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Tools to fetch and update paths, metadata and state for Mindscope Neuropixels sessions, in the cloud.

Project description

npc_lims

neuropixels cloud lab information management system Tools to fetch and update paths, metadata and state for Mindscope Neuropixels sessions, in the cloud.

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quickstart

  • make a new Python >=3.9 virtual environment with conda or venv (lighter option, since this package does not require pandas, numpy etc.):

    python -m venv .venv
    
  • activate the virtual environment:

    • Windows
    .venv\scripts\activate
    
    • Unix
    source .venv/bin/activate.sh
    
  • install the package:

    python -m pip install npc_lims
    
  • setup credentials

    • required environment variables:
      • AWS S3
        • AWS_DEFAULT_REGION
        • AWS_ACCESS_KEY_ID
        • AWS_SECRET_ACCESS_KEY
        • to find and read files on S3
        • must have read access on relevant aind buckets
        • can be in a standard ~/.aws location, as used by AWS CLI or boto3
      • CodeOcean API
        • CODE_OCEAN_API_TOKEN
        • CODE_OCEAN_DOMAIN
        • to find processed data in "data assets" via the Codeocean API
        • generated in CodeOcean:
          • right click on Account (bottom left, person icon)
          • click User Secrets - these are secrets than can be made available as environment variables in CodeOcean capsules
          • go to Access Tokens and click Generate new token - this is for programatically querying CodeOcean's databases
            • in Token Name enter Codeocean API (read) and check read on capsules and datasets
            • a token will be generated: click copy (storing it in a password manager, if you use one)
          • head back to User Secrets where we'll paste it into a new secret via Add secret > API credentials - in description enter Codeocean API (read) - in API key enter CODE_OCEAN_API_KEY - in API secret paste the copied secret from before (should start with cop_...) CODE_OCEAN_DOMAIN is the codeocean https address, up to and including .org
    • environment variables can also be specified in a file named .env in the current working directory
  • now in Python we can find sessions that are available to work with:

        >>> import npc_lims;
    
    # get a sequence of `SessionInfo` dataclass instances, one per session:
        >>> tracked_sessions: tuple[npc_lims.SessionInfo, ...] = npc_lims.get_session_info()
    
    # each `SessionInfo` instance has minimal metadata about its session:
        >>> tracked_sessions[0]                 # doctest: +SKIP
        npc_lims.SessionInfo(id='626791_2022-08-15', subject=626791, date='2022-08-15', idx=0, project='DRPilotSession', is_ephys=True, is_sync=True, allen_path=PosixUPath('//allen/programs/mindscope/workgroups/dynamicrouting/PilotEphys/Task 2 pilot/DRpilot_626791_20220815'))
            >>> tracked_sessions[0].is_ephys        # doctest: +SKIP
        False
    
    # currently, we're only tracking behavior and ephys sessions that use variants of https://github.com/samgale/DynamicRoutingTask/blob/main/TaskControl.py:
        >>> all(s.date.year >= 2022 for s in tracked_sessions)
        True
    
  • "tracked sessions" are discovered via 3 routes:

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