Skip to content

onconova.interoperability.fhir.schemas.primary_cancer_condition

PrimaryCancerConditionProfile

Bases: OnconovaFhirBaseSchema, OnconovaPrimaryCancerCondition

__model__ class-attribute instance-attribute

__schema__ class-attribute instance-attribute

fhir_to_onconova(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/primary_cancer_condition.py 
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
73
74
75
76
77
78
@classmethod
def fhir_to_onconova(
    cls, obj: fhir.OnconovaPrimaryCancerCondition
) -> schemas.NeoplasticEntityCreate:
    return schemas.NeoplasticEntityCreate(
        externalSource=None,
        externalSourceId=None,
        relationship=(
            NeoplasticEntityRelationshipChoices.LOCAL_RECURRENCE
            if obj.fhirpath_single(
                "Condition.clinicalStatus.coding.code = 'recurrence' and Condition.clinicalStatus.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-primary-cancer-recurrence-type').valueCodeableConcept.coding.code = '255470001'"
            )
            else (
                NeoplasticEntityRelationshipChoices.REGIONAL_RECURRENCE
                if obj.fhirpath_single(
                    "Condition.clinicalStatus.coding.code = 'recurrence' and Condition.clinicalStatus.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-primary-cancer-recurrence-type').valueCodeableConcept.coding.code = '410674003'"
                )
                else NeoplasticEntityRelationshipChoices.PRIMARY
            )
        ),
        caseId=obj.fhirpath_single(
            "Condition.subject.reference.getValue()"
        ).replace("Patient/", ""),
        topography=CodedConcept.model_validate(
            obj.fhirpath_single("Condition.bodySite.coding").model_dump()
        ),
        morphology=(
            CodedConcept.model_validate(
                obj.fhirpath_single(
                    "Condition.extension('http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-histology-morphology-behavior').valueCodeableConcept.coding"
                ).model_dump()
            )
        ),
        differentitation=(
            CodedConcept.model_validate(coding.model_dump())
            if (
                coding := obj.fhirpath_single(
                    "Condition.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-histological-differentiation').valueCodeableConcept.coding"
                )
            )
            else None
        ),
        relatedPrimaryId=obj.fhirpath_single(
            "Condition.clinicalStatus.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-primary-cancer-recurrence-of').valueReference.reference.getValue().replace('Condition/', '')"
        ),
        laterality=(
            CodedConcept.model_validate(coding.model_dump())
            if (
                coding := obj.fhirpath_single(
                    "Condition.bodySite.extension('http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality-qualifier').valueCodeableConcept.coding"
                )
            )
            else None
        ),
        assertionDate=obj.fhirpath_single(
            "Condition.extension('http://hl7.org/fhir/StructureDefinition/condition-assertedDate').valueDateTime.getValue()"
        ),
    )

onconova_to_fhir(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/primary_cancer_condition.py 
 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
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
@classmethod
def onconova_to_fhir(
    cls, obj: schemas.NeoplasticEntity
) -> fhir.OnconovaPrimaryCancerCondition:
    resource: fhir.OnconovaPrimaryCancerCondition = (
        fhir.OnconovaPrimaryCancerCondition.model_construct()
    )  # type: ignore
    resource.id = str(obj.id)
    resource.subject = Reference(
        reference=f"Patient/{obj.caseId}",
    )
    resource.text = Narrative(
        status="generated",
        div=f'<div xmlns="http://www.w3.org/1999/xhtml">{obj.description}</div>',
    )
    resource.bodySite = [
        fhir.OnconovaPrimaryCancerConditionBodySite(
            coding=construct_fhir_codeable_concept(obj.topography).coding,
            extension=(
                [
                    fhir.LateralityQualifier(
                        valueCodeableConcept=construct_fhir_codeable_concept(
                            obj.laterality
                        )
                    )
                ]
                if obj.laterality
                else None
            ),
        )
    ]
    resource.extension = [
        fhir.HistologyMorphologyBehavior(
            valueCodeableConcept=construct_fhir_codeable_concept(obj.morphology)
        ),
        fhir.AssertedDate(valueDateTime=obj.assertionDate.isoformat()),
    ]
    if obj.differentitation:
        resource.extension.append(
            fhir.HistologicalDifferentiation(
                valueCodeableConcept=construct_fhir_codeable_concept(
                    obj.differentitation
                )
            )
        )
    if obj.relationship == NeoplasticEntityRelationshipChoices.METASTATIC:
        raise ValueError(
            "NeoplasticEntity relationship cannot be 'metastatic' for PrimaryCancerCondition"
        )
    if (
        obj.relationship == NeoplasticEntityRelationshipChoices.LOCAL_RECURRENCE
        or obj.relationship
        == NeoplasticEntityRelationshipChoices.REGIONAL_RECURRENCE
    ):
        resource.clinicalStatus = fhir.OnconovaPrimaryCancerConditionClinicalStatus(
            coding=[
                fhir.Coding(
                    code="recurrence",
                    system="http://terminology.hl7.org/CodeSystem/condition-clinical",
                )
            ],
            extension=[
                fhir.PrimaryCancerRecurrenceType(
                    valueCodeableConcept=fhir.CodeableConcept(
                        coding=[
                            (
                                fhir.Coding(
                                    code="255470001",
                                    display="Local",
                                    system="http://snomed.info/sct",
                                )
                                if obj.relationship
                                == NeoplasticEntityRelationshipChoices.LOCAL_RECURRENCE
                                else fhir.Coding(
                                    code="410674003",
                                    display="Regional",
                                    system="http://snomed.info/sct",
                                )
                            )
                        ]
                    )
                ),
                fhir.PrimaryCancerRecurrenceOf(
                    valueReference=Reference(
                        reference=f"Condition/{obj.relatedPrimaryId}",
                    )
                ),
            ],
        )
    return resource
runner