/usr/share/pyshared/cfflib/loadsave.py is in python-cfflib 2.0.5-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 | """ Routines to load, save a connectome files """
#import cfflib_modified as cfflib
#import cfflib
import cfflib2 as cf
import os.path as op
from zipfile import ZipFile, ZIP_DEFLATED
def load(filename):
""" Load a connectome file either from meta.cml (default)
or from a zipped .cff file
Parameter
---------
filename : string
File to load, either a connectome markup file with ending .cml
or a zipped connectome file with ending .cff
Notes
-----
By the file name ending, the appropriate load function is selected.
They can be either .cml or .cff for unzipped or zipped connectome
files respectively.
"""
if isinstance(filename, basestring):
# check if file exists
from os.path import isfile, abspath
if isfile(filename):
if filename.endswith('.cff'):
fname = abspath(filename)
return _load_from_cff(fname)
elif filename.endswith('.cml'):
fname = abspath(filename)
return _load_from_meta_cml(fname)
else:
raise RuntimeError('%s must end with either .cml or .cff' % filename)
else:
raise RuntimeError('%s seems not to be a valid file string' % filename)
else:
raise RuntimeError('%s seems not to be a valid file string' % filename)
def _load_from_meta_cml(filename):
""" Load connectome file from a meta.cml file. """
with open(filename, 'r') as metacml:
metastr = metacml.read()
connectome = cf.parseString(metastr)
# update references
connectome._update_parent_reference()
connectome.iszip = False
connectome.fname = op.abspath(filename)
# check if names are unique!
connectome.check_names_unique()
return connectome
def _load_from_url(url, to_filename):
""" First downloads the connectome file to a file to_filename
load it and return the reference to the connectome object
Not tested.
"""
from util import download
download(url, to_filename)
return _load_from_cff(to_filename)
def _load_from_cff(filename, *args, **kwargs):
""" Load connectome file given filename
Returns
-------
connectome : ``Connectome``
Connectome Instance
"""
# XXX: take care to have allowZip64 = True (but not supported by unix zip/unzip, same for ubuntu?) ?
_zipfile = ZipFile(filename, 'a', ZIP_DEFLATED)
try:
metadata_string = _zipfile.read('meta.cml')
except: # XXX: what is the correct exception for read error?
raise RuntimeError('Can not extract meta.cml from connectome file.')
# create connectome instance
connectome = cf.parseString(metadata_string)
# update references
connectome._update_parent_reference()
# add additional attributes
connectome.src = filename
# it is from the zip file
connectome.iszip = True
# if it is a zip file, we can assume that the src paths are given relatively
connectome._zipfile = _zipfile
# check if all referenced container elements exist in the archive
connectome.check_file_in_cff()
# check if names are unique!
connectome.check_names_unique()
return connectome
def save_to_meta_cml(connectome, filename = 'meta.cml'):
""" Stores a Connectome Markup File to filename """
if connectome.get_connectome_meta() == None:
print "ERROR - there is no connectome metadata in this connectome"
return
elif connectome.get_connectome_meta().title == None or connectome.get_connectome_meta().title == '':
print "ERROR - the connectome metadata have to contain a unique title"
return
f = open(filename, 'w')
f.write('<?xml version="1.0" encoding="UTF-8"?>\n')
connectome.export(f, 0, namespacedef_='xmlns="http://www.connectomics.org/cff-2" xmlns:cml="http://www.connectomics.org/cff-2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:dcterms="http://purl.org/dc/terms/" xsi:schemaLocation="http://www.connectomics.org/cff-2 connectome.xsd"')
f.close()
def save_to_cff(connectome, filename):
""" Save connectome file to new .cff file on disk """
if connectome.get_connectome_meta() == None:
print "ERROR - there is no connectome metadata in this connectome"
return
elif connectome.get_connectome_meta().title == None or connectome.get_connectome_meta().title == '':
print "ERROR - the connectome metadata have to contain a unique title"
return
_newzip = ZipFile(filename, 'w', ZIP_DEFLATED, allowZip64 = True)
allcobj = connectome.get_all()
# tmpdir
import tempfile
import os
tmpdir = tempfile.gettempdir()
# check if names are unique!
connectome.check_names_unique()
for ele in allcobj:
print "----"
print "Storing element: ", str(ele)
# discover the relative path to use for the save
if hasattr(ele, 'src'):
if ele.src == '':
wt = ele.get_unique_relpath()
print "Created a unique path for element %s: %s" % (str(ele), wt)
else:
wt = ele.src
print "Used .src attribute for relative path: %s" % wt
else:
ele.src = ele.get_unique_relpath()
wt = ele.src
print "Element has no .src attribute. Create it and set it to %s" % ele.src
if not hasattr(ele, 'data'):
# Add if iszip is undefined
# if not hasattr(connectome, 'iszip'):
# connectome.iszip = False
if connectome.iszip:
# extract zip content and add it to new zipfile
if not wt in connectome._zipfile.namelist():
msg = """There exists no file %s in the connectome file you want to save to
"Please create .data and set the attributes right
"according to the documentation"""
raise Exception(msg)
else:
ftmp = connectome._zipfile.extract(wt)
else:
# connectome was not created from a zip
# but for example in an IPython session
# if now fname
if not hasattr(connectome, 'fname'):
connectome.fname = op.abspath(filename)
if hasattr(ele, 'tmpsrc'):
try:
ele.save()
except:
pass
ftmp = ele.tmpsrc
else:
# save the element
try:
ele.save()
except:
# e.g. there is nothing to save exception
ftmp = op.join(op.dirname(connectome.fname), wt)
# use the saved location
# ftmp = ele.tmpsrc
# create path coming from filesystem
#ftmp = op.join(op.dirname(connectome.fname), wt)
if not op.exists(ftmp):
msg = """There exists no file %s for element %s.
"Cannot save connectome file. Please update the element or bug report if it should work.""" % (ftmp, str(ele))
raise Exception(msg)
_newzip.write(ftmp, wt)
else:
# save content to a temporary file according to the objects specs
ele.save()
# get the path
ftmp = ele.tmpsrc
_newzip.write(ftmp, wt)
if connectome.iszip:
# remove file
os.remove(ftmp)
# update ele.src
ele.src = wt
# export and store meta.cml
mpth = op.join(tmpdir, 'meta.cml')
f = open(mpth, 'w')
f.write(connectome.to_xml())
f.close()
_newzip.write(mpth, 'meta.cml')
os.remove(mpth)
_newzip.close()
print "New connectome file written to %s " % op.abspath(filename)
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