def parseInputXML(self, inputXML):
dataDict = {}
xmltree = MU.parseXML(inputXML)
if xmltree:
header = xmltree.firstChild.getElementsByTagName('header')
dataRef = xmltree.firstChild.getElementsByTagName('dataReferences')
if header and dataRef:
header = header.pop()
dataRef = dataRef.pop()
jid = int(header.getAttribute('id'))
job = header.getElementsByTagName('job')
primFolder = dataRef.getElementsByTagName('tag')
if jid and job and primFolder:
job = job.pop()
primFolder = primFolder.pop()
paramsDict = {node.tagName: node.firstChild.data for node in job.childNodes if node.nodeType != 3 and node.firstChild}
cells = [l.firstChild.data for l in dataRef.getElementsByTagName('location')]
# cellPaths = map(lambda x: os.path.basename(x), cells)
# limsCodes = map(lambda x: '-'.join(LIMSMapper.limsCodeFromCellPath(x)), cellPaths)
if paramsDict.get('referenceSequenceName'):
dataDict['SecondaryReference'] = paramsDict.get('referenceSequenceName')
if paramsDict.get('protocolName'):
dataDict['SecondaryProtocol'] = paramsDict.get('protocolName')
if cells:
dataDict['InputPaths'] = cells
return dataDict
def parseReferenceXML(self, referenceXML):
dataDict = {}
xmltree = MU.parseXML(referenceXML)
if xmltree:
refInfo = xmltree.getElementsByTagName('reference_info')
if refInfo:
refInfo = refInfo.pop()
dataDict['name'] = refInfo.getAttribute('id')
dataDict['lastModified'] = refInfo.getAttribute('last_modified')
#dataDict['md5'] = 'unknown',#refInfo.getAttribute('')
dataDict['version'] = refInfo.getAttribute('version')
return dataDict
def parseJobXML(self, jobXML):
protocolDict = {}
xmltree = MU.parseXML(jobXML)
if xmltree:
protocolInfo = xmltree.getElementsByTagName('protocol')
moduleStageInfo = xmltree.getElementsByTagName('moduleStage')
if protocolInfo:
elemAttr = 'name' if self.isMartin else 'id'
protocolParams = {x.getAttribute(elemAttr): x.getElementsByTagName('param') for x in protocolInfo}
if protocolParams:
protocolDict['protocol'] = {x: {e.getAttribute('name'): self._getXMLParamValue(e) for e in y} for x,y in protocolParams.iteritems()}
if moduleStageInfo:
moduleParams = {x.getAttribute('name'): x.getElementsByTagName('param') for x in moduleStageInfo}
if moduleParams:
protocolDict['modules'] = {x: {e.getAttribute('name'): self._getXMLParamValue(e) for e in y} for x,y in moduleParams.iteritems()}
return protocolDict