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special_report_sections = configuration['special_sections']
# get any custom sections and locate them to make sure
# that they exist, otherwise raise an exception
custom_report_section_paths = configuration['custom_sections']
if custom_report_section_paths:
logger.info('Locating custom report sections')
custom_report_sections = Reporter.locate_custom_sections(custom_report_section_paths,
configuration.configdir)
else:
custom_report_sections = []
section_order = configuration['section_order']
# Initialize reporter
reporter = Reporter()
# check all sections values and order and get the
# ordered list of notebook files
chosen_notebook_files = reporter.get_ordered_notebook_files(general_report_sections,
special_report_sections,
custom_report_sections,
section_order,
subgroups,
model_type=None,
context='rsmsummarize')
# add chosen notebook files to configuration
configuration['chosen_notebook_files'] = chosen_notebook_files
# now generate the comparison report
logger.info('Starting report generation')
# what about the special or custom sections?
special_report_sections = config_obj['special_sections']
custom_report_section_paths = config_obj['custom_sections']
if custom_report_section_paths and configdir is not None:
logging.info('Locating custom report sections')
custom_report_sections = Reporter.locate_custom_sections(custom_report_section_paths,
configdir)
else:
custom_report_sections = []
section_order = config_obj['section_order']
chosen_notebook_files = Reporter().get_ordered_notebook_files(general_report_sections,
special_report_sections,
custom_report_sections,
section_order,
subgroups,
model_type=model_type,
context='rsmtool')
# Location of feature file
feature_field = config_obj['features']
feature_subset_field = config_obj['feature_subset']
# if the user requested feature_subset file and feature subset,
# read the file and check its format
if feature_subset is not None and feature_subset_field:
FeatureSubsetProcessor.check_feature_subset_file(feature_subset)
special_report_sections = configuration['special_sections']
# get any custom sections and locate them to make sure
# that they exist, otherwise raise an exception
custom_report_section_paths = configuration['custom_sections']
if custom_report_section_paths:
logger.info('Locating custom report sections')
custom_report_sections = Reporter.locate_custom_sections(custom_report_section_paths,
configuration.configdir)
else:
custom_report_sections = []
section_order = configuration['section_order']
# Initialize reporter
reporter = Reporter()
# check all sections values and order and get the
# ordered list of notebook files
chosen_notebook_files = reporter.get_ordered_notebook_files(general_report_sections,
special_report_sections,
custom_report_sections,
section_order,
subgroups,
model_type=None,
context='rsmsummarize')
# add chosen notebook files to configuration
configuration['chosen_notebook_files'] = chosen_notebook_files
# now generate the comparison report
logger.info('Starting report generation')
# Add processed data_container frames to pred_data_container
new_pred_data_container = pred_data_container + processed_container
logger.info('Running prediction analyses.')
(pred_analysis_config,
pred_analysis_data_container) = analyzer.run_prediction_analyses(new_pred_data_container,
pred_config)
# Write out files
writer.write_experiment_output(csvdir,
pred_analysis_data_container,
reset_index=True,
file_format=file_format)
# Initialize reporter
reporter = Reporter()
# generate the report
logger.info('Starting report generation.')
reporter.create_report(pred_analysis_config,
csvdir,
figdir)
def _get_all_general_section_names(self):
reporter = Reporter()
default_general_sections_value = DEFAULTS.get('general_sections', '')
default_special_sections_value = DEFAULTS.get('special_sections', '')
default_custom_sections_value = DEFAULTS.get('custom_sections', '')
# if we are told ot use subgroups then just make up a dummy subgroup
# value so that the subgroup-based sections will be included in the
# section list. This value is not actually used in configuration file.
subgroups_value = ['GROUP'] if self.use_subgroups else DEFAULTS.get('subgroups', '')
return reporter.determine_chosen_sections(default_general_sections_value,
default_special_sections_value,
default_custom_sections_value,
subgroups_value,
context=self.context)