def _request_list_input(self, key, text):
# type: (str, str) -> None
"""Request a list of values, either strings or 2-tuples of
strings.
Keyword Arguments:
key -- name of the parameter
text -- request message to display
"""
while True:
answer = input(text)
if (not answer):
if (not self[key]):
warnings.warn(': there is no default value')
else:
# Leave default value
break
else:
typeStr = self._parameters[key]['type']
answer = self._from_str_to_list(answer, typeStr)
# The validation process will warn about what was wrong
# if 'answer' is not valid
if ((typeStr == 'pairs')
and self._validate_pairs(key, answer, False)):
self._parameters[key]['value'] = answer
break
elif ((typeStr == 'multiselection')
and self._validate_multiselection(key, answer, False)):
self._parameters[key]['value'] = answer
break
def _request_str_input(self, key, text):
# type: (str, str) -> None
"""Request a string, either a path, one among several options or
a plain string.
Keyword Arguments:
key -- name of the parameter
text -- request message to display
"""
while True:
answer = input(text)
if (not answer):
if (not self[key]):
warnings.warn(': there is no default value')
else:
# Leave default value
break
else:
typeStr = self._parameters[key]['type']
# The validation process will warn about what was wrong
# if 'answer' is not valid
if ((typeStr == 'str')
and self._validate_literal(key, answer, False)):
self._parameters[key]['value'] = answer
break
elif ((typeStr == 'selection')
and self._validate_selection(key, answer, False)):
self._parameters[key]['value'] = answer
break
elif ((typeStr == 'path')
and self._validate_path(key, answer, False)):
self._parameters[key]['value'] = normalise_path(answer)
break
def _request_number(self, key, text):
# type: (str, str) -> None
"""Request a number value, either int or float.
Keyword Arguments:
key -- name of the parameter
text -- request message to display
"""
while True:
answer = input(text)
if (not answer):
if (self[key] is None):
warnings.warn(': there is no default value')
else:
# Leave default value
break
else:
try:
answer = ast.literal_eval(answer)
except ValueError:
typeStr = self._parameters[key]['type']
warnings.warn(": '{0}' type expected".format(typeStr))
else:
# The validation process will warn about what was
# wrong if 'answer' is not valid
if (self._validate_number(key, answer, False)):
self._parameters[key]['value'] = answer
break
def _request_bool(self, key, text):
# type: (str, str) -> None
"""Request a boolean value as "yes" or "no" answer.
Keyword Arguments:
key -- name of the parameter
text -- request message to display
"""
while True:
answer = input(text)
if (not answer):
# Leave default value
break
else:
if (answer.lower() in ['yes', 'y', 'no', 'n']):
answer = answer.lower()
# Translate "yes"/"y" to True and "no"/"n" to False
self._parameters[key]['value'] = answer.startswith('y')
break
else:
warnings.warn((": 'yes', 'y', 'no' or 'n' expected, '{0}' "
"inputted").format(answer))
def _request_range(self, key, text):
# type: (str, str) -> None
"""Request a numeric range of two elements (either integers or
floats).
Both numbers must be of the same type.
Keyword Arguments:
key -- name of the parameter
text -- request message to display
"""
while True:
answer = input(text)
if (not answer):
if (not self[key]):
warnings.warn(': there is no default value')
else:
# Leave default value
break
else:
answer = self._from_str_to_list(answer)
try:
# Convert each string in 'answer' to its
# corresponding numeric type (int or float)
answer = [ast.literal_eval(x) for x in answer]
except SyntaxError:
warnings.warn(": each number must be separated by ','")
except ValueError:
typeStr = self._parameters[key]['type'].split(' ')[0]
warnings.warn(
": list of two '{0}' types expected".format(typeStr))
else:
# The validation process will warn about what was
# wrong if 'answer' is not valid
if (self._validate_range(key, answer, False)):
self._parameters[key]['value'] = answer
break
def __init__(self, support=True, **kwargs):
# type: (bool, ...) -> LFParametersCLI
"""Constructor of the class LFParametersCLI.
First, the module's parameters template file is loaded. Next, if
a source JSON parameters file path is provided, the default
values are overwritten by the corresponding new (valid) values.
Finally, the question-answering system is executed.
Keyword Arguments:
support -- display help information together with the
description [default: True]
"""
LFParameters.__init__(self, **kwargs)
self._showHelp = support
# Launch a question-answering system to review the parameters
print(
("The next questions will help you review the parameters for "
"LipidFinder's{0}{1} module. A short description of the "
"parameter and its current value{0}are displayed. Next, you can "
"either introduce the new value(s) or press ENTER,{0}leaving the"
" default one(s).{0}").format(os.linesep, self._module))
for key in (x for x in self._parameters.keys() if self._is_active(x)):
data = self._parameters[key]
typeStr = data['type']
# Compose the main request message to display
text = '{0}{1}{2}{0}'.format(os.linesep, data['description'],
' [y/n]' if typeStr == 'bool' else '')
if (self._showHelp):
# Show help if available for the parameter
if (('help_cli' in data) and data['help_cli']):
# Some parameters might have an option available
# only for GUI, e.g. "Leave empty to include all."
text += 'Help: {0}{1}'.format(data['help_cli'], os.linesep)
elif ('help' in data):
text += 'Help: {0}{1}'.format(data['help'], os.linesep)
# Request the parameter value with a question-answering
# system
if (typeStr == 'bool'):
# Add the current value to the request message
text += '[current: {0}] '.format('YES' if self[key] else 'NO')
self._request_bool(key, text)
elif (typeStr in ['int', 'float']):
# Add the current value to the request message
if (self[key] is not None):
# Add the current value to the request message
text += '[current: {0}] '.format(self[key])
self._request_number(key, text)
elif (typeStr == 'selection'):
# Add the available options to the request message
text += 'Options: {0}{1}'.format(
self._from_list_to_str(data['options'], typeStr),
os.linesep)
if (self[key]):
# Add the current value to the request message
text += '[current: {0}] '.format(self[key])
self._request_str_input(key, text)
elif (typeStr in ['int range', 'float range']):
if (self[key]):
# Add the current value to the request message
text += '[current: {0}] '.format(
self._from_list_to_str(self[key], typeStr))
self._request_range(key, text)
elif (typeStr == 'multiselection'):
# Add the available options to the request message
text += 'Options: {0}{1}'.format(
self._from_list_to_str(data['options'], typeStr),
os.linesep)
if (self[key]):
# Add the current value to the request message
text += '[current: {0}] '.format(
self._from_list_to_str(self[key], typeStr))
self._request_list_input(key, text)
elif (typeStr == 'pairs'):
# Load the list of valid values for each 2-tuple from
# the first column of the file whose path is saved as
# value of another parameter ("file" key in the current
# parameter's information)
srcFilePath = self._parameters[data['file']]['value']
options = pandas.read_csv(srcFilePath).iloc[:, 0].tolist()
# Add the available options to the request message
text += 'Options: ' + self._from_list_to_str(options, typeStr) \
+ os.linesep
if (self[key]):
# Add the current value to the request message
text += '[current: {0}] '.format(
self._from_list_to_str(self[key], typeStr))
self._request_list_input(key, text)
else:
if (self[key]):
# Add the current value to the request message
text += '[current: {0}] '.format(self[key])
self._request_str_input(key, text)
# Question-answering system to save current parameters' values
text = ("{0}{0}Where do you want to save the new set of parameters "
"(path)?{0} ".format(os.linesep))
while True:
answer = input(text)
if (answer):
self.write(normalise_path(answer))
break