Fix ontology loads

build.gradle

@@ -49,6 +49,11 @@ dependencies {
     }
     implementation("ch.qos.logback:logback-classic:1.3.14")
     implementation("ch.qos.logback:logback-core:1.3.14")
+
+    //implementation("org.aksw.jena-sparql-api:jena-sparql-api-core:3.17.0-1")
+    implementation("org.apache.jena:jena-core:3.17.0")
+    implementation("org.apache.jena:jena-arq:3.17.0")
+
 }
 
 test {

src/config/container.xml

@@ -191,6 +191,8 @@
     <entry name="omero.client.import.mde.path">omero</entry>
     <!-- escape ice special characters, see https://doc.zeroc.com/ice/3.6/properties-and-configuration/configuration-file-syntax -->
     <entry name="omero.client.login_escape_characters">#=\s\\</entry>
+    <!-- sparql endpoint for sparql queries to parse the ontology terms used by mde-->
+    <entry name="omero.client.import.mde.sparqlEndpoint">http://sparql.hegroup.org/sparql/</entry>
   </services>
 
   <!--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

src/config/containerImporter.xml

@@ -172,6 +172,8 @@
     <entry name="omero.client.import.mde.path">omero</entry>
     <!-- escape ice special characters, see https://doc.zeroc.com/ice/3.6/properties-and-configuration/configuration-file-syntax -->
     <entry name="omero.client.login_escape_characters">#=\s\\</entry>
+    <!-- sparql endpoint for sparql queries to parse the ontology terms used by mde-->
+    <entry name="omero.client.import.mde.sparqlEndpoint">http://sparql.hegroup.org/sparql/</entry>
   </services>
 
   <!--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

src/main/java/org/openmicroscopy/shoola/agents/fsimporter/ImporterAgent.java

@@ -122,6 +122,10 @@ public static String getMDEPath() {
     	  Environment env = (Environment) registry.lookup(LookupNames.ENV);
     	  return env.getMDEConfigPath();
     }
+    public static String getMDESparqlEndpoint(){
+        Environment env = (Environment) registry.lookup(LookupNames.ENV);
+        return env.getMDESparqlEndpoint();
+    }
 
     /**
      * Returns <code>true</code> if the currently logged in user

src/main/java/org/openmicroscopy/shoola/agents/fsimporter/mde/util/OntologyElement.java

@@ -35,7 +35,7 @@ public OntologyElement(String val, String id, String uri) {
         this.val = val;
         parseId(id);
         this.uri=uri;
-        ImporterAgent.getRegistry().getLogger().debug(null,"[MDE] -- SET OntologyElement:"+toString());
+        //ImporterAgent.getRegistry().getLogger().debug(this,"[MDE] -- create OntologyElement:"+toString());
     }
 
     /**

src/main/java/org/openmicroscopy/shoola/agents/fsimporter/mde/util/inout/TagDataParser.java

@@ -21,14 +21,12 @@
 import org.openmicroscopy.shoola.agents.fsimporter.ImporterAgent;
 import org.openmicroscopy.shoola.agents.fsimporter.mde.util.OntologyElement;
 import org.openmicroscopy.shoola.agents.fsimporter.mde.util.TagData;
-import org.openmicroscopy.shoola.agents.fsimporter.mde.util.parser.BioPortal_Parser;
-import org.openmicroscopy.shoola.agents.fsimporter.mde.util.parser.OLS_Parser;
+import org.openmicroscopy.shoola.agents.fsimporter.mde.util.parser.OntologyParser_sparql;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 
-import java.util.ArrayList;
 import java.util.List;
 import java.util.stream.Collectors;
 
@@ -145,39 +143,26 @@ private List<OntologyElement> parseOntology(Element eElement) {
                 eElement = (Element) n;
             }
 
-            String ontology_RESTAPI_url=eElement.getAttribute(ATTR_RESTURL);
             String api_key = "";
             if(eElement.hasAttribute(ATTR_API_KEY)){
                 api_key=eElement.getAttribute(ATTR_API_KEY);
             }
             String ontologyAcronym = eElement.getAttribute(ATTR_ONTO_ACRO);
             String ontologyRef = eElement.getAttribute(ATTR_ONTO_REF);
 
-            ImporterAgent.getRegistry().getLogger().debug(null,"[MDE]"+
-                    String.format("Parse Ontology: {acronym:%s,id:%s}",ontologyAcronym,ontologyRef));
-
-            if(ontology_RESTAPI_url==null || ontology_RESTAPI_url.isEmpty() ||
-                ontologyAcronym==null || ontologyAcronym.isEmpty() ||
+            if(ontologyAcronym==null || ontologyAcronym.isEmpty() ||
                 ontologyRef==null || ontologyRef.isEmpty()){
                 return null;
             }
 
-            BioPortal_Parser oParser = new BioPortal_Parser(ontology_RESTAPI_url,api_key,ontologyAcronym);
-            try {
-                labelList = oParser.getSubLabels(ontologyAcronym, ontologyRef);
+            ImporterAgent.getRegistry().getLogger().debug(this,"[MDE]"+
+                    String.format("Parse Ontology: {acronym:%s,id:%s}",ontologyAcronym,ontologyRef));
 
-                if (labelList == null) {
-                    OLS_Parser olsParser = new OLS_Parser(ontology_RESTAPI_url,ontologyAcronym);
-                    labelList= olsParser.getSubLabels(ontologyAcronym, ontologyRef);
-                }
-                if (labelList ==null){
-                    ImporterAgent.getRegistry().getLogger().debug(null,"[MDE] "+String.format("Ontology element at %s has no childs",ontologyRef));
-                }
-            } catch (Exception e) {
-                ImporterAgent.getRegistry().getLogger().warn(this,
-                        "[MDE] can't parse given ontology item [" + ontologyAcronym + ", " + ontologyRef + "]");
-                e.printStackTrace();
-            }
+            OntologyParser_sparql parser= new OntologyParser_sparql();
+            labelList=parser.getSubLabels(ontologyAcronym,ontologyRef);
+
+            ImporterAgent.getRegistry().getLogger().debug(this,"[MDE]"+
+                    String.format("Retrieve subclasses: %d",labelList!=null?labelList.size():0));
         }
         return labelList;
     }