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`.
37 lines
1.3 KiB
Python
37 lines
1.3 KiB
Python
import os
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import yaml
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def flatten_ranges(path):
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with open(path, 'r') as f:
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lines = f.readlines()
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new_lines = []
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primitives = ["string", "integer", "float", "boolean", "date", "datetime", "uriorcurie", "uri", "ncname", "objectidentifier", "time", "decimal", "double"]
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modified = False
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for line in lines:
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stripped = line.strip()
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if stripped.startswith("range:") and ":" in stripped:
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parts = stripped.split(":")
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if len(parts) >= 2:
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range_val = parts[1].strip()
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if range_val not in primitives and not range_val.startswith("string"): # handle string(...)
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print(f"Flattening range in {path}: {range_val} -> uriorcurie")
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new_lines.append(f" range: uriorcurie\n")
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new_lines.append(f" # range: {range_val}\n")
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modified = True
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continue
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new_lines.append(line)
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if modified:
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with open(path, 'w') as f:
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f.writelines(new_lines)
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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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flatten_ranges(os.path.join(root, file))
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process_directory("schemas/20251121/linkml/modules/slots")
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