fc405445c6
- Removed obsolete slots: `has_or_had_custodian_observation`, `provider`, and `specificity_annotation`. - Updated `has_or_had_score` slot to use `SpecificityScore` class and modified its description and examples. - Added new slots: `end_seconds`, `end_time`, `has_archive_path`, `has_or_had_custodian_name`, `protocol_name`, and `protocol_version`. - Introduced a script `check_annotation_types.py` to validate the presence and structure of `custodian_types` in YAML files. - Added a script `update_specificity.py` to automate updates related to `SpecificityAnnotation` to `SpecificityScore`.
101 lines
3.4 KiB
Python
101 lines
3.4 KiB
Python
import os
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import re
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def update_file(path):
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with open(path, 'r') as f:
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content = f.read()
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original_content = content
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# Global replace of class name
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content = content.replace("SpecificityAnnotation", "SpecificityScore")
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content = content.replace("specificity_annotation.yaml", "specificity_annotation.yaml") # Wait, filename? imports usually omit extension or use it.
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# Check imports like: - ./SpecificityAnnotation
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# Regex for slot usage
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# If file contains "has_or_had_score", we need to be careful not to duplicate.
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has_score_slot = "has_or_had_score" in content
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lines = content.split('\n')
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new_lines = []
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skip_next = False
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for i, line in enumerate(lines):
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if skip_next:
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skip_next = False
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continue
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stripped = line.strip()
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# Handle Imports
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if "slots/specificity_annotation" in line:
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if has_score_slot:
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continue # Remove import if score already imported (assuming it is, based on check)
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# But wait, "has_or_had_score" string might be in comments.
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# Safer: Replace with has_or_had_score, then deduplicate later?
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# Or just check if "slots/has_or_had_score" is also in content.
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line = line.replace("specificity_annotation", "has_or_had_score")
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if "- ./SpecificityAnnotation" in line:
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line = line.replace("SpecificityAnnotation", "SpecificityScore")
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# Handle Slots list
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if stripped == "- specificity_annotation":
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if has_score_slot:
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# Check if has_or_had_score is in the file as a slot list item
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if re.search(r'-\s+has_or_had_score', content):
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continue # Remove duplicate
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line = line.replace("specificity_annotation", "has_or_had_score")
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# Handle slot_usage keys
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if stripped == "specificity_annotation:":
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line = line.replace("specificity_annotation:", "has_or_had_score:")
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# Handle range: SpecificityAnnotation -> range: SpecificityScore (Handled by global replace)
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new_lines.append(line)
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new_content = '\n'.join(new_lines)
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# Final deduplication of imports just in case
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# Convert to list of lines again
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final_lines = []
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seen_imports = set()
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in_imports = False
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for line in new_content.split('\n'):
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if line.strip() == "imports:":
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in_imports = True
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final_lines.append(line)
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continue
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if in_imports:
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if not line.strip().startswith("-"):
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in_imports = False
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else:
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import_stmt = line.strip()
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if import_stmt in seen_imports:
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continue
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seen_imports.add(import_stmt)
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final_lines.append(line)
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final_content = '\n'.join(final_lines)
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if final_content != original_content:
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print(f"Updating {path}")
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with open(path, 'w') as f:
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f.write(final_content)
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def process_directory(directory):
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for root, dirs, files in os.walk(directory):
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for file in files:
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if file.endswith(".yaml"):
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update_file(os.path.join(root, file))
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process_directory("schemas/20251121/linkml/modules/classes")
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process_directory("schemas/20251121/linkml/modules/slots")
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