clinvar_api.models package

Submodules

clinvar_api.models.query_response module

Data structures for internal representation of query response.

class clinvar_api.models.query_response.SubmissionStatus(*, actions: List[SubmissionStatusActions])

Bases: BaseModel

Internal submission status.

actions: List[SubmissionStatusActions]

The list of actions (one element only by the docs).

classmethod from_msg(other: SubmissionStatus)

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'actions': FieldInfo(annotation=List[SubmissionStatusActions], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class clinvar_api.models.query_response.SubmissionStatusActions(*, id: str, responses: List[SubmissionStatusResponse], status: str, target_db: str, updated: datetime)

Bases: BaseModel

classmethod from_msg(other: SubmissionStatusActions)

id: str

Identifier of the submission

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'id': FieldInfo(annotation=str, required=True), 'responses': FieldInfo(annotation=List[SubmissionStatusResponse], required=True), 'status': FieldInfo(annotation=str, required=True), 'target_db': FieldInfo(annotation=str, required=True), 'updated': FieldInfo(annotation=datetime, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

responses: List[SubmissionStatusResponse]

Entries in actions[*].responses, only one entry per the docs.

status: str

Status of the submission, one of “submitted”, “processing”, “processed”, “error”

target_db: str

Target database, usually “clinvar”

updated: datetime

Last updated time

class clinvar_api.models.query_response.SubmissionStatusFile(*, url: str)

Bases: BaseModel

classmethod from_msg(other: SubmissionStatusFile)

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'url': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

url: str

class clinvar_api.models.query_response.SubmissionStatusObject(*, accession: str | None, content: SubmissionStatusObjectContent, target_db: str)

Bases: BaseModel

accession: str | None

Optional object accession.

content: SubmissionStatusObjectContent

Object content.

classmethod from_msg(other: SubmissionStatusObject)

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'accession': FieldInfo(annotation=Union[str, NoneType], required=True), 'content': FieldInfo(annotation=SubmissionStatusObjectContent, required=True), 'target_db': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

target_db: str

Target database, usually “clinvar” per the docs.

class clinvar_api.models.query_response.SubmissionStatusObjectContent(*, clinvar_processing_status: str, clinvar_release_status: str)

Bases: BaseModel

clinvar_processing_status: str

Processing status

clinvar_release_status: str

Release status

classmethod from_msg(other: SubmissionStatusObjectContent)

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'clinvar_processing_status': FieldInfo(annotation=str, required=True), 'clinvar_release_status': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class clinvar_api.models.query_response.SubmissionStatusResponse(*, status: str, files: List[SubmissionStatusFile], message: SubmissionStatusResponseMessage | None, objects: List[SubmissionStatusObject])

Bases: BaseModel

files: List[SubmissionStatusFile]

Files in the response.

classmethod from_msg(other: SubmissionStatusResponse)

message: SubmissionStatusResponseMessage | None

Message

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'files': FieldInfo(annotation=List[SubmissionStatusFile], required=True), 'message': FieldInfo(annotation=Union[SubmissionStatusResponseMessage, NoneType], required=True), 'objects': FieldInfo(annotation=List[SubmissionStatusObject], required=True), 'status': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

objects: List[SubmissionStatusObject]

Objects

status: str

Status, one of “processing”, “processed”, “error”,

class clinvar_api.models.query_response.SubmissionStatusResponseMessage(*, error_code: ErrorCode | None, severity: str, text: str)

Bases: BaseModel

error_code: ErrorCode | None

The error code.

classmethod from_msg(other: SubmissionStatusResponseMessage)

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'error_code': FieldInfo(annotation=Union[ErrorCode, NoneType], required=True), 'severity': FieldInfo(annotation=str, required=True), 'text': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

severity: str

The message severity.

text: str

The message text.

clinvar_api.models.sub_payload module

Data structures for internal representation of submission payload.

class clinvar_api.models.sub_payload.SubmissionAssertionCriteria(*, db: CitationDb | None = None, id: str | None = None, url: str | None = None)

Bases: BaseModel

db: CitationDb | None

id: str | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'db': FieldInfo(annotation=Union[CitationDb, NoneType], required=False), 'id': FieldInfo(annotation=Union[str, NoneType], required=False), 'url': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

to_msg() → SubmissionAssertionCriteria

url: str | None

class clinvar_api.models.sub_payload.SubmissionChromosomeCoordinates(*, accession: str | None = None, alternate_allele: str | None = None, assembly: Assembly | None = None, chromosome: Chromosome | None = None, inner_start: int | None = None, inner_stop: int | None = None, outer_start: int | None = None, outer_stop: int | None = None, reference_allele: str | None = None, start: int | None = None, stop: int | None = None, variant_length: int | None = None)

Bases: BaseModel

accession: str | None

alternate_allele: str | None

assembly: Assembly | None

chromosome: Chromosome | None

inner_start: int | None

inner_stop: int | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'accession': FieldInfo(annotation=Union[str, NoneType], required=False), 'alternate_allele': FieldInfo(annotation=Union[str, NoneType], required=False), 'assembly': FieldInfo(annotation=Union[Assembly, NoneType], required=False), 'chromosome': FieldInfo(annotation=Union[Chromosome, NoneType], required=False), 'inner_start': FieldInfo(annotation=Union[int, NoneType], required=False), 'inner_stop': FieldInfo(annotation=Union[int, NoneType], required=False), 'outer_start': FieldInfo(annotation=Union[int, NoneType], required=False), 'outer_stop': FieldInfo(annotation=Union[int, NoneType], required=False), 'reference_allele': FieldInfo(annotation=Union[str, NoneType], required=False), 'start': FieldInfo(annotation=Union[int, NoneType], required=False), 'stop': FieldInfo(annotation=Union[int, NoneType], required=False), 'variant_length': FieldInfo(annotation=Union[int, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

outer_start: int | None

outer_stop: int | None

reference_allele: str | None

start: int | None

stop: int | None

to_msg() → SubmissionChromosomeCoordinates

variant_length: int | None

class clinvar_api.models.sub_payload.SubmissionCitation(*, db: CitationDb | None = None, id: str | None = None, url: str | None = None)

Bases: BaseModel

db: CitationDb | None

id: str | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'db': FieldInfo(annotation=Union[CitationDb, NoneType], required=False), 'id': FieldInfo(annotation=Union[str, NoneType], required=False), 'url': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

to_msg() → SubmissionCitation

url: str | None

class clinvar_api.models.sub_payload.SubmissionClinicalFeature(*, clinical_features_affected_status: ClinicalFeaturesAffectedStatus, db: ClinicalFeaturesDb | None = None, id: str | None = None, name: str | None = None)

Bases: BaseModel

clinical_features_affected_status: ClinicalFeaturesAffectedStatus

db: ClinicalFeaturesDb | None

id: str | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'clinical_features_affected_status': FieldInfo(annotation=ClinicalFeaturesAffectedStatus, required=True), 'db': FieldInfo(annotation=Union[ClinicalFeaturesDb, NoneType], required=False), 'id': FieldInfo(annotation=Union[str, NoneType], required=False), 'name': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

name: str | None

to_msg() → SubmissionClinicalFeature

class clinvar_api.models.sub_payload.SubmissionClinicalSignificance(*, clinical_significance_description: ClinicalSignificanceDescription, citation: List[SubmissionCitation] | None = None, comment: str | None = None, custom_assertion_score: float | None = None, date_last_evaluated: str | None = None, explanation_of_drug_response: str | None = None, explanation_of_other_clinical_significance: str | None = None, mode_of_inheritance: ModeOfInheritance | None = None)

Bases: BaseModel

citation: List[SubmissionCitation] | None

Must have at least one entry.

clinical_significance_description: ClinicalSignificanceDescription

comment: str | None

custom_assertion_score: float | None

date_last_evaluated: str | None

explanation_of_drug_response: str | None

explanation_of_other_clinical_significance: str | None

mode_of_inheritance: ModeOfInheritance | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'citation': FieldInfo(annotation=Union[List[SubmissionCitation], NoneType], required=False), 'clinical_significance_description': FieldInfo(annotation=ClinicalSignificanceDescription, required=True), 'comment': FieldInfo(annotation=Union[str, NoneType], required=False), 'custom_assertion_score': FieldInfo(annotation=Union[float, NoneType], required=False), 'date_last_evaluated': FieldInfo(annotation=Union[str, NoneType], required=False), 'explanation_of_drug_response': FieldInfo(annotation=Union[str, NoneType], required=False), 'explanation_of_other_clinical_significance': FieldInfo(annotation=Union[str, NoneType], required=False), 'mode_of_inheritance': FieldInfo(annotation=Union[ModeOfInheritance, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

to_msg() → SubmissionClinicalSignificance

class clinvar_api.models.sub_payload.SubmissionClinvarDeletion(*, accession_set: List[SubmissionClinvarDeletionAccessionSet])

Bases: BaseModel

accession_set: List[SubmissionClinvarDeletionAccessionSet]

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'accession_set': FieldInfo(annotation=List[SubmissionClinvarDeletionAccessionSet], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

to_msg() → SubmissionClinvarDeletion

class clinvar_api.models.sub_payload.SubmissionClinvarDeletionAccessionSet(*, accession: str, reason: str | None = None)

Bases: BaseModel

accession: str

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'accession': FieldInfo(annotation=str, required=True), 'reason': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

reason: str | None

to_msg() → SubmissionClinvarDeletionAccessionSet

class clinvar_api.models.sub_payload.SubmissionClinvarSubmission(*, clinical_significance: SubmissionClinicalSignificance, condition_set: SubmissionConditionSet, observed_in: List[SubmissionObservedIn], record_status: RecordStatus, clinvar_accession: str | None = None, compound_heterozygote_set: SubmissionCompoundHeterozygoteSet | None = None, diplotype_set: SubmissionDiplotypeSet | None = None, distinct_chromosomes_set: SubmissionDistinctChromosomesSet | None = None, haplotype_set: SubmissionHaplotypeSet | None = None, haplotype_single_variant_set: SubmissionHaplotypeSet | None = None, local_id: str | None = None, local_key: str | None = None, phase_unknown_set: SubmissionPhaseUnknownSet | None = None, variant_set: SubmissionVariantSet | None = None, extra_data: Dict[str, Any] | None = None)

Bases: BaseModel

clinical_significance: SubmissionClinicalSignificance

clinvar_accession: str | None

compound_heterozygote_set: SubmissionCompoundHeterozygoteSet | None

condition_set: SubmissionConditionSet

diplotype_set: SubmissionDiplotypeSet | None

distinct_chromosomes_set: SubmissionDistinctChromosomesSet | None

extra_data: Dict[str, Any] | None

Additional information from import. Will not be used for conversion to message but can be converted back to external formats.

haplotype_set: SubmissionHaplotypeSet | None

Has at least two elements in variants

haplotype_single_variant_set: SubmissionHaplotypeSet | None

Has exactly one elements in variants

local_id: str | None

local_key: str | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'clinical_significance': FieldInfo(annotation=SubmissionClinicalSignificance, required=True), 'clinvar_accession': FieldInfo(annotation=Union[str, NoneType], required=False), 'compound_heterozygote_set': FieldInfo(annotation=Union[SubmissionCompoundHeterozygoteSet, NoneType], required=False), 'condition_set': FieldInfo(annotation=SubmissionConditionSet, required=True), 'diplotype_set': FieldInfo(annotation=Union[SubmissionDiplotypeSet, NoneType], required=False), 'distinct_chromosomes_set': FieldInfo(annotation=Union[SubmissionDistinctChromosomesSet, NoneType], required=False), 'extra_data': FieldInfo(annotation=Union[Dict[str, Any], NoneType], required=False), 'haplotype_set': FieldInfo(annotation=Union[SubmissionHaplotypeSet, NoneType], required=False), 'haplotype_single_variant_set': FieldInfo(annotation=Union[SubmissionHaplotypeSet, NoneType], required=False), 'local_id': FieldInfo(annotation=Union[str, NoneType], required=False), 'local_key': FieldInfo(annotation=Union[str, NoneType], required=False), 'observed_in': FieldInfo(annotation=List[SubmissionObservedIn], required=True), 'phase_unknown_set': FieldInfo(annotation=Union[SubmissionPhaseUnknownSet, NoneType], required=False), 'record_status': FieldInfo(annotation=RecordStatus, required=True), 'variant_set': FieldInfo(annotation=Union[SubmissionVariantSet, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

observed_in: List[SubmissionObservedIn]

phase_unknown_set: SubmissionPhaseUnknownSet | None

record_status: RecordStatus

to_msg() → SubmissionClinvarSubmission

variant_set: SubmissionVariantSet | None

class clinvar_api.models.sub_payload.SubmissionCompoundHeterozygoteSet(*, hgvs: str, variant_sets: List[SubmissionCompoundHeterozygoteSetVariantSet])

Bases: BaseModel

hgvs: str

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'hgvs': FieldInfo(annotation=str, required=True), 'variant_sets': FieldInfo(annotation=List[SubmissionCompoundHeterozygoteSetVariantSet], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

to_msg() → SubmissionCompoundHeterozygoteSet

variant_sets: List[SubmissionCompoundHeterozygoteSetVariantSet]

class clinvar_api.models.sub_payload.SubmissionCompoundHeterozygoteSetVariantSet(*, variant_set: SubmissionVariantSet | None = None)

Bases: BaseModel

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'variant_set': FieldInfo(annotation=Union[SubmissionVariantSet, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

to_msg() → SubmissionCompoundHeterozygoteSetVariantSet

variant_set: SubmissionVariantSet | None

class clinvar_api.models.sub_payload.SubmissionCondition(*, db: ConditionDb | None = None, id: str | None = None, name: str | None = None)

Bases: BaseModel

db: ConditionDb | None

id: str | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'db': FieldInfo(annotation=Union[ConditionDb, NoneType], required=False), 'id': FieldInfo(annotation=Union[str, NoneType], required=False), 'name': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

name: str | None

to_msg() → SubmissionCondition

class clinvar_api.models.sub_payload.SubmissionConditionSet(*, condition: List[SubmissionCondition] | None = None, drug_response: List[SubmissionDrugResponse] | None = None, multiple_condition_explanation: MultipleConditionExplanation | None = None)

Bases: BaseModel

condition: List[SubmissionCondition] | None

drug_response: List[SubmissionDrugResponse] | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'condition': FieldInfo(annotation=Union[List[SubmissionCondition], NoneType], required=False), 'drug_response': FieldInfo(annotation=Union[List[SubmissionDrugResponse], NoneType], required=False), 'multiple_condition_explanation': FieldInfo(annotation=Union[MultipleConditionExplanation, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

multiple_condition_explanation: MultipleConditionExplanation | None

to_msg() → SubmissionConditionSet

class clinvar_api.models.sub_payload.SubmissionContainer(*, assertion_criteria: SubmissionAssertionCriteria | None = None, behalf_org_id: int | None = None, clinvar_deletion: SubmissionClinvarDeletion | None = None, clinvar_submission: List[SubmissionClinvarSubmission] | None = None, clinvar_submission_release_status: ReleaseStatus | None = None, submission_name: str | None = None)

Bases: BaseModel

assertion_criteria: SubmissionAssertionCriteria | None

behalf_org_id: int | None

clinvar_deletion: SubmissionClinvarDeletion | None

clinvar_submission: List[SubmissionClinvarSubmission] | None

clinvar_submission_release_status: ReleaseStatus | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'assertion_criteria': FieldInfo(annotation=Union[SubmissionAssertionCriteria, NoneType], required=False), 'behalf_org_id': FieldInfo(annotation=Union[int, NoneType], required=False), 'clinvar_deletion': FieldInfo(annotation=Union[SubmissionClinvarDeletion, NoneType], required=False), 'clinvar_submission': FieldInfo(annotation=Union[List[SubmissionClinvarSubmission], NoneType], required=False), 'clinvar_submission_release_status': FieldInfo(annotation=Union[ReleaseStatus, NoneType], required=False), 'submission_name': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

submission_name: str | None

to_msg() → SubmissionContainer

class clinvar_api.models.sub_payload.SubmissionDiplotypeSet(*, haplotype_sets: List[SubmissionHaplotypeSets], hgvs: str, star_allele_name: str | None = None)

Bases: BaseModel

haplotype_sets: List[SubmissionHaplotypeSets]

hgvs: str

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'haplotype_sets': FieldInfo(annotation=List[SubmissionHaplotypeSets], required=True), 'hgvs': FieldInfo(annotation=str, required=True), 'star_allele_name': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

star_allele_name: str | None

to_msg() → SubmissionDiplotypeSet

class clinvar_api.models.sub_payload.SubmissionDistinctChromosomesSet(*, hgvs: str, variants: List[SubmissionVariant])

Bases: BaseModel

hgvs: str

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'hgvs': FieldInfo(annotation=str, required=True), 'variants': FieldInfo(annotation=List[SubmissionVariant], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

to_msg() → SubmissionDistinctChromosomesSet

variants: List[SubmissionVariant]

Hast at least two elements

class clinvar_api.models.sub_payload.SubmissionDrugResponse(*, db: ConditionDb | None = None, drug_name: str | None = None, id: str | None = None, condition: List[SubmissionCondition] | None = None)

Bases: BaseModel

condition: List[SubmissionCondition] | None

db: ConditionDb | None

drug_name: str | None

id: str | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'condition': FieldInfo(annotation=Union[List[SubmissionCondition], NoneType], required=False), 'db': FieldInfo(annotation=Union[ConditionDb, NoneType], required=False), 'drug_name': FieldInfo(annotation=Union[str, NoneType], required=False), 'id': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

to_msg() → SubmissionDrugResponse

class clinvar_api.models.sub_payload.SubmissionHaplotypeSet(*, hgvs: str, variants: List[SubmissionVariant], star_allele_name: str | None = None)

Bases: BaseModel

hgvs: str

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'hgvs': FieldInfo(annotation=str, required=True), 'star_allele_name': FieldInfo(annotation=Union[str, NoneType], required=False), 'variants': FieldInfo(annotation=List[SubmissionVariant], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

star_allele_name: str | None

to_msg() → SubmissionHaplotypeSet

variants: List[SubmissionVariant]

class clinvar_api.models.sub_payload.SubmissionHaplotypeSets(*, haplotype_set: SubmissionHaplotypeSet | None = None, haplotype_single_variant_set: SubmissionHaplotypeSet | None = None)

Bases: BaseModel

haplotype_set: SubmissionHaplotypeSet | None

haplotype_single_variant_set: SubmissionHaplotypeSet | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'haplotype_set': FieldInfo(annotation=Union[SubmissionHaplotypeSet, NoneType], required=False), 'haplotype_single_variant_set': FieldInfo(annotation=Union[SubmissionHaplotypeSet, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

to_msg() → SubmissionHaplotypeSets

class clinvar_api.models.sub_payload.SubmissionObservedIn(*, affected_status: AffectedStatus, allele_origin: AlleleOrigin, collection_method: CollectionMethod, clinical_features: List[SubmissionClinicalFeature] | None = None, clinical_features_comment: str | None = None, number_of_individuals: int | None = None, struct_var_method_type: StructVarMethodType | None = None)

Bases: BaseModel

affected_status: AffectedStatus

allele_origin: AlleleOrigin

clinical_features: List[SubmissionClinicalFeature] | None

clinical_features_comment: str | None

collection_method: CollectionMethod

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'affected_status': FieldInfo(annotation=AffectedStatus, required=True), 'allele_origin': FieldInfo(annotation=AlleleOrigin, required=True), 'clinical_features': FieldInfo(annotation=Union[List[SubmissionClinicalFeature], NoneType], required=False), 'clinical_features_comment': FieldInfo(annotation=Union[str, NoneType], required=False), 'collection_method': FieldInfo(annotation=CollectionMethod, required=True), 'number_of_individuals': FieldInfo(annotation=Union[int, NoneType], required=False), 'struct_var_method_type': FieldInfo(annotation=Union[StructVarMethodType, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

number_of_individuals: int | None

struct_var_method_type: StructVarMethodType | None

to_msg() → SubmissionObservedIn

class clinvar_api.models.sub_payload.SubmissionPhaseUnknownSet(*, hgvs: str, variants: List[SubmissionVariant])

Bases: BaseModel

hgvs: str

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'hgvs': FieldInfo(annotation=str, required=True), 'variants': FieldInfo(annotation=List[SubmissionVariant], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

to_msg() → SubmissionPhaseUnknownSet

variants: List[SubmissionVariant]

class clinvar_api.models.sub_payload.SubmissionVariant(*, chromosome_coordinates: SubmissionChromosomeCoordinates | None = None, copy_number: str | None = None, gene: List[SubmissionVariantGene] | None = None, hgvs: str | None = None, reference_copy_number: int | None = None, variant_type: VariantType | None = None)

Bases: BaseModel

chromosome_coordinates: SubmissionChromosomeCoordinates | None

copy_number: str | None

gene: List[SubmissionVariantGene] | None

hgvs: str | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'chromosome_coordinates': FieldInfo(annotation=Union[SubmissionChromosomeCoordinates, NoneType], required=False), 'copy_number': FieldInfo(annotation=Union[str, NoneType], required=False), 'gene': FieldInfo(annotation=Union[List[SubmissionVariantGene], NoneType], required=False), 'hgvs': FieldInfo(annotation=Union[str, NoneType], required=False), 'reference_copy_number': FieldInfo(annotation=Union[int, NoneType], required=False), 'variant_type': FieldInfo(annotation=Union[VariantType, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

reference_copy_number: int | None

to_msg() → SubmissionVariant

variant_type: VariantType | None

class clinvar_api.models.sub_payload.SubmissionVariantGene(*, id: int | None = None, symbol: str | None = None)

Bases: BaseModel

id: int | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'id': FieldInfo(annotation=Union[int, NoneType], required=False), 'symbol': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

symbol: str | None

to_msg() → SubmissionVariantGene

class clinvar_api.models.sub_payload.SubmissionVariantSet(*, variant: List[SubmissionVariant])

Bases: BaseModel

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'variant': FieldInfo(annotation=List[SubmissionVariant], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

to_msg() → SubmissionVariantSet

variant: List[SubmissionVariant]

clinvar_api.models.sub_response module

Data structures for submission response.

class clinvar_api.models.sub_response.Created(*, id: str)

Bases: BaseModel

classmethod from_msg(other: Created)

id: str

The submission ID.

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'id': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class clinvar_api.models.sub_response.Error(*, message: str)

Bases: BaseModel

classmethod from_msg(other: Error)

message: str

The error response’s message.

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'message': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class clinvar_api.models.sub_response.SummaryResponse(*, batch_processing_status: BatchProcessingStatus, batch_release_status: BatchReleaseStatus, submission_date: str, submission_name: str, total_count: int, total_errors: int, total_public: int, total_success: int, deletions: List[SummaryResponseDeletion] | None = None, submissions: List[SummaryResponseSubmission] | None = None, total_delete_count: int | None = None, total_deleted: int | None = None, total_delete_errors: int | None = None, total_delete_success: int | None = None)

Bases: BaseModel

Represetation of server’s response to a submission.

batch_processing_status: BatchProcessingStatus

batch_release_status: BatchReleaseStatus

deletions: List[SummaryResponseDeletion] | None

classmethod from_msg(other: SummaryResponse)

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'batch_processing_status': FieldInfo(annotation=BatchProcessingStatus, required=True), 'batch_release_status': FieldInfo(annotation=BatchReleaseStatus, required=True), 'deletions': FieldInfo(annotation=Union[List[SummaryResponseDeletion], NoneType], required=False), 'submission_date': FieldInfo(annotation=str, required=True), 'submission_name': FieldInfo(annotation=str, required=True), 'submissions': FieldInfo(annotation=Union[List[SummaryResponseSubmission], NoneType], required=False), 'total_count': FieldInfo(annotation=int, required=True), 'total_delete_count': FieldInfo(annotation=Union[int, NoneType], required=False), 'total_delete_errors': FieldInfo(annotation=Union[int, NoneType], required=False), 'total_delete_success': FieldInfo(annotation=Union[int, NoneType], required=False), 'total_deleted': FieldInfo(annotation=Union[int, NoneType], required=False), 'total_errors': FieldInfo(annotation=int, required=True), 'total_public': FieldInfo(annotation=int, required=True), 'total_success': FieldInfo(annotation=int, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

submission_date: str

submission_name: str

submissions: List[SummaryResponseSubmission] | None

total_count: int

total_delete_count: int | None

total_delete_errors: int | None

total_delete_success: int | None

total_deleted: int | None

total_errors: int

total_public: int

total_success: int

class clinvar_api.models.sub_response.SummaryResponseDeletion(*, identifiers: SummaryResponseDeletionIdentifier, processing_status: str, delete_date: str | None = None, delete_status: str | None = None, errors: List[SummaryResponseError] | None = None)

Bases: BaseModel

delete_date: str | None

delete_status: str | None

errors: List[SummaryResponseError] | None

classmethod from_msg(other: SummaryResponseDeletion)

identifiers: SummaryResponseDeletionIdentifier

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'delete_date': FieldInfo(annotation=Union[str, NoneType], required=False), 'delete_status': FieldInfo(annotation=Union[str, NoneType], required=False), 'errors': FieldInfo(annotation=Union[List[SummaryResponseError], NoneType], required=False), 'identifiers': FieldInfo(annotation=SummaryResponseDeletionIdentifier, required=True), 'processing_status': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

processing_status: str

class clinvar_api.models.sub_response.SummaryResponseDeletionIdentifier(*, clinvar_accession: str, clinvar_local_key: str | None = None)

Bases: BaseModel

clinvar_accession: str

clinvar_local_key: str | None

classmethod from_msg(other: SummaryResponseDeletionIdentifier)

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'clinvar_accession': FieldInfo(annotation=str, required=True), 'clinvar_local_key': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class clinvar_api.models.sub_response.SummaryResponseError(*, input: List[SummaryResponseErrorInput], output: SummaryResponseErrorOutput)

Bases: BaseModel

classmethod from_msg(other: SummaryResponseError)

input: List[SummaryResponseErrorInput]

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'input': FieldInfo(annotation=List[SummaryResponseErrorInput], required=True), 'output': FieldInfo(annotation=SummaryResponseErrorOutput, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

output: SummaryResponseErrorOutput

class clinvar_api.models.sub_response.SummaryResponseErrorInput(*, value: str | None = None, field: str | None = None)

Bases: BaseModel

field: str | None

classmethod from_msg(other: SummaryResponseErrorInput)

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'field': FieldInfo(annotation=Union[str, NoneType], required=False), 'value': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

value: str | None

class clinvar_api.models.sub_response.SummaryResponseErrorOutput(*, errors: List[SummaryResponseErrorOutputError])

Bases: BaseModel

errors: List[SummaryResponseErrorOutputError]

classmethod from_msg(other: SummaryResponseErrorOutput)

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'errors': FieldInfo(annotation=List[SummaryResponseErrorOutputError], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class clinvar_api.models.sub_response.SummaryResponseErrorOutputError(*, user_message: str)

Bases: BaseModel

classmethod from_msg(other: SummaryResponseErrorOutputError)

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'user_message': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

user_message: str

class clinvar_api.models.sub_response.SummaryResponseSubmission(*, identifiers: SummaryResponseSubmissionIdentifiers, processing_status: str, clinvar_accession_version: str | None = None, errors: List[SummaryResponseError] | None = None, release_date: str | None = None, release_status: str | None = None)

Bases: BaseModel

clinvar_accession_version: str | None

errors: List[SummaryResponseError] | None

classmethod from_msg(other: SummaryResponseSubmission)

identifiers: SummaryResponseSubmissionIdentifiers

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'clinvar_accession_version': FieldInfo(annotation=Union[str, NoneType], required=False), 'errors': FieldInfo(annotation=Union[List[SummaryResponseError], NoneType], required=False), 'identifiers': FieldInfo(annotation=SummaryResponseSubmissionIdentifiers, required=True), 'processing_status': FieldInfo(annotation=str, required=True), 'release_date': FieldInfo(annotation=Union[str, NoneType], required=False), 'release_status': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

processing_status: str

release_date: str | None

release_status: str | None

class clinvar_api.models.sub_response.SummaryResponseSubmissionIdentifiers(*, clinvar_local_key: str, clinvar_accession: str | None = None, local_id: str | None = None, local_key: str | None = None)

Bases: BaseModel

clinvar_accession: str | None

clinvar_local_key: str

classmethod from_msg(other: SummaryResponseSubmissionIdentifiers)

local_id: str | None

local_key: str | None

model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'clinvar_accession': FieldInfo(annotation=Union[str, NoneType], required=False), 'clinvar_local_key': FieldInfo(annotation=str, required=True), 'local_id': FieldInfo(annotation=Union[str, NoneType], required=False), 'local_key': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

Module contents

Data structures for the internal “business logic” representation.

These data structure use the snake_case used throughout the program.