def action_model_template(model, version=None, doc_file=None):
'''
Returns a TSV model reporting template
'''
from flame.documentation import Documentation
documentation = Documentation(model, version, context='model')
if not model:
return False, 'Empty model label'
# get de model repo path
rdir = utils.model_path(model, version)
if not os.path.isfile(os.path.join(rdir, 'results.pkl')):
# compatibity method. use info.pkl
if not os.path.isfile(os.path.join(rdir, 'info.pkl')):
return False, 'Info file not found'
else:
# new method, use results.pkl
if not os.path.isfile(os.path.join(rdir, 'results.pkl')):
return False, 'Info file not found'
if doc_file is not None:
# use the param_file to update existing parameters at the model
# directory and save changes to make them persistent
success, message = documentation.delta(model,
0,
doc_file,
iformat='YAML')
print(success, message)
documentation.get_upf_template2()
return True, 'Model documentation template created'
def action_documentation(model, version=None, doc_file=None, oformat='YAML'):
''' Returns an object with whole results info for a given model and version '''
if model is None:
return False, 'Empty model label'
from flame.documentation import Documentation
# get de model repo path
rdir = utils.model_path(model, version)
if not os.path.isfile(os.path.join(rdir, 'model-results.pkl')):
return False, 'Info file not found'
doc = Documentation(model, version)
# INPUT, the doc_file will be applied to doc as a delta
if doc_file is not None:
success, message = doc.delta(model, version, doc_file, iformat=oformat)
return success, message
# CONSOLE PRINTING
if oformat == 'YAML':
yaml = doc.dumpYAML()
for line in yaml:
line = line.encode("ascii", "ignore")
line = line.decode("ascii", "ignore")
print(line)
return True, 'parameters listed'
# OUTPUT, the doc will be returened as a documentation object
return True, doc
def action_prediction_template(model, version=None):
'''
Returns a TSV model reporting template
'''
from flame.documentation import Documentation
if not model:
return False, 'Empty model label'
documentation = Documentation(model, version, context='prediction')
documentation.get_prediction_template()
return True, 'Prediction template created'
def verify_documentation(endpoint, version=None):
'''
Check that the required fields are completed
'''
blacklist = [
'Species', 'Limits_applicability', 'Experimental_protocol', 'location',
'description', 'endpoint_positive', 'endpoint_negative',
'raw_data_url', 'test_set_size', 'training_set_url', 'test_set_url',
'bootstrap', 'ccp_alpha', 'criterion', 'max_depth', 'max_features',
'max_leaf_nodes', 'max_samples', 'min_impurity_decrease',
'min_impurity_split', 'min_samples_leaf', 'min_samples_split',
'min_weight_fraction_leaf', 'n_estimators', 'n_jobs', 'oob_score',
'random_state', 'verbose', 'warm_start', 'confidence', 'ACP_sampler',
'KNN_NN', 'aggregated', 'aggregation_function', 'conformal_predictors',
'normalizing_model', 'Conformal_mean_interval', 'Conformal_accuracy',
'Q2', 'SDEP', 'Comments', 'Other_related_models', 'Date_of_QMRF',
'Date_of_QMRF_updates', 'QMRF_updates', 'References',
'QMRF_same_models', 'Mechanistic_basis', 'Mechanistic_references',
'Supporting_information', 'Comment_on_the_endpoint',
'Endpoint_data_quality_and_variability', 'Descriptor_selection',
'Internal_validation_2', 'External_validation'
]
if endpoint is None:
return False, 'Empty model label'
# get de model repo path
rdir = utils.model_path(endpoint, version)
if not os.path.isfile(os.path.join(rdir, 'model-results.pkl')):
return False, 'Info file not found'
doc = Documentation(endpoint, version)
fields = [field for field in doc.empty_fields() if field not in blacklist]
if fields:
result = {
'status': 'Failed',
'comments': 'fields not completed',
'Information': fields
}
else:
result = {
'status': 'Passed',
'comments': 'All fields required are completed',
'Information': []
}
return True, result
def action_documentation(model, version=None, doc_file=None, oformat='text'):
''' Returns an object with whole results info for a given model and version '''
if model is None:
return False, 'Empty model label'
from flame.documentation import Documentation
# get de model repo path
rdir = utils.model_path(model, version)
if not os.path.isfile(os.path.join(rdir, 'model-results.pkl')):
return False, 'Info file not found'
doc = Documentation(model, version)
if doc_file is not None:
if oformat == 'JSONS':
# use the param string to update existing parameters at the model
# directory and save changes to make them persistent
success, message = doc.delta(model, 0, doc_file, iformat='JSONS')
return True, 'OK'
else:
# use the param_file to update existing parameters at the model
# directory and save changes to make them persistent
success, message = doc.delta(model, 0, doc_file, iformat='YAML')
if not success:
return False, message
doc = Documentation(model, version)
if oformat != 'text':
return True, doc
else:
order = [
'ID', 'Version', 'Contact', 'Institution', 'Date', 'Endpoint',
'Endpoint_units', 'Interpretation', 'Dependent_variable',
'Species', 'Limits_applicability', 'Experimental_protocol',
'Model_availability', 'Data_info', 'Algorithm', 'Software',
'Descriptors', 'Algorithm_settings', 'AD_method', 'AD_parameters',
'Goodness_of_fit_statistics', 'Internal_validation_1',
'Internal_validation_2', 'External_validation', 'Comments',
'Other_related_models', 'Date_of_QMRF', 'Data_of_QMRF_updates',
'QMRF_updates', 'References', 'QMRF_same_models',
'Comment_on_the_endpoint', 'Endpoint_data_quality_and_variability',
'Descriptor_selection'
]
for ik in order:
if ik in doc.fields:
k = ik
v = doc.fields[k]
ivalue = ''
idescr = ''
ioptio = ''
## newest parameter formats are extended and contain
## rich metainformation for each entry
if 'value' in v:
if not isinstance(v['value'], dict):
ivalue = v['value']
else:
# print header of dictionary
print(f'{k} :')
# iterate keys assuming existence of value and description
for intk in v['value']:
intv = v['value'][intk]
if not isinstance(intv, dict):
print(f' {intk:27} : {str(intv):30}'
) #{iioptio} {iidescr}')
else:
#print(intk)
intv = v['value'][intk]
iivalue = ''
if "value" in intv:
iivalue = intv["value"]
# else:
# iivalue = intv
iidescr = ''
if "description" in intv and intv[
"description"] is not None:
iidescr = intv["description"]
iioptio = ''
if 'options' in intv:
toptio = intv['options']
if isinstance(toptio, list):
if toptio != [None]:
iioptio = f' {toptio}'
if isinstance(iivalue, float):
iivalue = f'{iivalue:f}'
elif iivalue is None:
iivalue = ''
print(
f' {intk:27} : {str(iivalue):30} #{iioptio} {iidescr}'
)
continue
if 'description' in v:
idescr = v['description']
if 'options' in v:
toptio = v['options']
if isinstance(toptio, list):
ioptio = f' {toptio}'
print(f'{k:30} : {str(ivalue):30} #{ioptio} {idescr}')
return True, 'parameters listed'