addTriplesToRdfFile.py

import csv
import time
import datetime
import argparse
from rdflib import Graph
from rdflib.namespace import DC, SKOS
from rdflib import URIRef, Literal
from rdflib.plugins.sparql import prepareQuery
import os

parser = argparse.ArgumentParser()
parser.add_argument('-r', '--rdfFileName', help='the RDF file to which triples \
will be added (include the extension). optional - if not provided, the script \
will ask for input')
parser.add_argument('-f', '--fileName', help='the CSV file of new triples \
(including \'.csv\'). optional - if not provided, the script will ask for \
input')
parser.add_argument('-d', '--directory', help='the directory for the input and \
output files. optional - if not provided, the script will assume null')
args = parser.parse_args()

if args.rdfFileName:
    rdfFileName = args.rdfFileName
else:
    rdfFileName = input('Enter the RDF file to which triples will be added \
    (include the extension): ')
if args.fileName:
    fileName = args.fileName
else:
    fileName = input('Enter the CSV file of headings to reconcile \
    (including \'.csv\'): ')
if args.directory:
    directory = args.directory
else:
    directory = ''

os.chdir(directory)
startTime = time.time()
date = datetime.datetime.today().strftime('%Y-%m-%d')
timeStamp = datetime.datetime.now().strftime('%Y-%m-%d %H.%M.%S')

# import rdf file into graph
g = Graph()
g.parse(rdfFileName, format='n3')
originalTripleCount = len(g)

# create backup of rdf file before updates
g.serialize(format='n3', destination=open(rdfFileName[:rdfFileName.index('.')]
            + 'Backup' + timeStamp + '.n3', 'w'))

# creating dict of existing labels for comparison
q = prepareQuery('SELECT ?s ?o WHERE { ?s skos:prefLabel ?o }',
                 initNs={'skos': SKOS})
existingLabels = {}
uriNums = []
results = g.query(q)
for row in results:
    uriNums.append(str(row[0]).replace('[Base URI]', ''))
    existingLabels[str(row[1])] = str(row[0])

# set uri starting point
uriNum = int(max(uriNums))

# create log file
f = csv.writer(open(os.path.join('triplesAdded',
               rdfFileName[:rdfFileName.index('.')] + 'TriplesAdded'
               + timeStamp + '.csv'), 'w'))
f.writerow(['label'] + ['rdfLabel'] + ['uri'] + ['date'])

# parse csv data and add triples to graph
with open(fileName) as csvfile:
    reader = csv.DictReader(csvfile)
    for row in reader:
        altLabel = row['originalLabel']
        prefLabel = row['standardizedLabel'].strip()
        try:
            subjectUri = existingLabels[prefLabel]
            if altLabel != prefLabel and altLabel != '':
                g.add((URIRef(subjectUri), SKOS.altLabel, Literal(altLabel)))
                f.writerow([subjectUri] + [SKOS.altLabel] + [altLabel])
                f.writerow([])
        except ValueError:
            uriNum += 1
            subjectUri = '[Base URI]' + str(uriNum)
            g.add((URIRef(subjectUri), SKOS.prefLabel, Literal(prefLabel)))
            f.writerow([subjectUri] + [SKOS.prefLabel] + [prefLabel])
            if altLabel != prefLabel:
                g.add((URIRef(subjectUri), SKOS.altLabel, Literal(altLabel)))
                f.writerow([subjectUri] + [SKOS.altLabel] + [altLabel])
            g.add((URIRef(subjectUri), DC.date, Literal(date)))
            f.writerow([subjectUri] + [DC.date] + [date])
            existingLabels[prefLabel] = subjectUri
            f.writerow([])

# create rdf file
g.serialize(format='n3', destination=open(rdfFileName, 'w'))
print('Original triples count: ', originalTripleCount)
print('Updated triples count: ', len(g))

# extract altLabels and prefLabels to csv for find and replace operations
f = csv.writer(open(os.path.join('findAndReplace',
               rdfFileName[:rdfFileName.index('.')] + 'FindAndReplace'
               + timeStamp + '.csv'), 'w'))
f.writerow(['replacedValue'] + ['replacementValue'])
q = prepareQuery('SELECT ?altLabel ?prefLabel WHERE { ?s skos:prefLabel \
?prefLabel. ?s skos:altLabel ?altLabel }', initNs={'skos': SKOS})
results = g.query(q)
for row in results:
    f.writerow([row[0]] + [row[1]])

# extract prefLabels to csv
f = csv.writer(open(os.path.join('prefLabels', 'prefLabels' + timeStamp
               + '.csv'), 'w'))
f.writerow(['uri'] + ['prefLabel'])
q = prepareQuery('SELECT ?s ?prefLabel WHERE { ?s skos:prefLabel ?prefLabel }',
                 initNs={'skos': SKOS})
results = g.query(q)
for row in results:
    f.writerow([row[0]] + [row[1]])

# extract all triples to csv
f = csv.writer(open(os.path.join('allTriples', 'allTriples' + timeStamp
               + '.csv'), 'w'))
f.writerow(['subject'] + ['predicate'] + ['object'])
for s, p, o in g:
    f.writerow([s] + [p] + [o])

elapsedTime = time.time() - startTime
m, s = divmod(elapsedTime, 60)
h, m = divmod(m, 60)
print('Total script run time: ', '%d:%02d:%02d' % (h, m, s))