Quick fix for the context download issue

pom.xml

@@ -86,15 +86,15 @@
         <dependency>
             <groupId>org.eclipse.rdf4j</groupId>
             <artifactId>rdf4j-rio-jsonld</artifactId>
-            <version>2.3.2</version>
+            <version>3.7.7</version>
             <scope>runtime</scope>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/org.eclipse.rdf4j/rdf4j-rio-api -->
         <dependency>
             <groupId>org.eclipse.rdf4j</groupId>
             <artifactId>rdf4j-rio-api</artifactId>
-            <version>2.3.2</version>
+            <version>3.7.7</version>
         </dependency>
 
         <!-- REASONERS -->

src/main/java/org/phyloref/jphyloref/helpers/JSONLDHelper.java

@@ -1,21 +1,34 @@
 package org.phyloref.jphyloref.helpers;
 
+import com.github.jsonldjava.core.DocumentLoader;
+import com.github.jsonldjava.core.JsonLdError;
+import com.github.jsonldjava.core.RemoteDocument;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.stream.Collectors;
 import org.eclipse.rdf4j.rio.RDFFormat;
 import org.eclipse.rdf4j.rio.RDFParser;
 import org.eclipse.rdf4j.rio.Rio;
+import org.eclipse.rdf4j.rio.helpers.JSONLDSettings;
 import org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormat;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration;
 import org.semanticweb.owlapi.rio.RioOWLRDFConsumerAdapter;
 import org.semanticweb.owlapi.util.AnonymousNodeChecker;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * JSONLDHelper provides methods to help read and process JSON-LD files.
  *
  * @author Gaurav Vaidya
  */
 public class JSONLDHelper {
+  private static final Logger logger = LoggerFactory.getLogger(JSONLDHelper.class);
+
   /**
    * Create an RDFParser for JSON-LD files. When the parser's <code>parse()</code> method is called,
    * its contents will be added to the OWLOntology passed to this method.
@@ -60,6 +73,59 @@ public boolean isAnonymousNode(IRI iri) {
     RDFParser parser = Rio.createParser(RDFFormat.JSONLD);
     parser.setRDFHandler(rdfHandler);
 
+    // We get some indistinct errors if any of the context URLs in the JSON-LD file are
+    // incorrect or inaccessible. However, we can set up our own document loader so we
+    // can detect when this occurs.)
+    parser.set(
+        JSONLDSettings.DOCUMENT_LOADER,
+        new DocumentLoader() {
+          {
+            // Load built-in context files as injected documents.
+            try {
+              this.addInjectedDoc(
+                  "https://www.phyloref.org/phyx.js/context/v1.0.0/phyx.json",
+                  loadResourceFileAsString("context/phyx-context-v1.0.0.json"));
+            } catch (IOException e) {
+              logger.error("Could not load Phyx context v1.0.0: " + e);
+            }
+
+            try {
+              this.addInjectedDoc(
+                  "https://www.phyloref.org/phyx.js/context/v1.1.0/phyx.json",
+                  loadResourceFileAsString("context/phyx-context-v1.1.0.json"));
+            } catch (IOException e) {
+              logger.error("Could not load Phyx context v1.1.0: " + e);
+            }
+          }
+
+          /**
+           * Load a text Resource as a String. Based on the code at
+           * https://stackoverflow.com/a/46613809/27310
+           *
+           * @return A String representation of the Resource specified.
+           */
+          private String loadResourceFileAsString(String fileName) throws IOException {
+            ClassLoader classLoader = ClassLoader.getSystemClassLoader();
+            try (InputStream is = classLoader.getResourceAsStream(fileName)) {
+              if (is == null) throw new IOException("Could not find resource: " + fileName);
+              try (InputStreamReader isr = new InputStreamReader(is);
+                  BufferedReader reader = new BufferedReader(isr)) {
+                return reader.lines().collect(Collectors.joining(System.lineSeparator()));
+              }
+            }
+          }
+
+          @Override
+          public RemoteDocument loadDocument(String url) throws JsonLdError {
+            try {
+              return super.loadDocument(url);
+            } catch (Exception err) {
+              logger.error("Error occurred while loading document " + url + ": " + err);
+              throw new JsonLdError(JsonLdError.Error.LOADING_REMOTE_CONTEXT_FAILED, url, err);
+            }
+          }
+        });
+
     return parser;
   }
 }

src/main/resources/context/phyx-context-v1.0.0.json

@@ -0,0 +1,143 @@
+{
+  "@context": {
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+    "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    "owl": "http://www.w3.org/2002/07/owl#",
+    "skos": "http://www.w3.org/2004/02/skos/core#",
+    "obo": "http://purl.obolibrary.org/obo/",
+    "dwc": "http://rs.tdwg.org/dwc/terms/",
+    "dct": "http://purl.org/dc/terms/",
+    "tc": "http://rs.tdwg.org/ontology/voc/TaxonConcept#",
+    "tn": "http://rs.tdwg.org/ontology/voc/TaxonName#",
+    "testcase": "http://vocab.phyloref.org/phyloref/testcase.owl#",
+    "pso": "http://purl.org/spar/pso/",
+    "tvc": "http://www.essepuntato.it/2012/04/tvc/",
+    "timeinterval": "http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl#",
+    "phyloref": "http://ontology.phyloref.org/phyloref.owl#",
+    "opentree": "http://purl.org/opentree/nexson#",
+    "subClasses": {
+      "@reverse": "rdfs:subClassOf"
+    },
+    "label": {
+      "@id": "rdfs:label",
+      "@type": "xsd:string"
+    },
+    "labels": {
+      "@id": "rdfs:label",
+      "@type": "xsd:string",
+      "@container": "@set"
+    },
+    "namePublishedIn": "dwc:namePublishedIn",
+    "definitionSource": "obo:IAO_0000119",
+    "definition": {
+      "@id": "obo:IAO_0000115",
+      "@type": "xsd:string"
+    },
+    "hasName": {
+      "@id": "tc:hasName",
+      "@type": "tn:TaxonName"
+    },
+    "nameComplete": {
+      "@id": "tn:nameComplete",
+      "@type": "xsd:string"
+    },
+    "nomenclaturalCode": {
+      "@id": "tn:nomenclaturalCode",
+      "@type": "@id"
+    },
+    "scientificName": {
+      "@id": "dwc:scientificName",
+      "@type": "xsd:string"
+    },
+    "genusPart": {
+      "@id": "tn:genusPart",
+      "@type": "xsd:string"
+    },
+    "specificEpithet": {
+      "@id": "tn:specificEpithet",
+      "@type": "xsd:string"
+    },
+    "basisOfRecord": "dwc:basisOfRecord",
+    "occurrenceID": "dwc:occurrenceID",
+    "catalogNumber": "dwc:catalogNumber",
+    "collectionCode": "dwc:collectionCode",
+    "institutionCode": "dwc:institutionCode",
+    "subClassOf": {
+      "@id": "rdfs:subClassOf",
+      "@type": "@id"
+    },
+    "parent": {
+      "@id": "obo:CDAO_0000179",
+      "@type": "@id"
+    },
+    "children": {
+      "@id": "obo:CDAO_0000149",
+      "@type": "@id"
+    },
+    "siblings": {
+      "@id": "phyloref:has_Sibling",
+      "@type": "@id"
+    },
+    "owl:imports": {
+      "@id": "owl:imports",
+      "@type": "@id"
+    },
+    "equivalentClass": "owl:equivalentClass",
+    "intersectionOf": {
+      "@id": "owl:intersectionOf",
+      "@container": "@list"
+    },
+    "onProperty": {
+      "@id": "owl:onProperty",
+      "@type": "@id"
+    },
+    "someValuesFrom": {
+      "@id": "owl:someValuesFrom",
+      "@container": "@set"
+    },
+    "unionOf": {
+      "@id": "owl:unionOf",
+      "@container": "@list"
+    },
+    "hasValue": {
+      "@id": "owl:hasValue",
+      "@type": "xsd:string"
+    },
+    "nodes": {
+      "@reverse": "obo:CDAO_0000200",
+      "@container": "@set"
+    },
+    "hasRootNode": {
+      "@id": "obo:CDAO_0000148",
+      "@type": "@id"
+    },
+    "newick": {
+      "@id": "phyloref:newick_expression",
+      "@type": "xsd:string"
+    },
+    "curator": {
+      "@id": "opentree:curatorName",
+      "@type": "xsd:string"
+    },
+    "scientificNameAuthorship": {
+      "@id": "dwc:scientificNameAuthorship",
+      "@type": "xsd:string"
+    },
+    "nameAccordingTo": "tc:accordingTo",
+    "phylogenies": {
+      "@reverse": "rdfs:isDefinedBy",
+      "@container": "@set"
+    },
+    "phylorefs": {
+      "@reverse": "rdfs:isDefinedBy",
+      "@container": "@set"
+    },
+    "title": "dct:title",
+    "source": "dct:source",
+    "bibliographicCitation": "dct:bibliographicCitation",
+    "doi": "http://prismstandard.org/namespaces/basic/2.0/doi",
+    "representsTaxonomicUnits": "obo:CDAO_0000187",
+    "apomorphy": "phyloref:apomorphy"
+  }
+}