[Biopython-dev] checker_function for the options in bio.application.abstractCommandline

[Brad Chapman]

Hi Bartek;

> I think, there's something not exactly consistent about the 
> parameter setting in AbstractCommandline class. 
[...]
> I'm not sure, whether the author meant checker_function to 
> raise an exception when the parameter is not valid, or he 
> just forgot to put the value assignement into another if-then 
> statement with the result of checker_function as condition, but
> I would really appreciate if someone made it more clear.
> 
> I would rather opt for the if-then statement, because it allows 
> me to write simple and self-explanatory checker functions

I can definitely see how this would be useful. Philosophically, I
like the raise an exception approach better (and is actually what I
intended when I wrote the code), but there is really no reason why
we can't support both ways.

What do you think about the attached patch, which clears up the
documentation a bit and adds support for having a 0/1 return value
specifying whether the value is good? I haven't really tested it out
yet (but will before I check it in, promise :-), and just wanted to
make sure it fulfilled what you were looking for.

Thanks much for the comments on the Application commandline stuff.
This is something I worked up until it was decent enough to use, but
haven't had enough time to make it actually be good. If you have any
other patches/comments, they'd be gratefully accepted. 

Thanks again.
Brad
-------------- next part --------------
Index: __init__.py
===================================================================
RCS file: /home/repository/biopython/biopython/Bio/Application/__init__.py,v
retrieving revision 1.1
diff -c -r1.1 __init__.py
*** __init__.py	14 Dec 2001 13:04:22 -0000	1.1
--- __init__.py	18 Jul 2003 17:53:02 -0000
***************
*** 89,103 ****
          for parameter in self.parameters:
              if name in parameter.names:
                  if value is not None:
!                     if parameter.checker_function is not None:
!                         paramater.checker_function(value)
! 
                      parameter.value = value
                  parameter.is_set = 1
                  set_option = 1
  
          if set_option == 0:
              raise ValueError("Option name %s was not found." % name)
                      
  class _AbstractParameter:
      """A class to hold information about a parameter for a commandline.
--- 89,117 ----
          for parameter in self.parameters:
              if name in parameter.names:
                  if value is not None:
!                     self._check_value(value, name, parameter.checker_function)
                      parameter.value = value
                  parameter.is_set = 1
                  set_option = 1
  
          if set_option == 0:
              raise ValueError("Option name %s was not found." % name)
+ 
+     def _check_value(self, value, name, check_function):
+         """Check whether the given value is valid.
+ 
+         This uses the passed function 'check_function', which can either
+         return a [0, 1] (bad, good) value or raise an error. Either way
+         this function will raise an error if the value is not valid, or
+         finish silently otherwise.
+         """
+         if check_function is not None:
+             is_good = check_function(value)
+             if is_good in [0, 1]: # if we are dealing with a good/bad check
+                 if not(is_good):
+                     raise ValueError(
+                             "Invalid parameter value %r for parameter %s" %
+                             (value, name))
                      
  class _AbstractParameter:
      """A class to hold information about a parameter for a commandline.
***************
*** 118,124 ****
      include 'input', 'output', 'file'
  
      o checker_function -- a reference to a function that will determine
!     if a given value is valid for this parameter.
  
      o description -- a description of the option.
  
--- 132,140 ----
      include 'input', 'output', 'file'
  
      o checker_function -- a reference to a function that will determine
!     if a given value is valid for this parameter. This function can either
!     raise an error when given a bad value, or return a [0, 1] decision on
!     whether the value is correct.
  
      o description -- a description of the option.