Source code for bioscons.utils

from os.path import join
import os.path

try:
    from SCons.Script import PathVariable
except ImportError:
    # we expect this to fail unless imported from within SConstruct
    pass

class verbose(object):
    """
    Decorator class to provide more verbose progress messages.
    """
    def __init__(self, f):
        self.f = f

    def __call__(self, *args, **kwargs):
        print("entering", self.f.__name__, 'called with arguments', args, kwargs)
        self.f(*args, **kwargs)
        print("exiting", self.f.__name__)


def getvars(config, secnames, indir=None, outdir=None,
            fmt_in='%(sec)s-infiles', fmt_out='%(sec)s-outfiles',
            fmt_params='%(sec)s-params'):
    """
    Return a tuple of configuration variables that may be passed to
    vars.AddVariables().

    * config - an instance of ConfigParser.SafeConfigParser()
    * secnames - a list of section names from which to import variables
    * indir - path to a directory to prepend to filenames if not found in cwd
    * outdir - path to a directory to prepend to output files.
    * fmt_* - formatting string defining sections corresponding to infiles,
      outfiles, and params for each section

    Example::

      vars = Variables()
      varlist = utils.getvars(config, ['ncbi','placefiles'],
                              indir=output, outdir=output)
      vars.AddVariables(*varlist)
    """

    vars = []

    # values from defaults section
    defaults = [k for k,v in config.items('DEFAULT')]
    for varname, val in config.items('DEFAULT'):
        if os.path.isdir(val):
            vars.append(PathVariable(
                varname, '%s (DEFAULT)' % varname, val, PathVariable.PathIsDir))
        if os.path.isfile(val):
            vars.append(
                PathVariable(varname, '%s (DEFAULT)' % varname, val,
                             PathVariable.PathIsFile))
        else:
            vars.append((varname, val, val))

    for sec in secnames:
        # input files and directories
        for varname,pth in config.items(fmt_in % locals()):
            if varname in defaults:
                continue
            elif os.path.exists(pth):
                pth = os.path.abspath(pth)
            elif indir:
                pth = join(indir, pth)
            else:
                raise OSError(
                    'Error in [%(sec)s] %(varname)s = %(pth)s: specify either an existing path or provide a default input directory using `indir`' % \
                        locals())

            vars.append(PathVariable(varname, '', pth))

        # output files and directories
        for varname,pth in config.items(fmt_out % locals()):
            if varname in defaults:
                continue
            elif outdir and not (pth.startswith(outdir) or pth.startswith('.')):
                pth = join(outdir, pth)
            else:
                pth = os.path.abspath(pth)

            # TODO: document this behavior (assume var is a directory if ends with 'dir')
            if varname.endswith('dir') or os.path.isdir(pth):
                pvar = PathVariable.PathIsDirCreate
            else:
                pvar = PathVariable.PathAccept

            vars.append(PathVariable(varname, '', pth, pvar))

        # ordinary variables; no path checking or directory creation
        params = fmt_params % locals()
        for varname, val in config.items(params):
            if varname in defaults:
                continue
            vars.append(
                (varname, '%(varname)s: defined in [%(params)s]' % locals(), val))

    return tuple(vars)