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Validator: check datasetId in visualizations table exists in measurem… #255

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Apr 19, 2024
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Validator: check datasetId in visualizations table exists in measurem… #255

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Validator: check datasetId in visualizations table exists in measurem… 
…ents table

Closes #229
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@dweindl
dweindl committed Apr 19, 2024
commit eb3143bb84cdd043ef9ca294396114053877eebd
14 changes: 14 additions & 0 deletions petab/visualize/lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,20 @@ def validate_visualization_df(problem: Problem) -> bool:
)
errors = True

if problem.measurement_df is not None:
referenced_datasets = set(filter(bool, vis_df[C.DATASET_ID].unique()))
if referenced_datasets:
existing_datasets = set(
filter(bool, problem.measurement_df[C.DATASET_ID].unique())
)
if not referenced_datasets.issubset(existing_datasets):
logger.error(
f"Visualization table references {C.DATASET_ID}(s) "
f"{referenced_datasets - existing_datasets}, but no such "
"dataset(s) exist in the measurement table."
)
errors = True

return errors


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31 changes: 27 additions & 4 deletions tests/test_visualization.py
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Expand Up @@ -178,11 +178,16 @@ def test_visualization_with_vis_and_sim(
simulation_file_Isensee,
close_fig,
):
validate_visualization_df(
petab.Problem(
condition_df=petab.get_condition_df(condition_file_Isensee),
visualization_df=petab.get_visualization_df(vis_spec_file_Isensee),
assert (
validate_visualization_df(
petab.Problem(
condition_df=petab.get_condition_df(condition_file_Isensee),
visualization_df=petab.get_visualization_df(
vis_spec_file_Isensee
),
)
)
is False
)
plot_with_vis_spec(
vis_spec_file_Isensee,
Expand Down Expand Up @@ -577,3 +582,21 @@ def test_validate(vis_file, request):
assert False is validate_visualization_df(
petab.Problem(visualization_df=petab.get_visualization_df(vis_file))
)


def test_validate_visualization_missing_dataset(
condition_file_Isensee,
data_file_Isensee,
vis_spec_file_Isensee,
simulation_file_Isensee,
):
petab_problem = petab.Problem(
condition_df=petab.get_condition_df(condition_file_Isensee),
measurement_df=petab.get_measurement_df(data_file_Isensee),
visualization_df=petab.get_visualization_df(vis_spec_file_Isensee),
)

assert validate_visualization_df(petab_problem) is False

petab_problem.visualization_df.loc[0, petab.DATASET_ID] = "missing_dataset"
assert validate_visualization_df(petab_problem) is True
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