Biobroker
Content
Biobroker
Code documentation
API
Authenticator
Generic
Input processor
Metadata entity
Output processor
Wrangler
Notebooks
Submit to biosamples
Submit your samples validating them against a checklist
Modifying the source input with a key:value map
Retrieving a sample
Updating submitted samples
Submitting complex metadata
Biobroker
Index
Index
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A
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B
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C
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D
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E
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F
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G
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I
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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__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)