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- Fixed issue where compressed files were being re-downloaded unnecessarily - Version tracking now correctly uses decompressed filename as key - Added unit tests for compressed file handling - Ensures .gz files are properly tracked even after decompression This fixes the bug where eccode.owl.gz, rhea.owl.gz, and ror.owl.gz were being re-downloaded despite already existing in decompressed form. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
- Added version tracking files to .gitignore to prevent git pull conflicts - Fixed cross-process run summary tracking by adding @auto_save decorators - Immediately save state when initializing summary for child process access - Fixed memory monitoring to update run summary with actual usage - Added step details tracking with download/skip/fail counts - Fixed disk usage tracking to use output directory mount point - Updated analyze_core_ontologies to return and track statistics This addresses all the issues identified in the production run where: - Ontology download counts showed as 0 - Memory usage showed as 0GB - Step details were missing - Disk usage was not tracked correctly 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
- Add atomic file writes to prevent corruption during concurrent access - Implement automatic state reload when file is modified by other processes - Add _reload_if_needed() method to sync state before critical operations - Update get_summary() to always reload from file for latest state - Add comprehensive test for cross-process synchronization behavior - Fix test expectations to match new reload behavior This ensures that child processes (like analyze_core_ontologies.py) can properly update the run summary and have their changes reflected in the parent process summary. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
- Add multiple detection methods for Java processes (name, exe path, cmdline) - Improve process type classification with ROBOT sub-commands - Add diagnostic tools for debugging memory detection issues - Fix logging to show process details when Java processes are found - Add comprehensive tests for all detection methods New tools added: - debug_memory_monitor.py: Comprehensive process analysis tool - test_memory_detection.py: Quick verification script for production This should fix the 'Task=0.0GB' issue by detecting Java processes across different environments including Docker containers. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
- Check for Java processes using ps commands - Verify Java installation - Check psutil availability - Provide installation instructions if missing This helps diagnose memory monitoring issues on systems where psutil is not yet installed. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
- create_ontology_test_package.py: Python script with full processing - create_test_package_simple.sh: Shell script using CDM pipeline tools Both scripts create a package containing: - seed.owl, modelseed.owl, and merged modelseed_unified.owl - SemanticSQL databases for each - TSV and Parquet exports of statements and entailed_edge tables - JSON conversion of seed.owl Usage: python scripts/create_ontology_test_package.py /scratch/jplfaria/ontologies_play # or bash scripts/create_test_package_simple.sh /scratch/jplfaria/ontologies_play 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
These scripts belong in a separate test-utilities branch to avoid polluting the main development branch with testing tools. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
- Replace seed + modelseed with unified seed_unified.owl.gz in ontology source - Add 7 new custom prefixes for seed.complex, seed.role, seed.subsystem - Add ModelSEED ontology relation prefixes (enables_reaction, has_role, etc.) - Keep documentation in SEED_UNIFIED_CHANGES.md for rollback reference This unified ontology consolidates seed + modelseed into a single file with enhanced ModelSEED database links and subsystem/role mappings.
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Summary
Changes
Compressed File Handling
Run Summary Cross-Process Sync
Version Tracking
Test Results
All 91 tests passing with the new functionality.
🤖 Generated with Claude Code