In c302 (https://github.com/openworm/CElegansNeuroML/tree/master/CElegans/pythonScripts/c302) reads each connection in excel file, generates .nml file for the pair of neurons and tests if the connection exists as stated in the excel file. Uses parameters_B which are still under development (OpenWorm)

c302_connection_test_B.py

import os

import sys
sys.path.append("..")
import SpreadsheetDataReader

from c302 import generate
import parameters_B as params

import neuroml.loaders as loaders

import unittest


class DataIntegrityTest(unittest.TestCase):

    def setUp(self):

        # read data from spread sheet
        self.cell_names, self.conns = SpreadsheetDataReader.readDataFromSpreadsheet(
            "../../../")
        print len(self.cell_names)

        # generate all nml files once
        self.checked_files = []
        counter = 0
        # self.specify_early_stop = 4     # early stopping
        # early_stop = self.specify_early_stop     # early stopping
        for index in self.conns:
            # if early_stop == 0:  # early stopping
            #     break  # and this

            origin = index.pre_cell
            target = index.post_cell

            fn = origin+"_"+target
            fnswap = target+"_"+origin

            if fn not in self.checked_files:
                if fnswap not in self.checked_files:
                    # generate xml and nml file
                    cells_to_plot = "["+origin+","+target+"]"
                    cells_to_stimulate = "["+origin+"]"

                    generate(fn, params, cells=cells_to_plot, cells_to_stimulate=cells_to_stimulate,            duration=500, validate=False)
                    # bashCommand = 'python c302.py '+fn+' parameters_A -cells '+cells_to_plot+' -cellstostimulate '+cells_to_stimulate+' -duration 500'
                    # os.system(bashCommand)

                    self.checked_files.append(fn)
                    counter += 1

            # early_stop -= 1         # early stopping
        print "Total files generated %i"%counter

    def test_c302_connections(self):

        # test each connection pair from the excel file
        # early_stop = self.specify_early_stop         # early stopping
        counter = 0
        for index in self.conns:

            # if early_stop == 0:  # early stopping
            #     break  # and this

            origin = index.pre_cell
            target = index.post_cell
            num = index.number
            synclass = index.synclass

            fn = origin+"_"+target
            fnswap = target+"_"+origin
            gap_junction = True

            if '_GJ' in synclass:
                test_id = 'NC_'+origin+'_'+target+'_'+synclass
                test_synapse = 'elec_syn_'+str(num)+'conns'
            elif 'GABA' in synclass:
                from_cell = origin+'[0]'
                to_cell = target+'[0]'
                test_synapse = 'inh_syn_'+str(num)+'conns'
                gap_junction = False
            else:
                from_cell = origin+'[0]'
                to_cell = target+'[0]'
                test_synapse = 'exc_syn_'+str(num)+'conns'
                gap_junction = False

            if fn in self.checked_files:
                nml_file = fn+'.nml'
            elif fnswap in self.checked_files:
                nml_file = fnswap+'.nml'
            else:
                print "File not found"

            doc = loaders.NeuroMLLoader.load(nml_file)
            print("Loaded NML file from: "+nml_file)

            synaptic_conn_list = doc.networks[0].synaptic_connections
            electrical_proj_list = doc.networks[0].electrical_projections

            # test if any connections exist
            flag = True if synaptic_conn_list or electrical_proj_list else False
            self.assertTrue(flag, 'Connection lists are empty for %s'+nml_file)

            # for Gap Junctions

            if gap_junction and electrical_proj_list:
                electrical_proj_test_list = []

                electrical_proj_test_list = [(connection.id, connection.electrical_connections[0].synapse) for connection in electrical_proj_list]

                print electrical_proj_test_list

               # test if this particular connection exists
                test_pair = (test_id, test_synapse)
                print test_pair
                self.assertIn(test_pair, electrical_proj_test_list, "connection not found")

            # for Synaptic Connections

            if not(gap_junction) and synaptic_conn_list:
                synaptic_conn_test_list = []

                synaptic_conn_test_list = [(connection.to, connection.from_, connection.synapse) for connection in synaptic_conn_list]

                print synaptic_conn_test_list

               # test if this particular connection exists
                test_pair = (to_cell, from_cell, test_synapse)
                print test_pair
                self.assertIn(test_pair, synaptic_conn_test_list, "connection not found")

            counter += 1

            # early_stop -= 1         # early stopping
        print "Total connections verified %i"%counter

    def tearDown(self):
        print "Cleaning up .. "
        for name in self.checked_files:
            bashCommand = "rm "+name+".nml "+"LEMS_"+name+".xml"
            os.system(bashCommand)

if __name__ == '__main__':
    unittest.main()