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neurobank is a simple data management system. It’s designed for neural and behavioral data, but could be used for other kinds of experiments. The software helps you generate unique identifiers for your 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.
The data management strategy behind neurobank is simple: every resource gets a unique identifier. 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.
The second component is an archive: a storage and retrieval
mechanism. That’s this package, which provides a basic filesystem-based
archive for your resources. 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. This package also provides a simple python and commandline
interface for querying the registry.
Install the neurobank Python package and its dependencies:
.. code:: bash
pip install neurobank
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.
- ``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 you can’t 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.
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 datatypesDepending 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
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.
nbank properties [options] id: queries the registry for all the
properties associated with id
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.
To be written
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.