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StepsLibrary.py
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StepsLibrary.py
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########################################################################################
## This file is a part of YAP package of scripts. https://github.com/shpakoo/YAP
## Distributed under the MIT license: http://www.opensource.org/licenses/mit-license.php
## Copyright (c) 2011-2013 Sebastian Szpakowski
########################################################################################
#################################################
## A library of "steps" or program wrappers to construct pipelines
## Pipeline steps orchestration, grid management and output handling.
#################################################
import sys, tempfile, shlex, glob, os, stat, hashlib, time, datetime, re, curses
from threading import *
from subprocess import *
from MothurCommandInfoWrapper import *
from collections import defaultdict
from collections import deque
from random import *
from Queue import *
import smtplib
from email.mime.text import MIMEText
from email.MIMEMultipart import MIMEMultipart
from email.MIMEBase import MIMEBase
from email.MIMEText import MIMEText
from email.Utils import COMMASPACE, formatdate
from email import Encoders
_author="Sebastian Szpakowski"
_date="2012/09/20"
_version="Version 2"
#################################################
## Classes
##
class BufferedOutputHandler(Thread):
def __init__(self, usecurses=False):
Thread.__init__(self)
self.shutdown=False
self.cache = deque()
self.registered=0
self.ids = list()
self.wrap = 140
self.starttime = time.time()
#### init log
try:
self.otptfile = open("logfile.txt", 'a')
self.toPrint("-----", "GLOBAL", "Appending to a logfile.txt...")
except:
self.otptfile = open("logfile.txt", 'w')
self.toPrint("-----", "GLOBAL", "Creating a new logfile.txt...")
command = " ".join(sys.argv)
self.otptfile.write("command: %s\n" % command)
#### init output (curses)
self.usecurses = usecurses
if (self.usecurses):
self.stdscr=curses.initscr()
curses.savetty()
curses.noecho()
curses.cbreak()
curses.curs_set(0)
self.textbuffer= list()
self.stdscr.clear()
self.stdscr.refresh()
self.cursestrackbuffer = 100
self.scrollpad = curses.newpad(self.cursestrackbuffer*2, self.wrap*2)
self.spacerpad = curses.newpad(1,1000)
self.updatepad = curses.newpad(10,1000)
self.rows, self.cols = self.stdscr.getmaxyx()
else:
self.stdscr=None
self.start()
def run(self):
self.toPrint("-----", "GLOBAL", "Setting up the pipeline...")
self.flush()
time.sleep(5)
while activeCount()>3 or self.registered>0 or len(self.cache) > 0:
self.flush()
time.sleep(1)
self.flush()
endtime = time.time()
text = "+%s [fin]" % (str(datetime.timedelta(seconds=round(endtime-self.starttime,0))).rjust(17))
self.toPrint("-----", "GLOBAL", text)
command = "%spython %straverser.py" % (binpath, scriptspath)
p = Popen(shlex.split(command), stdout = PIPE, stderr = PIPE, close_fds=True)
dot, err = p.communicate()
p.wait()
x = open("workflow.dot", "w")
x.write(dot)
x.write("\n")
x.close()
for format in ["svg", "svgz", "png", "pdf"]:
command = "%sdot -T%s -o workflow.%s" % (dotpath, format, format)
p = Popen(shlex.split(command), stdin = PIPE, stdout = PIPE, stderr = PIPE, close_fds=True)
out, err = p.communicate(dot)
p.wait()
self.toPrint("-----", "GLOBAL", "Check out workflow.{svg,png,jpg} for an overview of what happened.")
self.flush()
self.otptfile.close()
self.closeDisplay()
self.mailLog()
def register(self, id):
self.registered+=1
self.ids.append(id)
def deregister(self):
self.registered-=1
def collapseIDs(self, text ):
for id in self.ids:
if len(id)>5:
text = re.sub(id, "[{0}~]".format(id[:5]), text)
return (text)
def flush(self):
while len(self.cache) > 0:
id, name, line = self.cache.popleft()
tag = "[{0}] {1:<20} > ".format( id[:5], name)
line = "{0!s}".format(line)
line = self.collapseIDs(line)
otpt = "{0}{1}".format(tag, line[:self.wrap])
self.otptfile.write("{0}{1}\n".format(tag, line))
line = line[self.wrap:]
self.outputScroll(otpt)
while len(line)>=self.wrap:
otpt = "{0}\t{1}".format(tag, line[:self.wrap])
line = line[self.wrap:]
self.outputScroll(otpt)
if len(line)>0:
otpt = "{0:<30}\t\t{1}".format("", line)
line = line
self.outputScroll(otpt)
self.redrawScreen()
def mailLog(self):
log = loadLines("logfile.txt")
log.reverse()
paths = os.getcwd()
paths = "%s/" % (paths)
dirs = glob.glob("*OUTPUT*")
dirs.sort()
for d in dirs:
paths = "%s\n\t%s/*" % (paths, d)
header = "Hi,\nYAP has just finished. Most, if not all, of your data should be in:\n\n%s\n\n-see the log below just to make sure...\nThe attached work-flow graph can be opened in your browser.\nYours,\n\n~YAP" % (paths)
log = "".join(log)
msgtext = "%s\n\n<LOG>\n\n%s\n</LOG>\n\n" % (header, log)
try:
me = __email__
toaddr = [me]
msg = MIMEMultipart()
msg['To'] = COMMASPACE.join(toaddr)
msg['Date'] = formatdate(localtime=True)
msg['Subject'] = '[AUTOMATED] YAP is done.'
if me != __admin__:
ccaddr = [__admin__]
msg['BCC'] = COMMASPACE.join(ccaddr)
toaddr = toaddr + ccaddr
msg.attach(MIMEText(msgtext))
files = ["workflow.pdf"]
for f in files:
try:
part = MIMEBase('application', "octet-stream")
part.set_payload( open(f,"rb").read() )
Encoders.encode_base64(part)
part.add_header('Content-Disposition', 'attachment; filename="%s"' % os.path.basename(f))
msg.attach(part)
except:
pass
s = smtplib.SMTP('mail.jcvi.org')
s.sendmail(me, toaddr , msg.as_string())
s.quit()
except:
pass
def redrawScreen(self):
try:
y,x = self.stdscr.getmaxyx()
### enough screen to print:
if y>20 and x>20:
if len(self.textbuffer) < (y-10):
self.scrollpad.refresh(0, 0, 0, 0, y-10, x-5)
else:
self.scrollpad.refresh(self.cursestrackbuffer-y+10 , 0, 0, 0, y-10, x-5)
self.updatepad.refresh(0, 0, y-8, 10 , y-3, x-5)
### when screen too small
else:
self.scrollpad.refresh(0,0,0,0,0,0)
self.updatepad.refresh(0,0,0,0,0,0)
except:
self.closeDisplay()
self.usecurses=False
#
def toPrint(self, id, name, line):
self.cache.append((id, name, line))
def outputScroll(self, k):
if self.usecurses:
self.textbuffer.append("%s\n" %(k))
self.scrollpad.clear()
for k in self.textbuffer[-self.cursestrackbuffer:]:
self.scrollpad.addstr(k)
else:
print k
def outputUpdate(self,k):
if self.usecurses:
self.updatepad.clear()
for k in k.strip().split("\n"):
self.updatepad.addstr("%s\n" % k)
def closeDisplay(self):
if self.usecurses:
self.stdscr.clear()
self.stdscr.refresh()
curses.curs_set(1)
curses.nocbreak()
curses.echo()
curses.resetty()
curses.endwin()
class TaskQueueStatus(Thread):
def __init__(self, update=1, maxnodes=10):
Thread.__init__(self)
self.active=True
self.maxnodes = maxnodes
self.available = self.maxnodes
self.update = update
#### queue of grid jobs to run
self.scheduled = Queue()
#### to keep track of things popped off the queue
self.processing = dict()
#### inventory of what ran
#### tuple (jid, status) indexed by command
#### status: new/running/done/remove
#### new upon registering
#### running when submitted to the grid
#### done when completed
self.registered = dict()
#### inventory of completed jobs
self.bestqueue = "default.q"
self.pollqueues()
self.running=0
self.stats=dict()
self.previous =""
self.start()
def run(self):
BOH.outputUpdate("Setting up the grid...")
print "Setting up grid..."
time.sleep(5)
while activeCount()>3 or self.running>0 or self.scheduled.qsize()>0:
self.pollfinished()
self.pollqueues()
self.pollrunning()
self.dispatch()
self.cleanup()
BOH.outputUpdate("%s" % (self))
#print self
time.sleep(self.update)
BOH.outputUpdate("%s\nGrid Offline." % (self))
print self
print "Queue status shutting down."
def cleanup(self):
toremove = set()
for key, tup in self.registered.items():
id, status = tup
if status == "remove":
toremove.add(key)
for key in toremove:
del self.registered[key]
def flagRemoval(self, task):
id, status = self.registered[task.getUniqueID()]
if status =="done":
self.registered[task.getUniqueID()] = [id, "remove"]
else:
print "cannot flag yet:", id, status
def pollfinished(self):
# donejobs = set()
#
# ### only 100 recent jobs shown, which could be a problem ;-)
# p = Popen(shlex.split("qstat -s z"), stdout=PIPE, stderr=PIPE, close_fds=True)
# p.wait()
# out,err = p.communicate()
#
# lines = out.split("\n")
# tmp = set()
# if len(lines)>2:
# for line in lines[2:]:
# line = line.strip().split()
# if len(line)>0:
# donejobs.add(line[0])
#
#if len(donejobs)>0:
for key, tup in self.registered.items():
id, status = tup
#if (status == "running") and (id in donejobs):
if (status == "running") and (self.isJobDone(id)):
tmp = self.registered[key][1]= "done"
self.processing[key].setCompleted()
self.available += 1
del self.processing[key]
def isJobDone(self, jid):
p = Popen(shlex.split("qstat -j %s" % jid), stdout=PIPE, stderr=PIPE, close_fds=True)
p.wait()
out,err = p.communicate()
return err.find("jobs do not exist")>-1
def pollqueues(self):
command="qstat -g c"
p = Popen(shlex.split(command), stdout=PIPE, stderr=PIPE, close_fds=True )
p.wait()
out,err = p.communicate()
if err.find("neither submit nor admin host")==-1:
queues = defaultdict(float)
out = out.strip().split("\n")
fullqueues = set()
#cache queue information
for q in out[2:]:
queue, cqload, used, res, avail, total, acds, cdsu = q.split()
avail = float(avail)
total = float(total)
if total>0:
queues[queue] = avail
if avail==0:
fullqueues.add(queue)
# determine which queue is the best
#for k in ("default.q", "medium.q", "fast.q", "himem.q"):
#for k in ("fast.q", "medium.q", "default.q"):
#for k in ("himem.q", "medium.q", "default.q"):
if ("medium.q" in fullqueues) and ("default.q" in fullqueues) and "himem" in queues.keys() :
if queues["himem.q"]>0:
self.bestqueue = "himem.q"
else:
self.bestqueue = "medium.q"
else:
for k in ("medium.q", "default.q"):
if queues[k] >= queues[self.bestqueue]:
self.bestqueue = k
### sanity check, this should match the counters
def pollrunning(self):
tmp=defaultdict(int)
for jid, value in self.registered.values():
tmp[value]+=1
self.stats = tmp
self.running = self.stats["running"]
def dispatch(self):
while self.nodesAvailable():
if not self.scheduled.empty():
tmp = self.scheduled.get()
self.processing[tmp.getUniqueID()]=tmp
#print "submitting", tmp.getUniqueID()
jid = tmp.submit()
#print jid
if jid==-1:
print "???", tmp
self.registered[tmp.getUniqueID()] = [tmp.getGridId(), "running"]
self.available-=1
else:
break
def pickQ(self):
return self.bestqueue
def register(self, task):
self.scheduled.put(task)
self.registered[task.getUniqueID()]=[-1, "new"]
def shutdown(self):
self.active=False
print "Queue status shutting down..."
def nodesAvailable(self):
return (self.available > 0)
def __str__(self):
otpt ="Currently running/waiting: %s/%s\n" % (self.running, self.scheduled.qsize())
otpt ="%savailable/total: %s/%s" % (otpt, self.available, self.maxnodes)
# for key, tup in self.registered.items():
# id, status = tup
# if id != -1:
# otpt = "%s\n\t%s\t%s\t%s" % (otpt, id, status, key[0:10])
for key, val in self.stats.items():
otpt = "%s\n\t%s\t%s" % (otpt, key, val)
otpt = "%s\n\nbest queue: %s" % (otpt, self.bestqueue)
return (otpt)
#################################################
### a thread that will track of a qsub job
### templates adapted to JCVIs grid
###
class GridTask():
def __init__(self, template="default.q", command = "", name="default", cpu="1", dependson=list(), cwd=".", debug=False):
self.gridjobid=-1
self.completed=False
self.queue=template
self.inputcommand = command
self.cwd=cwd
self.project = __projectid__
self.email = __email__
### remove *e##, *pe## *o## *po##
self.retainstreams=" -o /dev/null -e /dev/null "
### debug flag
self.debugflag = debug
### the only queue that has more than 4 CPUs...
if int(cpu)>4:
self.queue = "himem.q"
if len(dependson)>0:
holdfor = "-hold_jid "
for k in dependson:
holdfor = "%s%s," % (holdfor, k.getJobid())
holdfor=holdfor.strip(",")
else:
holdfor = ""
### keep po pe o e streams for debugging purposes
if self.debugflag:
self.retainstreams=""
### to avoid long command problems, create a script with the command, and invoke that instead of the command directyly.
px = "tmp.%s.%s.%s.%s." % (randrange(1,100),randrange(1,100),randrange(1,100),randrange(1,100))
sx = ".%s.%s.%s.%s.sh" % (randrange(1,100),randrange(1,100),randrange(1,100),randrange(1,100))
##### to avoid too many opened files OSError
pool_open_files.acquire()
### bounded semaphore should limit throttle the files opening for tasks created around the same time
scriptfile, scriptfilepath = tempfile.mkstemp(suffix=sx, prefix=px, dir=self.cwd, text=True)
os.close(scriptfile)
self.scriptfilepath = scriptfilepath
os.chmod(self.scriptfilepath, 0777 )
input= "%s\n" % (self.inputcommand)
scriptfile = open(self.scriptfilepath, "w")
scriptfile.write(input)
scriptfile.close()
pool_open_files.release()
####
self.templates=dict()
self.templates["himem.q"] = 'qsub %s -P %s -N jh.%s -cwd -pe threaded %s -l "himem" -M %s -m a %s "%s" ' % (self.retainstreams, self.project, name, cpu, self.email, holdfor, self.scriptfilepath)
self.templates["default.q"] = 'qsub %s -P %s -N jd.%s -cwd -pe threaded %s -M %s -m a %s "%s" ' % (self.retainstreams, self.project, name, cpu, self.email, holdfor, self.scriptfilepath)
self.templates["fast.q"] = 'qsub %s -P %s -N jf.%s -cwd -pe threaded %s -l "fast" -M %s -m a %s "%s" ' % (self.retainstreams, self.project, name,cpu, self.email, holdfor, self.scriptfilepath)
self.templates["medium.q"] = 'qsub %s -P %s -N jm.%s -cwd -pe threaded %s -l "medium" -M %s -m a %s "%s" ' % (self.retainstreams, self.project, name, cpu, self.email, holdfor, self.scriptfilepath)
self.templates["himemCHEAT"] = 'qsub %s -P %s -N jH.%s -cwd -pe threaded %s -l "himem" -M %s -m a %s "%s" ' % (self.retainstreams, self.project, name, 1, self.email, holdfor, self.scriptfilepath)
self.templates["mpi"] = 'qsub %s -P %s -N jP.%s -cwd -pe orte %s -M %s -m a %s mpirun -np %s "%s" ' % (self.retainstreams, self.project, name, cpu, cpu, self.email, holdfor, self.scriptfilepath )
self.command = ""
QS.register(self);
def submit(self):
if not self.queue in self.templates.keys():
self.queue = QS.pickQ()
self.command = self.templates[self.queue]
#print self.command
p = Popen(shlex.split(self.command), stdout=PIPE, stderr=PIPE, cwd=self.cwd, close_fds=True)
p.wait()
out, err = p.communicate()
err = err.strip()
out = out.strip()
if err!="":
print err
if out.endswith("has been submitted"):
self.gridjobid = out.split(" ")[2]
else:
print ">>>", out
print "#FAIL"
return (self.getGridId())
def getGridId(self):
return self.gridjobid
def getUniqueID(self):
return "%s_%s_%s" % (id(self), self.cwd, self.inputcommand)
def setCompleted(self):
self.completed=True
try:
if not self.debugflag:
os.remove(self.scriptfilepath)
except OSError, error:
print( "%s already gone" % self.scriptfilepath)
QS.flagRemoval(self)
def isCompleted(self):
return (self.completed)
def wait(self):
while not self.isCompleted():
time.sleep(0.1)
#################################################
### Iterator over input fasta file.
### Only reading when requested
### Useful for very large FASTA files
### with many sequences
class FastaParser:
def __init__ (self, x):
self.filename = x
self.fp = open(x, "r")
self.currline = ""
self.currentFastaName = ""
self.currentFastaSequence = ""
self.lastitem=False
def __iter__(self):
return(self)
#####
def next(self):
for self.currline in self.fp:
if self.currline.startswith(">"):
self.currline = self.currline[1:]
if self.currentFastaName == "":
self.currentFastaName = self.currline
else:
otpt = (self.currentFastaName.strip(), self.currentFastaSequence.strip())
self.currentFastaName = self.currline
self.currentFastaSequence = ""
self.previoustell = self.fp.tell()
return (otpt)
else:
self.addSequence(self.currline)
if not self.lastitem:
self.lastitem=True
return (self.currentFastaName.strip(), self.currentFastaSequence.strip())
else:
raise StopIteration
def addSequence(self, x):
self.currentFastaSequence = "%s%s" % (self.currentFastaSequence, x.strip())
def __str__():
return ("reading file: %s" %self.filename)
#################################################
### Iterator over input file.
### every line is converted into a dictionary with variables referred to by their
### header name
class GeneralPurposeParser:
def __init__(self, file, skip=0, sep="\t"):
self.filename = file
self.fp = open(self.filename, "rU")
self.sep = sep
self.skip = skip
self.linecounter = 0
self.currline=""
while self.skip>0:
self.next()
self.skip-=1
def __iter__(self):
return (self)
def next(self):
otpt = dict()
for currline in self.fp:
currline = currline.strip().split(self.sep)
self.currline = currline
self.linecounter = self.linecounter + 1
return(currline)
raise StopIteration
def __str__(self):
return "%s [%s]\n\t%s" % (self.filename, self.linecounter, self.currline)
#################################################
### The mother of all Steps:
###
class DefaultStep(Thread):
def __init__(self):
#### thread init
Thread.__init__(self)
self.random = uniform(0, 10000)
self.name = ("%s[%s]" % (self.name, self.random))
#### hash of the current step-path (hash digest of previous steps + current inputs + arguments?)
self.workpathid = ""
#### path where the step stores its files
self.stepdir = ""
#### what needs to be completed for this step to proceed
#### a list of steps
self.previous = list()
#### mapping type - path for files
self.inputs = defaultdict(set)
#### mapping type - name for files
self.outputs = defaultdict(set)
#### mapping arg val for program's arguments
self.arguments= dict()
#### ID of the step...
self.stepname = ""
#### flag for completion
self.completed = False
self.completedpreviously=False
self.failed = False
#### keep track of time elapsed
self.starttime = 0
self.endtime = 0
#### special flag, some steps might not want to delete the inputs (argcheck)
self.removeinputs = True
####
def setInputs(self, x):
for k,v in x.items():
for elem in v:
self.inputs[k].add(elem)
def setArguments(self, x):
for k,v in x.items():
if v=="":
v=" "
self.arguments[k] = v
def setPrevious(self, x):
if not type(x) is list:
self.previous.append(x)
else:
for elem in x:
self.previous.append(elem)
def setName(self, x):
self.stepname=x
def run(self):
self.init()
if self.failed:
#self.message("Error detected... ")
BOH.deregister()
self.completed=True
elif not self.isDone():
try:
self.performStep()
self.finalize()
except Exception, inst:
self.message("...")
self.message( type(inst))
self.message( inst)
BOH.deregister()
self.completed=True
self.failed=True
else:
self.message("Completed (previously).")
BOH.deregister()
self.completed=True
self.completedpreviously=True
def performStep():
self.message("in a step...")
def init(self):
redo=False
### wait for previous steps to finish
for k in self.previous:
while not k.isDone():
#self.message( "waiting" )
time.sleep(1)
if k.hasFailed():
self.failed=True
redo=redo or (not k.isDonePreviously())
#self.message("needs a redo %s" % (redo))
if not self.failed:
### time stamp
self.starttime = time.time()
#### hash of the current step-path (hash digest of previous steps + current inputs + arguments?)
self.workpathid = self.makeWorkPathId()
####
### output handler
BOH.register(self.workpathid)
###
#self.message("Initializing %s %s" % (self.workpathid, self.name))
#### create directories if necessary
self.stepdir =""
self.prepareDir(redo=redo)
def makeWorkPathId(self):
tmp = list()
tmp.append(self.stepname)
if self.previous!=None:
for k in self.previous:
while k.getWorkPathId()==-1:
time.wait(1)
tmp.extend([k.getWorkPathId()])
for k,v in self.inputs.items():
tmp.extend(["%s=%s" % (k, ",".join(v) ) ] )
for k,v in self.arguments.items():
tmp.extend(["%s=%s" % (k, v) ] )
tmp.sort()
tmp = "\n".join(tmp)
workpathid = hashlib.sha224(tmp).hexdigest()[0:5]
return (workpathid)
def getWorkPathId(self):
return (self.workpathid)
def prepareDir(self, redo=False):
### make step's directory
self.stepdir = "Step_%s_%s" % (self.stepname, self.workpathid)
flush_old = False
try:
os.mkdir(self.stepdir)
except OSError, error:
self.message( "Step directory already exists...")
flush_old=True
if redo:
if flush_old:
self.message("Updating...")
k = "rm -r *"
task = GridTask(template="pick", name="redo_clean", command=k, cpu=1, cwd = self.stepdir)
task.wait()
else:
###supposedly no old step-data to flush
pass
else:
### has analysis been done already?
try:
self.parseManifest()
self.completed=True
self.completedpreviously=True
self.message("Using data generated previously...")
except IOError, inst:
#self.message("Will make new manifest...")
pass
except Exception, inst:
self.message("****ERROR***")
self.message(type(inst))
self.message(inst.args)
self.message(inst)
self.message("************")
def finalize(self):
if not self.failed:
self.categorizeAndTagOutputs()
self.makeManifest()
self.endtime = time.time()
self.message( "+%s\t[Done]" % (str(datetime.timedelta(seconds=round(self.endtime-self.starttime,0))).rjust(17)) )
else:
self.endtime = time.time()
self.message( "+%s\t[Fail]" % (str(datetime.timedelta(seconds=round(self.endtime-self.starttime,0))).rjust(17)) )
self.completed=True
BOH.deregister()
def makeManifest(self):
m = open("%s/%s.manifest" % (self.stepdir, self.workpathid), "w")
for type, files in self.inputs.items():
if len(files)>0:
m.write("input\t%s\t%s\n" % (type, ",".join(files)) )
for arg, val in self.arguments.items():
m.write("argument\t%s\t%s\n" % (arg, val ) )
for type, files in self.outputs.items():
if len(files)>0:
m.write("output\t%s\t%s\n" % (type, ",".join(files)) )
m.close()
def determineType(self, filename):
filename = filename.strip().split(".")
extension = filename[-1]
preextension = filename[-2]
if preextension == "scrap":
return "scrap"
elif preextension == "align" and extension == "report":
return "alignreport"
elif extension == "dist" and preextension == "phylip":
return "phylip"
elif extension == "dist":
return "column"
elif preextension == "tax" and extension =="summary":
return "taxsummary"
elif preextension == "cdhit" and extension =="clstr":
return "cdhitclstr"
elif preextension == "bak" and extension =="clstr":
return "cdhitbak"
elif extension == "cdhit":
return "fasta"
elif extension in ["align", "fna", "fa", "seq", "aln"]:
return "fasta"
elif extension == "qual":
return "qfile"
elif extension == "tax":
return "taxonomy"
elif extension == "names":
return "name"
elif extension == "groups":
return "group"
elif extension == "files":
return "file"
elif extension in ["tre", "tree", "dnd"]:
return "tre"
### sge job files
elif re.search("po\d{3}", extension) != None:
return "po"
elif re.search("pe\d{3}", extension) != None:
return "pe"
elif re.search("o\d{3}", extension) != None:
return "o"
elif re.search("e\d{3}", extension) != None:
return "e"
else:
return extension
def categorizeAndTagOutputs(self):
inputs = [x.split("/")[-1] for x in unlist( self.inputs.values()) ]
for file in glob.glob("%s/*" % self.stepdir):
file = file.split("/")[-1]
if file in inputs:
if self.removeinputs:
command = "unlink %s" % (file)
p = Popen(shlex.split(command), stdout=PIPE, stderr=PIPE, cwd=self.stepdir, close_fds=True)
out,err = p.communicate()
p.wait()
else:
self.message("kept %s" % file)
#pass
elif not file.endswith("manifest"):
#self.message( "output: %s" % (file))
### make sure that every output file except for the manifest starts with the workpathID
file = file.split(".")
if len(file[0]) == len(self.workpathid):
newfilename = "%s.%s" % (self.workpathid, ".".join(file[1:]))
else:
newfilename = "%s.%s" % (self.workpathid, ".".join(file[0:]))
if ".".join(file) != newfilename:
k="mv %s %s" % (".".join(file), newfilename)
p = Popen(shlex.split(k), stdout=PIPE, stderr=PIPE, cwd=self.stepdir, close_fds=True)
out,err = p.communicate()
p.wait()
self.outputs[self.determineType(newfilename)].add(newfilename)
def find(self, arg, ln=True, original=False):
files=list()
if not original:
if len(self.inputs[arg])==0:
tmp = {arg: self.getOutputs(arg)}
self.setInputs(tmp)
else:
tmp = {arg: self.getOriginal(arg)}
self.setInputs(tmp)
files = self.inputs[arg]
toreturn=list()
for file in files: