mcp-code-indexer 4.2.16__py3-none-any.whl → 4.2.17__py3-none-any.whl

mcp_code_indexer/database/database.py

@@ -35,7 +35,10 @@ from mcp_code_indexer.database.models import (
     WordFrequencyResult,
     WordFrequencyTerm,
 )
-from mcp_code_indexer.database.retry_executor import create_retry_executor
+from mcp_code_indexer.database.retry_executor import (
+    create_retry_executor,
+    DatabaseLockError,
+)
 from mcp_code_indexer.query_preprocessor import preprocess_search_query
 
 logger = logging.getLogger(__name__)
@@ -54,7 +57,7 @@ class DatabaseManager:
         db_path: Path,
         pool_size: int = 3,
         retry_count: int = 5,
-        timeout: float = 10.0,
+        timeout: float = 30.0,
         enable_wal_mode: bool = True,
         health_check_interval: float = 30.0,
         retry_min_wait: float = 0.1,
@@ -222,7 +225,7 @@ class DatabaseManager:
                 "PRAGMA cache_size = -64000",  # 64MB cache
                 "PRAGMA temp_store = MEMORY",  # Use memory for temp tables
                 "PRAGMA mmap_size = 268435456",  # 256MB memory mapping
-                "PRAGMA busy_timeout = 10000",  # 10s timeout (reduced from 30s)
+                f"PRAGMA busy_timeout = {int(self.timeout * 1000)}",  # Use configured timeout
                 "PRAGMA optimize",  # Enable query planner optimizations
             ]
         )
@@ -490,26 +493,39 @@ class DatabaseManager:
 
                 return result
 
-            except (aiosqlite.OperationalError, asyncio.TimeoutError) as e:
+            except aiosqlite.OperationalError as e:
                 # Record locking event for metrics
-                if self._metrics_collector and "locked" in str(e).lower():
+                error_msg = str(e).lower()
+                if self._metrics_collector and "locked" in error_msg:
                     self._metrics_collector.record_locking_event(operation_name, str(e))
 
-                # Classify the error for better handling
-                classified_error = classify_sqlite_error(e, operation_name)
-
-                # Record failed operation metrics for non-retryable errors
-                if not is_retryable_error(classified_error):
-                    if self._metrics_collector:
-                        self._metrics_collector.record_operation(
-                            operation_name,
-                            timeout_seconds * 1000,
-                            False,
-                            len(self._connection_pool),
-                        )
+                # For retryable errors (locked/busy), re-raise the ORIGINAL error
+                # so tenacity can retry. Only classify non-retryable errors.
+                if "locked" in error_msg or "busy" in error_msg:
+                    raise  # Let tenacity retry this
 
+                # Non-retryable OperationalError - classify and raise
+                classified_error = classify_sqlite_error(e, operation_name)
+                if self._metrics_collector:
+                    self._metrics_collector.record_operation(
+                        operation_name,
+                        timeout_seconds * 1000,
+                        False,
+                        len(self._connection_pool),
+                    )
                 raise classified_error
 
+            except asyncio.TimeoutError as e:
+                # Timeout on BEGIN IMMEDIATE - this is retryable
+                if self._metrics_collector:
+                    self._metrics_collector.record_locking_event(
+                        operation_name, "timeout waiting for lock"
+                    )
+                # Re-raise as OperationalError so tenacity can retry
+                raise aiosqlite.OperationalError(
+                    f"Timeout waiting for database lock: {e}"
+                ) from e
+
         try:
             # Create a temporary retry executor with custom max_retries if different
             # from default
@@ -534,8 +550,27 @@ class DatabaseManager:
                     execute_transaction, operation_name
                 )
 
+        except DatabaseLockError as e:
+            # Retries exhausted - record metrics and convert to DatabaseError
+            if self._metrics_collector:
+                self._metrics_collector.record_operation(
+                    operation_name,
+                    timeout_seconds * 1000,
+                    False,
+                    len(self._connection_pool),
+                )
+            # Convert to a proper DatabaseError for consistent error handling
+            raise DatabaseError(
+                f"Database operation failed after retries: {e.message}",
+                error_context={
+                    "operation": operation_name,
+                    "retry_count": e.retry_count,
+                    "retryable": False,  # Retries already exhausted
+                },
+            ) from e
+
         except DatabaseError:
-            # Record failed operation metrics for final failure
+            # Non-retryable DatabaseError from classification
             if self._metrics_collector:
                 self._metrics_collector.record_operation(
                     operation_name,
@@ -721,7 +756,7 @@ class DatabaseManager:
             cursor = await db.execute("SELECT changes()")
             changes = await cursor.fetchone()
             if changes[0] == 0:
-                raise ValueError(f"Project not found: {project_id}")
+                raise DatabaseError(f"Project not found: {project_id}")
 
             await db.commit()
             logger.debug(f"Set vector_mode={enabled} for project: {project_id}")
@@ -737,12 +772,18 @@ class DatabaseManager:
             projects = []
             for row in rows:
                 aliases = json.loads(row[2]) if row[2] else []
+                created = row[3]
+                last_accessed = row[4]
+                if isinstance(created, str):
+                    created = datetime.fromisoformat(created)
+                if isinstance(last_accessed, str):
+                    last_accessed = datetime.fromisoformat(last_accessed)
                 project = Project(
                     id=row[0],
                     name=row[1],
                     aliases=aliases,
-                    created=row[3],
-                    last_accessed=row[4],
+                    created=created,
+                    last_accessed=last_accessed,
                     vector_mode=bool(row[5]),
                 )
                 projects.append(project)
@@ -760,12 +801,18 @@ class DatabaseManager:
             projects = []
             for row in rows:
                 aliases = json.loads(row[2]) if row[2] else []
+                created = row[3]
+                last_accessed = row[4]
+                if isinstance(created, str):
+                    created = datetime.fromisoformat(created)
+                if isinstance(last_accessed, str):
+                    last_accessed = datetime.fromisoformat(last_accessed)
                 project = Project(
                     id=row[0],
                     name=row[1],
                     aliases=aliases,
-                    created=row[3],
-                    last_accessed=row[4],
+                    created=created,
+                    last_accessed=last_accessed,
                     vector_mode=bool(row[5]),
                 )
                 projects.append(project)
@@ -776,9 +823,7 @@ class DatabaseManager:
 
     async def create_file_description(self, file_desc: FileDescription) -> None:
         """Create or update a file description."""
-        async with self.get_write_connection_with_retry(
-            "create_file_description"
-        ) as db:
+        async def operation(db: aiosqlite.Connection) -> None:
             await db.execute(
                 """
                 INSERT INTO file_descriptions
@@ -806,8 +851,12 @@ class DatabaseManager:
                     file_desc.to_be_cleaned,
                 ),
             )
-            await db.commit()
-            logger.debug(f"Saved file description: {file_desc.file_path}")
+
+        await self.execute_transaction_with_retry(
+            operation,
+            "create_file_description"
+        )
+        logger.debug(f"Saved file description: {file_desc.file_path}")
 
     async def get_file_description(
         self, project_id: str, file_path: str
@@ -1018,7 +1067,7 @@ class DatabaseManager:
 
     async def create_project_overview(self, overview: ProjectOverview) -> None:
         """Create or update a project overview."""
-        async with self.get_write_connection() as db:
+        async def operation(db: aiosqlite.Connection) -> None:
             await db.execute(
                 """
                 INSERT OR REPLACE INTO project_overviews
@@ -1033,8 +1082,12 @@ class DatabaseManager:
                     overview.total_tokens,
                 ),
             )
-            await db.commit()
-            logger.debug(f"Created/updated overview for project {overview.project_id}")
+
+        await self.execute_transaction_with_retry(
+            operation,
+            "create_project_overview"
+        )
+        logger.debug(f"Created/updated overview for project {overview.project_id}")
 
     async def get_project_overview(self, project_id: str) -> Optional[ProjectOverview]:
         """Get project overview by ID."""
@@ -1373,7 +1426,7 @@ class DatabaseManager:
             cursor = await db.execute("SELECT changes()")
             changes = await cursor.fetchone()
             if changes[0] == 0:
-                raise ValueError(
+                raise DatabaseError(
                     f"Index metadata not found for project: {index_meta.project_id}"
                 )
 

mcp_code_indexer/database/database_factory.py

@@ -28,7 +28,7 @@ class DatabaseFactory:
         global_db_path: Path,
         pool_size: int = 3,
         retry_count: int = 5,
-        timeout: float = 10.0,
+        timeout: float = 30.0,
         enable_wal_mode: bool = True,
         health_check_interval: float = 30.0,
         retry_min_wait: float = 0.1,

mcp_code_indexer/database/exceptions.py

@@ -236,7 +236,7 @@ def classify_sqlite_error(error: Exception, operation_name: str = "") -> Databas
         for msg in [
             "no such table",
             "no such column",
-            "table already exists",
+            "already exists",
             "syntax error",
         ]
     ):

mcp_code_indexer/server/mcp_server.py

@@ -13,7 +13,7 @@ import random
 import re
 import time
 import uuid
-from datetime import datetime
+from datetime import datetime, timedelta
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Callable, cast
 
@@ -56,7 +56,7 @@ class MCPCodeIndexServer:
         cache_dir: Optional[Path] = None,
         db_pool_size: int = 3,
         db_retry_count: int = 5,
-        db_timeout: float = 10.0,
+        db_timeout: float = 30.0,
         enable_wal_mode: bool = True,
         health_check_interval: float = 30.0,
         retry_min_wait: float = 0.1,
@@ -882,8 +882,11 @@ class MCPCodeIndexServer:
             all_projects = await db_manager.get_all_projects()
             if all_projects:
                 project = all_projects[0]  # Use the first (and should be only) project
-                # Update last accessed time
-                await db_manager.update_project_access_time(project.id)
+
+                # Update last accessed time only if older than 5 minutes
+                if datetime.utcnow() - project.last_accessed > timedelta(minutes=5):
+                    await db_manager.update_project_access_time(project.id)
+
                 logger.info(
                     f"Using existing local project: {project.name} (ID: {project.id})"
                 )
@@ -1040,8 +1043,9 @@ class MCPCodeIndexServer:
         db_manager: DatabaseManager,
     ) -> None:
         """Update an existing project with new metadata and folder alias."""
-        # Update last accessed time
-        await db_manager.update_project_access_time(project.id)
+        # Update last accessed time only if older than 5 minutes
+        if datetime.utcnow() - project.last_accessed > timedelta(minutes=5):
+            await db_manager.update_project_access_time(project.id)
 
         should_update = False
 

{mcp_code_indexer-4.2.16.dist-info → mcp_code_indexer-4.2.17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mcp-code-indexer
-Version: 4.2.16
+Version: 4.2.17
 Summary: MCP server that tracks file descriptions across codebases, enabling AI agents to efficiently navigate and understand code through searchable summaries and token-aware overviews.
 License: MIT
 License-File: LICENSE
@@ -49,8 +49,8 @@ Description-Content-Type: text/markdown
 
 # MCP Code Indexer 🚀
 
-[![PyPI version](https://badge.fury.io/py/mcp-code-indexer.svg?63)](https://badge.fury.io/py/mcp-code-indexer)
-[![Python](https://img.shields.io/pypi/pyversions/mcp-code-indexer.svg?63)](https://pypi.org/project/mcp-code-indexer/)
+[![PyPI version](https://badge.fury.io/py/mcp-code-indexer.svg?64)](https://badge.fury.io/py/mcp-code-indexer)
+[![Python](https://img.shields.io/pypi/pyversions/mcp-code-indexer.svg?64)](https://pypi.org/project/mcp-code-indexer/)
 [![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 
 A production-ready **Model Context Protocol (MCP) server** that revolutionizes how AI agents navigate and understand codebases. Built for high-concurrency environments with advanced database resilience, the server provides instant access to intelligent descriptions, semantic search, and context-aware recommendations while maintaining 800+ writes/sec throughput.

{mcp_code_indexer-4.2.16.dist-info → mcp_code_indexer-4.2.17.dist-info}/RECORD

@@ -8,9 +8,9 @@ mcp_code_indexer/commands/makelocal.py,sha256=T_44so96jcs1FNlft9E3nAq0LlOzQLhjLd
 mcp_code_indexer/data/stop_words_english.txt,sha256=feRGP8WG5hQPo-wZN5ralJiSv1CGw4h3010NBJnJ0Z8,6344
 mcp_code_indexer/database/__init__.py,sha256=aPq_aaRp0aSwOBIq9GkuMNjmLxA411zg2vhdrAuHm-w,38
 mcp_code_indexer/database/connection_health.py,sha256=jZr3tCbfjUJujdXe_uxtm1N4c31dMV4euiSY4ulamOE,25497
-mcp_code_indexer/database/database.py,sha256=8sLr7fQ4whzOMnAYaKxO2Q7t27Dv_0gyixgBeI6aLXI,55705
-mcp_code_indexer/database/database_factory.py,sha256=zm942m72mqCYTGh1GFyVw-hBsbZcZnx3znJ2ZQPwISM,4316
-mcp_code_indexer/database/exceptions.py,sha256=bamoC-ssw_TMRA5-6lzX6d_1DlcXXrcmiCMBdUEQ9dI,10479
+mcp_code_indexer/database/database.py,sha256=GcXI6p99E4_fo9oMbbZXHIMpYm4Z7y2TdQJgSnZNvMI,57986
+mcp_code_indexer/database/database_factory.py,sha256=VMw0tlutGgZoTI7Q_PCuFy5zAimq2xuMtDFAlF_FKtc,4316
+mcp_code_indexer/database/exceptions.py,sha256=zciu7fDwF8y0Z4tkzTBFPPvXCvdnEJiA-Wd-cBLZBWw,10473
 mcp_code_indexer/database/models.py,sha256=w1U9zMGNt0LQeCiifYeXKW_Cia9BKV5uPChbOve-FZY,13467
 mcp_code_indexer/database/path_resolver.py,sha256=1Ubx6Ly5F2dnvhbdN3tqyowBHslABXpoA6wgL4BQYGo,3461
 mcp_code_indexer/database/retry_executor.py,sha256=r7eKn_xDc6hKz9qs9z9Dg8gyq4uZgnyrgFmQFTyDhdo,14409
@@ -33,7 +33,7 @@ mcp_code_indexer/migrations/005_remove_git_remotes.sql,sha256=vT84AaV1hyN4zq5W67
 mcp_code_indexer/migrations/006_vector_mode.sql,sha256=kN-UBPGoagqtpxpGEjdz-V3hevPAXxAdNmxF4iIPsY8,7448
 mcp_code_indexer/query_preprocessor.py,sha256=vi23sK2ffs4T5PGY7lHrbCBDL421AlPz2dldqX_3JKA,5491
 mcp_code_indexer/server/__init__.py,sha256=16xMcuriUOBlawRqWNBk6niwrvtv_JD5xvI36X1Vsmk,41
-mcp_code_indexer/server/mcp_server.py,sha256=cOFJETze1CzpTq2EieGGKD8Zl3MIRbd3Nepip_L1mfM,84183
+mcp_code_indexer/server/mcp_server.py,sha256=nkm7R_lOnD_XDxk1mEiZgrT6D-G-QIt0g34VHNb1p5g,84424
 mcp_code_indexer/tiktoken_cache/9b5ad71b2ce5302211f9c61530b329a4922fc6a4,sha256=Ijkht27pm96ZW3_3OFE-7xAPtR0YyTWXoRO8_-hlsqc,1681126
 mcp_code_indexer/token_counter.py,sha256=e6WsyCEWMMSkMwLbcVtr5e8vEqh-kFqNmiJErCNdqHE,8220
 mcp_code_indexer/tools/__init__.py,sha256=m01mxML2UdD7y5rih_XNhNSCMzQTz7WQ_T1TeOcYlnE,49
@@ -65,8 +65,8 @@ mcp_code_indexer/vector_mode/services/vector_mode_tools_service.py,sha256=K1_STy
 mcp_code_indexer/vector_mode/services/vector_storage_service.py,sha256=JI3VUc2mG8xZ_YqOvfKJivuMi4imeBLr2UFVrWgDWhk,21193
 mcp_code_indexer/vector_mode/types.py,sha256=M4lUF43FzjiVUezoRqozx_u0g1-xrX9qcRcRn-u65yw,1222
 mcp_code_indexer/vector_mode/utils.py,sha256=XtHrpOw0QJ0EjdzJ85jrbkmHy8Slkq_t7hz-q4RP-10,1283
-mcp_code_indexer-4.2.16.dist-info/METADATA,sha256=lZtjche-WN7CsUsb2eR22tZ0MvYOoxt3LF7IEpQR3zw,27689
-mcp_code_indexer-4.2.16.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
-mcp_code_indexer-4.2.16.dist-info/entry_points.txt,sha256=UABj7HZ0mC6rvF22gxaz2LLNLGQShTrFmp5u00iUtvo,67
-mcp_code_indexer-4.2.16.dist-info/licenses/LICENSE,sha256=JN9dyPPgYwH9C-UjYM7FLNZjQ6BF7kAzpF3_4PwY4rY,1086
-mcp_code_indexer-4.2.16.dist-info/RECORD,,
+mcp_code_indexer-4.2.17.dist-info/METADATA,sha256=hlxYys7f-3mK2L00ZbP7UHyVxBa5AQO1xDw8t5HZ3jo,27689
+mcp_code_indexer-4.2.17.dist-info/WHEEL,sha256=kJCRJT_g0adfAJzTx2GUMmS80rTJIVHRCfG0DQgLq3o,88
+mcp_code_indexer-4.2.17.dist-info/entry_points.txt,sha256=UABj7HZ0mC6rvF22gxaz2LLNLGQShTrFmp5u00iUtvo,67
+mcp_code_indexer-4.2.17.dist-info/licenses/LICENSE,sha256=JN9dyPPgYwH9C-UjYM7FLNZjQ6BF7kAzpF3_4PwY4rY,1086
+mcp_code_indexer-4.2.17.dist-info/RECORD,,

{mcp_code_indexer-4.2.16.dist-info → mcp_code_indexer-4.2.17.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.3.0
+Generator: poetry-core 2.3.1
 Root-Is-Purelib: true
 Tag: py3-none-any