chado.organism package¶

Module contents¶

Contains possible interactions with the Chado Organisms Module

class chado.organism.OrganismClient(engine, metadata, session, ci)¶

Access to the chado organism table

add_organism(genus, species, common, abbr, comment=None)¶

Add a new organism to the Chado database

Parameters:	genus (str) – The genus of the organism species (str) – The species of the organism common (str) – The common name of the organism abbr (str) – The abbreviation of the organism comment (str) – A comment / description
Return type:	dict
Returns:	Organism information

delete_all_organisms(confirm=False)¶

Delete all organisms

Parameters:	confirm (bool) – Confirm that you really do want to delete ALL of the organisms.
Return type:	None
Returns:	None

delete_organisms(organism_id=None, genus=None, species=None, common=None, abbr=None, comment=None)¶

Delete all organisms

Parameters:	organism_id (int) – organism_id filter genus (str) – genus filter species (str) – species filter common (str) – common filter abbr (str) – abbr filter comment (str) – comment filter
Return type:	None
Returns:	None

get_organisms(organism_id=None, genus=None, species=None, common=None, abbr=None, comment=None)¶

Get all or some organisms

Parameters:	organism_id (int) – organism_id filter genus (str) – genus filter species (str) – species filter common (str) – common filter abbr (str) – abbr filter comment (str) – comment filter
Return type:	list of dict
Returns:	Organisms information