tripal.organism package¶

Module contents¶

class tripal.organism.OrganismClient(tripalinstance, **requestArgs)¶

Manage Tripal organisms

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

Add a new organism to the 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 infraspecific_rank (str) – The type name of infraspecific name for any taxon below the rank of species. Must be one of [‘subspecies’, ‘varietas’, ‘subvariety’, ‘forma’, ‘subforma’] infraspecific_name (str) – The infraspecific name for this organism.
Return type:	dict
Returns:	Organism information

delete_orphans(job_name=None, no_wait=None)¶

Delete orphans Drupal organism nodes

Parameters:	job_name (str) – Name of the job no_wait (bool) – Return immediately without waiting for job completion
Return type:	str
Returns:	status

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

Get organisms from chado table

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

get_organisms_tripal(organism_id=None)¶

Get organism entities

Parameters:	organism_id (int) – An organism entity ID
Return type:	list of dict
Returns:	Organism entity information

get_taxonomic_ranks()¶

Get taxonomic ranks

Return type:	list of dict
Returns:	Taxonomic ranks

sync(organism=None, organism_id=None, job_name=None, no_wait=None)¶

Synchronize an organism

Parameters:	organism (str) – Common name of the organism to sync organism_id (str) – ID of the organism to sync job_name (str) – Name of the job no_wait (bool) – Return immediately without waiting for job completion
Return type:	str
Returns:	status