apollo.organisms package

Module contents

Contains possible interactions with the Apollo Organisms Module

class apollo.organisms.OrganismsClient(webapolloinstance, **requestArgs)

Bases: apollo.client.Client

CLIENT_BASE = '/organism/'
add_organism(common_name, directory, blatdb=None, genus=None, species=None, public=False, metadata=None, suppress_output=False)

Add an organism

Parameters:
  • common_name (str) – Organism common name
  • directory (str) – Server-side directory
  • blatdb (str) – Server-side path to 2bit index of the genome for Blat
  • genus (str) – Genus
  • species (str) – Species
  • public (bool) – Should the organism be public or not
  • metadata (str) – JSON formatted arbitrary metadata
  • suppress_output (bool) – Suppress output of all organisms (true / false) (default false)
Return type:

dict
Returns:

a dictionary with information about the new organism
delete_features(organism_id)

Remove features of an organism

Parameters:organism_id (str) – Organism ID Number
Return type:dict
Returns:an empty dictionary
delete_organism(organism_id, suppress_output=False)

Delete an organism

Parameters:
  • organism_id (str) – Organism ID Number
  • suppress_output (bool) – Suppress return of all organisms (true / false) (default false)
Return type:

list
Returns:

A list of all remaining organisms
get_organism_creator(organism_id)

Get the creator of an organism

Parameters:organism_id (str) – Organism ID Number
Return type:dict
Returns:a dictionary containing user information
get_organisms(common_name=None)

Get all organisms

Parameters:common_name (str) – Optionally filter on common name
Return type:list
Returns:Organism information
get_sequences(organism_id)

Get the sequences for an organism

Parameters:organism_id (str) – Organism ID Number
Return type:list of dict
Returns:The set of sequences associated with an organism
show_organism(common_name)

Get information about a specific organism.

Parameters:common_name (str) – Organism Common Name
Return type:dict
Returns:a dictionary containing the organism’s information
update_metadata(organism_id, metadata)

Update the metadata for an existing organism.

Parameters:
  • organism_id (str) – Organism ID Number
  • metadata (str) – Organism metadata. (Recommendation: use a structured format like JSON)
Return type:

dict
Returns:

An empty, useless dictionary
update_organism(organism_id, common_name, directory, blatdb=None, species=None, genus=None, public=False, no_reload_sequences=False, suppress_output=False)

Update an organism

Parameters:
  • organism_id (str) – Organism ID Number
  • common_name (str) – Organism common name
  • directory (str) – Server-side directory
  • blatdb (str) – Server-side Blat directory for the organism
  • genus (str) – Genus
  • species (str) – Species
  • public (bool) – User’s email
  • no_reload_sequences (bool) – Set this if you don’t want Apollo to reload genome sequences (no change in genome sequence)
  • suppress_output (bool) – Suppress output of all organisms (true / false) (default false)
Return type:

dict
Returns:

a dictionary with information about the updated organism