Update memory bank to reflect project directory reorganization
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@ -11,7 +11,6 @@ sim-search/
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├── query/
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│ ├── __init__.py
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│ ├── query_processor.py # Module for processing user queries
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│ ├── query_classifier.py # Module for classifying query types
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│ └── llm_interface.py # Module for interacting with LLM providers
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├── execution/
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│ ├── __init__.py
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@ -22,15 +21,68 @@ sim-search/
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│ ├── base_handler.py # Base class for search handlers
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│ ├── serper_handler.py # Handler for Serper API (Google search)
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│ ├── scholar_handler.py # Handler for Google Scholar via Serper
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│ ├── google_handler.py # Handler for Google search
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│ └── arxiv_handler.py # Handler for arXiv API
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├── ranking/
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│ ├── __init__.py
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│ ├── jina_reranker.py # Module for reranking documents using Jina AI
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│ └── filter_manager.py # Module for filtering documents
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├── test_search_execution.py # Test script for search execution
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├── test_all_handlers.py # Test script for all search handlers
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├── requirements.txt # Project dependencies
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└── search_execution_test_results.json # Test results
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│ └── jina_reranker.py # Module for reranking documents using Jina AI
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├── report/
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│ ├── __init__.py
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│ ├── report_generator.py # Module for generating reports
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│ ├── report_synthesis.py # Module for synthesizing reports
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│ ├── document_processor.py # Module for processing documents
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│ ├── document_scraper.py # Module for scraping documents
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│ ├── report_detail_levels.py # Module for managing report detail levels
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│ └── database/ # Database for storing reports
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│ ├── __init__.py
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│ └── db_manager.py # Module for managing the database
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├── ui/
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│ ├── __init__.py
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│ └── gradio_interface.py # Gradio-based web interface
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├── utils/
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│ ├── __init__.py
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│ ├── jina_similarity.py # Module for computing text similarity
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│ └── markdown_segmenter.py # Module for segmenting markdown documents
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├── scripts/
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│ └── query_to_report.py # Script for generating reports from queries
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├── tests/
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│ ├── __init__.py
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│ ├── query/ # Tests for query module
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│ │ ├── __init__.py
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│ │ ├── test_query_processor.py
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│ │ ├── test_query_processor_comprehensive.py
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│ │ └── test_llm_interface.py
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│ ├── execution/ # Tests for execution module
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│ │ ├── __init__.py
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│ │ ├── test_search.py
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│ │ ├── test_search_execution.py
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│ │ └── test_all_handlers.py
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│ ├── ranking/ # Tests for ranking module
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│ │ ├── __init__.py
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│ │ ├── test_reranker.py
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│ │ ├── test_similarity.py
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│ │ └── test_simple_reranker.py
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│ ├── report/ # Tests for report module
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│ │ ├── __init__.py
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│ │ ├── test_custom_model.py
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│ │ └── test_detail_levels.py
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│ ├── ui/ # Tests for UI module
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│ │ ├── __init__.py
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│ │ └── test_ui_search.py
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│ ├── integration/ # Integration tests
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│ │ ├── __init__.py
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│ │ ├── test_ev_query.py
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│ │ └── test_query_to_report.py
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│ ├── test_document_processor.py
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│ ├── test_document_scraper.py
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│ └── test_report_synthesis.py
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├── examples/
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│ ├── __init__.py
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│ ├── data/ # Example data files
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│ └── scripts/ # Example scripts
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│ └── __init__.py
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├── run_ui.py # Script to run the UI
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└── requirements.txt # Project dependencies
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```
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## Module Details
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@ -1,52 +1,55 @@
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# Current Focus: Google Gemini Integration, Reference Formatting, and NoneType Error Fixes
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# Current Focus: Project Directory Reorganization, Testing, and Embedding Usage
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## Active Work
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### Google Gemini Integration
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- ✅ Fixed the integration of Google Gemini models with LiteLLM
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- ✅ Updated message formatting for Gemini models
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- ✅ Added proper handling for the 'gemini' provider in environment variables
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- ✅ Fixed reference formatting issues with Gemini models
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- ✅ Converted LLM interface methods to async to fix runtime errors
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### Project Directory Reorganization
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- ✅ Reorganized project directory structure for better maintainability
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- ✅ Moved utility scripts to the `utils/` directory
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- ✅ Organized test files into subdirectories under `tests/`
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- ✅ Moved sample data to the `examples/data/` directory
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- ✅ Created proper `__init__.py` files for all packages
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- ✅ Verified pipeline functionality after reorganization
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### Gradio UI Updates
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- ✅ Updated the Gradio interface to handle async methods
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- ✅ Fixed parameter ordering in the report generation function
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- ✅ Improved error handling in the UI
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### Embedding Usage Analysis
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- ✅ Confirmed that the pipeline uses Jina AI's Embeddings API through the `JinaSimilarity` class
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- ✅ Verified that the `JinaReranker` class uses embeddings for document reranking
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- ✅ Analyzed how embeddings are integrated into the search and ranking process
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### Bug Fixes
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- ✅ Fixed NoneType error in report synthesis when chunk titles are None
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- ✅ Added defensive null checks throughout document processing and report synthesis
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- ✅ Improved chunk counter in map_document_chunks method
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### Pipeline Testing
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- ✅ Tested the pipeline after reorganization to ensure functionality
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- ✅ Verified that the UI works correctly with the new directory structure
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- ✅ Confirmed that all imports are working properly with the new structure
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## Recent Changes
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### Reference Formatting Improvements
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- Enhanced the instructions for reference formatting to ensure URLs are included
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- Added a recovery mechanism for truncated references
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- Improved context preparation to better extract URLs for references
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- Added duplicate URL fields in the context to emphasize their importance
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### Directory Structure Reorganization
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- Created a dedicated `utils/` directory for utility scripts
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- Moved `jina_similarity.py` to `utils/`
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- Added `__init__.py` to make it a proper Python package
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- Organized test files into subdirectories under `tests/`
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- Created subdirectories for each module (query, execution, ranking, report, ui, integration)
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- Added `__init__.py` files to all test directories
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- Created an `examples/` directory with subdirectories for data and scripts
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- Moved sample data to `examples/data/`
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- Added `__init__.py` files to make them proper Python packages
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- Added a dedicated `scripts/` directory for utility scripts
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- Moved `query_to_report.py` to `scripts/`
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### Async LLM Interface
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- Made `generate_completion`, `classify_query`, `enhance_query`, and `generate_search_queries` methods async
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- Updated dependent code to properly await these methods
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- Fixed runtime errors related to async/await patterns in the QueryProcessor
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### Error Handling Improvements
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- Added null checks for chunk titles in report synthesis
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- Improved chunk counter in map_document_chunks method
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- Added defensive code to ensure all chunks have titles
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- Updated document processor to handle None titles with default values
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### Pipeline Verification
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- Verified that the pipeline functions correctly after reorganization
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- Confirmed that the `JinaSimilarity` class in `utils/jina_similarity.py` is properly used for embeddings
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- Tested the reranking functionality with the `JinaReranker` class
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- Checked that the report generation process works with the new structure
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## Next Steps
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1. Continue testing with Gemini models to ensure stable operation
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2. Consider adding more robust error handling for LLM provider-specific issues
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3. Improve the reference formatting further if needed
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4. Update documentation to reflect the changes made to the LLM interface
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5. Consider adding more unit tests for the async methods
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6. Add more comprehensive null checks throughout the codebase
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7. Implement better error handling and recovery mechanisms
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1. Run comprehensive tests to ensure all functionality works with the new directory structure
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2. Update any remaining documentation to reflect the new directory structure
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3. Consider moving the remaining test files in the root of the `tests/` directory to appropriate subdirectories
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4. Review import statements throughout the codebase to ensure they follow the new structure
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5. Add more comprehensive documentation about the directory structure
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6. Consider creating a development guide for new contributors
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7. Implement automated tests to verify the directory structure remains consistent
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### Future Enhancements
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@ -644,6 +644,60 @@ Fixed reference formatting issues with Gemini models and updated the codebase to
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- Fixed the parameter order in the lambda function for async execution
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- Improved error handling in the UI
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## Session: 2025-03-11
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### Overview
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Reorganized the project directory structure to improve maintainability and clarity, ensuring all components are properly organized into their respective directories.
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### Key Activities
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1. **Directory Structure Reorganization**:
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- Created a dedicated `utils/` directory for utility scripts
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- Moved `jina_similarity.py` to `utils/`
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- Added `__init__.py` to make it a proper Python package
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- Organized test files into subdirectories under `tests/`
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- Created subdirectories for each module (query, execution, ranking, report, ui, integration)
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- Added `__init__.py` files to all test directories
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- Created an `examples/` directory with subdirectories for data and scripts
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- Moved sample data to `examples/data/`
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- Added `__init__.py` files to make them proper Python packages
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- Added a dedicated `scripts/` directory for utility scripts
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- Moved `query_to_report.py` to `scripts/`
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2. **Pipeline Verification**:
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- Tested the pipeline after reorganization to ensure functionality
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- Verified that the UI works correctly with the new directory structure
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- Confirmed that all imports are working properly with the new structure
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3. **Embedding Usage Analysis**:
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- Confirmed that the pipeline uses Jina AI's Embeddings API through the `JinaSimilarity` class
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- Verified that the `JinaReranker` class uses embeddings for document reranking
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- Analyzed how embeddings are integrated into the search and ranking process
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### Insights
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- A well-organized directory structure significantly improves code maintainability and readability
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- Using proper Python package structure with `__init__.py` files ensures clean imports
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- Separating tests, utilities, examples, and scripts into dedicated directories makes the codebase more navigable
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- The Jina AI embeddings are used throughout the pipeline for semantic similarity and document reranking
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### Challenges
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- Ensuring all import statements are updated correctly after moving files
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- Maintaining backward compatibility with existing code
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- Verifying that all components still work together after reorganization
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### Next Steps
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1. Run comprehensive tests to ensure all functionality works with the new directory structure
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2. Update any remaining documentation to reflect the new directory structure
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3. Consider moving the remaining test files in the root of the `tests/` directory to appropriate subdirectories
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4. Review import statements throughout the codebase to ensure they follow the new structure
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### Key Insights
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- Async/await patterns need to be consistently applied throughout the codebase
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- Reference formatting requires explicit instructions to include URLs
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