Skip to content

onconova.interoperability.fhir.schemas.surgical_procedure

SurgicalProcedureProfile

Bases: OnconovaFhirBaseSchema, OnconovaSurgicalProcedure

__model__ class-attribute instance-attribute

__schema__ class-attribute instance-attribute

fhir_to_onconova(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/surgical_procedure.py 
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
@classmethod
def fhir_to_onconova(
    cls, obj: fhir.OnconovaSurgicalProcedure
) -> schemas.SurgeryCreate:
    return schemas.SurgeryCreate(
        externalSource=None,
        externalSourceId=None,
        caseId=obj.fhirpath_single(
            "Procedure.subject.reference.getValue()"
        ).replace("Patient/", ""),
        date=obj.fhirpath_single("Procedure.performedDateTime.getValue()"),
        procedure=CodedConcept.model_validate(
            obj.fhirpath_single("Procedure.code.coding").model_dump()
        ),
        intent=cls.map_to_internal(
            "TreatmentIntents",
            obj.fhirpath_single(
                "Procedure.extension('http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-procedure-intent').valueCodeableConcept.coding"
            ),
        ),
        bodysite=(
            CodedConcept.model_validate(coding.model_dump())
            if (coding := obj.fhirpath_single("Procedure.bodySite.coding"))
            else None
        ),
        outcome=(
            CodedConcept.model_validate(coding.model_dump())
            if (coding := obj.fhirpath_single("Procedure.outcome.coding"))
            else None
        ),
        bodysiteQualifier=(
            CodedConcept.model_validate(coding.model_dump())
            if (
                coding := obj.fhirpath_single(
                    "Procedure.bodySite.extension('http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-body-location-qualifier').valueCodeableConcept.coding"
                )
            )
            else None
        ),
        bodysiteLaterality=(
            CodedConcept.model_validate(coding.model_dump())
            if (
                coding := obj.fhirpath_single(
                    "Procedure.bodySite.extension('http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality-qualifier').valueCodeableConcept.coding"
                )
            )
            else None
        ),
        targetedEntitiesIds=obj.fhirpath_values(
            "Procedure.reasonReference.reference.replace('Condition/','')"
        ),
        therapyLineId=obj.fhirpath_single(
            "Procedure.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-therapy-line-reference').valueReference.reference.replace('List/','')"
        ),
    )

onconova_to_fhir(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/surgical_procedure.py 
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
@classmethod
def onconova_to_fhir(cls, obj: schemas.Surgery) -> fhir.OnconovaSurgicalProcedure:
    resource = fhir.OnconovaSurgicalProcedure.model_construct()
    resource.id = str(obj.id)
    resource.text = Narrative(
        status="generated",
        div=f'<div xmlns="http://www.w3.org/1999/xhtml">{obj.description}</div>',
    )
    resource.performedDateTime = obj.date.isoformat()
    resource.subject = Reference(
        reference=f"Patient/{obj.caseId}",
    )
    resource.reasonReference = [
        Reference(
            reference=f"Condition/{conditionId}",
        )
        for conditionId in obj.targetedEntitiesIds or []
    ]
    resource.code = construct_fhir_codeable_concept(obj.procedure)
    resource.extension = [
        fhir.ProcedureIntent(
            valueCodeableConcept=construct_fhir_codeable_concept(
                cls.map_to_fhir("TreatmentIntents", obj.intent)
            )
        )
    ]
    if obj.therapyLineId:
        resource.extension.append(
            fhir.TherapyLineReference(
                valueReference=Reference(reference=f"List/{obj.therapyLineId}")
            )
        )
    if obj.bodysite:
        resource.bodySite = [
            fhir.CancerRelatedSurgicalProcedureBodySite(
                **construct_fhir_codeable_concept(obj.bodysite).model_dump(),
                extension=[
                    ext
                    for ext in [
                        (
                            fhir.BodyLocationQualifier(
                                valueCodeableConcept=construct_fhir_codeable_concept(
                                    obj.bodysiteQualifier
                                )
                            )
                            if obj.bodysiteQualifier
                            else None
                        ),
                        (
                            fhir.LateralityQualifier(
                                valueCodeableConcept=construct_fhir_codeable_concept(
                                    obj.bodysiteLaterality
                                )
                            )
                            if obj.bodysiteLaterality
                            else None
                        ),
                    ]
                    if ext is not None
                ],
            )
        ]
    if obj.outcome:
        resource.outcome = construct_fhir_codeable_concept(obj.outcome)
    return resource
runner