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Merge pull request #62 from linkml/rules-model
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rules model
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@cmungall
cmungall authored Oct 26, 2021
2 parents 2997d84 + d17b590 commit 6c222b2
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Showing 3 changed files with 61 additions and 168 deletions.
97 changes: 3 additions & 94 deletions linkml_runtime/linkml_model/meta.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Auto generated from meta.yaml by pythongen.py version: 0.9.0
# Generation date: 2021-10-25 15:29
# Generation date: 2021-10-25 20:23
# Schema: meta
#
# id: https://w3id.org/linkml/meta
Expand Down Expand Up @@ -1325,7 +1325,7 @@ class ClassDefinition(Definition):
tree_root: Optional[Union[bool, Bool]] = None
unique_keys: Optional[Union[Union[dict, "UniqueKey"], List[Union[dict, "UniqueKey"]]]] = empty_list()
rules: Optional[Union[Union[dict, "ClassRule"], List[Union[dict, "ClassRule"]]]] = empty_list()
classification_rules: Optional[Union[Union[dict, "ClassificationRule"], List[Union[dict, "ClassificationRule"]]]] = empty_list()
classification_rules: Optional[Union[Union[dict, AnonymousClassExpression], List[Union[dict, AnonymousClassExpression]]]] = empty_list()
is_a: Optional[Union[str, ClassDefinitionName]] = None
mixins: Optional[Union[Union[str, ClassDefinitionName], List[Union[str, ClassDefinitionName]]]] = empty_list()
apply_to: Optional[Union[Union[str, ClassDefinitionName], List[Union[str, ClassDefinitionName]]]] = empty_list()
Expand Down Expand Up @@ -1374,7 +1374,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):

if not isinstance(self.classification_rules, list):
self.classification_rules = [self.classification_rules] if self.classification_rules is not None else []
self.classification_rules = [v if isinstance(v, ClassificationRule) else ClassificationRule(**as_dict(v)) for v in self.classification_rules]
self.classification_rules = [v if isinstance(v, AnonymousClassExpression) else AnonymousClassExpression(**as_dict(v)) for v in self.classification_rules]

if self.is_a is not None and not isinstance(self.is_a, ClassDefinitionName):
self.is_a = ClassDefinitionName(self.is_a)
Expand Down Expand Up @@ -1532,97 +1532,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
super().__post_init__(**kwargs)


@dataclass
class ClassificationRule(ClassLevelRule):
"""
A rule that determines how to automatically classify an instance as a member of a class
"""
_inherited_slots: ClassVar[List[str]] = []

class_class_uri: ClassVar[URIRef] = LINKML.ClassificationRule
class_class_curie: ClassVar[str] = "linkml:ClassificationRule"
class_name: ClassVar[str] = "classification_rule"
class_model_uri: ClassVar[URIRef] = LINKML.ClassificationRule

instance_of: Optional[Union[str, ClassDefinitionName]] = None
slot_conditions: Optional[Union[Dict[Union[str, SlotDefinitionName], Union[dict, SlotDefinition]], List[Union[dict, SlotDefinition]]]] = empty_dict()
extensions: Optional[Union[Union[dict, Extension], List[Union[dict, Extension]]]] = empty_list()
annotations: Optional[Union[Union[dict, Annotation], List[Union[dict, Annotation]]]] = empty_list()
description: Optional[str] = None
alt_descriptions: Optional[Union[Dict[Union[str, AltDescriptionSource], Union[dict, "AltDescription"]], List[Union[dict, "AltDescription"]]]] = empty_dict()
title: Optional[str] = None
deprecated: Optional[str] = None
todos: Optional[Union[str, List[str]]] = empty_list()
notes: Optional[Union[str, List[str]]] = empty_list()
comments: Optional[Union[str, List[str]]] = empty_list()
examples: Optional[Union[Union[dict, "Example"], List[Union[dict, "Example"]]]] = empty_list()
in_subset: Optional[Union[Union[str, SubsetDefinitionName], List[Union[str, SubsetDefinitionName]]]] = empty_list()
from_schema: Optional[Union[str, URI]] = None
imported_from: Optional[str] = None
see_also: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = empty_list()
deprecated_element_has_exact_replacement: Optional[Union[str, URIorCURIE]] = None
deprecated_element_has_possible_replacement: Optional[Union[str, URIorCURIE]] = None

def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
if self.instance_of is not None and not isinstance(self.instance_of, ClassDefinitionName):
self.instance_of = ClassDefinitionName(self.instance_of)

self._normalize_inlined_as_dict(slot_name="slot_conditions", slot_type=SlotDefinition, key_name="name", keyed=True)

self._normalize_inlined_as_dict(slot_name="extensions", slot_type=Extension, key_name="tag", keyed=False)

self._normalize_inlined_as_dict(slot_name="annotations", slot_type=Annotation, key_name="tag", keyed=False)

if self.description is not None and not isinstance(self.description, str):
self.description = str(self.description)

self._normalize_inlined_as_dict(slot_name="alt_descriptions", slot_type=AltDescription, key_name="source", keyed=True)

if self.title is not None and not isinstance(self.title, str):
self.title = str(self.title)

if self.deprecated is not None and not isinstance(self.deprecated, str):
self.deprecated = str(self.deprecated)

if not isinstance(self.todos, list):
self.todos = [self.todos] if self.todos is not None else []
self.todos = [v if isinstance(v, str) else str(v) for v in self.todos]

if not isinstance(self.notes, list):
self.notes = [self.notes] if self.notes is not None else []
self.notes = [v if isinstance(v, str) else str(v) for v in self.notes]

if not isinstance(self.comments, list):
self.comments = [self.comments] if self.comments is not None else []
self.comments = [v if isinstance(v, str) else str(v) for v in self.comments]

if not isinstance(self.examples, list):
self.examples = [self.examples] if self.examples is not None else []
self.examples = [v if isinstance(v, Example) else Example(**as_dict(v)) for v in self.examples]

if not isinstance(self.in_subset, list):
self.in_subset = [self.in_subset] if self.in_subset is not None else []
self.in_subset = [v if isinstance(v, SubsetDefinitionName) else SubsetDefinitionName(v) for v in self.in_subset]

if self.from_schema is not None and not isinstance(self.from_schema, URI):
self.from_schema = URI(self.from_schema)

if self.imported_from is not None and not isinstance(self.imported_from, str):
self.imported_from = str(self.imported_from)

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, URIorCURIE) else URIorCURIE(v) for v in self.see_also]

if self.deprecated_element_has_exact_replacement is not None and not isinstance(self.deprecated_element_has_exact_replacement, URIorCURIE):
self.deprecated_element_has_exact_replacement = URIorCURIE(self.deprecated_element_has_exact_replacement)

if self.deprecated_element_has_possible_replacement is not None and not isinstance(self.deprecated_element_has_possible_replacement, URIorCURIE):
self.deprecated_element_has_possible_replacement = URIorCURIE(self.deprecated_element_has_possible_replacement)

super().__post_init__(**kwargs)


@dataclass
class Prefix(YAMLRoot):
"""
Expand Down
126 changes: 55 additions & 71 deletions linkml_runtime/linkml_model/model/schema/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -533,7 +533,52 @@ slots:
exact_mappings:
- sh:and
status: testing


preconditions:
aliases:
- if
- body
- antecedents
slot_uri: sh:condition
description: an expression that must hold in order for the rule to be applicable to an instance
range: anonymous_class_expression
inlined: true
close_mappings:
- swrl:body
postconditions:
aliases:
- then
- head
- consequents
description: an expression that must hold for an instance of the class, if the preconditions hold
range: anonymous_class_expression
inlined: true
close_mappings:
- swrl:body
elseconditions:
aliases:
- else
description: an expression that must hold for an instance of the class, if the preconditions no not hold
range: anonymous_class_expression
inlined: true
bidirectional:
aliases:
- iff
- if and only if
description: in addition to preconditions entailing postconditions, the postconditions entail the preconditions
range: boolean
open_world:
description: if true, the the postconditions may be omitted in instance data, but it is valid for an inference engine to add these
range: boolean
precedence:
description: the relative order in which the rule is applied
slot_uri: sh:order
range: integer
deactivated:
description: a deactivated rule is not executed by the rules engine
slot_uri: sh:deactivated
range: boolean

rules:
slot_uri: sh:rule
domain: class_definition
Expand All @@ -546,7 +591,7 @@ slots:
classification_rules:
domain: class_definition
multivalued: true
range: classification_rule
range: anonymous_class_expression
inlined: true
description: the collection of classification rules that apply to all members of this class
status: testing
Expand Down Expand Up @@ -1470,80 +1515,19 @@ classes:
- extensible
- annotatable
- common_metadata
attributes:
preconditions:
aliases:
- if
- body
- antecedents
slot_uri: sh:condition
description: an expression that must hold in order for the rule to be applicable to an instance
range: anonymous_class_expression
inlined: true
close_mappings:
- swrl:body
postconditions:
aliases:
- then
- head
- consequents
description: an expression that must hold for an instance of the class, if the preconditions hold
range: anonymous_class_expression
inlined: true
close_mappings:
- swrl:body
elseconditions:
aliases:
- else
description: an expression that must hold for an instance of the class, if the preconditions no not hold
range: anonymous_class_expression
inlined: true
bidirectional:
aliases:
- iff
- if and only if
description: in addition to preconditions entailing postconditions, the postconditions entail the preconditions
range: boolean
open_world:
description: if true, the the postconditions may be omitted in instance data, but it is valid for an inference engine to add these
range: boolean
precedence:
description: the relative order in which the rule is applied
slot_uri: sh:order
range: integer
deactivated:
description: a deactivated rule is not executed by the rules engine
slot_uri: sh:deactivated
range: boolean
slots:
- preconditions
- postconditions
- elseconditions
- bidirectional
- open_world
- precedence
- deactivated
close_mappings:
- sh:TripleRule
- swrl:Imp
status: testing

classification_rule:
is_a: class_level_rule
aliases:
- membership rule
description: A rule that determines how to automatically classify an instance as a member of a class
mixins:
- extensible
- annotatable
- common_metadata
attributes:
instance_of:
range: class_definition
slot_conditions:
aliases:
- differentiae
slot_uri: sh:condition
description: an expression that must hold in order for the classification rule to take effect
range: slot_definition
inlined: true
multivalued: true
close_mappings:
- swrl:body
status: testing

prefix:
description: prefix URI tuple
slots:
Expand Down
6 changes: 3 additions & 3 deletions tests/test_utils/input/rules-example.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -109,15 +109,15 @@ classes:
NoncodingGene:
is_a: Gene
classification_rules:
- instance_of: Gene
- is_a: Gene
slot_conditions:
encodes:
none_of:
range: Protein
ProteinCodingGene:
is_a: Gene
classification_rules:
- instance_of: Gene
- is_a: Gene
slot_conditions:
encodes:
range: Protein
Expand All @@ -129,7 +129,7 @@ classes:
GenomicSample:
is_a: Sample
classification_rules:
- instance_of: Sample
- is_a: Sample
slot_conditions:
analyte:
equals_string: DNA
Expand Down

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