def run(self, printProgress=PRINT_PROGRESS):
'''
Runs the statistic specified in self._analysis (from analysisDef) and returns an object of class Result
'''
#Should be there for batch runs.. Should never happen from GUI..
if self._statClass == None:
self._handleMissingStat()
return None
if USE_PROFILING:
profiler = Profiler()
resDict = {}
profiler.run('resDict[0] = StatJob.run(self, printProgress=printProgress)', globals(), locals())
res = resDict[0]
else:
res = StatJob.run(self, printProgress=printProgress)
res.setAnalysis(self._analysis)
res.setAnalysisText(str(self._analysis))
ResultsMemoizer.flushStoredResults()
if USE_PROFILING:
profiler.printStats()
return res
def runProfile(self):
from gold.util.Profiler import Profiler
profiler = Profiler()
import socket
import os
try:
profiler.run('self.run()', globals(), locals())
except:
pass
profiler.dumpStats(str(os.getpid()) + "-" + str(socket.gethostname()))
def run(self, printProgress=PRINT_PROGRESS):
'''
Runs the statistic specified in self._analysis (from analysisDef) and returns an object of class Result
'''
#Should be there for batch runs.. Should never happen from GUI..
if self._statClass == None:
self._handleMissingStat()
return None
if DebugConfig.USE_PROFILING:
from gold.util.Profiler import Profiler
profiler = Profiler()
resDict = {}
profiler.run('resDict[0] = StatJob.run(self, printProgress=printProgress)', globals(), locals())
res = resDict[0]
else:
res = StatJob.run(self, printProgress=printProgress)
res.setAnalysis(self._analysis)
res.setAnalysisText(str(self._analysis))
ResultsMemoizer.flushStoredResults()
if DebugConfig.USE_PROFILING:
profiler.printStats()
if DebugConfig.USE_CALLGRAPH and self._galaxyFn:
profiler.printLinkToCallGraph(['profile_AnalysisDefJob'], self._galaxyFn)
return res
def setUp(self):
if not self.VERBOSE:
sys.stdout = StringIO.StringIO()
if not hasattr(ProfiledIntegrationTest, '_svnRevision'):
ProfiledIntegrationTest._svnRevision = ProfilingStorage.getSvnRevision(
)
#print ProfiledIntegrationTest._svnRevision, self._getId(), ProfilingStorage.isStored(self._getId(), ProfiledIntegrationTest._svnRevision)
if ProfiledIntegrationTest._svnRevision != None and \
not ProfilingStorage.isStored(self._getId(), ProfiledIntegrationTest._svnRevision):
self._profiler = Profiler()
else:
self._profiler = None
def execute(cls, choices, galaxyFn=None, username=''):
# DebugUtil.insertBreakPoint()
cls._setDebugModeIfSelected(choices)
choices_queryTrack = choices.queryTrack
choices_gsuite = choices.gsuite
genome = choices.genome
# queryTrackNameAsList = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(genome, choices.queryTrack,
# printErrors=False,
# printProgress=False)
# gsuite = getGSuiteFromGalaxyTN(choices.gsuite)
analysisBins = UserBinMixin.getUserBinSource(choices)
import quick.gsuite.GuiBasedTsFactory as factory
queryTS = factory.getSingleTrackTS(genome, choices_queryTrack)
refTS = factory.getFlatTracksTS(genome, choices_gsuite)
ts = TrackStructureV2()
realTS = TrackStructureV2()
realTS["query"] = queryTS
realTS["reference"] = refTS
randQueryTS = queryTS
randTvProvider = cls.createTrackViewProvider(choices, refTS, analysisBins, genome)
localAnalysis = randTvProvider.supportsLocalAnalysis()
randRefTS = getRandomizedVersionOfTs(refTS, randTvProvider)
hypothesisKeyList = [sts.metadata["title"] for sts in randRefTS.values()]
for hypothesisKey in hypothesisKeyList:
realTS = TrackStructureV2()
realTS["query"] = queryTS
realTS["reference"] = refTS[hypothesisKey]
randTS = TrackStructureV2()
randTS["query"] = randQueryTS
randTS["reference"] = randRefTS[hypothesisKey]
hypothesisTS = TrackStructureV2()
hypothesisTS["real"] = realTS
hypothesisTS["rand"] = randTS
ts[hypothesisKey] = hypothesisTS
analysisSpec = cls._prepareAnalysisWithHypothesisTests(choices, localAnalysis)
if DebugConfig.USE_PROFILING:
from gold.util.Profiler import Profiler
profiler = Profiler()
resDict = {}
profiler.run('resDict[0] = doAnalysis(analysisSpec, analysisBins, ts)', globals(), locals())
res = resDict[0]
result = res.getGlobalResult()['Result']
profiler.printStats()
if DebugConfig.USE_CALLGRAPH and galaxyFn:
profiler.printLinkToCallGraph(['profile_AnalysisDefJob'], galaxyFn)
else:
result = doAnalysis(analysisSpec, analysisBins, ts).getGlobalResult()["Result"]
for trackTitle, res in result.iteritems():
print '{}: {}<br>'.format(trackTitle, repr(res.getResult()))
class ProfiledIntegrationTest(TestCaseWithImprovedAsserts):
VERBOSE = False
def setUp(self):
if not self.VERBOSE:
sys.stdout = StringIO.StringIO()
if not hasattr(ProfiledIntegrationTest, '_svnRevision'):
ProfiledIntegrationTest._svnRevision = ProfilingStorage.getSvnRevision(
)
#print ProfiledIntegrationTest._svnRevision, self._getId(), ProfilingStorage.isStored(self._getId(), ProfiledIntegrationTest._svnRevision)
if ProfiledIntegrationTest._svnRevision != None and \
not ProfilingStorage.isStored(self._getId(), ProfiledIntegrationTest._svnRevision):
self._profiler = Profiler()
else:
self._profiler = None
def _getId(self):
return self.id().split('.')[-1]
def _usesProfiling(self):
return self._profiler is not None
def _runWithProfiling(self, runStr, symbolDict={}):
aeval = Interpreter()
if symbolDict:
aeval.symtable.update(symbolDict)
if not self._usesProfiling():
return aeval(runStr)
else:
print 'Running with profiling..'
res = self._profiler.run('aeval(%s)' % runStr, globals, locals)
self._profiler.printStats()
return res
def _storeProfile(self, diskMemo=False):
if self.VERBOSE or not self._usesProfiling():
return
ProfilingStorage.parseAndStoreProfile(sys.stdout.getvalue(), self._getId(),\
ProfiledIntegrationTest._svnRevision, diskMemo)
def setUp(self):
if not self.VERBOSE:
sys.stdout = StringIO.StringIO()
if not hasattr(ProfiledIntegrationTest, '_svnRevision'):
ProfiledIntegrationTest._svnRevision = ProfilingStorage.getSvnRevision()
#print ProfiledIntegrationTest._svnRevision, self._getId(), ProfilingStorage.isStored(self._getId(), ProfiledIntegrationTest._svnRevision)
if ProfiledIntegrationTest._svnRevision != None and \
not ProfilingStorage.isStored(self._getId(), ProfiledIntegrationTest._svnRevision):
self._profiler = Profiler()
else:
self._profiler = None
class ProfiledIntegrationTest(TestCaseWithImprovedAsserts):
VERBOSE = False
def setUp(self):
if not self.VERBOSE:
sys.stdout = StringIO.StringIO()
if not hasattr(ProfiledIntegrationTest, '_svnRevision'):
ProfiledIntegrationTest._svnRevision = ProfilingStorage.getSvnRevision()
#print ProfiledIntegrationTest._svnRevision, self._getId(), ProfilingStorage.isStored(self._getId(), ProfiledIntegrationTest._svnRevision)
if ProfiledIntegrationTest._svnRevision != None and \
not ProfilingStorage.isStored(self._getId(), ProfiledIntegrationTest._svnRevision):
self._profiler = Profiler()
else:
self._profiler = None
def _getId(self):
return self.id().split('.')[-1]
def _usesProfiling(self):
return self._profiler is not None
def _runWithProfiling(self, runStr, globals, locals):
if not self._usesProfiling():
return eval(runStr, globals, locals)
else:
print 'Running with profiling..'
res = self._profiler.run(runStr, globals, locals)
self._profiler.printStats()
return res
def _storeProfile(self, diskMemo=False):
if self.VERBOSE or not self._usesProfiling():
return
ProfilingStorage.parseAndStoreProfile(sys.stdout.getvalue(), self._getId(),\
ProfiledIntegrationTest._svnRevision, diskMemo)
def runProfile(self):
from gold.util.Profiler import Profiler
profiler = Profiler()
import socket
import os
try:
profiler.run('self.run()', globals(), locals())
except:
pass
profiler.dumpStats(str(os.getpid()) + "-" + str(socket.gethostname()))