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