'QuantitationType_package':QuantitationTypePackage,
"BioAssayData_package": BioAssayDataPackage,
'Experiment_package':ExperimentPackage #"BioAssayData_assnlist":BioAssayData,
}
print "working..."
while 1:
print "starting cycle"
inDir = runRoot+"/XML_in/"
fileList = os.listdir(inDir)
for file in fileList:
if not file: break
if os.path.isfile(inDir+file):
if file.lower().endswith(".xml"):
fileRoot = file.split(".")[0]
try:
print "opening %s" %file
doc = Document()
doc.readDocument(inDir+file)
print "read document, beginning xml to rdf conversion"
doc.processSubSection(classDictionary = classDictionary)
doc.connectAllGraphs()
mastergraph = doc.mergeAllgraphs()
mastergraph.serialize(runRoot+'/RDF_out/%s.n3' %fileRoot, 'n3')
os.rename(inDir+file, runRoot+'/XML_processed/%s' %file )
print "converted %s" %fileRoot
except:
os.rename(inDir+file,runRoot+'/FailedXMLinfiles/%s' %file )
print 'Failed for %s' %fileRoot
print "fin!"
}
print "working..."
while 1:
print "starting cycle"
inDir = runRoot + "/XML_in/"
fileList = os.listdir(inDir)
for file in fileList:
if not file: break
if os.path.isfile(inDir + file):
if file.lower().endswith(".xml"):
fileRoot = file.split(".")[0]
try:
print "opening %s" % file
doc = Document()
doc.readDocument(inDir + file)
print "read document, beginning xml to rdf conversion"
doc.processSubSection(classDictionary=classDictionary)
doc.connectAllGraphs()
mastergraph = doc.mergeAllgraphs()
mastergraph.serialize(
runRoot + '/RDF_out/%s.n3' % fileRoot, 'n3')
os.rename(inDir + file,
runRoot + '/XML_processed/%s' % file)
print "converted %s" % fileRoot
except:
os.rename(inDir + file,
runRoot + '/FailedXMLinfiles/%s' % file)
print 'Failed for %s' % fileRoot
print "fin!"
