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