def submitProcessRow(runner, algName, inDir, outDir, paramDict):
inFnames = pubGeneric.findFiles(inDir, [".tab.gz"])
paramFname = join(runner.batchDir, "pubAlgParams.marshal.gz")
writeParamDict(paramDict, paramFname)
for relDir, fname in inFnames:
fname = abspath(fname)
outFname = join(abspath(outDir), basename(fname))
command = "%s %s %s %s %s {check out exists %s} %s" % \
(sys.executable, __file__ , algName, "processRow", fname, outFname, paramFname)
runner.submit(command)
runner.finish()
def submitCombine(runner, algName, mapReduceDir, outExt, paramDict, pieceCount):
" submits combiner jobs: they get a list of dicts and output a single dict "
inFnames = pubGeneric.findFiles(mapReduceDir, [MAPREDUCEEXT])
random.shuffle(inFnames)
parts = splitList(inFnames, pieceCount)
partFnames = writeParts(parts, runner.batchDir)
paramFname = join(runner.batchDir, "mapReduceParams.marshal.gz")
writeParamDict(paramDict, paramFname)
for fname in partFnames:
inBase = splitext(basename(fname))[0]
outFullname = join(mapReduceDir, inBase+".combined."+MAPREDUCEEXT.replace(".gz",""))
command = "%s %s %s %s %s {check out exists %s} %s" % \
(sys.executable, __file__ , algName, "combine", fname, outFullname, paramFname)
runner.submit(command)
runner.finish()
def concatFiles(inDir, outFname):
" concat all files in outDir and write to outFname. "
logging.info("Looking for tab.gz files in %s" % inDir)
inFnames = pubGeneric.findFiles(inDir, ".tab.gz")
ofh = open(outFname, "w")
pm = maxCommon.ProgressMeter(len(inFnames))
logging.info("Concatting...")
fno = 0
for relDir, fn in inFnames:
lno = 0
for line in gzip.open(fn):
if lno==0 and fno==0:
ofh.write(line)
if lno!=0:
ofh.write(line)
lno += 1
pm.taskCompleted()
fno += 1
ofh.close()
def runReduce(algName, paramDict, path, outFilename, quiet=False, inFnames=None):
""" parse pickled dicts from path, run through reduce function of alg and
write output to one file """
if outFilename!=None and isfile(outFilename):
logging.info("deleting existing file %s" % outFilename)
os.remove(outFilename)
if isinstance(algName, basestring):
alg = getAlg(algName, defClass="Map")
else:
alg = algName
if "map" not in dir(alg):
logging.error("There is not map() function in %s" % algName)
sys.exit(1)
if "startup" in dir(alg):
alg.startup(paramDict, {})
if inFnames!=None:
infiles = inFnames
elif isfile(path):
logging.debug("Filename specified, running only on a single file (debugging)")
infiles = [(dirname(path), path)]
else:
infiles = pubGeneric.findFiles(path, [MAPREDUCEEXT])
if len(infiles)==0:
logging.error("Could not find any %s files in %s" % (MAPREDUCEEXT, path))
sys.exit(1)
# read pickle files into data dict
data = {}
fileCount = 0
logging.info("Reading map output")
meter = maxCommon.ProgressMeter(len(infiles), quiet=quiet, stepCount=100)
for relDir, fileName in infiles:
binData = gzip.open(fileName, "rb").read()
nodeData = marshal.loads(binData)
del binData
for key, values in nodeData.iteritems():
if not hasattr(values, "__iter__"):
values = [values]
# major change: append instead of extend
# will break existing mr-scripts
data.setdefault(key, []).append(values)
fileCount += 1
logging.debug("Reading "+fileName)
meter.taskCompleted()
logging.info("Writing to %s" % outFilename)
if outFilename==None:
ofh = None
elif outFilename=="stdout":
ofh = sys.stdout
else:
ofh = open(outFilename, "w")
if "headers" in dir(alg) and ofh!=None:
ofh.write("\t".join(alg.headers))
ofh.write("\n")
if "reduceStartup" in dir(alg):
logging.info("Running reduceStartup")
alg.reduceStartup(data, paramDict, ofh)
logging.info("Running data through reducer")
meter = maxCommon.ProgressMeter(len(data))
for key, valList in data.iteritems():
tupleIterator = alg.reduce(key, valList)
for tuple in tupleIterator:
if tuple==None:
logging.debug("Got None, not writing anything")
continue
if type(tuple)==bytes: # make sure that returned value is a list
tuple = [tuple]
if type(tuple)==int: # make sure that it's a string
tuple = [str(tuple)]
tuple = [unicode(x).encode("utf8") for x in tuple] # convert to utf8
if ofh!=None:
ofh.write("\t".join(tuple))
ofh.write("\n")
meter.taskCompleted()
if ofh!=None:
ofh.close()
if "reduceEnd" in dir(alg):
logging.info("Running reduceEnd")
alg.reduceEnd(data)
