#!/bin/bash

# VisionFlow Pipeline Context Generator

# Extracts all files involved in GitHub → Neo4j → GPU → Client pipeline

# Output: context.txt with location metadata

OUTPUT_FILE="/mnt/mldata/githubs/AR-AI-Knowledge-Graph/context.txt"

PROJECT_ROOT="/mnt/mldata/githubs/AR-AI-Knowledge-Graph"

# Colors

GREEN='\033[0;32m'

BLUE='\033[0;34m'

YELLOW='\033[1;33m'

NC='\033[0m'

echo -e "${BLUE}VisionFlow Pipeline Context Generator${NC}"

echo -e "${BLUE}======================================${NC}\n"

# Clear output file

> "$OUTPUT_FILE"

# Header

cat >> "$OUTPUT_FILE" << 'EOF'

================================================================================

VISIONFLOW COMPLETE PIPELINE CONTEXT

GitHub → Markdown Parse → Neo4j → Metadata/Edges → GPU → Graph → Client

================================================================================

Generated: $(date)

Purpose: Complete source code context for LLM analysis of the VisionFlow pipeline

TABLE OF CONTENTS:

1. GitHub Interaction (Download & Fetch)

2. Markdown Parsing & Analysis

3. Neo4j Database Interaction

4. Metadata & Edge Building

5. GPU Computation (CUDA)

6. Graph Structure Building

7. Client Communication (WebSocket + HTTP)

================================================================================

EOF

# Function to add file with metadata

add_file() {

local filepath="$1"

local category="$2"

local description="$3"

if [ ! -f "$filepath" ]; then

echo -e "${YELLOW}⚠️ File not found: $filepath${NC}"

return

fi

local relative_path="${filepath#$PROJECT_ROOT/}"

local line_count=$(wc -l < "$filepath")

local file_size=$(stat -c%s "$filepath" 2>/dev/null || stat -f%z "$filepath" 2>/dev/null)

echo -e "${GREEN}✓${NC} $relative_path ($line_count lines)"

cat >> "$OUTPUT_FILE" << EOF

################################################################################

# FILE: $relative_path

# CATEGORY: $category

# DESCRIPTION: $description

# LINES: $line_count

# SIZE: $file_size bytes

################################################################################

EOF

cat "$filepath" >> "$OUTPUT_FILE"

echo -e "\n" >> "$OUTPUT_FILE"

}

# 1. GITHUB INTERACTION

echo -e "\n${BLUE}[1/7] GitHub Interaction Files${NC}"

cat >> "$OUTPUT_FILE" << 'EOF'

================================================================================

SECTION 1: GITHUB INTERACTION (Download & Fetch)

================================================================================

EOF

add_file "$PROJECT_ROOT/src/services/github/api.rs" "GitHub" "GitHub API client wrapper"

add_file "$PROJECT_ROOT/src/services/github/config.rs" "GitHub" "GitHub configuration and authentication"

add_file "$PROJECT_ROOT/src/services/github/content_enhanced.rs" "GitHub" "Enhanced content fetching API"

add_file "$PROJECT_ROOT/src/services/github/pr.rs" "GitHub" "Pull request API"

add_file "$PROJECT_ROOT/src/services/github/types.rs" "GitHub" "GitHub type definitions"

add_file "$PROJECT_ROOT/src/services/github/mod.rs" "GitHub" "GitHub module entry point"

add_file "$PROJECT_ROOT/src/services/github_sync_service.rs" "GitHub" "Main GitHub sync orchestration"

add_file "$PROJECT_ROOT/src/services/streaming_sync_service.rs" "GitHub" "Streaming sync for large repos"

add_file "$PROJECT_ROOT/src/services/local_markdown_sync.rs" "GitHub" "Local markdown synchronization"

add_file "$PROJECT_ROOT/src/handlers/admin_sync_handler.rs" "GitHub" "Admin endpoint for triggering sync"

# 2. MARKDOWN PARSING

echo -e "\n${BLUE}[2/7] Markdown Parsing & Analysis Files${NC}"

cat >> "$OUTPUT_FILE" << 'EOF'

================================================================================

SECTION 2: MARKDOWN PARSING & ANALYSIS

================================================================================

EOF

add_file "$PROJECT_ROOT/src/services/parsers/ontology_parser.rs" "Parsing" "Parse markdown for OWL ontologies"

add_file "$PROJECT_ROOT/src/services/parsers/knowledge_graph_parser.rs" "Parsing" "Parse markdown for graph structures"

add_file "$PROJECT_ROOT/src/ontology/parser/parser.rs" "Parsing" "Core ontology parsing logic"

add_file "$PROJECT_ROOT/src/ontology/parser/converter.rs" "Parsing" "Convert parsed data to OWL"

add_file "$PROJECT_ROOT/src/ontology/parser/assembler.rs" "Parsing" "Assemble OWL components"

add_file "$PROJECT_ROOT/src/services/semantic_analyzer.rs" "Parsing" "Extract semantic features from markdown"

add_file "$PROJECT_ROOT/src/services/owl_extractor_service.rs" "Parsing" "Extract OWL axioms from markdown"

add_file "$PROJECT_ROOT/src/services/ontology_enrichment_service.rs" "Parsing" "Enrich ontology with inferred data"

add_file "$PROJECT_ROOT/src/inference/owl_parser.rs" "Parsing" "Parse OWL syntax in markdown"

add_file "$PROJECT_ROOT/src/services/ontology_pipeline_service.rs" "Parsing" "Complete ontology processing pipeline"

add_file "$PROJECT_ROOT/src/services/ontology_reasoner.rs" "Parsing" "Reasoning over parsed ontologies"

add_file "$PROJECT_ROOT/src/services/ontology_reasoning_service.rs" "Parsing" "Reasoning service coordination"

add_file "$PROJECT_ROOT/src/services/ontology_converter.rs" "Parsing" "Convert between ontology formats"

add_file "$PROJECT_ROOT/src/reasoning/horned_integration.rs" "Parsing" "Horned-OWL reasoner integration"

add_file "$PROJECT_ROOT/src/reasoning/custom_reasoner.rs" "Parsing" "Custom reasoning logic"

# 3. NEO4J DATABASE

echo -e "\n${BLUE}[3/7] Neo4j Database Interaction Files${NC}"

cat >> "$OUTPUT_FILE" << 'EOF'

================================================================================

SECTION 3: NEO4J DATABASE INTERACTION

================================================================================

EOF

add_file "$PROJECT_ROOT/src/adapters/neo4j_adapter.rs" "Neo4j" "Main Neo4j connection adapter"

add_file "$PROJECT_ROOT/src/adapters/neo4j_ontology_repository.rs" "Neo4j" "Ontology CRUD operations"

add_file "$PROJECT_ROOT/src/adapters/neo4j_settings_repository.rs" "Neo4j" "Settings persistence"

add_file "$PROJECT_ROOT/src/utils/neo4j_helpers.rs" "Neo4j" "Neo4j query utilities"

add_file "$PROJECT_ROOT/src/ports/ontology_repository.rs" "Neo4j" "Ontology repository trait"

add_file "$PROJECT_ROOT/src/ports/knowledge_graph_repository.rs" "Neo4j" "Graph repository trait"

add_file "$PROJECT_ROOT/src/ports/graph_repository.rs" "Neo4j" "Generic graph port"

add_file "$PROJECT_ROOT/src/handlers/cypher_query_handler.rs" "Neo4j" "Execute Cypher queries"

add_file "$PROJECT_ROOT/src/services/natural_language_query_service.rs" "Neo4j" "NL to Cypher translation"

add_file "$PROJECT_ROOT/src/repositories/query_builder.rs" "Neo4j" "Dynamic query construction"

add_file "$PROJECT_ROOT/src/cqrs/handlers/ontology_handlers.rs" "Neo4j" "Ontology command handlers"

add_file "$PROJECT_ROOT/src/cqrs/queries/ontology_queries.rs" "Neo4j" "Ontology query handlers"

add_file "$PROJECT_ROOT/src/cqrs/handlers/graph_handlers.rs" "Neo4j" "Graph command handlers"

add_file "$PROJECT_ROOT/src/cqrs/queries/graph_queries.rs" "Neo4j" "Graph query handlers"

# 4. METADATA & EDGES

echo -e "\n${BLUE}[4/7] Metadata & Edge Building Files${NC}"

cat >> "$OUTPUT_FILE" << 'EOF'

================================================================================

SECTION 4: METADATA & EDGE BUILDING

================================================================================

EOF

add_file "$PROJECT_ROOT/src/models/metadata.rs" "Metadata" "Metadata data structures"

add_file "$PROJECT_ROOT/src/services/file_service.rs" "Metadata" "File metadata extraction"

add_file "$PROJECT_ROOT/src/actors/metadata_actor.rs" "Metadata" "Metadata processing actor"

add_file "$PROJECT_ROOT/src/services/edge_generation.rs" "Edges" "Generate edges from relationships"

add_file "$PROJECT_ROOT/src/services/edge_classifier.rs" "Edges" "Classify edge types"

add_file "$PROJECT_ROOT/src/models/edge.rs" "Edges" "Edge data model"

add_file "$PROJECT_ROOT/src/models/graph.rs" "Graph" "Graph data structures"

add_file "$PROJECT_ROOT/src/models/node.rs" "Graph" "Node data structures"

add_file "$PROJECT_ROOT/src/services/graph_serialization.rs" "Graph" "Serialize graph for transfer"

# 5. GPU COMPUTATION

echo -e "\n${BLUE}[5/7] GPU Computation Files${NC}"

cat >> "$OUTPUT_FILE" << 'EOF'

================================================================================

SECTION 5: GPU COMPUTATION (CUDA)

================================================================================

EOF

# GPU Actors

add_file "$PROJECT_ROOT/src/actors/gpu/gpu_manager_actor.rs" "GPU" "GPU resource orchestration"

add_file "$PROJECT_ROOT/src/actors/gpu/gpu_resource_actor.rs" "GPU" "GPU memory management"

add_file "$PROJECT_ROOT/src/actors/gpu/cuda_stream_wrapper.rs" "GPU" "CUDA stream wrapper"

add_file "$PROJECT_ROOT/src/actors/gpu/force_compute_actor.rs" "GPU" "Physics force computation"

add_file "$PROJECT_ROOT/src/actors/gpu/clustering_actor.rs" "GPU" "GPU clustering algorithms"

add_file "$PROJECT_ROOT/src/actors/gpu/anomaly_detection_actor.rs" "GPU" "Anomaly detection"

add_file "$PROJECT_ROOT/src/actors/gpu/constraint_actor.rs" "GPU" "Constraint enforcement"

add_file "$PROJECT_ROOT/src/actors/gpu/ontology_constraint_actor.rs" "GPU" "Ontology constraints to forces"

add_file "$PROJECT_ROOT/src/actors/gpu/stress_majorization_actor.rs" "GPU" "Stress majorization layout"

# Core GPU

add_file "$PROJECT_ROOT/src/utils/unified_gpu_compute.rs" "GPU" "PRIMARY: Unified GPU interface"

add_file "$PROJECT_ROOT/src/gpu/memory_manager.rs" "GPU" "GPU memory allocation"

add_file "$PROJECT_ROOT/src/gpu/dynamic_buffer_manager.rs" "GPU" "Dynamic buffer management"

add_file "$PROJECT_ROOT/src/gpu/streaming_pipeline.rs" "GPU" "Streaming GPU pipeline"

add_file "$PROJECT_ROOT/src/gpu/semantic_forces.rs" "GPU" "Semantic force computation"

# CUDA Kernels

add_file "$PROJECT_ROOT/src/utils/visionflow_unified.cu" "CUDA" "Main unified kernel"

add_file "$PROJECT_ROOT/src/utils/visionflow_unified_stability.cu" "CUDA" "Stability-enhanced kernel"

add_file "$PROJECT_ROOT/src/utils/dynamic_grid.cu" "CUDA" "Dynamic spatial grid"

add_file "$PROJECT_ROOT/src/utils/gpu_clustering_kernels.cu" "CUDA" "K-means, DBSCAN clustering"

add_file "$PROJECT_ROOT/src/utils/sssp_compact.cu" "CUDA" "Shortest path SSSP"

add_file "$PROJECT_ROOT/src/utils/gpu_landmark_apsp.cu" "CUDA" "All-pairs shortest path"

add_file "$PROJECT_ROOT/src/utils/ontology_constraints.cu" "CUDA" "Ontology constraint forces"

add_file "$PROJECT_ROOT/src/utils/semantic_forces.cu" "CUDA" "Semantic attraction/repulsion"

add_file "$PROJECT_ROOT/src/utils/stress_majorization.cu" "CUDA" "Stress majorization"

# GPU Utilities

add_file "$PROJECT_ROOT/src/utils/gpu_memory.rs" "GPU" "GPU memory utilities"

add_file "$PROJECT_ROOT/src/utils/gpu_diagnostics.rs" "GPU" "GPU diagnostics"

add_file "$PROJECT_ROOT/src/utils/gpu_safety.rs" "GPU" "GPU safety checks"

add_file "$PROJECT_ROOT/src/utils/cuda_error_handling.rs" "GPU" "CUDA error handling"

add_file "$PROJECT_ROOT/src/utils/ptx.rs" "GPU" "PTX loading utilities"

# GPU Adapters

add_file "$PROJECT_ROOT/src/adapters/gpu_semantic_analyzer.rs" "GPU" "GPU semantic analysis adapter"

add_file "$PROJECT_ROOT/src/adapters/actix_physics_adapter.rs" "GPU" "Physics actor adapter"

add_file "$PROJECT_ROOT/src/ports/gpu_physics_adapter.rs" "GPU" "GPU physics port"

# Constraint Translation

add_file "$PROJECT_ROOT/src/constraints/semantic_axiom_translator.rs" "Constraints" "Translate OWL axioms to forces"

add_file "$PROJECT_ROOT/src/constraints/gpu_converter.rs" "Constraints" "Convert constraints to GPU buffers"

add_file "$PROJECT_ROOT/src/constraints/semantic_gpu_buffer.rs" "Constraints" "GPU buffer management"

add_file "$PROJECT_ROOT/src/constraints/axiom_mapper.rs" "Constraints" "Map axioms to constraint types"

add_file "$PROJECT_ROOT/src/physics/ontology_constraints.rs" "Physics" "Physics constraint definitions"

add_file "$PROJECT_ROOT/src/physics/semantic_constraints.rs" "Physics" "Semantic constraint logic"

# 6. GRAPH STRUCTURE BUILDING

echo -e "\n${BLUE}[6/7] Graph Structure Building Files${NC}"

cat >> "$OUTPUT_FILE" << 'EOF'

================================================================================

SECTION 6: GRAPH STRUCTURE BUILDING

================================================================================

EOF

add_file "$PROJECT_ROOT/src/actors/graph_state_actor.rs" "Graph" "Central graph state management"

add_file "$PROJECT_ROOT/src/actors/physics_orchestrator_actor.rs" "Graph" "Physics orchestration"

add_file "$PROJECT_ROOT/src/actors/semantic_processor_actor.rs" "Graph" "Semantic processing"

add_file "$PROJECT_ROOT/src/actors/ontology_actor.rs" "Graph" "Ontology state management"

add_file "$PROJECT_ROOT/src/actors/client_coordinator_actor.rs" "Graph" "Client coordination"

add_file "$PROJECT_ROOT/src/application/knowledge_graph/queries.rs" "Graph" "Knowledge graph queries"

add_file "$PROJECT_ROOT/src/application/knowledge_graph/directives.rs" "Graph" "Knowledge graph directives"

add_file "$PROJECT_ROOT/src/application/graph/queries.rs" "Graph" "Generic graph queries"

add_file "$PROJECT_ROOT/src/physics/mod.rs" "Physics" "Physics module entry"

add_file "$PROJECT_ROOT/src/physics/stress_majorization.rs" "Physics" "Stress majorization layout"

# 7. CLIENT COMMUNICATION

echo -e "\n${BLUE}[7/7] Client Communication Files${NC}"

cat >> "$OUTPUT_FILE" << 'EOF'

================================================================================

SECTION 7: CLIENT COMMUNICATION (WebSocket + HTTP)

================================================================================

EOF

# WebSocket Handlers

add_file "$PROJECT_ROOT/src/handlers/socket_flow_handler.rs" "WebSocket" "PRIMARY: Main graph WebSocket"

add_file "$PROJECT_ROOT/src/handlers/realtime_websocket_handler.rs" "WebSocket" "Real-time updates"

add_file "$PROJECT_ROOT/src/handlers/websocket_settings_handler.rs" "WebSocket" "Settings WebSocket"

add_file "$PROJECT_ROOT/src/handlers/multi_mcp_websocket_handler.rs" "WebSocket" "Multi-agent visualization"

add_file "$PROJECT_ROOT/src/handlers/bots_visualization_handler.rs" "WebSocket" "Bot visualization WebSocket"

add_file "$PROJECT_ROOT/src/handlers/speech_socket_handler.rs" "WebSocket" "Speech interface WebSocket"

# Protocol & Messages

add_file "$PROJECT_ROOT/src/utils/socket_flow_messages.rs" "Protocol" "Binary graph protocol messages"

add_file "$PROJECT_ROOT/src/utils/standard_websocket_messages.rs" "Protocol" "Standard WebSocket messages"

add_file "$PROJECT_ROOT/src/handlers/websocket_utils.rs" "Protocol" "WebSocket utilities"

add_file "$PROJECT_ROOT/src/utils/websocket_heartbeat.rs" "Protocol" "WebSocket heartbeat"

add_file "$PROJECT_ROOT/src/protocols/binary_settings_protocol.rs" "Protocol" "Binary settings protocol"

# HTTP API

add_file "$PROJECT_ROOT/src/handlers/api_handler/graph/mod.rs" "HTTP" "Graph REST API"

add_file "$PROJECT_ROOT/src/handlers/api_handler/ontology/mod.rs" "HTTP" "Ontology REST API"

add_file "$PROJECT_ROOT/src/handlers/api_handler/analytics/mod.rs" "HTTP" "Analytics REST API"

add_file "$PROJECT_ROOT/src/handlers/api_handler/analytics/websocket_integration.rs" "HTTP" "Analytics WebSocket bridge"

add_file "$PROJECT_ROOT/src/handlers/graph_state_handler.rs" "HTTP" "Graph state HTTP endpoints"

add_file "$PROJECT_ROOT/src/handlers/graph_export_handler.rs" "HTTP" "Export graph data"

# Analytics

add_file "$PROJECT_ROOT/src/handlers/api_handler/analytics/clustering.rs" "Analytics" "Clustering results"

add_file "$PROJECT_ROOT/src/handlers/api_handler/analytics/anomaly.rs" "Analytics" "Anomaly detection results"

add_file "$PROJECT_ROOT/src/handlers/api_handler/analytics/community.rs" "Analytics" "Community detection"

# Footer

cat >> "$OUTPUT_FILE" << 'EOF'

================================================================================

END OF VISIONFLOW PIPELINE CONTEXT

================================================================================

PIPELINE FLOW SUMMARY:

1. GitHub API fetches markdown → src/services/github_sync_service.rs

2. Markdown parsed for OWL + semantics → src/services/ontology_parser.rs

3. Data stored in Neo4j → src/adapters/neo4j_ontology_repository.rs

4. Edges + metadata generated → src/services/edge_generation.rs

5. OWL axioms → GPU forces → src/constraints/semantic_axiom_translator.rs

6. CUDA kernels compute physics → src/utils/unified_gpu_compute.rs

7. Graph state built → src/actors/graph_state_actor.rs

8. WebSocket streams to client → src/handlers/socket_flow_handler.rs

Total pipeline files: ~120

Primary entry points: 8 (listed above)

================================================================================

EOF

echo -e "\n${GREEN}✓ Context file generated: $OUTPUT_FILE${NC}"

echo -e "${BLUE}File size: $(du -h "$OUTPUT_FILE" | cut -f1)${NC}"

echo -e "${BLUE}Total lines: $(wc -l < "$OUTPUT_FILE")${NC}\n"