glam/scripts/fix_alias_fields.py

#!/usr/bin/env python3
"""
Fix alias field names in YAML instance files to use canonical schema names.

LinkML aliases don't work in data validation - they're only for documentation.
This script renames fields to use canonical names defined in the schema.

Mappings:
- description (in DigitalPlatform) → platform_description
- description (in Collection) → collection_description  
- description (in Location) → location_description (needs to be added to schema)
- description (in Identifier) → identifier_description (needs to be added to schema)
- metadata_standards (in DigitalPlatform) → implemented_standards
- notes (in Provenance) → provenance_notes
- subject_areas (in Collection) → subjects
"""

import yaml
import sys
from pathlib import Path
from typing import Any, Dict, List


def fix_digital_platform(platform: Dict[str, Any]) -> Dict[str, Any]:
    """Fix DigitalPlatform field names."""
    if 'description' in platform:
        platform['platform_description'] = platform.pop('description')
    if 'metadata_standards' in platform:
        platform['implemented_standards'] = platform.pop('metadata_standards')
    return platform


def fix_collection(collection: Dict[str, Any]) -> Dict[str, Any]:
    """Fix Collection field names."""
    if 'description' in collection:
        collection['collection_description'] = collection.pop('description')
    if 'subject_areas' in collection:
        collection['subjects'] = collection.pop('subject_areas')
    return collection


def fix_location(location: Dict[str, Any]) -> Dict[str, Any]:
    """Fix Location field names."""
    if 'description' in location:
        # For now, store in a comment or remove
        # TODO: Add location_description to schema
        desc = location.pop('description')
        print(f"  ⚠️  Removed location description (not in schema yet): {desc[:50]}...")
    return location


def fix_identifier(identifier: Dict[str, Any]) -> Dict[str, Any]:
    """Fix Identifier field names."""
    if 'description' in identifier:
        # For now, store in a comment or remove
        # TODO: Add identifier_description to schema
        desc = identifier.pop('description')
        print(f"  ⚠️  Removed identifier description (not in schema yet): {desc[:50]}...")
    return identifier


def fix_provenance(provenance: Dict[str, Any]) -> Dict[str, Any]:
    """Fix Provenance field names."""
    if 'notes' in provenance:
        provenance['provenance_notes'] = provenance.pop('notes')
    return provenance


def fix_institution(institution: Dict[str, Any]) -> Dict[str, Any]:
    """Fix field names in a single institution record."""
    
    # Fix digital platforms
    if 'digital_platforms' in institution:
        institution['digital_platforms'] = [
            fix_digital_platform(p) for p in institution['digital_platforms']
        ]
    
    # Fix collections
    if 'collections' in institution:
        institution['collections'] = [
            fix_collection(c) for c in institution['collections']
        ]
    
    # Fix locations
    if 'locations' in institution:
        institution['locations'] = [
            fix_location(loc) for loc in institution['locations']
        ]
    
    # Fix identifiers
    if 'identifiers' in institution:
        institution['identifiers'] = [
            fix_identifier(ident) for ident in institution['identifiers']
        ]
    
    # Fix provenance
    if 'provenance' in institution:
        institution['provenance'] = fix_provenance(institution['provenance'])
    
    return institution


def fix_yaml_file(file_path: Path) -> bool:
    """
    Fix alias field names in a YAML file.
    
    Returns True if changes were made, False otherwise.
    """
    print(f"\n📄 Processing: {file_path.relative_to(file_path.parents[2])}")
    
    try:
        with open(file_path, 'r', encoding='utf-8') as f:
            data = yaml.safe_load(f)
        
        if not data:
            print("  ⚠️  Empty file, skipping")
            return False
        
        # Handle both single institution and list of institutions
        if isinstance(data, list):
            original_data = yaml.dump(data, default_flow_style=False, allow_unicode=True)
            fixed_data = [fix_institution(inst) for inst in data]
        else:
            original_data = yaml.dump(data, default_flow_style=False, allow_unicode=True)
            fixed_data = fix_institution(data)
        
        # Check if anything changed
        new_data_yaml = yaml.dump(fixed_data, default_flow_style=False, allow_unicode=True)
        if original_data == new_data_yaml:
            print("  ✅ No changes needed")
            return False
        
        # Write back to file
        with open(file_path, 'w', encoding='utf-8') as f:
            yaml.dump(fixed_data, f, default_flow_style=False, allow_unicode=True, sort_keys=False)
        
        print("  ✅ Fixed and saved")
        return True
        
    except Exception as e:
        print(f"  ❌ Error: {e}")
        return False


def main():
    """Process all YAML instance files."""
    
    # Find all YAML files in data/instances/
    base_dir = Path(__file__).parent.parent
    instances_dir = base_dir / 'data' / 'instances'
    
    if not instances_dir.exists():
        print(f"❌ Instances directory not found: {instances_dir}")
        sys.exit(1)
    
    yaml_files = list(instances_dir.rglob('*.yaml'))
    yaml_files.extend(instances_dir.rglob('*.yml'))
    
    if not yaml_files:
        print("⚠️  No YAML files found")
        sys.exit(0)
    
    print(f"🔍 Found {len(yaml_files)} YAML files")
    print("=" * 80)
    
    changed_files = []
    
    for yaml_file in sorted(yaml_files):
        if fix_yaml_file(yaml_file):
            changed_files.append(yaml_file)
    
    print("\n" + "=" * 80)
    print(f"✅ Processed {len(yaml_files)} files")
    print(f"📝 Modified {len(changed_files)} files")
    
    if changed_files:
        print("\nChanged files:")
        for f in changed_files:
            print(f"  - {f.relative_to(base_dir)}")
    
    print("\n⚠️  NOTE: Location and Identifier descriptions were removed.")
    print("   These fields need to be added to the schema before they can be used.")


if __name__ == '__main__':
    main()