Uses of Interface
org.phenopackets.phenopackettools.validator.core.PhenopacketValidator

Packages that use PhenopacketValidator

Package	Description
org.phenopackets.phenopackettools.validator.core	The package provides APIs and default implementations of phenopacket validation.
org.phenopackets.phenopackettools.validator.core.metadata	The package provides PhenopacketValidators for metadata validation - checking that MetaData of the top-level elements of the Phenopacket schema contains a Resource for all OntologyClasses of the element.
org.phenopackets.phenopackettools.validator.core.phenotype	Package with off-the-shelf validators that work with Human Phenotype Ontology (HPO).

Uses of PhenopacketValidator in org.phenopackets.phenopackettools.validator.core

Fields in org.phenopackets.phenopackettools.validator.core with type parameters of type PhenopacketValidator

Modifier and Type	Field	Description
protected final List<PhenopacketValidator<T>>	ValidationWorkflowRunnerBuilder.semanticValidators	Deprecated, for removal: This API element is subject to removal in a future version. use ValidationWorkflowRunnerBuilder.validators instead
protected final List<PhenopacketValidator<T>>	ValidationWorkflowRunnerBuilder.syntaxValidators	Deprecated, for removal: This API element is subject to removal in a future version. use ValidationWorkflowRunnerBuilder.validators instead
protected final List<PhenopacketValidator<T>>	ValidationWorkflowRunnerBuilder.validators

Methods in org.phenopackets.phenopackettools.validator.core with parameters of type PhenopacketValidator

Modifier and Type	Method	Description
ValidationWorkflowRunnerBuilder<T>	ValidationWorkflowRunnerBuilder.addSemanticValidator(PhenopacketValidator<T> semanticValidator)	Deprecated, for removal: This API element is subject to removal in a future version. use ValidationWorkflowRunnerBuilder.addValidator(PhenopacketValidator) instead
ValidationWorkflowRunnerBuilder<T>	ValidationWorkflowRunnerBuilder.addSyntaxValidator(PhenopacketValidator<T> syntaxValidator)	Deprecated, for removal: This API element is subject to removal in a future version. use ValidationWorkflowRunnerBuilder.addValidator(PhenopacketValidator) instead
ValidationWorkflowRunnerBuilder<T>	ValidationWorkflowRunnerBuilder.addValidator(PhenopacketValidator<T> validator)	Add a validator to the end of the workflow.

Method parameters in org.phenopackets.phenopackettools.validator.core with type arguments of type PhenopacketValidator

Modifier and Type	Method	Description
ValidationWorkflowRunnerBuilder<T>	ValidationWorkflowRunnerBuilder.addAllSemanticValidators(List<PhenopacketValidator<T>> validators)	Deprecated, for removal: This API element is subject to removal in a future version. use ValidationWorkflowRunnerBuilder.addValidators(Collection) instead
ValidationWorkflowRunnerBuilder<T>	ValidationWorkflowRunnerBuilder.addAllSyntaxValidators(List<PhenopacketValidator<T>> validators)	Deprecated, for removal: This API element is subject to removal in a future version. use ValidationWorkflowRunnerBuilder.addValidators(Collection) instead
ValidationWorkflowRunnerBuilder<T>	ValidationWorkflowRunnerBuilder.addValidators(Collection<? extends PhenopacketValidator<T>> validators)	Add validators to the end of the workflow.

Uses of PhenopacketValidator in org.phenopackets.phenopackettools.validator.core.metadata

Methods in org.phenopackets.phenopackettools.validator.core.metadata that return PhenopacketValidator

Modifier and Type	Method	Description
static PhenopacketValidator<org.phenopackets.schema.v2.CohortOrBuilder>	MetaDataValidators.cohortValidator()	Get PhenopacketValidator for checking that MetaData of CohortOrBuilder contains Resources for prefixes of all OntologyClass present in given CohortOrBuilder.
static PhenopacketValidator<org.phenopackets.schema.v2.FamilyOrBuilder>	MetaDataValidators.familyValidator()	Get PhenopacketValidator for checking that MetaData of FamilyOrBuilder contains Resources for prefixes of all OntologyClass present in given FamilyOrBuilder.
static PhenopacketValidator<org.phenopackets.schema.v2.PhenopacketOrBuilder>	MetaDataValidators.phenopacketValidator()	Get PhenopacketValidator for checking that MetaData of PhenopacketOrBuilder contains Resources for prefixes of all OntologyClass present in given PhenopacketOrBuilder.

Uses of PhenopacketValidator in org.phenopackets.phenopackettools.validator.core.phenotype

Methods in org.phenopackets.phenopackettools.validator.core.phenotype that return PhenopacketValidator

Modifier and Type	Method	Description
static PhenopacketValidator<org.phenopackets.schema.v2.CohortOrBuilder>	HpoPhenotypeValidators.Ancestry.cohortHpoAncestryValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Get PhenopacketValidator to validate ancestry Cohort using provided Ontology.
static PhenopacketValidator<org.phenopackets.schema.v2.CohortOrBuilder>	HpoPhenotypeValidators.OrganSystem.cohortHpoOrganSystemValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo, Collection<org.monarchinitiative.phenol.ontology.data.TermId> organSystemTermIds)	Get PhenopacketValidator to validate annotation of organ systems in a Cohort using provided Ontology and a collection of organ system TermIds.
static PhenopacketValidator<org.phenopackets.schema.v2.CohortOrBuilder>	HpoPhenotypeValidators.cohortHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Deprecated, for removal: This API element is subject to removal in a future version. use HpoPhenotypeValidators.Primary.cohortHpoPhenotypeValidator(Ontology) instead
static PhenopacketValidator<org.phenopackets.schema.v2.CohortOrBuilder>	HpoPhenotypeValidators.Primary.cohortHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Get PhenopacketValidator for performing primary validation Cohort using provided Ontology, as described in AbstractHpoPhenotypeValidator.
static PhenopacketValidator<org.phenopackets.schema.v2.FamilyOrBuilder>	HpoPhenotypeValidators.Ancestry.familyHpoAncestryValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Get PhenopacketValidator to validate ancestry Family using provided Ontology.
static PhenopacketValidator<org.phenopackets.schema.v2.FamilyOrBuilder>	HpoPhenotypeValidators.OrganSystem.familyHpoOrganSystemValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo, Collection<org.monarchinitiative.phenol.ontology.data.TermId> organSystemTermIds)	Get PhenopacketValidator to validate annotation of organ systems in a Family using provided Ontology and a collection of organ system TermIds.
static PhenopacketValidator<org.phenopackets.schema.v2.FamilyOrBuilder>	HpoPhenotypeValidators.familyHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Deprecated, for removal: This API element is subject to removal in a future version. use HpoPhenotypeValidators.Primary.familyHpoPhenotypeValidator(Ontology) instead
static PhenopacketValidator<org.phenopackets.schema.v2.FamilyOrBuilder>	HpoPhenotypeValidators.Primary.familyHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Get PhenopacketValidator for validate Family using provided Ontology.
static PhenopacketValidator<org.phenopackets.schema.v2.PhenopacketOrBuilder>	HpoPhenotypeValidators.Ancestry.phenopacketHpoAncestryValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Get PhenopacketValidator to validate ancestry Phenopacket using provided Ontology.
static PhenopacketValidator<org.phenopackets.schema.v2.PhenopacketOrBuilder>	HpoPhenotypeValidators.OrganSystem.phenopacketHpoOrganSystemValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo, Collection<org.monarchinitiative.phenol.ontology.data.TermId> organSystemTermIds)	Get PhenopacketValidator to validate annotation of organ systems in a Phenopacket using provided Ontology and a collection of organ system TermIds.
static PhenopacketValidator<org.phenopackets.schema.v2.PhenopacketOrBuilder>	HpoPhenotypeValidators.phenopacketHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Deprecated, for removal: This API element is subject to removal in a future version. use HpoPhenotypeValidators.Primary.phenopacketHpoPhenotypeValidator(Ontology) instead
static PhenopacketValidator<org.phenopackets.schema.v2.PhenopacketOrBuilder>	HpoPhenotypeValidators.Primary.phenopacketHpoPhenotypeValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Get PhenopacketValidator to validate Phenopacket using provided Ontology.