aind-session 0.1.3

User-friendly tools for accessing paths, metadata and assets related to AIND sessions.

aind-session

User-friendly tools for accessing paths, metadata and assets related to AIND sessions.

Under development!

Please check this out and make feature requests, but don't rely on the API to remain stable just yet..

Aim

This package is meant to provide easy access to session-related stuff required for common tasks in CodeOcean and beyond.

• when interacting with the CodeOcean API, it uses and returns objects from the official Python library - we will avoid duplicating functionality provided by that package, except to make convenience functions with assumptions baked-in (for example, getting a client with environment variables and a default domain; finding all the assets for a particular session)
• the core Session class should have a minimal set of methods and attributes that are common to sessions from all platforms - it should be fast to initialize and not do unnecessary work
• extensions provide additional functionality (e.g. for specific modalities, metadata, databases) - at the moment, this is implemented via registration of namespaces (like Pandas), which allows for extending without subclassing
• when searching for session data or information, methods should be exhaustive: for example, as naming conventions change, this package should support current and previous versions of names
• when searching is unsuccessful, as much information as possible should be provided to the user via logging messages and exceptions, so they can understand the reasons for failure

Usage

User secrets

Credentials are required for:

• S3
  • using the "assumable role" in CodeOcean should suffice
  • alternatively, access keys as environment variables or in a config file will be found by boto3 (see docs)
• CodeOcean API
  • an access token is required with at least "Datasets - Read" scope:
    • see CodeOcean's docs on how to create a token
    • CODE_OCEAN_API_TOKEN is the preferred environment variable name
    • if not found, the first environment variable with a value starting COP_ is used (case-insensitive)
  • domain name defaults to https://codeocean.allenneuraldynamics.org, but can be overridden by setting CODE_OCEAN_DOMAIN

For development, environment variables can be provided in a .env file in the project root directory or the user's home directory.

Install

pip install aind_session

Python

>>> from aind_session import Session

# Common attributes available for all sessions:
>>> session = Session('ecephys_676909_2023-12-13_13-43-40')
>>> session.platform
'ecephys'
>>> session.subject_id
'676909'
>>> session.dt
datetime.datetime(2023, 12, 13, 13, 43, 40)
>>> session.raw_data_asset.id
'16d46411-540a-4122-b47f-8cb2a15d593a'
>>> session.raw_data_dir.as_posix()
's3://aind-ephys-data/ecephys_676909_2023-12-13_13-43-40'

# Additional functionality in namespace extensions:
>>> session.metadata.subject['genotype']
'Pvalb-IRES-Cre/wt;Ai32(RCL-ChR2(H134R)_EYFP)/wt'
>>> session.ecephys.sorted_data_asset.name
'ecephys_676909_2023-12-13_13-43-40_sorted_2024-03-01_16-02-45'

Development

See instructions in CONTRIBUTING.md and the original template