def get(self, item_tag, prop="", child=None):
for in_text in self.xmlBlocks:
# this step is done to avoid confusion due to the "<<" and ">>" signs
root= ET.fromstring(in_text)
if root.tag == root_tag:
### we use XPath features of the xml.etree library here
root.findall('.%s' % child)
propSet= SettingParser(child.text)
if propSet.get(refProp) == refValue:
propSet.set(prop, value)
child.text= propText.tostring()
def set(self, item_tag, prop, value, refProp, refValue):
for i in range(len(self.xmlBlocks)):
# this step is done to avoid confusion due to the "<<" and ">>" signs
in_text= self.xmlBlocks[i]
root= ET.fromstring(in_text)
#print root.text
for item in root.iter():
#print item.tag
if item.tag == item_tag:
parser=SettingParser(item.text)
if refValue != "":
try:
if parser.get(refProp) == refValue:
parser.set(prop,value)
except:
pass
else:
parser.set(prop, value)
item.text= parser.tostring()
out_text = ET.tostring(root)
self.xmlBlocks[i]= out_text
class CircosConfigParser:
'''
circos implemented the apache config format which has no builtin parser in python. this class is intended to parse and manipulate the circos configuration files.
'''
def __init__(self, configType):
self.configType = configType
self.xmlParser=None
self.txtParser=None
self.conf_file= file_provider['circos_config'][configType]
self.parse()
def parse(self):
'''
returns a tuple with the first item as a dictionary of attributes outside xml blocks AND the second item as a list of xml blocks. the first item is straight forward. Second item should be further parsed iteratively by using the iPaseXML function
'''
with open(self.conf_file) as f:
text=f.read()
self.xmlParser= MyXMLParser(text)
xml_text= self.xmlParser.tostring()
non_xml_text= text.replace(xml_text, "")
self.txtParser= SettingParser(non_xml_text)
def set(self, prop, value, item_tag="", refProp="index", refValue= ""):
if item_tag != "": ## means coming from the xml part
self.xmlParser.set(item_tag, prop, value, refProp, refValue)
else: ### means coming from the text part
self.txtParser.set(prop, value)
self.write()
def write(self):
### !!! TODO: this part should be rewritten
### There is still a problem with the xmlparser.
with open(self.conf_file,'w') as f:
f.write(self.tostring())
def tostring(self):
if self.configType == 'plots':
self.doc= self.xmlParser.tostring()
else:
self.doc= self.txtParser.tostring() + self.xmlParser.tostring()
return self.doc
def parse(self):
'''
returns a tuple with the first item as a dictionary of attributes outside xml blocks AND the second item as a list of xml blocks. the first item is straight forward. Second item should be further parsed iteratively by using the iPaseXML function
'''
with open(self.conf_file) as f:
text=f.read()
self.xmlParser= MyXMLParser(text)
xml_text= self.xmlParser.tostring()
non_xml_text= text.replace(xml_text, "")
self.txtParser= SettingParser(non_xml_text)
