def test_pipe_error():
with pytest.raises(cmdy.CmdyActionError):
cmdy.cat().h() | cmdy.grep(cmdy_raise=False)
h = cmdy.cat().h()
h.stdout = sys.stderr
with pytest.raises(cmdy.CmdyActionError):
h.p() | cmdy.grep()
def pipeline(opts):
"""Construct the pipeline"""
# get the column index of the column name
colidx = cmdy.head(opts.infile, n=1, _pipe=True) | \
cmdy.tr("\t", "\n", _pipe=True) | \
cmdy.nl(_pipe=True) | \
cmdy.grep(w=opts.on)
colidx = colidx.strip().split()[0]
# sort by that column, make sure the first element we remain
# is the corresponding record
pSort.input = [opts.infile]
pSort.args.inopts.skip = 1
pSort.args.params.k = '%sg' % colidx
pTsvAggregate.depends = pSort
pTsvAggregate.args.sort = False
pTsvAggregate.args.aggrs.Padj_aggr = "$%s:%s" % (opts.method, opts.on)
#pTsvAggregate.args.on = "Case"
pTsvAggregate.args.origin = "keep0"
pTsvAggregate.output = "outfile:file:%s" % Path(opts.outfile).name
pTsvAggregate.config.export_dir = Path(opts.outfile).parent
return pSort
def test_mixed_actions_pipe_then():
# actions could be
# hold
# async_
# redirect
# fg
# iter
# pipe
c = cmdy.echo().h().pipe().r()
assert isinstance(c, CmdyHolding)
_CMDY_EVENT.clear()
with pytest.raises(CmdyActionError):
cmdy.echo().p().h()
c = cmdy.echo().p().a()
assert isinstance(c, CmdyHolding)
_CMDY_EVENT.clear()
c = cmdy.bash(
c='echo "1\n2\n3" 1>&2').p().r(STDERR) ^ STDOUT | cmdy.grep(2)
assert c.str() == '2\n'
with pytest.raises(CmdyActionError) as ex:
cmdy.echo().p().p()
assert 'Unconsumed piping' in str(ex.value)
def test_mixed_actions_pipe_then_iter(capsys):
c = cmdy.bash(c='echo "1\n2\n3" 1>&2').p(STDERR).iter(STDOUT)
d = c | cmdy.grep(2, cmdy_okcode='0,1')
assert isinstance(d, CmdyResult)
assert isinstance(c, CmdyHolding)
assert d == '2\n'
def test_mixed_actions_pipe_then_fg(capsys):
c = cmdy.bash(c='echo 123 1>&2 && echo 456').p(STDERR).fg() | cmdy.grep(
4, cmdy_okcode='0,1')
assert capsys.readouterr().out == '456\n'
assert c.str() == '' # have been redirected by fg
def test_multi_pipe():
c = cmdy.echo("11\n12\n22\n23").p() | cmdy.grep(2).p() | cmdy.grep(22)
assert c == '22\n'
def test_pipe():
c = cmdy.echo("1\n2\n3").p() | cmdy.grep(2)
assert c == '2\n'