mirror of
https://github.com/ISEAL-Community/iseal-core.git
synced 2024-11-17 20:37:04 +01:00
241 lines
9.0 KiB
Python
Executable File
241 lines
9.0 KiB
Python
Executable File
#!/usr/bin/env python
|
|
# 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, OWL.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, 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/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, OWL.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, 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)))
|
|
|
|
## 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")
|