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)