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Remove PEtab v2 mapping-table/YAML handling from petab.v1 #524

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28 changes: 0 additions & 28 deletions petab/v1/C.py
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Original file line number Diff line number Diff line change
Expand Up @@ -335,15 +335,6 @@
PROBLEMS = "problems"
#: SBML files key in the YAML file
SBML_FILES = "sbml_files"
#: Model files key in the YAML file
# (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
MODEL_FILES = "model_files"
#: Model location key in the YAML file
# (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
MODEL_LOCATION = "location"
#: Model language key in the YAML file
# (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
MODEL_LANGUAGE = "language"
#: Condition files key in the YAML file
CONDITION_FILES = "condition_files"
#: Measurement files key in the YAML file
Expand All @@ -352,25 +343,6 @@
OBSERVABLE_FILES = "observable_files"
#: Visualization files key in the YAML file
VISUALIZATION_FILES = "visualization_files"
#: Mapping files key in the YAML file
# (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
MAPPING_FILES = "mapping_files"
#: Extensions key in the YAML file
# (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
EXTENSIONS = "extensions"


# MAPPING

#: PEtab entity ID column in the mapping table
# (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
PETAB_ENTITY_ID = "petabEntityId"
#: Model entity ID column in the mapping table
# (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
MODEL_ENTITY_ID = "modelEntityId"
#: Required columns of the mapping table
# (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
MAPPING_DF_REQUIRED_COLS = [PETAB_ENTITY_ID, MODEL_ENTITY_ID]

# MORE

Expand Down
1 change: 0 additions & 1 deletion petab/v1/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,6 @@
from .core import *
from .format_version import __format_version__ # noqa: F401
from .lint import *
from .mapping import *
from .measurements import *
from .models import Model # noqa: F401
from .observables import *
Expand Down
63 changes: 1 addition & 62 deletions petab/v1/lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,15 +96,13 @@ def check_condition_df(
df: pd.DataFrame,
model: Model | None = None,
observable_df: pd.DataFrame | None = None,
mapping_df: pd.DataFrame | None = None,
) -> None:
"""Run sanity checks on PEtab condition table

Arguments:
df: PEtab condition DataFrame
model: Model for additional checking of parameter IDs
observable_df: PEtab observables DataFrame
mapping_df: PEtab mapping DataFrame

Raises:
AssertionError: in case of problems
Expand Down Expand Up @@ -141,11 +139,8 @@ def check_condition_df(
petab.get_output_parameters(
model=model,
observable_df=observable_df,
mapping_df=mapping_df,
)
)
if mapping_df is not None:
allowed_cols |= set(mapping_df.index.values)
for column_name in df.columns:
if (
column_name != CONDITION_NAME
Expand Down Expand Up @@ -217,7 +212,6 @@ def check_parameter_df(
observable_df: pd.DataFrame | None = None,
measurement_df: pd.DataFrame | None = None,
condition_df: pd.DataFrame | None = None,
mapping_df: pd.DataFrame | None = None,
) -> None:
"""Run sanity checks on PEtab parameter table

Expand All @@ -227,7 +221,6 @@ def check_parameter_df(
observable_df: PEtab observable table for additional checks
measurement_df: PEtab measurement table for additional checks
condition_df: PEtab condition table for additional checks
mapping_df: PEtab mapping table for additional checks

Raises:
AssertionError: in case of problems
Expand Down Expand Up @@ -286,7 +279,7 @@ def check_parameter_df(

if model and measurement_df is not None and condition_df is not None:
assert_all_parameters_present_in_parameter_df(
df, model, observable_df, measurement_df, condition_df, mapping_df
df, model, observable_df, measurement_df, condition_df
)


Expand Down Expand Up @@ -355,7 +348,6 @@ def assert_all_parameters_present_in_parameter_df(
observable_df: pd.DataFrame,
measurement_df: pd.DataFrame,
condition_df: pd.DataFrame,
mapping_df: pd.DataFrame = None,
) -> None:
"""Ensure all required parameters are contained in the parameter table
with no additional ones
Expand All @@ -366,7 +358,6 @@ def assert_all_parameters_present_in_parameter_df(
observable_df: PEtab observable table
measurement_df: PEtab measurement table
condition_df: PEtab condition table
mapping_df: PEtab mapping table for additional checks

Raises:
AssertionError: in case of problems
Expand All @@ -376,42 +367,19 @@ def assert_all_parameters_present_in_parameter_df(
condition_df=condition_df,
observable_df=observable_df,
measurement_df=measurement_df,
mapping_df=mapping_df,
)

allowed = parameters.get_valid_parameters_for_parameter_table(
model=model,
condition_df=condition_df,
observable_df=observable_df,
measurement_df=measurement_df,
mapping_df=mapping_df,
)

actual = set(parameter_df.index)
missing = required - actual
extraneous = actual - allowed

# missing parameters might be present under a different name based on
# the mapping table
if missing and mapping_df is not None:
model_to_petab_mapping = {}
for map_from, map_to in zip(
mapping_df.index.values, mapping_df[MODEL_ENTITY_ID], strict=True
):
if map_to in model_to_petab_mapping:
model_to_petab_mapping[map_to].append(map_from)
else:
model_to_petab_mapping[map_to] = [map_from]
missing = {
missing_id
for missing_id in missing
if missing_id not in model_to_petab_mapping
or all(
mapping_parameter not in actual
for mapping_parameter in model_to_petab_mapping[missing_id]
)
}

if missing:
raise AssertionError(
"Missing parameter(s) in the model or the "
Expand Down Expand Up @@ -893,13 +861,6 @@ def lint_problem(problem: "petab.Problem") -> bool:
# pylint: disable=too-many-statements
errors_occurred = False

if problem.extensions_config:
logger.warning(
"Validation of PEtab extensions is not yet implemented, "
"but the given problem uses the following extensions: "
f"{'', ''.join(problem.extensions_config.keys())}"
)

# Run checks on individual files
if problem.model is not None:
logger.info("Checking model...")
Expand All @@ -914,7 +875,6 @@ def lint_problem(problem: "petab.Problem") -> bool:
problem.condition_df,
model=problem.model,
observable_df=problem.observable_df,
mapping_df=problem.mapping_df,
)
except AssertionError as e:
logger.error(e)
Expand Down Expand Up @@ -963,7 +923,6 @@ def lint_problem(problem: "petab.Problem") -> bool:
problem.observable_df,
problem.measurement_df,
problem.condition_df,
problem.mapping_df,
)
except AssertionError as e:
logger.error(e)
Expand All @@ -981,7 +940,6 @@ def lint_problem(problem: "petab.Problem") -> bool:
problem.model,
problem.condition_df,
problem.parameter_df,
problem.mapping_df,
)
except AssertionError as e:
logger.error(e)
Expand Down Expand Up @@ -1017,7 +975,6 @@ def assert_model_parameters_in_condition_or_parameter_table(
model: Model,
condition_df: pd.DataFrame,
parameter_df: pd.DataFrame,
mapping_df: pd.DataFrame = None,
observable_df: pd.DataFrame = None,
measurement_df: pd.DataFrame = None,
) -> None:
Expand All @@ -1029,38 +986,20 @@ def assert_model_parameters_in_condition_or_parameter_table(
parameter_df: PEtab parameter DataFrame
model: PEtab model
condition_df: PEtab condition table
mapping_df: PEtab mapping table
observable_df: PEtab observable table
measurement_df: PEtab measurement table

Raises:
AssertionError: in case of problems
"""
allowed_in_condition_cols = set(model.get_valid_ids_for_condition_table())
if mapping_df is not None:
allowed_in_condition_cols |= {
from_id
for from_id, to_id in zip(
mapping_df.index.values,
mapping_df[MODEL_ENTITY_ID],
strict=True,
)
if not pd.isna(to_id)
and (
# mapping table entities mapping to already allowed parameters
to_id in allowed_in_condition_cols
# mapping table entities mapping to species
or model.is_state_variable(to_id)
)
}

allowed_in_parameter_table = (
parameters.get_valid_parameters_for_parameter_table(
model=model,
condition_df=condition_df,
observable_df=observable_df,
measurement_df=measurement_df,
mapping_df=mapping_df,
)
)

Expand Down
12 changes: 0 additions & 12 deletions petab/v1/observables.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,6 @@ def get_output_parameters(
model: Model,
observables: bool = True,
noise: bool = True,
mapping_df: pd.DataFrame = None,
) -> list[str]:
"""Get output parameters

Expand All @@ -92,7 +91,6 @@ def get_output_parameters(
model: The underlying model
observables: Include parameters from observableFormulas
noise: Include parameters from noiseFormulas
mapping_df: PEtab mapping table

Returns:
List of output parameter IDs
Expand All @@ -114,16 +112,6 @@ def get_output_parameters(
if model.symbol_allowed_in_observable_formula(sym):
continue

# does it map to a model entity?
if (
mapping_df is not None
and sym in mapping_df.index
and model.symbol_allowed_in_observable_formula(
mapping_df.loc[sym, MODEL_ENTITY_ID]
)
):
continue

output_parameters[sym] = None

return list(output_parameters.keys())
Expand Down
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