DatabaseStorageManager

class DatabaseStorageManager(hdf5_filepath, storage_name, force_new=False)

Database hdf5 storage manager.

Constructor for storage manager.

Parameters

• hdf5_filepath (str) – Path to hdf5 file

• storage_name (str) – Storage database name. Must match the one in storage file.

• force_new (bool) – If file exists the override it for new construction

Attributes

active_elements	Active storage elements that can be used.
element_state	Cached states per storage element.
has_accs	True if database storage contains sequence accessions, False otherwise.
has_align	True if database storage contains alignments, False otherwise.
has_repseq	True if database storage contains reference sequences, False otherwise.
has_tax	True if database storage contains reference taxonomy, False otherwise.
has_tree	True if database storage contains reference phylogeny, False otherwise.
hdf5_filepath	Path to hdf5 file.
repseq_ids	The rids present in the storage.
state	State of the storage manager.
storage_name	Storage database name/label.
summary	Cached storage database summary table.
taxon_ids	The tids present in the storage.

Methods

commit_to_storage(element_key, product_generator)	This is a primary function that commit changes to the storage.
compress_storage([complevel, complib, overwrite])	Compresses the storage file using the required parameters.
get_element_data_by_ids(element_key, ids)	Get partial data from storage element by ids.
get_index_by_element(element_key[, condition])	Get index of target storage element.
imprint_database(stamp_dict)	This is the final function that _local constructor must call.
initiate_memory_cache([level])	Load various elements based on level from storage to the memory for rapid data access.
retrieve_data_by_element(element_key[, …])	Retrieves data from storage element as whole or in chunks.
shutdown()	Shutdown the database and mark cache clean for garbage collector.
validate_storage(hdf5_filepath, storage_name)	Validates storage hdf5 file.