def validate_edge_property_values(self, subject: str, object: str, data: dict) -> list:
"""
Validate an edge property's value.
Parameters
----------
subject: str
Subject identifier
object: str
Object identifier
data: dict
Edge properties
Returns
-------
list
A list of errors for a given edge
"""
errors = []
error_type = ErrorType.INVALID_EDGE_PROPERTY_VALUE
if PrefixManager.is_curie(subject):
prefix = PrefixManager.get_prefix(subject)
if prefix and prefix not in self.get_all_prefixes():
message = f"Edge property 'subject' has a value '{subject}' with a CURIE prefix '{prefix}' that is not represented in Biolink Model JSON-LD context"
errors.append(ValidationError(f"{subject}-{object}", error_type, message, MessageLevel.ERROR))
else:
message = f"Edge property 'subject' has a value '{subject}' which is not a proper CURIE"
errors.append(ValidationError(f"{subject}-{object}", error_type, message, MessageLevel.ERROR))
if PrefixManager.is_curie(object):
prefix = PrefixManager.get_prefix(object)
if prefix not in self.prefixes:
message = f"Edge property 'object' has a value '{object}' with a CURIE prefix '{prefix}' that is not represented in Biolink Model JSON-LD context"
errors.append(ValidationError(f"{subject}-{object}", error_type, message, MessageLevel.ERROR))
else:
message = f"Edge property 'object' has a value '{object}' which is not a proper CURIE"
errors.append(ValidationError(f"{subject}-{object}", error_type, message, MessageLevel.ERROR))
if 'relation' in data:
if PrefixManager.is_curie(data['relation']):
prefix = PrefixManager.get_prefix(data['relation'])
if prefix not in self.prefixes:
message = f"Edge property 'relation' has a value '{data['relation']}' with a CURIE prefix '{prefix}' that is not represented in Biolink Model JSON-LD context"
errors.append(ValidationError(f"{subject}-{object}", error_type, message, MessageLevel.ERROR))
else:
message = f"Edge property 'relation' has a value '{data['relation']}' which is not a proper CURIE"
errors.append(ValidationError(f"{subject}-{object}", error_type, message, MessageLevel.ERROR))
return errors
def curie_lookup(curie: str) -> Optional[str]:
"""
Given a CURIE, find its label.
This method first does a lookup in predefined maps. If none found,
it makes use of CurieLookupService to look for the CURIE in a set
of preloaded ontologies.
Parameters
----------
curie: str
A CURIE
Returns
-------
Optional[str]
The label corresponding to the given CURIE
"""
cls = get_curie_lookup_service()
name: Optional[str] = None
prefix = PrefixManager.get_prefix(curie)
if prefix in ['OIO', 'OWL', 'owl', 'OBO', 'rdfs']:
name = stringcase.snakecase(curie.split(':', 1)[1])
elif curie in cls.curie_map:
name = cls.curie_map[curie]
elif curie in cls.ontology_graph:
name = cls.ontology_graph.nodes()[curie]['name']
return name
def validate_node_property_values(
self,
node: str,
data: dict
):
"""
Validate a node property's value.
Parameters
----------
node: str
Node identifier
data: dict
Node properties
"""
error_type = ErrorType.INVALID_NODE_PROPERTY_VALUE
if not PrefixManager.is_curie(node):
message = f"Node property 'id' is expected to be of type 'CURIE'"
self.log_error(node, error_type, message, MessageLevel.ERROR)
else:
prefix = PrefixManager.get_prefix(node)
if prefix and prefix not in self.get_all_prefixes():
message = f"Node property 'id' has a value '{node}' with a CURIE prefix '{prefix}'" + \
f" is not represented in Biolink Model JSON-LD context"
self.log_error(node, error_type, message, MessageLevel.ERROR)
def validate_node_property_values(node: str, data: dict) -> list:
"""
Validate a node property's value.
Parameters
----------
node: str
Node identifier
data: dict
Node properties
Returns
-------
list
A list of errors for a given node
"""
errors = []
error_type = ErrorType.INVALID_NODE_PROPERTY_VALUE
if not PrefixManager.is_curie(node):
message = f"Node property 'id' expected to be of type 'CURIE'"
errors.append(
ValidationError(node, error_type, message, MessageLevel.ERROR))
else:
prefix = PrefixManager.get_prefix(node)
if prefix and prefix not in Validator.get_all_prefixes():
message = f"Node property 'id' has a value '{node}' with a CURIE prefix '{prefix}' is not represented in Biolink Model JSON-LD context"
errors.append(
ValidationError(node, error_type, message,
MessageLevel.ERROR))
return errors
def get_category(self, curie: str, node: dict) -> Optional[str]:
"""
Get category for a given CURIE.
Parameters
----------
curie: str
Curie for node
node: dict
Node data
Returns
-------
Optional[str]
Category for the given node CURIE.
"""
category = None
# use meta.basicPropertyValues
if "meta" in node and "basicPropertyValues" in node["meta"]:
for p in node["meta"]["basicPropertyValues"]:
if p["pred"] == self.HAS_OBO_NAMESPACE:
category = p["val"]
element = self.toolkit.get_element(category)
if element:
category = f"biolink:{stringcase.pascalcase(stringcase.snakecase(element.name))}"
else:
element = self.toolkit.get_element_by_mapping(category)
if element:
category = f"biolink:{stringcase.pascalcase(stringcase.snakecase(element))}"
else:
category = "biolink:OntologyClass"
if not category or category == "biolink:OntologyClass":
prefix = PrefixManager.get_prefix(curie)
# TODO: the mapping should be via biolink-model lookups
if prefix == "HP":
category = "biolink:PhenotypicFeature"
elif prefix == "CHEBI":
category = "biolink:ChemicalSubstance"
elif prefix == "MONDO":
category = "biolink:Disease"
elif prefix == "UBERON":
category = "biolink:AnatomicalEntity"
elif prefix == "SO":
category = "biolink:SequenceFeature"
elif prefix == "CL":
category = "biolink:Cell"
elif prefix == "PR":
category = "biolink:Protein"
elif prefix == "NCBITaxon":
category = "biolink:OrganismalEntity"
else:
self.owner.log_error(
entity=f"{str(category)} for node {curie}",
error_type=ErrorType.MISSING_CATEGORY,
message=
f"Missing category; Defaulting to 'biolink:OntologyClass'",
message_level=MessageLevel.WARNING)
return category
def get_category(self, curie: str, node: dict) -> Optional[str]:
"""
Get category for a given CURIE.
Parameters
----------
curie: str
Curie for node
node: dict
Node data
Returns
-------
Optional[str]
Category for the given node CURIE.
"""
category = None
# use meta.basicPropertyValues
if 'meta' in node and 'basicPropertyValues' in node['meta']:
for p in node['meta']['basicPropertyValues']:
if p['pred'] == self.HAS_OBO_NAMESPACE:
category = p['val']
element = self.toolkit.get_element(category)
if element:
category = (
f"biolink:{stringcase.pascalcase(stringcase.snakecase(element.name))}"
)
else:
element = self.toolkit.get_element_by_mapping(category)
if element:
category = f"biolink:{stringcase.pascalcase(stringcase.snakecase(element.name))}"
else:
category = 'biolink:OntologyClass'
if not category or category == 'biolink:OntologyClass':
prefix = PrefixManager.get_prefix(curie)
# TODO: the mapping should be via biolink-model lookups
if prefix == 'HP':
category = "biolink:PhenotypicFeature"
elif prefix == 'CHEBI':
category = "biolink:ChemicalSubstance"
elif prefix == 'MONDO':
category = "biolink:Disease"
elif prefix == 'UBERON':
category = "biolink:AnatomicalEntity"
elif prefix == 'SO':
category = "biolink:SequenceFeature"
elif prefix == 'CL':
category = "biolink:Cell"
elif prefix == 'PR':
category = "biolink:Protein"
elif prefix == 'NCBITaxon':
category = "biolink:OrganismalEntity"
else:
log.debug(
f"{curie} Could not find a category mapping for '{category}'; Defaulting to 'biolink:OntologyClass'"
)
return category
def _compile_prefix_stats(self, n: str):
prefix = PrefixManager.get_prefix(n)
if not prefix:
error_type = ErrorType.MISSING_NODE_CURIE_PREFIX
self.mkg.log_error(entity=n,
error_type=error_type,
message="Node 'id' has no CURIE prefix",
message_level=MessageLevel.WARNING)
else:
if prefix not in self.category_stats["id_prefixes"]:
self.category_stats["id_prefixes"].add(prefix)
def validate_edge_property_values(
self,
subject: str,
object: str,
data: dict
):
"""
Validate an edge property's value.
Parameters
----------
subject: str
Subject identifier
object: str
Object identifier
data: dict
Edge properties
"""
error_type = ErrorType.INVALID_EDGE_PROPERTY_VALUE
prefixes = self.get_all_prefixes()
if PrefixManager.is_curie(subject):
prefix = PrefixManager.get_prefix(subject)
if prefix and prefix not in prefixes:
message = f"Edge property 'subject' has a value '{subject}' with a CURIE prefix " + \
f"'{prefix}' that is not represented in Biolink Model JSON-LD context"
self.log_error(f"{subject}->{object}", error_type, message, MessageLevel.ERROR)
else:
message = f"Edge property 'subject' has a value '{subject}' which is not a proper CURIE"
self.log_error(f"{subject}->{object}", error_type, message, MessageLevel.ERROR)
if PrefixManager.is_curie(object):
prefix = PrefixManager.get_prefix(object)
if prefix not in prefixes:
message = f"Edge property 'object' has a value '{object}' with a CURIE " + \
f"prefix '{prefix}' that is not represented in Biolink Model JSON-LD context"
self.log_error(f"{subject}->{object}", error_type, message, MessageLevel.ERROR)
else:
message = f"Edge property 'object' has a value '{object}' which is not a proper CURIE"
self.log_error(f"{subject}->{object}", error_type, message, MessageLevel.ERROR)
def analyse_node_category(self, n, data):
prefix = PrefixManager.get_prefix(n)
self.category_stats['count'] += 1
if prefix not in self.category_stats['id_prefixes']:
self.category_stats['id_prefixes'].add(prefix)
if 'provided_by' in data:
for s in data['provided_by']:
if s in self.category_stats['count_by_source']:
self.category_stats['count_by_source'][s] += 1
else:
self.category_stats['count_by_source'][s] = 1
else:
self.category_stats['count_by_source']['unknown'] += 1
def _capture_prefix(self, n: str):
prefix = PrefixManager.get_prefix(n)
if not prefix:
error_type = ErrorType.MISSING_NODE_CURIE_PREFIX
self.summary.log_error(entity=n,
error_type=error_type,
message="Node 'id' has no CURIE prefix",
message_level=MessageLevel.WARNING)
else:
if prefix in self.category_stats["count_by_id_prefix"]:
self.category_stats["count_by_id_prefix"][prefix] += 1
else:
self.category_stats["count_by_id_prefix"][prefix] = 1
def test_get_prefix(query):
"""
Test to check behavior of test_get_prefix method in PrefixManager.
"""
assert PrefixManager.get_prefix(query[0]) == query[1]