datacatalog.managers.sampleset package

class datacatalog.managers.sampleset.SampleSetProcessor(mongodb, agave=None, samples_file=None, samples_uri=None, path_prefix='/uploads', *args, **kwargs)[source]

Bases: datacatalog.managers.common.Manager

Manager class to process and load sample set JSON documents

contextualize(filename)[source]
get(doctype, identifier, identifier_value)[source]
process(strategy='merge')[source]

Recursiveley loads contents of a sample set into the catalog

Parameters:replace (bool, optional) – Replace existing records. Default is to merge.
Returns:Returns True on success
Return type:bool
process_experiment(parent_uuid=None, strategy='merge')[source]
process_files(parent_uuid=None, strategy='merge')[source]
process_measurements(parent_uuid=None, strategy='merge')[source]
process_samples(parent_uuid=None, strategy='merge')[source]
setup(samples_file=None, samples_uri=None)[source]

Submodules

datacatalog.managers.sampleset.processor module

class datacatalog.managers.sampleset.processor.SampleSetProcessor(mongodb, agave=None, samples_file=None, samples_uri=None, path_prefix='/uploads', *args, **kwargs)[source]

Bases: datacatalog.managers.common.Manager

Manager class to process and load sample set JSON documents

contextualize(filename)[source]
get(doctype, identifier, identifier_value)[source]
process(strategy='merge')[source]

Recursiveley loads contents of a sample set into the catalog

Parameters:replace (bool, optional) – Replace existing records. Default is to merge.
Returns:Returns True on success
Return type:bool
process_experiment(parent_uuid=None, strategy='merge')[source]
process_files(parent_uuid=None, strategy='merge')[source]
process_measurements(parent_uuid=None, strategy='merge')[source]
process_samples(parent_uuid=None, strategy='merge')[source]
setup(samples_file=None, samples_uri=None)[source]
exception datacatalog.managers.sampleset.processor.SampleSetProcessorError[source]

Bases: datacatalog.linkedstores.basestore.exceptions.CatalogError

exception datacatalog.managers.sampleset.processor.UnknownReference[source]

Bases: datacatalog.linkedstores.basestore.exceptions.CatalogError