# ---------------------------------------------------------------------------- # Copyright (c) 2014--, burrito development team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file LICENSE, distributed with this software. # ---------------------------------------------------------------------------- from copy import deepcopy from collections import Mapping def is_not_None(x): """Returns True if x is not None""" return x is not None class ParameterError(ValueError): """Error raised when field in parameter is bad""" pass class FilePath(str): """ Hold paths for proper handling Paths in this sense are filenames, directory paths, or filepaths. Some examples include: file.txt ./path/to/file.txt ./path/to/dir/ /path/to/file.txt . / The purpose of this class is to allow all paths to be handled the same since they sometimes need to be treated differently than simple strings. For example, if a path has a space in it, and it is being passed to system, it needs to be wrapped in quotes. But, you wouldn't want it as a string wrapped in quotes b/c, e.g., isabs('"/absolute/path"') == False, b/c the first char is a ", not a /. * This would make more sense to call Path, but that conflicts with the ResultPath.Path attribute. I'm not sure what to do about this and want to see what others think. Once finalized, a global replace should take care of making the switch. """ def __new__(cls, path): try: return str.__new__(cls, path.strip('"')) except AttributeError: return str.__new__(cls, '') def __str__(self): """ wrap self in quotes, or return the empty string if self == '' """ if self == '': return '' return ''.join(['"', self, '"']) def __add__(self, other): return FilePath(''.join([self, other])) class Parameter(object): """Stores information regarding a parameter to an application. An abstract class. """ def __init__(self, Prefix, Name, Value=None, Delimiter=None, Quote=None, IsPath=None): """Initialize the Parameter object. Prefix: the character(s) preceding the name of the parameter (eg. '-' for a '-a' parameter) Name: the name of the parameter (eg. 'a' for a '-a' parameter) Value: the value of the parameter (eg. '9' in a '-t=9' parameter) The value is also used in subclasses to turn parameters on and off Delimiter: the character separating the identifier and the value, (eg. '=' for a '-t=9' command or ' ' for a '-t 9' parameter) Quote: the character to use when quoting the value (eg. "\"" for a '-l="hello" parameter). At this point asymmetrical quotes are not possible (ie. [4]) WARNING: You must escape the quote in most cases. IsPath: boolean indicating whether Value is a file path, and should therefore be cast to a FilePath object WARNING: Don't set Quote='"' and set IsPath=True. This would result in two sets of double quotes being wrapped around the path when it is printed, and the application would most likely fail. We explicitly disallow this with: if self.IsPath and self.Quote == '"': self.Quote = None Id: The combination of Prefix and Name is called the identifier (Id) of the parameter. (eg. '-a' for a '-a' parameter, or '-t' for a '-t=9' parameter) This is intended to be an abstract class and has no use otherwise. To subclass Parameter, the subclass should implement the following methods: __str__(): returns the parameter as a string when turned on, or as an empty string when turned off on(): turns the parameter on isOn(): return True if a parameter is on, otherwise False off(): turns the parameter off isOff(): return True if a parameter is off, otherwise False Whether a parameter is on or off can be specified in different ways in subclasses, your isOn() and isOff() methods should define this. Optionally you can overwrite __init__, but you should be sure to either call the superclass init or handle the setting of the self._default attribute (or things will break!) """ self.Name = Name self.Prefix = Prefix self.Delimiter = Delimiter self.Quote = Quote self.Value = Value self.IsPath = IsPath if self.IsPath and self.Quote == '"': self.Quote = None def _get_id(self): """Construct and return the identifier""" return ''.join(map(str, filter(is_not_None, [self.Prefix, self.Name]))) Id = property(_get_id) def __eq__(self, other): """Return True if two parameters are equal""" return (self.IsPath == other.IsPath) and\ (self.Name == other.Name) and\ (self.Prefix == other.Prefix) and\ (self.Delimiter == other.Delimiter) and \ (self.Quote == other.Quote) and \ (self.Value == other.Value) def __ne__(self, other): """Return True if two parameters are not equal to each other""" return not self == other class FlagParameter(Parameter): """Stores information regarding a flag parameter to an application""" def __init__(self, Prefix, Name, Value=False): """Initialize a FlagParameter object Prefix: the character(s) preceding the name of the parameter (eg. '-' for a '-a' parameter) Name: the name of the parameter (eg. 'a' for a '-a' parameter) Value: determines whether the flag is turned on or not; should be True to turn on, or False to turn off, False by default Id: The combination of Prefix and Name is called the identifier (Id) of the parameter. (eg. '-a' for a '-a' parameter, or '-t' for a '-t=9' parameter) Usage: f = FlagParameter(Prefix='-',Name='a') Parameter f is turned off by default, so it won't be used by the application until turned on. or f = FlagParameter(Prefix='+',Name='d',Value=True) Parameter f is turned on. It will be used by the application. """ super(FlagParameter, self).__init__(Name=Name, Prefix=Prefix, Value=Value, Delimiter=None, Quote=None) def __str__(self): """Return the parameter as a string. When turned on: string representation of the parameter When turned off: empty string """ if self.isOff(): return '' else: return ''.join(map(str, [self.Prefix, self.Name])) def isOn(self): """Returns True if the FlagParameter is turned on. A FlagParameter is turned on if its Value is True or evaluates to True. A FlagParameter is turned off if its Value is False or evaluates to False. """ if self.Value: return True return False def isOff(self): """Returns True if the parameter is turned off A FlagParameter is turned on if its Value is True or evaluates to True. A FlagParameter is turned off if its Value is False or evaluates to False. """ return not self.isOn() def on(self): """Turns the FlagParameter ON by setting its Value to True""" self.Value = True def off(self): """Turns the FlagParameter OFF by setting its Value to False""" self.Value = False class ValuedParameter(Parameter): """Stores information regarding a valued parameter to an application""" def __init__(self, Prefix, Name, Value=None, Delimiter=None, Quote=None, IsPath=False): """Initialize a ValuedParameter object. Prefix: the character(s) preceding the name of the parameter (eg. '-' for a '-a' parameter) Name: the name of the parameter (eg. 'a' for a '-a' parameter) Value: the value of the parameter (eg. '9' in a '-t=9' parameter) Delimiter: the character separating the identifier and the value, (eg. '=' for a '-t=9' command or ' ' for a '-t 9' parameter) Quote: the character to use when quoting the value (eg. "\"" for a '-l="hello" parameter). At this point asymmetrical quotes are not possible (ie. [4]) WARNING: You must escape the quote in most cases. IsPath: boolean indicating whether Value is a file path, and should therefore be cast to a FilePath object Id: The combination of Prefix and Name is called the identifier (Id) of the parameter. (eg. '-a' for a '-a' parameter, or '-t' for a '-t=9' parameter) Default: the default value of the parameter; this is defined as what is passed into init for Value and can not be changed after object initialization Usage: v = ValuedParameter(Prefix='-',Name='a',Delimiter=' ',Value=3) the parameter is turned on by default (value=3) and will be used by the application as '-a 3'. or v = ValuedParameter(Prefix='-',Name='d',Delimiter='=') the parameter is turned off by default and won't be used by the application unless turned on with some value. """ if IsPath and Value: Value = FilePath(Value) super(ValuedParameter, self).__init__(Name=Name, Prefix=Prefix, Value=Value, Delimiter=Delimiter, Quote=Quote, IsPath=IsPath) self._default = Value def __str__(self): """Return the parameter as a string When turned on: string representation of the parameter When turned off: empty string """ if self.isOff(): return '' else: parts = [self.Prefix, self.Name, self.Delimiter, self.Quote, self.Value, self.Quote] return ''.join(map(str, filter(is_not_None, parts))) def __eq__(self, other): """Return True if two parameters are equal""" return (self.Name == other.Name) and\ (self.Prefix == other.Prefix) and\ (self.Delimiter == other.Delimiter) and \ (self.Quote == other.Quote) and \ (self.Value == other.Value) and\ (self._default == other._default) def _get_default(self): """Get the default value of the ValuedParameter Accessed as a property to avoid the user changing this after initialization. """ return self._default Default = property(_get_default) def reset(self): """Reset Value of the ValuedParameter to the default""" self.Value = self._default def isOn(self): """Returns True if the ValuedParameter is turned on A ValuedParameter is turned on if its Value is not None. A ValuedParameter is turned off if its Value is None. """ if self.Value is not None: return True return False def isOff(self): """Returns True if the ValuedParameter is turned off A ValuedParameter is turned on if its Value is not None. A ValuedParameter is turned off if its Value is None. """ return not self.isOn() def on(self, val): """Turns the ValuedParameter ON by setting its Value to val An attempt to turn the parameter on with value 'None' will result in an error, since this is the same as turning the parameter off. """ if val is None: raise ParameterError("Turning the ValuedParameter on with value " "None is the same as turning it off. " "Use another value.") elif self.IsPath: self.Value = FilePath(val) else: self.Value = val def off(self): """Turns the ValuedParameter OFF by setting its Value to None""" self.Value = None class MixedParameter(ValuedParameter): """Stores information regarding a mixed parameter to an application A mixed parameter is a mix between a FlagParameter and a ValuedParameter. When its Value is False, the parameter will be turned off. When its Value is set to None, the parameter will behave like a flag. When its Value is set to anything but None or False, it will behave like a ValuedParameter. Example: RNAfold [-d[0|1]] You can give either '-d' or '-d0' or '-d1' as input. """ def __init__(self, Prefix, Name, Value=False, Delimiter=None, Quote=None, IsPath=False): """Initialize a MixedParameter object Prefix: the character(s) preceding the name of the parameter (eg. '-' for a '-a' parameter) Name: the name of the parameter (eg. 'a' for a '-a' parameter) Value: the value of the parameter (eg. '9' in a '-t=9' parameter) Delimiter: the character separating the identifier and the value, (eg. '=' for a '-t=9' command or ' ' for a '-t 9' parameter) Quote: the character to use when quoting the value (eg. "\"" for a '-l="hello" parameter). At this point asymmetrical quotes are not possible (ie. [4]) WARNING: You must escape the quote in most cases. IsPath: boolean indicating whether Value is a file path, and should therefore be cast to a FilePath object Id: The combination of Prefix and Name is called the identifier (Id) of the parameter. (eg. '-a' for a '-a' parameter, or '-t' for a '-t=9' parameter) Default: the default value of the parameter; this is defined as what is passed into init for Value and can not be changed after object initialization Usage: m = MixedParameter(Prefix='-',Name='a',Delimiter=' ',Value=3) the parameter is turned on by default (value=3) and will be used by the application as '-a 3'. or m = MixedParameter(Prefix='-',Name='d',Delimiter='=',Value=None) the parameter is turned on by default as a flag parameter and will be used by the application as '-d'. or m = MixedParameter(Prefix='-',Name='d',Delimiter='=') the parameter is turned off by default (Value=False) and won't be used by the application unless turned on with some value. """ if IsPath and Value: Value = FilePath(Value) super(MixedParameter, self).__init__(Name=Name, Prefix=Prefix, Value=Value, Delimiter=Delimiter, Quote=Quote, IsPath=IsPath) def __str__(self): """Return the parameter as a string When turned on: string representation of the parameter When turned off: empty string """ if self.isOff(): return '' elif self.Value is None: return ''.join(map(str, [self.Prefix, self.Name])) else: parts = [self.Prefix, self.Name, self.Delimiter, self.Quote, self.Value, self.Quote] return ''.join(map(str, filter(is_not_None, parts))) def isOn(self): """Returns True if the MixedParameter is turned on A MixedParameter is turned on if its Value is not False. A MixedParameter is turned off if its Value is False. A MixedParameter is used as flag when its Value is None. A MixedParameter is used as ValuedParameter when its Value is anything but None or False. """ if self.Value is not False: return True return False def isOff(self): """Returns True if the MixedParameter is turned off A MixedParameter is turned on if its Value is not False. A MixedParameter is turned off if its Value is False. """ return not self.isOn() def on(self, val=None): """Turns the MixedParameter ON by setting its Value to val An attempt to turn the parameter on with value 'False' will result in an error, since this is the same as turning the parameter off. Turning the MixedParameter ON without a value or with value 'None' will let the parameter behave as a flag. """ if val is False: raise ParameterError("Turning the ValuedParameter on with value " "False is the same as turning it off. Use " "another value.") elif self.IsPath: self.Value = FilePath(val) else: self.Value = val def off(self): """Turns the MixedParameter OFF by setting its Value to False""" self.Value = False class Parameters(Mapping): """Parameters is a dictionary of Parameter objects. Parameters provides a mask that lets the user lookup and access parameters by its synonyms. """ def __init__(self, parameters={}, synonyms={}): """Initialize the Parameters object. parameters: a dictionary of Parameter objects keyed by their identifier synonyms: a dictionary of synonyms. Keys are synonyms, values are parameter identifiers. """ self._parameters = deepcopy(parameters) self._synonyms = deepcopy(synonyms) def __len__(self): return len(self._parameters) def __iter__(self): return iter(self._parameters) def __getitem__(self, key): try: key = self._synonyms[key] except KeyError: # the key is not a synonym pass return self._parameters[key] def all_off(self): """Turns all parameters in the dictionary off""" for v in self._parameters.values(): v.off()