class Person(YAMLRoot):
"""
Minimal information about a person
"""
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = SDO.Person
class_class_curie: ClassVar[str] = "sdo:Person"
class_name: ClassVar[str] = "Person"
class_model_uri: ClassVar[URIRef] = EX.Person
id: Union[str, PersonId] = None
first_name: Union[str, List[str]] = None
last_name: str = None
knows: Optional[Union[Union[str, PersonId],
List[Union[str, PersonId]]]] = empty_list()
def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
if self._is_empty(self.id):
raise ValueError("id must be supplied")
if not isinstance(self.id, PersonId):
self.id = PersonId(self.id)
if self._is_empty(self.first_name):
raise ValueError("first_name must be supplied")
if not isinstance(self.first_name, list):
self.first_name = [self.first_name]
self.first_name = [
v if isinstance(v, str) else str(v) for v in self.first_name
]
if self._is_empty(self.last_name):
raise ValueError("last_name must be supplied")
if not isinstance(self.last_name, str):
self.last_name = str(self.last_name)
if not isinstance(self.knows, list):
self.knows = [self.knows]
self.knows = [
v if isinstance(v, PersonId) else PersonId(v) for v in self.knows
]
super().__post_init__(**kwargs)
class MappingSet(YAMLRoot):
"""
Represents a set of mappings
"""
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = SSSOM.MappingSet
class_class_curie: ClassVar[str] = "sssom:MappingSet"
class_name: ClassVar[str] = "mapping set"
class_model_uri: ClassVar[URIRef] = SSSOM.MappingSet
mapping_set_id: Union[str, URI] = None
license: Union[str, URI] = None
mappings: Optional[Union[Union[dict, "Mapping"],
List[Union[dict, "Mapping"]]]] = empty_list()
mapping_set_version: Optional[str] = None
mapping_set_source: Optional[Union[Union[str, EntityReference], List[Union[
str, EntityReference]]]] = empty_list()
mapping_set_description: Optional[str] = None
creator_id: Optional[Union[Union[str, EntityReference],
List[Union[str,
EntityReference]]]] = empty_list()
creator_label: Optional[Union[str, List[str]]] = empty_list()
subject_source: Optional[Union[str, URI]] = None
subject_source_version: Optional[str] = None
object_source: Optional[Union[str, URI]] = None
object_source_version: Optional[str] = None
mapping_provider: Optional[Union[str, URI]] = None
mapping_tool: Optional[str] = None
mapping_date: Optional[Union[str, XSDDate]] = None
subject_match_field: Optional[Union[Union[
str, EntityReference], List[Union[str,
EntityReference]]]] = empty_list()
object_match_field: Optional[Union[Union[str, EntityReference], List[Union[
str, EntityReference]]]] = empty_list()
subject_preprocessing: Optional[
Union[Union[str, "PreprocessingMethodEnum"],
List[Union[str, "PreprocessingMethodEnum"]]]] = empty_list()
object_preprocessing: Optional[
Union[Union[str, "PreprocessingMethodEnum"],
List[Union[str, "PreprocessingMethodEnum"]]]] = empty_list()
match_term_type: Optional[Union[str, "MatchTermTypeEnum"]] = None
see_also: Optional[Union[str, List[str]]] = empty_list()
other: Optional[str] = None
comment: Optional[str] = None
def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
if self._is_empty(self.mapping_set_id):
self.MissingRequiredField("mapping_set_id")
if not isinstance(self.mapping_set_id, URI):
self.mapping_set_id = URI(self.mapping_set_id)
if self._is_empty(self.license):
self.MissingRequiredField("license")
if not isinstance(self.license, URI):
self.license = URI(self.license)
if not isinstance(self.mappings, list):
self.mappings = [self.mappings
] if self.mappings is not None else []
self.mappings = [
v if isinstance(v, Mapping) else Mapping(**as_dict(v))
for v in self.mappings
]
if self.mapping_set_version is not None and not isinstance(
self.mapping_set_version, str):
self.mapping_set_version = str(self.mapping_set_version)
if not isinstance(self.mapping_set_source, list):
self.mapping_set_source = [
self.mapping_set_source
] if self.mapping_set_source is not None else []
self.mapping_set_source = [
v if isinstance(v, EntityReference) else EntityReference(v)
for v in self.mapping_set_source
]
if self.mapping_set_description is not None and not isinstance(
self.mapping_set_description, str):
self.mapping_set_description = str(self.mapping_set_description)
if not isinstance(self.creator_id, list):
self.creator_id = [self.creator_id
] if self.creator_id is not None else []
self.creator_id = [
v if isinstance(v, EntityReference) else EntityReference(v)
for v in self.creator_id
]
if not isinstance(self.creator_label, list):
self.creator_label = [self.creator_label
] if self.creator_label is not None else []
self.creator_label = [
v if isinstance(v, str) else str(v) for v in self.creator_label
]
if self.subject_source is not None and not isinstance(
self.subject_source, URI):
self.subject_source = URI(self.subject_source)
if self.subject_source_version is not None and not isinstance(
self.subject_source_version, str):
self.subject_source_version = str(self.subject_source_version)
if self.object_source is not None and not isinstance(
self.object_source, URI):
self.object_source = URI(self.object_source)
if self.object_source_version is not None and not isinstance(
self.object_source_version, str):
self.object_source_version = str(self.object_source_version)
if self.mapping_provider is not None and not isinstance(
self.mapping_provider, URI):
self.mapping_provider = URI(self.mapping_provider)
if self.mapping_tool is not None and not isinstance(
self.mapping_tool, str):
self.mapping_tool = str(self.mapping_tool)
if self.mapping_date is not None and not isinstance(
self.mapping_date, XSDDate):
self.mapping_date = XSDDate(self.mapping_date)
if not isinstance(self.subject_match_field, list):
self.subject_match_field = [
self.subject_match_field
] if self.subject_match_field is not None else []
self.subject_match_field = [
v if isinstance(v, EntityReference) else EntityReference(v)
for v in self.subject_match_field
]
if not isinstance(self.object_match_field, list):
self.object_match_field = [
self.object_match_field
] if self.object_match_field is not None else []
self.object_match_field = [
v if isinstance(v, EntityReference) else EntityReference(v)
for v in self.object_match_field
]
if not isinstance(self.subject_preprocessing, list):
self.subject_preprocessing = [
self.subject_preprocessing
] if self.subject_preprocessing is not None else []
self.subject_preprocessing = [
v if isinstance(v, PreprocessingMethodEnum) else
PreprocessingMethodEnum(v) for v in self.subject_preprocessing
]
if not isinstance(self.object_preprocessing, list):
self.object_preprocessing = [
self.object_preprocessing
] if self.object_preprocessing is not None else []
self.object_preprocessing = [
v if isinstance(v, PreprocessingMethodEnum) else
PreprocessingMethodEnum(v) for v in self.object_preprocessing
]
if self.match_term_type is not None and not isinstance(
self.match_term_type, MatchTermTypeEnum):
self.match_term_type = MatchTermTypeEnum(self.match_term_type)
if not isinstance(self.see_also, list):
self.see_also = [self.see_also
] if self.see_also is not None else []
self.see_also = [
v if isinstance(v, str) else str(v) for v in self.see_also
]
if self.other is not None and not isinstance(self.other, str):
self.other = str(self.other)
if self.comment is not None and not isinstance(self.comment, str):
self.comment = str(self.comment)
super().__post_init__(**kwargs)
class Mapping(YAMLRoot):
"""
Represents an individual mapping between a pair of entities
"""
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = OWL.Axiom
class_class_curie: ClassVar[str] = "owl:Axiom"
class_name: ClassVar[str] = "mapping"
class_model_uri: ClassVar[URIRef] = SSSOM.Mapping
subject_id: Union[str, EntityReference] = None
predicate_id: Union[str, EntityReference] = None
object_id: Union[str, EntityReference] = None
match_type: Union[Union[str, "MatchTypeEnum"],
List[Union[str, "MatchTypeEnum"]]] = None
subject_label: Optional[str] = None
subject_category: Optional[str] = None
predicate_label: Optional[str] = None
predicate_modifier: Optional[Union[str, "PredicateModifierEnum"]] = None
object_label: Optional[str] = None
object_category: Optional[str] = None
author_id: Optional[Union[Union[str, EntityReference],
List[Union[str,
EntityReference]]]] = empty_list()
author_label: Optional[Union[str, List[str]]] = empty_list()
reviewer_id: Optional[Union[Union[str, EntityReference],
List[Union[str,
EntityReference]]]] = empty_list()
reviewer_label: Optional[Union[str, List[str]]] = empty_list()
creator_id: Optional[Union[Union[str, EntityReference],
List[Union[str,
EntityReference]]]] = empty_list()
creator_label: Optional[Union[str, List[str]]] = empty_list()
license: Optional[Union[str, URI]] = None
subject_source: Optional[Union[str, URI]] = None
subject_source_version: Optional[str] = None
object_source: Optional[Union[str, URI]] = None
object_source_version: Optional[str] = None
mapping_provider: Optional[Union[str, URI]] = None
mapping_cardinality: Optional[Union[str, "MappingCardinalityEnum"]] = None
mapping_tool: Optional[str] = None
mapping_tool_version: Optional[str] = None
mapping_date: Optional[Union[str, XSDDate]] = None
confidence: Optional[float] = None
subject_match_field: Optional[Union[Union[
str, EntityReference], List[Union[str,
EntityReference]]]] = empty_list()
object_match_field: Optional[Union[Union[str, EntityReference], List[Union[
str, EntityReference]]]] = empty_list()
match_string: Optional[Union[str, List[str]]] = empty_list()
subject_preprocessing: Optional[
Union[Union[str, "PreprocessingMethodEnum"],
List[Union[str, "PreprocessingMethodEnum"]]]] = empty_list()
object_preprocessing: Optional[
Union[Union[str, "PreprocessingMethodEnum"],
List[Union[str, "PreprocessingMethodEnum"]]]] = empty_list()
match_term_type: Optional[Union[str, "MatchTermTypeEnum"]] = None
semantic_similarity_score: Optional[float] = None
semantic_similarity_measure: Optional[str] = None
see_also: Optional[Union[str, List[str]]] = empty_list()
other: Optional[str] = None
comment: Optional[str] = None
def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
if self._is_empty(self.subject_id):
self.MissingRequiredField("subject_id")
if not isinstance(self.subject_id, EntityReference):
self.subject_id = EntityReference(self.subject_id)
if self._is_empty(self.predicate_id):
self.MissingRequiredField("predicate_id")
if not isinstance(self.predicate_id, EntityReference):
self.predicate_id = EntityReference(self.predicate_id)
if self._is_empty(self.object_id):
self.MissingRequiredField("object_id")
if not isinstance(self.object_id, EntityReference):
self.object_id = EntityReference(self.object_id)
if self._is_empty(self.match_type):
self.MissingRequiredField("match_type")
if not isinstance(self.match_type, list):
self.match_type = [self.match_type
] if self.match_type is not None else []
self.match_type = [
v if isinstance(v, MatchTypeEnum) else MatchTypeEnum(v)
for v in self.match_type
]
if self.subject_label is not None and not isinstance(
self.subject_label, str):
self.subject_label = str(self.subject_label)
if self.subject_category is not None and not isinstance(
self.subject_category, str):
self.subject_category = str(self.subject_category)
if self.predicate_label is not None and not isinstance(
self.predicate_label, str):
self.predicate_label = str(self.predicate_label)
if self.predicate_modifier is not None and not isinstance(
self.predicate_modifier, PredicateModifierEnum):
self.predicate_modifier = PredicateModifierEnum(
self.predicate_modifier)
if self.object_label is not None and not isinstance(
self.object_label, str):
self.object_label = str(self.object_label)
if self.object_category is not None and not isinstance(
self.object_category, str):
self.object_category = str(self.object_category)
if not isinstance(self.author_id, list):
self.author_id = [self.author_id
] if self.author_id is not None else []
self.author_id = [
v if isinstance(v, EntityReference) else EntityReference(v)
for v in self.author_id
]
if not isinstance(self.author_label, list):
self.author_label = [self.author_label
] if self.author_label is not None else []
self.author_label = [
v if isinstance(v, str) else str(v) for v in self.author_label
]
if not isinstance(self.reviewer_id, list):
self.reviewer_id = [self.reviewer_id
] if self.reviewer_id is not None else []
self.reviewer_id = [
v if isinstance(v, EntityReference) else EntityReference(v)
for v in self.reviewer_id
]
if not isinstance(self.reviewer_label, list):
self.reviewer_label = [
self.reviewer_label
] if self.reviewer_label is not None else []
self.reviewer_label = [
v if isinstance(v, str) else str(v) for v in self.reviewer_label
]
if not isinstance(self.creator_id, list):
self.creator_id = [self.creator_id
] if self.creator_id is not None else []
self.creator_id = [
v if isinstance(v, EntityReference) else EntityReference(v)
for v in self.creator_id
]
if not isinstance(self.creator_label, list):
self.creator_label = [self.creator_label
] if self.creator_label is not None else []
self.creator_label = [
v if isinstance(v, str) else str(v) for v in self.creator_label
]
if self.license is not None and not isinstance(self.license, URI):
self.license = URI(self.license)
if self.subject_source is not None and not isinstance(
self.subject_source, URI):
self.subject_source = URI(self.subject_source)
if self.subject_source_version is not None and not isinstance(
self.subject_source_version, str):
self.subject_source_version = str(self.subject_source_version)
if self.object_source is not None and not isinstance(
self.object_source, URI):
self.object_source = URI(self.object_source)
if self.object_source_version is not None and not isinstance(
self.object_source_version, str):
self.object_source_version = str(self.object_source_version)
if self.mapping_provider is not None and not isinstance(
self.mapping_provider, URI):
self.mapping_provider = URI(self.mapping_provider)
if self.mapping_cardinality is not None and not isinstance(
self.mapping_cardinality, MappingCardinalityEnum):
self.mapping_cardinality = MappingCardinalityEnum(
self.mapping_cardinality)
if self.mapping_tool is not None and not isinstance(
self.mapping_tool, str):
self.mapping_tool = str(self.mapping_tool)
if self.mapping_tool_version is not None and not isinstance(
self.mapping_tool_version, str):
self.mapping_tool_version = str(self.mapping_tool_version)
if self.mapping_date is not None and not isinstance(
self.mapping_date, XSDDate):
self.mapping_date = XSDDate(self.mapping_date)
if self.confidence is not None and not isinstance(
self.confidence, float):
self.confidence = float(self.confidence)
if not isinstance(self.subject_match_field, list):
self.subject_match_field = [
self.subject_match_field
] if self.subject_match_field is not None else []
self.subject_match_field = [
v if isinstance(v, EntityReference) else EntityReference(v)
for v in self.subject_match_field
]
if not isinstance(self.object_match_field, list):
self.object_match_field = [
self.object_match_field
] if self.object_match_field is not None else []
self.object_match_field = [
v if isinstance(v, EntityReference) else EntityReference(v)
for v in self.object_match_field
]
if not isinstance(self.match_string, list):
self.match_string = [self.match_string
] if self.match_string is not None else []
self.match_string = [
v if isinstance(v, str) else str(v) for v in self.match_string
]
if not isinstance(self.subject_preprocessing, list):
self.subject_preprocessing = [
self.subject_preprocessing
] if self.subject_preprocessing is not None else []
self.subject_preprocessing = [
v if isinstance(v, PreprocessingMethodEnum) else
PreprocessingMethodEnum(v) for v in self.subject_preprocessing
]
if not isinstance(self.object_preprocessing, list):
self.object_preprocessing = [
self.object_preprocessing
] if self.object_preprocessing is not None else []
self.object_preprocessing = [
v if isinstance(v, PreprocessingMethodEnum) else
PreprocessingMethodEnum(v) for v in self.object_preprocessing
]
if self.match_term_type is not None and not isinstance(
self.match_term_type, MatchTermTypeEnum):
self.match_term_type = MatchTermTypeEnum(self.match_term_type)
if self.semantic_similarity_score is not None and not isinstance(
self.semantic_similarity_score, float):
self.semantic_similarity_score = float(
self.semantic_similarity_score)
if self.semantic_similarity_measure is not None and not isinstance(
self.semantic_similarity_measure, str):
self.semantic_similarity_measure = str(
self.semantic_similarity_measure)
if not isinstance(self.see_also, list):
self.see_also = [self.see_also
] if self.see_also is not None else []
self.see_also = [
v if isinstance(v, str) else str(v) for v in self.see_also
]
if self.other is not None and not isinstance(self.other, str):
self.other = str(self.other)
if self.comment is not None and not isinstance(self.comment, str):
self.comment = str(self.comment)
super().__post_init__(**kwargs)
class Clique(YAMLRoot):
"""
A clique
"""
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = SSSOM.CS.Clique
class_class_curie: ClassVar[str] = "sssom.cs:Clique"
class_name: ClassVar[str] = "clique"
class_model_uri: ClassVar[URIRef] = SSSOM.CS.Clique
id: Union[str, CliqueId] = None
members: Optional[Union[str, List[str]]] = empty_list()
members_labels: Optional[Union[str, List[str]]] = empty_list()
num_members: Optional[int] = None
max_confidence: Optional[float] = None
min_confidence: Optional[float] = None
avg_confidence: Optional[float] = None
is_conflated: Optional[Union[bool, Bool]] = None
is_all_conflated: Optional[Union[bool, Bool]] = None
total_conflated: Optional[int] = None
proportion_conflated: Optional[float] = None
conflation_score: Optional[float] = None
members_count: Optional[int] = None
min_count_by_source: Optional[int] = None
max_count_by_source: Optional[int] = None
avg_count_by_source: Optional[float] = None
harmonic_mean_count_by_source: Optional[float] = None
def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
if self._is_empty(self.id):
self.MissingRequiredField("id")
if not isinstance(self.id, CliqueId):
self.id = CliqueId(self.id)
if not isinstance(self.members, list):
self.members = [self.members] if self.members is not None else []
self.members = [
v if isinstance(v, str) else str(v) for v in self.members
]
if not isinstance(self.members_labels, list):
self.members_labels = ([self.members_labels]
if self.members_labels is not None else [])
self.members_labels = [
v if isinstance(v, str) else str(v) for v in self.members_labels
]
if self.num_members is not None and not isinstance(
self.num_members, int):
self.num_members = int(self.num_members)
if self.max_confidence is not None and not isinstance(
self.max_confidence, float):
self.max_confidence = float(self.max_confidence)
if self.min_confidence is not None and not isinstance(
self.min_confidence, float):
self.min_confidence = float(self.min_confidence)
if self.avg_confidence is not None and not isinstance(
self.avg_confidence, float):
self.avg_confidence = float(self.avg_confidence)
if self.is_conflated is not None and not isinstance(
self.is_conflated, Bool):
self.is_conflated = Bool(self.is_conflated)
if self.is_all_conflated is not None and not isinstance(
self.is_all_conflated, Bool):
self.is_all_conflated = Bool(self.is_all_conflated)
if self.total_conflated is not None and not isinstance(
self.total_conflated, int):
self.total_conflated = int(self.total_conflated)
if self.proportion_conflated is not None and not isinstance(
self.proportion_conflated, float):
self.proportion_conflated = float(self.proportion_conflated)
if self.conflation_score is not None and not isinstance(
self.conflation_score, float):
self.conflation_score = float(self.conflation_score)
if self.members_count is not None and not isinstance(
self.members_count, int):
self.members_count = int(self.members_count)
if self.min_count_by_source is not None and not isinstance(
self.min_count_by_source, int):
self.min_count_by_source = int(self.min_count_by_source)
if self.max_count_by_source is not None and not isinstance(
self.max_count_by_source, int):
self.max_count_by_source = int(self.max_count_by_source)
if self.avg_count_by_source is not None and not isinstance(
self.avg_count_by_source, float):
self.avg_count_by_source = float(self.avg_count_by_source)
if self.harmonic_mean_count_by_source is not None and not isinstance(
self.harmonic_mean_count_by_source, float):
self.harmonic_mean_count_by_source = float(
self.harmonic_mean_count_by_source)
super().__post_init__(**kwargs)