ivoryos 1.3.8__py3-none-any.whl → 1.4.0__py3-none-any.whl

ivoryos/utils/script_runner.py

@@ -1,15 +1,18 @@
 import ast
 import asyncio
 import os
-import csv
 import threading
 import time
 from datetime import datetime
+from typing import List, Dict, Any
+
+import pandas as pd
 
 from ivoryos.utils import utils, bo_campaign
 from ivoryos.utils.db_models import Script, WorkflowRun, WorkflowStep, db, WorkflowPhase
 from ivoryos.utils.global_config import GlobalConfig
 from ivoryos.utils.decorators import BUILDING_BLOCKS
+from ivoryos.utils.nest_script import validate_and_nest_control_flow
 
 global_config = GlobalConfig()
 global deck
@@ -32,6 +35,8 @@ def pause(reason="Human intervention required"):
 
 class ScriptRunner:
     def __init__(self, globals_dict=None):
+        self.logger = None
+        self.socketio = None
         self.retry = False
         if globals_dict is None:
             globals_dict = globals()
@@ -74,13 +79,19 @@ class ScriptRunner:
         """Force stop everything, including ongoing tasks."""
         self.stop_current_event.set()
         self.abort_pending()
+        if self.lock.locked():
+            self.lock.release()
 
 
     def run_script(self, script, repeat_count=1, run_name=None, logger=None, socketio=None, config=None, bo_args=None,
-                   output_path="", compiled=False, current_app=None, history=None, optimizer=None):
+                   output_path="", compiled=False, current_app=None, history=None, optimizer=None, batch_mode=None,
+                   batch_size=1, objectives=None):
+        self.socketio = socketio
+        self.logger = logger
         global deck
         if deck is None:
             deck = global_config.deck
+
         # print("history", history)
         if self.current_app is None:
             self.current_app = current_app
@@ -97,12 +108,14 @@ class ScriptRunner:
         thread = threading.Thread(
             target=self._run_with_stop_check,
             args=(script, repeat_count, run_name, logger, socketio, config, bo_args, output_path, current_app, compiled,
-                  history, optimizer)
+                  history, optimizer, batch_mode, batch_size, objectives),
         )
         thread.start()
         return thread
 
-    def exec_steps(self, script, section_name, logger, socketio, phase_id, **kwargs):
+
+
+    async def exec_steps(self, script, section_name, phase_id, kwargs_list=None, batch_size=1):
         """
         Executes a function defined in a string line by line
         :param func_str: The function as a string
@@ -110,6 +123,8 @@ class ScriptRunner:
         :return: The final result of the function execution
         """
         _func_str = script.python_script or script.compile()
+        _, return_list = script.config_return()
+
         step_list: list = script.convert_to_lines(_func_str).get(section_name, [])
         global deck
         # global deck, registered_workflows
@@ -129,112 +144,54 @@ class ScriptRunner:
         # exec_globals = {"deck": deck, "time": time, "registered_workflows":registered_workflows}  # Add required global objects
         exec_globals.update(temp_connections)
 
-        # Inject all block categories
-        for category, data in BUILDING_BLOCKS.items():
-            for method_name, method in data.items():
-                exec_globals[method_name] = method["func"]
-
         exec_locals = {}  # Local execution scope
 
         # Define function arguments manually in exec_locals
-        exec_locals.update(kwargs)
+        # exec_locals.update(kwargs)
         index = 0
-
-        # Execute each line dynamically
-        while index < len(step_list):
-            if self.stop_current_event.is_set():
-                logger.info(f'Stopping execution during {section_name}')
-                step = WorkflowStep(
-                    phase_id=phase_id,
-                    # phase=section_name,
-                    # repeat_index=i_progress,
-                    step_index=index,
-                    method_name="stop",
-                    start_time=datetime.now(),
-                    end_time=datetime.now(),
-                    run_error=False,
-                )
-                db.session.add(step)
-                break
-            line = step_list[index]
-
-            method_name = line.strip()
-            # start_time = datetime.now()
-
-            step = WorkflowStep(
-                phase_id=phase_id,
-                # phase=section_name,
-                # repeat_index=i_progress,
-                step_index=index,
-                method_name=method_name,
-                start_time=datetime.now(),
-            )
-            db.session.add(step)
-            db.session.flush()
-
-            logger.info(f"Executing: {line}")
-            socketio.emit('execution', {'section': f"{section_name}-{index}"})
-
-            # if line.startswith("registered_workflows"):
-            #     line = line.replace("registered_workflows.", "")
-            try:
-                if line.startswith("time.sleep("): # add safe sleep for time.sleep lines
-                    duration_str = line.strip()[len("time.sleep("):-1]
-                    duration = float(duration_str)
-                    self.safe_sleep(duration)
+        if kwargs_list:
+            results = kwargs_list.copy()
+        else:
+            results = []
+        nest_script = validate_and_nest_control_flow(script.script_dict.get(section_name, []))
+
+        for step in nest_script:
+            action = step["action"]
+            instrument = step["instrument"]
+            action_id = step["id"]
+            if action == "if":
+                await self._execute_if_batched(step, results, phase_id=phase_id, step_index=action_id, section_name=section_name)
+            elif action == "repeat":
+                await self._execute_repeat_batched(step, results, phase_id=phase_id, step_index=action_id, section_name=section_name)
+            elif action == "while":
+                await self._execute_while_batched(step, results, phase_id=phase_id, step_index=action_id, section_name=section_name)
+            elif instrument == "variable":
+                await self._execute_variable_batched(step, results, phase_id=phase_id, step_index=action_id, section_name=section_name)
+                print("Variable executed", "current context", context)
+            else:
+                # Regular action - check if batch
+                if step.get("batch_action", False):
+                    # Execute once for all samples
+                    if results:
+                        await self._execute_action_once(step, results[0], phase_id=phase_id, step_index=action_id, section_name=section_name)
+                    else:
+                        await self._execute_action_once(step, {}, phase_id=phase_id, step_index=action_id, section_name=section_name)
                 else:
-                    if "await " in line:
-                        async_code = f"async def __async_exec_wrapper():\n"
-                        # indent all code lines by 4 spaces
-                        async_code += "\n".join("    " + line for line in line.splitlines())
-                        async_code += f"\n    return locals()"
-                        exec(async_code, exec_globals, exec_locals)
-                        func = exec_locals.get("__async_exec_wrapper") or exec_globals.get("__async_exec_wrapper")
-                        # Capture the return value from asyncio.run
-                        result_locals = asyncio.run(func())
-
-                        # Update exec_locals with the returned locals
-                        exec_locals.update(result_locals)
-
-
+                    # Execute for each sample
+                    if results:
+                        for context in results:
+                            await self._execute_action(step, context, phase_id=phase_id, step_index=action_id, section_name=section_name)
+                            self.pause_event.wait()
                     else:
-                        # print("just exec synchronously")
-                        exec(line, exec_globals, exec_locals)
-                        exec_globals.update(exec_locals)
-                        # return locals_dict
-                    # exec(line, exec_globals, exec_locals)
-                # step.run_error = False
-
-            except HumanInterventionRequired as e:
-                logger.warning(f"Human intervention required: {e}")
-                socketio.emit('human_intervention', {'message': str(e)})
-                # Instead of auto-resume, explicitly stay paused until user action
-                # step.run_error = False
-                self.toggle_pause()
-
-            except Exception as e:
-                logger.error(f"Error during script execution: {e}")
-                socketio.emit('error', {'message': str(e)})
-
-                step.run_error = True
-                self.toggle_pause()
-            exec_locals.pop("__async_exec_wrapper", None)
-            step.end_time = datetime.now()
-            step.output = exec_locals
-            db.session.commit()
-
-            self.pause_event.wait()
+                        for _ in range(batch_size):
+                            await self._execute_action(step, {}, phase_id=phase_id, step_index=action_id, section_name=section_name)
+                            self.pause_event.wait()
 
-            # todo update script during the run
-            # _func_str = script.compile()
-            # step_list: list = script.convert_to_lines(_func_str).get(section_name, [])
-            if not step.run_error or not self.retry:
-                index += 1
-
-        return exec_locals  # Return the 'results' variable
+        return results  # Return the 'results' variable
 
     def _run_with_stop_check(self, script: Script, repeat_count: int, run_name: str, logger, socketio, config, bo_args,
-                             output_path, current_app, compiled, history=None, optimizer=None):
+                             output_path, current_app, compiled, history=None, optimizer=None, batch_mode=None,
+                             batch_size=None, objectives=None):
         time.sleep(1)
         # _func_str = script.compile()
         # step_list_dict: dict = script.convert_to_lines(_func_str)
@@ -250,27 +207,40 @@ class ScriptRunner:
             db.session.add(run)
             db.session.flush()
             run_id = run.id  # Save the ID
-            try:
+            db.session.commit()
 
+            try:
+            # if True:
                 global_config.runner_status = {"id":run_id, "type": "workflow"}
                 # Run "prep" section once
-                self._run_actions(script, section_name="prep", logger=logger, socketio=socketio, run_id=run_id)
+                asyncio.run(self._run_actions(script, section_name="prep", logger=logger, socketio=socketio, run_id=run_id))
                 output_list = []
                 _, arg_type = script.config("script")
                 _, return_list = script.config_return()
                 # Run "script" section multiple times
                 if repeat_count:
-                    self._run_repeat_section(repeat_count, arg_type, bo_args, output_list, script,
+                    asyncio.run(
+                        self._run_repeat_section(repeat_count, arg_type, bo_args, output_list, script,
                                              run_name, return_list, compiled, logger, socketio,
-                                             history, output_path, run_id=run_id, optimizer=optimizer)
+                                             history, output_path, run_id=run_id, optimizer=optimizer,
+                                             batch_mode=batch_mode, batch_size=batch_size, objectives=objectives)
+                    )
                 elif config:
-                    self._run_config_section(config, arg_type, output_list, script, run_name, logger,
-                                             socketio, run_id=run_id, compiled=compiled)
+                    asyncio.run(
+                        self._run_config_section(
+                            config, arg_type, output_list, script, run_name, logger,
+                            socketio, run_id=run_id, compiled=compiled, batch_mode=batch_mode, batch_size=batch_size
+                        )
+                    )
+                    # self._run_config_section(config, arg_type, output_list, script, run_name, logger,
+                    #                          socketio, run_id=run_id, compiled=compiled)
                 # Run "cleanup" section once
-                self._run_actions(script, section_name="cleanup", logger=logger, socketio=socketio,run_id=run_id)
+                asyncio.run(self._run_actions(script, section_name="cleanup", logger=logger, socketio=socketio,run_id=run_id))
                 # Reset the running flag when done
                 # Save results if necessary
                 if not script.python_script and return_list:
+                    # print(output_list)
+
                     filename = self._save_results(run_name, arg_type, return_list, output_list, logger, output_path)
                 self._emit_progress(socketio, 100)
 
@@ -278,16 +248,20 @@ class ScriptRunner:
                 logger.error(f"Error during script execution: {e.__str__()}")
                 error_flag = True
             finally:
-                self.lock.release()
+                if self.lock.locked():
+                    self.lock.release()
         with current_app.app_context():
             run = db.session.get(WorkflowRun, run_id)
-            run.end_time = datetime.now()
-            run.data_path = filename
-            run.run_error = error_flag
-            db.session.commit()
+            if run is None:
+                logger.info("Error: Run not found in database.")
+            else:
+                run.end_time = datetime.now()
+                run.data_path = filename
+                run.run_error = error_flag
+                db.session.commit()
 
 
-    def _run_actions(self, script, section_name="", logger=None, socketio=None, run_id=None):
+    async def _run_actions(self, script, section_name="", logger=None, socketio=None, run_id=None):
         _func_str = script.python_script or script.compile()
         step_list: list = script.convert_to_lines(_func_str).get(section_name, [])
         if not step_list:
@@ -309,14 +283,15 @@ class ScriptRunner:
         db.session.flush()
         phase_id = phase.id
 
-        step_outputs = self.exec_steps(script, section_name, logger, socketio, phase_id=phase_id)
+        step_outputs = await self.exec_steps(script, section_name, phase_id=phase_id)
         # Save phase-level output
         phase.outputs = step_outputs
         phase.end_time = datetime.now()
         db.session.commit()
         return step_outputs
 
-    def _run_config_section(self, config, arg_type, output_list, script, run_name, logger, socketio, run_id, compiled=True):
+    async def _run_config_section(self, config, arg_type, output_list, script, run_name, logger, socketio, run_id,
+                                  compiled=True, batch_mode=False, batch_size=1):
         if not compiled:
             for i in config:
                 try:
@@ -327,13 +302,16 @@ class ScriptRunner:
                     compiled = False
                     break
         if compiled:
-            for i, kwargs in enumerate(config):
-                kwargs = dict(kwargs)
+            batch_size = int(batch_size)
+            nested_list = [config[i:i + batch_size] for i in range(0, len(config), batch_size)]
+
+            for i, kwargs_list in enumerate(nested_list):
+                # kwargs = dict(kwargs)
                 if self.stop_pending_event.is_set():
                     logger.info(f'Stopping execution during {run_name}: {i + 1}/{len(config)}')
                     break
-                logger.info(f'Executing {i + 1} of {len(config)} with kwargs = {kwargs}')
-                progress = ((i + 1) * 100 / len(config)) - 0.1
+                logger.info(f'Executing {i + 1} of {len(nested_list)} with kwargs = {kwargs_list}')
+                progress = ((i + 1) * 100 / len(nested_list)) - 0.1
                 self._emit_progress(socketio, progress)
                 # fname = f"{run_name}_script"
                 # function = self.globals_dict[fname]
@@ -342,30 +320,33 @@ class ScriptRunner:
                     run_id=run_id,
                     name="main",
                     repeat_index=i,
-                    parameters=kwargs,
+                    parameters=kwargs_list,
                     start_time=datetime.now()
                 )
                 db.session.add(phase)
                 db.session.flush()
 
                 phase_id = phase.id
-                output = self.exec_steps(script, "script", logger, socketio, phase_id, **kwargs)
+                output = await self.exec_steps(script, "script", phase_id, kwargs_list=kwargs_list, )
+                # print(output)
                 if output:
                     # kwargs.update(output)
-                    output_list.append(output)
-                    phase.outputs = {k:v for k, v in output.items() if k not in arg_type.keys()}
+                    for output_dict in output:
+                        output_list.append(output_dict)
+                    phase.outputs = output
                 phase.end_time = datetime.now()
                 db.session.commit()
+        return output_list
 
-    def _run_repeat_section(self, repeat_count, arg_types, bo_args, output_list, script, run_name, return_list, compiled,
-                            logger, socketio, history, output_path, run_id, optimizer=None):
+    async def _run_repeat_section(self, repeat_count, arg_types, bo_args, output_list, script, run_name, return_list, compiled,
+                            logger, socketio, history, output_path, run_id, optimizer=None, batch_mode=None,
+                            batch_size=None, objectives=None):
         if bo_args:
             logger.info('Initializing optimizer...')
             if compiled:
                 ax_client = bo_campaign.ax_init_opc(bo_args)
             else:
                 if history:
-                    import pandas as pd
                     file_path = os.path.join(output_path, history)
                     previous_runs = pd.read_csv(file_path).to_dict(orient='records')
                     ax_client = bo_campaign.ax_init_form(bo_args, arg_types, len(previous_runs))
@@ -378,12 +359,26 @@ class ScriptRunner:
                 else:
                     ax_client = bo_campaign.ax_init_form(bo_args, arg_types)
         elif optimizer and history:
-            import pandas as pd
             file_path = os.path.join(output_path, history)
 
             previous_runs = pd.read_csv(file_path)
+
+            expected_cols = list(arg_types.keys()) + list(return_list)
+
+            actual_cols = previous_runs.columns.tolist()
+
+            # NOT okay if it misses columns
+            if set(expected_cols) - set(actual_cols):
+                logger.warning(f"Missing columns from history .csv file. Expecting {expected_cols} but got {actual_cols}")
+                raise ValueError("Missing columns from history .csv file.")
+
+            # okay if there is extra columns
+            if set(actual_cols) - set(expected_cols):
+                logger.warning(f"Extra columns from history .csv file. Expecting {expected_cols} but got {actual_cols}")
+
             optimizer.append_existing_data(previous_runs)
-            for row in previous_runs:
+
+            for row in previous_runs.to_dict(orient='records'):
                 output_list.append(row)
 
 
@@ -409,12 +404,13 @@ class ScriptRunner:
             if bo_args:
                 try:
                     parameters, trial_index = ax_client.get_next_trial()
-                    logger.info(f'Output value: {parameters}')
+                    logger.info(f'Params value: {parameters}')
                     # fname = f"{run_name}_script"
                     # function = self.globals_dict[fname]
                     phase.parameters = parameters
-
-                    output = self.exec_steps(script, "script", logger, socketio, phase_id, **parameters)
+                    if not type(parameters) is list:
+                        parameters = [parameters]
+                    output = await self.exec_steps(script, "script", phase_id, parameters)
 
                     _output = {key: value for key, value in output.items() if key in return_list}
                     ax_client.complete_trial(trial_index=trial_index, raw_data=_output)
@@ -422,30 +418,41 @@ class ScriptRunner:
                 except Exception as e:
                     logger.info(f'Optimization error: {e}')
                     break
+            # Optimizer for UI
             elif optimizer:
                 try:
-                    parameters = optimizer.suggest(1)
-                    logger.info(f'Output value: {parameters}')
+                    parameters = optimizer.suggest(n=batch_size)
+                    logger.info(f'Parameters: {parameters}')
                     phase.parameters = parameters
-                    output = self.exec_steps(script, "script", logger, socketio, phase_id, **parameters)
+
+                    output = await self.exec_steps(script, "script",  phase_id, kwargs_list=parameters)
                     if output:
                         optimizer.observe(output)
-                        output.update(parameters)
+                        
+                    else:
+                        logger.info('No output from script')
+
+
                 except Exception as e:
                     logger.info(f'Optimization error: {e}')
                     break
             else:
                 # fname = f"{run_name}_script"
                 # function = self.globals_dict[fname]
-                output = self.exec_steps(script, "script", logger, socketio, phase_id)
-
+                output = await self.exec_steps(script, "script", phase_id, batch_size=batch_size)
             if output:
-                output_list.append(output)
+                # print("output: ", output)
+                output_list.extend(output)
                 logger.info(f'Output value: {output}')
                 phase.outputs = output
             phase.end_time = datetime.now()
             db.session.commit()
-
+            
+            early_stop = self._check_early_stop(output, objectives)
+            if early_stop:
+                logger.info('Early stopping')
+                break
+                
         if bo_args:
             ax_client.save_to_json_file(os.path.join(output_path, f"{run_name}_ax_client.json"))
             logger.info(
@@ -455,14 +462,14 @@ class ScriptRunner:
 
     @staticmethod
     def _save_results(run_name, arg_type, return_list, output_list, logger, output_path):
-        args = list(arg_type.keys()) if arg_type else []
-        args.extend(return_list)
+        output_columns = list(arg_type.keys()) + list(return_list)
+
         filename = run_name + "_" + datetime.now().strftime("%Y-%m-%d %H-%M") + ".csv"
         file_path = os.path.join(output_path, filename)
-        with open(file_path, "w", newline='') as file:
-            writer = csv.DictWriter(file, fieldnames=args)
-            writer.writeheader()
-            writer.writerows(output_list)
+        df = pd.DataFrame(output_list)
+        df = df.loc[:, [c for c in output_columns if c in df.columns]]
+
+        df. to_csv(file_path, index=False)
         logger.info(f'Results saved to {file_path}')
         return filename
 
@@ -486,4 +493,297 @@ class ScriptRunner:
                 "paused": self.paused,
                 "stop_pending": self.stop_pending_event.is_set(),
                 "stop_current": self.stop_current_event.is_set(),
-            }
+            }
+
+
+    async def _execute_steps_batched(self, steps: List[Dict], contexts: List[Dict[str, Any]], phase_id, step_index, section_name):
+        """
+        Execute a list of steps for multiple samples, batching where appropriate.
+        """
+        for step in steps:
+            action = step["action"]
+
+            if action == "if":
+                await self._execute_if_batched(step, contexts, phase_id, step_index, section_name)
+            elif action == "repeat":
+                await self._execute_repeat_batched(step, contexts, phase_id, step_index, section_name)
+            elif action == "while":
+                await self._execute_while_batched(step, contexts, phase_id, step_index, section_name)
+            else:
+                # Regular action - check if batch
+                if step.get("batch_action", False):
+                    # Execute once for all samples
+                    await self._execute_action_once(step, contexts[0], phase_id=phase_id, step_index=step_index, section_name=section_name)
+                else:
+                    # Execute for each sample
+                    for context in contexts:
+                        await self._execute_action(step, context, phase_id=phase_id, step_index=step_index, section_name=section_name)
+
+
+    async def _execute_if_batched(self, step: Dict, contexts: List[Dict[str, Any]], phase_id, step_index, section_name):
+        """Execute if/else block for multiple samples."""
+        # Evaluate condition for each sample
+        for context in contexts:
+            condition = self._evaluate_condition(step["args"]["statement"], context)
+
+            if condition:
+                await self._execute_steps_batched(step["if_block"], [context], phase_id=phase_id, step_index=step_index, section_name=section_name)
+            else:
+                await self._execute_steps_batched(step["else_block"], [context], phase_id=phase_id, step_index=step_index, section_name=section_name)
+
+
+    async def _execute_repeat_batched(self, step: Dict, contexts: List[Dict[str, Any]], phase_id, step_index, section_name):
+        """Execute repeat block for multiple samples."""
+        times = step["args"].get("times", 1)
+
+        for i in range(times):
+            # Add repeat index to all contexts
+            for context in contexts:
+                context["repeat_index"] = i
+
+            await self._execute_steps_batched(step["repeat_block"], contexts, phase_id=phase_id, step_index=step_index, section_name=section_name)
+
+
+    async def _execute_while_batched(self, step: Dict, contexts: List[Dict[str, Any]], phase_id, step_index, section_name):
+        """Execute while block for multiple samples."""
+        max_iterations = step["args"].get("max_iterations", 1000)
+        active_contexts = contexts.copy()
+        iteration = 0
+
+        while iteration < max_iterations and active_contexts:
+            # Filter contexts that still meet the condition
+            still_active = []
+
+            for context in active_contexts:
+                condition = self._evaluate_condition(step["args"]["statement"], context)
+
+                if condition:
+                    context["while_index"] = iteration
+                    still_active.append(context)
+
+            if not still_active:
+                break
+
+            # Execute for contexts that are still active
+            await self._execute_steps_batched(step["while_block"], still_active, phase_id=phase_id, step_index=step_index, section_name=section_name)
+            active_contexts = still_active
+            iteration += 1
+
+        if iteration >= max_iterations:
+            raise RuntimeError(f"While loop exceeded max iterations ({max_iterations})")
+
+    async def _execute_action(self, step: Dict, context: Dict[str, Any], phase_id=1, step_index=1, section_name=None):
+        """Execute a single action with parameter substitution."""
+        # Substitute parameters in args
+        substituted_args = self._substitute_params(step["args"], context)
+
+        # Get the component and method
+        instrument = step.get("instrument", "")
+        action = step["action"]
+        if instrument and "." in instrument:
+            instrument_type, instrument = instrument.split(".")
+        else:
+            instrument_type = ""
+        # Execute the action
+        step_db = WorkflowStep(
+            phase_id=phase_id,
+            step_index=step_index,
+            method_name=action,
+            start_time=datetime.now(),
+        )
+        db.session.add(step_db)
+        db.session.flush()
+        try:
+            self.socketio.emit('execution', {'section': f"{section_name}-{step_index}"})
+            if action == "wait":
+                duration = float(substituted_args["statement"])
+                self.safe_sleep(duration)
+
+            elif action == "pause":
+                msg = substituted_args.get("statement", "")
+                pause(msg)
+
+            elif instrument_type == "deck" and hasattr(deck, instrument):
+                component = getattr(deck, instrument)
+                if hasattr(component, action):
+                    method = getattr(component, action)
+
+                    # Execute and handle return value
+                    if step.get("coroutine", False):
+                        result = await method(**substituted_args)
+                    else:
+                        result = method(**substituted_args)
+
+                    # Store return value if specified
+                    return_var = step.get("return", "")
+                    if return_var:
+                        context[return_var] = result
+
+            elif instrument_type == "blocks" and instrument in BUILDING_BLOCKS.keys():
+                # Inject all block categories
+                method_collection = BUILDING_BLOCKS[instrument]
+                if action in method_collection.keys():
+                    method = method_collection[action]["func"]
+
+                    # Execute and handle return value
+                    # print(step.get("coroutine", False))
+                    if step.get("coroutine", False):
+                        result = await method(**substituted_args)
+                    else:
+                        result = method(**substituted_args)
+
+                    # Store return value if specified
+                    return_var = step.get("return", "")
+                    if return_var:
+                        context[return_var] = result
+        except HumanInterventionRequired as e:
+            self.logger.warning(f"Human intervention required: {e}")
+            self.socketio.emit('human_intervention', {'message': str(e)})
+            # Instead of auto-resume, explicitly stay paused until user action
+            # step.run_error = False
+            self.toggle_pause()
+
+        except Exception as e:
+            self.logger.error(f"Error during script execution: {e}")
+            self.socketio.emit('error', {'message': str(e)})
+
+            step_db.run_error = True
+            self.toggle_pause()
+        finally:
+            step_db.end_time = datetime.now()
+            step_db.output = context
+            db.session.commit()
+
+            self.pause_event.wait()
+
+        return context
+
+    async def _execute_action_once(self, step: Dict, context: Dict[str, Any], phase_id, step_index, section_name):
+        """Execute a batch action once (not per sample)."""
+        # print(f"Executing batch action: {step['action']}")
+        return await self._execute_action(step, context, phase_id=phase_id, step_index=step_index, section_name=section_name)
+
+    @staticmethod
+    def _substitute_params(args: Dict[str, Any], context: Dict[str, Any]) -> Dict[str, Any]:
+        """Substitute parameter placeholders like #param_1 with actual values."""
+        substituted = {}
+
+        for key, value in args.items():
+            if isinstance(value, str) and value.startswith("#"):
+                param_name = value[1:]  # Remove '#'
+                substituted[key] = context.get(param_name, value)
+            else:
+                substituted[key] = value
+
+        return substituted
+
+    @staticmethod
+    def _evaluate_condition(condition_str: str, context: Dict[str, Any]) -> bool:
+        """
+        Safely evaluate a condition string with context variables.
+        """
+        # Create evaluation context with all variables
+        eval_context = {}
+
+        # Substitute variables in the condition string
+        substituted = condition_str
+        for key, value in context.items():
+            # Replace #variable with actual variable name for eval
+            substituted = substituted.replace(f"#{key}", key)
+            # Add variable to eval context
+            eval_context[key] = value
+
+        try:
+            # Safe evaluation with variables in scope
+            result = eval(substituted, {"__builtins__": {}}, eval_context)
+            return bool(result)
+        except Exception as e:
+            raise ValueError(f"Error evaluating condition '{condition_str}': {e}")
+
+    def _check_early_stop(self, output, objectives):
+        for row in output:
+            all_met = True
+            for obj in objectives:
+                name = obj['name']
+                minimize = obj.get('minimize', True)
+                threshold = obj.get('early_stop', None)
+
+                if threshold is None:
+                    all_met = False
+                    break# Skip if no early stop defined
+
+                value = row[name]
+                if minimize and value > threshold:
+                    all_met = False
+                    break
+                elif not minimize and value < threshold:
+                    all_met = False
+                    break
+
+            if all_met:
+                return True  # At least one row meets all early stop thresholds
+
+        return False  # No row met all thresholds
+
+    async def _execute_variable_batched(self, step: Dict, contexts: List[Dict[str, Any]], phase_id, step_index,
+                                        section_name):
+        """Execute variable assignment for multiple samples."""
+        var_name = step["action"]  # "vial" in your example
+        var_value = step["args"]["statement"]
+        arg_type = step["arg_types"]["statement"]
+
+        for context in contexts:
+            # Substitute any variable references in the value
+            if isinstance(var_value, str):
+                substituted_value = var_value
+
+                # Replace all variable references (with or without #) with their values
+                for key, val in context.items():
+                    # Handle both #variable and variable (without #)
+                    substituted_value = substituted_value.replace(f"#{key}", str(val))
+                    # For expressions like "vial+10", replace variable name directly
+                    # Use word boundaries to avoid partial matches
+                    import re
+                    substituted_value = re.sub(r'\b' + re.escape(key) + r'\b', str(val), substituted_value)
+
+                # Handle based on type
+                if arg_type == "float":
+                    try:
+                        # Evaluate as expression (e.g., "10.0+10" becomes 20.0)
+                        result = eval(substituted_value, {"__builtins__": {}}, {})
+                        context[var_name] = float(result)
+                    except:
+                        # If eval fails, try direct conversion
+                        context[var_name] = float(substituted_value)
+
+                elif arg_type == "int":
+                    try:
+                        result = eval(substituted_value, {"__builtins__": {}}, {})
+                        context[var_name] = int(result)
+                    except:
+                        context[var_name] = int(substituted_value)
+
+                elif arg_type == "bool":
+                    try:
+                        # Evaluate boolean expressions
+                        result = eval(substituted_value, {"__builtins__": {}}, {})
+                        context[var_name] = bool(result)
+                    except:
+                        context[var_name] = substituted_value.lower() in ['true', '1', 'yes']
+
+                else:  # "str"
+                    # For strings, check if it looks like an expression
+                    if any(char in substituted_value for char in ['+', '-', '*', '/', '>', '<', '=', '(', ')']):
+                        try:
+                            # Try to evaluate as expression
+                            result = eval(substituted_value, {"__builtins__": {}}, {})
+                            context[var_name] = result
+                        except:
+                            # If eval fails, store as string
+                            context[var_name] = substituted_value
+                    else:
+                        context[var_name] = substituted_value
+            else:
+                # Direct numeric or boolean value
+                context[var_name] = var_value
+