def runJob(batchLine, genome, fullAccess, galaxyFn=None, printProgress=True):
bc = BatchRunner.parseBatchLine(batchLine, genome, fullAccess)
if bc.errorResult is not None:
return bc.errorResult
#Try a full run, and return either results or an exception
try:
#track = Track(trackName1)
#track2 = Track(trackName2)
#if 'tf1' in paramDict:
# track.setFormatConverter(formatConverter)
#results = StatRunner.run(userBinSource , Track(trackName1), Track(trackName2), \
# wrapClass(STAT_CLASS_DICT[statClassName], keywords=paramDict) )
#results = StatRunner.run(userBinSource , track, track2, \
# wrapClass(STAT_CLASS_DICT[statClassName], keywords=paramDict) )
fullRunParams = {}
if USE_PARALLEL:
#if galaxyFn == None: #then this is a test
uniqueId = time.time()
#else:
#uniqueId = extractIdFromGalaxyFn(galaxyFn)[1]
fullRunParams["uniqueId"] = uniqueId
if bc.cleanedTrackNameIntensity is not None:
fullRunParams['trackNameIntensity'] = '|'.join(tuple(bc.cleanedTrackNameIntensity))
analysisDefParams = [ '[' + key + '=' + value + ']' for key,value in bc.paramDict.items()]
analysisDef = ''.join(analysisDefParams) + '->' + bc.statClassName
from quick.application.GalaxyInterface import GalaxyInterface
GalaxyInterface._tempAnalysisDefHacks(analysisDef)
if printProgress:
print 'Corresponding batch command line:<br>' + \
GalaxyInterface._revEngBatchLine(bc.trackName1, bc.trackName2, bc.trackNameIntensity, analysisDef, bc.regSpec, bc.binSpec, genome) + '<br><br>'
results = AnalysisDefJob(analysisDef, bc.cleanedTrackName1, bc.cleanedTrackName2, bc.userBinSource, galaxyFn=galaxyFn, **fullRunParams).run(printProgress)
presCollectionType = results.getPresCollectionType()
if len(results.getResDictKeys()) > 0 and GalaxyInterface.APPEND_ASSEMBLY_GAPS and presCollectionType=='standard':
if USE_PARALLEL:
gapRes = AssemblyGapJob(bc.userBinSource, genome, uniqueId=uniqueId).run(printProgress)
else:
gapRes = AssemblyGapJob(bc.userBinSource, genome).run(printProgress)
results.includeAdditionalResults(gapRes, ensureAnalysisConsistency=False)
except Exception, e:
#print 'NOWAG BExc'
results = Results(bc.cleanedTrackName1, bc.cleanedTrackName2, bc.statClassName)
results.addError(e)
logException(e,message='Error in batch run')
if DebugConfig.PASS_ON_BATCH_EXCEPTIONS:
raise
return results
def runJob(batchLine, genome, fullAccess, galaxyFn=None, printProgress=True):
bc = BatchRunner.parseBatchLine(batchLine, genome, fullAccess)
if bc.errorResult is not None:
return bc.errorResult
#Try a full run, and return either results or an exception
try:
#track = Track(trackName1)
#track2 = Track(trackName2)
#if 'tf1' in paramDict:
# track.setFormatConverter(formatConverter)
#results = StatRunner.run(userBinSource , Track(trackName1), Track(trackName2), \
# wrapClass(STAT_CLASS_DICT[statClassName], keywords=paramDict) )
#results = StatRunner.run(userBinSource , track, track2, \
# wrapClass(STAT_CLASS_DICT[statClassName], keywords=paramDict) )
fullRunParams = {}
if USE_PARALLEL:
# TODO: Requirements for parallel runs should not be added in places like these. Parallelization
# should be a feature of the job runner somehow
#if galaxyFn == None: #then this is a test
uniqueId = time.time()
#else:
#uniqueId = extractIdFromGalaxyFn(galaxyFn)[1]
fullRunParams["uniqueId"] = uniqueId
from quick.application.GalaxyInterface import GalaxyInterface
analysisDefParams = [ '[' + key + '=' + value + ']' for key,value in bc.paramDict.items()]
analysisDef = ''.join(analysisDefParams) + '->' + bc.statClassName
# TODO: Keeping the ugly accesses to private methods in GalaxyInterface for now. To be refactored.
trackNames, analysisDef = GalaxyInterface._cleanUpAnalysisDef(bc.cleanedTrackNames, analysisDef)
if printProgress:
revEngBatchLine = RunDescription.getRevEngBatchLine(
analysisDef, bc.trackNames, bc.cleanedTrackNames, bc.regSpec, bc.binSpec, genome
)
print 'Corresponding batch command line:<br>{}<br><br>'.format(revEngBatchLine)
results = AnalysisDefJob(analysisDef, bc.cleanedTrackNames[0], bc.cleanedTrackNames[1], bc.userBinSource, galaxyFn=galaxyFn, **fullRunParams).run(printProgress)
presCollectionType = results.getPresCollectionType()
if len(results.getResDictKeys()) > 0 and GalaxyInterface.APPEND_ASSEMBLY_GAPS and presCollectionType=='standard':
if USE_PARALLEL:
gapRes = AssemblyGapJob(bc.userBinSource, genome, uniqueId=uniqueId).run(printProgress)
else:
gapRes = AssemblyGapJob(bc.userBinSource, genome).run(printProgress)
results.includeAdditionalResults(gapRes, ensureAnalysisConsistency=False)
except Exception, e:
#print 'NOWAG BExc'
results = Results(bc.cleanedTrackNames[0], bc.cleanedTrackNames[1], bc.statClassName)
results.addError(e)
logException(e,message='Error in batch run')
if DebugConfig.PASS_ON_BATCH_EXCEPTIONS:
raise
return results