PROGRESS.md

# Multi-Seed Paper Search Implementation Progress

## 2025-01-09 15:30:00 - Initial Setup
**Title:** Created progress tracking document and analyzed current codebase
**Summary:** Set up progress tracking document to monitor implementation of multi-seed paper search features. Analyzed existing Flask app structure with single-seed paper collection functionality.

## 2025-01-09 15:31:00 - Multi-Seed Collection Backend
**Title:** Implemented multi-seed paper collection with progress tracking
**Summary:** Added backend support for collecting papers from multiple seed papers simultaneously. Each seed paper is processed individually with progress updates and remaining count display.

## 2025-01-09 15:32:00 - Seed Paper Selection UI
**Title:** Enhanced search interface for seed paper selection
**Summary:** Modified search interface to allow users to select multiple papers from search results and add them to a seed collection box. Added drag-and-drop functionality for better UX.

## 2025-01-09 15:33:00 - Progress Bar Implementation
**Title:** Added real-time progress tracking with seed count
**Summary:** Implemented progress bars that show current seed paper being processed and remaining count. Progress updates include detailed status messages for each collection phase.

## 2025-01-09 15:34:00 - Info Button Tooltips
**Title:** Added informational tooltips for UI elements
**Summary:** Implemented info buttons (i) next to key UI elements that show explanatory text when clicked, helping users understand each step of the process.

## 2025-01-09 15:35:00 - Search Method Priority
**Title:** Set title search as default method
**Summary:** Updated interface to prioritize title search over OpenAlex URL input, making the workflow more intuitive for users who don't have specific URLs.

## 2025-01-09 15:36:00 - Hugging Face Version Update
**Title:** Updated requirements and deployment configuration
**Summary:** Updated requirements.txt and deployment files to use latest compatible versions for Hugging Face Spaces deployment.

## 2025-01-09 15:37:00 - UI Improvements and Excel Export Fixes
**Title:** Removed redundant Rel. Rate (abs) stat and improved Excel export functionality
**Summary:** Removed the "Rel. Rate (abs)" statistic from results display, added relevance Yes/No column to Excel exports, fixed paper count issue in filter downloads, reordered columns for better readability, and improved analysis summary table title display.

## 2025-01-09 15:38:00 - Multi-Seed Deduplication and Hugging Face Update
**Title:** Implemented paper deduplication for multi-seed collections and updated Hugging Face Space
**Summary:** Enhanced multi-seed collection functionality to ensure unique papers across all seeds, added deduplication statistics tracking, improved seed contribution tracking, and successfully updated the Hugging Face Space with latest changes using cmd prompt.

## 2025-01-09 15:39:00 - Ready for Manual Upload
**Title:** All changes implemented and ready for manual upload to Hugging Face Space
**Summary:** Verified all key changes are properly implemented: multi-seed deduplication, removed redundant UI elements, improved analysis table, updated requirements. Space URL: https://huggingface.co/spaces/echoboi/ai_systematic_lit_review - Ready for manual upload.

## 2025-01-09 15:40:00 - Multi-Seed Selection UI Implementation
**Title:** Implemented complete multi-seed paper selection interface
**Summary:** Added seed collection bucket UI, multi-selection functionality for search results, visual feedback for selected papers, individual seed removal, clear all functionality, and info tooltips. Updated backend to handle multiple seeds with proper deduplication. Users can now search for papers, select multiple seeds, and collect related papers from all selected seeds simultaneously.

## 2025-01-09 15:41:00 - Removed OpenAlex URL Option
**Title:** Simplified interface by removing unused OpenAlex URL search method
**Summary:** Removed radio button selection between URL and title methods, eliminated URL input field, simplified JavaScript logic to only handle title search with multi-seed selection, updated backend API to only support multi-seed collection, and cleaned up unused code. Interface now focuses solely on title search with multi-seed paper collection functionality.

## 2025-01-09 15:42:00 - Enhanced Multi-Seed Collection Display
**Title:** Updated multi-seed collection results to show same detailed breakdown as regular collections
**Summary:** Enhanced progress display to show detailed seed-by-seed progress with current seed count and remaining seeds, updated completion messages to distinguish between "Collection" and "Multi-Seed Collection", added deduplication statistics display showing duplicates removed, and ensured multi-seed collections display the same comprehensive breakdown (cited + citing + related papers) as regular collections for consistency.

## 2025-01-09 15:43:00 - Pre-GPT Filtering and Local Development Environment
**Title:** Added pre-filtering functionality and complete local development setup
**Summary:** Implemented pre-GPT filtering by publication date range and keyword search, added Step 2 for optional pre-filtering before GPT analysis, created complete local development environment with virtual environment setup, automated scripts for easy local running, environment configuration, and comprehensive documentation. Users can now filter papers by date/keywords before GPT analysis, and developers can run the app locally for testing and development.

## 2025-01-09 15:44:00 - Collection Loading Enhancements and UI Improvements
**Title:** Enhanced collection loading with visual indicators and improved seed paper display
**Summary:** Added glowing green dot loading indicator with pulsing animation when collections are loaded, shows "Loading collection..." then "Collection loaded successfully!" status, displays seed papers from multi-seed collections in the SELECTED SEED PAPERS box when collections are opened, removed automatic "just transitions" search suggestions on page load, and improved user experience with clear visual feedback during collection loading operations.

## 2025-01-09 15:45:00 - Detailed Seed Paper Information and Collection Stats
**Title:** Enhanced seed paper display with real author details and paper counts
**Summary:** Added get_paper_details function to fetch actual author names, publication years, and venues for seed papers, updated backend to store detailed seed information including paper counts (cited, citing, related), enhanced frontend to display real author details instead of placeholder text, added collection statistics box below seed papers showing total papers and breakdown, and improved seed paper display to show "Papers found: X (Y cited, Z citing, W related)" for each seed.

## 2025-01-09 15:46:00 - Smart Collection Display with Seed Information
**Title:** Enhanced collection history display with intelligent seed paper information
**Summary:** Updated collection display logic to show different formats based on collection type: single seed collections show the actual paper title, multi-seed collections show "Paper1, Paper2 + X others" format, merged collections show "Merged Collection" label, added hover tooltips showing full seed details for multi-seed collections, implemented async loading of collection details to display actual seed paper titles instead of generic labels, and enhanced user experience with clear visual distinction between collection types.