Mercurial > repos > shellac > sam_consensus_v3
view env/lib/python3.9/site-packages/cwltool/tests/test_iwdr.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
---|---|
date | Mon, 22 Mar 2021 18:12:50 +0000 |
parents | |
children |
line wrap: on
line source
from pathlib import Path from typing import Any from cwltool.main import main from .util import ( get_data, get_main_output, get_windows_safe_factory, needs_docker, needs_singularity, windows_needs_docker, ) @windows_needs_docker def test_newline_in_entry() -> None: """Files in a InitialWorkingDirectory are created with a newline character.""" factory = get_windows_safe_factory() echo = factory.make(get_data("tests/wf/iwdr-entry.cwl")) assert echo(message="hello") == {"out": "CONFIGVAR=hello\n"} @needs_docker def test_empty_file_creation() -> None: """An empty file can be created in InitialWorkingDirectory.""" err_code, _, _ = get_main_output([get_data("tests/wf/iwdr-empty.cwl")]) assert err_code == 0 @needs_docker def test_directory_literal_with_real_inputs_inside(tmp_path: Path) -> None: """Cope with unmoveable files in the output directory created by Docker+IWDR.""" err_code, _, _ = get_main_output( [ "--out", str(tmp_path), get_data("tests/iwdr_dir_literal_real_file.cwl"), "--example={}".format(get_data("tests/__init__.py")), ] ) assert err_code == 0 @needs_docker def test_iwdr_permutations(tmp_path_factory: Any) -> None: misc = tmp_path_factory.mktemp("misc") fifth = str(tmp_path_factory.mktemp("fifth")) sixth = str(tmp_path_factory.mktemp("sixth")) seventh = str(tmp_path_factory.mktemp("seventh")) eighth = str(tmp_path_factory.mktemp("eighth")) first = misc / "first" first.touch() second = misc / "second" second.touch() third = misc / "third" third.touch() fourth = misc / "fourth" fourth.touch() outdir = str(tmp_path_factory.mktemp("outdir")) assert ( main( [ "--outdir", outdir, "--enable-dev", get_data("tests/wf/iwdr_permutations.cwl"), "--first", str(first), "--second", str(second), "--third", str(third), "--fourth", str(fourth), "--fifth", fifth, "--sixth", sixth, "--seventh", seventh, "--eighth", eighth, ] ) == 0 ) @needs_docker def test_iwdr_permutations_inplace(tmp_path_factory: Any) -> None: misc = tmp_path_factory.mktemp("misc") fifth = str(tmp_path_factory.mktemp("fifth")) sixth = str(tmp_path_factory.mktemp("sixth")) seventh = str(tmp_path_factory.mktemp("seventh")) eighth = str(tmp_path_factory.mktemp("eighth")) first = misc / "first" first.touch() second = misc / "second" second.touch() third = misc / "third" third.touch() fourth = misc / "fourth" fourth.touch() outdir = str(tmp_path_factory.mktemp("outdir")) assert ( main( [ "--outdir", outdir, "--enable-ext", "--enable-dev", "--overrides", get_data("tests/wf/iwdr_permutations_inplace.yml"), get_data("tests/wf/iwdr_permutations.cwl"), "--first", str(first), "--second", str(second), "--third", str(third), "--fourth", str(fourth), "--fifth", fifth, "--sixth", sixth, "--seventh", seventh, "--eighth", eighth, ] ) == 0 ) @needs_singularity def test_iwdr_permutations_singularity(tmp_path_factory: Any) -> None: misc = tmp_path_factory.mktemp("misc") fifth = str(tmp_path_factory.mktemp("fifth")) sixth = str(tmp_path_factory.mktemp("sixth")) seventh = str(tmp_path_factory.mktemp("seventh")) eighth = str(tmp_path_factory.mktemp("eighth")) first = misc / "first" first.touch() second = misc / "second" second.touch() third = misc / "third" third.touch() fourth = misc / "fourth" fourth.touch() outdir = str(tmp_path_factory.mktemp("outdir")) assert ( main( [ "--outdir", outdir, "--enable-dev", "--singularity", get_data("tests/wf/iwdr_permutations.cwl"), "--first", str(first), "--second", str(second), "--third", str(third), "--fourth", str(fourth), "--fifth", fifth, "--sixth", sixth, "--seventh", seventh, "--eighth", eighth, ] ) == 0 ) @needs_singularity def test_iwdr_permutations_singularity_inplace(tmp_path_factory: Any) -> None: misc = tmp_path_factory.mktemp("misc") fifth = str(tmp_path_factory.mktemp("fifth")) sixth = str(tmp_path_factory.mktemp("sixth")) seventh = str(tmp_path_factory.mktemp("seventh")) eighth = str(tmp_path_factory.mktemp("eighth")) first = misc / "first" first.touch() second = misc / "second" second.touch() third = misc / "third" third.touch() fourth = misc / "fourth" fourth.touch() outdir = str(tmp_path_factory.mktemp("outdir")) assert ( main( [ "--outdir", outdir, "--singularity", "--enable-ext", "--enable-dev", "--overrides", get_data("tests/wf/iwdr_permutations_inplace.yml"), get_data("tests/wf/iwdr_permutations.cwl"), "--first", str(first), "--second", str(second), "--third", str(third), "--fourth", str(fourth), "--fifth", fifth, "--sixth", sixth, "--seventh", seventh, "--eighth", eighth, ] ) == 0 )