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linkml / linkml-owl

Extension of LinkML runtime for converting instances of LinkML classes to OWL (classes or instances)
https://linkml.io/linkml-owl
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"unknown_conforms_to" error while running pizza01-toppings example in https://linkml.io/linkml-owl/tutorial/pizza01/ #42

Closed samsontu closed 1 month ago

samsontu commented 2 months ago

After copying the pizza01-toppings-model.yaml and pizza01-toppings-data.yaml files from https://linkml.io/linkml-owl/tutorial/pizza01/, running

linkml-data2owl -s pizza01-toppings-model.yaml pizza01-toppings-data.yaml -o pizza01-toppings.ofn Result in: ERROR:root:Did not find unknown_conforms_to in PizzaTopping slots = [] Traceback (most recent call last): File "/Users/tu/opt/anaconda3/bin/linkml-data2owl", line 8, in sys.exit(cli()) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, **kwargs) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/linkml_owl/dumpers/owl_dumper.py", line 822, in cli doc = dumper.dumps(element, schemaview=sv, output_type=output_type) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/linkml_owl/dumpers/owl_dumper.py", line 185, in dumps doc = self.to_ontology_document(element, schema, iri=iri) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/linkml_owl/dumpers/owl_dumper.py", line 165, in to_ontology_document self.transform(e1, schema) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/linkml_owl/dumpers/owl_dumper.py", line 254, in transform raise ValueError(f'Lookup slot in {c.name} failed for {k} // element={element}') ValueError: Lookup slot in PizzaTopping failed for unknown_conforms_to // element=PizzaTopping(id='pizza:FishTopping', label='fish topping', conforms_to='PizzaTopping', subClassOf='pizza:PizzaTopping')

Taking out the conforms-to statements in pizza01-toppings-data.yaml and running

linkml-data2owl -C PizzaTopping -s pizza01-toppings-model.yaml pizza01-toppings-data-woconforms.yaml -o pizza01-toppings.ofn Result in: ERROR:root:Did not find unknown_conforms_to in PizzaTopping slots = [] Traceback (most recent call last): File "/Users/tu/opt/anaconda3/bin/linkml-data2owl", line 8, in sys.exit(cli()) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, **kwargs) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/linkml_owl/dumpers/owl_dumper.py", line 822, in cli doc = dumper.dumps(element, schemaview=sv, output_type=output_type) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/linkml_owl/dumpers/owl_dumper.py", line 185, in dumps doc = self.to_ontology_document(element, schema, iri=iri) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/linkml_owl/dumpers/owl_dumper.py", line 165, in to_ontology_document self.transform(e1, schema) File "/Users/tu/opt/anaconda3/lib/python3.9/site-packages/linkml_owl/dumpers/owl_dumper.py", line 254, in transform raise ValueError(f'Lookup slot in {c.name} failed for {k} // element={element}') ValueError: Lookup slot in PizzaTopping failed for unknown_conforms_to // element=PizzaTopping(id='pizza:FishTopping', label='fish topping', conforms_to='PizzaTopping', subClassOf='pizza:PizzaTopping')