7cf10084b4
- Added `fix_dual_class_link.py` to remove dual class link references from specified YAML files. - Created `fix_specific_ghosts.py` to apply specific replacements in YAML files based on defined mappings. - Introduced `migrate_staff_count.py` to migrate staff count references to a new structure in specified YAML files. - Developed `migrate_type_slots.py` to replace type-related slots with new identifiers across YAML files. - Implemented `scan_ghost_references.py` to identify and report ghost references to archived slots and classes in YAML files. - Added `verify_ontology_terms.py` to verify the presence of ontology terms in specified ontology files against schema definitions.
121 lines
4.8 KiB
Python
121 lines
4.8 KiB
Python
import os
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import re
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# Paths
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SCHEMA_ROOT = "/Users/kempersc/apps/glam/schemas/20251121/linkml/modules"
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CLASSES_DIR = os.path.join(SCHEMA_ROOT, "classes")
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SLOTS_DIR = os.path.join(SCHEMA_ROOT, "slots")
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ARCHIVED_SLOTS_FILE = "archived_slots.txt"
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ARCHIVED_CLASSES_FILE = "archived_classes.txt"
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def parse_archived_name(filename):
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# Removes _archived_YYYYMMDD.yaml suffix
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# Also handles cases without date if any (though list showed dates)
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# The pattern seems to be name_archived_date.yaml
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match = re.match(r"(.+)_archived_\d+\.yaml", filename)
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if match:
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return match.group(1)
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# Fallback if no date
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if filename.endswith(".yaml"):
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return filename[:-5]
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return filename
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def load_archived_entities(filepath):
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entities = set()
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try:
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with open(filepath, 'r') as f:
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for line in f:
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filename = line.strip()
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if filename:
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entity_name = parse_archived_name(filename)
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entities.add(entity_name)
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except FileNotFoundError:
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print(f"Warning: {filepath} not found.")
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return entities
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def scan_files(directory, archived_slots, archived_classes):
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print(f"Scanning {directory}...")
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issues = []
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for root, _, files in os.walk(directory):
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if "archive" in root: # Skip archive directories
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continue
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for file in files:
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if not file.endswith(".yaml"):
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continue
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filepath = os.path.join(root, file)
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try:
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with open(filepath, 'r') as f:
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content = f.read()
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lines = content.split('\n')
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for i, line in enumerate(lines):
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# Check for slot imports
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# Pattern: - ../slots/slot_name
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# or - ./slot_name (if in slots dir)
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# Check for slot usage in slots list
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# Pattern: - slot_name (indented)
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stripped = line.strip()
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# Check for archived slots
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for slot in archived_slots:
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# Explicit import check
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if f"../slots/{slot}" in stripped or f"./{slot}" in stripped:
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# Be strict about word boundaries to avoid partial matches
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# e.g. "slot" vs "slot_suffix"
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# But yaml references usually are explicit paths or items
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if stripped.endswith(slot) or f"/{slot}" in stripped:
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issues.append(f"{filepath}:{i+1}: Import of archived slot '{slot}'")
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# Usage check (simple heuristic)
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# We look for "- slot_name" in a slots list context
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if stripped == f"- {slot}":
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issues.append(f"{filepath}:{i+1}: Usage of archived slot '{slot}'")
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# Slot usage keys
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if stripped.startswith(f"{slot}:"):
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issues.append(f"{filepath}:{i+1}: Slot usage key for archived slot '{slot}'")
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# Check for archived classes
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for cls in archived_classes:
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if cls in stripped:
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# Exclude the file itself defining the class (if it were somehow here)
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# Check for imports or range references
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if f"/{cls}" in stripped or f"range: {cls}" in stripped:
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issues.append(f"{filepath}:{i+1}: Reference to archived class '{cls}'")
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except Exception as e:
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print(f"Error reading {filepath}: {e}")
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return issues
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def main():
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archived_slots = load_archived_entities(ARCHIVED_SLOTS_FILE)
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archived_classes = load_archived_entities(ARCHIVED_CLASSES_FILE)
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# Remove common metadata fields that collide with archived slot names
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archived_slots.discard("description")
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archived_slots.discard("title")
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archived_slots.discard("name") # "name" might be a slot too, but also metadata
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print(f"Loaded {len(archived_slots)} archived slots.")
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print(f"Loaded {len(archived_classes)} archived classes.")
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issues = scan_files(CLASSES_DIR, archived_slots, archived_classes)
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# Also scan slots dir, though less likely to have cross-slot dependencies that rot
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issues.extend(scan_files(SLOTS_DIR, archived_slots, archived_classes))
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if issues:
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print("\nFound potential ghost references:")
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for issue in issues:
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print(issue)
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else:
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print("\nNo obvious ghost references found.")
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if __name__ == "__main__":
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main()
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