fix: correctly parse and route implicit boolean flags from ini files (#90)

requirements.txt

@@ -26,6 +26,7 @@ contourpy==1.3.1
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
+defusedxml==0.7.1
 fonttools==4.59.2
     # via matplotlib
 gitdb==4.0.12

src/workflow/CommandExecutor.py

@@ -263,6 +263,10 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> b
 
         # Load parameters for non-defaults
         params = self.parameter_manager.get_parameters_from_json()
+
+        # NEW LOGIC: Ask the ParameterManager which keys are strictly booleans
+        bool_params = self.parameter_manager.get_boolean_parameters(tool)
+
         # Construct commands for each process
         for i in range(n_processes):
             command = [tool]
@@ -281,27 +285,38 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> b
                 # standard case, files was a list of strings, take the file name at index
                 else:
                     command += [value[i]]
+
             # Add non-default TOPP tool parameters
             if tool in params.keys():
                 for k, v in params[tool].items():
+                    # NEW LOGIC: Intercept boolean flags
+                    if k in bool_params:
+                        # Only add the implicit flag if True. If False, omit entirely.
+                        if str(v).lower() == "true":
+                            command += [f"-{k}"]
+                    else:
+                        # Existing logic for strings, ints, floats
+                        command += [f"-{k}"]
+                        if v != "" and v is not None:
+                            if isinstance(v, str) and "\n" in v:
+                                command += v.split("\n")
+                            else:
+                                command += [str(v)]
+
+            # Add custom parameters
+            for k, v in custom_params.items():
+                # NEW LOGIC: Intercept custom boolean flags
+                if k in bool_params:
+                    if str(v).lower() == "true":
+                        command += [f"-{k}"]
+                else:
                     command += [f"-{k}"]
-                    # Skip only empty strings (pass flag with no value)
-                    # Note: 0 and 0.0 are valid values, so use explicit check
                     if v != "" and v is not None:
-                        if isinstance(v, str) and "\n" in v:
-                            command += v.split("\n")
+                        if isinstance(v, list):
+                            command += [str(x) for x in v]
                         else:
                             command += [str(v)]
-            # Add custom parameters
-            for k, v in custom_params.items():
-                command += [f"-{k}"]
-                # Skip only empty strings (pass flag with no value)
-                # Note: 0 and 0.0 are valid values, so use explicit check
-                if v != "" and v is not None:
-                    if isinstance(v, list):
-                        command += [str(x) for x in v]
-                    else:
-                        command += [str(v)]
+
             # Add threads parameter for TOPP tools
             command += ["-threads", str(threads_per_command)]
             commands.append(command)

src/workflow/ParameterManager.py

@@ -3,6 +3,7 @@
 import shutil
 import subprocess
 import streamlit as st
+import defusedxml.ElementTree as ET
 from pathlib import Path
 
 class ParameterManager:
@@ -287,4 +288,68 @@ def clear_parameter_session_state(self) -> None:
             if key.startswith(self.param_prefix) or key.startswith(self.topp_param_prefix)
         ]
         for key in keys_to_delete:
-            del st.session_state[key]
+            del st.session_state[key]
+
+    def get_boolean_parameters(self, tool: str) -> list:
+        """
+        Parses the tool's generated .ini (XML) file to discover strictly boolean parameters.
+        This prevents implicit booleans from being passed as strings to the command line.
+
+        Args:
+            tool (str): The name of the TOPP tool (e.g., 'FeatureFinderMetabo').
+
+        Returns:
+            list: A list of hierarchical parameter keys that are explicitly typed as 'bool'.
+
+        Raises:
+            FileNotFoundError: If the .ini file does not exist.
+            RuntimeError: If the .ini file fails to generate.
+            ET.ParseError: If the XML parsing fails.
+        """
+        if not self.create_ini(tool):
+            # CodeRabbit Fix: Raise an explicit error instead of silently returning []
+            raise RuntimeError(f"Failed to generate .ini file for TOPP tool: {tool}")
+
+        ini_path = Path(self.ini_dir, f"{tool}.ini")
+        if not ini_path.exists():
+            # CodeRabbit Fix: Raise an explicit error instead of silently returning []
+            raise FileNotFoundError(f"Missing expected .ini file for TOPP tool at: {ini_path}")
+
+        bool_params = []
+        try:
+            # CodeRabbit Fix: Use defusedxml (imported as ET) to safely parse the file
+            tree = ET.parse(ini_path)
+            root = tree.getroot()
+
+            # Recursive function to build the hierarchical path from XML nodes
+            def traverse(node, current_path):
+                for child in node:
+                    if child.tag == "ITEM" and child.get("type") == "bool":
+                        name = child.get("name")
+                        if name:
+                            bool_params.append(current_path + name)
+                    elif child.tag == "NODE":
+                        name = child.get("name")
+                        if name:
+                            # Append the node name and a colon to the path
+                            traverse(child, current_path + name + ":")
+
+            # Start traversal from the XML root
+            traverse(root, "")
+
+            # OpenMS INI files usually encapsulate everything in a top-level <NODE name="ToolName">.
+            # We must strip this prefix so the keys perfectly match the JSON session state keys.
+            tool_prefix = f"{tool}:1:"
+            cleaned_params = [
+                p[len(tool_prefix):] if p.startswith(tool_prefix) else p 
+                for p in bool_params
+            ]
+
+            return cleaned_params
+
+        except ET.ParseError as e:
+            st.error(f"XML parsing failed for {tool}: {e}")
+            raise
+            print(f"Error parsing boolean parameters for {tool}: {e}")
+            pass # Safely return empty list if XML parsing fails
+        return []