improve error handling (#317)

Author: t0mdavid-m

src/workflow/CommandExecutor.py

@@ -27,7 +27,7 @@ def __init__(self, workflow_dir: Path, logger: Logger, parameter_manager: Parame
 
     def run_multiple_commands(
         self, commands: list[str]
-    ) -> None:
+    ) -> bool:
         """
         Executes multiple shell commands concurrently in separate threads.
 
@@ -38,17 +38,28 @@ def run_multiple_commands(
         Args:
             commands (list[str]): A list where each element is a list representing
                                         a command and its arguments.
+
+        Returns:
+            bool: True if all commands succeeded, False if any failed.
         """
         # Log the start of command execution
         self.logger.log(f"Running {len(commands)} commands in parallel...", 1)
         start_time = time.time()
 
+        results = []
+        lock = threading.Lock()
+
+        def run_and_track(cmd):
+            success = self.run_command(cmd)
+            with lock:
+                results.append(success)
+
         # Initialize a list to keep track of threads
         threads = []
 
         # Start a new thread for each command
         for cmd in commands:
-            thread = threading.Thread(target=self.run_command, args=(cmd,))
+            thread = threading.Thread(target=run_and_track, args=(cmd,))
             thread.start()
             threads.append(thread)
 
@@ -60,7 +71,9 @@ def run_multiple_commands(
         end_time = time.time()
         self.logger.log(f"Total time to run {len(commands)} commands: {end_time - start_time:.2f} seconds", 1)
 
-    def run_command(self, command: list[str]) -> None:
+        return all(results)
+
+    def run_command(self, command: list[str]) -> bool:
         """
         Executes a specified shell command and logs its execution details.
 
@@ -110,7 +123,9 @@ def run_command(self, command: list[str]) -> None:
 
         # Check for errors
         if process.returncode != 0:
-            self.logger.log(f"ERRORS OCCURRED: Process exited with code {process.returncode}", 2)
+            self.logger.log(f"ERROR: Command failed with exit code {process.returncode}: {command[0]}", 0)
+            return False
+        return True
 
     def _stream_output(self, process: subprocess.Popen) -> None:
         """
@@ -157,7 +172,7 @@ def read_stderr():
         stdout_thread.join()
         stderr_thread.join()
 
-    def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> None:
+    def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> bool:
         """
         Constructs and executes commands for the specified tool OpenMS TOPP tool based on the given
         input and output configurations. Ensures that all input/output file lists
@@ -176,6 +191,9 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> N
             input_output (dict): A dictionary specifying the input/output parameter names (as key) and their corresponding file paths (as value).
             custom_params (dict): A dictionary of custom parameters to pass to the tool.
 
+        Returns:
+            bool: True if all commands succeeded, False if any failed.
+
         Raises:
             ValueError: If the lengths of input/output file lists are inconsistent,
                         except for single string inputs.
@@ -240,9 +258,9 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> N
 
         # Run command(s)
         if len(commands) == 1:
-            self.run_command(commands[0])
+            return self.run_command(commands[0])
         elif len(commands) > 1:
-            self.run_multiple_commands(commands)
+            return self.run_multiple_commands(commands)
         else:
             raise Exception("No commands to execute.")
 

src/workflow/StreamlitUI.py

@@ -1081,10 +1081,10 @@ def execution_section(
             with open(log_path, "r", encoding="utf-8") as f:
                 content = f.read()
             # Check if workflow finished successfully
-            if "WORKFLOW FINISHED" not in content:
-                st.error("**Workflow did not complete. Check log file for errors.**")
-            elif "ERRORS OCCURRED" in content or "ERROR:" in content:
-                st.warning("**Workflow completed with errors. Some results may be missing.**")
+            if "WORKFLOW FINISHED" in content:
+                st.success("**Workflow completed successfully.**")
+            else:
+                st.error("**Errors occurred, check log file.**")
             st.code(content, language="neon", line_numbers=False)
 
     def _show_queue_status(self, status: dict) -> None:

src/workflow/WorkflowManager.py

@@ -101,8 +101,9 @@ def workflow_process(self) -> None:
             if results_dir.exists():
                 shutil.rmtree(results_dir)
             results_dir.mkdir(parents=True)
-            self.execution()
-            self.logger.log("WORKFLOW FINISHED")
+            success = self.execution()
+            if success:
+                self.logger.log("WORKFLOW FINISHED")
         except Exception as e:
             self.logger.log(f"ERROR: {e}")
             self.logger.log("".join(traceback.format_exception(e)))
@@ -258,14 +259,15 @@ def configure(self) -> None:
         ###################################
         pass
 
-    def execution(self) -> None:
+    def execution(self) -> bool:
         """
-        Add your workflow steps here
+        Add your workflow steps here.
+        Returns True on success, False on error.
         """
         ###################################
         # Add your workflow steps here
         ###################################
-        pass
+        return True
 
     def results(self) -> None:
         """