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v2: Remove redundant CheckAllObservablesDefined #399

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dweindl merged 3 commits into from
Jul 3, 2025
Merged

v2: Remove redundant CheckAllObservablesDefined #399

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v2: Remove redundant CheckAllObservablesDefined
dweindl Jul 2, 2025
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dweindl Jul 3, 2025
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dweindl Jul 3, 2025
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36 changes: 5 additions & 31 deletions petab/v2/lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,6 @@
"CheckUnusedExperiments",
"CheckObservablesDoNotShadowModelEntities",
"CheckUnusedConditions",
"CheckAllObservablesDefined",
"CheckPriorDistribution",
"lint_problem",
"default_validation_tasks",
Expand Down Expand Up @@ -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
Expand All @@ -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

Expand Down Expand Up @@ -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."""

Expand Down Expand Up @@ -1092,7 +1067,6 @@ def get_placeholders(
# CheckVisualizationTable(),
# TODO validate mapping table
CheckValidParameterInConditionOrParameterTable(),
CheckAllObservablesDefined(),
CheckAllParametersPresentInParameterTable(),
CheckValidConditionTargets(),
CheckPriorDistribution(),
Expand Down