Uploading using BaseSpace
Setting up Automated imports from BaseSpace¶
If a BaseSpace social connection is present for a user and there are adequate permissions for
importing from BaseSpace, an automated import can be set up.
It runs periodically and parses BaseSpace for the projects created in the last day whose names
contain the identifier. Biosamples from those BaseSpace projects are imported into Gencove
project to be run there.
Note
identifier is used as a search argument for BaseSpace projects. Any project name that
contains the identifier is returned. Letter case is ignored.
Identifier "cattle" will match BaseSpace project names like "Our cattle 1" and "Cattle New", but it won't match "Corn".
Listing autoimport jobs¶
Available autoimport jobs for a user can be listed using the
gencove basespace autoimports list command.
Creating an autoimport job¶
A new autoimport job can be created using the gencove basespace autoimports create command.
To assign the sample metadata for each sample set up to be imported this way --metadata-json can be used.
$ gencove basespace autoimports create <project-id> identifier-in-basespace-project-name --metadata-json '{"example-key": "example-value"}'
Note
When autoimport job is first created, it is immediately run. Afterwards it will periodically check if a new BaseSpace project with name containing the identifier is added in the last day and import the Biosamples according to the autoimport instructions.