refactor: extract INI creation into shared ParameterManager.create_ini() (#327)

- Add create_ini() method to ParameterManager for creating TOPP tool ini files
- Update save_parameters() to use create_ini() instead of skipping missing ini files
- Update input_TOPP() in StreamlitUI to use the shared method
- Removes code duplication and enables ini creation during parameter save

Author: t0mdavid-m

src/workflow/ParameterManager.py

@@ -1,6 +1,7 @@
 import pyopenms as poms
 import json
 import shutil
+import subprocess
 import streamlit as st
 from pathlib import Path
 
@@ -25,6 +26,25 @@ def __init__(self, workflow_dir: Path):
         self.param_prefix = f"{workflow_dir.stem}-param-"
         self.topp_param_prefix = f"{workflow_dir.stem}-TOPP-"
 
+    def create_ini(self, tool: str) -> bool:
+        """
+        Create an ini file for a TOPP tool if it doesn't exist.
+
+        Args:
+            tool: Name of the TOPP tool (e.g., "CometAdapter")
+
+        Returns:
+            True if ini file exists (created or already existed), False if creation failed
+        """
+        ini_path = Path(self.ini_dir, tool + ".ini")
+        if ini_path.exists():
+            return True
+        try:
+            subprocess.call([tool, "-write_ini", str(ini_path)])
+        except FileNotFoundError:
+            return False
+        return ini_path.exists()
+
     def save_parameters(self) -> None:
         """
         Saves the current parameters from Streamlit's session state to a JSON file.
@@ -54,11 +74,15 @@ def save_parameters(self) -> None:
         )
         # for each TOPP tool, open the ini file
         for tool in current_topp_tools:
+            if not self.create_ini(tool):
+                # Could not create ini file - skip this tool
+                continue
+            ini_path = Path(self.ini_dir, f"{tool}.ini")
             if tool not in json_params:
                 json_params[tool] = {}
             # load the param object
             param = poms.Param()
-            poms.ParamXMLFile().load(str(Path(self.ini_dir, f"{tool}.ini")), param)
+            poms.ParamXMLFile().load(str(ini_path), param)
             # get all session state param keys and values for this tool
             for key, value in st.session_state.items():
                 if key.startswith(f"{self.topp_param_prefix}{tool}:1:"):

src/workflow/StreamlitUI.py

@@ -641,12 +641,11 @@ def input_TOPP(
 
         # write defaults ini files
         ini_file_path = Path(self.parameter_manager.ini_dir, f"{topp_tool_name}.ini")
-        if not ini_file_path.exists():
-            try:
-                subprocess.call([topp_tool_name, "-write_ini", str(ini_file_path)])
-            except FileNotFoundError:
-                st.error(f"TOPP tool **'{topp_tool_name}'** not found.")
-                return
+        ini_existed = ini_file_path.exists()
+        if not self.parameter_manager.create_ini(topp_tool_name):
+            st.error(f"TOPP tool **'{topp_tool_name}'** not found.")
+            return
+        if not ini_existed:
             # update custom defaults if necessary
             if custom_defaults:
                 param = poms.Param()