cBioPortal #36
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cBioPortal #36
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added 3 commits
June 21, 2025 16:53
added 4 commits
June 24, 2025 18:01
- Sequential thinking moved from search(domain="thinking") to dedicated think tool - Think tool is now MANDATORY before any search operations - Search query parameter changed from optional to required with empty default Added: - Dedicated think tool for systematic biomedical analysis (required first step) - 10 individual tools restored: article_searcher/getter, trial_searcher/getter + 3 detail getters, trial_locations_getter, variant_searcher/getter - Thinking usage tracker with automatic reminders in search results - Enhanced cBioPortal integration in individual tools via include_cbioportal parameter - Centralized cbioportal_helper module to reduce code duplication - Location parameter validation for trial searches Fixed: - MyVariant.info timeout issues (now uses configured 120s timeout) - Added myvariant to aggressive retry domains - Optimized BRAF V600E query pattern to prevent timeouts - Improved timeout error messages with actionable suggestions Improved: - Total of 13 MCP tools: 3 core (think, search, fetch) + 10 individual - Better code organization with dedicated helper modules - Enhanced type safety with proper annotations - Consistent error handling and logging - ChatGPT compatibility with simplified query parameter Updated all documentation to reflect new tool structure and mandatory think-first workflow. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> This commit message follows conventional commit format with: - Clear feature description in the title - Breaking changes section highlighting API changes - Organized sections for Added/Fixed/Improved - Specific details about what changed - Attribution as requested
- Sequential thinking moved from search(domain="thinking") to dedicated think tool - Think tool is now MANDATORY before any search operations - Search query parameter changed from optional to required with empty default Added: - Dedicated think tool for systematic biomedical analysis (required first step) - 10 individual tools restored: article_searcher/getter, trial_searcher/getter + 3 detail getters, trial_locations_getter, variant_searcher/getter - Thinking usage tracker with automatic reminders in search results - Enhanced cBioPortal integration in individual tools via include_cbioportal parameter - Centralized cbioportal_helper module to reduce code duplication - Location parameter validation for trial searches Fixed: - MyVariant.info timeout issues (now uses configured 120s timeout) - Added myvariant to aggressive retry domains - Optimized BRAF V600E query pattern to prevent timeouts - Improved timeout error messages with actionable suggestions Improved: - Total of 13 MCP tools: 3 core (think, search, fetch) + 10 individual - Better code organization with dedicated helper modules - Enhanced type safety with proper annotations - Consistent error handling and logging - ChatGPT compatibility with simplified query parameter Updated all documentation to reflect new tool structure and mandatory think-first workflow. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> This commit message follows conventional commit format with: - Clear feature description in the title - Breaking changes section highlighting API changes - Organized sections for Added/Fixed/Improved - Specific details about what changed - Attribution as requested
imaurer
approved these changes
Jun 27, 2025
added 2 commits
June 27, 2025 15:22
- Sequential thinking moved from search(domain="thinking") to dedicated think tool - Think tool is now MANDATORY before any search operations - Search query parameter changed from optional to required with empty default Added: - Dedicated think tool for systematic biomedical analysis (required first step) - 10 individual tools restored: article_searcher/getter, trial_searcher/getter + 3 detail getters, trial_locations_getter, variant_searcher/getter - Thinking usage tracker with automatic reminders in search results - Enhanced cBioPortal integration in individual tools via include_cbioportal parameter - Centralized cbioportal_helper module to reduce code duplication - Location parameter validation for trial searches Fixed: - MyVariant.info timeout issues (now uses configured 120s timeout) - Added myvariant to aggressive retry domains - Optimized BRAF V600E query pattern to prevent timeouts - Improved timeout error messages with actionable suggestions Improved: - Total of 13 MCP tools: 3 core (think, search, fetch) + 10 individual - Better code organization with dedicated helper modules - Enhanced type safety with proper annotations - Consistent error handling and logging - ChatGPT compatibility with simplified query parameter Updated all documentation to reflect new tool structure and mandatory think-first workflow. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> This commit message follows conventional commit format with: - Clear feature description in the title - Breaking changes section highlighting API changes - Organized sections for Added/Fixed/Improved - Specific details about what changed - Attribution as requested
- Sequential thinking moved from search(domain="thinking") to dedicated think tool - Think tool is now MANDATORY before any search operations - Search query parameter changed from optional to required with empty default Added: - Dedicated think tool for systematic biomedical analysis (required first step) - 10 individual tools restored: article_searcher/getter, trial_searcher/getter + 3 detail getters, trial_locations_getter, variant_searcher/getter - Thinking usage tracker with automatic reminders in search results - Enhanced cBioPortal integration in individual tools via include_cbioportal parameter - Centralized cbioportal_helper module to reduce code duplication - Location parameter validation for trial searches Fixed: - MyVariant.info timeout issues (now uses configured 120s timeout) - Added myvariant to aggressive retry domains - Optimized BRAF V600E query pattern to prevent timeouts - Improved timeout error messages with actionable suggestions Improved: - Total of 13 MCP tools: 3 core (think, search, fetch) + 10 individual - Better code organization with dedicated helper modules - Enhanced type safety with proper annotations - Consistent error handling and logging - ChatGPT compatibility with simplified query parameter Updated all documentation to reflect new tool structure and mandatory think-first workflow. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> This commit message follows conventional commit format with: - Clear feature description in the title - Breaking changes section highlighting API changes - Organized sections for Added/Fixed/Improved - Specific details about what changed - Attribution as requested
jyeakley
added a commit
that referenced
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Aug 3, 2025
- cBioPortal Integration - Fixed lat/long for prompt - Added verbiage to biomcp to clarify usage to AI Clients BREAKING CHANGES: - Sequential thinking moved from search(domain="thinking") to dedicated think tool - Think tool is now MANDATORY before any search operations - Search query parameter changed from optional to required with empty default Added: - Dedicated think tool for systematic biomedical analysis (required first step) - 10 individual tools restored: article_searcher/getter, trial_searcher/getter + 3 detail getters, trial_locations_getter, variant_searcher/getter - Thinking usage tracker with automatic reminders in search results - Enhanced cBioPortal integration in individual tools via include_cbioportal parameter - Centralized cbioportal_helper module to reduce code duplication - Location parameter validation for trial searches Fixed: - MyVariant.info timeout issues (now uses configured 120s timeout) - Added myvariant to aggressive retry domains - Optimized BRAF V600E query pattern to prevent timeouts - Improved timeout error messages with actionable suggestions Improved: - Total of 13 MCP tools: 3 core (think, search, fetch) + 10 individual - Better code organization with dedicated helper modules - Enhanced type safety with proper annotations - Consistent error handling and logging - ChatGPT compatibility with simplified query parameter Updated all documentation to reflect new tool structure and mandatory think-first workflow.
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cBioPortal Integration
Fixed lat/long for prompt
Added verbiage to biomcp to clarify usage to AI Clients
BREAKING CHANGES:
Added:
Fixed:
Improved:
Updated all documentation to reflect new tool structure and mandatory think-first workflow.