def test_consume_commands_6():
parser = Parser(overall)
res = parser.consume()
print(res[5].parts)
res[5].alias.should.equal('6')
res[5].parts[4].should.equal('./somescript')
res[5].parts[5][0][0].should.equal(Input('1', 'somefile.1'))
res[5].parts[5][0][1].should.equal(Input('2', 'somefile.2'))
res[5].parts[5][0][2].should.equal(Input('3', 'somefile.3'))
res[5].parts[5][1][0].should.equal(Input('4', '*.counts'))
res[5]._dependencies.should.have.length_of(0)
def test_consume_commands_2():
parser = Parser(overall)
res = parser.consume()
res[1].alias.should.equal('2')
res[1].parts[4].should.equal(parser.paths[1])
res[1].parts[5].should.equal('somescript.sh')
res[1].parts[6].should.equal('-i')
res[1].parts[7][0][0].should.equal(Input('1.1'))
res[1].parts[7][1][0].should.equal(Input('1.2'))
res[1].parts[8].should.equal('-o')
res[1].parts[9].should.equal(Output('1'))
res[1].parts[10].should.equal('-fgh')
res[1].parts[11].should.equal('somefile.txt')
res[1]._dependencies.should.have.length_of(1)
res[1]._dependencies[0].alias.should.equal('1')
def test_consume_commands_9():
parser = Parser(overall)
res = parser.consume()
res[8].alias.should.equal('9')
res[8].parts[4].should.equal('cat')
res[8].parts[5][0][0].should.equal(Input('*.bam',
filename='*.bam'))
res[8]._dependencies.should.have.length_of(1)
def test_consume_commands_3():
parser = Parser(overall)
res = parser.consume()
res[2].alias.should.equal('3')
res[2].parts[4].should.equal(parser.paths[2])
res[2].parts[5].should.equal('somescript.rb')
res[2].parts[6].should.equal('-i')
res[2].parts[7][0][0].should.equal(Input('2.1'))
res[2].parts[7][1][0].should.equal(Input('2.2'))
res[2].parts[7][2][0].should.equal(Input('1.1'))
res[2].parts[7][2][1].should.equal(Input('1.2'))
res[2].parts[8].should.equal('>>')
res[2].parts[9].should.equal('somefile')
res[2]._dependencies.should.have.length_of(2)
aliases = [dep.alias for dep in res[2]._dependencies]
aliases.should.contain('2')
aliases.should.contain('1')
def test_consume_commands_8():
parser = Parser(overall)
res = parser.consume()
res[7].alias.should.equal('8')
res[7].parts[4].should.equal(parser.paths[0])
res[7].parts[5].should.equal('somescript.py')
res[7].parts[6].should.equal('-i')
res[7].parts[7][0][0].should.equal(Input('*.counts',
filename='*.counts'))
res[7].parts[9].should.equal(Output('', magic='*.bam'))
res[7]._dependencies.should.have.length_of(0)
def test_consume_commands_7():
parser = Parser(overall)
res = parser.consume()
res[6].alias.should.equal('7')
res[6].parts[4].should.equal(parser.paths[2])
res[6].parts[5].should.equal('somescript.rb')
res[6].parts[6].should.equal('-i')
res[6].parts[7][0][0].should.equal(Input('*.counts',
'*.counts'))
res[6].parts.should.have.length_of(8)
res[6]._dependencies.should.have.length_of(0)
def test_consume_commands_1():
parser = Parser(overall)
res = parser.consume()
res[0].alias.should.equal('1')
res[0].parts[4].should.equal(parser.paths[0])
res[0].parts[5].should.equal('somescript.py')
res[0].parts[6].should.equal('-i')
res[0].parts[7][0][0].should.equal(Input('1', filename='somefile.1'))
res[0].parts[7][0][1].should.equal(Input('2', filename='somefile.2'))
res[0].parts[7][0][2].should.equal(Input('3', filename='somefile.3'))
res[0].parts[7][1][0].should.equal(Input('4', filename='somefile.4'))
res[0].parts[7][1][1].should.equal(Input('5', filename='somefile.5'))
res[0].parts[7][1][2].should.equal(Input('6', filename='somefile.6'))
res[0].parts[8].should.equal('-o')
res[0].parts[9].should.equal(Output('1'))
res[0].parts[10].should.equal('-fgh')
res[0].parts[11].should.equal('somefile.txt')
res[0]._dependencies.should.have.length_of(0)
def test_consume_multiple_inputs():
parser = Parser(multiple_inputs)
res = parser.consume()
res[0].alias.should.equal('1')
res[0].parts[0].should.equal('bash')
res[0].parts[2][0][0].should.equal(Input('1',
filename='somefile.1'))
res[0].parts[2][1][0].should.equal(Input('2',
filename='somefile.2'))
res[0].parts[2][2][0].should.equal(Input('3',
filename='somefile.3'))
res[0].parts[4][0][0].should.equal(Input('4',
filename='somefile.4'))
res[0].parts[4][1][0].should.equal(Input('5',
filename='somefile.5'))
res[0].parts[4][2][0].should.equal(Input('6',
filename='somefile.6'))
res[0]._dependencies.should.have.length_of(0)