semantic update

backend/src/core/logger.py

@@ -35,7 +35,19 @@ class BeliefFormatter(logging.Formatter):
     def format(self, record):
         anchor_id = getattr(_belief_state, 'anchor_id', None)
         if anchor_id:
-            record.msg = f"[{anchor_id}][Action] {record.msg}"
+            msg = str(record.msg)
+            # Supported molecular topology markers
+            markers = ("[EXPLORE]", "[REASON]", "[REFLECT]", "[COHERENCE:", "[Action]", "[Entry]", "[Exit]")
+            
+            # Avoid duplicating anchor or overriding explicit markers
+            if msg.startswith(f"[{anchor_id}]"):
+                pass
+            elif any(msg.startswith(m) for m in markers):
+                record.msg = f"[{anchor_id}]{msg}"
+            else:
+                # Default covalent bond
+                record.msg = f"[{anchor_id}][Action] {msg}"
+                
         return super().format(record)
     # [/DEF:format:Function]
 # [/DEF:BeliefFormatter:Class]
@@ -75,12 +87,12 @@ def belief_scope(anchor_id: str, message: str = ""):
     try:
         yield
         # Log Coherence OK and Exit (DEBUG level to reduce noise)
-        logger.debug(f"[{anchor_id}][Coherence:OK]")
+        logger.debug("[COHERENCE:OK]")
         if _enable_belief_state:
-            logger.debug(f"[{anchor_id}][Exit]")
+            logger.debug("[Exit]")
     except Exception as e:
         # Log Coherence Failed (DEBUG level to reduce noise)
-        logger.debug(f"[{anchor_id}][Coherence:Failed] {str(e)}")
+        logger.debug(f"[COHERENCE:FAILED] {str(e)}")
         raise
     finally:
         # Restore old anchor
@@ -275,5 +287,33 @@ logger.addHandler(websocket_log_handler)
 # Example usage:
 # logger.info("Application started", extra={"context_key": "context_value"})
 # logger.error("An error occurred", exc_info=True)
+
+import types
+
+# [DEF:explore:Function]
+# @PURPOSE: Logs an EXPLORE message (Van der Waals force) for searching, alternatives, and hypotheses.
+# @SEMANTICS: log, explore, molecule
+def explore(self, msg, *args, **kwargs):
+    self.warning(f"[EXPLORE] {msg}", *args, **kwargs)
+# [/DEF:explore:Function]
+
+# [DEF:reason:Function]
+# @PURPOSE: Logs a REASON message (Covalent bond) for strict deduction and core logic.
+# @SEMANTICS: log, reason, molecule
+def reason(self, msg, *args, **kwargs):
+    self.info(f"[REASON] {msg}", *args, **kwargs)
+# [/DEF:reason:Function]
+
+# [DEF:reflect:Function]
+# @PURPOSE: Logs a REFLECT message (Hydrogen bond) for self-check and structural validation.
+# @SEMANTICS: log, reflect, molecule
+def reflect(self, msg, *args, **kwargs):
+    self.debug(f"[REFLECT] {msg}", *args, **kwargs)
+# [/DEF:reflect:Function]
+
+logger.explore = types.MethodType(explore, logger)
+logger.reason = types.MethodType(reason, logger)
+logger.reflect = types.MethodType(reflect, logger)
+
 # [/DEF:Logger:Global]
 # [/DEF:LoggerModule:Module]

backend/src/core/task_manager/context.py

@@ -6,9 +6,11 @@
 # @TIER: CRITICAL
 # @INVARIANT: Each TaskContext is bound to a single task execution.
 
+# [SECTION: IMPORTS]
 # [SECTION: IMPORTS]
 from typing import Dict, Any, Callable
 from .task_logger import TaskLogger
+from ..logger import belief_scope
 # [/SECTION]
 
 # [DEF:TaskContext:Class]
@@ -44,13 +46,14 @@ class TaskContext:
         params: Dict[str, Any],
         default_source: str = "plugin"
     ):
-        self._task_id = task_id
-        self._params = params
-        self._logger = TaskLogger(
-            task_id=task_id,
-            add_log_fn=add_log_fn,
-            source=default_source
-        )
+        with belief_scope("__init__"):
+            self._task_id = task_id
+            self._params = params
+            self._logger = TaskLogger(
+                task_id=task_id,
+                add_log_fn=add_log_fn,
+                source=default_source
+            )
     # [/DEF:__init__:Function]
     
     # [DEF:task_id:Function]
@@ -60,7 +63,8 @@ class TaskContext:
     # @RETURN: str - The task ID.
     @property
     def task_id(self) -> str:
-        return self._task_id
+        with belief_scope("task_id"):
+            return self._task_id
     # [/DEF:task_id:Function]
     
     # [DEF:logger:Function]
@@ -70,7 +74,8 @@ class TaskContext:
     # @RETURN: TaskLogger - The logger instance.
     @property
     def logger(self) -> TaskLogger:
-        return self._logger
+        with belief_scope("logger"):
+            return self._logger
     # [/DEF:logger:Function]
     
     # [DEF:params:Function]
@@ -80,7 +85,8 @@ class TaskContext:
     # @RETURN: Dict[str, Any] - The task parameters.
     @property
     def params(self) -> Dict[str, Any]:
-        return self._params
+        with belief_scope("params"):
+            return self._params
     # [/DEF:params:Function]
     
     # [DEF:get_param:Function]
@@ -91,7 +97,8 @@ class TaskContext:
     # @PARAM: default (Any) - Default value if key not found.
     # @RETURN: Any - Parameter value or default.
     def get_param(self, key: str, default: Any = None) -> Any:
-        return self._params.get(key, default)
+        with belief_scope("get_param"):
+            return self._params.get(key, default)
     # [/DEF:get_param:Function]
     
     # [DEF:create_sub_context:Function]
@@ -102,12 +109,13 @@ class TaskContext:
     # @RETURN: TaskContext - New context with different source.
     def create_sub_context(self, source: str) -> "TaskContext":
         """Create a sub-context with a different default source for logging."""
-        return TaskContext(
-            task_id=self._task_id,
-            add_log_fn=self._logger._add_log,
-            params=self._params,
-            default_source=source
-        )
+        with belief_scope("create_sub_context"):
+            return TaskContext(
+                task_id=self._task_id,
+                add_log_fn=self._logger._add_log,
+                params=self._params,
+                default_source=source
+            )
     # [/DEF:create_sub_context:Function]
 
 # [/DEF:TaskContext:Class]

backend/src/core/task_manager/manager.py

@@ -1,4 +1,5 @@
 # [DEF:TaskManagerModule:Module]
+# @TIER: CRITICAL
 # @SEMANTICS: task, manager, lifecycle, execution, state
 # @PURPOSE: Manages the lifecycle of tasks, including their creation, execution, and state tracking. It uses a thread pool to run plugins asynchronously.
 # @LAYER: Core
@@ -74,9 +75,10 @@ class TaskManager:
     # @POST: Logs are batch-written to database every LOG_FLUSH_INTERVAL seconds.
     def _flusher_loop(self):
         """Background thread that flushes log buffer to database."""
-        while not self._flusher_stop_event.is_set():
-            self._flush_logs()
-            self._flusher_stop_event.wait(self.LOG_FLUSH_INTERVAL)
+        with belief_scope("_flusher_loop"):
+            while not self._flusher_stop_event.is_set():
+                self._flush_logs()
+                self._flusher_stop_event.wait(self.LOG_FLUSH_INTERVAL)
     # [/DEF:_flusher_loop:Function]
     
     # [DEF:_flush_logs:Function]
@@ -85,23 +87,24 @@ class TaskManager:
     # @POST: All buffered logs are written to task_logs table.
     def _flush_logs(self):
         """Flush all buffered logs to the database."""
-        with self._log_buffer_lock:
-            task_ids = list(self._log_buffer.keys())
-        
-        for task_id in task_ids:
+        with belief_scope("_flush_logs"):
             with self._log_buffer_lock:
-                logs = self._log_buffer.pop(task_id, [])
+                task_ids = list(self._log_buffer.keys())
             
-            if logs:
-                try:
-                    self.log_persistence_service.add_logs(task_id, logs)
-                except Exception as e:
-                    logger.error(f"Failed to flush logs for task {task_id}: {e}")
-                    # Re-add logs to buffer on failure
-                    with self._log_buffer_lock:
-                        if task_id not in self._log_buffer:
-                            self._log_buffer[task_id] = []
-                        self._log_buffer[task_id].extend(logs)
+            for task_id in task_ids:
+                with self._log_buffer_lock:
+                    logs = self._log_buffer.pop(task_id, [])
+                
+                if logs:
+                    try:
+                        self.log_persistence_service.add_logs(task_id, logs)
+                    except Exception as e:
+                        logger.error(f"Failed to flush logs for task {task_id}: {e}")
+                        # Re-add logs to buffer on failure
+                        with self._log_buffer_lock:
+                            if task_id not in self._log_buffer:
+                                self._log_buffer[task_id] = []
+                            self._log_buffer[task_id].extend(logs)
     # [/DEF:_flush_logs:Function]
     
     # [DEF:_flush_task_logs:Function]
@@ -111,14 +114,15 @@ class TaskManager:
     # @PARAM: task_id (str) - The task ID.
     def _flush_task_logs(self, task_id: str):
         """Flush logs for a specific task immediately."""
-        with self._log_buffer_lock:
-            logs = self._log_buffer.pop(task_id, [])
-        
-        if logs:
-            try:
-                self.log_persistence_service.add_logs(task_id, logs)
-            except Exception as e:
-                logger.error(f"Failed to flush logs for task {task_id}: {e}")
+        with belief_scope("_flush_task_logs"):
+            with self._log_buffer_lock:
+                logs = self._log_buffer.pop(task_id, [])
+            
+            if logs:
+                try:
+                    self.log_persistence_service.add_logs(task_id, logs)
+                except Exception as e:
+                    logger.error(f"Failed to flush logs for task {task_id}: {e}")
     # [/DEF:_flush_task_logs:Function]
 
     # [DEF:create_task:Function]

backend/src/core/task_manager/persistence.py

@@ -1,4 +1,5 @@
 # [DEF:TaskPersistenceModule:Module]
+# @TIER: CRITICAL
 # @SEMANTICS: persistence, sqlite, sqlalchemy, task, storage
 # @PURPOSE: Handles the persistence of tasks using SQLAlchemy and the tasks.db database.
 # @LAYER: Core
@@ -19,42 +20,65 @@ from ..logger import logger, belief_scope
 # [/SECTION]
 
 # [DEF:TaskPersistenceService:Class]
+# @TIER: CRITICAL
 # @SEMANTICS: persistence, service, database, sqlalchemy
 # @PURPOSE: Provides methods to save and load tasks from the tasks.db database using SQLAlchemy.
+# @INVARIANT: Persistence must handle potentially missing task fields natively.
 class TaskPersistenceService:
+    # [DEF:_json_load_if_needed:Function]
+    # @PURPOSE: Safely load JSON strings from DB if necessary
+    # @PRE: value is an arbitrary database value
+    # @POST: Returns parsed JSON object, list, string, or primitive
     @staticmethod
     def _json_load_if_needed(value):
-        if value is None:
-            return None
-        if isinstance(value, (dict, list)):
-            return value
-        if isinstance(value, str):
-            stripped = value.strip()
-            if stripped == "" or stripped.lower() == "null":
+        with belief_scope("TaskPersistenceService._json_load_if_needed"):
+            if value is None:
                 return None
-            try:
-                return json.loads(stripped)
-            except json.JSONDecodeError:
+            if isinstance(value, (dict, list)):
                 return value
-        return value
+            if isinstance(value, str):
+                stripped = value.strip()
+                if stripped == "" or stripped.lower() == "null":
+                    return None
+                try:
+                    return json.loads(stripped)
+                except json.JSONDecodeError:
+                    return value
+            return value
+    # [/DEF:_json_load_if_needed:Function]
 
+    # [DEF:_parse_datetime:Function]
+    # @PURPOSE: Safely parse a datetime string from the database
+    # @PRE: value is an ISO string or datetime object
+    # @POST: Returns datetime object or None
     @staticmethod
     def _parse_datetime(value):
-        if value is None or isinstance(value, datetime):
-            return value
-        if isinstance(value, str):
-            try:
-                return datetime.fromisoformat(value)
-            except ValueError:
-                return None
-        return None
-
-    @staticmethod
-    def _resolve_environment_id(session: Session, env_id: Optional[str]) -> Optional[str]:
-        if not env_id:
+        with belief_scope("TaskPersistenceService._parse_datetime"):
+            if value is None or isinstance(value, datetime):
+                return value
+            if isinstance(value, str):
+                try:
+                    return datetime.fromisoformat(value)
+                except ValueError:
+                    return None
             return None
-        exists = session.query(Environment.id).filter(Environment.id == env_id).first()
-        return env_id if exists else None
+    # [/DEF:_parse_datetime:Function]
+
+    # [DEF:_resolve_environment_id:Function]
+    # @TIER: STANDARD
+    # @PURPOSE: Resolve environment id based on provided value or fallback to default
+    # @PRE: Session is active
+    # @POST: Environment ID is returned
+    @staticmethod
+    def _resolve_environment_id(session: Session, env_id: Optional[str]) -> str:
+        with belief_scope("_resolve_environment_id"):
+            if env_id:
+                return env_id
+            repo_env = session.query(Environment).filter_by(name="default").first()
+            if repo_env:
+                return str(repo_env.id)
+            return "default"
+    # [/DEF:_resolve_environment_id:Function]
 
     # [DEF:__init__:Function]
     # @PURPOSE: Initializes the persistence service.
@@ -90,13 +114,14 @@ class TaskPersistenceService:
                 
                 # Ensure params and result are JSON serializable
                 def json_serializable(obj):
-                    if isinstance(obj, dict):
-                        return {k: json_serializable(v) for k, v in obj.items()}
-                    elif isinstance(obj, list):
-                        return [json_serializable(v) for v in obj]
-                    elif isinstance(obj, datetime):
-                        return obj.isoformat()
-                    return obj
+                    with belief_scope("TaskPersistenceService.json_serializable"):
+                        if isinstance(obj, dict):
+                            return {k: json_serializable(v) for k, v in obj.items()}
+                        elif isinstance(obj, list):
+                            return [json_serializable(v) for v in obj]
+                        elif isinstance(obj, datetime):
+                            return obj.isoformat()
+                        return obj
 
                 record.params = json_serializable(task.params)
                 record.result = json_serializable(task.result)
@@ -227,9 +252,11 @@ class TaskLogPersistenceService:
     """
     
     # [DEF:__init__:Function]
-    # @PURPOSE: Initialize the log persistence service.
-    # @POST: Service is ready.
-    def __init__(self):
+    # @TIER: STANDARD
+    # @PURPOSE: Initializes the TaskLogPersistenceService
+    # @PRE: config is provided or defaults are used
+    # @POST: Service is ready for log persistence
+    def __init__(self, config=None):
         pass
     # [/DEF:__init__:Function]
     

backend/src/core/task_manager/task_logger.py

@@ -15,6 +15,7 @@ from typing import Dict, Any, Optional, Callable
 # @PURPOSE: A wrapper around TaskManager._add_log that carries task_id and source context.
 # @TIER: CRITICAL
 # @INVARIANT: All log calls include the task_id and source.
+# @TEST_DATA: task_logger -> {"task_id": "test_123", "source": "test_plugin"}
 # @UX_STATE: Idle -> Logging -> (system records log)
 class TaskLogger:
     """
@@ -71,6 +72,7 @@ class TaskLogger:
     # @PARAM: message (str) - Log message.
     # @PARAM: source (Optional[str]) - Override source for this log entry.
     # @PARAM: metadata (Optional[Dict]) - Additional structured data.
+    # @UX_STATE: Logging -> (writing internal log)
     def _log(
         self, 
         level: str, 
@@ -90,6 +92,8 @@ class TaskLogger:
     
     # [DEF:debug:Function]
     # @PURPOSE: Log a DEBUG level message.
+    # @PRE: message is a string.
+    # @POST: Log entry added via internally with DEBUG level.
     # @PARAM: message (str) - Log message.
     # @PARAM: source (Optional[str]) - Override source.
     # @PARAM: metadata (Optional[Dict]) - Additional data.
@@ -104,6 +108,8 @@ class TaskLogger:
     
     # [DEF:info:Function]
     # @PURPOSE: Log an INFO level message.
+    # @PRE: message is a string.
+    # @POST: Log entry added internally with INFO level.
     # @PARAM: message (str) - Log message.
     # @PARAM: source (Optional[str]) - Override source.
     # @PARAM: metadata (Optional[Dict]) - Additional data.
@@ -118,6 +124,8 @@ class TaskLogger:
     
     # [DEF:warning:Function]
     # @PURPOSE: Log a WARNING level message.
+    # @PRE: message is a string.
+    # @POST: Log entry added internally with WARNING level.
     # @PARAM: message (str) - Log message.
     # @PARAM: source (Optional[str]) - Override source.
     # @PARAM: metadata (Optional[Dict]) - Additional data.
@@ -132,6 +140,8 @@ class TaskLogger:
     
     # [DEF:error:Function]
     # @PURPOSE: Log an ERROR level message.
+    # @PRE: message is a string.
+    # @POST: Log entry added internally with ERROR level.
     # @PARAM: message (str) - Log message.
     # @PARAM: source (Optional[str]) - Override source.
     # @PARAM: metadata (Optional[Dict]) - Additional data.