def test_run_experiment_with_warnings():
source = 'lr-with-warnings'
experiment_id = 'lr_with_warnings'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
html_file = join('test_outputs', source, 'report',
experiment_id + '_report.html')
report_warnings = collect_warning_messages_from_report(html_file)
syntax_warnings = [
msg for msg in report_warnings if 'SyntaxWarning:' in msg
]
deprecation_warnings = [
msg for msg in report_warnings if 'DeprecationWarning:' in msg
]
unicode_warnings = [
msg for msg in report_warnings if 'UnicodeWarning:' in msg
]
runtime_warnings = [
msg for msg in report_warnings if 'RuntimeWarning:' in msg
]
user_warnings = [msg for msg in report_warnings if 'UserWarning:' in msg]
assert_equal(len(syntax_warnings), 1)
assert_equal(len(deprecation_warnings), 2)
assert_equal(len(unicode_warnings), 1)
assert_equal(len(runtime_warnings), 1)
assert_equal(len(user_warnings), 1)
def test_run_experiment_lr_with_cfg():
# basic experiment with a LinearRegression model
source = 'lr-cfg'
experiment_id = 'lr_cfg'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.cfg'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
output_dir = join('test_outputs', source, 'output')
expected_output_dir = join(rsmtool_test_dir, 'data', 'experiments', source, 'output')
html_report = join('test_outputs', source, 'report', '{}_report.html'.format(experiment_id))
csv_files = glob(join(output_dir, '*.csv'))
for csv_file in csv_files:
csv_filename = basename(csv_file)
expected_csv_file = join(expected_output_dir, csv_filename)
if exists(expected_csv_file):
yield check_file_output, csv_file, expected_csv_file
yield check_generated_output, csv_files, experiment_id, 'rsmtool'
yield check_scaled_coefficients, source, experiment_id
yield check_report, html_report
def test_run_experiment_lr_with_cfg():
# basic experiment with a LinearRegression model
source = 'lr-cfg'
experiment_id = 'lr_cfg'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.cfg'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
output_dir = join('test_outputs', source, 'output')
expected_output_dir = join(rsmtool_test_dir, 'data', 'experiments', source,
'output')
html_report = join('test_outputs', source, 'report',
'{}_report.html'.format(experiment_id))
csv_files = glob(join(output_dir, '*.csv'))
for csv_file in csv_files:
csv_filename = basename(csv_file)
expected_csv_file = join(expected_output_dir, csv_filename)
if exists(expected_csv_file):
yield check_file_output, csv_file, expected_csv_file
yield check_generated_output, csv_files, experiment_id, 'rsmtool'
yield check_scaled_coefficients, source, experiment_id
yield check_report, html_report
def test_run_experiment_empwtdropneg():
# rsmtool experiment with no longer supported empWtDropNeg model
source = 'empwtdropneg'
experiment_id = 'empWtDropNeg'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_truncations_no_features_field():
# rsmtool experiment with truncations, but no feature field
source = 'lr-with-truncations-no-features-field'
experiment_id = 'lr_with_truncations_no_features_field'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_truncations_no_features_columns():
# rsmtool experiment with truncations, but no min/max columns in feature file
source = 'lr-with-truncations-no-features-columns'
experiment_id = 'lr_with_truncations_no_features_columns'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_sc1_as_feature_name():
# rsmtool experiment with sc1 used as the name of a feature
source = 'lr-with-sc1-as-feature-name'
experiment_id = 'lr_with_sc1_as_feature_name'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_duplicate_feature_names():
# rsmtool experiment with duplicate feature names
source = 'lr-with-duplicate-feature-names'
experiment_id = 'lr_with_duplicate_feature_names'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_wrong_model_name():
# rsmtool experiment with incorrect model name
source = 'wrong-model-name'
experiment_id = 'wrong_model_name'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_requested_feature_zero_sd():
# rsmtool experiment when a requested feature has zero sd
source = 'lr-with-requested-feature-with-zero-sd'
experiment_id = 'lr_with_requested_feature_with_zero_sd'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_wrong_feature_file_path():
# basic experiment with the path in features field pointing to
# a non-existing file
source = 'lr-wrong-path-features'
experiment_id = 'lr'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_repeated_ids():
# rsmtool experiment with non-unique ids
source = 'lr-with-repeated-ids'
experiment_id = 'lr_with_repeated_ids'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_h2_column_and_feature():
# rsmtool experiment that has second rater column but
# the same column as a model feature
source = 'lr-with-h2-and-feature'
experiment_id = 'lr_with_h2_and_feature'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_length_column_and_feature_list():
# experiment with feature as list instead of file name
# and length included in feature list and as length column
source = 'lr-with-length-and-feature-list'
experiment_id = 'lr_with_length_and_feature'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_subset_feature_file_and_feature_file():
# basic experiment with LinearRegression model and a feature file and
# also a subset file. This is not allowed and so should raise a ValueError.
source = 'lr-with-feature-subset-file-and-feature-file'
experiment_id = 'lr_with_feature_subset_file'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_length_as_feature_name():
# rsmtool experiment with 'length' used as feature name
# when a length analysis is requested using a different feature
source = 'lr-with-length-as-feature-name'
experiment_id = 'lr_with_length_as_feature_name'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_subgroup_as_feature_name():
# rsmtool experiment with a subgroup name used as feature
# when the user also requests subgroup analysis with that subgroup
source = 'lr-with-subgroup-as-feature-name'
experiment_id = 'lr_with_subgroup_as_feature_name'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_same_h1_and_h2():
# rsmtool experiment that has label column
# and second rater column set the same
source = 'lr-same-h1-and-h2'
experiment_id = 'lr_same_h1_and_h2'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_sc2_as_feature_name():
# rsmtool experiment with sc2 used as a feature name
# when the user also requests h2 analysis using a different
# column
source = 'lr-with-sc2-as-feature-name'
experiment_id = 'lr_with_sc2_as_feature_name'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_all_non_numeric_scores():
# rsmtool experiment with all values for `sc1`
# being non-numeric and all getting filtered out
# which should raise an exception
source = 'lr-with-all-non-numeric-scores'
experiment_id = 'lr_with_all_non_numeric_scores'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_truncations_no_features_columns():
# rsmtool experiment with truncations, but no min/max columns in feature file
source = 'lr-with-truncations-no-features-columns'
experiment_id = 'lr_with_truncations_no_features_columns'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_requested_feature_zero_sd():
# rsmtool experiment when a requested feature has zero sd
source = 'lr-with-requested-feature-with-zero-sd'
experiment_id = 'lr_with_requested_feature_with_zero_sd'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_wrong_model_name():
# rsmtool experiment with incorrect model name
source = 'wrong-model-name'
experiment_id = 'wrong_model_name'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_duplicate_feature_names():
# rsmtool experiment with duplicate feature names
source = 'lr-with-duplicate-feature-names'
experiment_id = 'lr_with_duplicate_feature_names'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_repeated_ids():
# rsmtool experiment with non-unique ids
source = 'lr-with-repeated-ids'
experiment_id = 'lr_with_repeated_ids'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_wrong_feature_file_path():
# basic experiment with the path in features field pointing to
# a non-existing file
source = 'lr-wrong-path-features'
experiment_id = 'lr'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_one_fully_non_numeric_feature():
# rsmtool experiment with all values for one of the
# features being non-numeric and all getting filtered out
# which should raise an exception
source = 'lr-with-one-fully-non-numeric-feature'
experiment_id = 'lr_with_one_fully_non_numeric_feature'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_none_flagged():
# rsmtool experiment where all responses have the bad flag
# value and so they all get filtered out which should
# raise an exception
source = 'lr-with-none-flagged'
experiment_id = 'lr_with_none_flagged'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_empwtdropneg():
# rsmtool experiment with no longer supported empWtDropNeg model
source = 'empwtdropneg'
experiment_id = 'empWtDropNeg'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_truncations_no_features_field():
# rsmtool experiment with truncations, but no feature field
source = 'lr-with-truncations-no-features-field'
experiment_id = 'lr_with_truncations_no_features_field'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_sc1_as_feature_name():
# rsmtool experiment with sc1 used as the name of a feature
source = 'lr-with-sc1-as-feature-name'
experiment_id = 'lr_with_sc1_as_feature_name'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_length_column_and_feature_list():
# experiment with feature as list instead of file name
# and length included in feature list and as length column
source = 'lr-with-length-and-feature-list'
experiment_id = 'lr_with_length_and_feature'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_subset_feature_file_and_feature_file():
# basic experiment with LinearRegression model and a feature file and
# also a subset file. This is not allowed and so should raise a ValueError.
source = 'lr-with-feature-subset-file-and-feature-file'
experiment_id = 'lr_with_feature_subset_file'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_length_as_feature_name():
# rsmtool experiment with 'length' used as feature name
# when a length analysis is requested using a different feature
source = 'lr-with-length-as-feature-name'
experiment_id = 'lr_with_length_as_feature_name'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_h2_column_and_feature():
# rsmtool experiment that has second rater column but
# the same column as a model feature
source = 'lr-with-h2-and-feature'
experiment_id = 'lr_with_h2_and_feature'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_subgroup_as_feature_name():
# rsmtool experiment with a subgroup name used as feature
# when the user also requests subgroup analysis with that subgroup
source = 'lr-with-subgroup-as-feature-name'
experiment_id = 'lr_with_subgroup_as_feature_name'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_same_h1_and_h2():
# rsmtool experiment that has label column
# and second rater column set the same
source = 'lr-same-h1-and-h2'
experiment_id = 'lr_same_h1_and_h2'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_feature_json():
# basic experiment with a LinearRegression model but using
# feature json file
source = 'lr-feature-json'
experiment_id = 'lr'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
# run this experiment but suppress the expected deprecation warnings
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=DeprecationWarning)
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_sc2_as_feature_name():
# rsmtool experiment with sc2 used as a feature name
# when the user also requests h2 analysis using a different
# column
source = 'lr-with-sc2-as-feature-name'
experiment_id = 'lr_with_sc2_as_feature_name'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_old_config():
# basic experiment with a LinearRegression model but using an
# old style configuration file
source = 'lr-old-config'
experiment_id = 'empWt'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
# run this experiment but suppress the expected deprecation warnings
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=DeprecationWarning)
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_all_non_numeric_scores():
# rsmtool experiment with all values for `sc1`
# being non-numeric and all getting filtered out
# which should raise an exception
source = 'lr-with-all-non-numeric-scores'
experiment_id = 'lr_with_all_non_numeric_scores'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_none_flagged():
# rsmtool experiment where all responses have the bad flag
# value and so they all get filtered out which should
# raise an exception
source = 'lr-with-none-flagged'
experiment_id = 'lr_with_none_flagged'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_one_fully_non_numeric_feature():
# rsmtool experiment with all values for one of the
# features being non-numeric and all getting filtered out
# which should raise an exception
source = 'lr-with-one-fully-non-numeric-feature'
experiment_id = 'lr_with_one_fully_non_numeric_feature'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_feature_json():
# basic experiment with a LinearRegression model but using
# feature json file
source = 'lr-feature-json'
experiment_id = 'lr'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
# run this experiment but suppress the expected deprecation warnings
do_run_experiment(source,
experiment_id,
config_file,
suppress_warnings_for=[DeprecationWarning])
def test_run_experiment_lr_old_config():
# basic experiment with a LinearRegression model but using an
# old style configuration file
source = 'lr-old-config'
experiment_id = 'empWt'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
# run this experiment but suppress the expected deprecation warnings
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=DeprecationWarning)
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_feature_json():
# basic experiment with a LinearRegression model but using
# feature json file
source = 'lr-feature-json'
experiment_id = 'lr'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
# run this experiment but suppress the expected deprecation warnings
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=DeprecationWarning)
do_run_experiment(source, experiment_id, config_file)
def test_run_experiment_lr_with_object():
# basic experiment with a LinearRegression model
source = 'lr-object'
experiment_id = 'lr_object'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
config_dict = {
"train_file": "../../files/train.csv",
"id_column": "ID",
"use_scaled_predictions": True,
"test_label_column": "score",
"train_label_column": "score",
"test_file": "../../files/test.csv",
"trim_max": 6,
"features": "features.csv",
"trim_min": 1,
"model": "LinearRegression",
"experiment_id": "lr_object",
"description": "Using all features with an LinearRegression model."
}
config_parser = ConfigurationParser()
config_parser.load_config_from_dict(config_dict)
config_obj = config_parser.normalize_validate_and_process_config()
config_obj = config_file
do_run_experiment(source, experiment_id, config_obj)
output_dir = join('test_outputs', source, 'output')
expected_output_dir = join(rsmtool_test_dir, 'data', 'experiments', source,
'output')
html_report = join('test_outputs', source, 'report',
'{}_report.html'.format(experiment_id))
csv_files = glob(join(output_dir, '*.csv'))
for csv_file in csv_files:
csv_filename = basename(csv_file)
expected_csv_file = join(expected_output_dir, csv_filename)
if exists(expected_csv_file):
yield check_file_output, csv_file, expected_csv_file
yield check_generated_output, csv_files, experiment_id, 'rsmtool'
yield check_scaled_coefficients, source, experiment_id
yield check_report, html_report
def test_run_experiment_lr_with_object():
# basic experiment with a LinearRegression model
source = 'lr-object'
experiment_id = 'lr_object'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
config_dict = {"train_file": "../../files/train.csv",
"id_column": "ID",
"use_scaled_predictions": True,
"test_label_column": "score",
"train_label_column": "score",
"test_file": "../../files/test.csv",
"trim_max": 6,
"features": "features.csv",
"trim_min": 1,
"model": "LinearRegression",
"experiment_id": "lr_object",
"description": "Using all features with an LinearRegression model."}
config_parser = ConfigurationParser()
config_parser.load_config_from_dict(config_dict)
config_obj = config_parser.normalize_validate_and_process_config()
config_obj = config_file
do_run_experiment(source, experiment_id, config_obj)
output_dir = join('test_outputs', source, 'output')
expected_output_dir = join(rsmtool_test_dir, 'data', 'experiments', source, 'output')
html_report = join('test_outputs', source, 'report', '{}_report.html'.format(experiment_id))
csv_files = glob(join(output_dir, '*.csv'))
for csv_file in csv_files:
csv_filename = basename(csv_file)
expected_csv_file = join(expected_output_dir, csv_filename)
if exists(expected_csv_file):
yield check_file_output, csv_file, expected_csv_file
yield check_generated_output, csv_files, experiment_id, 'rsmtool'
yield check_scaled_coefficients, source, experiment_id
yield check_report, html_report
def test_run_experiment_lr_rsmtool_and_rsmpredict():
# this test is to make sure that both rsmtool
# and rsmpredict generate the same files
source = 'lr-rsmtool-rsmpredict'
experiment_id = 'lr_rsmtool_rsmpredict'
rsmtool_config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, rsmtool_config_file)
rsmpredict_config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'rsmpredict.json')
do_run_prediction(source, rsmpredict_config_file)
output_dir = join('test_outputs', source, 'output')
expected_output_dir = join(rsmtool_test_dir, 'data', 'experiments', source, 'output')
csv_files = glob(join(output_dir, '*.csv'))
html_report = join('test_outputs', source, 'report', '{}_report.html'.format(experiment_id))
# Check the results for rsmtool
for csv_file in csv_files:
csv_filename = basename(csv_file)
expected_csv_file = join(expected_output_dir, csv_filename)
if exists(expected_csv_file):
yield check_file_output, csv_file, expected_csv_file
yield check_scaled_coefficients, source, experiment_id
yield check_generated_output, csv_files, experiment_id, 'rsmtool'
yield check_report, html_report
# check that the rsmpredict generated the same results
for csv_pair in [('predictions.csv',
'{}_pred_processed.csv'.format(experiment_id)),
('preprocessed_features.csv',
'{}_test_preprocessed_features.csv'.format(experiment_id))]:
output_file = join(output_dir, csv_pair[0])
expected_output_file = join(expected_output_dir, csv_pair[1])
yield check_file_output, output_file, expected_output_file
def test_load_rsmtool_output(self):
source = 'lr-subgroups-with-h2'
experiment_id = 'lr_subgroups_with_h2'
test_dir = dirname(__file__)
config_file = join(test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
output_dir = join('test_outputs', source, 'output')
figure_dir = join('test_outputs', source, 'figure')
comparer = Comparer()
csvs, figs, file_format = comparer.load_rsmtool_output(
output_dir, figure_dir, experiment_id, 'scale', ['QUESTION', 'L1'])
expected_csv_keys = [
'df_coef', 'df_confmatrix', 'df_consistency', 'df_degradation',
'df_descriptives', 'df_disattenuated_correlations',
'df_disattenuated_correlations_by_L1',
'df_disattenuated_correlations_by_L1_overview',
'df_disattenuated_correlations_by_QUESTION',
'df_disattenuated_correlations_by_QUESTION_overview', 'df_eval',
'df_eval_by_L1', 'df_eval_by_L1_m_sd', 'df_eval_by_L1_overview',
'df_eval_by_QUESTION', 'df_eval_by_QUESTION_m_sd',
'df_eval_by_QUESTION_overview', 'df_eval_for_degradation',
'df_feature_cors', 'df_mcor_sc1', 'df_mcor_sc1_L1_overview',
'df_mcor_sc1_QUESTION_overview', 'df_mcor_sc1_by_L1',
'df_mcor_sc1_by_QUESTION', 'df_mcor_sc1_overview', 'df_model_fit',
'df_outliers', 'df_pca', 'df_pcavar', 'df_pcor_sc1',
'df_pcor_sc1_L1_overview', 'df_pcor_sc1_QUESTION_overview',
'df_pcor_sc1_by_L1', 'df_pcor_sc1_by_QUESTION',
'df_pcor_sc1_overview', 'df_percentiles', 'df_score_dist',
'df_scores', 'df_train_features'
]
expected_fig_keys = [
'betas', 'eval_barplot_by_L1', 'eval_barplot_by_QUESTION',
'feature_boxplots_by_L1_svg', 'feature_boxplots_by_QUESTION_svg',
'feature_distplots', 'pca_scree_plot'
]
assert_equal(file_format, 'csv')
assert_equal(expected_csv_keys, sorted(csvs.keys()))
assert_equal(expected_fig_keys, sorted(figs.keys()))
def test_run_experiment_lr_rsmtool_and_rsmpredict():
'''
this test is to make sure that both rsmtool
and rsmpredict generate the same files
'''
source = 'lr-rsmtool-rsmpredict'
experiment_id = 'lr_rsmtool_rsmpredict'
rsmtool_config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, rsmtool_config_file)
rsmpredict_config_file = join(rsmtool_test_dir, 'data', 'experiments',
source, 'rsmpredict.json')
do_run_prediction(source, rsmpredict_config_file)
output_dir = join('test_outputs', source, 'output')
expected_output_dir = join(rsmtool_test_dir, 'data', 'experiments', source,
'output')
csv_files = glob(join(output_dir, '*.csv'))
html_report = join('test_outputs', source, 'report',
'{}_report.html'.format(experiment_id))
# Check the results for rsmtool
for csv_file in csv_files:
csv_filename = basename(csv_file)
expected_csv_file = join(expected_output_dir, csv_filename)
if exists(expected_csv_file):
yield check_file_output, csv_file, expected_csv_file
yield check_scaled_coefficients, source, experiment_id
yield check_generated_output, csv_files, experiment_id, 'rsmtool'
yield check_report, html_report
# check that the rsmpredict generated the same results
for csv_pair in [
('predictions.csv', '{}_pred_processed.csv'.format(experiment_id)),
('preprocessed_features.csv',
'{}_test_preprocessed_features.csv'.format(experiment_id))
]:
output_file = join(output_dir, csv_pair[0])
expected_output_file = join(expected_output_dir, csv_pair[1])
yield check_file_output, output_file, expected_output_file
def test_run_experiment_lr_with_notebook_rerun():
# basic experiment with LinearRegression model and notebook
# run-run after the experiment after `RSM_REPORT_DIR` is deleted
# to ensure that the `.environ.json` file can be located
source = 'lr-with-notebook-rerun'
experiment_id = 'lr'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
report_ipynb = join('test_outputs', source, 'report',
'{}_report.ipynb'.format(experiment_id))
report_html = join('test_outputs', source, 'report',
'{}_report.html'.format(experiment_id))
del os.environ['RSM_REPORT_DIR']
Reporter.convert_ipynb_to_html(report_ipynb, report_html)
check_report(report_html)
def test_run_experiment_lr_with_notebook_rerun():
# basic experiment with LinearRegression model and notebook
# run-run after the experiment after `RSM_REPORT_DIR` is deleted
# to ensure that the `.environ.json` file can be located
source = 'lr-with-notebook-rerun'
experiment_id = 'lr'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
report_ipynb = join('test_outputs', source, 'report', '{}_report.ipynb'.format(experiment_id))
report_html = join('test_outputs', source, 'report', '{}_report.html'.format(experiment_id))
del os.environ['RSM_REPORT_DIR']
Reporter.convert_ipynb_to_html(report_ipynb, report_html)
check_report(report_html)
def test_run_experiment_lr_with_notebook_rerun_fail():
# basic experiment with LinearRegression model and notebook
# run-run after the experiment after `RSM_REPORT_DIR` is deleted
# and `.environ.json` is deleted, so the notebook execution will fail
source = 'lr-with-notebook-rerun-fail'
experiment_id = 'lr'
config_file = join(rsmtool_test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
report_env = join('test_outputs', source, 'report', '.environ.json'.format(experiment_id))
report_ipynb = join('test_outputs', source, 'report', '{}_report.ipynb'.format(experiment_id))
report_html = join('test_outputs', source, 'report', '{}_report.html'.format(experiment_id))
del os.environ['RSM_REPORT_DIR']
os.remove(report_env)
Reporter.convert_ipynb_to_html(report_ipynb, report_html)
def test_run_experiment_lr_with_notebook_rerun_fail():
# basic experiment with LinearRegression model and notebook
# run-run after the experiment after `RSM_REPORT_DIR` is deleted
# and `.environ.json` is deleted, so the notebook execution will fail
source = 'lr-with-notebook-rerun-fail'
experiment_id = 'lr'
config_file = join(rsmtool_test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
report_env = join('test_outputs', source, 'report',
'.environ.json'.format(experiment_id))
report_ipynb = join('test_outputs', source, 'report',
'{}_report.ipynb'.format(experiment_id))
report_html = join('test_outputs', source, 'report',
'{}_report.html'.format(experiment_id))
del os.environ['RSM_REPORT_DIR']
os.remove(report_env)
Reporter.convert_ipynb_to_html(report_ipynb, report_html)
def test_load_rsmtool_output(self):
source = 'lr-subgroups-with-h2'
experiment_id = 'lr_subgroups_with_h2'
test_dir = dirname(__file__)
config_file = join(test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
output_dir = join('test_outputs', source, 'output')
figure_dir = join('test_outputs', source, 'figure')
comparer = Comparer()
csvs, figs, file_format = comparer.load_rsmtool_output(output_dir,
figure_dir,
experiment_id,
'scale',
['QUESTION', 'L1'])
expected_csv_keys = ['df_coef',
'df_confmatrix',
'df_consistency',
'df_degradation',
'df_descriptives',
'df_disattenuated_correlations',
'df_disattenuated_correlations_by_L1',
'df_disattenuated_correlations_by_L1_overview',
'df_disattenuated_correlations_by_QUESTION',
'df_disattenuated_correlations_by_QUESTION_overview',
'df_eval',
'df_eval_by_L1',
'df_eval_by_L1_m_sd',
'df_eval_by_L1_overview',
'df_eval_by_QUESTION',
'df_eval_by_QUESTION_m_sd',
'df_eval_by_QUESTION_overview',
'df_eval_for_degradation',
'df_feature_cors',
'df_mcor_sc1',
'df_mcor_sc1_L1_overview',
'df_mcor_sc1_QUESTION_overview',
'df_mcor_sc1_by_L1',
'df_mcor_sc1_by_QUESTION',
'df_mcor_sc1_overview',
'df_model_fit',
'df_outliers',
'df_pca',
'df_pcavar',
'df_pcor_sc1',
'df_pcor_sc1_L1_overview',
'df_pcor_sc1_QUESTION_overview',
'df_pcor_sc1_by_L1',
'df_pcor_sc1_by_QUESTION',
'df_pcor_sc1_overview',
'df_percentiles',
'df_score_dist',
'df_scores',
'df_train_features']
expected_fig_keys = ['betas',
'eval_barplot_by_L1',
'eval_barplot_by_QUESTION',
'feature_boxplots_by_L1_svg',
'feature_boxplots_by_QUESTION_svg',
'feature_distplots',
'pca_scree_plot']
assert_equal(file_format, 'csv')
assert_equal(expected_csv_keys, sorted(csvs.keys()))
assert_equal(expected_fig_keys, sorted(figs.keys()))