test_compatibility.py

'''
A test script to quickly check the compatibility of NWB files with NWB Explorer

See https://github.com/MetaCell/nwb-explorer/issues/293

'''

import sys
import pynwb
from pynwb import NWBHDF5IO


def test_compatibility(nwb_file):
    print("-------------------------------------------------------")

    print("NWB file to be examined:", nwb_file)

    metadata_list = ['institution', 'lab', 'experimenter', 'experiment_description','modules', 'acquisition']

    io = NWBHDF5IO(nwb_file, mode="r")
    nwbfile = io.read()

    # get pynwb info
    notes = getattr(nwbfile,'notes')
    # if field is not None
    if bool(notes):
        # print file's pynwb info
        print('Info:"\t %s' % (notes))
        # print explorer's pynwb info
        print('pynwb version: %s' % (pynwb.__version__))
        # split notes to get pynwb ver elements
        notes_str = notes.split()
        # get file's pynwb version to match with explorer's version
        pynwb_file_ver = notes_str[notes_str.index('pynwb')+1]
        pynwb_explorer_ver = 'v'+str(pynwb.__version__)
        if pynwb_file_ver == pynwb_explorer_ver:
            print('pynwb versions match')
        else:
            print('pynbw versions do not match - potential file loading failure')
    else:
        print('No information present in file on pynwb version')

    # print other information
    for meta_ind in metadata_list:
        # get attribute from nwbfile
        metadata = getattr(nwbfile,meta_ind)
        if bool(metadata):
            # get number of acquisition timeseries
            if meta_ind =='acquisition':
                print('Field: acquisition (number):\t %s' % (len(metadata)))
            else:
                if type(metadata) == tuple:
                    metadata = ', '.join(metadata)
                md = str(metadata).replace('\n','\n\t\t\t   ')
                print('Field:\t%s:\t %s' % (meta_ind,md))

    print("-------------------------------------------------------")

if __name__ == "__main__":

    if len(sys.argv)==1:
        print('Please specify the NWB file to be tested')
        exit()

    test_compatibility(str(sys.argv[1]))