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_buildscript(tmpdir, caplog): p13 = Proc() p13.props.template = TemplateLiquid p13._buildScript() assert 'No script specified' in caplog.text scriptfile = tmpdir / 'test_buildscript.txt' scriptfile.write_text('# script') p13.script = 'file:%s' % scriptfile fs.remove(scriptfile) with pytest.raises(ProcScriptError): p13._buildScript() scriptfile.write_text('''# script # PYPPL INDENT REMOVE abs bin # PYPPL INDENT KEEP callable def''') caplog.clear() p13.lang = 'python' p13._buildScript() assert 'Using template file: ' in caplog.text assert p13.script.render() == '''#!/usr/bin/env python
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_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