Index

_

__contains__() (Biosample method) (GenericEntity method) __delitem__() (Biosample method) (GenericEntity method) __getitem__() (Biosample method) (GenericEntity method) __setitem__() (Biosample method) (GenericEntity method) _build_search_query() (BsdApi static method) _check_structured_data() (BsdApi method) _flatten_characteristics() (Biosample method) _flatten_relationships() (Biosample method) _flatten_urls() (Biosample method) _is_invalid_for_update() (BsdApi static method) _request() (GenericAuthenticator method) _retrieve() (BsdApi method) (GenericApi method)

_retrieve_multiple() (BsdApi method) (GenericApi method) _save() (GenericOutputProcessor method) (TsvOutputProcessor method) (XlsxOutputProcessor method) _submit() (BsdApi method) (GenericApi method) _submit_errors() (BsdApi method) _submit_multiple() (BsdApi method) (GenericApi method) _tag_is_valid() (Biosample static method) _update() (BsdApi method) (GenericApi method) _update_multiple() (BsdApi method) (GenericApi method)

A

accession (Biosample property) (GenericEntity property) AccessionHasIncorrectFormat add_external_reference() (Biosample method)

add_organization() (Biosample method) add_relationship() (Biosample method) auth_endpoint (GenericAuthenticator property) (WebinAuthenticator property)

B

biobroker.api module biobroker.api.exceptions module biobroker.authenticator module biobroker.authenticator.exceptions module biobroker.generic module biobroker.generic.exceptions module biobroker.generic.logger module biobroker.generic.pydantic_model module biobroker.generic.utilities module

biobroker.input_processor module biobroker.input_processor.exceptions module biobroker.metadata_entity module biobroker.metadata_entity.exceptions module biobroker.output_processor module biobroker.wrangler module biobroker.wrangler.exceptions module Biosample (class in biobroker.metadata_entity) BiosampleGeneralModel (class in biobroker.generic.pydantic_model) BiosamplesNoErrorMessageError BiosamplesValidationError BsdApi (class in biobroker.api)

C

CantBeUpdatedApiError CantBeUpdatedLocalError

check_accession() (Biosample static method) ChecklistValidationError

D

delete() (GenericAuthenticator method)

DomainAlreadyExists

E

entity (Biosample property) (GenericEntity property)

EntityValidationError EXTERNAL_REFERENCE_FIELD (Biosample attribute)

F

flatten() (Biosample method) (GenericEntity method)

G

GenericApi (class in biobroker.api) GenericAuthenticator (class in biobroker.authenticator) GenericEntity (class in biobroker.metadata_entity) GenericInputProcessor (class in biobroker.input_processor)

GenericOutputProcessor (class in biobroker.output_processor) get() (GenericAuthenticator method) guidelines() (Biosample static method) (GenericEntity static method)

I

id (Biosample property) (GenericEntity property)

input_data (GenericInputProcessor property) (TsvInputProcessor property) (XlsxInputProcessor property)

M

MandatoryFunctionNotSet model_computed_fields (BiosampleGeneralModel attribute) (StructuredDataModel attribute) model_config (BiosampleGeneralModel attribute) (StructuredDataModel attribute) model_fields (BiosampleGeneralModel attribute) (StructuredDataModel attribute) module biobroker.api biobroker.api.exceptions biobroker.authenticator biobroker.authenticator.exceptions biobroker.generic biobroker.generic.exceptions biobroker.generic.logger biobroker.generic.pydantic_model biobroker.generic.utilities biobroker.input_processor biobroker.input_processor.exceptions biobroker.metadata_entity biobroker.metadata_entity.exceptions biobroker.output_processor biobroker.wrangler biobroker.wrangler.exceptions

N

NameShouldBeStringError NoNameSetError

NoOrganismSetError NoResults

O

ORGANIZATION (Biosample attribute)

P

parse_checklist_validation_errors() (in module biobroker.api.exceptions) parse_pydantic_errors() (in module biobroker.generic.utilities) patch() (GenericAuthenticator method)

post() (GenericAuthenticator method) process() (GenericInputProcessor method) process_relationships() (BsdApi method) put() (GenericAuthenticator method)

R

RelationshipInvalidSourceError RelationshipInvalidTargetError

retrieve() (GenericApi method) retrieve_entities() (Wrangler method) ROOT_PROPERTIES (Biosample attribute)

S

save() (GenericOutputProcessor method) save_results() (Wrangler method) search_samples() (BsdApi method) set_up_logger() (in module biobroker.generic.logger) slice_list() (in module biobroker.generic.utilities)

StructuredDataError StructuredDataModel (class in biobroker.generic.pydantic_model) StructuredDataSubmissionError submit() (GenericApi method) (Wrangler method) submit_structured_data() (BsdApi method)

T

to_json() (GenericEntity method) token (GenericAuthenticator property) (WebinAuthenticator property)

transform() (GenericInputProcessor method) TsvInputProcessor (class in biobroker.input_processor) TsvOutputProcessor (class in biobroker.output_processor)

U

update() (GenericApi method)

UsernameNotValid

V

VALID_RELATIONSHIPS (Biosample attribute) VALID_TAGS (Biosample attribute)

validate() (GenericEntity method) validate_sample() (BsdApi method) validate_username() (WebinAuthenticator method)

W

WebinAuthenticator (class in biobroker.authenticator)

Wrangler (class in biobroker.wrangler) WrongUserOrPassword

X

XlsxInputProcessor (class in biobroker.input_processor)

XlsxOutputProcessor (class in biobroker.output_processor)