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✨ Add Encounter framework #19

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Merged
RobertJCarroll merged 1 commit into from
Mar 9, 2026
Merged

✨ Add Encounter framework #19

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151 changes: 150 additions & 1 deletion src/include_access_model/datamodel/include_access_model.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Auto generated from include_access_model.yaml by pythongen.py version: 0.0.1
# Generation date: 2026-03-09T10:45:00
# Generation date: 2026-03-09T12:08:53
# Schema: include-access-model
#
# id: https://includedcc.org/include-access-model
Expand Down Expand Up @@ -125,6 +125,18 @@ class AliquotAliquotId(extended_str):
pass


class EncounterEncounterId(extended_str):
pass


class EncounterDefinitionEncounterDefinitionId(extended_str):
pass


class ActivityDefinitionActivityDefinitionId(extended_str):
pass


@dataclass(repr=False)
class Record(YAMLRoot):
"""
Expand Down Expand Up @@ -554,6 +566,7 @@ class SubjectAssertion(Record):

assertion_id: Union[str, SubjectAssertionAssertionId] = None
subject_id: Optional[Union[str, SubjectSubjectId]] = None
encounter_id: Optional[Union[str, EncounterEncounterId]] = None
assertion_provenance: Optional[Union[str, "EnumAssertionProvenance"]] = None
age_at_assertion: Optional[int] = None
age_at_event: Optional[int] = None
Expand All @@ -575,6 +588,9 @@ def __post_init__(self, *_: str, **kwargs: Any):
if self.subject_id is not None and not isinstance(self.subject_id, SubjectSubjectId):
self.subject_id = SubjectSubjectId(self.subject_id)

if self.encounter_id is not None and not isinstance(self.encounter_id, EncounterEncounterId):
self.encounter_id = EncounterEncounterId(self.encounter_id)

if self.assertion_provenance is not None and not isinstance(self.assertion_provenance, EnumAssertionProvenance):
self.assertion_provenance = EnumAssertionProvenance(self.assertion_provenance)

Expand Down Expand Up @@ -717,6 +733,7 @@ class BiospecimenCollection(Record):
site: Optional[Union[str, "EnumSite"]] = None
spatial_qualifier: Optional[Union[str, "EnumSpatialQualifiers"]] = None
laterality: Optional[Union[str, "EnumLaterality"]] = None
encounter_id: Optional[Union[str, EncounterEncounterId]] = None

def __post_init__(self, *_: str, **kwargs: Any):
if self._is_empty(self.biospecimen_collection_id):
Expand All @@ -727,6 +744,9 @@ def __post_init__(self, *_: str, **kwargs: Any):
if self.age_at_collection is not None and not isinstance(self.age_at_collection, float):
self.age_at_collection = float(self.age_at_collection)

if self.encounter_id is not None and not isinstance(self.encounter_id, EncounterEncounterId):
self.encounter_id = EncounterEncounterId(self.encounter_id)

super().__post_init__(**kwargs)


Expand Down Expand Up @@ -777,6 +797,111 @@ def __post_init__(self, *_: str, **kwargs: Any):
super().__post_init__(**kwargs)


@dataclass(repr=False)
class Encounter(Record):
"""
An event at which data was collected about a participant, an intervention was made, or information about a
participant was recorded.
"""
_inherited_slots: ClassVar[list[str]] = []

class_class_uri: ClassVar[URIRef] = INCLUDEDCC["Encounter"]
class_class_curie: ClassVar[str] = "includedcc:Encounter"
class_name: ClassVar[str] = "Encounter"
class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Encounter

encounter_id: Union[str, EncounterEncounterId] = None
subject_id: Optional[Union[str, SubjectSubjectId]] = None
encounter_definition_id: Optional[Union[str, EncounterDefinitionEncounterDefinitionId]] = None
age_at_event: Optional[int] = None

def __post_init__(self, *_: str, **kwargs: Any):
if self._is_empty(self.encounter_id):
self.MissingRequiredField("encounter_id")
if not isinstance(self.encounter_id, EncounterEncounterId):
self.encounter_id = EncounterEncounterId(self.encounter_id)

if self.subject_id is not None and not isinstance(self.subject_id, SubjectSubjectId):
self.subject_id = SubjectSubjectId(self.subject_id)

if self.encounter_definition_id is not None and not isinstance(self.encounter_definition_id, EncounterDefinitionEncounterDefinitionId):
self.encounter_definition_id = EncounterDefinitionEncounterDefinitionId(self.encounter_definition_id)

if self.age_at_event is not None and not isinstance(self.age_at_event, int):
self.age_at_event = int(self.age_at_event)

super().__post_init__(**kwargs)


@dataclass(repr=False)
class EncounterDefinition(Record):
"""
A definition of an encounter type in this study, ie, an event at which data was collected about a participant, an
intervention was made, or information about a participant was recorded. This may be something planned by a study
or a type of data collection.
"""
_inherited_slots: ClassVar[list[str]] = []

class_class_uri: ClassVar[URIRef] = INCLUDEDCC["EncounterDefinition"]
class_class_curie: ClassVar[str] = "includedcc:EncounterDefinition"
class_name: ClassVar[str] = "EncounterDefinition"
class_model_uri: ClassVar[URIRef] = INCLUDEDCC.EncounterDefinition

encounter_definition_id: Union[str, EncounterDefinitionEncounterDefinitionId] = None
name: Optional[str] = None
description: Optional[str] = None
activity_definition_id: Optional[Union[Union[str, ActivityDefinitionActivityDefinitionId], list[Union[str, ActivityDefinitionActivityDefinitionId]]]] = empty_list()

def __post_init__(self, *_: str, **kwargs: Any):
if self._is_empty(self.encounter_definition_id):
self.MissingRequiredField("encounter_definition_id")
if not isinstance(self.encounter_definition_id, EncounterDefinitionEncounterDefinitionId):
self.encounter_definition_id = EncounterDefinitionEncounterDefinitionId(self.encounter_definition_id)

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

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

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

super().__post_init__(**kwargs)


@dataclass(repr=False)
class ActivityDefinition(Record):
"""
A definition of an activity in this study, eg, a biospecimen collection, intervention, survey, or assessment.
"""
_inherited_slots: ClassVar[list[str]] = []

class_class_uri: ClassVar[URIRef] = INCLUDEDCC["ActivityDefinition"]
class_class_curie: ClassVar[str] = "includedcc:ActivityDefinition"
class_name: ClassVar[str] = "ActivityDefinition"
class_model_uri: ClassVar[URIRef] = INCLUDEDCC.ActivityDefinition

activity_definition_id: Union[str, ActivityDefinitionActivityDefinitionId] = None
name: Optional[str] = None
description: Optional[str] = None

def __post_init__(self, *_: str, **kwargs: Any):
if self._is_empty(self.activity_definition_id):
self.MissingRequiredField("activity_definition_id")
if not isinstance(self.activity_definition_id, ActivityDefinitionActivityDefinitionId):
self.activity_definition_id = ActivityDefinitionActivityDefinitionId(self.activity_definition_id)

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

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

super().__post_init__(**kwargs)


# Enumerations
class EnumProgram(EnumDefinitionImpl):
"""
Expand Down Expand Up @@ -1493,6 +1618,18 @@ class slots:
slots.laterality = Slot(uri=INCLUDEDCC.laterality, name="laterality", curie=INCLUDEDCC.curie('laterality'),
model_uri=INCLUDEDCC.laterality, domain=None, range=Optional[Union[str, "EnumLaterality"]])

slots.encounter_id = Slot(uri=INCLUDEDCC.encounter_id, name="encounter_id", curie=INCLUDEDCC.curie('encounter_id'),
model_uri=INCLUDEDCC.encounter_id, domain=None, range=Optional[Union[str, EncounterEncounterId]])

slots.description = Slot(uri=INCLUDEDCC.description, name="description", curie=INCLUDEDCC.curie('description'),
model_uri=INCLUDEDCC.description, domain=None, range=Optional[str])

slots.encounter_definition_id = Slot(uri=INCLUDEDCC.encounter_definition_id, name="encounter_definition_id", curie=INCLUDEDCC.curie('encounter_definition_id'),
model_uri=INCLUDEDCC.encounter_definition_id, domain=None, range=Optional[Union[str, EncounterDefinitionEncounterDefinitionId]])

slots.activity_definition_id = Slot(uri=INCLUDEDCC.activity_definition_id, name="activity_definition_id", curie=INCLUDEDCC.curie('activity_definition_id'),
model_uri=INCLUDEDCC.activity_definition_id, domain=None, range=Optional[Union[str, ActivityDefinitionActivityDefinitionId]])

slots.Study_study_id = Slot(uri=INCLUDEDCC.study_id, name="Study_study_id", curie=INCLUDEDCC.curie('study_id'),
model_uri=INCLUDEDCC.Study_study_id, domain=Study, range=Union[str, StudyStudyId])

Expand Down Expand Up @@ -1525,3 +1662,15 @@ class slots:

slots.Aliquot_aliquot_id = Slot(uri=INCLUDEDCC.aliquot_id, name="Aliquot_aliquot_id", curie=INCLUDEDCC.curie('aliquot_id'),
model_uri=INCLUDEDCC.Aliquot_aliquot_id, domain=Aliquot, range=Union[str, AliquotAliquotId])

slots.Encounter_encounter_id = Slot(uri=INCLUDEDCC.encounter_id, name="Encounter_encounter_id", curie=INCLUDEDCC.curie('encounter_id'),
model_uri=INCLUDEDCC.Encounter_encounter_id, domain=Encounter, range=Union[str, EncounterEncounterId])

slots.EncounterDefinition_encounter_definition_id = Slot(uri=INCLUDEDCC.encounter_definition_id, name="EncounterDefinition_encounter_definition_id", curie=INCLUDEDCC.curie('encounter_definition_id'),
model_uri=INCLUDEDCC.EncounterDefinition_encounter_definition_id, domain=EncounterDefinition, range=Union[str, EncounterDefinitionEncounterDefinitionId])

slots.EncounterDefinition_activity_definition_id = Slot(uri=INCLUDEDCC.activity_definition_id, name="EncounterDefinition_activity_definition_id", curie=INCLUDEDCC.curie('activity_definition_id'),
model_uri=INCLUDEDCC.EncounterDefinition_activity_definition_id, domain=EncounterDefinition, range=Optional[Union[Union[str, ActivityDefinitionActivityDefinitionId], list[Union[str, ActivityDefinitionActivityDefinitionId]]]])

slots.ActivityDefinition_activity_definition_id = Slot(uri=INCLUDEDCC.activity_definition_id, name="ActivityDefinition_activity_definition_id", curie=INCLUDEDCC.curie('activity_definition_id'),
model_uri=INCLUDEDCC.ActivityDefinition_activity_definition_id, domain=ActivityDefinition, range=Union[str, ActivityDefinitionActivityDefinitionId])
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