cleaning code to generate rdf
This commit is contained in:
Marie-Angélique Laporte
parent
4e34581797
commit
78e3dce29e
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@ -4,23 +4,25 @@
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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_core():
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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 = "http://iseal.org/terms/"
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NS = "https://alanorth.github.io/iseal-schema/#"
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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("../data/iseal-core.csv")
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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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@ -31,9 +33,14 @@ def make_core():
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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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# controlled_vocab = row["element controlled values or terms"]
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module = row["idss element cluster"]
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module_cat = row["idss schema module"]
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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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@ -43,99 +50,70 @@ def make_core():
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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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##element
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# if '-' not in element_name:
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if True: ## lazy reindenting
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concept = module_cat # element_name.split(' - ')[0]
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# element = element_name.strip()
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## code from Alan
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# Make sure element name is URL friendly because we need to use it in
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# the file system and in the URL.
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#
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# Replace two or more whitespaces with one
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element_name = re.sub(r"\s{2,}", " ", element_name)
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# Replace unnecessary stuff in some element names (I should tell Peter
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# that these belong in the description)
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element_name = re.sub(r"\s?\(\w+\)", "", element_name)
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# Remove commas and question marks
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element_name = re.sub(r"[,?]", "", element_name)
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# Replace ": " with a dash (as in "Evaluation: ")
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element_name = element_name.replace(": ", "-")
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# Replace " / " with a dash (as in "biome / zone")
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element_name = element_name.replace(" / ", "-")
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# Replace whitespace, colons, and slashes with dashes
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element_name = re.sub(r"[\s/]", "-", element_name)
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# Lower case it
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element_name = element_name.lower()
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# Strip just in case
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element_name = element_name.strip()
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# For example Certifying Body, FSC audit, Certificate, etc
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cluster = row["idss element cluster"].capitalize()
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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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# For example Assurance, Certification, Core, Impact, etc
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module = row["idss schema module"].capitalize()
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# Generate a "safe" version of the element name for use in URLs and
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# files by combining the cluster and the element name. This could
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# change in the future.
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element_name_safe = cluster.replace(" ", "-").lower() + "-" + element_name
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element = element_name_safe
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conceptUri = URIRef(NS + concept.replace(" ", "_"))
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if not (None, SKOS.prefLabel, Literal(concept)) 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(concept)))
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g.add((conceptUri, RDFS.subClassOf, moduleUri))
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## create properties
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elementURI = URIRef(NS + element.replace(" ", "_"))
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if prop_type == "CONTROLLED VALUE": ## object property
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g.add((elementURI, SKOS.prefLabel, Literal(element)))
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g.add((elementURI, RDF.type, OWL.ObjectProperty))
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g.add((elementURI, OWL.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 "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(
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"http://www.w3.org/2003/01/geo/wgs84_pos#" + dct
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),
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)
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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, OWL.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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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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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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## create controlled vocab
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cvURI = URIRef(NS + "VOCAB_" + element.replace(" ", "_"))
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g.add(
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(cvURI, RDF.type, OWL.Class)
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) ## SKOS.Concept ## SKOS.Collection??
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g.add((cvURI, SKOS.prefLabel, Literal("VOCAB " + element)))
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for term in controlled_vocab.split("||"):
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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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)
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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, OWL.range, cvURI))
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## add the controlled vocab information on properties directly
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@ -144,324 +122,119 @@ def make_core():
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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/alanorth/iseal-schema/main/data/controlled-vocabularies/"
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+ element
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"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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## 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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# elif prop_type == 'URL': ## object property
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# g.add((elementURI, RDF.type, OWL.ObjectProperty))
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# g.add((elementURI, OWL.domain, conceptUri))
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# g.add((elementURI, OWL.range, URIRef("") ))
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# g.add((elementURI, SKOS.prefLabel, Literal(element)))
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else: ## datatype properties
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g.add((elementURI, SKOS.prefLabel, Literal(element)))
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g.add((elementURI, RDF.type, OWL.DatatypeProperty))
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g.add((elementURI, OWL.domain, conceptUri))
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if dc:
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dct = dc.split(":")[1]
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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(
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"http://www.w3.org/2003/01/geo/wgs84_pos#" + dct
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),
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)
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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, OWL.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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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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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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range = None
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if prop_type == "DATE":
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g.add((elementURI, OWL.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, OWL.range, XSD.float))
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range = XSD.float
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else:
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g.add((elementURI, OWL.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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)
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range = None
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if prop_type == "DATE":
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g.add((elementURI, OWL.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, OWL.range, XSD.float))
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range = XSD.float
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else:
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g.add((elementURI, OWL.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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# else:
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# print(element_name)
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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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g.serialize(destination="idds_new3.ttl", format="turtle")
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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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def make_fsc():
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g = Graph()
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##namespace
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# NS = "http://iseal.org/terms/"
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NS = "https://alanorth.github.io/iseal-schema/FSC#"
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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_excel("./idss_schema_fields_new2.xlsx", "fsc extension")
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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 = row["fsc extension module"]
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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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##element
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# if '-' not in element_name:
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if True: ## lazy reindenting
|
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concept = module_cat # element_name.split(' - ')[0]
|
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# element = element_name.strip()
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## code from Alan
|
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# Make sure element name is URL friendly because we need to use it in
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# the file system and in the URL.
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#
|
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# Replace two or more whitespaces with one
|
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element_name = re.sub(r"\s{2,}", " ", element_name)
|
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# Replace unnecessary stuff in some element names (I should tell Peter
|
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# that these belong in the description)
|
||||
element_name = re.sub(r"\s?\(\w+\)", "", element_name)
|
||||
# Remove commas and question marks
|
||||
element_name = re.sub(r"[,?]", "", element_name)
|
||||
# Replace ": " with a dash (as in "Evaluation: ")
|
||||
element_name = element_name.replace(": ", "-")
|
||||
# Replace " / " with a dash (as in "biome / zone")
|
||||
element_name = element_name.replace(" / ", "-")
|
||||
# Replace whitespace, colons, and slashes with dashes
|
||||
element_name = re.sub(r"[\s/]", "-", element_name)
|
||||
# Lower case it
|
||||
element_name = element_name.lower()
|
||||
# Strip just in case
|
||||
element_name = element_name.strip()
|
||||
|
||||
# For example Certifying Body, FSC audit, Certificate, etc
|
||||
cluster = row["idss element cluster"].capitalize()
|
||||
|
||||
# For example Assurance, Certification, Core, Impact, etc
|
||||
module = row["fsc extension module"].capitalize()
|
||||
|
||||
# Generate a "safe" version of the element name for use in URLs and
|
||||
# files by combining the cluster and the element name. This could
|
||||
# change in the future.
|
||||
element_name_safe = cluster.replace(" ", "-").lower() + "-" + element_name
|
||||
|
||||
element = element_name_safe
|
||||
# remove extra fsc in name
|
||||
element = element.replace("fsc-fsc-", "fsc-")
|
||||
|
||||
conceptUri = URIRef(NS + concept.replace(" ", "_"))
|
||||
if not (None, SKOS.prefLabel, Literal(concept)) in g:
|
||||
##create concept as skos concept
|
||||
g.add((conceptUri, RDF.type, OWL.Class)) ## SKOS.Concept
|
||||
g.add((conceptUri, SKOS.prefLabel, Literal(concept)))
|
||||
g.add((conceptUri, RDFS.subClassOf, moduleUri))
|
||||
|
||||
## create properties
|
||||
elementURI = URIRef(NS + element.replace(" ", "_"))
|
||||
if prop_type == "CONTROLLED VALUE": ## object property
|
||||
g.add((elementURI, SKOS.prefLabel, Literal(element)))
|
||||
g.add((elementURI, RDF.type, OWL.ObjectProperty))
|
||||
g.add((elementURI, OWL.domain, conceptUri))
|
||||
## add suproperty link
|
||||
if dc:
|
||||
dct = dc.split(":")[1]
|
||||
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.replace(" ", "_"))
|
||||
g.add(
|
||||
(cvURI, RDF.type, OWL.Class)
|
||||
) ## SKOS.Concept ## SKOS.Collection??
|
||||
g.add((cvURI, SKOS.prefLabel, Literal("VOCAB " + element)))
|
||||
for term in controlled_vocab.split("||"):
|
||||
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, OWL.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/alanorth/iseal-schema/main/data/controlled-vocabularies/"
|
||||
+ element
|
||||
+ ".txt"
|
||||
),
|
||||
)
|
||||
)
|
||||
|
||||
## 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))
|
||||
|
||||
# elif prop_type == 'URL': ## object property
|
||||
# g.add((elementURI, RDF.type, OWL.ObjectProperty))
|
||||
# g.add((elementURI, OWL.domain, conceptUri))
|
||||
# g.add((elementURI, OWL.range, URIRef("") ))
|
||||
# g.add((elementURI, SKOS.prefLabel, Literal(element)))
|
||||
else: ## datatype properties
|
||||
g.add((elementURI, SKOS.prefLabel, Literal(element)))
|
||||
g.add((elementURI, RDF.type, OWL.DatatypeProperty))
|
||||
g.add((elementURI, OWL.domain, conceptUri))
|
||||
if dc:
|
||||
dct = dc.split(":")[1]
|
||||
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, OWL.range, XSD.date))
|
||||
range = XSD.date
|
||||
elif prop_type == "NUMERIC VALUE":
|
||||
g.add((elementURI, OWL.range, XSD.float))
|
||||
range = XSD.float
|
||||
else:
|
||||
g.add((elementURI, OWL.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)))
|
||||
# else:
|
||||
# print(element_name)
|
||||
|
||||
## save graph
|
||||
g.serialize(destination="fsc.ttl", format="turtle")
|
||||
|
||||
|
||||
make_core()
|
||||
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")
|
||||
|
|
|
|||
Loading…
Reference in New Issue