glam/scripts/fix_alias_fields_v2.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 (remove for now)
- description (in Identifier) → identifier_description (remove for now)
- metadata_standards (in DigitalPlatform) → implemented_standards
- notes (in Provenance) → provenance_notes
- subject_areas (in Collection) → subjects
"""

import yaml
import sys
from pathlib import Path


def fix_digital_platform(platform):
    """Fix DigitalPlatform field names."""
    changed = False
    if 'description' in platform:
        platform['platform_description'] = platform.pop('description')
        changed = True
    if 'metadata_standards' in platform:
        platform['implemented_standards'] = platform.pop('metadata_standards')
        changed = True
    return changed


def fix_collection(collection):
    """Fix Collection field names."""
    changed = False
    if 'description' in collection:
        collection['collection_description'] = collection.pop('description')
        changed = True
    if 'subject_areas' in collection:
        collection['subjects'] = collection.pop('subject_areas')
        changed = True
    return changed


def fix_location(location):
    """Fix Location field names."""
    changed = False
    if 'description' in location:
        # Remove for now - not in schema yet
        location.pop('description')
        changed = True
    return changed


def fix_identifier(identifier):
    """Fix Identifier field names."""
    changed = False
    if 'description' in identifier:
        # Remove for now - not in schema yet
        identifier.pop('description')
        changed = True
    return changed


def fix_provenance(provenance):
    """Fix Provenance field names."""
    changed = False
    if 'notes' in provenance:
        provenance['provenance_notes'] = provenance.pop('notes')
        changed = True
    return changed


def fix_institution(institution):
    """Fix field names in a single institution record."""
    changed = False
    
    # Fix digital platforms
    if 'digital_platforms' in institution:
        for platform in institution['digital_platforms']:
            if fix_digital_platform(platform):
                changed = True
    
    # Fix collections
    if 'collections' in institution:
        for collection in institution['collections']:
            if fix_collection(collection):
                changed = True
    
    # Fix locations
    if 'locations' in institution:
        for location in institution['locations']:
            if fix_location(location):
                changed = True
    
    # Fix identifiers
    if 'identifiers' in institution:
        for identifier in institution['identifiers']:
            if fix_identifier(identifier):
                changed = True
    
    # Fix provenance
    if 'provenance' in institution:
        if fix_provenance(institution['provenance']):
            changed = True
    
    return changed


def fix_yaml_file(file_path):
    """Fix alias field names in a YAML file."""
    try:
        with open(file_path, 'r', encoding='utf-8') as f:
            data = yaml.safe_load(f)
        
        if not data:
            return False, "Empty file"
        
        # Handle both single institution and list of institutions
        changed = False
        if isinstance(data, list):
            for inst in data:
                if fix_institution(inst):
                    changed = True
        else:
            changed = fix_institution(data)
        
        if changed:
            # Write back to file
            with open(file_path, 'w', encoding='utf-8') as f:
                yaml.dump(data, f, default_flow_style=False, allow_unicode=True, sort_keys=False)
            return True, "Fixed"
        else:
            return False, "No changes needed"
        
    except Exception as e:
        return False, f"Error: {e}"


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\n")
    
    changed_count = 0
    unchanged_count = 0
    error_count = 0
    
    for i, yaml_file in enumerate(sorted(yaml_files), 1):
        rel_path = yaml_file.relative_to(base_dir)
        changed, msg = fix_yaml_file(yaml_file)
        
        if changed:
            print(f"{i:3d}. ✅ {rel_path}: {msg}")
            changed_count += 1
        elif "Error" in msg:
            print(f"{i:3d}. ❌ {rel_path}: {msg}")
            error_count += 1
        else:
            unchanged_count += 1
    
    print(f"\n{'='*80}")
    print(f"✅ Modified: {changed_count} files")
    print(f"⏭️  Unchanged: {unchanged_count} files")
    print(f"❌ Errors: {error_count} files")
    print(f"📊 Total: {len(yaml_files)} files")


if __name__ == '__main__':
    main()