def restoreSequence( molecule, sequenceFile ):
"""Restore sequence from sequenceFile.
Return self or None on error.
"""
if (not os.path.exists( sequenceFile ) ):
io.error('Molecule.restoreSequence: sequenceFile "{0}" not found\n',
sequenceFile
)
return None
#end if
# compatibility
if molecule.content.version < 0.92:
fileObject = open(sequenceFile, 'r')
for line in fileObject:
exec(line)
#end for
fileObject.close()
else:
sequence = xmlTools.xML2obj( sequenceFile )
if sequence is None:
io.error('restoreSequence: error parsing xml-file "{0}"', sequenceFile)
return None
for chainId, resName, resNum, convention in sequence:
molecule.addResidue( chainId, resName, resNum, convention )
#end for
#end if
return molecule
def restoreStereoAssignments( molecule, stereoFileName ):
"""
Restore the stereo assignments from xml stereoFileName,
return count or -1 on error
"""
if not os.path.exists( stereoFileName ):
return -1
stereo = xmlTools.xML2obj(stereoFileName)
if stereo is None:
io.error('restoreStereoAssignment: parsing xml-file "{0}"\n', stereoFileName)
return -1
#end if
count = 0
for nameTuple in stereo:
atm = molecule.decodeNameTuple( nameTuple )
if atm is None:
io.error('restoreStereoAssignment: invalid atom nameTuple ({0})', nameTuple)
else:
atm.stereoAssigned = True
count += 1
#end if
#end for
#nTdebug('Molecule.restoreStereoAssignments: restored %d stereo assignments from "%s\n',count, stereoFileName)
return count
def decode(string, backend=None, keys=False, referenceObject=None):
"""
Convert a JSON string into a Python object.
The keyword argument 'keys' defaults to False.
If set to True then jsonpickle will decode non-string dictionary keys
into python objects via the jsonpickle protocol.
referenceObject is passed as attribute to to the unpickler instance (available as 'context'
attribute in custom handlers that are derived from the Basehandler class).
GWV changed to return a tuple
return (obj, metadata) tuple
>>> str(decode('"my string"'))
'my string'
>>> decode('36')
36
"""
from cing.Libs.jsonTools import unpickler
if backend is None:
backend = json
#GWV: unwrap the metadata and the object
metadata,obj = unpickler.decode(string, backend=backend, keys=keys, referenceObject=referenceObject)
if metadata is None:
io.error('jsonTools.decode: failed to decode metadata\n')
if obj is None:
io.error('jsonTools.decode: failed to decode object\n')
return obj, metadata
def restore(self, fromPath=None, restoreLinkages=True):
"""
restore validation data fromPath (set to default if None);
establish linkage to project if restoreLinkages == True
return True on error
"""
if fromPath is None:
fromPath = self.project.path() / cdefs.directories.validation
else:
fromPath = disk.Path(fromPath)
if not fromPath.exists():
io.error('ValidationData.restore: path "{0}" does not exist\n', fromPath)
error = False # used to track if decoding of any of the json files generated an error
for vfile in fromPath.glob('*.json'):
io.debug('ValidationData.restore: restoring {0}, restoreLinkages = \n',
vfile, restoreLinkages)
if restoreLinkages:
if self._restoreWithLinkages(vfile): error = True
else:
if self._restoreWithoutLinkages(vfile): error = True
#end if
#end for
return error
def getResult(self, theObject, key, default=None):
"""v3:Returns validation result from theObject for key,
None if not present or value set to None,
unless default is defined which is then set and returned
(in the spirit of dict.setdefault())
"""
#io.debug('>get> {0!s} {1!s} {2!s}\n', theObject, key, default)
if theObject is None:
io.error('ValidationData.getResult: invalid object\n')
return None
if key is None:
io.error('ValidationData.getResult: invalid key\n')
return None
#v3: use attribute method so v3 will not 'suffer'
if not hasattr(theObject, ValidationResultsContainer.KEY):
if default is not None:
self.setResult(theObject, key, default)
return default # ==None or default
#end if
container = getattr(theObject, ValidationResultsContainer.KEY)
if key not in container:
if default is not None:
self.setResult(theObject, key, default)
return default # ==None or default
#endif
result = container[key]
if result is None and default is not None:
self.setResult(theObject, key, default)
return default # ==None or default
return result # ==result
def quote(inputString):
"return a single or double quoted string"
single = (find(inputString, "'") >= 0)
double = (find(inputString, '"') >= 0)
if single and double:
io.error("in quote: both single and double quotes in [{0}]\n", inputString)
return None
if double:
return "'" + inputString + "'"
return '"' + inputString + '"'
def upgrade100(project, restore):
"""
Do all things to upgrade project to current configuration
All versions <= 1.00
"""
nTmessage('*** upgrade100: upgrading %s from version %s ***', project, project.version)
verbosity = cing.verbosity
# make sure we get all if we heave debug on
if cing.verbosity < cing.verbosityDebug:
cing.verbosity = cing.verbosityWarning
# Molecules
for molName in project.moleculeNames:
pathName = project.molecules.path(molName)
mol = Molecule.open(pathName)
if mol:
mol.status = 'keep'
project.appendMolecule(mol)
#end if
nTdebug('upgrade100: restored %s', mol)
#end for
# restore the lists
for pl in [project.peaks, project.distances, project.dihedrals, project.rdcs, project.coplanars]:
pl.restore()
#end for
# Now patch talos+
nTmessage('==> upgrade100: talosPlus')
if restoreTalosPlus100(project):
io.error('upgrade100: restoring talosPlus data failed\n')
# Now patch queeny
# nTmessage('==> upgrade100: queeny')
# if restoreQueeny100(project):
# nTerror('upgrade100: restoring queeny data failed')
# project.saveQueeny()
#
# # Now patch shiftx
# if restoreShiftx100(project):
# nTerror('upgrade100: restoring shiftx data failed')
# return None
# project.saveShiftx()
# Plugin registered functions
nTdebug('upgrade100: calling plugins')
project._callPluginRestores()
# save to consolidate
project.save()
cing.verbosity = verbosity
return Project.open(project.name, constants.PROJECT_OLD, restore=restore)
def nThandle(node):
"""Handle a given node, return object of None in case of Error
"""
if node is None:
io.error("nThandle: None node\n")
return None
#end if
if node.nodeName not in XMLhandlers:
io.error('nThandle: no handler for XML <{0}>\n', node.nodeName)
return None
#end if
return XMLhandlers[node.nodeName].handle(node)
def handleMultipleElements(self, node):
'For each child handle XML'
self.printDebugNode(node)
if node.nodeName != self.name:
io.error('XML%Handler: invalid XML handler for node <{0}>\n', node.nodeName)
return None
#end if
result = []
for subNode in node.childNodes:
if subNode.nodeType == Node.ELEMENT_NODE:
result.append(nThandle(subNode))
#end if
#end for
# nTdebug("==>%s %s",repr(node), result)
return result
def modify(self, index, newId, type=None):
"""
Return new pid with position index modified by newId
"""
parts = self._split()
idparts = parts[1:]
try:
# NB this allows negative indices also, according to normal Python rules
idparts[index] = newId
except IndexError:
io.error('Pid.modify: invalid index ({0})\n', index+1)
parts[1:] = idparts
if type is not None:
parts[0] = type
return Pid.new(*parts)
def json2obj(path, referenceObject=None):
"""return object from serialised representation in json file
or None on error
"""
from cing.Libs.disk import Path
p = Path(str(path)) # assure path instance
if not p.exists():
io.error('json2obj: path "{0}" does not exist\n', path)
return None, None
with open(p,'r') as fp:
try:
obj, keyedMetadata = decode(fp.read(), referenceObject=referenceObject)
except ValueError:
io.error('json2obj: trying to decode object from "{0}" failed\n', path)
return None, None
return obj, keyedMetadata
def decodePid(sourceObject, thePid):
"""
try to decode thePid relative to sourceObject
return decoded pid object or None on not found or Error
"""
if thePid is None:
return None
# assure a Pid object
if not isinstance(thePid, Pid):
if hasattr(thePid, 'asPid'):
# we probably did get passed an object
thePid = thePid.asPid
else:
# just try it as a string
thePid = Pid(str(thePid))
#end if
#end if
if not thePid.isValid:
io.error('decodePid: pid "{0}" is invalid', thePid)
return None
#end if
# check if thePid describes the source object
if hasattr(sourceObject,'asPid'):
if sourceObject.asPid == thePid:
return sourceObject
#end if
# apparently not, let try to traverse down to find the elements of thePid
obj = sourceObject
for p in thePid:
#print( 'decodePid>>', p, object)
if p not in obj:
return None
obj = obj[p]
#end for
# found an object, check if it is the right kind
if thePid.type != obj.__class__.__name__:
io.error('decodePid: type "{0}" does not match object type "{1}"',
thePid.type, obj.__class__.__name__)
return None
return obj
def xML2obj(path=None, string=None):
"""Convert XML file to object
returns object or None on error
"""
if path == None and string==None:
io.error("xML2obj: no input defined\n")
return None
# nTdebug("Starting to read XML from path: " + repr(path)+ " or string: " + repr(string))
if path:
doc = minidom.parse(path)
else:
doc = minidom.parseString(string)
# nTdebug("Done reading XML")
root = doc.documentElement
result = nThandle(root)
doc.unlink()
return result
def restoreTalosPlus100(project):
"""
Restore talos+ results by parsing files.
Return True on error
"""
if project is None:
io.error("restoreTalosPlus100: No project defined\n")
return True
if project.molecule is None:
return True # Gracefully returns
talosDefs = project.getStatusDict('talosPlus')
if not talosDefs.completed:
io.error('restoreTalosPlus100: talosPlus not completed\n')
return True
return project.parseTalosPlus()
def openMol_075( path ) :
"""Static method to restore molecule from directory path
implements the <=0.75 storage model
returns Molecule instance or None on error
"""
# old format
content = xmlTools.xML2obj( path=os.path.join( path, NTmolParameters.contentFile ) )
if not content:
io.error('openMol_075: error reading xml file "{0}"\n',
os.path.join( path, NTmolParameters.contentFile )
)
return None
#end if
content.keysformat()
io.debug('openMol_075: content from xml-file: %s', content.format())
mol = molecule.Molecule( name = content.name )
if not mol:
io.error('openMol_075: initializing molecule\n')
return None
#end if
mol.content = content
if content.has_key('sequenceFile') and \
restoreSequence(mol, os.path.join(path, content.sequenceFile)) is None:
return None
if content.has_key('resonanceFile') and \
restoreResonances(mol, os.path.join(path, content.resonanceFile), append=False) < 0:
return None
if content.has_key('stereoFile') and \
restoreStereoAssignments(mol, os.path.join(path, content.stereoFile)) < 0:
return None
if content.has_key('coordinateFile') and \
restoreCoordinates(mol, os.path.join(path, content.coordinateFile), append=False) is None:
return None
mol._check()
mol.updateAll()
return mol
def openMol_094(path) :
"""Static method to restore molecule from SML file path: 0.75< version <= 0.90
returns Molecule instance or None on error
"""
#print '*** Opening using Molecule.openMol_094'
if (not os.path.exists( path )):
io.error('Molecule.open: smlFile "{0}" not found\n', path)
return None
#end if
mol = Molecule.SMLhandler.fromFile(path) # pylint: disable=E1101
if not mol:
io.error('openMol_094: open from "{0}" failed\n', path)
return None
#end if
mol._check()
mol.updateAll()
return mol
def execute(self, cutoff = 0.1):
"""Do the steps for a full analysis
"""
if self.project is None:
io.error('Queeny.execute: undefined project')
return True
if self.molecule is None:
io.error('Queeny.execute: undefined molecule')
return True
self.reset()
# do the topology
self.initTopology()
self.triangulateAll( cutoff=cutoff, maxDepth = 4 )
self.setUncertainty(constants.QUEENY_UNCERTAINTY1_STR)
# do the restraints
self.initRestraints()
self.triangulateAll( cutoff=cutoff, maxDepth = 3 )
self.setUncertainty(constants.QUEENY_UNCERTAINTY2_STR)
# calculate the information content for each atom, residue
self.setInformation(constants.QUEENY_UNCERTAINTY1_STR, constants.QUEENY_UNCERTAINTY2_STR, constants.QUEENY_INFORMATION_STR)
return False
def setResult(self, theObject, key, result):
"""v3: Add result to theObject's validation container instance under key,
add reverse linkage to result under constants.OBJECT_KEY
add container to self
return True on error
"""
#io.debug('>set> {0!s} {1!s} {2!s}\n', theObject, key, result)
if theObject is None:
io.error('ValidationData.setResult: invalid object\n')
return True
if key is None:
io.error('ValidationData.setResult: invalid key\n')
return True
#v3: use attribute method so v3 will not 'suffer'
# check if theObject has a validation container, create one if needed
if not hasattr(theObject, ValidationResultsContainer.KEY):
container = ValidationResultsContainer()
# add this container
self.addContainer(theObject, container)
# setattr(theObject, ValidationResultsContainer.KEY, container)
# container.setattrOnly(constants.OBJECT_KEY, theObject)
else:
container = getattr(theObject, ValidationResultsContainer.KEY)
#end if
# add the result and set the object's reference
# conditionally adjust the the pid of result instance
container[key] = result
if result is not None:
result[constants.OBJECT_KEY] = theObject
if hasattr(theObject,'asPid'):
result.setPid(theObject.asPid.id,
ValidationResultsContainer.KEY,
key
)
#end if
#end if
return False
def _restoreWithLinkages(self, vfile):
"""
restore validation results in vfile, reestablish linkages to project objects
"""
vdata, metadeta = jsonTools.json2obj(vfile, self.project)
if vdata is None:
io.error('ValidationData._restoreWithLinkages: unable to restore objects from "{0}"\n',
vfile)
return True
#end if
for result in vdata:
#print 'ValidationData.restore> ', result
obj = self.project.getByPid(result[constants.OBJECT_KEY])
if obj is None:
io.error('ValidationData._restoreWithLinkages: unable to decode pid "{0} (file {1})"\n',
result[constants.OBJECT_KEY], vfile
)
return True
#end if
self.project.validationData.setResult(obj, result.KEY, result)
#end for
return False
def _restoreWithoutLinkages(self, vfile):
"""
restore validation results in vfile, do not decode pid's into linkages
Add containers to self.data when needed
"""
# everything is maintained as pid's
vdata, metadeta = jsonTools.json2obj(vfile)
if vdata is None:
io.error('ValidationData._restoreWithoutLinkages: unable to restore objects from "{0}"\n',
vfile)
return True
for result in vdata:
# check for the presence of appropriate container
objPid = result[constants.OBJECT_KEY]
if objPid in self.data:
container = self.data[objPid]
else:
container = ValidationResultsContainer()
self.data[objPid] = container
#end if
container[result.KEY] = result
def parseTalosPlus( project, tmp=None ):
"""Import talosPlus results.
Return True on error.
"""
if project is None:
io.warning("parseTalosPlus: No project defined\n")
return False
if project.molecule is None:
io.warning("parseTalosPlus: No molecule defined\n")
return False
talosDefs = project.getStatusDict(constants.TALOSPLUS_KEY, **talosDefaults)
if not talosDefs.completed:
io.warning("parseTalosPlus: No talos+ was run\n")
return False
path = project.validationPath(talosDefs.directory)
if not path:
io.error('parseTalosPlus: directory "{0}" with talosPlus data not found\n', path)
return True
if _findTalosOutputFiles(path, talosDefs):
return True
predFile = path / talosDefs.predFile
if not predFile.exists() or predFile.isdir():
io.error('parseTalosPlus: file "{0}" with talosPlus predictions not found\n', predFile)
return True
predSSFile = path / talosDefs.predSSFile
if not predSSFile.exists() or predSSFile.isdir():
io.error('parseTalosPlus: file "{0}" with talosPlus SS predictions not found\n', predSSFile)
return True
_resetTalosPlus(project)
if _importTalosPlus(project, predFile, predSSFile):
return True
talosDefs.parsed = True
if talosPlus2restraints(project):
io.error("parseTalosPlus: Failed talosPlus2restraints\n")
return True
return False
def restoreResonances( molecule, fileName, append = True ):
"""Restore resonances from fileName
Optionally append to existing settings
Return resonanceCount or -1 on error
"""
if not os.path.exists( fileName ):
io.error('restoreResonances: file "{0}" not found\n', fileName )
return -1
#end if
if not append:
molecule.initResonances()
#end if
#execfile( fileName )
# 25 Sep 2007: Explicit coding, less memory, better:
file = open(fileName, 'r')
for line in file:
exec(line)
#end for
file.close()
resonanceCount = len(molecule.resonanceSources)
#nTdebug('Molecule.restoreResonances: %s (%d)', fileName, resonanceCount)
return resonanceCount
def restoreCoordinates( molecule, fileName, append = True ):
"""Restore coordinates from fileName
Optionally append to existing settings
Return self or None on error
"""
if not os.path.exists( fileName ):
io.error('restoreCoordinates: file "{0}" not found\n', fileName )
return None
#end if
if not append:
for atm in molecule.allAtoms():
atm.coordinates = ntu.NTlist()
#end for
#end if
#execfile(fileName);
# 25 Sep 2007: Explicit coding, less memory, better:
file = open(fileName, 'r')
for line in file:
exec(line)
#end for
file.close()
#nTdebug('Molecule.restoreCoordinates: %s (%d)', fileName, self.modelCount)
return molecule
#end def
def obj2XML(obj, stream=None, path=None):
"""Convert an object to XML
output to stream or path
gwv 13 Jun08: return object or None on error
"""
if obj is None:
io.error("obj2XML: no object\n")
return None
if stream is None and path is None:
io.error("obj2XML: no output defined\n")
return None
closeFile = 0
if not stream:
stream = open(path, 'w')
closeFile = 1
fprintf(stream, '<?xml version="1.0" encoding="ISO-8859-1"?>\n')
nTtoXML(obj, depth=0, stream=stream, indent=' ')
if closeFile:
stream.close()
return obj
def handleSingleElement(self, node):
"""Returns single element below node from DOM tree"""
self.printDebugNode(node)
if node.nodeName != self.name:
io.error('XML%sHandler: invalid XML handler for node <{0}>\n', node.nodeName)
return None
#end if
if len(node.childNodes) != 1:
io.error("XML%sHandler: malformed DOM tree ({0})\n", self.name)
return None
#end if
if node.childNodes[0].nodeType != Node.TEXT_NODE:
io.error("XML%sHandler: malformed DOM tree ({0}), expected TEXT_NODE containing value\n", self.name)
return None
#end if
result = node.childNodes[0].nodeValue
# nTdebug("==>%s %s",repr(node), result)
return result
def upgrade075(project, restore):
"""
Upgrade project from 075 or earlier conventions
return upgraded project or None on error
"""
io.message('upgrade075: converting from CING version {0}\n', project.version)
# 0.75 version had moleculeNames stored in molecules attribute
# >=0.76 version molecules is a ProjectList instance
project.moleculeNames = project.molecules
# store the project file and reopen to have correct settings
project._save2json()
pr = classes.Project._restoreFromJson(project.path(cing.cingPaths.project))
if pr == None:
io.error('upgrade075: conversion from version %s failed on read\n', project.version)
return None
for molName in pr.moleculeNames:
pathName = pr.path(cing.directories.molecules, molName) # old reference, versions 0.48-0.75
if pr.version <= 0.48:
pathName = pr.path('Molecules', molName) # old reference
# end if
io.debug('upgrade075: trying molecule conversion from {0}\n', pathName)
if not pathName.exists():
io.error('upgrade075: old molecule pathName "{0}" does not exist\n', pathName)
return None
mol = openMol_075(pathName)
if not mol:
io.error('upgrade075: conversion from version {0} failed on molecule {1}\n', project.version, molName)
return None
pathName.removedir()
# Save molecule to new format
mol.save(pr.molecules.path(molName))
#end for
# restore
pr.restore()
# Save to consolidate
pr.save()
return cing.Legacy.Legacy100.upgrade100.upgrade100(pr, restore)
from cing.Libs.NTutils import NTsort
from cing.Libs.NTutils import nTerror
from cing.Libs.NTutils import nTtracebackError
from cing.Libs.NTutils import nTwarning
from cing.Libs.NTutils import nTmessage
from cing.Libs.NTutils import nTdebug
from cing.Libs.NTutils import nTfill
from cing.Libs.NTutils import nTzap
from cing.Libs.NTutils import Odict
from cing.Libs.io import sprintf
try:
import pyximport
except ImportError:
io.error('Importing pyximport routines for queeny\n')
raise ImportError
pyximport.install()
try:
import cing.Libs.cython.superpose as superpose
except ImportError:
io.error('Importing cython routines for queeny\n')
raise ImportError
# versions < 0.95 not logged with version number
# cing versions >1.0 first ones to include this
__version__ = cing.__version__
# defaults for the queeny status dict
def _parseShiftxOutput(fileName, project, chainId):
"""
Parse shiftx generated output (gv_version!).
Store result in shiftx attribute (which is a NTlist type) of each atom
format file:
# Entries marked with a * may have inaccurate shift predictions.
# Entries marked with a value < -600 should be ignored
501 H N 116.3173
501 H CA 55.4902
501 H CB 29.9950
501 H C 169.8446
501 H H 8.4401
or in 1y4o:
1 G N 109.7404
1 G CA 45.2787
or in 1afp
10 K HZ3 3.7795 # A HZ3 that might not be present.
Return True on error; eg. when the file is absent.
"""
if not os.path.exists(fileName):
nTerror("_parseShiftxOutput: Failed to find %s" % fileName)
return True
if project is None:
nTerror("_parseShiftxOutput: no project defined")
return True
molecule = project.molecule
nTdebug("_parseShiftxOutput: parsing %s", fileName)
atomDict = molecule.getAtomDict(constants.IUPAC, chainId)
for line in AwkLike(fileName, commentString="#", minNF=4):
shift = line.float(4)
if shift != -666.000:
lineCol1 = int(line.dollar[1].strip("*"))
atmName = line.dollar[3]
if chainId is not None:
atm = molecule.decodeNameTuple((constants.IUPAC, chainId, lineCol1, atmName))
# happens for all N-terminal H because the Nterminal residue has H1/2/3
# fix:
if atm is None and atmName == "H":
atm = molecule.decodeNameTuple((constants.IUPAC, chainId, lineCol1, "H1"))
else:
atm = None
if atomDict.has_key((lineCol1, atmName)):
atm = atomDict[(lineCol1, atmName)]
# end if
# print '>>', atm
if not atm:
pass
nTdebug("parseShiftxOutput: chainId [%s] line %d (%s)", chainId, line.NR, line.dollar[0])
# happens for all LYS without HZ3.
else:
result = project.validationData.getResult(atm, constants.SHIFTX_KEY, ShiftxResult())
if result is None:
io.error("_parseShiftxOutput: retrieving ShiftxResult for atom {0}\n", atm)
else:
result.DATA.append(shift)
# LEGACY:
atm.shiftx.append(shift)
def nTtoXML(obj, depth=0, stream=sys.stdout, indent='\t', lineEnd='\n'):
"""Generate XML:
check for method toXML
or
standard types int, float, tuple, list, dict
"""
if (obj == None):
nTindent(depth, stream, indent)
fprintf(stream, "<None/>")
fprintf(stream, lineEnd)
elif hasattr(obj, 'toXML'):
obj.toXML(depth, stream, indent, lineEnd)
elif (type(obj) == int):
nTindent(depth, stream, indent)
fprintf(stream, "<int>%s</int>", repr(obj))
fprintf(stream, lineEnd)
elif (type(obj) == bool):
nTindent(depth, stream, indent)
fprintf(stream, "<bool>%s</bool>", repr(obj))
fprintf(stream, lineEnd)
elif (type(obj) == float):
nTindent(depth, stream, indent)
fprintf(stream, "<float>%s</float>", repr(obj))
fprintf(stream, lineEnd)
elif (type(obj) == str):
nTindent(depth, stream, indent)
# fprintf( stream, "<string>%s</string>", saxutils.escape( obj ) )
fprintf(stream, "<string>%s</string>", unicode(saxutils.escape(obj)))
fprintf(stream, lineEnd)
elif (type(obj) == unicode):
nTindent(depth, stream, indent)
fprintf(stream, "<unicode>%s</unicode>", unicode(saxutils.escape(obj)))
fprintf(stream, lineEnd)
elif (type(obj) == list):
nTindent(depth, stream, indent)
fprintf(stream, "<list>")
fprintf(stream, lineEnd)
for a in obj:
nTtoXML(a, depth+1, stream, indent, lineEnd)
#end for
nTindent(depth, stream, indent)
fprintf(stream, "</list>")
fprintf(stream, lineEnd)
elif (type(obj) == tuple):
nTindent(depth, stream, indent)
fprintf(stream, "<tuple>")
fprintf(stream, lineEnd)
for a in list(obj):
nTtoXML(a, depth+1, stream, indent, lineEnd)
#end for
nTindent(depth, stream, indent)
fprintf(stream, "</tuple>")
fprintf(stream, lineEnd)
elif (type(obj) == dict):
nTindent(depth, stream, indent)
fprintf(stream, "<dict>")
fprintf(stream, lineEnd)
for key, value in obj.iteritems():
nTindent(depth+1, stream, indent)
fprintf(stream, "<key name=%s>", quote(key))
fprintf(stream, lineEnd)
nTtoXML(value, depth+2, stream, indent, lineEnd)
nTindent(depth+1, stream, indent)
fprintf(stream, "</key>")
fprintf(stream, lineEnd)
#end for
nTindent(depth, stream, indent)
fprintf(stream, "</dict>")
fprintf(stream, lineEnd)
else:
pass
io.error('nTtoXML: undefined object "{0}": cannot generate XML\n', obj) # reenable when done testing.
def handleDictElements(self, node):
'For dictionary elements return another dictionary.'
self.printDebugNode(node)
if node.nodeName != self.name:
io.error('XML%sHandler: invalid XML handler for node <{0}>\n', node.nodeName)
return None
#end if
result = {}
# We have two dict formats
# original 'NT' format:
##
##<dict>
## <key name="noot">
## <int>2</int>
## </key>
## <key name="mies">
## <int>3</int>
## </key>
## <key name="aap">
## <int>1</int>
## </key>
##</dict>
##
# Or Apple plist dict's
##<dict>
## <key>Key</key>
## <string>3F344E56-C8C2-4A1C-B6C7-CD84EAA1E70A</string>
## <key>Title</key>
## <string>New on palm</string>
## <key>Type</key>
## <string>com.apple.ical.sources.naivereadwrite</string>
##</dict>
# first collect all element nodes, skipping the 'empty' text nodes
subNodes = []
for n in node.childNodes:
# print '>>',n
if n.nodeType == Node.ELEMENT_NODE:
subNodes.append(n)
#end for
if len(subNodes) == 0:
return result
#append all keys, checking for 'format' as outlined above
i = 0
while (i < len(subNodes)):
#print '>>', len(subNodes), i, str(subNodes[i]), 'childnodes:', len(subNodes[i].childNodes), str(subNodes[i].childNodes[0])
self.printDebugNode(subNodes[i])
try:
keyName = subNodes[i].attributes.get('name').nodeValue
#test for valid childNodes; have seen cases they don't exits (!?)
if len(subNodes[i].childNodes) > 1:
value = nThandle(subNodes[i].childNodes[1])
else:
#nTdebug('XMLhandler.handleDictElements: empty key "%s", value set to None', keyName)
value = None
i += 1
except AttributeError:
keyName = subNodes[i].childNodes[0].nodeValue
value = nThandle(subNodes[i+1])
i += 2
# print ">>", keyName, value
result[keyName] = value
#end while
# nTdebug("==>%s %s",repr(node), result)
return result
