def dsIdToSuffix(dsId):
"""Translate a MetaType/ID into a file suffix"""
dsIds = DataSetMetaTypes.ALL
suffixMap = {dsId: dsIdToName(dsId) for dsId in dsIds}
suffixMap[toDsId("DataSet")] = 'DataSet'
if DataSetMetaTypes.isValid(dsId):
suffix = suffixMap[dsId]
suffix = suffix.lower()
suffix += '.xml'
return suffix
else:
raise InvalidDataSetIOError("Invalid DataSet MetaType")
def __parseMetadata(xsd_name, tag_name, return_type, filename):
fileLocation = uri2fn(filename)
tree = ET.parse(fileLocation)
dsm_tag = (".//{http://pacificbiosciences.com/" + xsd_name + "}" +
tag_name)
try:
metadata = _eleToDictList(tree.getroot().find(dsm_tag))
except AttributeError:
# the tag wasn't found, we're trying to do something with None
raise InvalidDataSetIOError("Unable to parse metadata from "
"{f}".format(f=filename))
return return_type(metadata)
def parseMetadata(filename):
fileLocation = uri2fn(filename)
tree = ET.parse(fileLocation)
dsm_tag = (".//{http://pacificbiosciences.com/PacBioDatasets.xsd}"
"DataSetMetadata")
try:
metadata = _parseXmlDataSetMetadata(tree.getroot().find(dsm_tag))
except AttributeError:
# the tag wasn't found, we're trying to do something with None
raise InvalidDataSetIOError("Unable to parse metadata from "
"{f}".format(f=filename))
return metadata
def dsIdToName(dsId):
"""Translate a MetaType/ID into a class name"""
if DataSetMetaTypes.isValid(dsId):
return dsId.split('.')[-1]
else:
raise InvalidDataSetIOError("Invalid DataSet MetaType")