Merge pull request #25 from phyloref/use_local_ontologies_in_webserver

TestCommand (`java -jar jphyloref.jar test ...`) already supports the use of local ontologies if they are available. This PR adds support for reading ontologies from the same folder to WebserverCommand (`java -jar jphyloref.jar webserver ...`) as well.

CHANGELOG.md

@@ -9,6 +9,7 @@ Based on the suggestion at https://keepachangelog.com/en/1.0.0/.
 - Removed Eclipse files that should not have been added in [phyloref/jphyloref#13].
 - Moved code for determining Phyloref statuses to PhylorefHelper. This is part of
   [phyloref/jphyloref#8].
+- WebserverCommand now looks for ontologies in the local 'ontologies/' directory.
 
 ## 0.2 - 2018-06-20
 - Added support for phyloreference statuses using the Publication Status Ontology

src/main/java/org/phyloref/jphyloref/commands/WebserverCommand.java

@@ -40,6 +40,7 @@
 import org.semanticweb.owlapi.rio.RioOWLRDFConsumerAdapter;
 import org.semanticweb.owlapi.search.EntitySearcher;
 import org.semanticweb.owlapi.util.AnonymousNodeChecker;
+import org.semanticweb.owlapi.util.AutoIRIMapper;
 import org.semanticweb.owlapi.util.VersionInfo;
 
 import fi.iki.elonen.NanoHTTPD;
@@ -160,6 +161,13 @@ public JSONObject serveReason(File jsonldFile) throws OWLOntologyCreationExcepti
 
       // Prepare an ontology to fill with the provided JSON-LD file.
       OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+
+      // Is purl.obolibrary.org down? No worries, you can access local copies
+      // of your ontologies in the 'ontologies/' folder.
+      AutoIRIMapper mapper = new AutoIRIMapper(new File("ontologies"), true);
+      System.err.println("Found local ontologies: " + mapper.getOntologyIRIs());
+      manager.addIRIMapper(mapper);
+
       OWLOntology ontology = manager.createOntology();
       OWLOntologyLoaderConfiguration config = new OWLOntologyLoaderConfiguration();