def testRunErr(self):
ex = None
try:
procOps.runProc(["false"], stdin=self.getInputFile("simple1.txt"))
except Exception as ex:
pass
self.failUnless(isinstance(ex, Pipeline.ProcException))
self.failUnlessEqual(str(ex), 'process exited 1: false')
def testRead(self):
inf = self.getInputFile("simple1.txt")
infGz = self.getOutputFile(".txt.gz")
procOps.runProc(("gzip", "-c", inf), stdout=infGz)
pl = Pipeline(("gzip", "-dc"), "r", otherEnd=infGz)
self.cpPlToFile(pl, ".out")
pl.wait()
self.diffExpected(".out")
def testRead(self):
inf = self.getInputFile("simple1.txt")
infGz = self.getOutputFile(".txt.gz")
procOps.runProc(("gzip", "-c", inf), stdout=infGz)
pl = Pipeline(("gzip", "-dc"), "r", otherEnd=infGz)
self.cpPlToFile(pl, ".out")
pl.wait()
self.diffExpected(".out")
def testWrite(self):
outf = self.getOutputFile(".out")
outfGz = self.getOutputFile(".out.gz")
pl = Pipeline(("gzip", "-1"), "w", otherEnd=outfGz)
self.cpFileToPl("simple1.txt", pl)
pl.wait()
procOps.runProc(("zcat", outfGz), stdout=outf)
self.diffExpected(".out")
def testWrite(self):
outf = self.getOutputFile(".out")
outfGz = self.getOutputFile(".out.gz")
pl = Pipeline(("gzip", "-1"), "w", otherEnd=outfGz)
self.cpFileToPl("simple1.txt", pl)
pl.wait()
procOps.runProc(("zcat", outfGz), stdout=outf)
self.diffExpected(".out")
def XXtestPassWrite(self):
"using FIFO to pass pipe to another process for writing"
# FIXME: should this be supported somehow
inf = self.getInputFile("simple1.txt")
outf = self.getOutputFile(".out")
pipePath = self.getOutputFile(".fifo")
pl = Pipeline(("sort", "-r"), "w", otherEnd=outf, pipePath=pipePath)
procOps.runProc(["cat"], stdin=inf, stdout=pl.pipePath)
pl.wait()
self.diffExpected(".out")
def XXtestPassWrite(self):
"using FIFO to pass pipe to another process for writing"
# FIXME: should this be supported somehow
inf = self.getInputFile("simple1.txt")
outf = self.getOutputFile(".out")
pipePath = self.getOutputFile(".fifo")
pl = Pipeline(("sort", "-r"), "w", otherEnd=outf, pipePath=pipePath)
procOps.runProc(["cat"], stdin=inf, stdout=pl.pipePath)
pl.wait()
self.diffExpected(".out")
def XXtestPassRead(self):
"using FIFO to pass pipe to another process for reading"
# FIXME: should this be supported somehow
inf = self.getInputFile("simple1.txt")
infGz = self.getOutputFile(".txt.gz")
cpOut = self.getOutputFile(".out")
procOps.runProc(("gzip", "-c", inf), stdout=infGz)
pl = Pipeline(("gzip", "-dc"), "r", otherEnd=infGz)
procOps.runProc(["cat"], stdin=pl.pipePath, stdout=cpOut)
pl.wait()
self.diffExpected(".out")
def XXtestPassRead(self):
"using FIFO to pass pipe to another process for reading"
# FIXME: should this be supported somehow
inf = self.getInputFile("simple1.txt")
infGz = self.getOutputFile(".txt.gz")
cpOut = self.getOutputFile(".out")
procOps.runProc(("gzip", "-c", inf), stdout=infGz)
pl = Pipeline(("gzip", "-dc"), "r", otherEnd=infGz)
procOps.runProc(["cat"], stdin=pl.pipePath, stdout=cpOut)
pl.wait()
self.diffExpected(".out")
def testRunInOut(self):
outf = self.getOutputFile(".txt")
ret = procOps.runProc(["sort"], stdin=self.getInputFile("simple1.txt"), stdout=outf)
self.failUnlessEqual(ret, 0)
self.diffExpected(".txt")
def testReadBzip2(self):
tsvBz = self.getOutputFile("tsv.bz2")
procOps.runProc(["bzip2", "-c", self.getInputFile("mrna1.tsv")], stdout=tsvBz)
self.readMRna1(tsvBz)
def testReadGzip(self):
tsvGz = self.getOutputFile("tsv.gz")
procOps.runProc(["gzip", "-c", self.getInputFile("mrna1.tsv")], stdout=tsvGz)
self.readMRna1(tsvGz)
def testReadBzip2(self):
tsvBz = self.getOutputFile("tsv.bz2")
procOps.runProc(
["bzip2", "-c", self.getInputFile("mrna1.tsv")], stdout=tsvBz)
self.readMRna1(tsvBz)
def testReadGzip(self):
tsvGz = self.getOutputFile("tsv.gz")
procOps.runProc(
["gzip", "-c", self.getInputFile("mrna1.tsv")], stdout=tsvGz)
self.readMRna1(tsvGz)