Note for Docker users
The export commands will need to run inside the container, perhaps
dcanto shell function.
Exporting to JSON
The curation data can be exported in JSON
format with the
canto_export.pl script from the
script directory. This
JSON file can then be loaded into a Chado database (see below).
To export the data from sessions that have been "approved" by the administrators using the admin interface use:
script/canto_export.pl canto-json --dump-approved > canto_approved.json
(From the canto top level directory).
If you use the flag
--export-approved instead of
exported sessions with be marked as "EXPORTED" in the Canto database. These
sessions won't be exported next time. This option is provided so that
annotation will be exported only once from Canto.
To export the data from all the sessions, regardless of its state use:
script/canto_export.pl canto-json --all > canto_all.json
Reading Canto data into Chado
./script/pombase-import.pl load-config-example.yaml canto --organism-taxonid=4896 \ --db-prefix=PomBase $HOST DB_NAME $USER $PASSWORD < canto_approved.json
PASSWORD are the details of your local
pombase-import.pl command will never delete or alter existing data it
only adds annotation.
To test loading without modifying the Chado database, add the
--dry-run option to the command line.