v2: Remove redundant CheckAllObservablesDefined (#399)

There is already `CheckMeasuredObservablesDefined`.

Co-authored-by: Dilan Pathirana <[email protected]>

Author: dweindl

petab/v2/lint.py

@@ -39,7 +39,6 @@
     "CheckUnusedExperiments",
     "CheckObservablesDoNotShadowModelEntities",
     "CheckUnusedConditions",
-    "CheckAllObservablesDefined",
     "CheckPriorDistribution",
     "lint_problem",
     "default_validation_tasks",
@@ -261,8 +260,9 @@ def run(self, problem: Problem) -> ValidationIssue | None:
         }
         if undefined_observables := (used_observables - defined_observables):
             return ValidationError(
-                f"Observables {undefined_observables} used in "
-                "measurement table but not defined in observable table."
+                f"Observable(s) {undefined_observables} are used in the "
+                "measurement table but are not defined in the observable "
+                "table."
             )
 
         return None
@@ -289,8 +289,8 @@ def run(self, problem: Problem) -> ValidationIssue | None:
                 expected = observable_parameters_count[m.observable_id]
             except KeyError:
                 messages.append(
-                    f"Observable {m.observable_id} used in measurement "
-                    f"table is not defined."
+                    f"Observable {m.observable_id} is used in the measurement "
+                    f"table but is not defined in the observable table."
                 )
                 continue
 
@@ -443,31 +443,6 @@ def run(self, problem: Problem) -> ValidationIssue | None:
         return None
 
 
-class CheckAllObservablesDefined(ValidationTask):
-    """A task to validate that all observables in the measurement table are
-    defined in the observable table."""
-
-    def run(self, problem: Problem) -> ValidationIssue | None:
-        if problem.measurement_df is None:
-            return None
-
-        measurement_df = problem.measurement_df
-        observable_df = problem.observable_df
-        used_observables = set(measurement_df[OBSERVABLE_ID].values)
-        defined_observables = (
-            set(observable_df.index.values)
-            if observable_df is not None
-            else set()
-        )
-        if undefined_observables := (used_observables - defined_observables):
-            return ValidationError(
-                f"Observables {undefined_observables} are used in the"
-                "measurements table but are not defined in observables table."
-            )
-
-        return None
-
-
 class CheckUniquePrimaryKeys(ValidationTask):
     """Check that all primary keys are unique."""
 
@@ -1092,7 +1067,6 @@ def get_placeholders(
     # CheckVisualizationTable(),
     # TODO validate mapping table
     CheckValidParameterInConditionOrParameterTable(),
-    CheckAllObservablesDefined(),
     CheckAllParametersPresentInParameterTable(),
     CheckValidConditionTargets(),
     CheckPriorDistribution(),