="obs1", formula="x + y", non_petab=1).non_petab == 1
+    assert (
+        Observable(
+            id="obs1",
+            formula="x + y",
+            noise_formula="x + y",
+            non_petab=1,
+        ).non_petab
+        == 1
+    )
 
-    o = Observable(id="obs1", formula=x + y)
+    o = Observable(id="obs1", formula=x + y, noise_formula=1)
     assert o.observable_placeholders == []
     assert o.noise_placeholders == []
 
@@ -492,14 +500,14 @@ def test_modify_problem():
         problem.condition_df, exp_condition_df, check_dtype=False
     )
 
-    problem.add_observable("observable1", "1")
+    problem.add_observable("observable1", "1", noise_formula=1)
     problem.add_observable("observable2", "2", noise_formula=2.2)
 
     exp_observable_df = pd.DataFrame(
         data={
             OBSERVABLE_ID: ["observable1", "observable2"],
             OBSERVABLE_FORMULA: [1, 2],
-            NOISE_FORMULA: [np.nan, 2.2],
+            NOISE_FORMULA: [1, 2.2],
         }
     ).set_index([OBSERVABLE_ID])
     assert_frame_equal(