# mtypes.py ---
#
# Filename: mtypes.py
# Description:
# Author:
# Maintainer:
# Created: Fri Feb 8 11:29:36 2013 (+0530)
# Version:
# Last-Updated: Tue Mar 1 02:52:35 2016 (-0500)
# By: subha
# Update #: 182
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# Utility to detect the model type in a file
#
#
# Change log:
#
#
#
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 3, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; see the file COPYING. If not, write to
# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
# Floor, Boston, MA 02110-1301, USA.
#
#
# Code:
from __future__ import print_function
import re
import moose
##!!!!!!!!!!!!!!!!!!!!!!!!!!!!
## !! This was stolen from
## http://eli.thegreenplace.net/2011/10/19/perls-guess-if-file-is-text-or-binary-implemented-in-python/#id2
import sys
PY3 = sys.version_info[0] >= 3
# A function that takes an integer in the 8-bit range and returns
# a single-character byte object in py3 / a single-character string
# in py2.
#
int2byte = (lambda x: bytes((x,))) if PY3 else chr
_text_characters = (
b''.join(int2byte(i) for i in range(32, 127)) +
b'\n\r\t\f\b')
def istextfile(fileobj, blocksize=512):
""" Uses heuristics to guess whether the given file is text or binary,
by reading a single block of bytes from the file.
If more than 30% of the chars in the block are non-text, or there
are NUL ('\x00') bytes in the block, assume this is a binary file.
- Originally written by Eli Bendersky from the algorithm used
in Perl:
http://eli.thegreenplace.net/2011/10/19/perls-guess-if-file-is-text-or-binary-implemented-in-python/#id2
"""
block = fileobj.read(blocksize)
if b'\x00' in block:
# Files with null bytes are binary
return False
elif not block:
# An empty file is considered a valid text file
return True
# Use translate's 'deletechars' argument to efficiently remove all
# occurrences of _text_characters from the block
nontext = block.translate(None, _text_characters)
return float(len(nontext)) / len(block) <= 0.30
## Eli Bendersky till here !!
##!!!!!!!!!!!!!!!!!!!!!!!!!!!!
def getType(filename, mode='t'):
"""Returns the type of the model in file `filename`. Returns None
if type is not known.
mode: 'b' for binary, 't' for text. Not used currently.
"""
mtype = None
msubtype = None
if mode == 't':
for typename, typefunc in list(typeChecks.items()):
if typefunc(filename):
return typename
return None
def getSubtype(filename, typename):
"""Returns what subtype of the specified `typename` is the model file.
None if could not resolve the subtype.
"""
for subtype in subtypes[typename]:
subtypeFunc = subtypeChecks['%s/%s' % (typename, subtype)]
if subtypeFunc(filename):
return subtype
return ''
# Dictionary of model description types and functions to detect them.
#
# Fri Feb 8 11:07:41 IST 2013 - as of now we only recognize GENESIS .g
# XML .xml extensions
#
# Fri Feb 22 16:29:43 IST 2013 - added .cspace
isCSPACE = lambda x: x.lower().endswith('.cspace')
isGENESIS = lambda x: x.lower().endswith('.g') or x.endswith('.p')
isXML = lambda x: x.lower().endswith('.xml')
isProto = lambda x: x.lower().endswith('.p')
import xml.dom.minidom as md
def isNeuroML(filename):
"""Check if a model is in neuroml format. An xml document is
considered a neuroml if the top level element is either
'networkml', morphml', 'channelml' or 'neuroml'.
"""
doc = md.parse(filename)
for child in doc.childNodes:
print(child.nodeName, child.nodeType == child.ELEMENT_NODE)
if child.nodeType == child.ELEMENT_NODE and \
(child.nodeName == 'networkml' or \
child.nodeName == 'morphml' or \
child.nodeName == 'channelml'or \
child.nodeName == 'neuroml'):
return True
return False
def isSBML(filename):
"""Check model in `filename` is in SBML format."""
doc = md.parse(filename)
for child in doc.childNodes:
if child.nodeType == child.ELEMENT_NODE and \
child.nodeName == 'sbml':
return True
return False
def isKKIT(filename):
"""Check if `filename` is a GENESIS/KINETIKIT file.
"""
pattern = re.compile('include\s+kkit') # KKIT files must have "include kkit" statement somewhere
with open(filename, 'r') as infile:
while True:
sentence = ''
contd = False # Flags if we are inside a multi-line entry
line = infile.readline()
if not line: # End of file
return False
line = line.strip()
# print 'read:', line
if line.find('//') == 0: # skip c++ style comment lines
# print 'c++ comment'
continue
# Skip C style multi-line comments
comment_start = line.find('/*')
if comment_start >= 0:
sentence = line[:comment_start]
# print 'cstart', comment_start, sentence
while comment_start >= 0 and line:
# print '#', line
comment_end = line.find('*/')
if comment_end >= 0:
comment_start = -1;
line = line[comment_end+2:] # keep the rest of the line
break
line = infile.readline()
if line:
line = line.strip()
# Keep extending the sentence with next line if current
# line ends with continuation token '\'
if line:
contd = line.endswith('\\')
while line and contd:
sentence += ' ' + line[:-1]
line = infile.readline()
if line:
line = line.strip()
contd = line.endswith('\\')
# if contd turned false, the last line came out of the
# while loop unprocessed
if line:
sentence += ' ' + line
# print '>', sentence
if re.search(pattern, sentence):
return True
return False
# Mapping model types to functions to check them. These functions
# should take the filename as the single argument and return True or
# False. Define new functions for new model type checks and add them
# here.
typeChecks = {
'cspace': isCSPACE,
'genesis': isGENESIS,
'xml': isXML,
}
# These are "type/subtype": function maps for checking model subtype
# New model types with subtypes should be added here with
# corresponding checker function.
subtypeChecks = {
'genesis/kkit': isKKIT,
'genesis/proto': isProto,
'xml/neuroml': isNeuroML,
'xml/sbml': isSBML,
}
# Mapping types to list of subtypes.
subtypes = {
'cspace': [],
'genesis': ['kkit', 'proto'],
'xml': ['neuroml', 'sbml'],
}
#
# mtypes.py ends here