neurobank 0.11.1
Simple data management system for neuroscience
License: BSD 3-Clause License
Requires Python: >=3.8

neurobank
=========

|ProjectStatus|_ |Version|_ |BuildStatus|_ |License|_ |PythonVersions|_

.. |ProjectStatus| image:: https://www.repostatus.org/badges/latest/active.svg
.. _ProjectStatus: https://www.repostatus.org/#active

.. |Version| image:: https://img.shields.io/pypi/v/neurobank.svg
.. _Version: https://pypi.python.org/pypi/neurobank/

.. |BuildStatus| image:: https://github.com/melizalab/neurobank/actions/workflows/python_tests.yml/badge.svg
.. _BuildStatus: https://github.com/melizalab/neurobank/actions/workflows/python_tests.yml

.. |License| image:: https://img.shields.io/pypi/l/neurobank.svg
.. _License: https://opensource.org/license/bsd-3-clause/

.. |PythonVersions| image:: https://img.shields.io/pypi/pyversions/neurobank.svg
.. _PythonVersions: https://pypi.python.org/pypi/neurobank/

**neurobank** is the Meliza lab's data management system. It’s designed for
neural and behavioral data, but could be used for other kinds of
experiments. The software helps generate unique identifiers for
data resources, including stimuli, protocols, and recording units. No
more guessing what version of a stimulus you presented in an experiment,
where you stored an important recording, and whether you’ve backed it up
or archived it.

You can think of **neurobank** like git for your data. Every resource gets a
unique identifier and doesn't get changed once the identifier is assigned. This
provides you with the confidence that some stimulus "xyzzy" that you used in an
experiment in 2005 is the same as the one you used last week.

What are resources? Resources include *sources*, which are used to control an
experiment, and *data*, which result from running the experiment. Resources do
not include things that evolve, like code, figures, or manuscripts. These should
be managed in a version control system.

There are two components to the **neurobank** system. One part is the
**registry**, a service that stores identifiers, ensures they’re unique, and
resolves identifiers to the location where the resource is stored.
`django-neurobank <https://github.com/melizalab/django-neurobank>`__ is an
implementation of this service that uses a postgres backend and the django REST
framework. This package provides a simple python and commandline interface for
querying the registry.

The second component is an **archive**, a storage and retrieval mechanism, which
is also provided by this package. We keep our archives on a filesystem shared
over NFS to our local compute cluster for fast, filesystem-based access. These
archives have a simple directory structure with a little nesting so that you
don't have single directories filling up with hundreds of thousands of files.
This package also provides some mechanisms for moving older data to and from
cold storage on tape.

You can also use an external cloud-based service or a distributed filesystem
like `IPFS <https://ipfs.io/>`__, but for i/o-intensive pipelines you’ll want to
have your data on a local disk. 

Installation
------------

Install the **neurobank** Python package and its dependencies:

.. code:: bash

   pip install neurobank

Archive setup
-------------

First, initialize an archive:

.. code:: bash

   nbank [-a username:password] [-r registry-url] init [-n name] my-archive-path

``my-archive-path`` must be a directory on a locallly-accessible
filesystem (which could be an NFS or SSHFS mount).

``registry-url`` specifies the registry to use, which can be any service
that implements the API defined in
`django-neurobank <https://github.com/melizalab/django-neurobank>`__ can
be used. If not supplied, the script will try to use the value of the
environment variable ``NBANK_REGISTRY``. The registry URL also
determines the base URL for the resource identifiers. For example, if
the registry is at ``http://melizalab.org/neurobank/resources/`` and you
deposit a resource with the identifier ``st32_1_2_1``, the full
identifier is ``http://melizalab.org/neurobank/resources/st32_1_2_1/``.
``st32_1_2_1`` is guaranteed to be unique within this domain.

If your registry requires authentication, this must be supplied with the
``-a`` flag, or in your
`netrc <https://www.gnu.org/software/inetutils/manual/html_node/The-_002enetrc-file.html>`__
file.

The script will attempt to contact the registry service through the
supplied URL and add the archive. By default, the archive is named after
the basename of the archive path. For example,
``/home/data/intracellular`` would have the name ``intracellular``. You
can can override this behavior with the ``-n`` flag; however, the
registry may only allow you to have one archive name for each path to
avoid confusion. Then the script will create and initialize the archive
under ``my-archive-path``. You’ll get an error if the target directory
already exists, or if the registry already has an archive with the same
name.

Set archive policies
~~~~~~~~~~~~~~~~~~~~

Edit the ``README.md`` and ``nbank.json`` files created in the archive
directory to describe your project. The ``nbank.json`` file is also
where you’ll need to set some key variables and policies. These are the
settings you may want to modify:

-  ``auto_identifiers``: If set to false (the default), when files are deposited, their names are used as identifiers unless the user asks for an automatically generated id. If set to true, every resource is given an automatic id.
- ``auto_id_type``: If set to ``null`` (or not set at all), automatic ids are assigned by the registry. This is usually a short, random base-36 string. If set to ``"uuid"``, the ``nbank`` script will generate 128-bit UUIDs as identifiers, which are guaranteed to work everywhere but a little painful to manipulate by hand.
-  ``require_hash``: If set to true (the default), every resource will have a hash value calculated and stored in the registry. The registry will then be able to prevent duplicate files from being deposited under multiple identifiers.
   - ``keep_extensions``: If set to true (the default), files keep their extensions when deposited. Only one file with a given base identifier can be deposited, so if you have a ``st32_1_2_1.wav``, the identifier is ``st32_1_2_1``, and therefore you can’t also have an ``st32_1_2_1.json`` file. If set to false, the extension is stripped, so ``st32_1_2_1.wav`` would be deposited as ``st32_1_2_1``. Usually you want this to be true, unless your archive only contains one kind of file.
   -  ``allow_directories``: If set to true, directories and their contents can be deposited as resources. The identifier is given to the directory, and the user is responsible for knowing how to interpret the contents. If set to false (the default), only regular files can be deposited.
   -  ``access``: Specify the ``user`` and ``group`` who will own deposited files, and the ``umask`` to modify access mode. If these are not set, files will be owned by the user who deposited them.

Registering and storing resources
---------------------------------

Before you start an experiment, register all the resources you plan to
use. For example, let’s say you’re presenting a set of acoustic stimuli
to an animal while recording neural responses. To register the stimuli:

.. code:: bash

   nbank [-a user:pass] deposit [options] my-archive-path stimfile-1 stimfile-2 ...

Each stimulus will be given an identifier and moved to the archive. The
command will output a JSON-encoded list of the resources that were
deposited, including a mapping from the identifiers to the old
filenames, if automatic identifiers were used.

The ``deposit`` command takes several options:

-  ``-d, --dtype``: specify the datatype for the deposited resources.
   Your registry may require this.
-  ``-k``: specify a metadata key-value pair. You can use this flag
   multiple times to set multiple fields.
-  ``-H, --hash``: if set, ``nbank`` will calculate a SHA1 hash of each
   file and store it in the registry. Use this if you expect the
   contents of the file to be unique.
-  ``-A, --auto-id``: if set, ``nbank`` will ask the registry to assign
   each file an automatically generated identifier, overriding the
   ``auto_identifiers`` policy if it is set to false.
-  ``-j, --json-out``: if set, the script will output info about each
   deposited file as line-deliminated JSON

Now run your experiment, making sure to record the identifiers of the stimuli.
The short identifier suffices in most cases, but make sure you record the
registry URL somewhere, too. If you're running the experiment on machine that
doesn't have direct access to the archive, you can use the ``nbank fetch`` command
on the experiment machine to retrieve the resources.

After the experiment, deposit the data files into the archive using the
same command. If you deposit containers or directories, you’re
responsible for organizing the contents and assigning any internal
identifiers.

Resource datatypes
~~~~~~~~~~~~~~~~~~

Depending on your registry implementation, you may be required to
specify a datatype for each deposited resource. This feature allows a
single registry to store information about different kinds of resources.
Each datatype has a name and a MIME content-type. Content-types can be
from the `official
list <https://www.iana.org/assignments/media-types/media-types.xhtml>`__,
or they can be user-defined, like the content-type for
`pprox <https://meliza.org/spec:2/pprox/>`__. You can get a list of the
known datatypes with

.. code:: bash

   nbank [-r registry-url] dtype list

You may be able to add datatypes to the registry with:

.. code:: bash

   nbank [-a user:pass] [-r registry-url] dtype add dtype-name content-type

Retrieving resources
--------------------

The ``deposit`` command moves resource files to the archive under the
``resources`` directory, so you can always manually locate your files
based on the identifier. Resources are sorted into subdirectories using
the first two characters of the identifier to avoid having too many
files in one directory. For example, if the identifier is
``edd0ccae-c34c-48cb-b515-a5e6f9ed91bc``, you’ll find the file under
``resources/ed``.

``nbank`` also acts as a command-line interface to the registry. You can
perform the following operations:

- ``nbank locate [options] id-1 [id-2 [id-3] ...]``: look up the location(s) of the resources associated with each identifier. You can supply full URL-based identifiers, or short ids. If short ids are used, the default registry (specified with ``-r`` argument or ``NBANK_REGISTRY`` environment variable) is used to resolve the full URL. Use the ``-L`` flag to create symbolic links or the ``-0`` flag to pipe the paths to another program.
-  ``nbank info id``: returns the registry information on the resource in json format.
-  ``nbank search [options] query``: searches the database for resources that match ``query``. The default is to search by identifier, but you can also search by hash, dtype, archive, or any metadata fields. The default is to return only the identifiers of the resources, but you can use the ``-j`` flag to output json instead, which is useful if you want to distribute the metadata with the archive.
-  ``nbank verify [options] files``: computes a SHA1 hash for each file and searches the registry for a match. Running this is a good idea before starting an experiment, as you’ll be able to tell if any of your stimulus files have changed. It’s also useful if the same identifier is used in more than one domain or if you have a data file that was inadvertently renamed.
-  ``nbank modify [-k key=value] id``: update the metadata for ``id``. Multiple ``-k`` flags can be used.

Managing archives
-----------------

You can check whether an archive contains all the files it's supposed to by running ``nbank archive check <path_to_archive>``. This command will compare each resource in the archive to its record in the registry and provide a summary of any resources missing from the archive and files that don't have matches in the registry (which might indicate corrupted data).

Some resources, like raw extracellular data, can be moved to cold storage when they are no longer needed. The Meliza lab uses tape for this because of its long shelf life, low cost, and low environmental impact (no need for power). Moving resources to cold storage is a multi-step process:

- Identify the resources to archive, using lists of identifiers from project directories or ``nbank search``.
- Copy the resource files to a tar file. For example, ``cat <list_of_identifiers> | xargs nbank locate -0 | xargs -0 tar -cvf <name_of_tar_file>``
- Write the tar file to tape (or some other media)
- Register the tar file with neurobank using ``nbank archive register-tar -n <name_of_archive> <name_of_tape> <tape_index> <tar_file>``. This will create a record for the tape archive and update the records for the resources in the tar file.
- To remove the tape-archived resources from live storage, run ``nbank archive prune <live_archive_name> <list_of_identifiers>``. This command will delete files from the local filesystem archive and update records for the resources. It will only do this for resources that have another location.
- To copy data back to live storage, extract the tar file from the tape and run ``nbank archive import-tar <tar_file> <path_of_archive>``

Development
-----------

Recommend using `uv <https://docs.astral.sh/uv/>`__ for development.

Run ``uv sync`` to create a virtual environment and install
dependencies. ``uv sync --no-dev --frozen`` for deployment.

Testing: ``uv run pytest``

Python interface
----------------

To be written

Best Practices
--------------

See `docs/examples <docs/examples.md>`__ for some additional notes on
how the Meliza Lab uses neurobank.

Controlling access
~~~~~~~~~~~~~~~~~~

One of the primary uses for neurobank is to allow multiple users to
share a common set of data, thereby reducing the need for temporary
copies and ensuring that a canonical, centralized backup of critical
data can be maintained. In this case, the following practices are
suggested for POSIX operating systems:

1. For each project, create a separate group and make the archive owned
   by the group. To give a user access to the data, add them to the
   group.
2. To restrict access to users not in the project group, set your umask
   to 027 before creating the archive.
3. Set the setgid (or setuid) bit on the subdirectories of the archive,
   so that files added to the archive become owned by the group.
   (``chmod 2770 resources metadata``). You may also consider setting
   the sticky bit so that files and directories can’t be accidentally
   deleted.
4. If your filesystem supports it, set the default ACL on subdirectories
   so that added files are accessible only to the group.
   (``setfacl -d -m u::rwx,g::rwx,o::- resources metadata``).

License
-------

**neurobank** is licensed under the GNU Public License, version 2. That
means you are free to use the code for anything you want, including a
commerical work, but you have to provide the source code, including any
modifications you make. You still own your data files and any associated
metadata. See COPYING for more details.