Merge pull request #1248 from common-workflow-language/add-doc-to-helpmsg

Add `doc` field message to the output of `--help`

Author: mr-c

cwltool/argparser.py

@@ -799,6 +799,7 @@ def generate_parser(
     records: List[str],
     input_required: bool = True,
 ) -> argparse.ArgumentParser:
+    toolparser.description = tool.tool.get("doc", None)
     toolparser.add_argument("job_order", nargs="?", help="Job input json file")
     namemap["job_order"] = "job_order"
 

tests/test_toolargparse.py

@@ -1,11 +1,15 @@
+import argparse
 import os
 import sys
 from io import BytesIO, StringIO
 from tempfile import NamedTemporaryFile
 
 import pytest
 
+from cwltool.argparser import generate_parser
+from cwltool.context import LoadingContext
 import cwltool.executors
+from cwltool.load_tool import load_tool
 from cwltool.main import main
 
 from .util import get_data, needs_docker
@@ -162,3 +166,21 @@ def test_dont_require_inputs():
     finally:
         if script and script.name and os.path.exists(script.name):
             os.unlink(script.name)
+
+
+def test_argparser_with_doc():
+    """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():
+    """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)

tests/with_doc.cwl

@@ -0,0 +1,7 @@
+cwlVersion: v1.0
+class: CommandLineTool
+inputs: []
+baseCommand: echo
+outputs: []
+
+doc: This should be shown in help message

tests/without_doc.cwl

@@ -0,0 +1,5 @@
+cwlVersion: v1.0
+class: CommandLineTool
+inputs: []
+baseCommand: echo
+outputs: []