diff env/lib/python3.9/site-packages/cwltool/tests/test_toolargparse.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_toolargparse.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,156 @@
+import argparse
+from io import StringIO
+from pathlib import Path
+from typing import Callable
+
+import pytest
+
+import cwltool.executors
+from cwltool.argparser import generate_parser
+from cwltool.context import LoadingContext
+from cwltool.load_tool import load_tool
+from cwltool.main import main
+
+from .util import get_data, needs_docker
+
+script_a = """
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"
+inputs:
+  #Give it a list of input files
+  - id: input
+    type: File
+    inputBinding:
+      position: 0
+outputs:
+  - id: output
+    type: File
+    outputBinding:
+      glob: test.txt
+stdout: test.txt
+baseCommand: [cat]
+"""
+
+script_b = """
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+  - id: bdg
+    type: "boolean"
+outputs:
+  - id: output
+    type: File
+    outputBinding:
+      glob: foo
+baseCommand:
+  - echo
+  - "ff"
+stdout: foo
+"""
+
+script_c = """
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: ExpressionTool
+
+inputs:
+  foo:
+    type:
+      type: record
+      fields:
+        one: File
+        two: string
+
+expression: $(inputs.foo.two)
+
+outputs: []
+"""
+
+scripts_argparse_params = [
+    ("help", script_a, lambda x: ["--debug", x, "--input", get_data("tests/echo.cwl")]),
+    ("boolean", script_b, lambda x: [x, "--help"]),
+    ("help with c", script_c, lambda x: [x, "--help"]),
+    (
+        "foo with c",
+        script_c,
+        lambda x: [x, "--foo.one", get_data("tests/echo.cwl"), "--foo.two", "test"],
+    ),
+]
+
+
+@needs_docker
[e-mail]("name,script_contents,params", scripts_argparse_params)
+def test_argparse(
+    name: str, script_contents: str, params: Callable[[str], str], tmp_path: Path
+) -> None:
+    script_name = tmp_path / "script"
+    try:
+        with script_name.open(mode="w") as script:
+            script.write(script_contents)
+
+        my_params = ["--outdir", str(tmp_path / "outdir")]
+        my_params.extend(params(script.name))
+        assert main(my_params) == 0, name
+
+    except SystemExit as err:
+        assert err.code == 0, name
+
+
+def test_dont_require_inputs(tmp_path: Path) -> None:
+    stream = StringIO()
+
+    script_name = tmp_path / "script"
+    try:
+        with script_name.open(mode="w") as script:
+            script.write(script_a)
+
+        assert (
+            main(
+                argsl=["--debug", str(script_name), "--input", str(script_name)],
+                executor=cwltool.executors.NoopJobExecutor(),
+                stdout=stream,
+            )
+            == 0
+        )
+        assert (
+            main(
+                argsl=["--debug", str(script_name)],
+                executor=cwltool.executors.NoopJobExecutor(),
+                stdout=stream,
+            )
+            == 2
+        )
+        assert (
+            main(
+                argsl=["--debug", str(script_name)],
+                executor=cwltool.executors.NoopJobExecutor(),
+                input_required=False,
+                stdout=stream,
+            )
+            == 0
+        )
+
+    except SystemExit as err:
+        assert err.code == 0, script_name if script else None
+
+
+def test_argparser_with_doc() -> None:
+    """The `desription` field is set if `doc` field is provided."""
+    loadingContext = LoadingContext()
+    tool = load_tool(get_data("tests/with_doc.cwl"), loadingContext)
+    p = argparse.ArgumentParser()
+    parser = generate_parser(p, tool, {}, [], False)
+    assert parser.description is not None
+
+
+def test_argparser_without_doc() -> None:
+    """The `desription` field is None if `doc` field is not provided."""
+    loadingContext = LoadingContext()
+    tool = load_tool(get_data("tests/without_doc.cwl"), loadingContext)
+    p = argparse.ArgumentParser()
+    parser = generate_parser(p, tool, {}, [], False)
+    assert parser.description is None