Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/cwltool/tests/test_iwdr.py @ 2:6af9afd405e9 draft
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author | shellac |
---|---|
date | Thu, 14 May 2020 14:56:58 -0400 |
parents | 26e78fe6e8c4 |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/cwltool/tests/test_iwdr.py Thu May 14 14:56:58 2020 -0400 @@ -0,0 +1,129 @@ +import tempfile +import os +from cwltool.main import main +from cwltool import load_tool +from .util import (get_data, get_windows_safe_factory, windows_needs_docker, + needs_docker, temp_dir, needs_singularity, get_main_output) + +@windows_needs_docker +def test_newline_in_entry(): + """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(): + """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_iwdr_permutations(): + saved_tempdir = tempfile.tempdir + with temp_dir() as misc: + tempfile.tempdir = os.path.realpath(misc) + with temp_dir() as fifth: + with temp_dir() as sixth: + with temp_dir() as seventh: + with temp_dir() as eighth: + with tempfile.NamedTemporaryFile() as first: + with tempfile.NamedTemporaryFile() as second: + with tempfile.NamedTemporaryFile() as third: + with tempfile.NamedTemporaryFile() as fourth: + with temp_dir() as outdir: + assert(main( + ['--outdir', outdir, + get_data("tests/wf/iwdr_permutations.cwl"), + '--first', first.name, + '--second', second.name, + '--third', third.name, + '--fourth', fourth.name, + '--fifth', fifth, + '--sixth', sixth, + '--seventh', seventh, + '--eighth', eighth]) == 0) + tempfile.tempdir = saved_tempdir + +@needs_docker +def test_iwdr_permutations_inplace(): + saved_tempdir = tempfile.tempdir + with temp_dir() as misc: + tempfile.tempdir = os.path.realpath(misc) + with temp_dir() as fifth: + with temp_dir() as sixth: + with temp_dir() as seventh: + with temp_dir() as eighth: + with tempfile.NamedTemporaryFile() as first: + with tempfile.NamedTemporaryFile() as second: + with tempfile.NamedTemporaryFile() as third: + with tempfile.NamedTemporaryFile() as fourth: + with temp_dir() as outdir: + assert(main( + ['--outdir', outdir, + '--enable-ext', + '--overrides', + get_data("tests/wf/iwdr_permutations_inplace.yml"), + get_data("tests/wf/iwdr_permutations.cwl"), + '--first', first.name, + '--second', second.name, + '--third', third.name, + '--fourth', fourth.name, + '--fifth', fifth, + '--sixth', sixth, + '--seventh', seventh, + '--eighth', eighth]) == 0) + tempfile.tempdir = saved_tempdir + +@needs_singularity +def test_iwdr_permutations_singularity(): + with temp_dir() as fifth: + with temp_dir() as sixth: + with temp_dir() as seventh: + with temp_dir() as eighth: + with tempfile.NamedTemporaryFile() as first: + with tempfile.NamedTemporaryFile() as second: + with tempfile.NamedTemporaryFile() as third: + with tempfile.NamedTemporaryFile() as fourth: + with temp_dir() as outdir: + assert(main( + ['--outdir', outdir, + '--singularity', + get_data("tests/wf/iwdr_permutations.cwl"), + '--first', first.name, + '--second', second.name, + '--third', third.name, + '--fourth', fourth.name, + '--fifth', fifth, + '--sixth', sixth, + '--seventh', seventh, + '--eighth', eighth]) == 0) + +@needs_singularity +def test_iwdr_permutations_singularity_inplace(): + with temp_dir() as fifth: + with temp_dir() as sixth: + with temp_dir() as seventh: + with temp_dir() as eighth: + with tempfile.NamedTemporaryFile() as first: + with tempfile.NamedTemporaryFile() as second: + with tempfile.NamedTemporaryFile() as third: + with tempfile.NamedTemporaryFile() as fourth: + with temp_dir() as outdir: + assert(main( + ['--outdir', outdir, + '--singularity', + '--enable-ext', + '--overrides', + get_data("tests/wf/iwdr_permutations_inplace.yml"), + get_data("tests/wf/iwdr_permutations.cwl"), + '--first', first.name, + '--second', second.name, + '--third', third.name, + '--fourth', fourth.name, + '--fifth', fifth, + '--sixth', sixth, + '--seventh', seventh, + '--eighth', eighth]) == 0)