A tool for cleaning up external DataJoint stores
DataJoint-Cleaner is a tool used to clean external DataJoint stores.
How It Works
The user provides information pointing to a particular external table and external store combination. Using this information DataJoint-Cleaner will delete all objects in the external store that have no corresponding entry in the external table, thus freeing storage space.
The creation of a backup is highly recommended before using DataJoint-Cleaner to avoid a potential loss of data due to an user error or a bug.
DataJoint-Cleaner should not be used to clean external stores that are used by multiple database servers or multiple storage protocols (e.g. file & s3). If done so it could potentially delete objects that are still referenced in the database.
Recommended installation method
To avoid messing up the system Python environment, the most recommended way to install DataJoint-Cleaner is via pipx:
pipx install datajoint-cleaner
Other installation methods
Install DataJoint-Cleaner into user site with
pip install --user datajoint-cleaner
DataJoint-Cleaner will look for a TOML file called
datajoint-cleaner.toml in the current working directory (by default) to configure itself. The configuration file must have two top-level tables called
storage_servers and an array of tables called
Specifying Database Servers
Database servers are specified in the top-level
database_servers table. Each key in the table corresponds to a distinct database server. The value of each key must be a table that contains the following keys:
The values of the
password keys correspond to the host name of the database server, the name of a user present on said server and the password of said user, respectively.
[database_servers.my_db_server] host = "184.108.40.206" user = "me" password = "mypassword"
Specifying Storage Servers
Storage servers are specified in a sub-table of the
storage_servers table based on their kind. Currently only MinIO servers are supported which are specified in the
minio sub table. The keys necessary to specify a MinIO server are
The values of these keys correspond to the endpoint of the MinIO server, your access and private key and whether a secure connection should be established or not, respectively.
[storage_servers.minio.my_minio_server] endpoint = "192.543.5.61" access_key = "my_access_key" secret_key = "my_secret_key" secure = true
Specifying Cleaning Runs
Individual cleaning runs are specified in the top-level array of tables called
cleaning_runs. Each table in the array corresponds to a distinct cleaning run and must have the following keys:
database_server: Name of a database server specified in the
schema: Name of a schema on said database server
store: Name of a DataJoint store for which an external table exists in said schema
storage_server: A storage server specified in the
storage_serverstable in the
bucket: Name of a bucket on said MinIO server
location: Location of externally stored objects in said bucket
[[cleaning_runs]] database_server = "my_db_server" schema = "my_schema" store = "my_store" storage_server = "minio.my_minio_server" bucket = "my_bucket" location = "my_location"
The cleaning process can be started like so:
The command above will execute all cleaning runs defined in the configuration file. The
--config-file option can be used to pass a custom path to a configuration file to DataJoint-Cleaner:
dj-cleaner --config-file /path/to/config/file
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