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onconova.interoperability.fhir.models.TumorMarker

NoneType module-attribute

OnconovaTumorMarker

Bases: TumorMarkerTest

Measurements and simple assertions

bodySite class-attribute instance-attribute

code class-attribute instance-attribute

component class-attribute instance-attribute

device class-attribute instance-attribute

effective property

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

value property

FHIR_o_tma_req_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_o_tma_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-tma-req-1',
        severity='error',
    )

FHIR_o_tma_req_2_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_o_tma_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-tma-req-2',
        severity='error',
    )

FHIR_o_tma_req_3_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_o_tma_req_3_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression="code.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-tumor-marker-analyte').exists()",
        human='The tumorMarkerAnalyte element is required and must be provided.',
        key='o-tma-req-3',
        severity='error',
    )

FHIR_obs_3_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.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',
    )

FHIR_us_core_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_us_core_1_constraint_validator(self):
    return validate_element_constraint( 
        self,
        elements="effectiveDateTime",
        expression='$this is DateTime implies $this.toString().length() >= 10',
        human='Datetime must be at least to day.',
        key='us-core-1',
        severity='error',
    )

FHIR_us_core_4_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_us_core_4_constraint_validator(self):
    return validate_element_constraint( 
        self,
        elements="valueRatio",
        expression="value.ofType(CodeableConcept).coding.system.empty() or value.ofType(CodeableConcept).coding.system = 'http://snomed.info/sct'",
        human='SHOULD use Snomed CT for coded Results',
        key='us-core-4',
        severity='warning',
    )

effective_type_choice_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.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/TumorMarker.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/TumorMarker.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', 'Ratio'],
        field_name_base="value",
        required=True,
    )

OnconovaTumorMarkerCode

Bases: CodeableConcept

The name of the clinical test or procedure performed on a patient. A LOINC SHALL be used if the concept is present in LOINC.

extension class-attribute instance-attribute

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMarker.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",
    )

OnconovaTumorMarkerRelatedCondition

Bases: Extension, 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/TumorMarker.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/TumorMarker.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',
    )

OnconovaTumorMarkerTumorMarkerAnalyte

Bases: TumorMarkerAnalyte, 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

RelatedCondition

Bases: Extension

A condition that has a relationship with the resource.

extension class-attribute instance-attribute

url class-attribute instance-attribute

value property

valueCodeableConcept class-attribute instance-attribute

valueReference class-attribute instance-attribute

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.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/TumorMarker.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/us/mcode/StructureDefinition/mcode-related-condition',
    )

extension_slicing_cardinality_validator(value) classmethod

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

TumorMarkerAnalyte

Bases: Extension

The specific analyte or substance being measured as a tumor marker, such as PSA, CA-125, or CEA.

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/TumorMarker.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/TumorMarker.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-marker-analyte',
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMarker.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/TumorMarker.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,
    )

TumorMarkerTest

Bases: USCoreLaboratoryResultObservationProfile

Measurements and simple assertions

effective property

extension class-attribute instance-attribute

subject class-attribute instance-attribute

value property

FHIR_us_core_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_us_core_1_constraint_validator(self):
    return validate_element_constraint( 
        self,
        elements="effectivePeriod",
        expression='$this is DateTime implies $this.toString().length() >= 10',
        human='Datetime must be at least to day.',
        key='us-core-1',
        severity='error',
    )

FHIR_us_core_2_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_us_core_2_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='(component.empty() and hasMember.empty()) implies (dataAbsentReason.exists() or value.exists())',
        human='If there is no component or hasMember element then either a value[x] or a data absent reason must be present',
        key='us-core-2',
        severity='error',
    )

FHIR_us_core_4_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_us_core_4_constraint_validator(self):
    return validate_element_constraint( 
        self,
        elements="valueRatio",
        expression="value.ofType(CodeableConcept).coding.system.empty() or value.ofType(CodeableConcept).coding.system = 'http://snomed.info/sct'",
        human='SHOULD use Snomed CT for coded Results',
        key='us-core-4',
        severity='warning',
    )

effective_type_choice_validator()

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

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMarker.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/TumorMarker.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', 'Ratio'],
        field_name_base="value",
        required=True,
    )

TumorMarkerTestRelatedCondition

Bases: RelatedCondition, FHIRSliceModel

Associates the tumor marker test with a condition, if one exists. Condition can be given by a reference or a code. In the case of a screening test such as prostate-specific antigen (PSA), there may be no existing condition to reference.

max_cardinality class-attribute

min_cardinality class-attribute

FHIR_ele_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.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/TumorMarker.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',
    )

USCoreLaboratoryResultObservationProfile

Bases: USCoreObservationClinicalResultProfile

Measurements and simple assertions

category class-attribute instance-attribute

specimen 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_us_core_2_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_us_core_2_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='(component.empty() and hasMember.empty()) implies (dataAbsentReason.exists() or value.exists())',
        human='If there is no component or hasMember element then either a value[x] or a data absent reason must be present',
        key='us-core-2',
        severity='error',
    )

FHIR_us_core_4_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_us_core_4_constraint_validator(self):
    return validate_element_constraint( 
        self,
        elements="valuePeriod",
        expression="value.ofType(CodeableConcept).coding.system.empty() or value.ofType(CodeableConcept).coding.system = 'http://snomed.info/sct'",
        human='SHOULD use Snomed CT for coded Results',
        key='us-core-4',
        severity='warning',
    )

category_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMarker.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",
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.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=False,
    )

USCoreLaboratoryResultObservationProfileUsCore

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_Category_pattern_constraint()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_Category_pattern_constraint(self):
    return validate_FHIR_model_pattern( 
        self,
        pattern=CodeableConcept(coding=[Coding(code='laboratory', system='http://terminology.hl7.org/CodeSystem/observation-category')]),
    )

USCoreObservationClinicalResultProfile

Bases: Observation

Measurements and simple assertions

category class-attribute instance-attribute

code class-attribute instance-attribute

dataAbsentReason class-attribute instance-attribute

effective property

effectiveDateTime class-attribute instance-attribute

effectiveInstant class-attribute instance-attribute

effectivePeriod class-attribute instance-attribute

effectiveTiming 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_us_core_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_us_core_1_constraint_validator(self):
    return validate_element_constraint( 
        self,
        elements="effectiveInstant",
        expression='$this is DateTime implies $this.toString().length() >= 10',
        human='Datetime must be at least to day.',
        key='us-core-1',
        severity='error',
    )

FHIR_us_core_2_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_us_core_2_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='(component.empty() and hasMember.empty()) implies (dataAbsentReason.exists() or value.exists())',
        human='If there is no component or hasMember element then either a value[x] or a data absent reason must be present',
        key='us-core-2',
        severity='error',
    )

FHIR_us_core_3_constraint_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.py 
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@model_validator(mode="after")
def FHIR_us_core_3_constraint_validator(self):
    return validate_element_constraint( 
        self,
        elements="valuePeriod",
        expression="value.ofType(Quantity).system.empty() or value.ofType(Quantity).system = 'http://unitsofmeasure.org'",
        human='SHALL use UCUM for coded quantity units.',
        key='us-core-3',
        severity='error',
    )

category_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/TumorMarker.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",
    )

effective_type_choice_validator()

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

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/TumorMarker.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=False,
    )

USCoreObservationClinicalResultProfileUsCore

Bases: CodeableConcept, FHIRSliceModel

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

max_cardinality class-attribute

min_cardinality class-attribute

runner