def test_split_cmdline_args_with_expandable_tags(self):
splitted = ToolSpecification.split_cmdline_args("@@optional_inputs@@")
self.assertEqual(splitted, ["@@optional_inputs@@"])
splitted = ToolSpecification.split_cmdline_args(
"@@url:database name with spaces@@")
self.assertEqual(splitted, ["@@url:database name with spaces@@"])
splitted = ToolSpecification.split_cmdline_args(
"@@url:spaced name@@ -a @@url:another spaced tag@@")
self.assertEqual(
splitted,
["@@url:spaced name@@", "-a", "@@url:another spaced tag@@"])
def test_find_optional_input_files_without_wildcards(self):
with TemporaryDirectory() as temp_dir:
optional_file = pathlib.Path(temp_dir, "1.txt")
optional_file.touch()
pathlib.Path(temp_dir, "should_not_be_found.txt").touch()
logger = mock.MagicMock()
optional_input_files = ["1.txt", "does_not_exist.dat"]
tool_specification = ToolSpecification(
"spec name",
"Python",
temp_dir, [],
None,
logger,
inputfiles_opt=optional_input_files)
executable = ExecutableItem(
"executable name",
work_dir=temp_dir,
output_dir="",
tool_specification=tool_specification,
cmd_line_args=[],
logger=logger,
)
resources = [
ProjectItemResource(None, "file", optional_file.as_uri())
]
file_paths = executable._find_optional_input_files(resources)
self.assertEqual(file_paths, {"1.txt": [str(optional_file)]})
def test_find_optional_input_files_in_sub_directory(self):
with TemporaryDirectory() as temp_dir:
pathlib.Path(temp_dir, "subdir").mkdir()
optional_file1 = pathlib.Path(temp_dir, "subdir", "1.txt")
optional_file1.touch()
optional_file2 = pathlib.Path(temp_dir, "subdir", "data.dat")
optional_file2.touch()
pathlib.Path(temp_dir, "should_not_be_found.jpg").touch()
logger = mock.MagicMock()
optional_input_files = ["subdir/*.txt", "subdir/data.dat"]
tool_specification = ToolSpecification(
"spec name",
"Python",
temp_dir, [],
None,
logger,
inputfiles_opt=optional_input_files)
executable = ExecutableItem(
"executable name",
work_dir=temp_dir,
output_dir="",
tool_specification=tool_specification,
cmd_line_args=[],
logger=logger,
)
resources = [
ProjectItemResource(None, "file", optional_file1.as_uri()),
ProjectItemResource(None, "file", optional_file2.as_uri()),
]
file_paths = executable._find_optional_input_files(resources)
self.assertEqual(
file_paths, {
"subdir/*.txt": [str(optional_file1)],
"subdir/data.dat": [str(optional_file2)]
})
def test_get_cmdline_args_with_optional_inputs(self):
specification = ToolSpecification("", "", "", [], None, None)
specification.cmdline_args = ["@@optional_inputs@@"]
args = specification.get_cmdline_args([], {}, {})
self.assertEqual(args, [""])
specification.cmdline_args = ["@@optional_inputs@@"]
args = specification.get_cmdline_args(["file.dat", "table.csv"], {},
{})
self.assertEqual(args, ["file.dat", "table.csv"])
specification.cmdline_args = ["--inputs=@@optional_inputs@@"]
args = specification.get_cmdline_args(["file.dat", "table.csv"], {},
{})
self.assertEqual(args, ["--inputs=file.dat", "table.csv"])
def test_get_cmdline_args_with_datastore_urls(self):
specification = ToolSpecification("", "", "", [], None, None)
specification.cmdline_args = ["@@url:ds1@@"]
args = specification.get_cmdline_args(
[], {"ds1": "sqlite:///Q:\\databases\\base.sqlite"}, {})
self.assertEqual(args, ["sqlite:///Q:\\databases\\base.sqlite"])
specification.cmdline_args = ["--url=@@url:ds1@@"]
args = specification.get_cmdline_args(
[], {}, {"ds1": "sqlite:///Q:\\databases\\base.sqlite"})
self.assertEqual(args, ["--url=sqlite:///Q:\\databases\\base.sqlite"])
def test_split_cmdline_args(self):
splitted = ToolSpecification.split_cmdline_args("")
self.assertFalse(bool(splitted))
splitted = ToolSpecification.split_cmdline_args("--version")
self.assertEqual(splitted, ["--version"])
splitted = ToolSpecification.split_cmdline_args(
"--input=data.dat -h 5")
self.assertEqual(splitted, ["--input=data.dat", "-h", "5"])
splitted = ToolSpecification.split_cmdline_args(
'--output="a long file name.txt"')
self.assertEqual(splitted, ['--output=a long file name.txt'])
splitted = ToolSpecification.split_cmdline_args(
"--file='file name with spaces.dat' -i 3")
self.assertEqual(splitted,
["--file=file name with spaces.dat", "-i", "3"])
splitted = ToolSpecification.split_cmdline_args(
"'quotation \"within\" a quotation'")
self.assertEqual(splitted, ['quotation \"within\" a quotation'])
def test_get_cmdline_args_without_expansion(self):
specification = ToolSpecification("", "", "", [], None, None)
self.assertFalse(specification.get_cmdline_args([], {}, {}))
specification.cmdline_args = ["-a", "--version", "-xvf"]
self.assertEqual(specification.get_cmdline_args([], {}, {}),
["-a", "--version", "-xvf"])
def test_split_cmdline_args_with_consecutive_tags(self):
splitted = ToolSpecification.split_cmdline_args(
"@@optional_inputs@@@@optional_inputs@@")
self.assertEqual(splitted, ["@@optional_inputs@@@@optional_inputs@@"])