def test_03_input(instance_path):
"""Check the essential input parameters."""
whale = Path(instance_path) / 'whale.txt'
whale.touch()
argv = [
'echo',
'-f',
'-i42',
'--example-string',
'hello',
'--file=whale.txt',
]
tool = CommandLineToolFactory(argv,
directory=instance_path,
working_dir=instance_path).generate_tool()
assert tool.arguments[0].to_argv() == ['-f']
assert tool.inputs[0].default == 42
assert tool.inputs[0].type == 'int'
assert tool.inputs[0].inputBinding.prefix == '-i'
assert tool.inputs[0].inputBinding.separate is False
assert tool.inputs[1].default == 'hello'
assert tool.inputs[1].type == 'string'
assert tool.inputs[1].inputBinding.prefix == '--example-string'
assert tool.inputs[1].inputBinding.separate is True
assert tool.inputs[2].default.path.samefile(whale)
assert tool.inputs[2].type == 'File'
assert tool.inputs[2].inputBinding.prefix == '--file='
assert tool.inputs[2].inputBinding.separate is False
assert tool.to_argv() == argv
def test_09_array_inputs(instance_path):
"""Test specification of input parameters in arrays."""
argv = [
'echo',
'-A',
'one',
'two',
'three',
'-B=four',
'-B=five',
'-B=six',
'-C=seven,eight,nine',
]
tool = CommandLineToolFactory(argv,
directory=instance_path,
working_dir=instance_path).generate_tool()
# TODO add grouping for -A and -B
assert tool.inputs[-1].type == 'string[]'
assert tool.inputs[-1].default == ['seven', 'eight', 'nine']
assert tool.inputs[-1].inputBinding.prefix == '-C='
assert tool.inputs[-1].inputBinding.itemSeparator == ','
assert tool.inputs[-1].inputBinding.separate is False
assert tool.to_argv() == argv
def test_short_base_command_detection():
"""Test base command detection without arguments."""
tool = CommandLineToolFactory(('echo', 'A')).generate_tool()
assert tool.cwlVersion == 'v1.0'
assert tool.__class__.__name__ == 'CommandLineTool'
assert tool.inputs[0].default == 'A'
assert tool.to_argv() == ['echo', 'A']
def test_short_base_command_detection(client):
"""Test base command detection without arguments."""
tool = CommandLineToolFactory(
('echo', 'A')).generate_process_run(client=client,
commit=client.repo.head.commit,
path='dummy.yaml')
tool = tool.association.plan
assert 'A' == tool.arguments[0].value
assert ['echo', 'A'] == tool.to_argv()
def test_base_command_detection(instance_path):
"""Test base command detection."""
hello = Path(instance_path) / 'hello.tar'
hello.touch()
argv = ['tar', 'xf', 'hello.tar']
tool = CommandLineToolFactory(argv,
directory=instance_path,
working_dir=instance_path).generate_tool()
assert tool.baseCommand == ['tar', 'xf']
assert tool.inputs[0].default.path.samefile(hello)
assert tool.inputs[0].type == 'File'
assert tool.inputs[0].inputBinding.prefix is None
assert tool.inputs[0].inputBinding.separate is True
assert tool.to_argv() == argv
def test_base_command_detection(client):
"""Test base command detection."""
hello = Path(client.path) / 'hello.tar'
hello.touch()
client.repo.index.add([str(hello)])
client.repo.index.commit('add hello.tar')
argv = ['tar', 'xf', 'hello.tar']
tool = CommandLineToolFactory(
argv, directory=client.path,
working_dir=client.path).generate_process_run(
client=client, commit=client.repo.head.commit, path='dummy.yaml')
tool = tool.association.plan
assert 'tar xf' == tool.command
assert tool.inputs[0].consumes.path == 'hello.tar'
assert isinstance(tool.inputs[0].consumes, Entity)
assert not isinstance(tool.inputs[0].consumes, Collection)
assert tool.inputs[0].prefix is None
assert argv == tool.to_argv()
def test_03_input(client):
"""Check the essential input parameters."""
whale = Path(client.path) / 'whale.txt'
whale.touch()
client.repo.index.add([str(whale)])
client.repo.index.commit('add whale.txt')
argv = [
'echo',
'-f',
'-i42',
'--example-string',
'hello',
'--file=whale.txt',
]
tool = CommandLineToolFactory(
argv, directory=client.path,
working_dir=client.path).generate_process_run(
client=client, commit=client.repo.head.commit, path='dummy.yaml')
tool = tool.association.plan
assert ['-f'] == tool.arguments[0].to_argv()
assert 42 == tool.arguments[1].value
assert '-i' == tool.arguments[1].prefix
assert 'hello' == tool.arguments[2].value
assert '--example-string ' == tool.arguments[2].prefix
assert tool.inputs[0].consumes.path == 'whale.txt'
assert isinstance(tool.inputs[0].consumes, Entity)
assert not isinstance(tool.inputs[0].consumes, Collection)
assert '--file=' == tool.inputs[0].prefix
assert argv == tool.to_argv()
def test_03_input(client):
"""Check the essential input parameters."""
whale = Path(client.path) / "whale.txt"
whale.touch()
client.repo.index.add([str(whale)])
client.repo.index.commit("add whale.txt")
argv = [
"echo",
"-f",
"-i42",
"--example-string",
"hello",
"--file=whale.txt",
]
tool = CommandLineToolFactory(
argv, directory=client.path,
working_dir=client.path).generate_process_run(
client=client, commit=client.repo.head.commit, path="dummy.yaml")
tool = tool.association.plan
assert ["-f"] == tool.arguments[0].to_argv()
assert 42 == tool.arguments[1].value
assert "-i" == tool.arguments[1].prefix
assert "hello" == tool.arguments[2].value
assert "--example-string " == tool.arguments[2].prefix
assert tool.inputs[0].consumes.path == "whale.txt"
assert isinstance(tool.inputs[0].consumes, Entity)
assert not isinstance(tool.inputs[0].consumes, Collection)
assert "--file=" == tool.inputs[0].prefix
assert argv == tool.to_argv()
def test_09_array_inputs(client):
"""Test specification of input parameters in arrays."""
argv = [
'echo',
'-A',
'one',
'two',
'three',
'-B=four',
'-B=five',
'-B=six',
'-C=seven,eight,nine',
]
tool = CommandLineToolFactory(
argv, directory=client.path,
working_dir=client.path).generate_process_run(
client=client, commit=client.repo.head.commit, path='dummy.yaml')
tool = tool.association.plan
assert 'seven,eight,nine' == tool.arguments[-1].value
assert '-C=' == tool.arguments[-1].prefix
assert argv == tool.to_argv()
def test_09_array_inputs(client):
"""Test specification of input parameters in arrays."""
argv = [
"echo",
"-A",
"one",
"two",
"three",
"-B=four",
"-B=five",
"-B=six",
"-C=seven,eight,nine",
]
tool = CommandLineToolFactory(
argv, directory=client.path,
working_dir=client.path).generate_process_run(
client=client, commit=client.repo.head.commit, path="dummy.yaml")
tool = tool.association.plan
assert "seven,eight,nine" == tool.arguments[-1].value
assert "-C=" == tool.arguments[-1].prefix
assert argv == tool.to_argv()
def test_09_array_inputs(instance_path):
"""Test specification of input parameters in arrays."""
argv = [
'echo',
'-A',
'one',
'two',
'three',
'-B=four',
'-B=five',
'-B=six',
'-C=seven,eight,nine',
]
tool = CommandLineToolFactory(argv,
directory=instance_path,
working_dir=instance_path).generate_tool()
assert 'string[]' == tool.inputs[-1].type
assert ['seven', 'eight', 'nine'] == tool.inputs[-1].default
assert '-C=' == tool.inputs[-1].inputBinding.prefix
assert ',' == tool.inputs[-1].inputBinding.itemSeparator
assert tool.inputs[-1].inputBinding.separate is False
assert argv == tool.to_argv()
