Skip to content

onconova.interoperability.fhir.models.GenomicsBase

NoneType module-attribute

BodyStructureReference

Bases: Extension, FHIRSliceModel

Record details about the anatomical location of a specimen or body part. This resource may be used when a coded concept does not provide the necessary detail needed for the use case.

extension class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

url class-attribute instance-attribute

value property

valueReference class-attribute instance-attribute

FHIR_url_fixed_value_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicsBase.py 
157
158
159
160
161
162
163
164
@field_validator(*("url",), mode="after", check_fields=None)
@classmethod
def FHIR_url_fixed_value_constraint(cls, value):
    return validate_FHIR_element_fixed_value(
        cls,
        value,
        constant="http://hl7.org/fhir/StructureDefinition/bodySite",
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicsBase.py 
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element(
        self,
        field_types=["Reference"],
        field_name_base="value",
        required=True,
        non_allowed_types=[
            "Base64Binary",
            "Boolean",
            "Canonical",
            "Code",
            "Date",
            "DateTime",
            "Decimal",
            "Id",
            "Instant",
            "Integer",
            "Markdown",
            "Oid",
            "PositiveInt",
            "String",
            "Time",
            "UnsignedInt",
            "Uri",
            "Url",
            "Uuid",
            "Address",
            "Age",
            "Annotation",
            "Attachment",
            "CodeableConcept",
            "Coding",
            "ContactPoint",
            "Count",
            "Distance",
            "Duration",
            "HumanName",
            "Identifier",
            "Money",
            "Period",
            "Quantity",
            "Range",
            "Ratio",
            "SampledData",
            "Signature",
            "Timing",
            "ContactDetail",
            "Contributor",
            "DataRequirement",
            "Expression",
            "ParameterDefinition",
            "RelatedArtifact",
            "TriggerDefinition",
            "UsageContext",
            "Dosage",
            "Meta",
        ],
    )

GenomicsBase

Bases: Observation

Base profile that defines characteristics shared by all genetic observations.

category class-attribute instance-attribute

component class-attribute instance-attribute

extension class-attribute instance-attribute

meta class-attribute instance-attribute

note class-attribute instance-attribute

category_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicsBase.py 
381
382
383
384
385
386
387
388
@field_validator(*("category",), mode="after", check_fields=None)
@classmethod
def category_slicing_cardinality_validator(cls, value):
    return validate_slicing_cardinalities(
        cls,
        value,
        field_name="category",
    )

component_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicsBase.py 
390
391
392
393
394
395
396
397
@field_validator(*("component",), mode="after", check_fields=None)
@classmethod
def component_slicing_cardinality_validator(cls, value):
    return validate_slicing_cardinalities(
        cls,
        value,
        field_name="component",
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicsBase.py 
372
373
374
375
376
377
378
379
@field_validator(*("extension",), mode="after", check_fields=None)
@classmethod
def extension_slicing_cardinality_validator(cls, value):
    return validate_slicing_cardinalities(
        cls,
        value,
        field_name="extension",
    )

GenomicsBaseConclusionString

Bases: BackboneElement, FHIRSliceModel

Clinical Conclusion

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueString class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicsBase.py 
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
@field_validator(*("code",), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):
    return validate_FHIR_element_pattern(
        cls,
        value,
        pattern=CodeableConcept(
            coding=[
                Coding(
                    code="conclusion-string",
                    system="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
                )
            ]
        ),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicsBase.py 
304
305
306
307
308
309
310
311
312
@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element(
        self,
        field_types=["String"],
        field_name_base="value",
        required=False,
        non_allowed_types=[],
    )

GenomicsBaseLabCategory

Bases: CodeableConcept, FHIRSliceModel

Classification of type of observation

coding class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

FHIR_coding_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicsBase.py 
244
245
246
247
248
249
250
251
252
253
254
@field_validator(*("coding",), mode="after", check_fields=None)
@classmethod
def FHIR_coding_pattern_constraint(cls, value):
    return validate_FHIR_element_pattern(
        cls,
        value,
        pattern=Coding(
            code="laboratory",
            system="http://terminology.hl7.org/CodeSystem/observation-category",
        ),
    )

ObsSecondaryFinding

Bases: Extension, FHIRSliceModel

Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.

For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings.

extension class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

url class-attribute instance-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_url_fixed_value_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicsBase.py 
60
61
62
63
64
65
66
67
@field_validator(*("url",), mode="after", check_fields=None)
@classmethod
def FHIR_url_fixed_value_constraint(cls, value):
    return validate_FHIR_element_fixed_value(
        cls,
        value,
        constant="http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding",
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicsBase.py 
 69
 70
 71
 72
 73
 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
@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element(
        self,
        field_types=["CodeableConcept"],
        field_name_base="value",
        required=True,
        non_allowed_types=[
            "Base64Binary",
            "Boolean",
            "Canonical",
            "Code",
            "Date",
            "DateTime",
            "Decimal",
            "Id",
            "Instant",
            "Integer",
            "Markdown",
            "Oid",
            "PositiveInt",
            "String",
            "Time",
            "UnsignedInt",
            "Uri",
            "Url",
            "Uuid",
            "Address",
            "Age",
            "Annotation",
            "Attachment",
            "Coding",
            "ContactPoint",
            "Count",
            "Distance",
            "Duration",
            "HumanName",
            "Identifier",
            "Money",
            "Period",
            "Quantity",
            "Range",
            "Ratio",
            "Reference",
            "SampledData",
            "Signature",
            "Timing",
            "ContactDetail",
            "Contributor",
            "DataRequirement",
            "Expression",
            "ParameterDefinition",
            "RelatedArtifact",
            "TriggerDefinition",
            "UsageContext",
            "Dosage",
            "Meta",
        ],
    )
runner