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`.
79 lines
2.6 KiB
Python
79 lines
2.6 KiB
Python
import os
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def populate_imports(main_schema_path, classes_dir):
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with open(main_schema_path, 'r') as f:
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lines = f.readlines()
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# Find start and end of imports section
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start_idx = -1
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end_idx = -1
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for i, line in enumerate(lines):
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if line.strip() == "imports:":
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start_idx = i
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break
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if start_idx == -1:
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print("imports: section not found")
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return
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# Find where imports block ends (next top-level key or end of file)
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for i in range(start_idx + 1, len(lines)):
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line = lines[i]
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if line.strip() and not line.startswith(" ") and not line.startswith("#"):
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end_idx = i
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break
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if end_idx == -1:
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end_idx = len(lines)
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# Keep existing non-class imports (slots, enums, metadata, types)
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# Filter out modules/classes/* imports
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preserved_imports = []
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for i in range(start_idx + 1, end_idx):
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line = lines[i]
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stripped = line.strip()
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if stripped.startswith("- modules/classes/"):
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continue # We will regenerate these
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if stripped.startswith("- ./"): # Should not happen in 01_...
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continue
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if stripped.strip():
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preserved_imports.append(line)
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# Collect all class files
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class_imports = []
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for root, dirs, files in os.walk(classes_dir):
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if 'archive' in dirs:
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dirs.remove('archive')
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if 'deprecated' in dirs:
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dirs.remove('deprecated')
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if 'archive' in root.split(os.sep):
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continue
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if 'deprecated' in root.split(os.sep):
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continue
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for file in files:
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if file.endswith(".yaml"):
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# Path relative to 01_... location (schemas/20251121/linkml)
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# classes_dir is schemas/20251121/linkml/modules/classes
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# relative path: modules/classes/Filename
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# Check for duplicate base names? e.g. .yaml vs .yaml.bak?
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# assume clean dir.
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rel_path = f"modules/classes/{file.replace('.yaml', '')}"
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class_imports.append(f" - {rel_path}\n")
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class_imports.sort()
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# Reassemble file
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new_lines = lines[:start_idx + 1] + preserved_imports + class_imports + lines[end_idx:]
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with open(main_schema_path, 'w') as f:
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f.writelines(new_lines)
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print(f"Updated {main_schema_path} with {len(class_imports)} class imports.")
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populate_imports("schemas/20251121/linkml/01_custodian_name_modular.yaml", "schemas/20251121/linkml/modules/classes")
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