The gemma-client syntax to “register” a dataset stored within an external S3 bucket looks like this:
gemma-client register --no-verify --hostname <host> --no-warnings --username <user> <UUID> "<data_format>" <s3://path-to-dataset(s)> --screen-name <screen_name>
Where:
<host> is the IP or domain name of the SImA server
<user> is the SImA user account into which the data is to be imported
<UUID> is unique identifier for the screen (this would need to be manually inserted/created)
<data_format> is the file format being imported, e.g. “Columbus IDX/TIF”, “Harmony IDX/TIF”, etc.
<s3://path-to-dataset(s)> is the path to the dataset stored in an external S3 bucket
<screen_name> is the Screen name of the imported data set as it would appear in SImA
Real-World example:
gemma-client register --no-verify --hostname simaserver.com --username john $(uuidgen) "Columbus IDX/TIF" s3://imaging-sima-original/dataset-59a6dbee-c9bd-11ed-a2f7-02420a00011a/ --screen-name "MyScreen"
In the above example the Linux uuidgen program was used to generate the Screen UUID. The uuidgen program creates a new universally unique identifier (UUID) using the libuuid library. Similar UUID generators could be used when working with the gemma-client in a Windows environment.
Uploading on behalf of other users:
As of SImA v1.2 it is possible to use the admin user account to upload data on behalf of another user using the --owner-username parameter. In that case the syntax looks like this:
gemma-client register --no-verify --hostname <host> --no-warnings --username <admin_user> <UUID> "<data_format>" <s3://path-to-dataset(s)> --screen-name <screen_name> --owner-username <user_name>
Where the --owner-username parameter is used to pass the <user> account into which the data should be imported.
Real-World example:
gemma-client register --no-verify --hostname simaserver.com --username admin $(uuidgen) "Columbus IDX/TIF" s3://imaging-external-bucket/Dataset/ --screen-name "MyScreen" --owner-username john
In the above example the admin user registers the data on behalf of user john.
Note - data generated by SImA and/or stored in the SImA format is not currently supported by the registration tool.