def create_executable_template(command: str):
commands_builder = CommandsBuilder(
command, image=self._image_with_compatible_icommands,
get_path_arguments_to_mount=IrodsBaseExecutablesController._GET_POSITIONAL_ARGUMENTS_TO_MOUNT,
mounts=self._run_container_commands_builder.mounts,
other_docker=self._run_container_commands_builder.other_docker)
return Executable(commands_builder, False)
def test_create_executable_commands_with_no_running_container(self):
commands_builder = CommandsBuilder("echo",
image=UBUNTU_IMAGE_TO_TEST_WITH,
executable_arguments=[_CONTENT])
commands = self.controller.create_executable_commands(
Executable(commands_builder, False))
out, error = self._run_commands(commands)
self.assertEqual(_CONTENT, out)
def test_create_executable_commands_with_positional_parameter_needing_mounting_for_read(
self):
_, read_file = self._temp_manager.create_temp_file()
with open(read_file, "w") as file:
file.write(_CONTENT)
commands_builder = CommandsBuilder(
"cat",
image=UBUNTU_IMAGE_TO_TEST_WITH,
get_path_arguments_to_mount=_CAT_MOUNTED_ARGUMENT_PARSER)
commands = self.controller.create_executable_commands(
Executable(commands_builder, False))
out, error = self._run_commands(commands, [read_file])
self.assertEqual(_CONTENT, out)
def create_simple_executable_commands(
self,
containerised_executable: str,
executable_arguments=CLI_ARGUMENTS) -> str:
"""
TODO
:param containerised_executable:
:param executable_arguments:
:return:
"""
containerised_executable = containerised_executable.replace('"', '\\"')
to_execute = CommandsBuilder(
executable=containerised_executable,
container=self._cached_container_name,
executable_arguments=[executable_arguments])
return self.create_executable_commands(Executable(to_execute, True))
def test_create_executable_commands_with_named_parameters_needing_mounting(
self):
with tempfile.TemporaryDirectory(
dir=MOUNTABLE_TEMP_DIRECTORY) as temp_directory:
commands_builder = CommandsBuilder(
"touch",
image=UBUNTU_IMAGE_TO_TEST_WITH,
get_path_arguments_to_mount=_TOUCH_MOUNTED_ARGUMENT_PARSER,
mounts={temp_directory: temp_directory})
commands = self.persistent_run_controller.create_executable_commands(
Executable(commands_builder, False))
test_file = os.path.join(temp_directory, "test-file")
_, reference = self._temp_manager.create_temp_file()
os.utime(reference, (0, 0))
self._run_commands(commands, ["-r", reference, test_file])
self.assertEqual(0.0, os.path.getmtime(test_file))
def test_create_executable_commands_with_positional_parameter_needing_mounting_for_write(
self):
with tempfile.TemporaryDirectory(
dir=MOUNTABLE_TEMP_DIRECTORY) as temp_directory:
file_locations = [
os.path.join(temp_directory, str(uuid4())) for _ in range(5)
]
commands_builder = CommandsBuilder(
"touch",
image=UBUNTU_IMAGE_TO_TEST_WITH,
get_path_arguments_to_mount=_TOUCH_MOUNTED_ARGUMENT_PARSER)
commands = self.controller.create_executable_commands(
Executable(commands_builder, False))
self._run_commands(commands, file_locations)
for location in file_locations:
self.assertTrue(os.path.exists(location))
def _register_named_executables(self):
"""
Registers the executables that can be written by this controller.
"""
for icommand in IrodsBaseExecutablesController._ICOMMAND_EXECUTABLES - {"iget", "iput"}:
self.named_executables[icommand] = Executable(CommandsBuilder(icommand), True)
def create_executable_template(command: str):
commands_builder = CommandsBuilder(
command, image=self._image_with_compatible_icommands,
get_path_arguments_to_mount=IrodsBaseExecutablesController._GET_POSITIONAL_ARGUMENTS_TO_MOUNT,
mounts=self._run_container_commands_builder.mounts,
other_docker=self._run_container_commands_builder.other_docker)
return Executable(commands_builder, False)
# Note: if `-` is the second positional argument with `iget`, `-` is suspected as a file, relative to the
# current directory. This leads to an unnecessary mount and the use of `-w` to change the working directory.
self.named_executables["iget"] = create_executable_template("iget")
self.named_executables["iput"] = create_executable_template("iput")
from useintest.executables.builders import CommandsBuilder
from useintest.executables.common import get_all_path_like_arguments_for_mounting
from useintest.executables.controllers import DefinedExecutablesControllerTypeBuilder
from useintest.executables.models import Executable
Samtools1_3_1ExecutablesController = DefinedExecutablesControllerTypeBuilder(
"Samtools1_3_1ExecutablesController",
{
"samtools":
Executable(
CommandsBuilder(
image="comics/samtools:1.3.1",
executable="samtools",
# There are so many ways in which Samtools accepts file paths that the creation of a parser for it would
# be a massive task. Instead, we'll overzealously bind mount anything that looks like a file path.
get_path_arguments_to_mount=
get_all_path_like_arguments_for_mounting),
False)
}).build()
SamtoolsExecutablesController = Samtools1_3_1ExecutablesController
samtools_executable_controllers = {Samtools1_3_1ExecutablesController}