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# Handling of data files for tests
#############################################################################
#############################################################################
# #
# Copyright (C) 2013 - 2014 Genome Research Ltd. #
# #
# Author: Hannes Ponstingl (hp3@sanger.ac.uk) #
# #
# This file is part of SMALT. #
# #
# SMALT is free software: you can redistribute it and/or modify it under #
# the terms of the GNU General Public License as published by the Free #
# Software Foundation, either version 3 of the License, or (at your #
# option) any later version. #
# #
# This program is distributed in the hope that it will be useful, but #
# WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU #
# General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License along #
# with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
#############################################################################
#############################################################################
class DataFiles:
INPUTDIR = "./data"
WORKDIR = "./tmp"
LOGFILNAM = "LOGFILE"
def __init__(self, df=[]):
from os import access, F_OK, mkdir, path
if not access(DataFiles.WORKDIR, F_OK):
mkdir(DataFiles.WORKDIR)
logfilnam = path.join(DataFiles.WORKDIR, DataFiles.LOGFILNAM)
self.tmpfiles = [logfilnam + ".out", logfilnam + ".err"]
self.datafiles = []
self.logfil_out = openFile(self.tmpfiles[0], 'w')
self.logfil_err = openFile(self.tmpfiles[1], 'w')
self.addPackedSourceFiles(df)
def __delete_(self):
self.logfil_out.flush()
self.logfil_out.close()
self.logfil_err.flush()
self.logfil_err.close()
def joinData(self, filnam):
from os import path
return path.join(DataFiles.INPUTDIR, filnam)
def addPackedSourceFiles(self, filnams):
for fn in filnams:
self.unpack(fn)
def unpack(self, filnam):
from os import path
fn_from = path.join(DataFiles.INPUTDIR, filnam)
if len(filnam) < 4 or filnam[-3:] != '.gz': fn_from = fn_from + '.gz'
fn_to = path.join(DataFiles.WORKDIR, filnam)
infil = openFile(fn_from, 'r')
oufil = openFile(fn_to, 'wb')
self.logfil_out.write("unpacking '%s' -> '%s'\n" % (fn_from, fn_to))
while 1:
lin = infil.readline()
if not lin:
break
oufil.write(lin)
oufil.close()
infil.close()
self.datafiles.append(fn_to)
return fn_to
def addIndex(self, filnam):
from os import path
fn = path.join(DataFiles.WORKDIR, filnam)
for f in (fn + '.smi', fn + '.sma'):
if f not in self.tmpfiles:
self.tmpfiles.append(f)
return fn
def addTMP(self, filnam):
from os import path
fn = path.join(DataFiles.WORKDIR, filnam)
if fn not in self.tmpfiles:
self.tmpfiles.append(fn)
return fn
def call(self, tup, errmsg="", oufilnam=None):
from subprocess import call
if oufilnam:
oufil = openFile(oufilnam, 'w')
else:
oufil = self.logfil_out
self.addLog(tup)
rc = call(tup, stdout=oufil, stderr=self.logfil_err)
if oufilnam:
oufil.close()
if rc != 0:
if not errmsg:
errmsg = "when calling %s" % (tup[0])
self.exitErr("ERROR %s: returned with code %i" % (errmsg, rc))
self.logfil_out.flush()
self.logfil_err.flush()
def addLog(self, tup):
if not tup:
return
self.logfil_out.write("%s" % tup[0])
if len(tup) > 1:
for t in tup[1:]:
self.logfil_out.write(" %s" % t)
self.logfil_out.write("\n")
self.logfil_err.flush()
return
def addErr(self, msg):
self.logfil_err.write(msg + "\n")
self.logfil_out.flush()
self.logfil_err.flush()
def exitErr(self, msg):
from sys import exit
self.addErr(msg)
exit(msg)
def cleanup(self, is_verbose=False):
from os import access, F_OK, remove, removedirs
self.logfil_out.close()
self.logfil_err.close()
for filnam in (self.datafiles + self.tmpfiles):
if access(filnam, F_OK):
remove(filnam)
if is_verbose: print("Removed file '%s'" % filnam)
else:
print("Could not access file '%s'" % filnam)
self.datafiles = []
self.tmpfiles = []
try:
removedirs(DataFiles.WORKDIR)
except:
"Could not remove temporary directory %s" % DataFiles.WORKDIR
def openFile(filnam, mode = 'r'):
import gzip
is_compressed = len(filnam) > 3 and filnam[-3:] == ".gz"
try:
if is_compressed:
oufil = gzip.open(filnam, mode)
else:
oufil = open(filnam, mode)
except:
print("ERROR when opening file '%s'" % filnam)
exit(1)
return oufil
def areFilesIdentical(filnamA, filnamB, ignore_key=""):
# compare text files line by line
# ignore lines that start with ignore_key
infilA = openFile(filnamA)
infilB = openFile(filnamB)
kl = len(ignore_key)
okflg = True
while okflg:
linA = infilA.readline()
linB = infilB.readline()
if not linA or not linB:
okflg = not linA and not linB
break
if linA != linB and \
(kl < 1 or \
linA[:kl] != linB[:kl] or \
linA[:kl] != ignore_key):
okflg = False
return okflg
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