initial implementation of parameter groups

Author: mr-c

cwltool/argparser.py

@@ -17,7 +17,7 @@
 from .process import Process, shortname
 from .resolver import ga4gh_tool_registries
 from .software_requirements import SOFTWARE_REQUIREMENTS_ENABLED
-from .utils import DEFAULT_TMP_PREFIX
+from .utils import DEFAULT_TMP_PREFIX, CWLObjectType
 
 
 class _env_var_table(Table):
@@ -933,7 +933,7 @@ def __call__(
 
 
 def add_argument(
-    toolparser: argparse.ArgumentParser,
+    toolparser: argparse.ArgumentParser | "argparse._ArgumentGroup",
     name: str,
     inptype: Any,
     records: list[str],
@@ -1047,14 +1047,18 @@ def generate_parser(
     toolparser.add_argument("job_order", nargs="?", help="Job input json file")
     namemap["job_order"] = "job_order"
 
-    for inp in tool.tool["inputs"]:
-        name = shortname(inp["id"])
+    inps = tool.tool["inputs"]
+
+    def process_input(
+        inp: CWLObjectType, parser: argparse.ArgumentParser | "argparse._ArgumentGroup"
+    ) -> None:
+        name = shortname(cast(str, inp["id"]))
         namemap[name.replace("-", "_")] = name
         inptype = inp["type"]
-        description = inp.get("doc", inp.get("label", ""))
+        description = cast(str, inp.get("doc", inp.get("label", "")))
         default = inp.get("default", None)
         add_argument(
-            toolparser,
+            parser,
             name,
             inptype,
             records,
@@ -1065,6 +1069,31 @@ def generate_parser(
             base_uri,
         )
 
+    if (groups_req := tool.get_requirement("http://commonwl.org/cwltool#Groups")[0]) is not None:
+        groups = cast(CWLObjectType, groups_req["groups"])
+        for group_name in groups.keys():
+            group_inputs: list[CWLObjectType] = []
+            group_definition = cast(CWLObjectType, groups[group_name])
+            for input_name in cast(list[str], group_definition["groupMembers"]):
+                new_inps: list[CWLObjectType] = []
+                for inp in inps:
+                    if shortname(inp["id"]) == input_name:
+                        group_inputs.append(inp)
+                    else:
+                        new_inps.append(inp)
+                inps = new_inps
+
+            if len(group_inputs) > 0:
+                group = toolparser.add_argument_group(
+                    title=cast(str, group_definition.get("label", group_name)),
+                    description=cast(str | None, group_definition.get("doc", None)),
+                )
+                for inp in group_inputs:
+                    process_input(inp, group)
+
+    for inp in inps:
+        process_input(inp, toolparser)
+
     toolparser.add_argument(
         "--generate-help-preview",
         action=HelpPreviewAction,

cwltool/builder.py

@@ -597,7 +597,7 @@ def tostr(self, value: MutableMapping[str, str] | Any) -> str:
             case {"class": "File" | "Directory" as class_name, **rest}:
                 if "path" not in rest:
                     raise WorkflowException(
-                        '{} object missing "path": {}'.format(class_name, value)
+                        f'{class_name} object missing "path": {value}'
                     )
                 return str(rest["path"])
             case ScalarFloat():

cwltool/extensions-v1.2.yml

@@ -245,6 +245,7 @@ $graph:
         - Specify the desired method of dealing with loop outputs
         - Default. Propagates only the last computed element to the subsequent steps when the loop terminates.
         - Propagates a single array with all output values to the subsequent steps when the loop terminates.
+
 - name: ShmSize
   type: record
   extends: cwl:ProcessRequirement
@@ -263,3 +264,34 @@ $graph:
         than 0. Unit is optional and can be `b` (bytes), `k` (kilobytes), `m`
         (megabytes), or `g` (gigabytes). If you omit the unit, the default is
         bytes. If you omit the size entirely, the value is `64m`."
+
+- name: Grouping
+  type: record
+  extends: [ sld:Documented ]
+  fields:
+    - name: GroupName
+      type: string
+    - name: groupMembers
+      type: string[]
+      jsonldPredicate:
+        "_type": "@id"
+        "_container": "@list"
+        refScope: 0
+
+- name: Groups
+  type: record
+  extends: cwl:ProcessRequirement
+  inVocab: false
+  fields:
+    class:
+      type: string
+      doc: 'cwltool:Groups'
+      jsonldPredicate:
+        "_id": "@type"
+        "_type": "@vocab"
+    group:
+      type:
+        - type: array
+          items: "#Grouping"
+      jsonldPredicate:
+        mapSubject: GroupName

tests/echo-groups.cwl

@@ -0,0 +1,34 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+  first:
+    type: string
+    inputBinding: {}
+  second:
+    type: string
+    inputBinding: {}
+  third:
+    type: string
+    label: groupless
+outputs:
+  - id: out
+    type: string
+    outputBinding:
+      glob: out.txt
+      loadContents: true
+      outputEval: $(self[0].contents)
+baseCommand: echo
+stdout: out.txt
+
+
+$namespaces:
+  cwltool: "http://commonwl.org/cwltool#"
+
+hints:
+  cwltool:Groups:
+    groups:
+      my_groups:
+        groupMembers: [first, second]
+        label: my great inputs
+        doc: "parameters related to the foobar feature"

tests/test_ext.py

@@ -293,3 +293,16 @@ def test_ext_in_dollarsign_graph() -> None:
         ["--validate", "--enable-ext", get_data("tests/wf/hello_gpu.cwl")]
     )
     assert error_code == 0
+
+
+def test_ext_groups_help(capsys: pytest.CaptureFixture[str]) -> None:
+    error_code, stdout, stderr = get_main_output([get_data("tests/echo-groups.cwl"), "--help"])
+    assert error_code == 0
+    assert (
+        """my great inputs:
+  parameters related to the foobar feature
+
+  --first FIRST
+  --second SECOND"""
+        in capsys.readouterr().out
+    )