/usr/share/pyshared/nipype/utils/docparse.py is in python-nipype 0.5.3-2wheezy2.
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# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Utilities to pull in documentation from command-line tools.
Examples
--------
# Instantiate bet object
from nipype.interfaces import fsl
from nipype.utils import docparse
better = fsl.Bet()
docstring = docparse.get_doc(better.cmd, better.opt_map)
"""
import subprocess
from nipype.interfaces.base import CommandLine
from nipype.utils.misc import is_container
def grab_doc(cmd, trap_error=True):
"""Run cmd without args and grab documentation.
Parameters
----------
cmd : string
Command line string
trap_error : boolean
Ensure that returncode is 0
Returns
-------
doc : string
The command line documentation
"""
proc = subprocess.Popen(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
stdout, stderr = proc.communicate()
if trap_error and proc.returncode:
msg = 'Attempting to run %s. Returned Error: %s'%(cmd,stderr)
raise IOError(msg)
if stderr:
# A few programs, like fast and fnirt, send their help to
# stderr instead of stdout.
# XXX: Test for error vs. doc in stderr
return stderr
return stdout
def reverse_opt_map(opt_map):
"""Reverse the key/value pairs of the option map in the interface classes.
Parameters
----------
opt_map : dict
Dictionary mapping the attribute name to a command line flag.
Each interface class defines these for the command it wraps.
Returns
-------
rev_opt_map : dict
Dictionary mapping the flags to the attribute name.
"""
# For docs, we only care about the mapping from our attribute
# names to the command-line flags. The 'v.split()[0]' below
# strips off the string format characters.
# if (k != 'flags' and v) , key must not be flags as it is generic,
# v must not be None or it cannot be parsed by this line
revdict = {}
for key, value in opt_map.items():
if is_container(value):
# The value is a tuple where the first element is the
# format string and the second element is a docstring.
value = value[0]
if (key != 'flags' and value is not None):
revdict[value.split()[0]] = key
return revdict
def format_params(paramlist, otherlist=None):
"""Format the parameters according to the nipy style conventions.
Since the external programs do not conform to any conventions, the
resulting docstrings are not ideal. But at a minimum the
Parameters section is reasonably close.
Parameters
----------
paramlist : list
List of strings where each list item matches exactly one
parameter and it's description. These items will go into the
'Parameters' section of the docstring.
otherlist : list
List of strings, similar to paramlist above. These items will
go into the 'Other Parameters' section of the docstring.
Returns
-------
doc : string
The formatted docstring.
"""
hdr = 'Parameters'
delim = '----------'
paramlist.insert(0, delim)
paramlist.insert(0, hdr)
params = '\n'.join(paramlist)
otherparams = []
doc = ''.join(params)
if otherlist:
hdr = 'Others Parameters'
delim = '-----------------'
otherlist.insert(0, delim)
otherlist.insert(0, hdr)
otherlist.insert(0, '\n')
otherparams = '\n'.join(otherlist)
doc = ''.join([doc, otherparams])
return doc
def insert_doc(doc, new_items):
"""Insert ``new_items`` into the beginning of the ``doc``
Docstrings in ``new_items`` will be inserted right after the
*Parameters* header but before the existing docs.
Parameters
----------
doc : str
The existing docstring we're inserting docmentation into.
new_items : list
List of strings to be inserted in the ``doc``.
Examples
--------
>>> from nipype.utils.docparse import insert_doc
>>> doc = '''Parameters
... ----------
... outline :
... something about an outline'''
>>> new_items = ['infile : str', ' The name of the input file']
>>> new_items.extend(['outfile : str', ' The name of the output file'])
>>> newdoc = insert_doc(doc, new_items)
>>> print newdoc
Parameters
----------
infile : str
The name of the input file
outfile : str
The name of the output file
outline :
something about an outline
"""
# Insert new_items after the Parameters header
doclist = doc.split('\n')
tmpdoc = doclist[:2]
# Add new_items
tmpdoc.extend(new_items)
# Add rest of documents
tmpdoc.extend(doclist[2:])
# Insert newlines
newdoc = []
for line in tmpdoc:
newdoc.append(line)
newdoc.append('\n')
# We add one too many newlines, remove it.
newdoc.pop(-1)
return ''.join(newdoc)
def build_doc(doc, opts):
"""Build docstring from doc and options
Parameters
----------
rep_doc : string
Documentation string
opts : dict
Dictionary of option attributes and keys. Use reverse_opt_map
to reverse flags and attrs from opt_map class attribute.
Returns
-------
newdoc : string
The docstring with flags replaced with attribute names and
formated to match nipy standards (as best we can).
"""
# Split doc into line elements. Generally, each line is an
# individual flag/option.
doclist = doc.split('\n')
newdoc = []
flags_doc = []
for line in doclist:
linelist = line.split()
if not linelist:
# Probably an empty line
continue
# For lines we care about, the first item is the flag
if ',' in linelist[0]: #sometimes flags are only seperated by comma
flag = linelist[0].split(',')[0]
else:
flag = linelist[0]
attr = opts.get(flag)
if attr is not None:
#newline = line.replace(flag, attr)
# Replace the flag with our attribute name
linelist[0] = '%s :' % str(attr)
# Add some line formatting
linelist.insert(1, '\n ')
newline = ' '.join(linelist)
newdoc.append(newline)
else:
if line[0].isspace():
# For all the docs I've looked at, the flags all have
# indentation (spaces) at the start of the line.
# Other parts of the docs, like 'usage' statements
# start with alpha-numeric characters. We only care
# about the flags.
flags_doc.append(line)
return format_params(newdoc, flags_doc)
def get_doc(cmd, opt_map, help_flag=None, trap_error=True):
"""Get the docstring from our command and options map.
Parameters
----------
cmd : string
The command whose documentation we are fetching
opt_map : dict
Dictionary of flags and option attributes.
help_flag : string
Provide additional help flag. e.g., -h
trap_error : boolean
Override if underlying command returns a non-zero returncode
Returns
-------
doc : string
The formated docstring
"""
res = CommandLine('which %s' % cmd.split(' ')[0]).run()
cmd_path = res.runtime.stdout.strip()
if cmd_path == '':
raise Exception('Command %s not found'%cmd.split(' ')[0])
if help_flag:
cmd = ' '.join((cmd,help_flag))
doc = grab_doc(cmd,trap_error)
opts = reverse_opt_map(opt_map)
return build_doc(doc, opts)
def _parse_doc(doc, style=['--']):
"""Parses a help doc for inputs
Parameters
----------
doc : string
Documentation string
style : string default ['--']
The help command style (--, -)
Returns
-------
optmap : dict of input parameters
"""
# Split doc into line elements. Generally, each line is an
# individual flag/option.
doclist = doc.split('\n')
optmap = {}
if isinstance(style,str):
style = [style]
for line in doclist:
linelist = line.split()
flag =[item for i,item in enumerate(linelist) if i<2 and \
any([item.startswith(s) for s in style]) and \
len(item)>1]
if flag:
if len(flag)==1:
style_idx = [flag[0].startswith(s) for s in style].index(True)
flag = flag[0]
else:
style_idx = []
for f in flag:
for i,s in enumerate(style):
if f.startswith(s):
style_idx.append(i)
break
flag = flag[style_idx.index(min(style_idx))]
style_idx = min(style_idx)
optmap[flag.split(style[style_idx])[1]] = '%s %%s'%flag
return optmap
def get_params_from_doc(cmd, style='--', help_flag=None, trap_error=True):
"""Auto-generate option map from command line help
Parameters
----------
cmd : string
The command whose documentation we are fetching
style : string default ['--']
The help command style (--, -). Multiple styles can be provided in a
list e.g. ['--','-'].
help_flag : string
Provide additional help flag. e.g., -h
trap_error : boolean
Override if underlying command returns a non-zero returncode
Returns
-------
optmap : dict
Contains a mapping from input to command line variables
"""
res = CommandLine('which %s' % cmd.split(' ')[0]).run()
cmd_path = res.runtime.stdout.strip()
if cmd_path == '':
raise Exception('Command %s not found'%cmd.split(' ')[0])
if help_flag:
cmd = ' '.join((cmd,help_flag))
doc = grab_doc(cmd,trap_error)
return _parse_doc(doc,style)
def replace_opts(rep_doc, opts):
"""Replace flags with parameter names.
This is a simple operation where we replace the command line flags
with the attribute names.
Parameters
----------
rep_doc : string
Documentation string
opts : dict
Dictionary of option attributes and keys. Use reverse_opt_map
to reverse flags and attrs from opt_map class attribute.
Returns
-------
rep_doc : string
New docstring with flags replaces with attribute names.
Examples
--------
doc = grab_doc('bet')
opts = reverse_opt_map(fsl.Bet.opt_map)
rep_doc = replace_opts(doc, opts)
"""
# Replace flags with attribute names
for key, val in opts.items():
rep_doc = rep_doc.replace(key, val)
return rep_doc
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