2025-11-21 16:08:38,580 - INFO - Discovered incarnation type: CODE_ANALYSIS_=code_analysis_
2025-11-21 16:08:38,580 - INFO - Added simplified alias: CODE=code_analysis_
2025-11-21 16:08:38,580 - INFO - Discovered incarnation type: CODING_=coding_
2025-11-21 16:08:38,580 - INFO - Added simplified alias: CODING=coding_
2025-11-21 16:08:38,580 - INFO - Discovered incarnation type: DATA_ANALYSIS_=data_analysis_
2025-11-21 16:08:38,580 - INFO - Added simplified alias: DATA=data_analysis_
2025-11-21 16:08:38,580 - INFO - Discovered incarnation type: DECISION_=decision_
2025-11-21 16:08:38,580 - INFO - Added simplified alias: DECISION=decision_
2025-11-21 16:08:38,580 - INFO - Discovered incarnation type: KNOWLEDGE_GRAPH_=knowledge_graph_
2025-11-21 16:08:38,580 - INFO - Added simplified alias: KNOWLEDGE=knowledge_graph_
2025-11-21 16:08:38,580 - INFO - Discovered incarnation type: RESEARCH_=research_
2025-11-21 16:08:38,580 - INFO - Added simplified alias: RESEARCH=research_
2025-11-21 16:08:38,581 - INFO - Discovered incarnation identifiers: ['code_analysis_', 'coding_', 'data_analysis_', 'decision_', 'knowledge_graph_', 'research_']
2025-11-21 16:08:38,581 - INFO - Searching for incarnations in: /home/ty/Repositories/NeoCoder-neo4j-ai-workflow/src/mcp_neocoder/incarnations
2025-11-21 16:08:38,581 - INFO - Found incarnation class via 'name' attribute: CodeAnalysisIncarnation, name: code_analysis
2025-11-21 16:08:38,581 - INFO - Registered incarnation: code_analysis (CodeAnalysisIncarnation)
2025-11-21 16:08:38,581 - INFO - Found incarnation class via 'name' attribute: CodingIncarnation, name: coding
2025-11-21 16:08:38,581 - INFO - Registered incarnation: coding (CodingIncarnation)
2025-11-21 16:08:39,528 - INFO - Found incarnation class via 'name' attribute: DataAnalysisIncarnation, name: data_analysis
2025-11-21 16:08:39,528 - INFO - Registered incarnation: data_analysis (DataAnalysisIncarnation)
2025-11-21 16:08:39,529 - INFO - Found incarnation class via 'name' attribute: DecisionIncarnation, name: decision_support
2025-11-21 16:08:39,529 - INFO - Registered incarnation: decision_support (DecisionIncarnation)
2025-11-21 16:08:39,529 - INFO - Found incarnation class via 'name' attribute: KnowledgeGraphIncarnation, name: knowledge_graph
2025-11-21 16:08:39,529 - INFO - Registered incarnation: knowledge_graph (KnowledgeGraphIncarnation)
2025-11-21 16:08:39,530 - INFO - Found incarnation class via 'name' attribute: ResearchIncarnation, name: research_orchestration
2025-11-21 16:08:39,530 - INFO - Registered incarnation: research_orchestration (ResearchIncarnation)
2025-11-21 16:08:39,531 - INFO - Registered signal handlers for SIGTERM and SIGINT
2025-11-21 16:08:39,531 - INFO - Registered atexit cleanup handler
2025-11-21 16:08:39,531 - INFO - Process cleanup handlers registered
2025-11-21 16:08:39,531 - INFO - Scanning for zombie NeoCoder MCP server instances...
2025-11-21 16:08:39,601 - INFO - No zombie processes found
2025-11-21 16:08:39,602 - INFO - NEO4J_URL from environment: bolt://localhost:7687
2025-11-21 16:08:39,602 - INFO - NEO4J_USERNAME from environment: neo4j
2025-11-21 16:08:39,602 - INFO - NEO4J_PASSWORD from environment: Set
2025-11-21 16:08:39,602 - INFO - NEO4J_DATABASE from environment: neo4j
2025-11-21 16:08:39,602 - INFO - Starting NeoCoder MCP Server
2025-11-21 16:08:39,602 - INFO - Starting NeoCoder Neo4j Workflow Server
2025-11-21 16:08:39,602 - INFO - Scanning for zombie NeoCoder MCP server instances...
2025-11-21 16:08:39,653 - INFO - No zombie processes found
2025-11-21 16:08:39,654 - INFO - Loaded environment variables from .env file
2025-11-21 16:08:39,654 - INFO - Set log level to DEBUG
2025-11-21 16:08:39,654 - INFO - Neo4j connection: bolt://localhost:7687, database: neo4j
2025-11-21 16:08:39,655 - INFO - Using existing event loop
2025-11-21 16:08:39,655 - DEBUG - Found event loop for current thread
2025-11-21 16:08:39,655 - INFO - Initializing main event loop for Neo4j operations
2025-11-21 16:08:39,655 - INFO - Initialized main event loop for Neo4j operations
2025-11-21 16:08:39,655 - INFO - Creating Neo4j driver (URL: bolt://localhost:7687, database: neo4j)
2025-11-21 16:08:39,656 - DEBUG - Tracking Neo4j driver, total: 1
2025-11-21 16:08:40,312 - INFO - HTTP Request: GET http://localhost:6333 "HTTP/1.1 200 OK"
2025-11-21 16:08:40,312 - INFO - Qdrant client initialized successfully
2025-11-21 16:08:40,312 - INFO - No running event loop - will create server with async setup
2025-11-21 16:08:40,312 - INFO - No running loop - using run_until_complete for setup
2025-11-21 16:08:40,312 - DEBUG - Tracking Neo4j session, total: 1
2025-11-21 16:08:40,359 - INFO - Neo4j driver connection verified successfully
2025-11-21 16:08:40,359 - DEBUG - Untracked Neo4j session, remaining: 0
2025-11-21 16:08:40,359 - DEBUG - Cleanup handlers already registered
2025-11-21 16:08:40,359 - INFO - Cleanup handlers registered
2025-11-21 16:08:40,359 - DEBUG - Tracking Neo4j driver, total: 1
2025-11-21 16:08:40,365 - INFO - Basic protocol handlers registered
2025-11-21 16:08:40,365 - INFO - Neo4jWorkflowServer created successfully
2025-11-21 16:08:40,365 - INFO - Waiting for server initialization to complete...
2025-11-21 16:08:40,367 - INFO - Registered basic protocol handlers via direct attribute assignment
2025-11-21 16:08:40,367 - INFO - Checking database initialization status
2025-11-21 16:08:40,367 - DEBUG - Tracking Neo4j session, total: 1
2025-11-21 16:08:40,375 - WARNING - Received notification from DBMS server: {severity: WARNING} {code: Neo.ClientNotification.Statement.UnknownLabelWarning} {category: UNRECOGNIZED} {title: The provided label is not in the database.} {description: One of the labels in your query is not available in the database, make sure you didn't misspell it or that the label is available when you run this statement in your application (the missing label name is: ActionTemplate)} {position: line: 1, column: 10, offset: 9} for query: 'MATCH (t:ActionTemplate) RETURN count(t) > 0 as exists'
2025-11-21 16:08:40,376 - DEBUG - Untracked Neo4j session, remaining: 0
2025-11-21 16:08:40,376 - INFO - Database needs initialization, running setup
2025-11-21 16:08:40,376 - INFO - Discovered incarnation name: code_analysis from code_analysis_incarnation.py
2025-11-21 16:08:40,376 - INFO - Discovered incarnation name: coding from coding_incarnation.py
2025-11-21 16:08:40,376 - INFO - Discovered incarnation name: data_analysis from data_analysis_incarnation.py
2025-11-21 16:08:40,376 - INFO - Discovered incarnation name: decision from decision_incarnation.py
2025-11-21 16:08:40,376 - INFO - Discovered incarnation name: knowledge_graph from knowledge_graph_incarnation.py
2025-11-21 16:08:40,376 - INFO - Discovered incarnation name: research from research_incarnation.py
2025-11-21 16:08:40,376 - INFO - Discovered incarnation types: ['code_analysis', 'coding', 'data_analysis', 'decision', 'knowledge_graph', 'research']
2025-11-21 16:08:40,376 - DEBUG - Tracking Neo4j session, total: 1
2025-11-21 16:08:40,420 - DEBUG - Untracked Neo4j session, remaining: 0
2025-11-21 16:08:40,420 - INFO - Successfully connected to Neo4j
2025-11-21 16:08:40,420 - INFO - Initializing base schema...
2025-11-21 16:08:40,421 - DEBUG - Tracking Neo4j session, total: 1
2025-11-21 16:08:40,422 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT hub_id IF NOT EXISTS FOR (e:AiGuidanceHub) REQUIRE (e.id) IS UNIQUE` has no effect.} {description: `CONSTRAINT hub_id FOR (e:AiGuidanceHub) REQUIRE (e.id) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT hub_id IF NOT EXISTS FOR (hub:AiGuidanceHub) REQUIRE hub.id IS UNIQUE'
2025-11-21 16:08:40,424 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT proposal_id IF NOT EXISTS FOR (e:ToolProposal) REQUIRE (e.id) IS UNIQUE` has no effect.} {description: `CONSTRAINT proposal_id FOR (e:ToolProposal) REQUIRE (e.id) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT proposal_id IF NOT EXISTS FOR (p:ToolProposal) REQUIRE p.id IS UNIQUE'
2025-11-21 16:08:40,425 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT request_id IF NOT EXISTS FOR (e:ToolRequest) REQUIRE (e.id) IS UNIQUE` has no effect.} {description: `CONSTRAINT request_id FOR (e:ToolRequest) REQUIRE (e.id) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT request_id IF NOT EXISTS FOR (r:ToolRequest) REQUIRE r.id IS UNIQUE'
2025-11-21 16:08:40,426 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT snippet_id IF NOT EXISTS FOR (e:CypherSnippet) REQUIRE (e.id) IS UNIQUE` has no effect.} {description: `CONSTRAINT snippet_id FOR (e:CypherSnippet) REQUIRE (e.id) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT snippet_id IF NOT EXISTS FOR (s:CypherSnippet) REQUIRE s.id IS UNIQUE'
2025-11-21 16:08:40,428 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT tag_name IF NOT EXISTS FOR (e:Tag) REQUIRE (e.name) IS UNIQUE` has no effect.} {description: `CONSTRAINT tag_name FOR (e:Tag) REQUIRE (e.name) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT tag_name IF NOT EXISTS FOR (t:Tag) REQUIRE t.name IS UNIQUE'
2025-11-21 16:08:40,430 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE RANGE INDEX hub_type IF NOT EXISTS FOR (e:AiGuidanceHub) ON (e.type)` has no effect.} {description: `RANGE INDEX hub_type FOR (e:AiGuidanceHub) ON (e.type)` already exists.} {position: None} for query: 'CREATE INDEX hub_type IF NOT EXISTS FOR (hub:AiGuidanceHub) ON (hub.type)'
2025-11-21 16:08:40,431 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE RANGE INDEX proposal_status IF NOT EXISTS FOR (e:ToolProposal) ON (e.status)` has no effect.} {description: `RANGE INDEX proposal_status FOR (e:ToolProposal) ON (e.status)` already exists.} {position: None} for query: 'CREATE INDEX proposal_status IF NOT EXISTS FOR (p:ToolProposal) ON (p.status)'
2025-11-21 16:08:40,433 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE RANGE INDEX request_status IF NOT EXISTS FOR (e:ToolRequest) ON (e.status)` has no effect.} {description: `RANGE INDEX request_status FOR (e:ToolRequest) ON (e.status)` already exists.} {position: None} for query: 'CREATE INDEX request_status IF NOT EXISTS FOR (r:ToolRequest) ON (r.status)'
2025-11-21 16:08:40,434 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE RANGE INDEX snippet_name IF NOT EXISTS FOR (e:CypherSnippet) ON (e.name)` has no effect.} {description: `RANGE INDEX snippet_name FOR (e:CypherSnippet) ON (e.name)` already exists.} {position: None} for query: 'CREATE INDEX snippet_name IF NOT EXISTS FOR (s:CypherSnippet) ON (s.name)'
2025-11-21 16:08:40,435 - DEBUG - Untracked Neo4j session, remaining: 0
2025-11-21 16:08:40,435 - INFO - Base schema initialized successfully
2025-11-21 16:08:40,435 - INFO - Initializing research schema...
2025-11-21 16:08:40,435 - DEBUG - Tracking Neo4j session, total: 1
2025-11-21 16:08:40,436 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT research_hypothesis_id IF NOT EXISTS FOR (e:Hypothesis) REQUIRE (e.id) IS UNIQUE` has no effect.} {description: `CONSTRAINT research_hypothesis_id FOR (e:Hypothesis) REQUIRE (e.id) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT research_hypothesis_id IF NOT EXISTS FOR (h:Hypothesis) REQUIRE h.id IS UNIQUE'
2025-11-21 16:08:40,438 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT research_experiment_id IF NOT EXISTS FOR (e:Experiment) REQUIRE (e.id) IS UNIQUE` has no effect.} {description: `CONSTRAINT research_experiment_id FOR (e:Experiment) REQUIRE (e.id) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT research_experiment_id IF NOT EXISTS FOR (e:Experiment) REQUIRE e.id IS UNIQUE'
2025-11-21 16:08:40,439 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT research_protocol_id IF NOT EXISTS FOR (e:Protocol) REQUIRE (e.id) IS UNIQUE` has no effect.} {description: `CONSTRAINT research_protocol_id FOR (e:Protocol) REQUIRE (e.id) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT research_protocol_id IF NOT EXISTS FOR (p:Protocol) REQUIRE p.id IS UNIQUE'
2025-11-21 16:08:40,441 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT research_observation_id IF NOT EXISTS FOR (e:Observation) REQUIRE (e.id) IS UNIQUE` has no effect.} {description: `CONSTRAINT research_observation_id FOR (e:Observation) REQUIRE (e.id) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT research_observation_id IF NOT EXISTS FOR (o:Observation) REQUIRE o.id IS UNIQUE'
2025-11-21 16:08:40,442 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT research_run_id IF NOT EXISTS FOR (e:Run) REQUIRE (e.id) IS UNIQUE` has no effect.} {description: `CONSTRAINT research_run_id FOR (e:Run) REQUIRE (e.id) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT research_run_id IF NOT EXISTS FOR (r:Run) REQUIRE r.id IS UNIQUE'
2025-11-21 16:08:40,444 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE RANGE INDEX research_hypothesis_status IF NOT EXISTS FOR (e:Hypothesis) ON (e.status)` has no effect.} {description: `RANGE INDEX research_hypothesis_status FOR (e:Hypothesis) ON (e.status)` already exists.} {position: None} for query: 'CREATE INDEX research_hypothesis_status IF NOT EXISTS FOR (h:Hypothesis) ON (h.status)'
2025-11-21 16:08:40,445 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE RANGE INDEX research_experiment_status IF NOT EXISTS FOR (e:Experiment) ON (e.status)` has no effect.} {description: `RANGE INDEX research_experiment_status FOR (e:Experiment) ON (e.status)` already exists.} {position: None} for query: 'CREATE INDEX research_experiment_status IF NOT EXISTS FOR (e:Experiment) ON (e.status)'
2025-11-21 16:08:40,446 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE RANGE INDEX research_protocol_name IF NOT EXISTS FOR (e:Protocol) ON (e.name)` has no effect.} {description: `RANGE INDEX research_protocol_name FOR (e:Protocol) ON (e.name)` already exists.} {position: None} for query: 'CREATE INDEX research_protocol_name IF NOT EXISTS FOR (p:Protocol) ON (p.name)'
2025-11-21 16:08:40,448 - DEBUG - Untracked Neo4j session, remaining: 0
2025-11-21 16:08:40,448 - INFO - Research schema initialized successfully
2025-11-21 16:08:40,448 - INFO - Initializing decision support schema...
2025-11-21 16:08:40,448 - DEBUG - Tracking Neo4j session, total: 1
2025-11-21 16:08:40,450 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT decision_id IF NOT EXISTS FOR (e:Decision) REQUIRE (e.id) IS UNIQUE` has no effect.} {description: `CONSTRAINT decision_id FOR (e:Decision) REQUIRE (e.id) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT decision_id IF NOT EXISTS FOR (d:Decision) REQUIRE d.id IS UNIQUE'
2025-11-21 16:08:40,451 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT alternative_id IF NOT EXISTS FOR (e:Alternative) REQUIRE (e.id) IS UNIQUE` has no effect.} {description: `CONSTRAINT alternative_id FOR (e:Alternative) REQUIRE (e.id) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT alternative_id IF NOT EXISTS FOR (a:Alternative) REQUIRE a.id IS UNIQUE'
2025-11-21 16:08:40,452 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT metric_id IF NOT EXISTS FOR (e:Metric) REQUIRE (e.id) IS UNIQUE` has no effect.} {description: `CONSTRAINT metric_id FOR (e:Metric) REQUIRE (e.id) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT metric_id IF NOT EXISTS FOR (m:Metric) REQUIRE m.id IS UNIQUE'
2025-11-21 16:08:40,454 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE CONSTRAINT evidence_id IF NOT EXISTS FOR (e:Evidence) REQUIRE (e.id) IS UNIQUE` has no effect.} {description: `CONSTRAINT evidence_id FOR (e:Evidence) REQUIRE (e.id) IS UNIQUE` already exists.} {position: None} for query: 'CREATE CONSTRAINT evidence_id IF NOT EXISTS FOR (e:Evidence) REQUIRE e.id IS UNIQUE'
2025-11-21 16:08:40,455 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE RANGE INDEX decision_status IF NOT EXISTS FOR (e:Decision) ON (e.status)` has no effect.} {description: `RANGE INDEX decision_status FOR (e:Decision) ON (e.status)` already exists.} {position: None} for query: 'CREATE INDEX decision_status IF NOT EXISTS FOR (d:Decision) ON (d.status)'
2025-11-21 16:08:40,456 - INFO - Received notification from DBMS server: {severity: INFORMATION} {code: Neo.ClientNotification.Schema.IndexOrConstraintAlreadyExists} {category: SCHEMA} {title: `CREATE RANGE INDEX alternative_name IF NOT EXISTS FOR (e:Alternative) ON (e.name)` has no effect.} {description: `RANGE INDEX alternative_name FOR (e:Alternative) ON (e.name)` already exists.} {position: None} for query: 'CREATE INDEX alternative_name IF NOT EXISTS FOR (a:Alternative) ON (a.name)'
2025-11-21 16:08:40,458 - DEBUG - Untracked Neo4j session, remaining: 0
2025-11-21 16:08:40,458 - INFO - Decision schema initialized successfully
2025-11-21 16:08:40,458 - INFO - Creating basic schema for incarnation: code_analysis
2025-11-21 16:08:40,459 - DEBUG - Tracking Neo4j session, total: 1
2025-11-21 16:08:40,460 - INFO - Created hub for code_analysis
2025-11-21 16:08:40,461 - DEBUG - Untracked Neo4j session, remaining: 0
2025-11-21 16:08:40,461 - INFO - Creating basic schema for incarnation: coding
2025-11-21 16:08:40,461 - DEBUG - Tracking Neo4j session, total: 1
2025-11-21 16:08:40,462 - INFO - Created hub for coding
2025-11-21 16:08:40,463 - DEBUG - Untracked Neo4j session, remaining: 0
2025-11-21 16:08:40,463 - INFO - Creating basic schema for incarnation: data_analysis
2025-11-21 16:08:40,463 - DEBUG - Tracking Neo4j session, total: 1
2025-11-21 16:08:40,464 - INFO - Created hub for data_analysis
2025-11-21 16:08:40,465 - DEBUG - Untracked Neo4j session, remaining: 0
2025-11-21 16:08:40,465 - INFO - Creating basic schema for incarnation: knowledge_graph
2025-11-21 16:08:40,465 - DEBUG - Tracking Neo4j session, total: 1
2025-11-21 16:08:40,466 - INFO - Created hub for knowledge_graph
2025-11-21 16:08:40,467 - DEBUG - Untracked Neo4j session, remaining: 0
2025-11-21 16:08:40,467 - INFO - Creating main guidance hub...
2025-11-21 16:08:40,467 - DEBUG - Tracking Neo4j session, total: 1
2025-11-21 16:08:40,469 - DEBUG - Untracked Neo4j session, remaining: 0
2025-11-21 16:08:40,469 - INFO - Main guidance hub created successfully
2025-11-21 16:08:40,469 - INFO - Creating dynamic links between hubs...
2025-11-21 16:08:40,469 - DEBUG - Tracking Neo4j session, total: 1
2025-11-21 16:08:40,473 - INFO - Created link for incarnation: code_analysis
2025-11-21 16:08:40,475 - INFO - Created link for incarnation: coding
2025-11-21 16:08:40,477 - INFO - Created link for incarnation: data_analysis
2025-11-21 16:08:40,479 - INFO - Created link for incarnation: decision
2025-11-21 16:08:40,481 - INFO - Created link for incarnation: knowledge_graph
2025-11-21 16:08:40,483 - INFO - Created link for incarnation: research
2025-11-21 16:08:40,484 - DEBUG - Untracked Neo4j session, remaining: 0
2025-11-21 16:08:40,484 - INFO - Hub links created successfully
2025-11-21 16:08:40,484 - INFO - Database initialization complete!
2025-11-21 16:08:40,484 - INFO - Database initialization completed
2025-11-21 16:08:40,484 - INFO - Database initialization completed successfully
2025-11-21 16:08:40,484 - INFO - Registered tool 'get_guidance_hub' in category 'navigation'
2025-11-21 16:08:40,484 - INFO - Registered tool 'list_action_templates' in category 'navigation'
2025-11-21 16:08:40,484 - INFO - Registered tool 'get_action_template' in category 'navigation'
2025-11-21 16:08:40,484 - INFO - Registered tool 'get_best_practices' in category 'navigation'
2025-11-21 16:08:40,484 - INFO - Registered tool 'suggest_tool' in category 'navigation'
2025-11-21 16:08:40,484 - INFO - Registered tool 'get_project' in category 'project'
2025-11-21 16:08:40,484 - INFO - Registered tool 'list_projects' in category 'project'
2025-11-21 16:08:40,484 - INFO - Registered tool 'log_workflow_execution' in category 'workflow'
2025-11-21 16:08:40,484 - INFO - Registered tool 'get_workflow_history' in category 'workflow'
2025-11-21 16:08:40,484 - INFO - Registered tool 'add_template_feedback' in category 'workflow'
2025-11-21 16:08:40,484 - INFO - Registered tool 'run_custom_query' in category 'query'
2025-11-21 16:08:40,484 - INFO - Registered tool 'write_neo4j_cypher' in category 'query'
2025-11-21 16:08:40,484 - INFO - Registered tool 'check_connection' in category 'query'
2025-11-21 16:08:40,484 - INFO - Registered tool 'list_cypher_snippets' in category 'cypher'
2025-11-21 16:08:40,484 - INFO - Registered tool 'get_cypher_snippet' in category 'cypher'
2025-11-21 16:08:40,484 - INFO - Registered tool 'search_cypher_snippets' in category 'cypher'
2025-11-21 16:08:40,484 - INFO - Registered tool 'create_cypher_snippet' in category 'cypher'
2025-11-21 16:08:40,484 - INFO - Registered tool 'update_cypher_snippet' in category 'cypher'
2025-11-21 16:08:40,484 - INFO - Registered tool 'delete_cypher_snippet' in category 'cypher'
2025-11-21 16:08:40,484 - INFO - Registered tool 'get_cypher_tags' in category 'cypher'
2025-11-21 16:08:40,484 - INFO - Registered tool 'propose_tool' in category 'proposal'
2025-11-21 16:08:40,485 - INFO - Registered tool 'request_tool' in category 'proposal'
2025-11-21 16:08:40,485 - INFO - Registered tool 'get_tool_proposal' in category 'proposal'
2025-11-21 16:08:40,485 - INFO - Registered tool 'get_tool_request' in category 'proposal'
2025-11-21 16:08:40,485 - INFO - Registered tool 'list_tool_proposals' in category 'proposal'
2025-11-21 16:08:40,485 - INFO - Registered tool 'list_tool_requests' in category 'proposal'
2025-11-21 16:08:40,485 - INFO - Registered tool 'get_current_incarnation' in category 'incarnation'
2025-11-21 16:08:40,485 - INFO - Registered tool 'list_incarnations' in category 'incarnation'
2025-11-21 16:08:40,485 - INFO - Registered tool 'switch_incarnation' in category 'incarnation'
2025-11-21 16:08:40,485 - INFO - Registered tool 'get_cleanup_status' in category 'monitoring'
2025-11-21 16:08:40,485 - INFO - Registered all core tools with ToolRegistry
2025-11-21 16:08:40,485 - INFO - Core tools registered
2025-11-21 16:08:40,485 - INFO - Discovering available incarnation classes
2025-11-21 16:08:40,485 - INFO - Discovered incarnation type: CODE_ANALYSIS_=code_analysis_
2025-11-21 16:08:40,485 - INFO - Added simplified alias: CODE=code_analysis_
2025-11-21 16:08:40,485 - INFO - Discovered incarnation type: CODING_=coding_
2025-11-21 16:08:40,485 - INFO - Added simplified alias: CODING=coding_
2025-11-21 16:08:40,485 - INFO - Discovered incarnation type: DATA_ANALYSIS_=data_analysis_
2025-11-21 16:08:40,485 - INFO - Added simplified alias: DATA=data_analysis_
2025-11-21 16:08:40,485 - INFO - Discovered incarnation type: DECISION_=decision_
2025-11-21 16:08:40,485 - INFO - Added simplified alias: DECISION=decision_
2025-11-21 16:08:40,485 - INFO - Discovered incarnation type: KNOWLEDGE_GRAPH_=knowledge_graph_
2025-11-21 16:08:40,485 - INFO - Added simplified alias: KNOWLEDGE=knowledge_graph_
2025-11-21 16:08:40,485 - INFO - Discovered incarnation type: RESEARCH_=research_
2025-11-21 16:08:40,485 - INFO - Added simplified alias: RESEARCH=research_
2025-11-21 16:08:40,485 - INFO - Discovered incarnation identifiers: ['code_analysis_', 'coding_', 'data_analysis_', 'decision_', 'knowledge_graph_', 'research_']
2025-11-21 16:08:40,485 - INFO - Searching for incarnations in: /home/ty/Repositories/NeoCoder-neo4j-ai-workflow/src/mcp_neocoder/incarnations
2025-11-21 16:08:40,485 - DEBUG - Module code_analysis_incarnation already loaded, skipping
2025-11-21 16:08:40,485 - DEBUG - Module coding_incarnation already loaded, skipping
2025-11-21 16:08:40,485 - DEBUG - Module data_analysis_incarnation already loaded, skipping
2025-11-21 16:08:40,485 - DEBUG - Module decision_incarnation already loaded, skipping
2025-11-21 16:08:40,485 - DEBUG - Module knowledge_graph_incarnation already loaded, skipping
2025-11-21 16:08:40,485 - DEBUG - Module research_incarnation already loaded, skipping
2025-11-21 16:08:40,485 - INFO - Registering 6 incarnations with server
2025-11-21 16:08:40,485 - INFO - Attempting to register incarnation: code_analysis (CodeAnalysisIncarnation)
2025-11-21 16:08:40,485 - INFO - Registered incarnation: code_analysis -> CodeAnalysisIncarnation
2025-11-21 16:08:40,485 - INFO - Registered incarnation: code_analysis (CodeAnalysisIncarnation)
2025-11-21 16:08:40,485 - INFO - Created instance of CodeAnalysisIncarnation
2025-11-21 16:08:40,485 - DEBUG - Checking methods in CodeAnalysisIncarnation
2025-11-21 16:08:40,485 - INFO - Using predefined tool list for CodeAnalysisIncarnation: ['analyze_codebase', 'analyze_file', 'compare_versions', 'find_code_smells', 'generate_documentation', 'explore_code_structure', 'search_code_constructs']
2025-11-21 16:08:40,485 - INFO - Found 7 tool methods in code_analysis (will register later)
2025-11-21 16:08:40,485 - INFO - Attempting to register incarnation: coding (CodingIncarnation)
2025-11-21 16:08:40,485 - INFO - Registered incarnation: coding -> CodingIncarnation
2025-11-21 16:08:40,485 - INFO - Registered incarnation: coding (CodingIncarnation)
2025-11-21 16:08:40,485 - INFO - Created instance of CodingIncarnation
2025-11-21 16:08:40,485 - DEBUG - Checking methods in CodingIncarnation
2025-11-21 16:08:40,485 - INFO - Using predefined tool list for CodingIncarnation: []
2025-11-21 16:08:40,485 - INFO - Found 0 tool methods in coding (will register later)
2025-11-21 16:08:40,485 - INFO - Attempting to register incarnation: data_analysis (DataAnalysisIncarnation)
2025-11-21 16:08:40,485 - INFO - Registered incarnation: data_analysis -> DataAnalysisIncarnation
2025-11-21 16:08:40,485 - INFO - Registered incarnation: data_analysis (DataAnalysisIncarnation)
2025-11-21 16:08:40,486 - INFO - Created instance of DataAnalysisIncarnation
2025-11-21 16:08:40,486 - INFO - Found 16 tool methods in data_analysis (will register later)
2025-11-21 16:08:40,486 - INFO - Attempting to register incarnation: decision_support (DecisionIncarnation)
2025-11-21 16:08:40,486 - INFO - Registered incarnation: decision_support -> DecisionIncarnation
2025-11-21 16:08:40,486 - INFO - Registered incarnation: decision_support (DecisionIncarnation)
2025-11-21 16:08:40,486 - INFO - Created instance of DecisionIncarnation
2025-11-21 16:08:40,486 - DEBUG - Checking methods in DecisionIncarnation
2025-11-21 16:08:40,486 - INFO - Using predefined tool list for DecisionIncarnation: ['create_decision', 'list_decisions', 'get_decision', 'add_alternative', 'add_metric', 'add_evidence']
2025-11-21 16:08:40,486 - INFO - Found 6 tool methods in decision_support (will register later)
2025-11-21 16:08:40,486 - INFO - Attempting to register incarnation: knowledge_graph (KnowledgeGraphIncarnation)
2025-11-21 16:08:40,486 - INFO - Registered incarnation: knowledge_graph -> KnowledgeGraphIncarnation
2025-11-21 16:08:40,486 - INFO - Registered incarnation: knowledge_graph (KnowledgeGraphIncarnation)
2025-11-21 16:08:40,486 - INFO - Created instance of KnowledgeGraphIncarnation
2025-11-21 16:08:40,486 - DEBUG - Checking methods in KnowledgeGraphIncarnation
2025-11-21 16:08:40,486 - INFO - Using predefined tool list for KnowledgeGraphIncarnation: ['create_entities', 'create_relations', 'add_observations', 'add_single_observation', 'delete_entities', 'delete_observations', 'delete_relations', 'read_graph', 'search_nodes', 'open_nodes']
2025-11-21 16:08:40,486 - INFO - Found 10 tool methods in knowledge_graph (will register later)
2025-11-21 16:08:40,486 - INFO - Attempting to register incarnation: research_orchestration (ResearchIncarnation)
2025-11-21 16:08:40,486 - INFO - Registered incarnation: research_orchestration -> ResearchIncarnation
2025-11-21 16:08:40,486 - INFO - Registered incarnation: research_orchestration (ResearchIncarnation)
2025-11-21 16:08:40,486 - INFO - Created instance of ResearchIncarnation
2025-11-21 16:08:40,486 - DEBUG - Checking methods in ResearchIncarnation
2025-11-21 16:08:40,486 - INFO - Using predefined tool list for ResearchIncarnation: ['register_hypothesis', 'list_hypotheses', 'get_hypothesis', 'update_hypothesis', 'create_protocol', 'list_protocols', 'get_protocol', 'create_experiment', 'list_experiments', 'get_experiment', 'update_experiment', 'record_observation', 'list_observations', 'compute_statistics', 'create_publication_draft']
2025-11-21 16:08:40,486 - INFO - Found 15 tool methods in research_orchestration (will register later)
2025-11-21 16:08:40,486 - INFO - Loaded 6 incarnations successfully
2025-11-21 16:08:40,486 - INFO - Incarnations loaded
2025-11-21 16:08:40,486 - INFO - Registering tools from all incarnations...
2025-11-21 16:08:40,486 - INFO - Registering core tools with MCP server...
2025-11-21 16:08:40,486 - DEBUG - Tools available for registration: ['get_guidance_hub', 'list_action_templates', 'get_action_template', 'get_best_practices', 'suggest_tool', 'get_project', 'list_projects', 'log_workflow_execution', 'get_workflow_history', 'add_template_feedback', 'run_custom_query', 'write_neo4j_cypher', 'check_connection', 'list_cypher_snippets', 'get_cypher_snippet', 'search_cypher_snippets', 'create_cypher_snippet', 'update_cypher_snippet', 'delete_cypher_snippet', 'get_cypher_tags', 'propose_tool', 'request_tool', 'get_tool_proposal', 'get_tool_request', 'list_tool_proposals', 'list_tool_requests', 'get_current_incarnation', 'list_incarnations', 'switch_incarnation', 'get_cleanup_status']
2025-11-21 16:08:40,487 - INFO - Added tool 'get_guidance_hub' to MCP server
2025-11-21 16:08:40,488 - INFO - Added tool 'list_action_templates' to MCP server
2025-11-21 16:08:40,488 - INFO - Added tool 'get_action_template' to MCP server
2025-11-21 16:08:40,489 - INFO - Added tool 'get_best_practices' to MCP server
2025-11-21 16:08:40,490 - INFO - Added tool 'suggest_tool' to MCP server
2025-11-21 16:08:40,490 - INFO - Added tool 'get_project' to MCP server
2025-11-21 16:08:40,491 - INFO - Added tool 'list_projects' to MCP server
2025-11-21 16:08:40,493 - INFO - Added tool 'log_workflow_execution' to MCP server
2025-11-21 16:08:40,494 - INFO - Added tool 'get_workflow_history' to MCP server
2025-11-21 16:08:40,495 - INFO - Added tool 'add_template_feedback' to MCP server
2025-11-21 16:08:40,496 - INFO - Added tool 'run_custom_query' to MCP server
2025-11-21 16:08:40,497 - INFO - Added tool 'write_neo4j_cypher' to MCP server
2025-11-21 16:08:40,497 - INFO - Added tool 'check_connection' to MCP server
2025-11-21 16:08:40,498 - INFO - Added tool 'list_cypher_snippets' to MCP server
2025-11-21 16:08:40,499 - INFO - Added tool 'get_cypher_snippet' to MCP server
2025-11-21 16:08:40,500 - INFO - Added tool 'search_cypher_snippets' to MCP server
2025-11-21 16:08:40,501 - INFO - Added tool 'create_cypher_snippet' to MCP server
2025-11-21 16:08:40,503 - INFO - Added tool 'update_cypher_snippet' to MCP server
2025-11-21 16:08:40,503 - INFO - Added tool 'delete_cypher_snippet' to MCP server
2025-11-21 16:08:40,504 - INFO - Added tool 'get_cypher_tags' to MCP server
2025-11-21 16:08:40,505 - INFO - Added tool 'propose_tool' to MCP server
2025-11-21 16:08:40,506 - INFO - Added tool 'request_tool' to MCP server
2025-11-21 16:08:40,507 - INFO - Added tool 'get_tool_proposal' to MCP server
2025-11-21 16:08:40,507 - INFO - Added tool 'get_tool_request' to MCP server
2025-11-21 16:08:40,508 - INFO - Added tool 'list_tool_proposals' to MCP server
2025-11-21 16:08:40,509 - INFO - Added tool 'list_tool_requests' to MCP server
2025-11-21 16:08:40,510 - INFO - Added tool 'get_current_incarnation' to MCP server
2025-11-21 16:08:40,510 - INFO - Added tool 'list_incarnations' to MCP server
2025-11-21 16:08:40,510 - INFO - Added tool 'switch_incarnation' to MCP server
2025-11-21 16:08:40,511 - INFO - Added tool 'get_cleanup_status' to MCP server
2025-11-21 16:08:40,511 - INFO - Registered 30 core tools with MCP server
2025-11-21 16:08:40,511 - INFO - Processing 6 incarnation types
2025-11-21 16:08:40,511 - INFO - Processing incarnation: code_analysis
2025-11-21 16:08:40,511 - INFO - Registering tools from code_analysis incarnation
2025-11-21 16:08:40,511 - DEBUG - Checking methods in CodeAnalysisIncarnation
2025-11-21 16:08:40,511 - INFO - Using predefined tool list for CodeAnalysisIncarnation: ['analyze_codebase', 'analyze_file', 'compare_versions', 'find_code_smells', 'generate_documentation', 'explore_code_structure', 'search_code_constructs']
2025-11-21 16:08:40,511 - INFO - Found 7 tools via list_tool_methods: ['analyze_codebase', 'analyze_file', 'compare_versions', 'find_code_smells', 'generate_documentation', 'explore_code_structure', 'search_code_constructs']
2025-11-21 16:08:40,511 - INFO - Registered tool 'analyze_codebase' in category 'code_analysis'
2025-11-21 16:08:40,511 - INFO - Registered tool 'analyze_file' in category 'code_analysis'
2025-11-21 16:08:40,511 - INFO - Registered tool 'compare_versions' in category 'code_analysis'
2025-11-21 16:08:40,511 - INFO - Registered tool 'find_code_smells' in category 'code_analysis'
2025-11-21 16:08:40,511 - INFO - Registered tool 'generate_documentation' in category 'code_analysis'
2025-11-21 16:08:40,511 - INFO - Registered tool 'explore_code_structure' in category 'code_analysis'
2025-11-21 16:08:40,511 - INFO - Registered tool 'search_code_constructs' in category 'code_analysis'
2025-11-21 16:08:40,511 - INFO - Registered 7 tools from class CodeAnalysisIncarnation
2025-11-21 16:08:40,511 - INFO - Found 7 tools in code_analysis incarnation
2025-11-21 16:08:40,511 - INFO - Tools in category code_analysis: {'search_code_constructs', 'explore_code_structure', 'compare_versions', 'analyze_codebase', 'generate_documentation', 'find_code_smells', 'analyze_file'}
2025-11-21 16:08:40,512 - INFO - Added tool 'search_code_constructs' from code_analysis to MCP server
2025-11-21 16:08:40,513 - INFO - Added tool 'explore_code_structure' from code_analysis to MCP server
2025-11-21 16:08:40,514 - INFO - Added tool 'compare_versions' from code_analysis to MCP server
2025-11-21 16:08:40,515 - INFO - Added tool 'analyze_codebase' from code_analysis to MCP server
2025-11-21 16:08:40,516 - INFO - Added tool 'generate_documentation' from code_analysis to MCP server
2025-11-21 16:08:40,517 - INFO - Added tool 'find_code_smells' from code_analysis to MCP server
2025-11-21 16:08:40,518 - INFO - Added tool 'analyze_file' from code_analysis to MCP server
2025-11-21 16:08:40,518 - INFO - Successfully registered 7 tools from code_analysis incarnation
2025-11-21 16:08:40,518 - INFO - Registered 7 tools from code_analysis incarnation
2025-11-21 16:08:40,518 - INFO - Processing incarnation: coding
2025-11-21 16:08:40,518 - INFO - Registering tools from coding incarnation
2025-11-21 16:08:40,518 - DEBUG - Checking methods in CodingIncarnation
2025-11-21 16:08:40,518 - INFO - Using predefined tool list for CodingIncarnation: []
2025-11-21 16:08:40,518 - INFO - Found 0 tools via list_tool_methods: []
2025-11-21 16:08:40,518 - INFO - Registered 0 tools from class CodingIncarnation
2025-11-21 16:08:40,519 - INFO - Found 0 tools in coding incarnation
2025-11-21 16:08:40,519 - INFO - Attempting direct method inspection for coding
2025-11-21 16:08:40,519 - INFO - Found potential tool method: add_template_feedback
2025-11-21 16:08:40,519 - DEBUG - Tool 'add_template_feedback' already registered, skipping.
2025-11-21 16:08:40,519 - INFO - Found potential tool method: get_action_template
2025-11-21 16:08:40,519 - DEBUG - Tool 'get_action_template' already registered, skipping.
2025-11-21 16:08:40,519 - INFO - Found potential tool method: get_base_guidance
2025-11-21 16:08:40,519 - INFO - Registered tool 'get_base_guidance' in category 'coding'
2025-11-21 16:08:40,519 - INFO - Found potential tool method: get_best_practices
2025-11-21 16:08:40,519 - DEBUG - Tool 'get_best_practices' already registered, skipping.
2025-11-21 16:08:40,519 - INFO - Found potential tool method: get_project
2025-11-21 16:08:40,519 - DEBUG - Tool 'get_project' already registered, skipping.
2025-11-21 16:08:40,519 - INFO - Found potential tool method: get_workflow_history
2025-11-21 16:08:40,519 - DEBUG - Tool 'get_workflow_history' already registered, skipping.
2025-11-21 16:08:40,519 - INFO - Found potential tool method: list_action_templates
2025-11-21 16:08:40,519 - DEBUG - Tool 'list_action_templates' already registered, skipping.
2025-11-21 16:08:40,519 - INFO - Found potential tool method: list_projects
2025-11-21 16:08:40,519 - DEBUG - Tool 'list_projects' already registered, skipping.
2025-11-21 16:08:40,519 - INFO - Found potential tool method: log_workflow_execution
2025-11-21 16:08:40,519 - DEBUG - Tool 'log_workflow_execution' already registered, skipping.
2025-11-21 16:08:40,519 - INFO - Tools in category coding: {'get_base_guidance'}
2025-11-21 16:08:40,520 - INFO - Added tool 'get_base_guidance' from coding to MCP server
2025-11-21 16:08:40,520 - INFO - Successfully registered 1 tools from coding incarnation
2025-11-21 16:08:40,520 - INFO - Registered 1 tools from coding incarnation
2025-11-21 16:08:40,520 - INFO - Processing incarnation: data_analysis
2025-11-21 16:08:40,520 - INFO - Registering tools from data_analysis incarnation
2025-11-21 16:08:40,520 - INFO - Found 16 tools via list_tool_methods: ['load_dataset', 'explore_dataset', 'profile_data', 'calculate_statistics', 'analyze_correlations', 'filter_data', 'aggregate_data', 'compare_datasets', 'export_results', 'list_datasets', 'get_analysis_history', 'visualize_data', 'detect_anomalies', 'cluster_analysis', 'time_series_analysis', 'generate_insights']
2025-11-21 16:08:40,520 - INFO - Registered tool 'load_dataset' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'explore_dataset' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'profile_data' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'calculate_statistics' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'analyze_correlations' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'filter_data' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'aggregate_data' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'compare_datasets' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'export_results' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'list_datasets' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'get_analysis_history' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'visualize_data' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'detect_anomalies' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'cluster_analysis' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'time_series_analysis' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered tool 'generate_insights' in category 'data_analysis'
2025-11-21 16:08:40,520 - INFO - Registered 16 tools from class DataAnalysisIncarnation
2025-11-21 16:08:40,520 - INFO - Found 16 tools in data_analysis incarnation
2025-11-21 16:08:40,520 - INFO - Tools in category data_analysis: {'profile_data', 'export_results', 'aggregate_data', 'time_series_analysis', 'visualize_data', 'calculate_statistics', 'analyze_correlations', 'list_datasets', 'compare_datasets', 'get_analysis_history', 'generate_insights', 'load_dataset', 'filter_data', 'detect_anomalies', 'cluster_analysis', 'explore_dataset'}
2025-11-21 16:08:40,521 - INFO - Added tool 'profile_data' from data_analysis to MCP server
2025-11-21 16:08:40,522 - INFO - Added tool 'export_results' from data_analysis to MCP server
2025-11-21 16:08:40,522 - INFO - Added tool 'aggregate_data' from data_analysis to MCP server
2025-11-21 16:08:40,523 - INFO - Added tool 'time_series_analysis' from data_analysis to MCP server
2025-11-21 16:08:40,525 - INFO - Added tool 'visualize_data' from data_analysis to MCP server
2025-11-21 16:08:40,526 - INFO - Added tool 'calculate_statistics' from data_analysis to MCP server
2025-11-21 16:08:40,526 - INFO - Added tool 'analyze_correlations' from data_analysis to MCP server
2025-11-21 16:08:40,527 - INFO - Added tool 'list_datasets' from data_analysis to MCP server
2025-11-21 16:08:40,528 - INFO - Added tool 'compare_datasets' from data_analysis to MCP server
2025-11-21 16:08:40,529 - INFO - Added tool 'get_analysis_history' from data_analysis to MCP server
2025-11-21 16:08:40,530 - INFO - Added tool 'generate_insights' from data_analysis to MCP server
2025-11-21 16:08:40,531 - INFO - Added tool 'load_dataset' from data_analysis to MCP server
2025-11-21 16:08:40,531 - INFO - Added tool 'filter_data' from data_analysis to MCP server
2025-11-21 16:08:40,532 - INFO - Added tool 'detect_anomalies' from data_analysis to MCP server
2025-11-21 16:08:40,533 - INFO - Added tool 'cluster_analysis' from data_analysis to MCP server
2025-11-21 16:08:40,534 - INFO - Added tool 'explore_dataset' from data_analysis to MCP server
2025-11-21 16:08:40,534 - INFO - Successfully registered 16 tools from data_analysis incarnation
2025-11-21 16:08:40,534 - INFO - Registered 16 tools from data_analysis incarnation
2025-11-21 16:08:40,534 - INFO - Processing incarnation: decision_support
2025-11-21 16:08:40,534 - INFO - Registering tools from decision_support incarnation
2025-11-21 16:08:40,534 - DEBUG - Checking methods in DecisionIncarnation
2025-11-21 16:08:40,534 - INFO - Using predefined tool list for DecisionIncarnation: ['create_decision', 'list_decisions', 'get_decision', 'add_alternative', 'add_metric', 'add_evidence']
2025-11-21 16:08:40,534 - INFO - Found 6 tools via list_tool_methods: ['create_decision', 'list_decisions', 'get_decision', 'add_alternative', 'add_metric', 'add_evidence']
2025-11-21 16:08:40,534 - INFO - Registered tool 'create_decision' in category 'decision_support'
2025-11-21 16:08:40,534 - INFO - Registered tool 'list_decisions' in category 'decision_support'
2025-11-21 16:08:40,534 - INFO - Registered tool 'get_decision' in category 'decision_support'
2025-11-21 16:08:40,534 - INFO - Registered tool 'add_alternative' in category 'decision_support'
2025-11-21 16:08:40,534 - INFO - Registered tool 'add_metric' in category 'decision_support'
2025-11-21 16:08:40,534 - INFO - Registered tool 'add_evidence' in category 'decision_support'
2025-11-21 16:08:40,534 - INFO - Registered 6 tools from class DecisionIncarnation
2025-11-21 16:08:40,534 - INFO - Found 6 tools in decision_support incarnation
2025-11-21 16:08:40,534 - INFO - Tools in category decision_support: {'add_alternative', 'add_metric', 'create_decision', 'get_decision', 'list_decisions', 'add_evidence'}
2025-11-21 16:08:40,536 - INFO - Added tool 'add_alternative' from decision_support to MCP server
2025-11-21 16:08:40,537 - INFO - Added tool 'add_metric' from decision_support to MCP server
2025-11-21 16:08:40,538 - INFO - Added tool 'create_decision' from decision_support to MCP server
2025-11-21 16:08:40,539 - INFO - Added tool 'get_decision' from decision_support to MCP server
2025-11-21 16:08:40,540 - INFO - Added tool 'list_decisions' from decision_support to MCP server
2025-11-21 16:08:40,541 - INFO - Added tool 'add_evidence' from decision_support to MCP server
2025-11-21 16:08:40,542 - INFO - Successfully registered 6 tools from decision_support incarnation
2025-11-21 16:08:40,542 - INFO - Registered 6 tools from decision_support incarnation
2025-11-21 16:08:40,542 - INFO - Processing incarnation: knowledge_graph
2025-11-21 16:08:40,542 - INFO - Registering tools from knowledge_graph incarnation
2025-11-21 16:08:40,542 - DEBUG - Checking methods in KnowledgeGraphIncarnation
2025-11-21 16:08:40,542 - INFO - Using predefined tool list for KnowledgeGraphIncarnation: ['create_entities', 'create_relations', 'add_observations', 'add_single_observation', 'delete_entities', 'delete_observations', 'delete_relations', 'read_graph', 'search_nodes', 'open_nodes']
2025-11-21 16:08:40,542 - INFO - Found 10 tools via list_tool_methods: ['create_entities', 'create_relations', 'add_observations', 'add_single_observation', 'delete_entities', 'delete_observations', 'delete_relations', 'read_graph', 'search_nodes', 'open_nodes']
2025-11-21 16:08:40,542 - INFO - Registered tool 'create_entities' in category 'knowledge_graph'
2025-11-21 16:08:40,542 - INFO - Registered tool 'create_relations' in category 'knowledge_graph'
2025-11-21 16:08:40,542 - INFO - Registered tool 'add_observations' in category 'knowledge_graph'
2025-11-21 16:08:40,542 - INFO - Registered tool 'add_single_observation' in category 'knowledge_graph'
2025-11-21 16:08:40,542 - INFO - Registered tool 'delete_entities' in category 'knowledge_graph'
2025-11-21 16:08:40,542 - INFO - Registered tool 'delete_observations' in category 'knowledge_graph'
2025-11-21 16:08:40,542 - INFO - Registered tool 'delete_relations' in category 'knowledge_graph'
2025-11-21 16:08:40,542 - INFO - Registered tool 'read_graph' in category 'knowledge_graph'
2025-11-21 16:08:40,542 - INFO - Registered tool 'search_nodes' in category 'knowledge_graph'
2025-11-21 16:08:40,542 - INFO - Registered tool 'open_nodes' in category 'knowledge_graph'
2025-11-21 16:08:40,542 - INFO - Registered 10 tools from class KnowledgeGraphIncarnation
2025-11-21 16:08:40,542 - INFO - Found 10 tools in knowledge_graph incarnation
2025-11-21 16:08:40,542 - INFO - Tools in category knowledge_graph: {'create_relations', 'read_graph', 'open_nodes', 'create_entities', 'add_single_observation', 'delete_observations', 'search_nodes', 'add_observations', 'delete_relations', 'delete_entities'}
2025-11-21 16:08:40,543 - INFO - Added tool 'create_relations' from knowledge_graph to MCP server
2025-11-21 16:08:40,543 - INFO - Added tool 'read_graph' from knowledge_graph to MCP server
2025-11-21 16:08:40,544 - INFO - Added tool 'open_nodes' from knowledge_graph to MCP server
2025-11-21 16:08:40,544 - INFO - Added tool 'create_entities' from knowledge_graph to MCP server
2025-11-21 16:08:40,545 - INFO - Added tool 'add_single_observation' from knowledge_graph to MCP server
2025-11-21 16:08:40,546 - INFO - Added tool 'delete_observations' from knowledge_graph to MCP server
2025-11-21 16:08:40,546 - INFO - Added tool 'search_nodes' from knowledge_graph to MCP server
2025-11-21 16:08:40,547 - INFO - Added tool 'add_observations' from knowledge_graph to MCP server
2025-11-21 16:08:40,547 - INFO - Added tool 'delete_relations' from knowledge_graph to MCP server
2025-11-21 16:08:40,548 - INFO - Added tool 'delete_entities' from knowledge_graph to MCP server
2025-11-21 16:08:40,548 - INFO - Successfully registered 10 tools from knowledge_graph incarnation
2025-11-21 16:08:40,548 - INFO - Registered 10 tools from knowledge_graph incarnation
2025-11-21 16:08:40,548 - INFO - Processing incarnation: research_orchestration
2025-11-21 16:08:40,548 - INFO - Registering tools from research_orchestration incarnation
2025-11-21 16:08:40,548 - DEBUG - Checking methods in ResearchIncarnation
2025-11-21 16:08:40,548 - INFO - Using predefined tool list for ResearchIncarnation: ['register_hypothesis', 'list_hypotheses', 'get_hypothesis', 'update_hypothesis', 'create_protocol', 'list_protocols', 'get_protocol', 'create_experiment', 'list_experiments', 'get_experiment', 'update_experiment', 'record_observation', 'list_observations', 'compute_statistics', 'create_publication_draft']
2025-11-21 16:08:40,548 - INFO - Found 15 tools via list_tool_methods: ['register_hypothesis', 'list_hypotheses', 'get_hypothesis', 'update_hypothesis', 'create_protocol', 'list_protocols', 'get_protocol', 'create_experiment', 'list_experiments', 'get_experiment', 'update_experiment', 'record_observation', 'list_observations', 'compute_statistics', 'create_publication_draft']
2025-11-21 16:08:40,548 - INFO - Registered tool 'register_hypothesis' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'list_hypotheses' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'get_hypothesis' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'update_hypothesis' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'create_protocol' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'list_protocols' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'get_protocol' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'create_experiment' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'list_experiments' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'get_experiment' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'update_experiment' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'record_observation' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'list_observations' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'compute_statistics' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered tool 'create_publication_draft' in category 'research_orchestration'
2025-11-21 16:08:40,548 - INFO - Registered 15 tools from class ResearchIncarnation
2025-11-21 16:08:40,548 - INFO - Found 15 tools in research_orchestration incarnation
2025-11-21 16:08:40,548 - INFO - Tools in category research_orchestration: {'get_experiment', 'create_protocol', 'get_protocol', 'record_observation', 'update_hypothesis', 'list_protocols', 'create_publication_draft', 'update_experiment', 'list_hypotheses', 'list_observations', 'get_hypothesis', 'register_hypothesis', 'compute_statistics', 'list_experiments', 'create_experiment'}
2025-11-21 16:08:40,549 - INFO - Added tool 'get_experiment' from research_orchestration to MCP server
2025-11-21 16:08:40,550 - INFO - Added tool 'create_protocol' from research_orchestration to MCP server
2025-11-21 16:08:40,551 - INFO - Added tool 'get_protocol' from research_orchestration to MCP server
2025-11-21 16:08:40,552 - INFO - Added tool 'record_observation' from research_orchestration to MCP server
2025-11-21 16:08:40,554 - INFO - Added tool 'update_hypothesis' from research_orchestration to MCP server
2025-11-21 16:08:40,554 - INFO - Added tool 'list_protocols' from research_orchestration to MCP server
2025-11-21 16:08:40,556 - INFO - Added tool 'create_publication_draft' from research_orchestration to MCP server
2025-11-21 16:08:40,557 - INFO - Added tool 'update_experiment' from research_orchestration to MCP server
2025-11-21 16:08:40,558 - INFO - Added tool 'list_hypotheses' from research_orchestration to MCP server
2025-11-21 16:08:40,558 - INFO - Added tool 'list_observations' from research_orchestration to MCP server
2025-11-21 16:08:40,559 - INFO - Added tool 'get_hypothesis' from research_orchestration to MCP server
2025-11-21 16:08:40,560 - INFO - Added tool 'register_hypothesis' from research_orchestration to MCP server
2025-11-21 16:08:40,561 - INFO - Added tool 'compute_statistics' from research_orchestration to MCP server
2025-11-21 16:08:40,562 - INFO - Added tool 'list_experiments' from research_orchestration to MCP server
2025-11-21 16:08:40,563 - INFO - Added tool 'create_experiment' from research_orchestration to MCP server
2025-11-21 16:08:40,563 - INFO - Successfully registered 15 tools from research_orchestration incarnation
2025-11-21 16:08:40,563 - INFO - Registered 15 tools from research_orchestration incarnation
2025-11-21 16:08:40,563 - INFO - Tool registration complete. Total tools registered: 85
2025-11-21 16:08:40,563 - INFO - - Core tools: 30
2025-11-21 16:08:40,563 - INFO - - Incarnation tools: 55
2025-11-21 16:08:40,563 - INFO - Registered 85 tools from all incarnations
2025-11-21 16:08:40,563 - INFO - Server initialization completed successfully
2025-11-21 16:08:40,563 - INFO - Server initialization complete
2025-11-21 16:08:40,563 - INFO - Server created successfully, starting MCP transport
2025-11-21 16:08:40,570 - INFO - Processing request of type CallToolRequest
2025-11-21 16:08:40,570 - DEBUG - Tracking Neo4j session, total: 1
2025-11-21 16:08:40,571 - ERROR - Read access test failed: Task <Task pending name='Task-311' coro=<StreamReader.read() running at /home/ty/.pyenv/versions/3.11.12/lib/python3.11/asyncio/streams.py:711> cb=[_release_waiter(<Future pendi...ask_wakeup()]>)() at /home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/shims/__init__.py:38]> got Future <Future pending> attached to a different loop
2025-11-21 16:08:40,571 - ERROR - Write access test failed: Task <Task pending name='Task-313' coro=<StreamReader.read() running at /home/ty/.pyenv/versions/3.11.12/lib/python3.11/asyncio/streams.py:711> cb=[_release_waiter(<Future pendi...ask_wakeup()]>)() at /home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/shims/__init__.py:38]> got Future <Future pending> attached to a different loop
2025-11-21 16:08:40,571 - WARNING - Couldn't get server info: Task <Task pending name='Task-315' coro=<StreamReader.read() running at /home/ty/.pyenv/versions/3.11.12/lib/python3.11/asyncio/streams.py:711> cb=[_release_waiter(<Future pendi...ask_wakeup()]>)() at /home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/shims/__init__.py:38]> got Future <Future pending> attached to a different loop
2025-11-21 16:08:40,572 - ERROR - Error in Neo4j session: Task <Task pending name='Task-318' coro=<StreamReader.read() running at /home/ty/.pyenv/versions/3.11.12/lib/python3.11/asyncio/streams.py:711> cb=[_release_waiter(<Future pendi...ask_wakeup()]>)() at /home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/shims/__init__.py:38]> got Future <Future pending> attached to a different loop
2025-11-21 16:08:40,572 - ERROR - Event loop mismatch detected. This is likely due to asyncio objects being used across different event loops.
2025-11-21 16:08:40,572 - ERROR - Recommendation: Ensure all Neo4j operations use the same event loop context.
2025-11-21 16:08:40,572 - DEBUG - Untracked Neo4j session, remaining: 0
2025-11-21 16:08:40,572 - ERROR - Connection check error: Task <Task pending name='Task-318' coro=<StreamReader.read() running at /home/ty/.pyenv/versions/3.11.12/lib/python3.11/asyncio/streams.py:711> cb=[_release_waiter(<Future pendi...ask_wakeup()]>)() at /home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/shims/__init__.py:38]> got Future <Future pending> attached to a different loop
2025-11-21 16:08:40,575 - ERROR - Error details: Traceback (most recent call last):
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/work/session.py", line 222, in close
await self._connection.fetch_all()
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/io/_bolt.py", line 879, in fetch_all
detail_delta, summary_delta = await self.fetch_message()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/io/_bolt.py", line 861, in fetch_message
tag, fields = await self.inbox.pop(
^^^^^^^^^^^^^^^^^^^^^
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/io/_common.py", line 77, in pop
await self._buffer_one_chunk()
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/io/_common.py", line 54, in _buffer_one_chunk
await receive_into_buffer(self._socket, self._buffer, 2)
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/io/_common.py", line 345, in receive_into_buffer
n = await sock.recv_into(
^^^^^^^^^^^^^^^^^^^^^
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/network/_bolt_socket.py", line 156, in recv_into
res = await self._wait_for_io(self._reader.read, nbytes)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/network/_bolt_socket.py", line 116, in _wait_for_io
return await wait_for(io_fut, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/shims/__init__.py", line 118, in wait_for
return fut.result()
^^^^^^^^^^^^
File "/home/ty/.pyenv/versions/3.11.12/lib/python3.11/asyncio/streams.py", line 711, in read
await self._wait_for_data('read')
File "/home/ty/.pyenv/versions/3.11.12/lib/python3.11/asyncio/streams.py", line 543, in _wait_for_data
await self._waiter
RuntimeError: Task <Task pending name='Task-316' coro=<StreamReader.read() running at /home/ty/.pyenv/versions/3.11.12/lib/python3.11/asyncio/streams.py:711> cb=[_release_waiter(<Future pendi...ask_wakeup()]>)() at /home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/shims/__init__.py:38]> got Future <Future pending> attached to a different loop
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/src/mcp_neocoder/server.py", line 1091, in check_connection
async with safe_neo4j_session(self.driver, self.database or "neo4j") as session:
File "/home/ty/.pyenv/versions/3.11.12/lib/python3.11/contextlib.py", line 217, in __aexit__
await anext(self.gen)
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/src/mcp_neocoder/event_loop_manager.py", line 118, in safe_neo4j_session
async with session_cm as session:
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/work/session.py", line 130, in __aexit__
await self.close()
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/work/session.py", line 233, in close
await self._disconnect()
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/work/session.py", line 145, in _disconnect
return await super()._disconnect(sync=sync)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/work/workspace.py", line 301, in _disconnect
await self._pool.release(self._connection)
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/io/_pool.py", line 484, in release
await connection.reset()
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/io/_bolt5.py", line 447, in reset
await self.fetch_all()
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/io/_bolt.py", line 879, in fetch_all
detail_delta, summary_delta = await self.fetch_message()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/io/_bolt.py", line 861, in fetch_message
tag, fields = await self.inbox.pop(
^^^^^^^^^^^^^^^^^^^^^
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/io/_common.py", line 77, in pop
await self._buffer_one_chunk()
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/io/_common.py", line 54, in _buffer_one_chunk
await receive_into_buffer(self._socket, self._buffer, 2)
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async/io/_common.py", line 345, in receive_into_buffer
n = await sock.recv_into(
^^^^^^^^^^^^^^^^^^^^^
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/network/_bolt_socket.py", line 156, in recv_into
res = await self._wait_for_io(self._reader.read, nbytes)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/network/_bolt_socket.py", line 116, in _wait_for_io
return await wait_for(io_fut, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/shims/__init__.py", line 118, in wait_for
return fut.result()
^^^^^^^^^^^^
File "/home/ty/.pyenv/versions/3.11.12/lib/python3.11/asyncio/streams.py", line 711, in read
await self._wait_for_data('read')
File "/home/ty/.pyenv/versions/3.11.12/lib/python3.11/asyncio/streams.py", line 543, in _wait_for_data
await self._waiter
RuntimeError: Task <Task pending name='Task-318' coro=<StreamReader.read() running at /home/ty/.pyenv/versions/3.11.12/lib/python3.11/asyncio/streams.py:711> cb=[_release_waiter(<Future pendi...ask_wakeup()]>)() at /home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/shims/__init__.py:38]> got Future <Future pending> attached to a different loop
Starting server process...
Sending initialize request...
Reading initialize response...
Initialize Response: {"jsonrpc":"2.0","id":0,"result":{"protocolVersion":"2024-11-05","capabilities":{"experimental":{},"prompts":{"listChanged":false},"resources":{"subscribe":false,"listChanged":false},"tools":{"listChanged":false}},"serverInfo":{"name":"mcp-neocoder","version":"1.9.4"}}}
Sending check_connection request...
Reading check_connection response...
Check Connection Response: {"jsonrpc":"2.0","id":1,"result":{"content":[{"type":"text","text":"# Neo4j Connection Status\n\n❌ **Connection Failed**\n\nUnable to connect to Neo4j database.\n\n- **Connection:** Not Connected\n- **Database:** neo4j\n- **Read Access:** False\n- **Write Access:** False\n\n## Error Details\n\n```\nTask <Task pending name='Task-318' coro=<StreamReader.read() running at /home/ty/.pyenv/versions/3.11.12/lib/python3.11/asyncio/streams.py:711> cb=[_release_waiter(<Future pendi...ask_wakeup()]>)() at /home/ty/Repositories/NeoCoder-neo4j-ai-workflow/.venv/lib/python3.11/site-packages/neo4j/_async_compat/shims/__init__.py:38]> got Future <Future pending> attached to a different loop\n```\nThis error may help with troubleshooting database connection issues.\n\n## Connection Settings\n\n- **URL:** bolt://localhost:7687\n- **Username:** neo4j\n- **Password:** 00000000\n- **Database:** neo4j\n\n## Troubleshooting Tips\n\n1. Verify Neo4j is running: `sudo systemctl status neo4j`\n2. Check connection settings in environment variables\n3. Try restarting Neo4j: `sudo systemctl restart neo4j`\n4. Check Neo4j logs: `sudo journalctl -u neo4j`\n"}],"isError":false}}
2025-11-21 16:08:40,576 - INFO - Received signal 15, initiating graceful shutdown
2025-11-21 16:09:10,576 - ERROR - Error waiting for cleanup future:
2025-11-21 16:09:10,576 - INFO - Starting process cleanup...
2025-11-21 16:09:10,577 - INFO - Closing 1 Neo4j drivers
2025-11-21 16:09:10,577 - ERROR - Error closing Neo4j driver: Task <Task pending name='Task-319' coro=<cleanup_processes() running at /home/ty/Repositories/NeoCoder-neo4j-ai-workflow/src/mcp_neocoder/process_manager.py:262> cb=[_chain_future.<locals>._call_set_state() at /home/ty/.pyenv/versions/3.11.12/lib/python3.11/asyncio/futures.py:394]> got Future <Future pending> attached to a different loop
2025-11-21 16:09:10,577 - INFO - Process cleanup completed
2025-11-21 16:09:10,577 - INFO - Performing final cleanup...
2025-11-21 16:09:10,577 - ERROR - Error during server cleanup: There is no current event loop in thread 'MainThread'.
2025-11-21 16:09:10,577 - INFO - No running event loop, creating new one for cleanup.
2025-11-21 16:09:10,578 - INFO - Starting process cleanup...
2025-11-21 16:09:10,578 - INFO - Process cleanup completed
2025-11-21 16:09:10,578 - INFO - Synchronous cleanup completed via new loop.
2025-11-21 16:09:10,578 - INFO - Final cleanup completed
2025-11-21 16:09:10,578 - INFO - No running event loop, creating new one for cleanup.
2025-11-21 16:09:10,578 - INFO - Starting process cleanup...
2025-11-21 16:09:10,578 - INFO - Process cleanup completed
2025-11-21 16:09:10,578 - INFO - Synchronous cleanup completed via new loop.
