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Fix bug with unknown_conforms_to message when running tutorial. #43

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merged 1 commit into from
May 13, 2024
Merged

Fix bug with unknown_conforms_to message when running tutorial. #43

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21 changes: 20 additions & 1 deletion linkml_owl/dumpers/owl_dumper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,9 @@
OP_KEY = Tuple[LEVEL, OPERAND, AXIOM_TYPE_NAME]


def _skip_key_in_element(k: str, element: YAMLRoot) -> bool:
return k.startswith("unknown_") and k.replace("unknown_", "") in vars(element)

@dataclass
class EntityAxiomIndex:
"""
Expand Down Expand Up @@ -248,10 +251,12 @@ def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_o
unprocessed_parents = []
# set subj = IRI for element
for k, v in vars(element).items():
if _skip_key_in_element(k, element):
continue
slot: SlotDefinition
slot = self._lookup_slot(c, k)
if slot is None:
raise ValueError(f'Lookup slot in {c.name} failed for {k} // element={element}')
raise ValueError(f'Cannot find slot {c.name}.{k} // {vars(element)} element={element}')
if slot.identifier:
subj = URIRef(self._get_IRI_str(v))
logging.debug(f"set subj from {slot.name}={v} asURI: {subj}")
Expand All @@ -275,6 +280,8 @@ def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_o
# iterate through all slot-value assignments for element;
# generate axioms or add axioms to EntityAxiomIndex for each
for k, v in vars(element).items():
if _skip_key_in_element(k, element):
continue
slot: SlotDefinition
# TODO: unify slot/schema_level_slot
slot = self._lookup_slot(c, k)
Expand Down Expand Up @@ -518,6 +525,9 @@ def _instance_of_linkml_class(self, v) -> bool:
return False

def _lookup_slot(self, cls: ClassDefinition, field: str) -> SlotDefinition:
"""
Lookup a slot in a class by name
"""
matching_slot = None
for s in self.schemaview.class_induced_slots(cls.name):
if underscore(s.name) == field:
Expand Down Expand Up @@ -798,6 +808,13 @@ def cli(inputfile: str, schema: str, target_class, module, output, output_type,
https://linkml.io/linkml-owl/
"""
logger = logging.getLogger()
# Set handler for the root logger to output to the console
console_handler = logging.StreamHandler()
console_handler.setFormatter(logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s"))
# Clear existing handlers to avoid duplicate messages if function runs multiple times
logger.handlers = []
# Add the newly created console handler to the logger
logger.addHandler(console_handler)
if verbose >= 2:
logger.setLevel(level=logging.DEBUG)
elif verbose == 1:
Expand All @@ -806,6 +823,7 @@ def cli(inputfile: str, schema: str, target_class, module, output, output_type,
logger.setLevel(level=logging.WARNING)
if quiet:
logger.setLevel(level=logging.ERROR)
logger.info(f"Loading and compiling schema {schema}")
if module is None:
if schema is None:
raise Exception('must pass one of module OR schema')
Expand All @@ -814,6 +832,7 @@ def cli(inputfile: str, schema: str, target_class, module, output, output_type,
else:
python_module = compile_python(module)
sv = SchemaView(schema)
logger.info(f"Loading {inputfile} into schema {sv.schema.name}")
element = load_structured_file(inputfile, target_class=target_class, python_module=python_module, schemaview=sv, fmt=format)

dumper = OWLDumper()
Expand Down
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