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

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /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
+    )