#!/usr/bin/env python
"""
REDCap Data Dictionary to OWL Converter
=======================================
This script provides a conversion utility for modeling REDCap Data
Dictionaries as an OWL Ontology, where instances are specific implementations
of a given REDCap Form.
"""
__author__ = '<NAME> <https://orcid.org/0000-0003-1099-3328>'

import os
import csv
import sys
import hashlib

import rdflib

verbose = None

ns = dict(nidm=rdflib.Namespace('http://purl.org/nidash/nidm/'),
          owl=rdflib.OWL)


def datatype_property(term):
    triple = [term,
              rdflib.RDF.term('type'),
              rdflib.OWL.term('DatatypeProperty')]
    return triple


def rdfs_label(term, label):
    triple = [term,
              rdflib.RDFS.term('label'),
              rdflib.Literal(label)]
    return triple


def nidm_term(term):
    nidm = ns.get('nidm')
    return nidm.term('nidm_{}'.format(hashlib.sha1(term).hexdigest()))


def header_to_owl(header):
    g = rdflib.Graph()
    [g.bind(k, v) for k, v in ns.iteritems()]
    for idx, prop in enumerate(header):
        term = nidm_term(prop)
        g.add(datatype_property(term))
        g.add(rdfs_label(term, prop))
    return g


def row_to_instance(rows):
    g = rdflib.Graph()
    [g.bind(k, v) for k, v in ns.iteritems()]
    hdr = rows.pop(0)
    for row in rows:
        term = nidm_term(row[0])
        for idx, column in enumerate(row):
            prop = nidm_term(hdr[idx])
            g.add([term, prop, rdflib.Literal(column)])
            g.add([term, rdflib.RDF.term('type'), nidm_term('DataElement')])
            g.add(rdfs_label(term, row[0]))
    return g


def owl_class():
    g = rdflib.Graph()
    [g.bind(k, v) for k, v in ns.iteritems()]
    g.add([nidm_term('DataElement'), rdflib.RDF.term('type'), rdflib.OWL.term('Class')])
    g.add(rdfs_label(nidm_term('DataElement'), 'Data Element'))
    return g


def main(args=None):
    with open(args.input, mode='rb') as fi:
        csvreader = csv.reader(fi)
        rows = list(csvreader)
        hdr = rows[0]
        fi.close()
    g = owl_class()
    g += header_to_owl(hdr)
    g += row_to_instance(rows)
    print g.serialize(args.output, format='turtle')


if __name__ == "__main__":
    import argparse

    formatter = argparse.RawDescriptionHelpFormatter
    default = 'default: %(default)s'
    parser = argparse.ArgumentParser(prog="redcap_datadict_to_owl.py",
                                     description=__doc__,
                                     formatter_class=formatter)
    parser.add_argument('-i', '--input',
                        required=True,
                        help="Input REDCap data dictionary as a csv file")
    parser.add_argument('-o', '--output',
                        default='redcap.owl',
                        help="Output file in turtle OWL format. {}".format(default))
    parser.add_argument('-v', '--verbose',
                        action='store_true',
                        help='Enable verbose {}'.format(default))
    argv = parser.parse_args()
    verbose = argv.verbose
    sys.exit(main(args=argv))

#!/usr/bin/env python
"""
REDCap Data Dictionary to OWL Converter
=======================================
This script provides a conversion utility for modeling REDCap Data
Dictionaries as an OWL Ontology, where instances are specific implementations
of a given REDCap Form.
"""
__author__ = '<NAME> <https://orcid.org/0000-0003-1099-3328>'

import os
import csv
import sys
import hashlib

import rdflib

verbose = None

ns = dict(nidm=rdflib.Namespace('http://purl.org/nidash/nidm/'),
          owl=rdflib.OWL)


def datatype_property(term):
    triple = [term,
              rdflib.RDF.term('type'),
              rdflib.OWL.term('DatatypeProperty')]
    return triple


def rdfs_label(term, label):
    triple = [term,
              rdflib.RDFS.term('label'),
              rdflib.Literal(label)]
    return triple


def nidm_term(term):
    nidm = ns.get('nidm')
    return nidm.term('nidm_{}'.format(hashlib.sha1(term).hexdigest()))


def header_to_owl(header):
    g = rdflib.Graph()
    [g.bind(k, v) for k, v in ns.iteritems()]
    for idx, prop in enumerate(header):
        term = nidm_term(prop)
        g.add(datatype_property(term))
        g.add(rdfs_label(term, prop))
    return g


def row_to_instance(rows):
    g = rdflib.Graph()
    [g.bind(k, v) for k, v in ns.iteritems()]
    hdr = rows.pop(0)
    for row in rows:
        term = nidm_term(row[0])
        for idx, column in enumerate(row):
            prop = nidm_term(hdr[idx])
            g.add([term, prop, rdflib.Literal(column)])
            g.add([term, rdflib.RDF.term('type'), nidm_term('DataElement')])
            g.add(rdfs_label(term, row[0]))
    return g


def owl_class():
    g = rdflib.Graph()
    [g.bind(k, v) for k, v in ns.iteritems()]
    g.add([nidm_term('DataElement'), rdflib.RDF.term('type'), rdflib.OWL.term('Class')])
    g.add(rdfs_label(nidm_term('DataElement'), 'Data Element'))
    return g


def main(args=None):
    with open(args.input, mode='rb') as fi:
        csvreader = csv.reader(fi)
        rows = list(csvreader)
        hdr = rows[0]
        fi.close()
    g = owl_class()
    g += header_to_owl(hdr)
    g += row_to_instance(rows)
    print g.serialize(args.output, format='turtle')


if __name__ == "__main__":
    import argparse

    formatter = argparse.RawDescriptionHelpFormatter
    default = 'default: %(default)s'
    parser = argparse.ArgumentParser(prog="redcap_datadict_to_owl.py",
                                     description=__doc__,
                                     formatter_class=formatter)
    parser.add_argument('-i', '--input',
                        required=True,
                        help="Input REDCap data dictionary as a csv file")
    parser.add_argument('-o', '--output',
                        default='redcap.owl',
                        help="Output file in turtle OWL format. {}".format(default))
    parser.add_argument('-v', '--verbose',
                        action='store_true',
                        help='Enable verbose {}'.format(default))
    argv = parser.parse_args()
    verbose = argv.verbose
    sys.exit(main(args=argv))

#!/usr/bin/env python REDCap Data Dictionary to OWL Converter ======================================= This script provides a conversion utility for modeling REDCap Data Dictionaries as an OWL Ontology, where instances are specific implementations of a given REDCap Form.