clinvar_api package
Subpackages
- clinvar_api.models package
- Submodules
- clinvar_api.models.query_response module
- clinvar_api.models.sub_payload module
SubmissionAssertionCriteria
SubmissionChromosomeCoordinates
SubmissionChromosomeCoordinates.accession
SubmissionChromosomeCoordinates.alternate_allele
SubmissionChromosomeCoordinates.assembly
SubmissionChromosomeCoordinates.chromosome
SubmissionChromosomeCoordinates.inner_start
SubmissionChromosomeCoordinates.inner_stop
SubmissionChromosomeCoordinates.model_config
SubmissionChromosomeCoordinates.model_fields
SubmissionChromosomeCoordinates.outer_start
SubmissionChromosomeCoordinates.outer_stop
SubmissionChromosomeCoordinates.reference_allele
SubmissionChromosomeCoordinates.start
SubmissionChromosomeCoordinates.stop
SubmissionChromosomeCoordinates.to_msg()
SubmissionChromosomeCoordinates.variant_length
SubmissionCitation
SubmissionClinicalFeature
SubmissionClinicalSignificance
SubmissionClinicalSignificance.citation
SubmissionClinicalSignificance.clinical_significance_description
SubmissionClinicalSignificance.comment
SubmissionClinicalSignificance.custom_assertion_score
SubmissionClinicalSignificance.date_last_evaluated
SubmissionClinicalSignificance.explanation_of_drug_response
SubmissionClinicalSignificance.explanation_of_other_clinical_significance
SubmissionClinicalSignificance.mode_of_inheritance
SubmissionClinicalSignificance.model_config
SubmissionClinicalSignificance.model_fields
SubmissionClinicalSignificance.to_msg()
SubmissionClinvarDeletion
SubmissionClinvarDeletionAccessionSet
SubmissionClinvarSubmission
SubmissionClinvarSubmission.clinical_significance
SubmissionClinvarSubmission.clinvar_accession
SubmissionClinvarSubmission.compound_heterozygote_set
SubmissionClinvarSubmission.condition_set
SubmissionClinvarSubmission.diplotype_set
SubmissionClinvarSubmission.distinct_chromosomes_set
SubmissionClinvarSubmission.extra_data
SubmissionClinvarSubmission.haplotype_set
SubmissionClinvarSubmission.haplotype_single_variant_set
SubmissionClinvarSubmission.local_id
SubmissionClinvarSubmission.local_key
SubmissionClinvarSubmission.model_config
SubmissionClinvarSubmission.model_fields
SubmissionClinvarSubmission.observed_in
SubmissionClinvarSubmission.phase_unknown_set
SubmissionClinvarSubmission.record_status
SubmissionClinvarSubmission.to_msg()
SubmissionClinvarSubmission.variant_set
SubmissionCompoundHeterozygoteSet
SubmissionCompoundHeterozygoteSetVariantSet
SubmissionCondition
SubmissionConditionSet
SubmissionContainer
SubmissionContainer.assertion_criteria
SubmissionContainer.behalf_org_id
SubmissionContainer.clinvar_deletion
SubmissionContainer.clinvar_submission
SubmissionContainer.clinvar_submission_release_status
SubmissionContainer.model_config
SubmissionContainer.model_fields
SubmissionContainer.submission_name
SubmissionContainer.to_msg()
SubmissionDiplotypeSet
SubmissionDistinctChromosomesSet
SubmissionDrugResponse
SubmissionHaplotypeSet
SubmissionHaplotypeSets
SubmissionObservedIn
SubmissionObservedIn.affected_status
SubmissionObservedIn.allele_origin
SubmissionObservedIn.clinical_features
SubmissionObservedIn.clinical_features_comment
SubmissionObservedIn.collection_method
SubmissionObservedIn.model_config
SubmissionObservedIn.model_fields
SubmissionObservedIn.number_of_individuals
SubmissionObservedIn.struct_var_method_type
SubmissionObservedIn.to_msg()
SubmissionPhaseUnknownSet
SubmissionVariant
SubmissionVariantGene
SubmissionVariantSet
- clinvar_api.models.sub_response module
Created
Error
SummaryResponse
SummaryResponse.batch_processing_status
SummaryResponse.batch_release_status
SummaryResponse.deletions
SummaryResponse.from_msg()
SummaryResponse.model_config
SummaryResponse.model_fields
SummaryResponse.submission_date
SummaryResponse.submission_name
SummaryResponse.submissions
SummaryResponse.total_count
SummaryResponse.total_delete_count
SummaryResponse.total_delete_errors
SummaryResponse.total_delete_success
SummaryResponse.total_deleted
SummaryResponse.total_errors
SummaryResponse.total_public
SummaryResponse.total_success
SummaryResponseDeletion
SummaryResponseDeletionIdentifier
SummaryResponseError
SummaryResponseErrorInput
SummaryResponseErrorOutput
SummaryResponseErrorOutputError
SummaryResponseSubmission
SummaryResponseSubmission.clinvar_accession_version
SummaryResponseSubmission.errors
SummaryResponseSubmission.from_msg()
SummaryResponseSubmission.identifiers
SummaryResponseSubmission.model_config
SummaryResponseSubmission.model_fields
SummaryResponseSubmission.processing_status
SummaryResponseSubmission.release_date
SummaryResponseSubmission.release_status
SummaryResponseSubmissionIdentifiers
SummaryResponseSubmissionIdentifiers.clinvar_accession
SummaryResponseSubmissionIdentifiers.clinvar_local_key
SummaryResponseSubmissionIdentifiers.from_msg()
SummaryResponseSubmissionIdentifiers.local_id
SummaryResponseSubmissionIdentifiers.local_key
SummaryResponseSubmissionIdentifiers.model_config
SummaryResponseSubmissionIdentifiers.model_fields
- Module contents
- clinvar_api.msg package
- Submodules
- clinvar_api.msg.query_response module
- clinvar_api.msg.sub_payload module
AffectedStatus
AlleleOrigin
Assembly
Chromosome
Chromosome.CHR1
Chromosome.CHR10
Chromosome.CHR11
Chromosome.CHR12
Chromosome.CHR13
Chromosome.CHR14
Chromosome.CHR15
Chromosome.CHR16
Chromosome.CHR17
Chromosome.CHR18
Chromosome.CHR19
Chromosome.CHR2
Chromosome.CHR20
Chromosome.CHR21
Chromosome.CHR22
Chromosome.CHR3
Chromosome.CHR4
Chromosome.CHR5
Chromosome.CHR6
Chromosome.CHR7
Chromosome.CHR8
Chromosome.CHR9
Chromosome.CHRMT
Chromosome.CHRX
Chromosome.CHRY
CitationDb
ClinicalFeaturesAffectedStatus
ClinicalFeaturesDb
ClinicalSignificanceDescription
ClinicalSignificanceDescription.AFFECTED
ClinicalSignificanceDescription.ASSOCIATION
ClinicalSignificanceDescription.BENIGN
ClinicalSignificanceDescription.CONFERS_SENSITIVITY
ClinicalSignificanceDescription.DRUG_RESPONSE
ClinicalSignificanceDescription.ESTABLISHED_RISK_ALLELE
ClinicalSignificanceDescription.LIKELY_BENIGN
ClinicalSignificanceDescription.LIKELY_PATHOGENIC
ClinicalSignificanceDescription.LIKELY_PATHOGENIC_LOW_PENETRANCE
ClinicalSignificanceDescription.LIKELY_RISK_ALLELE
ClinicalSignificanceDescription.NOT_PROVIDED
ClinicalSignificanceDescription.OTHER
ClinicalSignificanceDescription.PATHOGENIC
ClinicalSignificanceDescription.PATHOGENIC_LOW_PENETRANCE
ClinicalSignificanceDescription.PROTECTIVE
ClinicalSignificanceDescription.UNCERTAIN_RISK_ALLELE
ClinicalSignificanceDescription.UNCERTAIN_SIGNIFICANCE
CollectionMethod
CollectionMethod.CASE_CONTROL
CollectionMethod.CLINICAL_TESTING
CollectionMethod.CURATION
CollectionMethod.IN_VITRO
CollectionMethod.IN_VIVO
CollectionMethod.LITERATURE_ONLY
CollectionMethod.NOT_PROVIDED
CollectionMethod.PHENOTYPING_ONLY
CollectionMethod.PROVIDER_INTERPRETATION
CollectionMethod.REFERENCE_POPULATION
CollectionMethod.RESEARCH
ConditionDb
ModeOfInheritance
ModeOfInheritance.AUTOSOMAL_DOMINANT_INHERITANCE
ModeOfInheritance.AUTOSOMAL_DOMINANT_INHERITANCE_WITH_MATERNAL_IMPRINTING
ModeOfInheritance.AUTOSOMAL_DOMINANT_INHERITANCE_WITH_PATERNAL_IMPRINTING
ModeOfInheritance.AUTOSOMAL_RECESSIVE_INHERITANCE
ModeOfInheritance.AUTOSOMAL_UNKNOWN
ModeOfInheritance.CODOMINANT
ModeOfInheritance.DEMIDOMINANT_INHERITANCE
ModeOfInheritance.GENETIC_ANTICIPATION
ModeOfInheritance.MITOCHONDRIAL_INHERITANCE
ModeOfInheritance.MULTIFACTORIAL_INHERITANCE
ModeOfInheritance.OLIGOGENIC_INHERITANCE
ModeOfInheritance.OTHER
ModeOfInheritance.SEX_LIMITED_AUTOSOMAL_DOMINANT
ModeOfInheritance.SOMATIC_MUTATION
ModeOfInheritance.SPORADIC
ModeOfInheritance.UNKNOWN_MECHANISM
ModeOfInheritance.X_LINKED_DOMINANT_INHERITANCE
ModeOfInheritance.X_LINKED_INHERITANCE
ModeOfInheritance.X_LINKED_RECESSIVE_INHERITANCE
ModeOfInheritance.Y_LINKED_INHERITANCE
MultipleConditionExplanation
RecordStatus
ReleaseStatus
StructVarMethodType
SubmissionAssertionCriteria
SubmissionChromosomeCoordinates
SubmissionChromosomeCoordinates.accession
SubmissionChromosomeCoordinates.alternateAllele
SubmissionChromosomeCoordinates.assembly
SubmissionChromosomeCoordinates.chromosome
SubmissionChromosomeCoordinates.innerStart
SubmissionChromosomeCoordinates.innerStop
SubmissionChromosomeCoordinates.model_config
SubmissionChromosomeCoordinates.model_fields
SubmissionChromosomeCoordinates.outerStart
SubmissionChromosomeCoordinates.outerStop
SubmissionChromosomeCoordinates.referenceAllele
SubmissionChromosomeCoordinates.start
SubmissionChromosomeCoordinates.stop
SubmissionChromosomeCoordinates.variantLength
SubmissionCitation
SubmissionClinicalFeature
SubmissionClinicalSignificance
SubmissionClinicalSignificance.citation
SubmissionClinicalSignificance.clinicalSignificanceDescription
SubmissionClinicalSignificance.comment
SubmissionClinicalSignificance.customAssertionScore
SubmissionClinicalSignificance.dateLastEvaluated
SubmissionClinicalSignificance.explanationOfDrugResponse
SubmissionClinicalSignificance.explanationOfOtherClinicalSignificance
SubmissionClinicalSignificance.modeOfInheritance
SubmissionClinicalSignificance.model_config
SubmissionClinicalSignificance.model_fields
SubmissionClinvarDeletion
SubmissionClinvarDeletionAccessionSet
SubmissionClinvarSubmission
SubmissionClinvarSubmission.clinicalSignificance
SubmissionClinvarSubmission.clinvarAccession
SubmissionClinvarSubmission.compoundHeterozygoteSet
SubmissionClinvarSubmission.conditionSet
SubmissionClinvarSubmission.diplotypeSet
SubmissionClinvarSubmission.distinctChromosomesSet
SubmissionClinvarSubmission.haplotypeSet
SubmissionClinvarSubmission.haplotypeSingleVariantSet
SubmissionClinvarSubmission.localID
SubmissionClinvarSubmission.localKey
SubmissionClinvarSubmission.model_config
SubmissionClinvarSubmission.model_fields
SubmissionClinvarSubmission.observedIn
SubmissionClinvarSubmission.phaseUnknownSet
SubmissionClinvarSubmission.recordStatus
SubmissionClinvarSubmission.variantSet
SubmissionCompoundHeterozygoteSet
SubmissionCompoundHeterozygoteSetVariantSet
SubmissionCondition
SubmissionConditionSet
SubmissionContainer
SubmissionDiplotypeSet
SubmissionDistinctChromosomesSet
SubmissionDrugResponse
SubmissionHaplotypeSet
SubmissionHaplotypeSets
SubmissionObservedIn
SubmissionObservedIn.affectedStatus
SubmissionObservedIn.alleleOrigin
SubmissionObservedIn.clinicalFeatures
SubmissionObservedIn.clinicalFeaturesComment
SubmissionObservedIn.collectionMethod
SubmissionObservedIn.model_config
SubmissionObservedIn.model_fields
SubmissionObservedIn.numberOfIndividuals
SubmissionObservedIn.structVarMethodType
SubmissionPhaseUnknownSet
SubmissionVariant
SubmissionVariantGene
SubmissionVariantSet
VariantType
- clinvar_api.msg.sub_response module
BatchProcessingStatus
BatchReleaseStatus
Created
Error
SummaryResponse
SummaryResponse.batchProcessingStatus
SummaryResponse.batchReleaseStatus
SummaryResponse.deletions
SummaryResponse.model_config
SummaryResponse.model_fields
SummaryResponse.submissionDate
SummaryResponse.submissionName
SummaryResponse.submissions
SummaryResponse.totalCount
SummaryResponse.totalDeleteCount
SummaryResponse.totalDeleteErrors
SummaryResponse.totalDeleteSuccess
SummaryResponse.totalDeleted
SummaryResponse.totalErrors
SummaryResponse.totalPublic
SummaryResponse.totalSuccess
SummaryResponseDeletion
SummaryResponseDeletionIdentifier
SummaryResponseError
SummaryResponseErrorInput
SummaryResponseErrorOutput
SummaryResponseErrorOutputError
SummaryResponseSubmission
SummaryResponseSubmission.clinvarAccessionVersion
SummaryResponseSubmission.errors
SummaryResponseSubmission.identifiers
SummaryResponseSubmission.model_config
SummaryResponseSubmission.model_fields
SummaryResponseSubmission.processingStatus
SummaryResponseSubmission.releaseDate
SummaryResponseSubmission.releaseStatus
SummaryResponseSubmissionIdentifiers
- Module contents
Submodules
clinvar_api.client module
REST API client code for communicating with server endpoints.
- class clinvar_api.client.AsyncClient(config: Config)[source]
Bases:
object
NCBI ClinVar REST API client (async).
- async retrieve_status(submission_id: str) RetrieveStatusResult [source]
Retrieve submission status from API.
- Parameters:
submission_id – The identifier of the submission as returned earlier from API.
- Returns:
The information about the created submission.
- Raises:
exceptions.QueryFailed – on problems with the communication to the server.
- async submit_data(payload: SubmissionContainer) Created [source]
Submit new data to ClinVar API.
- Parameters:
payload – The submission data.
- Returns:
The information about the created submission.
- Raises:
exceptions.SubmissionFailed – on problems with the submission.
- class clinvar_api.client.Client(config: Config)[source]
Bases:
object
NCBI ClinVar REST API client (sync).
- retrieve_status(submission_id: str) RetrieveStatusResult [source]
Retrieve submission status from API.
- Parameters:
submission_id – The identifier of the submission as returned earlier from API.
- Returns:
The information about the created submission.
- Raises:
exceptions.QueryFailed – on problems with the communication to the server.
- submit_data(payload: SubmissionContainer) Created [source]
Submit new data to ClinVar API.
- Parameters:
payload – The submission data.
- Returns:
The information about the created submission.
- Raises:
exceptions.SubmissionFailed – on problems with the submission.
- class clinvar_api.client.Config(*, auth_token: SecretStr, use_testing: bool = False, use_dryrun: bool = False, presubmission_validation: bool = True, verify_ssl: bool = True)[source]
Bases:
BaseModel
Configuration for the
Client
class.- auth_token: SecretStr
Token to use for authentication.
- 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]] = {'auth_token': FieldInfo(annotation=SecretStr, required=True), 'presubmission_validation': FieldInfo(annotation=bool, required=False, default=True), 'use_dryrun': FieldInfo(annotation=bool, required=False, default=False), 'use_testing': FieldInfo(annotation=bool, required=False, default=False), 'verify_ssl': FieldInfo(annotation=bool, required=False, default=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.
- presubmission_validation: bool
Whether to validate submission payload before posting.
- use_dryrun: bool
Whether to use dry running.
- use_testing: bool
Whether to use the test endpoint.
- verify_ssl: bool
Whether or not to verify SSL on submission.
- clinvar_api.client.ENDPOINT_URL_PROD = 'https://submit.ncbi.nlm.nih.gov/api/v1/submissions/'
URL of the server endpoint (non-test/production).
- clinvar_api.client.ENDPOINT_URL_TEST = 'https://submit.ncbi.nlm.nih.gov/apitest/v1/submissions/'
URL of the test endpoint.
- class clinvar_api.client.RetrieveStatusResult(*, status: SubmissionStatus, summaries: Dict[str, SummaryResponse])[source]
Bases:
BaseModel
Result type for
retrieve_status
function.- 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]] = {'status': FieldInfo(annotation=SubmissionStatus, required=True), 'summaries': FieldInfo(annotation=Dict[str, SummaryResponse], 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.
- status: SubmissionStatus
The submission status.
- summaries: Dict[str, SummaryResponse]
A dict mapping file URLs to the parsed
Sum
.
- clinvar_api.client.SUFFIX_DRYRUN = '?dry-run=true'
URL suffix for enabling dry-run.
- async clinvar_api.client.async_retrieve_status(submission_id: str, config: Config) RetrieveStatusResult [source]
Retrieve submission status from API.
- Parameters:
submission_id – The identifier of the submission as returned earlier from API.
config – The connfiguration to use.
- Returns:
The information about the created submission.
- Raises:
exceptions.QueryFailed – on problems with the communication to the server.
- async clinvar_api.client.async_submit_data(submission_container: SubmissionContainer, config: Config) Created [source]
Submit new data to ClinVar API via async API (async).
- Parameters:
submission_container – The submission data.
config – The connfiguration to use.
- Returns:
The information about the created submission.
- Raises:
exceptions.SubmissionFailed – on problems with the submission.
- clinvar_api.client.retrieve_status(submission_id: str, config: Config) RetrieveStatusResult [source]
Retrieve submission status from API.
- Parameters:
submission_id – The identifier of the submission as returned earlier from API.
config – The connfiguration to use.
- Returns:
The information about the created submission.
- Raises:
exceptions.QueryFailed – on problems with the communication to the server.
- clinvar_api.client.submit_data(submission_container: SubmissionContainer, config: Config) Created [source]
Submit new data to ClinVar API (sync).
- Parameters:
submission_container – The submission data.
config – The connfiguration to use.
- Returns:
The information about the created submission.
- Raises:
exceptions.SubmissionFailed – on problems with the submission.
clinvar_api.common module
clinvar_api.constants module
clinvar_api.exceptions module
Module with the exception classes.
- exception clinvar_api.exceptions.ClinvarApiException[source]
Bases:
Exception
Base exception for
clinvar_api
.
- exception clinvar_api.exceptions.QueryFailed[source]
Bases:
ClinvarApiException
Raised when the status query failed.
- exception clinvar_api.exceptions.SubmissionFailed[source]
Bases:
ClinvarApiException
Raised when there was a problem with submitting to ClinVar.