def testCmdErr(self):
"handling of pipes when process has error"
er = ExRun(verbFlags=set())
ifp = er.getFile(self.getInputFile("numbers.txt"))
ofp1 = er.getFile(self.getOutputFile(".txt.gz"))
ofp2 = er.getFile(self.getOutputFile(".txt"))
r1 = er.addCmd(
(["sort", "-r", FileIn(ifp)], ["tee", FileOut(ofp1)]),
stdout="/dev/null")
r2 = er.addCmd(
(["zcat", FileIn(ofp1, autoDecompress=False)], ["false"]),
stdout=FileOut(ofp2))
ex = None
try:
er.run()
except ExRunException, ex:
self.failUnlessEqual("Experiment failed: 1 error(s) encountered",
str(ex))
ex1 = er.errors[0]
self.failUnless(isinstance(ex1, ExRunException))
ex2 = ex1.cause
self.failUnless(isinstance(ex2, ExRunException))
ex3 = ex2.cause
self.failUnless(isinstance(ex3, ProcException))
exre = "process exited 1: false"
self.failUnless(str(ex3), exre)
def testArgs(self):
er = ExRun(verbFlags=verbFlags)
ifp = er.getFile(self.getInputFile("numbers.txt"))
ofp1 = er.getFile(self.getOutputFile(".txt.gz"))
ofp2 = er.getFile(self.getOutputFile(".txt"))
er.addCmd((["sort", "-r", FileIn(ifp)], ["tee", FileOut(ofp1)]),
stdout="/dev/null")
er.addCmd(["sed", "-e", "s/^/= /", FileIn(ofp1)], stdout=FileOut(ofp2))
try:
er.run()
except Exception, ex:
prExceptions(er, ex)
raise
def testSort2RulesSub(self):
"two commands in separate rules, with file ref subtitution"
er = ExRun(verbFlags=verbFlags)
ifp = er.getFile(self.getInputFile("numbers.txt"))
ofp1 = er.getFile(self.getOutputFile(".txt"))
ofp2 = er.getFile(self.getOutputFile(".linecnt"))
c1 = Cmd((("sort", "-r", FileIn(ifp)), ("sort", "-nr"),
("tee", FileOut(ofp1))),
stdout="/dev/null")
c2 = Cmd((("cat", FileIn(ofp1)), ("wc", "-l"), ("sed", "-e", "s/ //g"),
("tee", FileOut(ofp2))),
stdout="/dev/null")
er.addRule(CmdRule(c2))
er.addRule(CmdRule(c1))
try:
er.run()
except Exception, ex:
prExceptions(er, ex)
raise
def testSortPipe(self):
"pipeline command to sort a file"
er = ExRun(verbFlags=verbFlags)
ifp = er.getFile(self.getInputFile("numbers.txt"))
ofp = er.getFile(self.getOutputFile(".txt"))
c = Cmd((("sort", "-r", FileIn(ifp)), ("sort", "-nr")), stdout=ofp)
er.addRule(CmdRule(c, requires=ifp, produces=ofp))
try:
er.run()
except Exception, ex:
prExceptions(er, ex)
raise
def testFilePrefix(self):
"test prefixes to FileIn/FileOut"
er = ExRun(verbFlags=verbFlags)
ifp = er.getFile(self.getInputFile("numbers.txt"))
ofp = er.getFile(self.getOutputFile(".txt"))
c = Cmd(("dd", "if=" + FileIn(ifp), "of=" + FileOut(ofp)))
er.addRule(CmdRule(c))
try:
er.run()
except Exception, ex:
prExceptions(er, ex)
raise
def testStdio(self):
er = ExRun(verbFlags=verbFlags)
ifp = er.getFile(self.getInputFile("numbers.txt"))
ofp1 = er.getFile(self.getOutputFile(".txt.gz"))
ofp2 = er.getFile(self.getOutputFile(".txt"))
er.addCmd(["sort", "-r"], stdin=ifp, stdout=ofp1)
er.addCmd((["zcat", FileIn(ofp1, autoDecompress=False)
], ["sed", "-e", "s/^/= /"]),
stdout=ofp2)
try:
er.run()
except Exception, ex:
prExceptions(er, ex)
raise
def testSort2(self):
"two commands"
er = ExRun(verbFlags=verbFlags)
ifp = er.getFile(self.getInputFile("numbers.txt"))
ofp1 = er.getFile(self.getOutputFile(".txt"))
ofp2 = er.getFile(self.getOutputFile(".linecnt"))
c1 = Cmd((("sort", "-r", FileIn(ifp)), ("sort", "-nr")), stdout=ofp1)
c2 = Cmd((("wc", "-l"), ("sed", "-e", "s/ //g")),
stdin=ofp1,
stdout=ofp2)
er.addRule(CmdRule((c1, c2), requires=ifp))
try:
er.run()
except Exception, ex:
prExceptions(er, ex)
raise