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.