"""
Functions for creating an overview report of a PEtab problem
"""
import os
from shutil import copyfile
import pandas as pd
import petab
from petab.C import *
[docs]def create_report(problem: petab.Problem, model_name: str) -> None:
"""Create an HTML overview data / model overview report
Arguments:
problem: PEtab problem
model_name: Name of the model, used for file name for report
"""
template_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'templates')
template_file = "report.html"
data_per_observable = get_data_per_observable(problem.measurement_df)
num_conditions = (len(problem.condition_df.columns)
- 1 * (CONDITION_NAME in problem.condition_df.columns))
# Setup template engine
import jinja2
template_loader = jinja2.FileSystemLoader(
searchpath=template_dir)
template_env = jinja2.Environment(loader=template_loader)
template = template_env.get_template(template_file)
# Render and save
output_text = template.render(problem=problem, model_name=model_name,
data_per_observable=data_per_observable,
num_conditions=num_conditions)
with open(model_name + '.html', 'w') as html_file:
html_file.write(output_text)
copyfile(os.path.join(template_dir, 'mystyle.css'), 'mystyle.css')
[docs]def get_data_per_observable(measurement_df: pd.DataFrame) -> pd.DataFrame:
"""Get table with number of data points per observable and condition
Arguments:
measurement_df: PEtab measurement data frame
Returns:
data_per_observable:
Pivot table with number of data points per observable and condition
"""
my_measurements = measurement_df.copy()
my_measurements[PREEQUILIBRATION_CONDITION_ID].fillna('', inplace=True)
data_per_observable = pd.pivot_table(
my_measurements, values=MEASUREMENT, aggfunc='count',
index=[SIMULATION_CONDITION_ID, PREEQUILIBRATION_CONDITION_ID],
columns=[OBSERVABLE_ID], fill_value=0)
# Add row and column sums
data_per_observable.loc['SUM', :] = data_per_observable.sum(axis=0).values
data_per_observable['SUM'] = data_per_observable.sum(axis=1).values
data_per_observable = data_per_observable.astype(int)
return data_per_observable
[docs]def main():
"""Data overview generation with example data from the repository for
testing
"""
root_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'..', '..', 'doc/example/example_Fujita/')
problem = petab.Problem.from_files(
sbml_file=os.path.join(root_path, 'Fujita_model.xml'),
condition_file=os.path.join(root_path,
'Fujita_experimentalCondition.tsv'),
measurement_file=os.path.join(root_path, 'Fujita_measurementData.tsv'),
parameter_file=os.path.join(root_path, 'Fujita_parameters.tsv'),
)
create_report(problem, 'Fujita')
if __name__ == '__main__':
main()