Load medic and NIFST ontologies from the classpath

Author: arteymix

pom.xml

@@ -275,6 +275,7 @@
 			<resource>
 				<directory>src</directory>
 				<includes>
+					<include>**/*.owl.gz</include>
 					<include>**/*.properties</include>
 				</includes>
 				<filtering>false</filtering>

src/data/loader/ontology/medic.owl.gz

@@ -34,7 +34,6 @@ url.obiOntology=http://purl.obolibrary.org/obo/obi.owl
 
 
 # no longer actively used.
-url.nifstdOntology=http://ontology.neuinfo.org/NIF/nif-gemma.owl
 url.fmaOntology=http://purl.obolibrary.org/obo/fma.owl
 
 ontology.index.dir=ontology.index.dir

src/data/loader/ontology/nif-gemma.owl.gz

@@ -24,6 +24,7 @@
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.util.zip.GZIPInputStream;
 
 /**
  * MEDIC ONTOLOGY USED BY PHENOCARTA, its represents MESH terms as a tree so with can use the parent structure that a
@@ -39,7 +40,7 @@ public class MedicOntologyService extends AbstractOntologyService {
     /**
      * FIXME this shouldn't be hard-coded like this, we should load it like any other ontology service.
      */
-    private static final String MEDIC_ONTOLOGY_FILE = "/data/loader/ontology/medic.owl";
+    private static final String MEDIC_ONTOLOGY_FILE = "/data/loader/ontology/medic.owl.gz";
 
     @Override
     protected String getOntologyName() {
@@ -48,7 +49,7 @@ protected String getOntologyName() {
 
     @Override
     protected String getOntologyUrl() {
-        return MEDIC_ONTOLOGY_FILE;
+        return "classpath:" + MEDIC_ONTOLOGY_FILE;
     }
 
     @Override
@@ -57,7 +58,7 @@ protected OntModel loadModel() {
             if ( is == null ) {
                 throw new RuntimeException( String.format( "The MEDIC ontology was not found in classpath at %s.", MEDIC_ONTOLOGY_FILE ) );
             }
-            return loadModelFromStream( is );
+            return loadModelFromStream( new GZIPInputStream( is ) );
         } catch ( IOException e ) {
             throw new RuntimeException( e );
         }

src/ontology.properties

@@ -1,29 +1,32 @@
 /*
  * The baseCode project
- * 
+ *
  * Copyright (c) 2011 University of British Columbia
- * 
+ *
  * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with
  * the License. You may obtain a copy of the License at
- * 
+ *
  * http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on
  * an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the
  * specific language governing permissions and limitations under the License.
  */
 package ubic.basecode.ontology.providers;
 
+import com.hp.hpl.jena.ontology.OntModel;
 import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.zip.GZIPInputStream;
 
 /**
  * @author paul
- * 
  */
 public class NIFSTDOntologyService extends AbstractOntologyMemoryBackedService {
 
-    private static final String NIFSTD_ONTOLOGY_URL = "url.nifstdOntology";
+    private static final String NIFSTD_ONTOLOGY_FILE = "/data/loader/ontology/nif-gemma.owl.gz";
 
     @Override
     protected String getOntologyName() {
@@ -32,7 +35,23 @@ protected String getOntologyName() {
 
     @Override
     protected String getOntologyUrl() {
-        return Configuration.getString( NIFSTD_ONTOLOGY_URL );
+        return "classpath:" + NIFSTD_ONTOLOGY_FILE;
+    }
+
+    @Override
+    protected boolean getProcessImport() {
+        return false;
     }
 
+    @Override
+    protected OntModel loadModel() {
+        try ( InputStream stream = getClass().getResourceAsStream( NIFSTD_ONTOLOGY_FILE ) ) {
+            if ( stream == null ) {
+                throw new RuntimeException( String.format( "The NIF ontology was not found in classpath at %s.", NIFSTD_ONTOLOGY_FILE ) );
+            }
+            return loadModelFromStream( new GZIPInputStream( stream ) );
+        } catch ( IOException e ) {
+            throw new RuntimeException( e );
+        }
+    }
 }