Add support for JSON and YAML files, closes #20

- add dependency on jena-arq
    - used to convert JSON-LD to RDF
    - this will also be used for SPARQL
- add dependency on snakeyaml
- update IOHelper.loadOntology(File, boolean) to
    - detect and convert YAML to JSON
    - detect and convert JSON to RDF
- add simple.json translation of simple.owl
- add simple.yaml translation of simple.owl
- update unit tests

robot-core/pom.xml

@@ -12,10 +12,20 @@
     <description>Core library for ROBOT, the OBO tool</description>
 
     <dependencies>
+        <dependency>
+            <groupId>org.apache.jena</groupId>
+            <artifactId>jena-arq</artifactId>
+            <version>2.13.0</version>
+        </dependency>
         <dependency>
             <groupId>com.github.jsonld-java</groupId>
             <artifactId>jsonld-java</artifactId>
             <version>0.5.1</version>
         </dependency>
+        <dependency>
+            <groupId>org.yaml</groupId>
+            <artifactId>snakeyaml</artifactId>
+            <version>1.15</version>
+        </dependency>
     </dependencies>
 </project>

robot-core/src/main/java/org/obolibrary/robot/IOHelper.java

@@ -2,9 +2,10 @@
 
 import java.io.InputStream;
 import java.io.File;
-import java.io.FileInputStream;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -17,11 +18,14 @@
 
 import com.github.jsonldjava.core.Context;
 import com.github.jsonldjava.core.JsonLdApi;
+import com.github.jsonldjava.core.JsonLdError;
 import com.github.jsonldjava.core.JsonLdOptions;
 import com.github.jsonldjava.core.JsonLdProcessor;
 import com.github.jsonldjava.utils.JsonUtils;
-import org.apache.commons.io.FilenameUtils;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
 import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.io.IOUtils;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.IRI;
@@ -36,6 +40,7 @@
 import org.semanticweb.owlapi.model.PrefixManager;
 import org.semanticweb.owlapi.util.DefaultPrefixManager;
 import org.semanticweb.owlapi.vocab.PrefixOWLOntologyFormat;
+import org.yaml.snakeyaml.Yaml;
 
 /**
  * Provides convenience methods for working with ontology and term files.
@@ -236,17 +241,49 @@ public OWLOntology loadOntology(File ontologyFile, File catalogFile)
         logger.debug("Loading ontology {} with catalog file {}",
                 ontologyFile, catalogFile);
 
-        OWLOntology ontology = null;
+        Object jsonObject = null;
+
         try {
-            OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+            String extension =
+                FilenameUtils.getExtension(ontologyFile.getName());
+            extension = extension.trim().toLowerCase();
+            if (extension.equals("yml") || extension.equals("yaml")) {
+                logger.debug("Converting from YAML to JSON");
+                String yamlString = FileUtils.readFileToString(ontologyFile);
+                jsonObject = new Yaml().load(yamlString);
+            } else if (extension.equals("js")
+                       || extension.equals("json")
+                       || extension.equals("jsonld")) {
+                String jsonString = FileUtils.readFileToString(ontologyFile);
+                jsonObject = JsonUtils.fromString(jsonString);
+            }
+
+            // Use Jena to convert a JSON-LD string to RDFXML, then load it
+            if (jsonObject != null) {
+                logger.debug("Converting from JSON to RDF");
+                jsonObject = new JsonLdApi().expand(getContext(), jsonObject);
+                String jsonString = JsonUtils.toString(jsonObject);
+                Model model = ModelFactory.createDefaultModel();
+                model.read(IOUtils.toInputStream(jsonString), null, "JSON-LD");
+                ByteArrayOutputStream output = new ByteArrayOutputStream();
+                //model.write(System.out);
+                model.write(output);
+                byte[] data = output.toByteArray();
+                ByteArrayInputStream input = new ByteArrayInputStream(data);
+                return loadOntology(input);
+            }
+
+            OWLOntologyManager manager =
+                OWLManager.createOWLOntologyManager();
             if (catalogFile != null && catalogFile.isFile()) {
                 manager.addIRIMapper(new CatalogXmlIRIMapper(catalogFile));
             }
-            ontology = manager.loadOntologyFromOntologyDocument(ontologyFile);
+            return manager.loadOntologyFromOntologyDocument(ontologyFile);
+        } catch (JsonLdError e) {
+            throw new IOException(e);
         } catch (OWLOntologyCreationException e) {
             throw new IOException(e);
         }
-        return ontology;
     }
 
     /**

robot-core/src/test/java/org/obolibrary/robot/IOHelperTest.java

@@ -1,5 +1,6 @@
 package org.obolibrary.robot;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -18,6 +19,32 @@
  * Tests for {@link IOHelper}.
  */
 public class IOHelperTest extends CoreTest {
+    /**
+     * Test loading JSON files.
+     *
+     * @throws IOException on file problem
+     */
+    @Test
+    public void testJSON() throws IOException {
+        IOHelper ioh = new IOHelper();
+        String jsonPath = this.getClass().getResource("/simple.json").getFile();
+        File jsonFile = new File(jsonPath);
+        assertIdentical("/simple.owl", ioh.loadOntology(jsonFile));
+    }
+
+    /**
+     * Test loading YAML files.
+     *
+     * @throws IOException on file problem
+     */
+    @Test
+    public void testYAML() throws IOException {
+        IOHelper ioh = new IOHelper();
+        String yamlPath = this.getClass().getResource("/simple.yaml").getFile();
+        File yamlFile = new File(yamlPath);
+        assertIdentical("/simple.owl", ioh.loadOntology(yamlFile));
+    }
+
     /**
      * Test getting the default context.
      *

robot-core/src/test/resources/simple.json

@@ -0,0 +1,31 @@
+{
+    "@context": {
+        "resources": "https://github.com/ontodev/robot/robot-core/src/test/resources/",
+        "simple": "resources:simple.owl#",
+        "label": "rdfs:label",
+        "parent": {
+            "@id": "rdfs:subClassOf",
+            "@type": "@id"
+        }
+    },
+
+    "@graph": [
+        {
+            "@id": "resources:simple.owl",
+            "@type": "owl:Ontology"
+        },
+        {
+            "@id": "simple:test1",
+            "@type": "owl:Class",
+            "label": [
+                {"@value": "test one"},
+                {"@value": "Test 1"}
+            ]
+        },
+        {
+            "@id": "simple:test2",
+            "@type": "owl:Class",
+            "parent": "simple:test1"
+        }
+    ]
+}

robot-core/src/test/resources/simple.yaml

@@ -0,0 +1,20 @@
+---
+"@context":
+    resources: https://github.com/ontodev/robot/robot-core/src/test/resources/
+    simple: resources:simple.owl#
+    label: rdfs:label
+    parent:
+        "@id": rdfs:subClassOf
+        "@type": "@id"
+
+"@graph":
+    - "@id": resources:simple.owl
+      "@type": owl:Ontology
+    - "@id": simple:test1
+      "@type": owl:Class
+      label:
+          - "@value": test one
+          - "@value": Test 1
+    - "@id": simple:test2
+      "@type": owl:Class
+      parent: simple:test1