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onconova.interoperability.fhir.models.TumorMutationalBurden

NoneType module-attribute

AnnotationCode

Bases: Extension

Codifies the content of an Annotation

extension class-attribute instance-attribute

url class-attribute instance-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

FHIR_url_fixed_value_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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/uv/genomics-reporting/StructureDefinition/annotation-code',
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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",
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=False,
    )

BodyStructureReference

Bases: Extension

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

url class-attribute instance-attribute

value property

valueReference class-attribute instance-attribute

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

FHIR_url_fixed_value_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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',
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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",
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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,
    )

CodedAnnotation

Bases: Annotation

A text note which also contains information about who made the statement and when.

extension class-attribute instance-attribute

FHIR_ele_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ele_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='hasValue() or (children().count() > id.count())',
        human='All FHIR elements must have a @value or children',
        key='ele-1',
        severity='error',
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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",
    )

CodedAnnotationCode

Bases: AnnotationCode, FHIRSliceModel

May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

max_cardinality class-attribute

min_cardinality class-attribute

FHIR_ele_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ele_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='hasValue() or (children().count() > id.count())',
        human='All FHIR elements must have a @value or children',
        key='ele-1',
        severity='error',
    )

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

GenomicsBase

Bases: Observation

Measurements and simple assertions made about a patient, device or other subject.

category class-attribute instance-attribute

component class-attribute instance-attribute

extension class-attribute instance-attribute

note class-attribute instance-attribute

FHIR_obs_6_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_obs_6_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='dataAbsentReason.empty() or value.empty()',
        human='dataAbsentReason SHALL only be present if Observation.value[x] is not present',
        key='obs-6',
        severity='error',
    )

FHIR_obs_7_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_obs_7_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()',
        human='If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present',
        key='obs-7',
        severity='error',
    )

category_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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/TumorMutationalBurden.py 
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@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/TumorMutationalBurden.py 
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@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",
    )

GenomicsBaseBodyStructure

Bases: BodyStructureReference, FHIRSliceModel

May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

max_cardinality class-attribute

min_cardinality class-attribute

FHIR_ele_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ele_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='hasValue() or (children().count() > id.count())',
        human='All FHIR elements must have a @value or children',
        key='ele-1',
        severity='error',
    )

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

GenomicsBaseConclusionString

Bases: ObservationComponent, FHIRSliceModel

Concise and clinically contextualized summary conclusion (interpretation/impression) of the observation

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/TumorMutationalBurden.py 
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@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/TumorMutationalBurden.py 
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@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,
    )

GenomicsBaseLabCategory

Bases: CodeableConcept, FHIRSliceModel

A code that classifies the general type of observation being made.

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/TumorMutationalBurden.py 
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@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'),
    )

GenomicsBaseSecondaryFinding

Bases: SecondaryFinding, FHIRSliceModel

May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

max_cardinality class-attribute

min_cardinality class-attribute

FHIR_ele_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ele_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='hasValue() or (children().count() > id.count())',
        human='All FHIR elements must have a @value or children',
        key='ele-1',
        severity='error',
    )

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

OnconovaTumorMutationalBurden

Bases: TMB

Measurements and simple assertions made about a patient, device or other subject.

bodySite class-attribute instance-attribute

component class-attribute instance-attribute

device class-attribute instance-attribute

effective property

effectiveDateTime class-attribute instance-attribute

encounter class-attribute instance-attribute

extension class-attribute instance-attribute

focus class-attribute instance-attribute

hasMember class-attribute instance-attribute

interpretation class-attribute instance-attribute

issued class-attribute instance-attribute

performer class-attribute instance-attribute

referenceRange class-attribute instance-attribute

specimen class-attribute instance-attribute

status class-attribute instance-attribute

subject class-attribute instance-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

FHIR_o_sig_req_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_o_sig_req_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='subject.exists()',
        human='The subject element is required and must be provided.',
        key='o-sig-req-1',
        severity='error',
    )

FHIR_o_sig_req_2_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_o_sig_req_2_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='effectiveDateTime.exists() and effectiveDateTime.hasValue()',
        human='The effectiveDateTime element is required and must be provided.',
        key='o-sig-req-2',
        severity='error',
    )

FHIR_o_sig_req_3_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_o_sig_req_3_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='valueQuantity.exists()',
        human='The valueQuantity element is required and must be provided.',
        key='o-sig-req-3',
        severity='error',
    )

FHIR_obs_3_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_obs_3_constraint_validator(self):
    return validate_element_constraint( 
        self,
        elements="referenceRange",
        expression='low.exists() or high.exists() or text.exists()',
        human='Must have at least a low or a high or text',
        key='obs-3',
        severity='error',
    )

component_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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",
    )

effective_type_choice_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def effective_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['DateTime'],
        field_name_base="effective",
        required=True,
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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",
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=True,
    )

OnconovaTumorMutationalBurdenStatus

Bases: TumorMutationalBurdenStatus, FHIRSliceModel

May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

max_cardinality class-attribute

min_cardinality class-attribute

FHIR_ele_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ele_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='hasValue() or (children().count() > id.count())',
        human='All FHIR elements must have a @value or children',
        key='ele-1',
        severity='error',
    )

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

SecondaryFinding

Bases: Extension

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

url class-attribute instance-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

FHIR_url_fixed_value_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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',
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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",
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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,
    )

TMB

Bases: GenomicsBase

Measurements and simple assertions made about a patient, device or other subject.

code class-attribute instance-attribute

interpretation class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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='94076-7', system='http://loinc.org')]),
    )

FHIR_obs_6_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_obs_6_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='dataAbsentReason.empty() or value.empty()',
        human='dataAbsentReason SHALL only be present if Observation.value[x] is not present',
        key='obs-6',
        severity='error',
    )

FHIR_obs_7_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_obs_7_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()',
        human='If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present',
        key='obs-7',
        severity='error',
    )

FHIR_valueQuantity_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@field_validator(*('valueQuantity',), mode="after", check_fields=None)
@classmethod
def FHIR_valueQuantity_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=Quantity(code='1/1000000{Base}', system='http://unitsofmeasure.org'),
    )

TMBValueQuantity

Bases: Quantity

The information determined as a result of making the observation, if the information has a simple value.

code class-attribute instance-attribute

system class-attribute instance-attribute

unit class-attribute instance-attribute

FHIR_ValueQuantity_pattern_constraint()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ValueQuantity_pattern_constraint(self):
    return validate_FHIR_model_pattern( 
        self,
        pattern=Quantity(code='1/1000000{Base}', system='http://unitsofmeasure.org'),
    )

FHIR_unit_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@field_validator(*('unit',), mode="after", check_fields=None)
@classmethod
def FHIR_unit_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern='Mutations/Megabase',
    )

TumorMutationalBurdenStatus

Bases: Extension

The categorical classification of the TMB status interpreted from its value.

extension class-attribute instance-attribute

url class-attribute instance-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

FHIR_url_fixed_value_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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://onconova.github.io/fhir/StructureDefinition/onconova-ext-tumor-mutational-burden-status',
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@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",
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/TumorMutationalBurden.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=False,
    )
runner