Remove unreachable dead code (#1176)

* Remove unreachable dead code

Delete symbols with no callers anywhere in the codebase, tests, or docs,
confirmed by a repo-wide search. These are internal/private or app-layer
(explorer) symbols, not part of the importable library's public API
(no __all__ / package re-export), so there is no user-facing change.

Removed:
- poc_runner.py: parse_import_csv_row (unused nested helper)
- change_management/version_storage.py: create_graph_snapshot_record
- context/graph_schema.py: drop_decision_schema
- explorer/dependencies.py: get_ws_manager (+ now-unused ConnectionManager import)
- explorer/routes/graph.py: _extract_node_embeddings (+ stale cross-ref comment)
- explorer/routes/ontology.py: ProposalState
- explorer/schemas.py: ErrorResponse, TemporalSnapshotResponse, ExportResponse,
  StandardMessageResponse
- semantic_extract/methods.py: _parse_entity_result, _parse_triplet_result
- triplet_store/methods.py: _get_query_engine (+ now-unused _global_query_engine)

Co-Authored-By: Vinv-AI <309466812+Vinv-AI@users.noreply.github.com>

* Address review: drop now-orphaned helper and fix stale docstring

- Remove _coerce_embedding_vector from explorer/routes/graph.py: its only
  non-recursive caller was _extract_node_embeddings (removed in this PR), so
  it is now dead. The live coercion logic lives in
  GraphSession._coerce_embedding_vector.
- Update explorer/dependencies.py module docstring: it no longer injects
  ConnectionManager (get_ws_manager was removed); note that websocket manager
  access is via app.state.ws_manager.

Co-Authored-By: Vinv-AI <309466812+Vinv-AI@users.noreply.github.com>

* Keep public helpers with a DeprecationWarning instead of removing them

create_graph_snapshot_record() and drop_decision_schema() are not
underscore-prefixed, so downstream users can import them directly from
their modules even though they are not re-exported from the package
__init__.py. A repo search only proves there are no in-tree callers.

Restore both unchanged and emit a DeprecationWarning on call, with a
matching ".. deprecated::" note in each docstring pointing at the
replacement. This keeps the PR non-breaking; the actual removal can
happen in a future major version.

The underscore-prefixed helper removals are unaffected.

---------

Co-authored-by: noQbot <noQbot@users.noreply.github.com>
Co-authored-by: Vinv-AI <309466812+Vinv-AI@users.noreply.github.com>
Co-authored-by: noQbot <anshul@vinv.ai>

poc_runner.py

@@ -187,15 +187,6 @@ def poc_vuln3():
             })
         return nodes
 
-    # Simulate the CSV parser — mirrors export_import.py lines 131-133
-    def parse_import_csv_row(row: dict) -> dict:
-        """Mirrors export_import.py CSV node ID extraction (no sanitization)."""
-        node_id = row.get("id") or row.get("node_id") or row.get(":ID") or row.get("_id")
-        return {
-            "id": str(node_id),  # ← UNSANITIZED
-            "type": row.get("type", "entity"),
-        }
-
     # Attack payloads
     payloads = [
         # Header injection payload (chained with VULN-1)

semantica/change_management/version_storage.py

@@ -31,6 +31,7 @@ import hashlib
 import json
 import sqlite3
 import threading
+import warnings
 from abc import ABC, abstractmethod
 from datetime import datetime
 from pathlib import Path
@@ -62,6 +63,12 @@ def create_graph_snapshot_record(
     """
     Creates a standardized snapshot metadata record for a named graph.
 
+    .. deprecated::
+        ``create_graph_snapshot_record()`` is deprecated and will be removed in
+        a future major version. It has no callers inside Semantica; build the
+        record inline and checksum it with
+        :func:`semantica.change_management.compute_checksum` instead.
+
     Args:
         version_id: Unique identifier for this snapshot
         graph_uri: The underlying named graph URI in the triplet store
@@ -69,6 +76,13 @@ def create_graph_snapshot_record(
         description: Purpose or context of the snapshot
         metadata: Additional tags or pipeline context
     """
+    warnings.warn(
+        "create_graph_snapshot_record() is deprecated and will be removed in a "
+        "future major version. Build the snapshot record inline and use "
+        "semantica.change_management.compute_checksum() instead.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
     
     record = {
         "label": version_id,

semantica/context/graph_schema.py

@@ -6,6 +6,7 @@ including node labels, relationship types, and indexes for graph databases.
 """
 
 import json
+import warnings
 from typing import Dict, Any, List
 
 from ..graph_store import GraphStore
@@ -460,11 +461,25 @@ def drop_decision_schema(graph_store: GraphStore) -> None:
     """
     Drop decision tracking schema (for cleanup/testing).
     
+    .. deprecated::
+        ``drop_decision_schema()`` is deprecated and will be removed in a future
+        major version. It has no callers inside Semantica; issue the DROP
+        CONSTRAINT / DROP INDEX / DETACH DELETE statements directly against your
+        :class:`~semantica.graph_store.GraphStore` instead.
+
     Args:
         graph_store: Graph database instance
     """
     logger = get_logger(__name__)
     
+    warnings.warn(
+        "drop_decision_schema() is deprecated and will be removed in a future "
+        "major version. Issue the DROP CONSTRAINT / DROP INDEX / DETACH DELETE "
+        "statements directly against your GraphStore instead.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+    
     try:
         # Drop constraints
         constraints = [

semantica/explorer/dependencies.py

@@ -2,8 +2,9 @@
 Semantica Explorer : FastAPI Dependencies
 
 Provides ``Depends()``-compatible callables for injecting the
-current ``GraphSession`` and ``ConnectionManager`` into route handlers,
+current ``GraphSession`` into route handlers, and for enforcing API-key
-and for enforcing API-key authentication on protected routes.
+authentication on protected routes. WebSocket manager access is handled
+directly via ``app.state.ws_manager``.
 """
 
 import hmac
@@ -14,7 +15,6 @@ from fastapi import Request, HTTPException, Security, status
 from fastapi.security.api_key import APIKeyHeader
 
 from .session import GraphSession
-from .ws import ConnectionManager
 
 _api_key_header = APIKeyHeader(name="X-API-Key", auto_error=False)
 
@@ -80,13 +80,3 @@ def get_session(request: Request) -> GraphSession:
             detail="GraphSession not initialized."
         )
     return request.app.state.session
-
-
-def get_ws_manager(request: Request) -> ConnectionManager:
-    """Retrieve the ConnectionManager stored on ``app.state``."""
-    if not hasattr(request.app.state, "ws_manager") or request.app.state.ws_manager is None:
-        raise HTTPException(
-            status_code=status.HTTP_503_SERVICE_UNAVAILABLE,
-            detail="WebSocket manager not initialized.",
-        )
-    return request.app.state.ws_manager

semantica/explorer/routes/graph.py

@@ -78,66 +78,6 @@ def _parse_bbox(raw_bbox: Optional[str]) -> Optional[tuple[float, float, float,
     return min_x, min_y, max_x, max_y
 
 
-def _coerce_embedding_vector(value: object) -> Optional[List[float]]:
-    if isinstance(value, dict):
-        # Probe keys in priority order: generic first, then framework-specific.
-        # Must stay aligned with the top-level keys in _extract_node_embeddings.
-        for key in ("embedding", "embeddings", "vector", "values", "node2vec", "semantic"):
-            nested = _coerce_embedding_vector(value.get(key))
-            if nested is not None:
-                return nested
-        return None
-
-    if not isinstance(value, (list, tuple)):
-        return None
-
-    vector: List[float] = []
-    for item in value:
-        try:
-            vector.append(float(item))
-        except (TypeError, ValueError):
-            return None
-
-    return vector if vector else None
-
-
-def _extract_node_embeddings(graph_dict: dict) -> dict[str, List[float]]:
-    """Extract embeddings from graph dictionary."""
-    # Top-level keys to probe on each entity (and its metadata/properties dicts).
-    # Priority: generic names first, then KG-extras-specific names.
-    # Must stay aligned with the inner probe list in _coerce_embedding_vector.
-    embedding_keys = (
-        "embedding",
-        "embeddings",
-        "vector",
-        "node_embedding",
-        "node2vec_embedding",
-        "semantic_embedding",
-        "reasoning_embedding",
-    )
-
-    embeddings: dict[str, List[float]] = {}
-    for entity in graph_dict.get("entities") or graph_dict.get("nodes") or []:
-        if not isinstance(entity, dict):
-            continue
-        node_id = entity.get("id") or entity.get("node_id")
-        if not node_id:
-            continue
-
-        metadata = entity.get("metadata") if isinstance(entity.get("metadata"), dict) else {}
-        properties = entity.get("properties") if isinstance(entity.get("properties"), dict) else {}
-
-        for key in embedding_keys:
-            vector = _coerce_embedding_vector(
-                entity.get(key, metadata.get(key, properties.get(key)))
-            )
-            if vector is not None:
-                embeddings[str(node_id)] = vector
-                break
-
-    return embeddings
-
-
 def _get_cached_embeddings(session: GraphSession) -> dict[str, List[float]]:
     """Get embeddings from session cache for optimal performance."""
     return session.get_cached_embeddings()

semantica/explorer/routes/ontology.py

@@ -456,10 +456,6 @@ class DraftResponse(BaseModel):
     updated_at: str
 
 
-class ProposalState(BaseModel):
-    state: Literal["draft", "proposed", "approved", "published", "rejected"]
-
-
 class ProposalRequest(BaseModel):
     draft_id: str
     ontology_uri: str

semantica/explorer/schemas.py

@@ -8,11 +8,6 @@ from typing import Any, Dict, List, Literal, Optional, Tuple
 from pydantic import BaseModel, Field, field_validator
 
 
-class ErrorResponse(BaseModel):
-    detail: str
-    status_code: int = 500
-
-
 class NodeResponse(BaseModel):
     id: str
     type: str
@@ -187,12 +182,6 @@ class ComplianceResponse(BaseModel):
     violations: List[Dict[str, Any]] = Field(default_factory=list)
 
 
-class TemporalSnapshotResponse(BaseModel):
-    timestamp: str
-    active_nodes: List[NodeResponse]
-    active_node_count: int
-
-
 class TemporalDiffResponse(BaseModel):
     from_time: str
     to_time: str
@@ -256,13 +245,6 @@ class ExportRequest(BaseModel):
     node_ids: Optional[List[str]] = None
 
 
-class ExportResponse(BaseModel):
-    format: str
-    content_type: str
-    filename: str
-    size_bytes: int = 0
-
-
 class ImportResponse(BaseModel):
     status: str = "success"
     message: str = "Import successful"
@@ -272,11 +254,6 @@ class ImportResponse(BaseModel):
     edges_imported: Optional[int] = None
 
 
-class StandardMessageResponse(BaseModel):
-    status: str
-    message: str
-
-
 class AnnotationCreate(BaseModel):
     node_id: str
     content: str

semantica/semantic_extract/methods.py

@@ -1124,47 +1124,6 @@ Text to extract from:
         return []
 
 
-def _parse_entity_result(result: Any, provider: str, model: Optional[str]) -> List[Entity]:
-    """Helper to parse raw LLM result into Entity objects."""
-    entities = []
-    items = []
-    
-    if isinstance(result, list):
-        items = result
-    elif isinstance(result, dict):
-        # Handle cases where LLM wraps the list in a key
-        for key in ["entities", "data", "results"]:
-            if key in result and isinstance(result[key], list):
-                items = result[key]
-                break
-        if not items and "text" in result: # Single object instead of list
-            items = [result]
-
-    for item in items:
-        if not isinstance(item, dict):
-            continue
-            
-        text = item.get("text", "")
-        if not text:
-            continue
-            
-        entities.append(
-            Entity(
-                text=text,
-                label=item.get("label", "UNKNOWN"),
-                start_char=item.get("start", 0),
-                end_char=item.get("end", 0),
-                confidence=item.get("confidence", 0.9),
-                metadata={
-                    "provider": provider,
-                    "model": model,
-                    "extraction_method": "llm",
-                },
-            )
-        )
-    return entities
-
-
 def _extract_entities_chunked(
     text: str,
     provider: str,
@@ -2559,48 +2518,6 @@ Text to extract from:
         return []
 
 
-def _parse_triplet_result(result: Any, provider: str, model: Optional[str]) -> List[Triplet]:
-    """Helper to parse raw LLM result into Triplet objects."""
-    triplets = []
-    items = []
-    
-    if isinstance(result, list):
-        items = result
-    elif isinstance(result, dict):
-        for key in ["triplets", "data", "results"]:
-            if key in result and isinstance(result[key], list):
-                items = result[key]
-                break
-        if not items and "subject" in result:
-            items = [result]
-
-    for item in items:
-        if not isinstance(item, dict):
-            continue
-            
-        subject = item.get("subject", "")
-        predicate = item.get("predicate", "")
-        obj = item.get("object", "")
-        
-        if not subject or not predicate or not obj:
-            continue
-            
-        triplets.append(
-            Triplet(
-                subject=str(subject),
-                predicate=str(predicate),
-                object=str(obj),
-                confidence=item.get("confidence", 0.9),
-                metadata={
-                    "provider": provider,
-                    "model": model,
-                    "extraction_method": "llm",
-                },
-            )
-        )
-    return triplets
-
-
 def _extract_triplets_chunked(
     text: str,
     provider: str,

semantica/triplet_store/methods.py

@@ -101,7 +101,6 @@ from .triplet_store import TripletStore
 # Global store registry
 _global_stores: Dict[str, TripletStore] = {}
 _default_store_id: Optional[str] = None
-_global_query_engine: Optional[QueryEngine] = None
 _global_bulk_loader: Optional[BulkLoader] = None
 
 
@@ -131,25 +130,6 @@ def _get_store(store_id: Optional[str] = None) -> TripletStore:
     return _global_stores[target_id]
 
 
-def _get_query_engine() -> QueryEngine:
-    """Get or create global QueryEngine instance."""
-    global _global_query_engine
-    if _global_query_engine is None:
-        # We need a store backend for the engine, but QueryEngine in this module
-        # seems to be initialized with config in the old code.
-        # In the new code, TripletStore has its own query_engine.
-        # If we use this standalone function, we might need to rely on the store's engine.
-        # But let's keep a standalone one if needed, or better, delegate to store.
-        config = triplet_store_config.get_all()
-        # QueryEngine now expects a backend, but we can initialize it without one 
-        # if we pass the backend at execution time? 
-        # Checking QueryEngine implementation... it takes `store_backend` in __init__.
-        # So we can't easily have a global one without a store.
-        # We'll rely on the store's engine.
-        pass
-    return None # Deprecated use of global engine
-
-
 def _get_bulk_loader() -> BulkLoader:
     """Get or create global BulkLoader instance."""
     global _global_bulk_loader