def test_preruntidy(tmpdir, caplog):
p20 = Proc()
p20.input = 'a, b'
p20.input = [(1, 2), (3, 4), (5, 6)]
p20.callfront = lambda p: setattr(p, 'forks', 20)
p20._preRunTidy()
assert 'Calling callfront ...' in caplog.text
assert p20.forks == 20
assert p20.size == 3
def test_suffix_input(tmpdir):
p82 = Proc()
p82.input = 'a'
p82.input = [1]
sigs = OBox()
sigs.argv0 = str(Path(sys.argv[0]).resolve())
sigs.id = 'p82'
sigs.tag = 'notag'
assert p82.config.input == {'a': [1]}
sigs.input = {'a': "[1]"}
assert p82.suffix == uid(sigs.to_json())
def test_runjobs(tmpdir):
p21 = Proc()
p21.forks = 3
p21.input = 'a, b'
p21.input = [(1, 2), (3, 4), (5, 6)]
p21.output = 'a:{{i.a}}, b:{{i.b}}'
p21.script = 'echo Hello world!'
p21._preRunTidy()
p21._runJobs()
assert p21.channel == [('1', '2'), ('3', '4'), ('5', '6')]
assert p21.channel.a.flatten() == ['1', '3', '5']
assert p21.channel.b.flatten() == ['2', '4', '6']
def test_proc_setattr(tmpdir, caplog):
p3 = Proc()
with pytest.raises(ProcAttributeError):
p3.x = 1
p3.preCmd = 'ls'
assert 'beforeCmd' in p3.sets
p4 = Proc()
ps = ProcSet(p4)
p3.depends = p4
assert p3.depends == [p4]
p3.depends = [p4], ps
assert p3.depends == [p4, ps.p4]
assert p4.tag == 'notag'
assert ps.p4.tag == 'notag@ps'
with pytest.raises(ProcAttributeError):
p3.depends = p3
with pytest.raises(ProcAttributeError):
p3.depends = object()
p3.script = 'file:%s' % Path(__file__).name
assert p3.config.script == 'file:%s' % Path(__file__).resolve()
p31 = Proc(script='file:%s' % Path(__file__).name)
assert p31.config.script == 'file:%s' % Path(__file__).resolve()
with pytest.raises(ProcAttributeError):
p3.script = 'file:nosuchfile'
p3.args = {'a': 1}
assert p3.args.a == 1
p3.input = 'a, b'
p3.input = [1, 2]
assert p3.config.input == {'a, b': [1, 2]}
p3.input = {'a': [1], 'b': [2]}
caplog.clear()
p3.input = [3, 4]
assert 'Previous input is a dict with multiple keys and key order may be changed.' in caplog.text
assert 'Now the key order is:' in caplog.text
p3.runner = 'sge'
assert p3.config.runner == 'sge'
assert p3.props.runner == 'sge'
with pytest.raises(ProcAttributeError):
p3.tag = 'a@b'
def test_buildinput(tmpdir, caplog):
p10 = Proc()
p10.input = 'a, b:file, '
p10.input = ('1', 'infile')
p10._buildInput()
assert len(p10.input) == 2
assert p10.input['a'] == ('var', ['1'])
assert p10.input['b'] == ('file', ['infile'])
assert p10.size == 1
p10.input = 'a:x:y'
with pytest.raises(ProcInputError):
p10._buildInput()
p101 = Proc()
p101.props.channel = Channel.create([(1, 3), (2, 4)])
p10.depends = p101
p10.input = 'a, b, c'
p10.input = lambda ch: ch.cbind(1).cbind(2)
caplog.clear()
p10._buildInput()
assert 'Not all data are used as input' in caplog.text
assert len(p10.input) == 3
assert p10.size == 2
assert p10.input['a'] == ('var', [1, 2])
assert p10.input['b'] == ('var', [3, 4])
assert p10.input['c'] == ('var', [1, 1])
p10.input = 'a:files, b:files, c'
p10.input = Channel.create([['infile1'], ['infile2']])
p10._buildInput()
assert 'No data found for input key "b"' in caplog.text
assert 'No data found for input key "c"' in caplog.text
caplog.clear()
assert len(p10.input) == 3
assert p10.size == 2
assert p10.input['a'] == ('files', [['infile1'], ['infile2']])
assert p10.input['b'] == ('files', [[], []])
assert p10.input['c'] == ('var', ['', ''])
p10.props.template = TemplateLiquid
p10.props.workdir = tmpdir / 'test_buildinput_p10'
p10.resume = 'resume'
fs.remove(Path(p10.workdir) / 'proc.settings.yaml')
with pytest.raises(ProcInputError):
p10._buildInput()
fs.mkdir(p10.workdir)
p10.props.input = OBox()
p10.input['a'] = ('files', [['infile1'], ['infile2']])
p10.input['b'] = ('files', [[], []])
p10.input['c'] = ('var', ['', ''])
p10._saveSettings()
p10.props.input = None
p10._buildInput()
assert len(p10.input) == 3
assert p10.size == 2
assert p10.input['a'] == ('files', [['infile1'], ['infile2']])
assert p10.input['b'] == ('files', [[], []])
assert p10.input['c'] == ('var', ['', ''])
def test_suffix_compute(tmpdir):
p76 = Proc()
p81 = Proc()
p81.depends = p76
p81.input = 'a'
sigs = OBox()
sigs.argv0 = str(Path(sys.argv[0]).resolve())
sigs.id = 'p81'
sigs.tag = 'notag'
sigs.input = 'a'
sigs.depends = ['p76#' + p76.suffix]
assert p81.suffix == uid(sigs.to_json())
def test_postruntidy(tmpdir, caplog):
p22 = Proc()
p22.resume = 'skip+'
p22.callback = lambda p: p.props.update({'channel': p.channel.cbind(1, 2)})
p22._postRunTidy()
assert p22.channel == [(1, 2)]
p23 = Proc()
p23.forks = 5
p23.input = 'a, b'
p23.input = [(1, 2), (3, 4), (5, 6), (7, 8), (9, 10)]
p23.output = 'a:{{i.a}}, b:{{i.b}}'
p23.script = 'echo Hello world!'
p23.errhow = 'ignore'
p23.callback = lambda p: setattr(p, 'forks', 10)
p23._preRunTidy()
p23._runJobs()
p23.jobs[0].state = STATES.BUILTFAILED
p23.jobs[1].state = STATES.SUBMITFAILED
p23.jobs[2].state = STATES.DONE
p23.jobs[3].state = STATES.DONECACHED
p23.jobs[4].state = STATES.ENDFAILED
p23._postRunTidy()
assert ' Jobs (Cached: 1, Succ: 1, B.Fail: 1, S.Fail: 1, R.Fail: 1)' in caplog.text
assert 'Failed but ignored (totally 3).' in caplog.text
assert p23.forks == 10
p23.errhow = 'terminate'
caplog.clear()
with pytest.raises(SystemExit):
p23._postRunTidy()
assert 'Cached: 4' in caplog.text
assert 'Succeeded: 3' in caplog.text
assert 'Building failed: 1' in caplog.text
assert 'Submission failed: 2' in caplog.text
assert 'Running failed: 5' in caplog.text