input_TOPP: exclude or include a whole parameter section with a trailing ':'

src/workflow/StreamlitUI.py

@@ -28,6 +28,31 @@
 )
 
 
+def _matches_topp_parameter(pattern: str, key: bytes) -> bool:
+    """
+    Match an include/exclude pattern against a TOPP parameter key.
+
+    Key format: b"ToolName:1:section:subsection:param_name"
+
+    A pattern matches the end of the parameter path, bounded by ':' or the
+    start of the path ("tol" matches "FD:tol"). A pattern ending in ':' names
+    a whole section from the top of the path instead ("fd:" matches every
+    parameter under "fd:", but not "FD:" or "algorithm:fd:").
+    """
+    pattern = pattern.lstrip(":")  # Strip legacy leading colon
+    key_str = key.decode()
+
+    # Extract param path after "ToolName:1:"
+    parts = key_str.split(":")
+    param_path = ":".join(parts[2:]) if len(parts) > 2 else key_str
+
+    if pattern.endswith(":"):
+        return param_path.startswith(pattern)
+
+    # Check if pattern matches as a suffix, bounded by ':' or start
+    return param_path == pattern or param_path.endswith(":" + pattern)
+
+
 def _mounted_data_root() -> Union[Path, None]:
     """Return the validated mount root from the ``local_data_dir`` setting.
 
@@ -866,7 +891,7 @@ def input_TOPP(
         Args:
             topp_tool_name (str): The name of the TOPP tool for which to generate inputs.
             num_cols (int, optional): Number of columns to use for the layout. Defaults to 3.
-            exclude_parameters (List[str], optional): List of parameter names to exclude from the widget. Defaults to an empty list.
+            exclude_parameters (List[str], optional): List of parameter names to exclude from the widget. A name ending in ":" excludes that whole top-level section (e.g. "fd:"). Defaults to an empty list.
             include_parameters (List[str], optional): List of parameter names to include in the widget. Defaults to an empty list.
             flag_parameters (List[str], optional): List of parameter names that should
                 be treated as no-value CLI flags during command construction.
@@ -1054,24 +1079,6 @@ def _input_TOPP_impl(
         param = poms.Param()
         poms.ParamXMLFile().load(str(ini_file_path), param)
 
-        def _matches_parameter(pattern: str, key: bytes) -> bool:
-            """
-            Match pattern against TOPP parameter key using suffix matching.
-
-            Key format: b"ToolName:1:section:subsection:param_name"
-
-            Returns True if pattern matches the end of the param path,
-            bounded by ':' or start of path.
-            """
-            pattern = pattern.lstrip(":")  # Strip legacy leading colon
-            key_str = key.decode()
-
-            # Extract param path after "ToolName:1:"
-            parts = key_str.split(":")
-            param_path = ":".join(parts[2:]) if len(parts) > 2 else key_str
-
-            # Check if pattern matches as a suffix, bounded by ':' or start
-            return param_path == pattern or param_path.endswith(":" + pattern)
 
         # Always apply base exclusions (input/output files, standard excludes)
         excluded_keys = [
@@ -1090,15 +1097,15 @@ def _matches_parameter(pattern: str, key: bytes) -> bool:
             if not (
                 b"input file" in param.getTags(key)
                 or b"output file" in param.getTags(key)
-                or any([_matches_parameter(k, key) for k in excluded_keys])
+                or any([_matches_topp_parameter(k, key) for k in excluded_keys])
             )
         ]
 
         # Track which keys are "included" (shown by default) vs "non-included" (advanced only)
         if include_parameters:
             included_keys = {
                 key for key in valid_keys
-                if any([_matches_parameter(k, key) for k in include_parameters])
+                if any([_matches_topp_parameter(k, key) for k in include_parameters])
             }
         else:
             included_keys = set(valid_keys)  # All are included when no filter specified

tests/test_topp_parameter_matching.py

@@ -0,0 +1,66 @@
+"""
+``_matches_topp_parameter()`` — how ``input_TOPP(exclude_parameters=...,
+include_parameters=...)`` patterns select TOPP parameters.
+
+A plain name matches the end of the parameter path, bounded by ':'. A name
+ending in ':' selects a whole top-level section, so a tool can hide a
+subsection (e.g. FLASHTnT's ``fd:`` parameters, which only apply to raw input)
+without listing every parameter in it.
+"""
+import os
+import sys
+from unittest.mock import MagicMock
+
+import pytest
+
+PROJECT_ROOT = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+sys.path.append(PROJECT_ROOT)
+
+# Same sys.modules mocking as tests/test_streamlit_ui_param_read.py.
+mock_streamlit = MagicMock()
+mock_streamlit.session_state = {}
+
+_originals = {
+    name: sys.modules.get(name)
+    for name in ("streamlit", "pyopenms", "src.common.common")
+}
+sys.modules["streamlit"] = mock_streamlit
+if _originals["pyopenms"] is None:
+    sys.modules["pyopenms"] = MagicMock()
+if _originals["src.common.common"] is None:
+    sys.modules["src.common.common"] = MagicMock()
+
+from src.workflow.StreamlitUI import _matches_topp_parameter
+
+for name, module in _originals.items():
+    if module is not None:
+        sys.modules[name] = module
+    else:
+        sys.modules.pop(name, None)
+
+for _key in list(sys.modules.keys()):
+    if _key.startswith("src.workflow"):
+        sys.modules.pop(_key, None)
+
+
+@pytest.mark.parametrize(
+    "pattern, key, expected",
+    [
+        # suffix matching, bounded by ':'
+        ("tol", b"FLASHTnT:1:fd:FD:tol", True),
+        ("FD:tol", b"FLASHTnT:1:fd:FD:tol", True),
+        ("ol", b"FLASHTnT:1:fd:FD:tol", False),
+        ("prsm_fdr", b"FLASHTnT:1:prsm_fdr", True),
+        # legacy leading colon is ignored
+        (":prsm_fdr", b"FLASHTnT:1:prsm_fdr", True),
+        # a trailing ':' names a top-level section
+        ("fd:", b"FLASHTnT:1:fd:FD:tol", True),
+        ("fd:FD:", b"FLASHTnT:1:fd:FD:tol", True),
+        ("fd:", b"FLASHTnT:1:fdr", False),
+        ("fd:", b"FLASHTnT:1:prsm_fdr", False),
+        ("FD:", b"FLASHTnT:1:fd:FD:tol", False),
+        ("fd:", b"FLASHTnT:1:tag:fd:x", False),
+    ],
+)
+def test_matches_topp_parameter(pattern, key, expected):
+    assert _matches_topp_parameter(pattern, key) is expected