organism¶
This section is auto-generated from the help text for the tripaille command
organism
.
add_organism
command¶
Usage:
tripaille organism add_organism [OPTIONS] GENUS SPECIES
Help
Add a new organism to the database
Output
Organism information
Options:
--common TEXT The common name of the organism
--abbr TEXT The abbreviation of the organism
--comment TEXT A comment / description
--infraspecific_rank TEXT 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 TEXT The infraspecific name for this organism.
-h, --help Show this message and exit.
delete_orphans
command¶
Usage:
tripaille organism delete_orphans [OPTIONS]
Help
Delete orphans Drupal organism nodes
Output
status
Options:
--job_name TEXT Name of the job
--no_wait Return immediately without waiting for job completion
-h, --help Show this message and exit.
get_organisms
command¶
Usage:
tripaille organism get_organisms [OPTIONS]
Help
Get organisms from chado table
Output
Organism information
Options:
--organism_id TEXT An organism ID
--genus TEXT The genus of the organism
--species TEXT The species of the organism
--common TEXT The common name of the organism
--abbr TEXT The abbreviation of the organism
--comment TEXT A comment / description
-h, --help Show this message and exit.
get_organisms_tripal
command¶
Usage:
tripaille organism get_organisms_tripal [OPTIONS]
Help
Get organism entities
Output
Organism entity information
Options:
--organism_id INTEGER An organism entity ID
-h, --help Show this message and exit.
get_taxonomic_ranks
command¶
Usage:
tripaille organism get_taxonomic_ranks [OPTIONS]
Help
Get taxonomic ranks
Output
Taxonomic ranks
Options:
-h, --help Show this message and exit.
sync
command¶
Usage:
tripaille organism sync [OPTIONS]
Help
Synchronize an organism
Output
status
Options:
--organism TEXT Common name of the organism to sync
--organism_id TEXT ID of the organism to sync
--job_name TEXT Name of the job
--no_wait Return immediately without waiting for job completion
-h, --help Show this message and exit.