Install & setup¶

Installation¶

pyversions

pip install lamindb

You can configure the installation using extras, e.g.,

pip install 'lamindb[jupyter,bionty]'

Supported extras are:

# commonly used
jupyter   # parse Jupyter notebook metadata
bionty    # basic biological ontologies
# cloud backends (AWS is assumed)
gcp       # Google Cloud (gcfs, etc.)
# biological artifact formats
fcs       # FCS artifacts (flow cytometry)
# storage backends
zarr      # store & stream arrays with zarr

If you’d like to install from GitHub, see here.

If you’d like a docker container, here is a way: github.com/laminlabs/lamindb-docker.

Sign up & log in¶

Sign up for a free account (see more info) and copy the API key.
Log in on the command line:
```
lamin login
```
You will be prompted for your API key. You can create your API key in your account settings on LaminHub.

Note

An account is free & signing up takes 1 min.

Through signing up, Lamin does not store or see any of your data, but only basic metadata about you (email address, etc.).

If you register a LaminDB instance to LaminHub, we store metadata about the involved infrastructure (database server, storage locations, etc.). But we don’t store any secrets when you call lamin init and can’t see your data or metadata. If you want to connect your instance to LaminHub for exploration with read-write access: please reach out.

For more, see doc, the source code, or the privacy policy.

On the command line, you can log in with your handle if you have a cached API-key:

lamin login testuser1

Log out:

lamin logout

Init an instance¶

Initialize an instance using lamin init on the commmand line and these options:

storage: a default storage location for the instance (e.g. s3://my-bucket, gs://my-bucket, ./my-data-dir)
name (optional): a name for the instance (e.g., my-assets)
db (optional): a Postgres database connection URL, do not pass for SQLite
schema (optional): comma-separated string of schema modules

If you are only interested in tracking artifacts and their transformations, init your local SQLite instance via:

lamin init --storage ./mydata

Mount the Bionty schema module:

lamin init --storage mydata --schema bionty

You can also pass an AWS S3 bucket.

lamin init --storage s3://<bucket_name> --schema bionty

Instead of SQLite, you can pass a Postgres connection string.

lamin init --storage gs://<bucket_name> --db postgresql://<user>:<pwd>@<hostname>:<port>/<dbname> --schema bionty

Connecting to an instance¶

Connect to your own instance:

lamin connect <instance_name>

Connect to somebody else’s instance:

lamin connect <account_handle/instance_name>

Access settings¶

Now, let’s look at a specific example:

!lamin init --storage mydata --schema bionty

→ connected lamindb: testuser1/mydata

Print settings:

!lamin settings

Configure: see `lamin settings --help`
Current user: testuser1
- handle: testuser1
- email: [email protected]
- uid: DzTjkKse
Auto-connect in Python: True
Private Django API: True
Cache directory: /home/runner/.cache/lamindb
Current instance: testuser1/mydata
- owner: testuser1
- name: mydata
- storage root: /home/runner/work/lamindb/lamindb/docs/mydata
- storage region: None
- db: sqlite:////home/runner/work/lamindb/lamindb/docs/mydata/bad64064a38a5d18ae1654872904d661.lndb
- schema: {'bionty'}
- git_repo: None

Settings persist in ~/.lamin/ and can also be accessed via lamindb.setup.settings.

The settings directory can also be configured using LAMIN_SETTINGS_DIR environment variable.

import lamindb as ln

→ connected lamindb: testuser1/mydata

ln.setup.settings.user

Current user: testuser1
- handle: testuser1
- email: [email protected]
- uid: DzTjkKse

ln.setup.settings.instance

Current instance: testuser1/mydata
- owner: testuser1
- name: mydata
- storage root: /home/runner/work/lamindb/lamindb/docs/mydata
- storage region: None
- db: sqlite:////home/runner/work/lamindb/lamindb/docs/mydata/bad64064a38a5d18ae1654872904d661.lndb
- schema: {'bionty'}
- git_repo: None

Note

The user who creates an instance is its owner. Ownership can be transferred in the hub.
Advanced users could also consider the Python setup API: lamindb.setup.

Update the default storage¶

It’s easiest to see and update the default storage for the current Python session in the Python API using storage:

import lamindb as ln
ln.settings.storage  # set via ln.settings.storage = "s3://other-bucket"
#> s3://default-bucket

Manage cache¶

lamindb mantains cache for cloud instances, i.e. instances having storage set to an AWS S3 bucket.

Cache directory can be accessed via lamindb.settings.

ln.settings.cache_dir

PosixUPath('/home/runner/.cache/lamindb')

or print the cache directory path with CLI

!lamin cache get

The cache directory is /home/runner/.cache/lamindb

It can be also configured via

lamin cache set some/path/to/cache

Cache directory can also be set using LAMIN_CACHE_DIR environment variable.

Dsiconnect from an instance¶

Connecting to an instance means loading an environment for managing your data.

When connecting to a new instance, you automatically disconnect from the previously connected instance.

If you want to disconnect from the instance without connecting to a new instance, use lamin disconnect

Migrate an instance¶

If you are an admin and you haven’t set up automated deployments of migrations, you can use two commands to create and deploy migrations:

lamin migrate create
lamin migrate deploy

Unless you manage a custom plugin schema, you’ll never need to create a migration.

You’ll receive a logged warning when deploying a migration is advisable.

Create a migration¶

You need to have the schema package installed locally:

git clone https://github.com/my-org/lnschema-custom
cd lnschema-custom
pip install -e .

Edit the registries in your schema.

Then, call

lamin migrate create

to create the migration script.

When you’re happy, commit them to your GitHub repo, and ideally make a new release.

To deploy the migration call lamin migrate deploy.

Note

The lamin migration commands are a wrapper around Django’s migration manager.

Delete an instance¶

This works as follows. It won’t delete your data, just the metadata managed by LaminDB:

!lamin delete --force mydata

• deleting instance testuser1/mydata