glam/scripts/migrate_slots.py

#!/usr/bin/env python3
"""
Migrate old-style slot files to concise naming convention.

Transforms:
- is_or_was_X -> X  
- has_or_had_X -> has_X
- contains_or_contained_X -> contains_X
"""

import os
import re
import yaml
from pathlib import Path
from datetime import datetime

SLOTS_DIR = Path("/Users/kempersc/apps/glam/schemas/20251121/linkml/modules/slots")
NEW_SLOTS_DIR = SLOTS_DIR / "20260202_matang"
ARCHIVE_DIR = SLOTS_DIR / "archive"

# Create directories if they don't exist
NEW_SLOTS_DIR.mkdir(exist_ok=True)
ARCHIVE_DIR.mkdir(exist_ok=True)

def to_camel_case(snake_str: str) -> str:
    """Convert snake_case to camelCase."""
    components = snake_str.split('_')
    return components[0] + ''.join(x.title() for x in components[1:])

def migrate_slot_name(old_name: str) -> str:
    """Convert old slot name to new concise name."""
    if old_name.startswith("is_or_was_"):
        return old_name.replace("is_or_was_", "")
    elif old_name.startswith("has_or_had_"):
        return old_name.replace("has_or_had_", "has_")
    elif old_name.startswith("contains_or_contained_"):
        return old_name.replace("contains_or_contained_", "contains_")
    return old_name

def create_new_slot_file(old_file: Path, new_name: str) -> str:
    """Create new slot file content from old file."""
    with open(old_file, 'r') as f:
        old_content = yaml.safe_load(f)
    
    old_name = old_file.stem
    
    # Get old slot data
    old_slots = old_content.get('slots', {})
    if old_name not in old_slots:
        # Try without suffix
        for key in old_slots:
            if key.startswith(old_name.replace('_slot', '')):
                old_name = key
                break
    
    old_slot = old_slots.get(old_name, {})
    
    # Extract key properties from old slot
    description = old_slot.get('description', f'Migrated from {old_name}')
    slot_uri = old_slot.get('slot_uri', f'hc:{to_camel_case(new_name)}')
    range_val = old_slot.get('range', 'string')
    multivalued = old_slot.get('multivalued', True)
    
    # Get mappings
    exact_mappings = old_slot.get('exact_mappings', [])
    close_mappings = old_slot.get('close_mappings', [])
    related_mappings = old_slot.get('related_mappings', [])
    broad_mappings = old_slot.get('broad_mappings', [])
    narrow_mappings = old_slot.get('narrow_mappings', [])
    
    # Get annotations
    annotations = old_slot.get('annotations', {'custodian_types': '["*"]'})
    
    # Get examples and comments
    examples = old_slot.get('examples', [])
    comments = old_slot.get('comments', [])
    
    # Build new slot content
    new_slot = {
        'slot_uri': f'hc:{to_camel_case(new_name)}',
        'description': f'{description}\n\nMIGRATED {datetime.now().strftime("%Y-%m-%d")} from {old_name} for conciseness.',
        'range': range_val,
        'multivalued': multivalued,
        'aliases': [old_name],
    }
    
    # Add mappings if present
    if exact_mappings:
        new_slot['exact_mappings'] = exact_mappings
    if close_mappings:
        new_slot['close_mappings'] = close_mappings
    if related_mappings:
        new_slot['related_mappings'] = related_mappings
    if broad_mappings:
        new_slot['broad_mappings'] = broad_mappings
    if narrow_mappings:
        new_slot['narrow_mappings'] = narrow_mappings
    
    # Add annotations
    new_slot['annotations'] = annotations
    
    # Add examples if present
    if examples:
        new_slot['examples'] = examples
    
    # Add comments if present
    if comments:
        new_slot['comments'] = comments
    
    # Build full YAML structure
    new_content = {
        'id': f'https://nde.nl/ontology/hc/slot/{new_name}',
        'name': new_name,
        'title': new_name.replace('_', ' '),
        'prefixes': {
            'linkml': 'https://w3id.org/linkml/',
            'hc': 'https://nde.nl/ontology/hc/',
            'schema': 'http://schema.org/',
            'dcterms': 'http://purl.org/dc/terms/',
            'rico': 'https://www.ica.org/standards/RiC/ontology#',
            'org': 'http://www.w3.org/ns/org#',
            'oa': 'http://www.w3.org/ns/oa#',
        },
        'default_prefix': 'hc',
        'imports': ['linkml:types'],
        'slots': {
            new_name: new_slot
        }
    }
    
    return yaml.dump(new_content, default_flow_style=False, allow_unicode=True, sort_keys=False)

def process_slots():
    """Process all old-style slot files."""
    patterns = [
        ('is_or_was_*.yaml', lambda x: x.replace('is_or_was_', '')),
        ('has_or_had_*.yaml', lambda x: x.replace('has_or_had_', 'has_')),
        ('contains_or_contained_*.yaml', lambda x: x.replace('contains_or_contained_', 'contains_')),
    ]
    
    created = 0
    skipped = 0
    
    for pattern, transform_fn in patterns:
        for old_file in SLOTS_DIR.glob(pattern):
            if old_file.is_file():
                old_name = old_file.stem
                new_name = transform_fn(old_name)
                new_file = NEW_SLOTS_DIR / f'{new_name}.yaml'
                
                # Check if new file already exists
                if new_file.exists():
                    print(f"SKIP (exists): {old_name} -> {new_name}")
                    skipped += 1
                    continue
                
                # Create new slot file
                try:
                    new_content = create_new_slot_file(old_file, new_name)
                    with open(new_file, 'w') as f:
                        f.write(new_content)
                    print(f"CREATED: {old_name} -> {new_name}")
                    created += 1
                except Exception as e:
                    print(f"ERROR: {old_name} -> {e}")
    
    print(f"\nSummary: Created {created}, Skipped {skipped}")
    return created, skipped

if __name__ == '__main__':
    process_slots()