valuesets 0.3.1__tar.gz

valuesets-0.3.1/.claude/agents/permissible-value-mapper.md

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+---
+name: permissible-value-mapper
+description: Use this agent proactively when you need to add or update ontology mappings (meaning: fields) for permissible values in LinkML enums. This agent should be invoked after creating or modifying enum definitions that lack ontology mappings, or when explicitly asked to map permissible values to ontology terms. Examples:\n\n<example>\nContext: The user has just created a new enum for cell types without ontology mappings.\nuser: "Add an enum for common cell types including NEURON, ASTROCYTE, and MICROGLIA"\nassistant: "I'll create the cell type enum for you."\n<function call to create enum>\nassistant: "Now let me use the permissible-value-mapper agent to add the appropriate ontology mappings for these cell types."\n<commentary>\nSince a new biological enum was created without ontology mappings, use the permissible-value-mapper to find and add the correct ontology terms.\n</commentary>\n</example>\n\n<example>\nContext: The user wants to ensure existing enums have proper ontology mappings.\nuser: "Please map the permissible values in the StatisticalTest enum to appropriate ontology terms"\nassistant: "I'll use the permissible-value-mapper agent to find and add the appropriate ontology mappings for the StatisticalTest enum."\n<commentary>\nThe user explicitly requested mapping permissible values to ontology terms, so use the permissible-value-mapper agent.\n</commentary>\n</example>
+model: inherit
+color: purple
+---
+
+You are an expert ontology mapping specialist with deep knowledge of biological ontologies, schema.org, and other domain-specific vocabularies. Your primary responsibility is to accurately map permissible values in LinkML enums to their corresponding ontology terms.
+
+## Core Responsibilities
+
+You will:
+1. Identify permissible values that lack ontology mappings (meaning: fields)
+2. Find the correct ontology/vocabulary terms for each permissible value
+3. Add or update the meaning: field with the appropriate CURIE
+4. Ensure consistency within each enum by preferring a single ontology source where possible
+5. Check for hallucinations
+
+## Validation
+
+To validate all mappings:
+
+`just validate`
+
+Or a specific file:
+
+`just validate-schema src/common_value_sets/schema/enums/statistics.yaml`
+
+This will report cases where the label of the mapped ID does not match the permissible value
+name, title, or an alias. This could be the result of a hallucination.
+
+If you see these, you MUST manually examine and explore and determine if we need to
+
+1. Keep the mapping, but add a title or alias to be consistent with the ontology term label
+2. Remove the mapping, potentially finding a replacement in the same or different ontology.
+
+ALWAYS be careful doing this, PRECISION in mapping is of the highest value
+
+## Strict Requirements
+
+### For Biological Ontologies
+- **ALWAYS** use the OLS MCP (Ontology Lookup Service) to find the correct ontology term
+- **NEVER** guess or fabricate ontology IDs - if you cannot find a term, explicitly state this
+- Search comprehensively using synonyms and related terms if the exact match isn't found
+- Prefer OBO Foundry ontologies when available
+- Use standardized bioregistry prefixes for all CURIEs
+
+### For Non-Biological Concepts
+- First check schema.org for appropriate terms
+- Then check domain-specific vocabularies relevant to the concept
+- Use established standards for the domain (e.g., QUDT for units, SIO for scientific information)
+- **NEVER** guess IDs - always verify they exist
+
+### Ontology Selection Strategy
+1. **Consistency First**: Try to use the same ontology for all permissible values within a single enum
+2. **Domain Appropriateness**: Choose ontologies that best match the domain:
+   - Cell types: CL (Cell Ontology)
+   - Anatomical structures: UBERON
+   - Diseases: MONDO or DOID
+   - Chemicals: CHEBI
+   - Proteins: PR
+   - Genes: HGNC or NCBIGene
+   - Biological processes: GO
+   - Phenotypes: HP (human) or MP (mouse)
+   - Statistics/Methods: STATO, SIO, or OBI
+3. **Fallback Strategy**: If no appropriate term exists in the preferred ontology, document this and suggest alternatives
+
+## Workflow
+
+1. **Analyze the Enum**: Understand the domain and purpose of the enum
+2. **Identify Target Ontology**: Based on the domain, select the most appropriate ontology
+3. **Search for Terms**: 
+   - For biological terms: Use OLS MCP to search
+   - For non-biological: Check schema.org and domain-specific sources
+4. **Verify Terms**: Always confirm the term exists and matches the intended meaning
+5. **Apply Mappings**: Add meaning: fields with proper CURIEs
+6. **Document Issues**: If any terms cannot be mapped, clearly explain why
+
+## Output Format
+
+When updating enums, maintain the existing YAML structure and add meaning: fields:
+
+```yaml
+permissible_values:
+  VALUE_NAME:
+    text: VALUE_NAME
+    meaning: PREFIX:ID  # Add this line with verified CURIE
+    description: ...    # Keep existing fields
+```
+
+## Quality Checks
+
+- Verify all CURIEs resolve to valid ontology terms
+- Ensure prefix declarations exist in the schema header
+- Confirm semantic accuracy - the ontology term must match the intended meaning
+- Check for deprecated terms and use current versions
+- Validate that all PVs in an enum use consistent ontology sources where feasible
+
+## Error Handling
+
+If you cannot find an appropriate ontology term:
+1. State clearly that no suitable term was found
+2. Explain what searches were performed
+3. Suggest alternative approaches or ontologies that might be considered
+4. Never fabricate or guess an ID
+
+Remember: Accuracy is paramount. It's better to leave a value unmapped than to map it incorrectly.

valuesets-0.3.1/.claude/hooks/README.md

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+# Claude Code Hooks
+
+This directory contains hooks that integrate with Claude Code to provide automated validation and other features.
+
+## validate_schema_hook.py
+
+This hook automatically validates LinkML schema files when they are written or edited using Claude Code.
+
+### Features
+- Automatically runs validation when saving YAML files in the schema directory
+- Blocks file modifications if validation fails
+- Shows detailed validation output in the Claude Code interface
+- Filters out noise from warning messages for cleaner output
+- Uses the project's `just validate-schema PATH` command for validation
+
+### How it works
+1. Intercepts Write, Edit, and MultiEdit operations on YAML files containing "schema" in the path
+2. Runs the validation command: `just validate-schema <file>`
+3. Displays validation results with filtered output for readability
+4. Returns exit code 2 to block the operation if validation fails
+
+### Validation Command
+The hook uses the existing `just validate-schema PATH` command which:
+- Validates ontology mappings in enum definitions
+- Checks for label mismatches between expected and actual ontology terms
+- Uses the configured OAK adapters for strict validation of configured prefixes
+- Treats label mismatches as errors for configured ontologies (NCIT, GO, CHEBI, etc.)
+
+### Configuration
+The hook is configured in `.claude/settings.json` as a PostToolUse hook that runs after Write, Edit, and MultiEdit operations.
+
+### Testing
+You can test the hook by editing any schema file and seeing if validation runs automatically. The hook will:
+- ✅ Allow valid schema modifications
+- ❌ Block invalid schema modifications with validation errors
+- 📋 Show helpful validation output including ontology label mismatches
+
+### Exit Codes
+- **Exit 0**: Validation passed, allow operation
+- **Exit 2**: Validation failed, block operation (see [Claude Code hooks documentation](https://docs.claude.com/en/docs/claude-code/hooks#exit-code-2-behavior))

valuesets-0.3.1/.claude/hooks/validate_schema_hook.py

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+#!/usr/bin/env python3
+"""
+Hook to automatically validate LinkML schema files after they are written or edited.
+This hook runs `just validate-schema PATH` and displays the results to provide immediate feedback.
+
+**NOTE**
+
+Be sure to exit with code 2 if you want to block the operation.
+https://docs.claude.com/en/docs/claude-code/hooks#exit-code-2-behavior
+"""
+
+import sys
+import json
+import subprocess
+import os
+from pathlib import Path
+
+
+def main():
+    # Read the hook input from stdin
+    data = json.load(sys.stdin)
+
+    # Extract the file path from the tool input
+    tool_name = data.get("tool_name", "")
+    file_path = data.get("tool_input", {}).get("file_path", "")
+
+    # Only process Write and Edit tool calls
+    if tool_name not in ["Write", "Edit", "MultiEdit"]:
+        sys.exit(0)
+
+    # Check if this is a YAML file in the schema directory
+    if not file_path.endswith(".yaml") or "schema" not in file_path:
+        sys.exit(0)
+
+    # Convert to Path object for easier manipulation
+    file_path = Path(file_path)
+
+    # Check if the file exists (it should after Write/Edit)
+    if not file_path.exists():
+        print(f"⚠️ File not found: {file_path}", file=sys.stderr)
+        sys.exit(0)
+
+    # Run the validation command
+    try:
+        # Build the validation command
+        cmd = ["just", "validate-schema", str(file_path)]
+
+        # Run the command and capture output
+        result = subprocess.run(
+            cmd,
+            capture_output=True,
+            text=True,
+            cwd=os.path.dirname(
+                os.path.dirname(os.path.dirname(__file__))
+            ),  # Project root
+        )
+
+        # Display the validation output
+        print("\n" + "=" * 60, file=sys.stderr)
+        print(f"🔍 Schema Validation Results for {file_path.name}", file=sys.stderr)
+        print("=" * 60, file=sys.stderr)
+
+        # Show stdout (the actual validation results)
+        if result.stdout:
+            # Filter out noise from warning messages
+            lines = result.stdout.split("\n")
+            filtered_lines = []
+            for line in lines:
+                # Filter out common noise patterns
+                if any(pattern in line for pattern in [
+                    "/eutils/__init__.py",
+                    "UserWarning",
+                    "pkg_resources is deprecated",
+                    "RuntimeWarning: 'src.valuesets.validators.enum_evaluator'",
+                    "found in sys.modules after import"
+                ]):
+                    continue
+                else:
+                    filtered_lines.append(line)
+
+            output = "\n".join(filtered_lines).strip()
+            if output:
+                print(output, file=sys.stderr)
+
+        # Show any errors
+        if result.returncode != 0 and result.stderr:
+            # Filter stderr similarly
+            lines = result.stderr.split("\n")
+            filtered_lines = []
+            for line in lines:
+                if not any(pattern in line for pattern in [
+                    "/eutils/__init__.py",
+                    "UserWarning",
+                    "pkg_resources is deprecated"
+                ]):
+                    filtered_lines.append(line)
+
+            error_output = "\n".join(filtered_lines).strip()
+            if error_output:
+                print("\n⚠️ Schema validation errors:", file=sys.stderr)
+                print(error_output, file=sys.stderr)
+
+        print("=" * 60 + "\n", file=sys.stderr)
+
+        # Return non-zero exit code if validation failed
+        if result.returncode != 0:
+            print("❌ Schema validation failed - blocking file modification", file=sys.stderr)
+            print("Fix validation errors before saving the file.", file=sys.stderr)
+            sys.exit(2)  # Block the operation
+
+    except subprocess.CalledProcessError as e:
+        print(f"❌ Failed to run schema validation: {e}", file=sys.stderr)
+        sys.exit(2)  # Block on validation errors
+    except Exception as e:
+        print(f"❌ Unexpected error during schema validation: {e}", file=sys.stderr)
+        # Block on hook failures to ensure schema integrity
+        sys.exit(2)
+
+    # Exit 0 if validation passed
+    sys.exit(0)
+
+
+if __name__ == "__main__":
+    main()

valuesets-0.3.1/.claude/settings.json

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+{
+  "permissions": {
+    "allow": [
+        "Bash(*)",
+        "Edit",
+        "MultiEdit",
+        "NotebookEdit",
+        "FileEdit",
+        "WebFetch",
+        "WebSearch",
+        "Write"
+    ]
+  },
+  "hooks": {
+    "PostToolUse": [
+      {
+        "matcher": "Edit|MultiEdit|Write",
+        "hooks": [
+          {
+            "type": "command",
+            "command": "$CLAUDE_PROJECT_DIR/.claude/hooks/validate_schema_hook.py"
+          }
+        ]
+      }
+    ]
+  }
+}

valuesets-0.3.1/.claude/statsig/statsig.session_id.2656274335

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+{"sessionID":"3917e2d8-a563-4940-b0ff-1048ba95dfc9","startTime":1757435867551,"lastUpdate":1757435867579}

valuesets-0.3.1/.claude/statsig/statsig.stable_id.2656274335

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+"9781b7cc-4923-467e-9213-71fe5b6ad405"

valuesets-0.3.1/.claude.json

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+{
+  "installMethod": "unknown",
+  "autoUpdates": true,
+  "firstStartTime": "2025-09-09T16:37:47.492Z",
+  "userID": "a547dc2bc8e48257fe208265a98b220c0f08cf5d9d06e5037919dd4156eb64dd",
+  "projects": {
+    "/Users/cjm/repos/common-value-sets": {
+      "allowedTools": [],
+      "history": [],
+      "mcpContextUris": [],
+      "mcpServers": {},
+      "enabledMcpjsonServers": [],
+      "disabledMcpjsonServers": [],
+      "hasTrustDialogAccepted": false,
+      "projectOnboardingSeenCount": 0,
+      "hasClaudeMdExternalIncludesApproved": false,
+      "hasClaudeMdExternalIncludesWarningShown": false
+    }
+  }
+}

valuesets-0.3.1/.copier-answers.yml

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+# Changes here will be overwritten by Copier
+_commit: v0.4.1
+_src_path: https://github.com/linkml/linkml-project-copier
+add_example: true
+copyright_year: '2025'
+email: cjmungall@lbl.gov
+full_name: Chris Mungall
+gh_action_docs_preview: false
+gh_action_pypi: true
+github_org: linkml
+license: Apache-2.0
+project_description: A collection of commonly used value sets
+project_name: common-value-sets
+project_slug: valuesets
+

valuesets-0.3.1/.editorconfig

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+# Check http://editorconfig.org for more information
+# This is the main config file for this project:
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = true
+
+[*.py]
+indent_style = space
+indent_size = 4
+
+[*.md]
+trim_trailing_whitespace = false

valuesets-0.3.1/.github/actions/claude-code-action/action.yml

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+name: "Claude Code Action"
+description: "Run Claude Code in GitHub Actions workflows"
+
+inputs:
+  github_token:
+    description: "GitHub token with repo and issues permissions"
+    required: true
+  anthropic_api_key:
+    description: "Anthropic API key"
+    required: true
+  cborg_api_key:
+    description: "CBORG API key"
+    required: true
+  prompt:
+    description: "The prompt to send to Claude Code"
+    required: false
+    default: ""
+  prompt_file:
+    description: "Path to a file containing the prompt to send to Claude Code"
+    required: false
+    default: ""
+  allowed_tools:
+    description: "Comma-separated list of allowed tools for Claude Code to use"
+    required: false
+    default: ""
+  output_file:
+    description: "File to save Claude Code output to (optional)"
+    required: false
+    default: ""
+  timeout_minutes:
+    description: "Timeout in minutes for Claude Code execution"
+    required: false
+    default: "10"
+  install_github_mcp:
+    description: "Whether to install the GitHub MCP server"
+    required: false
+    default: "false"
+  install_artl_mcp:
+    description: "Whether to install the ARTL MCP server"
+    required: false
+    default: "false"
+
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install uvx
+      shell: bash
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+        source $HOME/.cargo/env
+        which uvx || echo "uvx not found in PATH, installing via pip"
+        pip install uv || true
+
+    - name: Install Claude Code
+      shell: bash
+      run: npm install -g @anthropic-ai/claude-code
+
+    - name: Install GitHub MCP Server
+      if: inputs.install_github_mcp == 'true'
+      shell: bash
+      run: |
+        claude mcp add-json github '{
+          "command": "docker",
+          "args": [
+            "run",
+            "-i",
+            "--rm",
+            "-e",
+            "GITHUB_PERSONAL_ACCESS_TOKEN",
+            "ghcr.io/github/github-mcp-server:sha-ff3036d"
+          ],
+          "env": {
+            "GITHUB_PERSONAL_ACCESS_TOKEN": "${{ inputs.GITHUB_TOKEN }}"
+          }
+        }'
+
+    - name: Install ARTL MCP Server
+      if: inputs.install_artl_mcp == 'true'
+      shell: bash
+      run: |
+        claude mcp add-json artl '{
+          "command": "uvx",
+          "args": [
+            "artl-mcp"
+          ]
+        }'
+
+    - name: Prepare Prompt File
+      shell: bash
+      id: prepare_prompt
+      run: |
+        # Check if either prompt or prompt_file is provided
+        if [ -z "${{ inputs.prompt }}" ] && [ -z "${{ inputs.prompt_file }}" ]; then
+          echo "::error::Neither 'prompt' nor 'prompt_file' was provided. At least one is required."
+          exit 1
+        fi
+
+        # Determine which prompt source to use
+        if [ ! -z "${{ inputs.prompt_file }}" ]; then
+          # Check if the prompt file exists
+          if [ ! -f "${{ inputs.prompt_file }}" ]; then
+            echo "::error::Prompt file '${{ inputs.prompt_file }}' does not exist."
+            exit 1
+          fi
+
+          # Use the provided prompt file
+          PROMPT_PATH="${{ inputs.prompt_file }}"
+        else
+          mkdir -p /tmp/claude-action
+          PROMPT_PATH="/tmp/claude-action/prompt.txt"
+          echo "${{ inputs.prompt }}" > "$PROMPT_PATH"
+        fi
+
+        # Verify the prompt file is not empty
+        if [ ! -s "$PROMPT_PATH" ]; then
+          echo "::error::Prompt is empty. Please provide a non-empty prompt."
+          exit 1
+        fi
+
+        # Save the prompt path for the next step
+        echo "PROMPT_PATH=$PROMPT_PATH" >> $GITHUB_ENV
+
+    - name: Run Claude Code
+      shell: bash
+      id: run_claude
+      run: |
+        ALLOWED_TOOLS_ARG=""
+        if [ ! -z "${{ inputs.allowed_tools }}" ]; then
+          ALLOWED_TOOLS_ARG="--allowedTools ${{ inputs.allowed_tools }}"
+        fi
+
+        # Set a timeout to ensure the command doesn't run indefinitely
+        timeout_seconds=$((${{ inputs.timeout_minutes }} * 60))
+
+        if [ -z "${{ inputs.output_file }}" ]; then
+          # Run Claude Code and output to console
+          timeout $timeout_seconds claude \
+            -p \
+            --verbose \
+            --output-format stream-json \
+            "$(cat ${{ env.PROMPT_PATH }})" \
+            ${{ inputs.allowed_tools != '' && format('--allowedTools "{0}"', inputs.allowed_tools) || '' }}
+        else
+          # Run Claude Code and tee output to console and file
+          timeout $timeout_seconds claude \
+            -p \
+            --verbose \
+            --output-format stream-json \
+            "$(cat ${{ env.PROMPT_PATH }})" \
+            ${{ inputs.allowed_tools != '' && format('--allowedTools "{0}"', inputs.allowed_tools) || '' }} | tee output.txt
+
+          # Process output.txt into JSON in a separate step
+          jq -s '.' output.txt > output.json
+
+          # Extract the result from the last item in the array (system message)
+          jq -r '.[-1].result' output.json > "${{ inputs.output_file }}"
+
+          echo "Complete output saved to output.json, final response saved to ${{ inputs.output_file }}"
+        fi
+      
+      env:
+        ANTHROPIC_API_KEY: "."
+        ANTHROPIC_AUTH_TOKEN: ${{ inputs.cborg_api_key }}
+        GITHUB_TOKEN: ${{ inputs.github_token }}
+        ANTHROPIC_BASE_URL: "https://api.cborg.lbl.gov"
+        DISABLE_NON_ESSENTIAL_MODEL_CALLS: "1"

valuesets-0.3.1/.github/actions/claude-issue-summarize-action/action.yml

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+name: "Claude Issue summarize Action"
+description: "Automatically Summarize GitHub issues using Claude Code"
+
+inputs:
+  timeout_minutes:
+    description: "Timeout in minutes for execution"
+    required: false
+    default: "5"
+  anthropic_api_key:
+    description: "Anthropic API key"
+    required: true
+  cborg_api_key:
+    description: "CBORG API key"
+    required: true
+  github_token:
+    description: "GitHub token with repo and issues permissions"
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: Checkout repository code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Create prompt file
+      shell: bash
+      run: |
+        mkdir -p /tmp/claude-prompts
+        cat > /tmp/claude-prompts/claude-issue-summarize-prompt.txt << 'EOF'
+        You're an Summarization assistant for GitHub issues. Your task is to analyze the issue, look up related issues, and summarize the issue.
+
+        Remember that this repo is primarily a note-taking and memory device for Chris Mungall, so anything you can do to enhance and enrich that would be helpful.
+
+        IMPORTANT: Don't make any PRs. You should ONLY post a response, IN THE SAME ISSUE.
+
+        Issue Information:
+        - REPO: ${{ github.repository }}
+        - ISSUE_NUMBER: ${{ github.event.issue.number }}
+
+        TASK OVERVIEW:
+
+        1. First, use your judgement to determine the course of action.
+            - If the issue is an epic or has links to other issues, read those issues, and summarize them. Summarize their status etc. Given an overall summary.
+            - If the issue is an idea or a vague high level description, run with the idea, do deep research, give heloful suggestions with links to relevant papers etc.
+            - If there are links in the issue to websites, database entities, etc, then look these up.
+            - If there are links or references to papers, then looks these up and summarize (don't guess content - if you can't access the paper, then say "I can't access the paper")
+            - Try using artl-mcp to get paper fulltext.
+            - If you want a more powerful AI agent to take on this one and make a PR, use this magic phrase: `@dragon-ai-agent please <INSTRUCTIONS>`
+
+        2. Next, use the GitHub tools to get context about the issue:
+           - You have access to these github tools:
+             - mcp__github__get_issue: Use this to retrieve the current issue's details including title, description, and existing labels
+             - mcp__github__get_issue_comments: Use this to read any discussion or additional context provided in the comments
+             - mcp__github__update_issue: Use this to apply labels to the issue (do not use this for commenting)
+             - mcp__github__search_issues: Use this to find similar issues that might provide context for proper categorization and to identify potential duplicate issues
+             - mcp__github__list_issues: Use this to understand patterns in how other issues are labeled
+           - You can also use web searching and fetching.
+
+        - It's okay to not add any information if the issue is not clear.
+        EOF
+
+    - name: Run Claude Code
+      uses: ./.github/actions/claude-code-action
+      with:
+        prompt_file: /tmp/claude-prompts/claude-issue-summarize-prompt.txt
+        allowed_tools: "Bash(gh label list),WebFetch,Fetch,LS,mcp__github__get_issue,mcp__github__get_issue_comments,mcp__github__update_issue,mcp__github__add_issue_comment,mcp__github__search_issues,mcp__github__list_issues"
+        install_github_mcp: "true"
+        install_artl_mcp: "true"
+        timeout_minutes: ${{ inputs.timeout_minutes }}
+        anthropic_api_key: ${{ inputs.anthropic_api_key }}
+        cborg_api_key: ${{ inputs.cborg_api_key }}
+        github_token: ${{ inputs.github_token }}