#!/usr/bin/env python3 # coding: utf-8 import json import os import re import argparse import sys import pandas as pd from rdflib import BNode, Graph, Literal, URIRef from rdflib.namespace import DC, DCTERMS, OWL, RDF, RDFS, SKOS, XSD def make_rdf(file, ns): g = Graph() ##namespace # NS = "https://iseal-community.github.io/iseal-core#" NS = ns ## create ontology iseal = URIRef(NS) g.add((iseal, RDF.type, OWL.Ontology)) df = pd.read_csv(file) df.dropna(how="all", axis=1) df.fillna("", inplace=True) for index, row in df.iterrows(): element_name = row["element name"] element_description = row["element description"] comment = row["element guidance"] example = row["element link for more information"] cardinality = row["element options"] prop_type = row["element type"] # controlled_vocab = row["element controlled values or terms"] module = row["idss element cluster"] module_cat = "" try: ## for extensions module_cat = row["idss schema module"] except: module_cat_name = [col for col in df.columns if "module" in col][0] module_cat = row[module_cat_name] dc = row["element link for dublin core attributes"] dspace = row["dspace field name"] ##module moduleUri = URIRef(NS + module) if not (None, SKOS.prefLabel, Literal(module)) in g: ##create module as skos concept g.add((moduleUri, RDF.type, OWL.Class)) ## SKOS.Concept g.add((moduleUri, SKOS.prefLabel, Literal(module))) conceptUri = URIRef(NS + module_cat.replace(" ", "_")) if not (None, SKOS.prefLabel, Literal(module_cat)) in g: ##create concept as skos concept g.add((conceptUri, RDF.type, OWL.Class)) ## SKOS.Concept g.add((conceptUri, SKOS.prefLabel, Literal(module_cat))) g.add((conceptUri, RDFS.subClassOf, moduleUri)) ## create properties elementURI = URIRef(NS + dspace.replace(".", "-").lower()) if prop_type == "controlled value": ## object property g.add((elementURI, SKOS.prefLabel, Literal(element_name))) g.add((elementURI, RDF.type, OWL.ObjectProperty)) g.add((elementURI, RDFS.domain, conceptUri)) ## add suproperty link if dc: dct = dc.split(":")[1] if "||" in dct: dct = dc.split(":")[0] if "wgs84" in dc: g.add( ( elementURI, RDFS.subPropertyOf, URIRef("http://www.w3.org/2003/01/geo/wgs84_pos#" + dct), ) ) else: g.add( ( elementURI, RDFS.subPropertyOf, URIRef("http://purl.org/dc/terms/" + dct), ) ) ## add dspace alternative ID g.add( ( elementURI, URIRef("http://purl.org/dc/terms/alternative"), Literal(dspace), ) ) ## create controlled vocab cvURI = URIRef(NS + "VOCAB_" + element_name.replace(" ", "_")) g.add((cvURI, RDF.type, OWL.Class)) ## SKOS.Concept ## SKOS.Collection?? g.add((cvURI, SKOS.prefLabel, Literal("VOCAB " + element_name))) ## open controlled vocab file ## open controlled vocab file try: with open( "data/controlled-vocabularies/" + dspace.replace(".", "-").lower() + ".txt", "r", encoding="utf-8", ) as f: lines = f.readlines() for line in lines: term = line.strip() termURI = URIRef(NS + term.replace(" ", "_").replace("|", "")) g.add((termURI, RDF.type, OWL.Class)) ## SKOS.Concept g.add((termURI, SKOS.prefLabel, Literal(term))) g.add((termURI, RDFS.subClassOf, cvURI)) ## SKOS.member??? g.add((elementURI, RDFS.range, cvURI)) ## add the controlled vocab information on properties directly g.add( ( elementURI, URIRef("http://purl.org/dc/dcam/rangeIncludes"), Literal( "https://raw.githubusercontent.com/iseal-community/iseal-core/main/data/controlled-vocabularies/" + dspace.replace(".", "-").lower() + ".txt" ), ) ) except FileNotFoundError: continue ## cardinality if cardinality == "multi select from control list": br = BNode() g.add((br, RDF.type, OWL.Restriction)) g.add((br, OWL.onProperty, elementURI)) g.add((br, OWL.minQualifiedCardinality, Literal(1))) g.add((br, OWL.someValuesFrom, cvURI)) g.add((conceptUri, RDFS.subClassOf, br)) else: br = BNode() g.add((br, RDF.type, OWL.Restriction)) g.add((br, OWL.onProperty, elementURI)) g.add((br, OWL.maxQualifiedCardinality, Literal(1))) g.add((br, OWL.onClass, cvURI)) g.add((conceptUri, RDFS.subClassOf, br)) else: ## datatype properties g.add((elementURI, SKOS.prefLabel, Literal(element_name))) g.add((elementURI, RDF.type, OWL.DatatypeProperty)) g.add((elementURI, RDFS.domain, conceptUri)) if dc: dct = dc.split(":")[1] if "||" in dct: dct = dc.split(":")[0] if "wgs84" in dc: g.add( ( elementURI, RDFS.subPropertyOf, URIRef("http://www.w3.org/2003/01/geo/wgs84_pos#" + dct), ) ) else: g.add( ( elementURI, RDFS.subPropertyOf, URIRef("http://purl.org/dc/terms/" + dct), ) ) ## add dspace alternative ID g.add( ( elementURI, URIRef("http://purl.org/dc/terms/alternative"), Literal(dspace), ) ) range = None if prop_type == "date": g.add((elementURI, RDFS.range, XSD.date)) range = XSD.date elif prop_type == "numeric value": g.add((elementURI, RDFS.range, XSD.float)) range = XSD.float else: g.add((elementURI, RDFS.range, XSD.string)) range = XSD.string ##cardinality if cardinality == "repeat values": br = BNode() g.add((br, RDF.type, OWL.Restriction)) g.add((br, OWL.onProperty, elementURI)) g.add((br, OWL.someValuesFrom, range)) g.add((conceptUri, RDFS.subClassOf, br)) else: br = BNode() g.add((br, RDF.type, OWL.Restriction)) g.add((br, OWL.onProperty, elementURI)) g.add((br, OWL.maxQualifiedCardinality, Literal(1))) g.add((br, OWL.onDataRange, range)) g.add((conceptUri, RDFS.subClassOf, br)) if comment: g.add((elementURI, SKOS.scopeNote, Literal(comment))) if example: g.add((elementURI, RDFS.comment, Literal(example))) if element_description: g.add((elementURI, SKOS.definition, Literal(element_description))) ## save graph head, tail = os.path.split(file) filename = tail.split(".")[0] g.serialize(destination="data/rdf/" + filename + ".ttl", format="turtle") parser = argparse.ArgumentParser( description="Parse an ISEAL schema CSV file to export it as RDF." ) parser.add_argument( "-i", "--input-file", help="Path to schema fields file (ie, iseal-core.csv).", required=True, type=argparse.FileType("r"), ) parser.add_argument( "-ns", "--namespace", help="Namespace of the schema. Used to create the URIs, should point to the website (ie. https://iseal-community.github.io/iseal-core#).", required=True, ) args = parser.parse_args() try: make_rdf(args.input_file.name, args.namespace) except FileNotFoundError: sys.stderr.write(f" Could not open {args.input_file.name}\n")