Michael Hanke
c332abbd1b
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72 lines
2.2 KiB
Python
72 lines
2.2 KiB
Python
import sys
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from argparse import ArgumentParser
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import yaml
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from linkml_runtime.utils.schemaview import SchemaView
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# Patch linkml
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from dump_things_service.patches import enabled # noqa: F401 -- patches LinkML
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parser = ArgumentParser(
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prog='Create a static schema with all imported schemas integrated',
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)
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parser.add_argument('schema', help='File containing a schema definition')
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def update_uris_for_elements(
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all_elements: dict, attribute_name: str, prefix_index: dict
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):
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for name, info in all_elements.items():
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uri = getattr(info, attribute_name)
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if uri is None:
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source = info.from_schema + '/'
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if source in prefix_index:
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source = prefix_index[source] + ':'
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uri = source + name
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setattr(info, attribute_name, uri)
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def update_uris(schema_view: SchemaView):
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"""Update element-defining URIs to the original element source
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Element-defining URIs (e.g., slot_uri, class_uri) are by default set to
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the schema in which the element is defined. In this case, that would be the
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root-schema of the merged schema. The merged schema would then contain different
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element-defining URIs than the individual schemas that were merged. That
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means that records that are based on the individual schemas would not be
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valid in the merged schema.
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This function updates the element-defining URIs to the original source.
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"""
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prefix_index = {
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p.prefix_reference: p.prefix_prefix
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for p in schema_view.schema.prefixes.values()
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}
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update_uris_for_elements(schema_view.schema.slots, 'slot_uri', prefix_index)
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update_uris_for_elements(schema_view.schema.types, 'uri', prefix_index)
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update_uris_for_elements(schema_view.schema.enums, 'enum_uri', prefix_index)
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update_uris_for_elements(schema_view.schema.classes, 'class_uri', prefix_index)
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def main():
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args = parser.parse_args()
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schema_view = SchemaView(
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schema=args.schema,
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importmap=None,
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merge_imports=True,
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)
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update_uris(schema_view)
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text = yaml.dump(
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schema_view.schema,
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Dumper=yaml.SafeDumper,
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allow_unicode=True,
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sort_keys=False,
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)
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print(text)
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return 0
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if __name__ == '__main__':
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sys.exit(main())
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