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#############################################################
# #
# Author: Herve Menager #
# Organization:'Biological Software and Databases' Group, #
# Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the #
# COPYING.LIB document. #
# #
#############################################################
"""
Mobyle.IndexBase
Provides mechanisms to generate, cache, and load Mobyle indexes
"""
import os
from logging import getLogger
i_log = getLogger(__name__)
from Mobyle.ConfigManager import Config
_cfg = Config()
from Mobyle.Registry import registry, ProgramDef, WorkflowDef, ViewerDef, TutorialDef
from lxml import etree
import pickle
parser = etree.XMLParser( no_network = False )
class IndexGenerator(object):
def __init__(self, cls):
self.indexClass = cls
def load(self, type):
index_path = os.path.join(_cfg.index_path(), type + self.indexClass.indexFileName)
try:
input = open(index_path, 'rb')
idx = pickle.load(input)
input.close()
except IOError:
idx = {}
i_log.warning("index file '%s' could not be found, set as empty. Please check documentation: %s." % (index_path,os.path.join(os.environ.get('MOBYLEHOME','$MOBYLEHOME'),'Tools','README')))
return idx
def dump(self, type, dir, registry=registry):
output = open(os.path.join(dir, type + self.indexClass.indexFileName), 'wb')
idx = {}
for s in getattr( registry, type + 's'):
try:
doc = etree.parse(s.path)
doc.xinclude()
if (isinstance(s, ProgramDef)):
idx[registry.getProgramUrl(s.name, s.server.name)] = self.indexClass.getIndexEntry(doc, s)
elif (isinstance(s, WorkflowDef)):
idx[registry.getWorkflowUrl(s.name, s.server.name)] = self.indexClass.getIndexEntry(doc, s)
elif (isinstance(s, ViewerDef)):
idx[registry.getViewerUrl(s.name)] = self.indexClass.getIndexEntry(doc, s)
elif (isinstance(s, TutorialDef)):
idx[registry.getTutorialUrl(s.name)] = self.indexClass.getIndexEntry(doc, s)
except:
i_log.error("Error while generating %s entry for %s/%s" %\
(self.indexClass.__name__, s.server.name, \
s.name), exc_info=True)
i_log.error(s.name)
i_log.error(s.path)
i_log.error(s.url)
pickle.dump(idx, output, 2)
output.close()
class Index(object):
indexFileName=""
def __init__(self, type):
ig =IndexGenerator(self.__class__)
self.index = ig.load(type)
self.type = type
@classmethod
def generate(cls, type, dir, registry):
ig =IndexGenerator(cls)
ig.dump(type, dir, registry)
@classmethod
def getIndexEntry(cls, doc):
raise NotImplementedError
def _XPathQuery(node, query, returnType="valueString"):
"""
_XPathQuery is a helper function to get property values from the XML
@param node: the node which is queried
@type node: Element
@param query: Compiled XPath Query
@type query: varies
@param returnType: the type we want returned by the function valueString|valueList|rawResult
@type string
"""
try:
if returnType == "rawResult":
rawResult = node.xpath(query)
return rawResult
else:
valueList = [n for n in node.xpath(query) \
if n and n.strip()!='']
if returnType == "valueList":
return valueList
valueString = ' '.join(valueList)
if returnType == "valueString":
return valueString
raise Exception("unauthorized returnType value (%s), \
authorized values are rawResult|valueList|valueString"\
% valueString)
except Exception, e:
i_log.error(e)
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