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Update to give local URIs to SVOs
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@dgarijo
dgarijo committed Jan 5, 2021
1 parent 81f973e commit 200f2f0
Showing 1 changed file with 46 additions and 40 deletions.
86 changes: 46 additions & 40 deletions CSVToRDF/src/main/java/edu/isi/csvtordf/CSV2RDF.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,11 +21,8 @@
import org.apache.jena.ontology.OntModel;
import org.apache.jena.ontology.OntProperty;
import org.apache.jena.ontology.OntResource;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.ResultSet;
import org.apache.jena.query.*;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.Property;
import org.apache.jena.vocabulary.XSD;
Expand All @@ -35,6 +32,7 @@
*/
public class CSV2RDF {
OntModel instances;
OntModel variables;
OntModel mcOntology;
String instance_URI = "https://w3id.org/okn/i/mint/";
JsonObject unitDictionary;
Expand All @@ -45,13 +43,15 @@ public class CSV2RDF {
*/
public CSV2RDF(String unitDictionaryFile, String scientificVariableFile) throws FileNotFoundException{
instances = ModelFactory.createOntologyModel();
variables = ModelFactory.createOntologyModel();
//create class
instances.createClass("https://w3id.org/okn/o/sd/#SoftwareConfiguration");
//we read all the variables, as they will be part of the model catalog.
instances.read(scientificVariableFile);
//we read all the variables separately, as we will use them to link contents.
variables.read(scientificVariableFile);
mcOntology = ModelFactory.createOntologyModel();
mcOntology.read("https://w3id.org/okn/o/sdm#");
mcOntology.read("https://w3id.org/okn/o/sd#");
mcOntology.createObjectProperty("http://www.w3.org/2002/07/owl#sameAs");
//for some reason it's not doing the right redirect
// mcOntology.read("https://mintproject.github.io/Mint-ModelCatalog-Ontology/release/1.4.0/ontology.xml");
// mcOntology.read("http://ontosoft.org/ontology/software/ontosoft-v1.0.owl");//for some reason, it doesn't do the negotiation rihgt.
Expand Down Expand Up @@ -106,29 +106,31 @@ private void checkFile (String path){
* @param rowValue
*/
private void processSVO(Individual ind, Property p, String rowValue, boolean index){
Individual mint_svo = instances.createClass("https://w3id.org/okn/o/sd#StandardVariable").createIndividual(instance_URI+encode(rowValue));
mint_svo.addLabel(rowValue, null);
//assign the variable to target node.
ind.addProperty(p, mint_svo);
/**
read label, try to find one in the svo file (there should be).
* If found, then use that URI. IF not found, then create one.
* If found, then copy description and label into instance, and add owl:sameAs.
**/
Query query = QueryFactory.create("select ?var where {"
+ "?var <http://www.w3.org/2000/01/rdf-schema#label> \""+rowValue+"\"}");
// Execute the query and obtain results
QueryExecution qe = QueryExecutionFactory.create(query, instances);
ResultSet rs = qe.execSelect();
if(rs.hasNext()){
ind.addProperty(p, rs.next().getResource("?var"));
}else{
//no variable found: create variable, add label
Individual userInstance;
//if(index){
// userInstance = instances.createClass("https://w3id.org/okn/o/sdm#NumericalIndex").createIndividual(instance_URI+encode(rowValue));
//}else{
userInstance = instances.createClass("http://www.geoscienceontology.org/svo/svu#Variable").createIndividual(instance_URI+encode(rowValue));
//}
userInstance.addLabel(rowValue, null);
//assign the variable to target node.
ind.addProperty(p, userInstance);
}
Query query = QueryFactory.create("select ?var ?desc where {"
+ "?var <http://www.w3.org/2000/01/rdf-schema#label> \""+rowValue+"\"" +
"optional {?var <https://schema.org/description> ?desc}}");
QueryExecution qe = QueryExecutionFactory.create(query, variables);
ResultSet rs = qe.execSelect();
// if found in SVO, copy description and owl:sameAs
if(rs.hasNext()){
QuerySolution qs = rs.next();
OntProperty pSameAs = (OntProperty)mcOntology.getProperty("http://www.w3.org/2002/07/owl#sameAs");
mint_svo.addProperty(pSameAs, qs.getResource("?var"));
Literal desc = qs.getLiteral("?desc");
if (!"".equals(desc) && desc!= null){
//svo comes with html tags. remove them
mint_svo.addProperty(mcOntology.getOntProperty("https://w3id.org/okn/o/sd#description"),
desc.getString().replace("<p>","\n").replaceAll("\\<[^>]*>",""));
}
}
}

private void processFile(String path) throws Exception{
Expand Down Expand Up @@ -176,10 +178,10 @@ private void processFile(String path) throws Exception{
System.err.println("ERROR: "+rowValue+" is not a URI. Ind: "+ind.getLocalName());
}
break;
case "http://www.w3.org/2001/XMLSchema#int":
case "http://www.w3.org/2001/XMLSchema#integer":
try{
Integer.parseInt(rowValue);
ind.addProperty(p, rowValue,XSDDatatype.XSDint);
ind.addProperty(p, rowValue,XSDDatatype.XSDinteger);
}catch (NumberFormatException e){
System.err.println("ERROR: "+rowValue+" is not an Integer. Ind: "+ind.getLocalName());
}
Expand All @@ -189,7 +191,7 @@ private void processFile(String path) throws Exception{
Float.parseFloat(rowValue);
ind.addProperty(p, rowValue,XSDDatatype.XSDfloat);
}catch (NumberFormatException e){
System.err.println("ERROR: "+rowValue+" is not an Integer. Ind: "+ind.getLocalName());
System.err.println("ERROR: "+rowValue+" is not a float. Ind: "+ind.getLocalName());
}
break;
default:
Expand Down Expand Up @@ -248,9 +250,6 @@ private void processFile(String path) throws Exception{
}else if(p.toString().contains("hasStandardVariable")){
processSVO(ind, p, rowValue,false);
}
//else if(p.toString().contains("usefulForCalculatingIndex")){
// processSVO(ind, p, rowValue,true);
//}
else if(p.toString().contains("hasSoftwareImage")){
//seaparated because here we will do the link to Dockerpedia when appropriate.
//at the moment just create a URI and link with label
Expand Down Expand Up @@ -366,10 +365,16 @@ public static void main(String[] args){
// String pathToTransformationsDataFolder = "C:\\Users\\dgarijo\\Documents\\GitHub\\ModelCatalog\\Data\\Transformations";

//MINT
String version = "1.6.0";
String pathToInstancesDataFolder = "C:\\Users\\dgarijo\\Documents\\GitHub\\ModelCatalog\\Data\\MINT\\"+version;
String version = "1.6_to_1.7";
// Unix
String pathToGitFolder = "/home/dgarijo/Documents/GitHub/ModelCatalog";

// WIN
// String pathToGitFolder = "C:\\Users\\dgarijo\\Documents\\GitHub";
String pathToInstancesDataFolder = pathToGitFolder+"/Data/MINT/"+version;
String [] graphs = {"[email protected]"};//, "[email protected]", "[email protected]", "[email protected]","[email protected]"};
//end mint
//end MINT

//COVID models example
// pathToInstancesDataFolder = "C:\\Users\\dgarijo\\Documents\\GitHub\\ModelCatalog\\Data\\COVID";
// processDataFolder(pathToInstancesDataFolder, false, catalog);
Expand All @@ -382,11 +387,12 @@ public static void main(String[] args){
//end wifire
for (String graph:graphs){
//a new catalog should be made per graph; otherwise graphs will be aggregated.
CSV2RDF catalog = new CSV2RDF("C:\\Users\\dgarijo\\Documents\\GitHub\\ModelCatalog\\Data\\Units\\dict.json",
"C:\\Users\\dgarijo\\Documents\\GitHub\\ModelCatalog\\Data\\SVO\\variable-23-10-2019.ttl");
processDataFolder(pathToInstancesDataFolder+"\\"+graph, false, catalog);
exportRDFFile("modelCatalog_"+graph+".ttl", catalog.instances, "TTL");
CSV2RDF catalog = new CSV2RDF(pathToGitFolder+"/Data/Units/dict.json",
pathToGitFolder+"/Data/SVO/variable-23-10-2019.ttl");
processDataFolder(pathToInstancesDataFolder+"/"+graph, false, catalog);
exportRDFFile("modelCatalog_"+graph+"_"+version+".ttl", catalog.instances, "TTL");
}
System.out.println("Import process finished successfully");
}catch (Exception e){
System.err.println("Error: "+e);
}
Expand Down

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