# -*- coding: utf-8 -*-
# This software and supporting documentation are distributed by
# Institut Federatif de Recherche 49
# CEA/NeuroSpin, Batiment 145,
# 91191 Gif-sur-Yvette cedex
# France
#
# This software is governed by the CeCILL-B license under
# French law and abiding by the rules of distribution of free software.
# You can use, modify and/or redistribute the software under the
# terms of the CeCILL-B license as circulated by CEA, CNRS
# and INRIA at the following URL "http://www.cecill.info".
#
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
#
# In this respect, the user's attention is drawn to the risks associated
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean that it is complicated to manipulate, and that also
# therefore means that it is reserved for developers and experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or
# data to be ensured and, more generally, to use and operate it in the
# same conditions as regards security.
#
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL-B license and that you accept its terms.
'''
This module contains all the framework necessary to customize, read and
write minf files. A minf file is composed of structured data saved in
XML or Python format. The minf framework provides tools to read and write
minf files but also to customize the way Python objects are read an written.
There are several submodules in this package but main functions and classes
can be imported from :py:mod:`soma.minf.api`:
- for reading minf files: :func:`iterateMinf`, :func:`readMinf`
- for writing minf files: :func:`createMinfWriter`, :func:`writeMinf`
- for customizing minf files: :func:`createReducerAndExpander`, :func:`registerClass`, :func:`registerClassAs`
* author: Yann Cointepas
* organization: NeuroSpin
* license: `CeCILL B <http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html>`_
'''
from __future__ import print_function
from __future__ import absolute_import
__docformat__ = "restructuredtext en"
import gzip
import six
import sys
from soma.translation import translate as _
from soma.minf.error import MinfError
from soma.bufferandfile import BufferAndFile
from soma.minf.reader import MinfReader
from soma.minf.writer import MinfWriter
from soma.minf.tree import createReducerAndExpander, registerClass, \
registerClassAs, createMinfExpander, \
EndStructure, MinfReducer, MinfExpander, \
listStructure, dictStructure
from soma.undefined import Undefined
defaultReducer = MinfReducer.defaultReducer
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
def _setTarget(target, source):
try:
from soma.signature.api import HasSignature
except ImportError:
class HasSignature(object):
pass
if isinstance(source, dict):
if isinstance(target, dict):
target.update(source)
return True
elif isinstance(target, HasSignature):
for k, v in six.iteritems(source):
attrTarget = getattr(target, k, Undefined)
if attrTarget is Undefined:
setattr(target, k, v)
else:
if not _setTarget(attrTarget, v):
setattr(target, k, v)
return True
return False
#------------------------------------------------------------------------------
[docs]def iterateMinf(source, targets=None, stop_on_error=True, exceptions=[]):
'''
Returns an iterator over all objects stored in a minf file.
Example:
::
from soma.minf.api import iterateMinf
for item in iterateMinf('test.minf'):
print(repr(item))
Parameters
----------
source: string
Input file name or file object. If it is a file name, it is
opened with C{open( source )}.
'''
if targets is not None:
targets = iter(targets)
initial_source = source
if not hasattr(initial_source, 'readline') and not six.PY2:
# in python3 the encoding of a file should be specified when opening
# it: it cannot be changed afterwards. So in python3 we cannot read
# the encoding within the file (for instance in a XML file).
# This is completely silly, but here it is...
# So we just have to try several encodings...
try_encodings = ['UTF-8', 'latin1']
else:
try_encodings = [None]
for encoding in try_encodings:
opened_source_file = None
if not hasattr(initial_source, 'readline'):
if six.PY2:
opened_source_file = open(initial_source)
else:
opened_source_file = open(initial_source, encoding=encoding)
source = BufferAndFile(opened_source_file)
elif not isinstance(source, BufferAndFile):
source.seek(0)
source = BufferAndFile(source)
try:
# Check first non white character to see if the minf file is XML or not
start = source.read(5)
source.unread(start)
if start == 'attri':
try:
import numpy
d = {'nan': numpy.nan}
except Exception:
d = {'nan': None}
try:
six.exec_(source.read().replace("\r\n", "\n"), d)
except Exception as e:
x = source
if hasattr(source, '_BufferAndFile__file'):
x = source._BufferAndFile__file
x = 'Error in iterateMinf while reading ' + str(x) + ': '
# e.args = ( x + e.args[0], ) + e.args[1:]
print(x)
raise
minf = d['attributes']
if targets is not None:
result = next(targets)
_setTarget(result, minf)
yield result
else:
yield minf
return
elif start != '<?xml':
# Try gzip compressed file
gzSource = gzip.open(source.name, mode='rt', encoding=encoding)
if gzSource.read(5) != '<?xml':
raise MinfError(_('Invalid minf file: %s')
% (source.name, ))
source = BufferAndFile(gzSource)
source.unread('<?xml')
r = MinfReader.createReader('XML')
iterator = r.nodeIterator(source)
minfNode = next(iterator)
expander = createMinfExpander(minfNode.attributes['reduction'])
count = 0
for nodeItem in iterator:
count += 1
if isinstance(nodeItem, EndStructure):
break
target = None
if targets is not None:
try:
target = next(targets)
except StopIteration:
targets = None
yield expander.expand(iterator, nodeItem, target=target,
stop_on_error=stop_on_error,
exceptions=exceptions)
except UnicodeDecodeError as e:
if encoding == try_encodings[-1]:
raise
continue
finally:
if opened_source_file is not None:
opened_source_file.close()
break # no error, don't process next encoding
#------------------------------------------------------------------------------
[docs]def readMinf(source, targets=None, stop_on_error=True, exceptions=[]):
'''
Entirerly reads a minf file and returns its content in a tuple.
Equivalent to tuple(iterateMinf(source)).
see: :func`iterateMinf`
'''
return tuple(iterateMinf(source, targets=targets,
stop_on_error=stop_on_error,
exceptions=exceptions))
#------------------------------------------------------------------------------
[docs]def createMinfWriter(destFile, format='XML', reducer='minf_2.0'):
'''
Create a writer for storing objects in destFile.
Example:
::
from soma.minf.api import createMinfWriter
writer = createMinfWriter( '/tmp/test.minf' )
writer.write( 'A string' )
writer.write( { 'A dict key': [ 'A list', 'with two elements' ] } )
writer.close()
Parameters
----------
format: string
name of the format to write.
reducer: string
name of the reducer to use (see L{soma.minf.tree} for
more information about reducers).
'''
return MinfWriter.createWriter(destFile, format, reducer)
#------------------------------------------------------------------------------
[docs]def writeMinf(destFile, args, format='XML', reducer=None):
'''
Creates a minf writer with :func:`createMinfWriter` and write the content
of args in it.
Parameters
----------
destFile:
see :func:`createMinfWriter`
args: sequence or iterator
series of values to write
format:
see :func:`createMinfWriter`
reducer:
see :func:`createMinfWriter`
'''
it = iter(args)
try:
firstItem = next(it)
except StopIteration:
firstItem = Undefined
if reducer is None:
if firstItem is not Undefined:
reducer = MinfReducer.defaultReducer(firstItem)
if reducer is None:
reducer = 'minf_2.0'
writer = createMinfWriter(destFile, format, reducer)
if firstItem is not Undefined:
writer.write(firstItem)
for item in it:
writer.write(item)
writer.close()
#------------------------------------------------------------------------------
# xml_reader and xml_writer are not used directly but importing
# them register the XML minf format
import soma.minf.xml_reader
import soma.minf.xml_writer
#------------------------------------------------------------------------------
from soma.minf.xhtml import XHTML
from soma.uuid import Uuid
minf_2_0_reducer = MinfReducer('minf_2.0')
minf_2_0_reducer.registerAtomType(None.__class__)
minf_2_0_reducer.registerAtomType(bool)
for t in six.integer_types:
minf_2_0_reducer.registerAtomType(t)
minf_2_0_reducer.registerAtomType(float)
minf_2_0_reducer.registerAtomType(str)
minf_2_0_reducer.registerAtomType(six.text_type) # unicode in Python 2
minf_2_0_reducer.registerAtomType(XHTML)
minf_2_0_reducer.registerClass(list, minf_2_0_reducer.sequenceReducer)
minf_2_0_reducer.registerClass(tuple, minf_2_0_reducer.sequenceReducer)
minf_2_0_reducer.registerClass(dict, minf_2_0_reducer.dictReducer)
minf_2_0_expander = MinfExpander('minf_2.0')
minf_2_0_expander.registerStructure(
listStructure, minf_2_0_expander.sequenceExpander)
minf_2_0_expander.registerStructure(
dictStructure, minf_2_0_expander.dictExpander)
registerClass('minf_2.0', Uuid, 'Uuid')
#------------------------------------------------------------------------------
minf_1_0_reducer = MinfReducer('minf_1.0', ('minf_2.0', ))
minf_1_0_expander = MinfExpander('minf_1.0', ('minf_2.0', ))