def __init__(self,file=None,level=soya.World,verbose=False,volume_class=soya.Volume,elementtree=None):
self.soyaVolume=volume_class
self.infile=file
if file:
print "Reading:",file
self.tree=ElementTree.parse(file)
elif elementtree:
self.tree=elementtree
self.root=root=self.tree.getroot()
ElementInclude.include(root)
self.level=level()
self.level_static=soya.World(self.level)
self.materials={}
self.verbose=verbose
iter=root.getchildren()
for element in iter:
if verbose: print "Main Element:", element.tag,
try:
self.handle_element(element)
if verbose: print "ok"
except:
raise LevelError('main error handling %s' % element.tag)
self.done()
def envelopewrite(self,node):
''' write envelope for XML messages'''
self.normalisetree(node)
#~ xmltree = ET.ElementTree(self._node2xml(node))
xmltree = BotsElementTree(self._node2xml(node))
root=xmltree.getroot()
ETI.include(root)
xmltree.write(self.ta_info['filename'],encoding=self.ta_info['charset'],ta_info=self.ta_info)
def envelopewrite(self,node_instance):
''' write envelope for XML messages'''
self._initwrite()
self.checkmessage(node_instance,self.defmessage)
xmltree = ET.ElementTree(self._node2xml(node_instance))
root = xmltree.getroot()
ETI.include(root)
self._xmlcorewrite(xmltree,root)
self._closewrite()
def envelopewrite(self,node):
''' write envelope for XML messages'''
self._initwrite()
self.normalisetree(node)
xmltree = ET.ElementTree(self._node2xml(node))
root = xmltree.getroot()
ETI.include(root)
self._xmlcorewrite(xmltree,root)
self._closewrite()
def envelopewrite(self, node_instance):
""" write envelope for XML messages"""
self._initwrite()
self.checkmessage(node_instance, self.defmessage)
self.checkforerrorlist()
xmltree = ET.ElementTree(self._node2xml(node_instance))
root = xmltree.getroot()
ETI.include(root)
self._xmlcorewrite(xmltree, root)
self._closewrite()
def envelopewrite(self, node):
''' write envelope for XML messages'''
self.normalisetree(node)
#~ xmltree = ET.ElementTree(self._node2xml(node))
xmltree = BotsElementTree(self._node2xml(node))
root = xmltree.getroot()
ETI.include(root)
xmltree.write(self.ta_info['filename'],
encoding=self.ta_info['charset'],
ta_info=self.ta_info)
def get_repository_install_dir(self, tool_shed_repository):
for tool_config in self.tool_configs:
tree = ElementTree.parse(tool_config)
root = tree.getroot()
ElementInclude.include(root)
tool_path = root.get('tool_path', None)
if tool_path:
tool_shed = galaxy.util.shed_util_common.clean_tool_shed_url(
tool_shed_repository.tool_shed)
relative_path = os.path.join(
tool_path, tool_shed, 'repos', tool_shed_repository.owner,
tool_shed_repository.name,
tool_shed_repository.installed_changeset_revision)
if os.path.exists(relative_path):
return relative_path
return None
def get_repository_install_dir( self, tool_shed_repository ):
for tool_config in self.tool_configs:
tree = ElementTree.parse( tool_config )
root = tree.getroot()
ElementInclude.include( root )
tool_path = root.get( 'tool_path', None )
if tool_path:
tool_shed = galaxy.util.shed_util.clean_tool_shed_url( tool_shed_repository.tool_shed )
relative_path = os.path.join( tool_path,
tool_shed,
'repos',
tool_shed_repository.owner,
tool_shed_repository.name,
tool_shed_repository.installed_changeset_revision )
if os.path.exists( relative_path ):
return relative_path
return None
def parse_xml(fname):
"""Returns a parsed xml tree"""
tree = ElementTree.parse(fname)
root = tree.getroot()
ElementInclude.include(root)
return tree
def parse_xml(fname):
"""Returns a parsed xml tree"""
tree = ElementTree.parse(fname)
root = tree.getroot()
ElementInclude.include(root)
return tree
def __init__(self, data):
self.tree = ElementTree.parse(data)
self.root = self.tree.getroot()
ElementInclude.include(self.root)
def parse_xml(fname):
"""Parse XML file using elemenTree"""
tree=ElementTree.parse(fname)
root=tree.getroot()
ElementInclude.include(root)
return tree
def __init__( self, data ):
self.tree = ElementTree.parse( data )
self.root = self.tree.getroot()
ElementInclude.include(self.root)