Validating NWB filesΒΆ

Validating NWB files is handled by a command-line tool available in pynwb. The validator can be invoked like so:

python -m pynwb.validate test.nwb

This will validate the file test.nwb against the core NWB specification. In case of success the output looks like

Validating test.nwb against cached namespace information using namespace core.
 - no errors found.

and the program exit code is 0. On error the program exit code is 1 and the list of errors is outputted.

If possible the file is validated against the cached namespace specification read from the file itself. This can be tweaked with the command line options given below.

CURRENTLY BROKEN!!!

Validating against other specifications i.e. extensions can be done using the -p and -n flags. For example, the following command will validate against the specifications referenced in the namespace file mylab.namespace.yaml in addition to the core specification.

python -m pynwb.validate -p mylab.namespace.yaml test.nwb
$python -m pynwb.validate --help
usage: validate.py [-h] [-p NSPATH] [-n NS] [-lns]
                   [--cached-namespace | --no-cached-namespace]
                   paths [paths ...]

Validate an NWB file

positional arguments:
  paths                 NWB file paths

optional arguments:
  -h, --help            show this help message and exit
  -p NSPATH, --nspath NSPATH
                        the path to the namespace YAML file
  -n NS, --ns NS        the namespace to validate against
  -lns, --list-namespaces
                        List the available namespaces and exit.
  --cached-namespace    Use the cached namespace (default).
  --no-cached-namespace
                        Don't use the cached namespace.

use --nspath to validate against an extension. If --ns is not specified,
validate against all namespaces in namespace file.