Mercurial > repos > shellac > sam_consensus_v3
diff env/lib/python3.9/site-packages/cwltool/tests/test_iwdr.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/cwltool/tests/test_iwdr.py Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,230 @@ +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 + )