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Generated schema (from gen-doc)
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‎src/fair_mappings_schema/datamodel/fair_mappings_schema.py‎

Lines changed: 126 additions & 86 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,9 @@
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# Auto generated from fair_mappings_schema.yaml by pythongen.py version: 0.0.1
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# Generation date: 2025-10-04T08:59:50
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# Generation date: 2025-10-04T12:17:23
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# Schema: fair-mappings-schema
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#
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# id: https://w3id.org/mapping-commons/fair-mappings-schema
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# description: A basic metadata schema for FAIR mapping specifications
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# description: A minimal metadata schema for FAIR mapping specifications
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# license: Apache-2.0
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99
import dataclasses
@@ -56,8 +56,7 @@
5656
URIRef
5757
)
5858

59-
from linkml_runtime.linkml_model.types import Date, Integer, String, Uriorcurie
60-
from linkml_runtime.utils.metamodelcore import URIorCURIE, XSDDate
59+
from linkml_runtime.linkml_model.types import String
6160

6261
metamodel_version = "1.7.0"
6362
version = None
@@ -75,151 +74,192 @@
7574
# Types
7675

7776
# Class references
78-
class NamedThingId(URIorCURIE):
79-
pass
80-
81-
82-
class PersonId(NamedThingId):
77+
class AgentId(extended_str):
8378
pass
8479

8580

8681
@dataclass(repr=False)
87-
class NamedThing(YAMLRoot):
82+
class Agent(YAMLRoot):
8883
"""
89-
A generic grouping for any identifiable entity
84+
An entity that can create or contribute to a digital object, such as an author or creator.
9085
"""
9186
_inherited_slots: ClassVar[list[str]] = []
9287

93-
class_class_uri: ClassVar[URIRef] = SCHEMA["Thing"]
94-
class_class_curie: ClassVar[str] = "schema:Thing"
95-
class_name: ClassVar[str] = "NamedThing"
96-
class_model_uri: ClassVar[URIRef] = FAIR_MAPPINGS_SCHEMA.NamedThing
88+
class_class_uri: ClassVar[URIRef] = FAIR_MAPPINGS_SCHEMA["Agent"]
89+
class_class_curie: ClassVar[str] = "fair_mappings_schema:Agent"
90+
class_name: ClassVar[str] = "Agent"
91+
class_model_uri: ClassVar[URIRef] = FAIR_MAPPINGS_SCHEMA.Agent
9792

98-
id: Union[str, NamedThingId] = None
93+
id: Union[str, AgentId] = None
9994
name: Optional[str] = None
100-
description: Optional[str] = None
10195

10296
def __post_init__(self, *_: str, **kwargs: Any):
10397
if self._is_empty(self.id):
10498
self.MissingRequiredField("id")
105-
if not isinstance(self.id, NamedThingId):
106-
self.id = NamedThingId(self.id)
99+
if not isinstance(self.id, AgentId):
100+
self.id = AgentId(self.id)
107101

108102
if self.name is not None and not isinstance(self.name, str):
109103
self.name = str(self.name)
110104

111-
if self.description is not None and not isinstance(self.description, str):
112-
self.description = str(self.description)
113-
114105
super().__post_init__(**kwargs)
115106

116107

117108
@dataclass(repr=False)
118-
class Person(NamedThing):
109+
class Source(YAMLRoot):
119110
"""
120-
Represents a Person
111+
A data source from which entities are drawn, such as a database, ontology, or vocabulary.
121112
"""
122113
_inherited_slots: ClassVar[list[str]] = []
123114

124-
class_class_uri: ClassVar[URIRef] = FAIR_MAPPINGS_SCHEMA["Person"]
125-
class_class_curie: ClassVar[str] = "fair_mappings_schema:Person"
126-
class_name: ClassVar[str] = "Person"
127-
class_model_uri: ClassVar[URIRef] = FAIR_MAPPINGS_SCHEMA.Person
115+
class_class_uri: ClassVar[URIRef] = FAIR_MAPPINGS_SCHEMA["Source"]
116+
class_class_curie: ClassVar[str] = "fair_mappings_schema:Source"
117+
class_name: ClassVar[str] = "Source"
118+
class_model_uri: ClassVar[URIRef] = FAIR_MAPPINGS_SCHEMA.Source
128119

129-
id: Union[str, PersonId] = None
130-
primary_email: Optional[str] = None
131-
birth_date: Optional[Union[str, XSDDate]] = None
132-
age_in_years: Optional[int] = None
133-
vital_status: Optional[Union[str, "PersonStatus"]] = None
120+
name: Optional[str] = None
121+
version: Optional[str] = None
122+
type: Optional[str] = None
123+
documentation: Optional[str] = None
124+
content: Optional[str] = None
125+
content_type: Optional[str] = None
134126

135127
def __post_init__(self, *_: str, **kwargs: Any):
136-
if self._is_empty(self.id):
137-
self.MissingRequiredField("id")
138-
if not isinstance(self.id, PersonId):
139-
self.id = PersonId(self.id)
128+
if self.name is not None and not isinstance(self.name, str):
129+
self.name = str(self.name)
130+
131+
if self.version is not None and not isinstance(self.version, str):
132+
self.version = str(self.version)
140133

141-
if self.primary_email is not None and not isinstance(self.primary_email, str):
142-
self.primary_email = str(self.primary_email)
134+
if self.type is not None and not isinstance(self.type, str):
135+
self.type = str(self.type)
143136

144-
if self.birth_date is not None and not isinstance(self.birth_date, XSDDate):
145-
self.birth_date = XSDDate(self.birth_date)
137+
if self.documentation is not None and not isinstance(self.documentation, str):
138+
self.documentation = str(self.documentation)
146139

147-
if self.age_in_years is not None and not isinstance(self.age_in_years, int):
148-
self.age_in_years = int(self.age_in_years)
140+
if self.content is not None and not isinstance(self.content, str):
141+
self.content = str(self.content)
149142

150-
if self.vital_status is not None and not isinstance(self.vital_status, PersonStatus):
151-
self.vital_status = PersonStatus(self.vital_status)
143+
if self.content_type is not None and not isinstance(self.content_type, str):
144+
self.content_type = str(self.content_type)
152145

153146
super().__post_init__(**kwargs)
154147

155148

156149
@dataclass(repr=False)
157-
class PersonCollection(YAMLRoot):
150+
class MappingSpecification(YAMLRoot):
158151
"""
159-
A holder for Person objects
152+
A formal description of correspondences between entities in a source and a target, expressed as rules, functions,
153+
or mapping statements.
160154
"""
161155
_inherited_slots: ClassVar[list[str]] = []
162156

163-
class_class_uri: ClassVar[URIRef] = FAIR_MAPPINGS_SCHEMA["PersonCollection"]
164-
class_class_curie: ClassVar[str] = "fair_mappings_schema:PersonCollection"
165-
class_name: ClassVar[str] = "PersonCollection"
166-
class_model_uri: ClassVar[URIRef] = FAIR_MAPPINGS_SCHEMA.PersonCollection
157+
class_class_uri: ClassVar[URIRef] = FAIR_MAPPINGS_SCHEMA["MappingSpecification"]
158+
class_class_curie: ClassVar[str] = "fair_mappings_schema:MappingSpecification"
159+
class_name: ClassVar[str] = "MappingSpecification"
160+
class_model_uri: ClassVar[URIRef] = FAIR_MAPPINGS_SCHEMA.MappingSpecification
167161

168-
entries: Optional[Union[dict[Union[str, PersonId], Union[dict, Person]], list[Union[dict, Person]]]] = empty_dict()
162+
author: Optional[Union[dict, Agent]] = None
163+
creator: Optional[Union[dict, Agent]] = None
164+
publication_date: Optional[str] = None
165+
license: Optional[str] = None
166+
version: Optional[str] = None
167+
description: Optional[str] = None
168+
type: Optional[str] = None
169+
mapping_method: Optional[str] = None
170+
documentation: Optional[str] = None
171+
content: Optional[str] = None
172+
subject_source: Optional[Union[dict, Source]] = None
173+
object_source: Optional[Union[dict, Source]] = None
169174

170175
def __post_init__(self, *_: str, **kwargs: Any):
171-
self._normalize_inlined_as_list(slot_name="entries", slot_type=Person, key_name="id", keyed=True)
176+
if self.author is not None and not isinstance(self.author, Agent):
177+
self.author = Agent(**as_dict(self.author))
178+
179+
if self.creator is not None and not isinstance(self.creator, Agent):
180+
self.creator = Agent(**as_dict(self.creator))
181+
182+
if self.publication_date is not None and not isinstance(self.publication_date, str):
183+
self.publication_date = str(self.publication_date)
184+
185+
if self.license is not None and not isinstance(self.license, str):
186+
self.license = str(self.license)
187+
188+
if self.version is not None and not isinstance(self.version, str):
189+
self.version = str(self.version)
190+
191+
if self.description is not None and not isinstance(self.description, str):
192+
self.description = str(self.description)
193+
194+
if self.type is not None and not isinstance(self.type, str):
195+
self.type = str(self.type)
196+
197+
if self.mapping_method is not None and not isinstance(self.mapping_method, str):
198+
self.mapping_method = str(self.mapping_method)
199+
200+
if self.documentation is not None and not isinstance(self.documentation, str):
201+
self.documentation = str(self.documentation)
202+
203+
if self.content is not None and not isinstance(self.content, str):
204+
self.content = str(self.content)
205+
206+
if self.subject_source is not None and not isinstance(self.subject_source, Source):
207+
self.subject_source = Source(**as_dict(self.subject_source))
208+
209+
if self.object_source is not None and not isinstance(self.object_source, Source):
210+
self.object_source = Source(**as_dict(self.object_source))
172211

173212
super().__post_init__(**kwargs)
174213

175214

176215
# Enumerations
177-
class PersonStatus(EnumDefinitionImpl):
178-
179-
ALIVE = PermissibleValue(
180-
text="ALIVE",
181-
description="the person is living",
182-
meaning=PATO["0001421"])
183-
DEAD = PermissibleValue(
184-
text="DEAD",
185-
description="the person is deceased",
186-
meaning=PATO["0001422"])
187-
UNKNOWN = PermissibleValue(
188-
text="UNKNOWN",
189-
description="the vital status is not known")
190-
191-
_defn = EnumDefinition(
192-
name="PersonStatus",
193-
)
216+
194217

195218
# Slots
196219
class slots:
197220
pass
198221

199-
slots.id = Slot(uri=SCHEMA.identifier, name="id", curie=SCHEMA.curie('identifier'),
222+
slots.id = Slot(uri=FAIR_MAPPINGS_SCHEMA.id, name="id", curie=FAIR_MAPPINGS_SCHEMA.curie('id'),
200223
model_uri=FAIR_MAPPINGS_SCHEMA.id, domain=None, range=URIRef)
201224

202-
slots.name = Slot(uri=SCHEMA.name, name="name", curie=SCHEMA.curie('name'),
225+
slots.name = Slot(uri=FAIR_MAPPINGS_SCHEMA.name, name="name", curie=FAIR_MAPPINGS_SCHEMA.curie('name'),
203226
model_uri=FAIR_MAPPINGS_SCHEMA.name, domain=None, range=Optional[str])
204227

205-
slots.description = Slot(uri=SCHEMA.description, name="description", curie=SCHEMA.curie('description'),
228+
slots.creator = Slot(uri=FAIR_MAPPINGS_SCHEMA.creator, name="creator", curie=FAIR_MAPPINGS_SCHEMA.curie('creator'),
229+
model_uri=FAIR_MAPPINGS_SCHEMA.creator, domain=None, range=Optional[Union[dict, Agent]])
230+
231+
slots.author = Slot(uri=FAIR_MAPPINGS_SCHEMA.author, name="author", curie=FAIR_MAPPINGS_SCHEMA.curie('author'),
232+
model_uri=FAIR_MAPPINGS_SCHEMA.author, domain=None, range=Optional[Union[dict, Agent]])
233+
234+
slots.publication_date = Slot(uri=FAIR_MAPPINGS_SCHEMA.publication_date, name="publication_date", curie=FAIR_MAPPINGS_SCHEMA.curie('publication_date'),
235+
model_uri=FAIR_MAPPINGS_SCHEMA.publication_date, domain=None, range=Optional[str])
236+
237+
slots.license = Slot(uri=FAIR_MAPPINGS_SCHEMA.license, name="license", curie=FAIR_MAPPINGS_SCHEMA.curie('license'),
238+
model_uri=FAIR_MAPPINGS_SCHEMA.license, domain=None, range=Optional[str])
239+
240+
slots.version = Slot(uri=FAIR_MAPPINGS_SCHEMA.version, name="version", curie=FAIR_MAPPINGS_SCHEMA.curie('version'),
241+
model_uri=FAIR_MAPPINGS_SCHEMA.version, domain=None, range=Optional[str])
242+
243+
slots.description = Slot(uri=FAIR_MAPPINGS_SCHEMA.description, name="description", curie=FAIR_MAPPINGS_SCHEMA.curie('description'),
206244
model_uri=FAIR_MAPPINGS_SCHEMA.description, domain=None, range=Optional[str])
207245

208-
slots.primary_email = Slot(uri=SCHEMA.email, name="primary_email", curie=SCHEMA.curie('email'),
209-
model_uri=FAIR_MAPPINGS_SCHEMA.primary_email, domain=None, range=Optional[str])
246+
slots.type = Slot(uri=FAIR_MAPPINGS_SCHEMA.type, name="type", curie=FAIR_MAPPINGS_SCHEMA.curie('type'),
247+
model_uri=FAIR_MAPPINGS_SCHEMA.type, domain=None, range=Optional[str])
248+
249+
slots.mapping_method = Slot(uri=FAIR_MAPPINGS_SCHEMA.mapping_method, name="mapping_method", curie=FAIR_MAPPINGS_SCHEMA.curie('mapping_method'),
250+
model_uri=FAIR_MAPPINGS_SCHEMA.mapping_method, domain=None, range=Optional[str])
210251

211-
slots.birth_date = Slot(uri=SCHEMA.birthDate, name="birth_date", curie=SCHEMA.curie('birthDate'),
212-
model_uri=FAIR_MAPPINGS_SCHEMA.birth_date, domain=None, range=Optional[Union[str, XSDDate]])
252+
slots.documentation = Slot(uri=FAIR_MAPPINGS_SCHEMA.documentation, name="documentation", curie=FAIR_MAPPINGS_SCHEMA.curie('documentation'),
253+
model_uri=FAIR_MAPPINGS_SCHEMA.documentation, domain=None, range=Optional[str])
213254

214-
slots.age_in_years = Slot(uri=FAIR_MAPPINGS_SCHEMA.age_in_years, name="age_in_years", curie=FAIR_MAPPINGS_SCHEMA.curie('age_in_years'),
215-
model_uri=FAIR_MAPPINGS_SCHEMA.age_in_years, domain=None, range=Optional[int])
255+
slots.content = Slot(uri=FAIR_MAPPINGS_SCHEMA.content, name="content", curie=FAIR_MAPPINGS_SCHEMA.curie('content'),
256+
model_uri=FAIR_MAPPINGS_SCHEMA.content, domain=None, range=Optional[str])
216257

217-
slots.vital_status = Slot(uri=FAIR_MAPPINGS_SCHEMA.vital_status, name="vital_status", curie=FAIR_MAPPINGS_SCHEMA.curie('vital_status'),
218-
model_uri=FAIR_MAPPINGS_SCHEMA.vital_status, domain=None, range=Optional[Union[str, "PersonStatus"]])
258+
slots.content_type = Slot(uri=FAIR_MAPPINGS_SCHEMA.content_type, name="content_type", curie=FAIR_MAPPINGS_SCHEMA.curie('content_type'),
259+
model_uri=FAIR_MAPPINGS_SCHEMA.content_type, domain=None, range=Optional[str])
219260

220-
slots.personCollection__entries = Slot(uri=FAIR_MAPPINGS_SCHEMA.entries, name="personCollection__entries", curie=FAIR_MAPPINGS_SCHEMA.curie('entries'),
221-
model_uri=FAIR_MAPPINGS_SCHEMA.personCollection__entries, domain=None, range=Optional[Union[dict[Union[str, PersonId], Union[dict, Person]], list[Union[dict, Person]]]])
261+
slots.subject_source = Slot(uri=FAIR_MAPPINGS_SCHEMA.subject_source, name="subject_source", curie=FAIR_MAPPINGS_SCHEMA.curie('subject_source'),
262+
model_uri=FAIR_MAPPINGS_SCHEMA.subject_source, domain=None, range=Optional[Union[dict, Source]])
222263

223-
slots.Person_primary_email = Slot(uri=SCHEMA.email, name="Person_primary_email", curie=SCHEMA.curie('email'),
224-
model_uri=FAIR_MAPPINGS_SCHEMA.Person_primary_email, domain=Person, range=Optional[str],
225-
pattern=re.compile(r'^\S+@[\S+\.]+\S+'))
264+
slots.object_source = Slot(uri=FAIR_MAPPINGS_SCHEMA.object_source, name="object_source", curie=FAIR_MAPPINGS_SCHEMA.curie('object_source'),
265+
model_uri=FAIR_MAPPINGS_SCHEMA.object_source, domain=None, range=Optional[Union[dict, Source]])

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