view env/lib/python3.9/site-packages/cwltool/tests/test_singularity.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

import distutils.spawn
import os
import sys
from pathlib import Path

from cwltool.main import main

from .util import (
    get_data,
    get_main_output,
    needs_singularity,
    needs_singularity_2_6,
    working_directory,
)

sys.argv = [""]


@needs_singularity_2_6
def test_singularity_pullfolder(tmp_path: Path) -> None:
    workdir = tmp_path / "working_dir_new"
    workdir.mkdir()
    os.chdir(workdir)
    pullfolder = tmp_path / "pullfolder"
    pullfolder.mkdir()
    env = os.environ.copy()
    env["SINGULARITY_PULLFOLDER"] = str(pullfolder)
    result_code, stdout, stderr = get_main_output(
        [
            "--singularity",
            get_data("tests/sing_pullfolder_test.cwl"),
            "--message",
            "hello",
        ],
        env=env,
    )
    print(stdout)
    print(stderr)
    assert result_code == 0
    image = pullfolder / "debian.img"
    assert image.exists()


@needs_singularity
def test_singularity_workflow(tmp_path: Path) -> None:
    with working_directory(tmp_path):
        error_code, _, stderr = get_main_output(
            [
                "--singularity",
                "--default-container",
                "debian",
                "--debug",
                get_data("tests/wf/hello-workflow.cwl"),
                "--usermessage",
                "hello",
            ]
        )
    assert "completed success" in stderr, stderr
    assert error_code == 0


def test_singularity_iwdr() -> None:
    result_code = main(
        [
            "--singularity",
            "--default-container",
            "debian",
            get_data("tests/wf/iwdr-entry.cwl"),
            "--message",
            "hello",
        ]
    )
    singularity_installed = bool(distutils.spawn.find_executable("singularity"))
    if singularity_installed:
        assert result_code == 0
    else:
        assert result_code != 0


@needs_singularity
def test_singularity_incorrect_image_pull() -> None:
    result_code, _, stderr = get_main_output(
        [
            "--singularity",
            "--default-container",
            "non-existant-weird-image",
            get_data("tests/wf/hello-workflow.cwl"),
            "--usermessage",
            "hello",
        ]
    )
    assert result_code != 0


@needs_singularity
def test_singularity_local(tmp_path: Path) -> None:
    workdir = tmp_path / "working_dir"
    workdir.mkdir()
    os.chdir(workdir)
    result_code, stdout, stderr = get_main_output(
        [
            "--singularity",
            get_data("tests/sing_pullfolder_test.cwl"),
            "--message",
            "hello",
        ]
    )
    assert result_code == 0


@needs_singularity_2_6
def test_singularity_docker_image_id_in_tool(tmp_path: Path) -> None:
    workdir = tmp_path / "working_dir"
    workdir.mkdir()
    os.chdir(workdir)
    result_code, stdout, stderr = get_main_output(
        [
            "--singularity",
            get_data("tests/sing_pullfolder_test.cwl"),
            "--message",
            "hello",
        ]
    )
    result_code1, stdout, stderr = get_main_output(
        ["--singularity", get_data("tests/debian_image_id.cwl"), "--message", "hello"]
    )
    assert result_code1 == 0