tripal.organism package¶
Module contents¶
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class
tripal.organism.
OrganismClient
(tripalinstance, **requestArgs)¶ Bases:
tripal.client.Client
Manage Tripal organisms
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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
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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
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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
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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
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get_taxonomic_ranks
()¶ Get taxonomic ranks
Return type: list of dict Returns: Taxonomic ranks
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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
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