def trackPrepare(self, inputTracks, genome) : #just filter out the -- All subtypes -- tag if it exists
output = []
for track in inputTracks :
if isinstance(track, basestring) :
track = track.split(":")
if track[-1] == "-- All subtypes --" :
output.append(track[:-1])
else :
output.append(track)
output = GalaxyInterface._cleanUpTracks(output, genome, realPreProc=True)
return output
def parseBatchLine(batchLine, genome, fullAccess):
if batchLine[0] == '#' or batchLine.strip() == '':
return
from urllib import unquote
#Split and check number of columns
cols = [x for x in batchLine.strip().split(BATCH_COL_SEPARATOR)]
if len(cols) != 6:
results = Results(['N/A'], ['N/A'], 'N/A')
#results.addResultComponent( 'Invalid',InvalidRunResultComponent('Error in batch specification. 6 columns are required, while '\
# + str(len(cols)) + ' are given.'))
results.addError(InvalidRunSpecException('Error in batch specification. 6 columns are required, while '\
+ str(len(cols)) + ' are given: ' + batchLine))
return results, None, None, None, None
bc = BatchContents()
bc.regSpec = cols[1]
bc.binSpec = unquote(cols[2])
from quick.application.ExternalTrackManager import ExternalTrackManager
if ExternalTrackManager.isGalaxyTrack(bc.binSpec.split(':')):
bc.binSpec = ExternalTrackManager.extractFnFromGalaxyTN(
bc.binSpec.split(':'))
try:
from quick.application.GalaxyInterface import GalaxyInterface
bc.trackName1 = [unquote(x) for x in cols[3].split(':')]
bc.trackName2 = [unquote(x) for x in cols[4].split(':')]
bc.cleanedTrackName1, bc.cleanedTrackName2 = GalaxyInterface._cleanUpTracks(
[bc.trackName1, bc.trackName2], genome, realPreProc=True)
bc.cleanedTrackName1 = BatchRunner._inferTrackName(
bc.cleanedTrackName1, genome, fullAccess)
bc.cleanedTrackName2 = BatchRunner._inferTrackName(
bc.cleanedTrackName2, genome, fullAccess)
except (InvalidRunSpecException, IdenticalTrackNamesError), e:
if DebugConfig.PASS_ON_BATCH_EXCEPTIONS:
raise
bc.errorResult = Results(['N/A'], ['N/A'], 'N/A')
bc.errorResult.addError(e)
return bc
def parseBatchLine(batchLine, genome, fullAccess):
if batchLine[0] == '#' or batchLine.strip() == '':
return
from urllib import unquote
# Split and check number of columns
cols = [x for x in batchLine.strip().split(BATCH_COL_SEPARATOR)]
if len(cols) != 6:
results = Results(['N/A'], ['N/A'], 'N/A')
results.addError(InvalidRunSpecException('Error in batch specification. 6 columns are required, while '\
+ str(len(cols)) + ' are given: ' + batchLine))
return results, None, None, None, None
bc = BatchContents()
bc.regSpec = cols[1]
bc.binSpec = unquote(cols[2])
from quick.application.ExternalTrackManager import ExternalTrackManager
if ExternalTrackManager.isGalaxyTrack(bc.binSpec.split(':')):
bc.binSpec = ExternalTrackManager.extractFnFromGalaxyTN(bc.binSpec.split(':'))
bc.statClassName, bc.paramDict = BatchRunner._parseClassAndParams(cols[5])
bc.trackNames = [[unquote(x) for x in cols[i].split(':')] for i in [3, 4]]
if 'trackNameIntensity' in bc.paramDict:
bc.trackNames.append(convertTNstrToTNListFormat(bc.paramDict['trackNameIntensity'], doUnquoting=True))
from quick.application.GalaxyInterface import GalaxyInterface
partlyCleanedTrackNames = GalaxyInterface._cleanUpTracks(bc.trackNames, genome, realPreProc=True)
try:
bc.cleanedTrackNames = BatchRunner._inferTrackNames(partlyCleanedTrackNames, genome, fullAccess)
except (InvalidRunSpecException,IdenticalTrackNamesError), e:
if DebugConfig.PASS_ON_BATCH_EXCEPTIONS:
raise
bc.errorResult = Results(['N/A'],['N/A'],'N/A')
bc.errorResult.addError(e)
return bc
def runJob(batchLine, genome, fullAccess):
if batchLine[0] == '#' or batchLine.strip()=='':
return
from urllib import unquote
#Split and check number of columns
cols = [x for x in batchLine.strip().split(BATCH_COL_SEPARATOR)]
if len(cols) != 6:
results = Results(['N/A'],['N/A'],'N/A')
#results.addResultComponent( 'Invalid',InvalidRunResultComponent('Error in batch specification. 6 columns are required, while '\
# + str(len(cols)) + ' are given.'))
results.addError(InvalidRunSpecException('Error in batch specification. 6 columns are required, while '\
+ str(len(cols)) + ' are given: ' + batchLine))
return results
#print 'COL2: ',cols[2]
cols[2] = unquote(cols[2])
#print 'COL2: ',cols[2]
from quick.application.ExternalTrackManager import ExternalTrackManager
if ExternalTrackManager.isGalaxyTrack(cols[2].split(':')):
cols[2] = ExternalTrackManager.extractFnFromGalaxyTN(cols[2].split(':'))
#print 'COL2: ',cols[2]
try:
from quick.application.GalaxyInterface import GalaxyInterface
trackName1 = [unquote(x) for x in cols[3].split(':')]
trackName2 = [unquote(x) for x in cols[4].split(':')]
cleanedTrackName1, cleanedTrackName2 = GalaxyInterface._cleanUpTracks([trackName1, trackName2], genome, realPreProc=True)
cleanedTrackName1 = BatchRunner._inferTrackName(':'.join(cleanedTrackName1), genome, fullAccess)
cleanedTrackName2 = BatchRunner._inferTrackName(':'.join(cleanedTrackName2), genome, fullAccess)
except (InvalidRunSpecException,IdenticalTrackNamesError), e:
if DebugConfig.PASS_ON_BATCH_EXCEPTIONS:
raise
results = Results(['N/A'],['N/A'],'N/A')
results.addError(e)
return results
class BatchRunner(object):
@staticmethod
def runFromFn(batchFn, genome, fullAccess):
return BatchRunner.runManyLines(
[line for line in open(batchFn, genome, fullAccess)])
@staticmethod
def runManyLines(batchLines,
genome,
fullAccess,
useBatchId=True,
galaxyFn=None,
printProgress=True):
#fixme: useBatchId is currently ignored! Do something with it if this was a meaningful name from a standard batch run....
resList = []
for line in batchLines:
resList.append(
BatchRunner.runJob(line,
genome,
fullAccess,
galaxyFn=galaxyFn,
printProgress=printProgress))
return resList
@staticmethod
def parseBatchLine(batchLine, genome, fullAccess):
if batchLine[0] == '#' or batchLine.strip() == '':
return
from urllib import unquote
#Split and check number of columns
cols = [x for x in batchLine.strip().split(BATCH_COL_SEPARATOR)]
if len(cols) != 6:
results = Results(['N/A'], ['N/A'], 'N/A')
#results.addResultComponent( 'Invalid',InvalidRunResultComponent('Error in batch specification. 6 columns are required, while '\
# + str(len(cols)) + ' are given.'))
results.addError(InvalidRunSpecException('Error in batch specification. 6 columns are required, while '\
+ str(len(cols)) + ' are given: ' + batchLine))
return results, None, None, None, None
bc = BatchContents()
bc.regSpec = cols[1]
bc.binSpec = unquote(cols[2])
from quick.application.ExternalTrackManager import ExternalTrackManager
if ExternalTrackManager.isGalaxyTrack(bc.binSpec.split(':')):
bc.binSpec = ExternalTrackManager.extractFnFromGalaxyTN(
bc.binSpec.split(':'))
try:
from quick.application.GalaxyInterface import GalaxyInterface
bc.trackName1 = [unquote(x) for x in cols[3].split(':')]
bc.trackName2 = [unquote(x) for x in cols[4].split(':')]
bc.cleanedTrackName1, bc.cleanedTrackName2 = GalaxyInterface._cleanUpTracks(
[bc.trackName1, bc.trackName2], genome, realPreProc=True)
bc.cleanedTrackName1 = BatchRunner._inferTrackName(
bc.cleanedTrackName1, genome, fullAccess)
bc.cleanedTrackName2 = BatchRunner._inferTrackName(
bc.cleanedTrackName2, genome, fullAccess)
except (InvalidRunSpecException, IdenticalTrackNamesError), e:
if DebugConfig.PASS_ON_BATCH_EXCEPTIONS:
raise
bc.errorResult = Results(['N/A'], ['N/A'], 'N/A')
bc.errorResult.addError(e)
return bc
bc.errorResult, bc.userBinSource = BatchRunner._constructBins(
bc.regSpec, bc.binSpec, genome, bc.cleanedTrackName1,
bc.cleanedTrackName2)
if bc.errorResult is not None:
return bc
bc.statClassName, bc.paramDict = BatchRunner._parseClassAndParams(
cols[5])
bc.trackNameIntensity = []
if 'trackNameIntensity' in bc.paramDict:
#fullRunParams['trackNameIntensity'] = paramDict['trackNameIntensity'].replace('_',' ').split(':')
from quick.application.GalaxyInterface import GalaxyInterface
import re
#trackNameIntensity = re.split(':|\|', paramDict['trackNameIntensity'])
bc.trackNameIntensity = convertTNstrToTNListFormat(
bc.paramDict['trackNameIntensity'], doUnquoting=True)
#print "HERE: ",trackNameIntensity
bc.cleanedTrackNameIntensity = GalaxyInterface._cleanUpTracks(
[bc.trackNameIntensity], genome, realPreProc=True)[0]
bc.cleanedTrackNameIntensity = BatchRunner._inferTrackName(
bc.cleanedTrackNameIntensity, genome, fullAccess)
del bc.paramDict['trackNameIntensity']
return bc
