Validating NWB files

Note

The pynwb validation CLI checks for structural compliance of NWB files with the NWB schema. It is recommended to use the NWBInspector CLI for more comprehensive validation of both structural compliance with the NWB schema and compliance of data with NWB best practices. The NWBInspector runs both PyNWB validation as described here and additional data checks.

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

pynwb-validate test.nwb

If the file contains no NWB extensions, then this command will validate the file test.nwb against the core NWB specification. On success, the output will be:

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 the file contains NWB extensions, then the above validation command will validate the file test.nwb against all extensions in the file and the core NWB specification.

To validate against only one NWB extension that is cached within the file, use the -n flag. For example, the following command will validate against the “ndx-my-extension” namespace that is cached within the test.nwb file.

pynwb-validate -n ndx-my-extension test.nwb

To validate against the version of the core NWB specification that is included with the installed version of PyNWB, use the --no-cached-namespace flag. This can be useful in validating files against newer or older versions of the core NWB specification that are installed with newer or older versions of PyNWB.

pynwb-validate --no-cached-namespace test.nwb

$pynwb-validate --help
usage: pynwb-validate [-h] [-lns] [-n NS] [--json-output-path JSON_OUTPUT_PATH] [--no-cached-namespace] paths [paths ...]

Validate an NWB file

positional arguments:
  paths                 NWB file paths

options:
  -h, --help            show this help message and exit
  -lns, --list-namespaces
                        List the available namespaces and exit.
  -n NS, --ns NS        the namespace to validate against
  --json-output-path JSON_OUTPUT_PATH
                        Write json output to this location.
  --no-cached-namespace
                        Use the namespaces installed by PyNWB (true) or use the cached namespaces (false; default).

If --ns is not specified, validate against all namespaces in the NWB file.

Validation against a namespace that is not cached within the schema is not currently possible but is a planned feature.