Refactored package structuring

src/main/java/de/cebitec/common/dbxref/DbXRefService.java → src/main/java/de/cebitec/common/dbxref/api/DbXRefService.java

@@ -14,7 +14,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package de.cebitec.common.dbxref;
+package de.cebitec.common.dbxref.api;
 
 import de.cebitec.common.dbxref.api.DbXRef;
 import de.cebitec.common.dbxref.api.Resource;
@@ -44,7 +44,7 @@ public interface DbXRefService {
         if (it.hasNext()) {
             return it.next();
         } else {
-            return DbXRefResourceRegistry.getDefault();
+            throw new IllegalStateException("No DbXRefService provided");
         }
     }
 

src/main/java/de/cebitec/common/dbxref/DbXRefResourceRegistry.java → src/main/java/de/cebitec/common/dbxref/impl/DbXRefResourceRegistry.java

@@ -14,8 +14,9 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package de.cebitec.common.dbxref;
+package de.cebitec.common.dbxref.impl;
 
+import de.cebitec.common.dbxref.api.DbXRefService;
 import com.google.common.collect.Iterables;
 import de.cebitec.common.dbxref.api.DbXRef;
 import de.cebitec.common.dbxref.api.Resource;
@@ -38,21 +39,10 @@ import org.kohsuke.MetaInfServices;
  *
  * @author cb
  * @author Lukas Jelonek {@literal <ljelonek at cebitec.uni-bielefeld.de>}
- * @deprecated Don't use this class directly. Use the service interface instead. The visibility of this implementation
- * will be changed to package private in a future release.
  */
 @MetaInfServices
 public class DbXRefResourceRegistry implements DbXRefService {
 
-    private static DbXRefResourceRegistry instance;
-
-    public static DbXRefResourceRegistry getDefault() {
-        if (instance == null) {
-            instance = new DbXRefResourceRegistry();
-        }
-        return instance;
-    }
-
     Iterable<? extends DbXRefResolver> getResolvers() {
         // service provider lookup von resolvern
         Iterator<DbXRefResolver> it = ServiceLoader.load(DbXRefResolver.class, this.getClass().getClassLoader()).iterator();

src/main/java/de/cebitec/common/dbxref/DbXrefParser.java → src/main/java/de/cebitec/common/dbxref/impl/DbXrefParser.java

@@ -14,7 +14,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package de.cebitec.common.dbxref;
+package de.cebitec.common.dbxref.impl;
 
 import de.cebitec.common.dbxref.persistence.SimpleDbXRef;
 import de.cebitec.common.dbxref.api.DbXRef;

src/main/java/de/cebitec/common/dbxref/DbXrefParserException.java → src/main/java/de/cebitec/common/dbxref/impl/DbXrefParserException.java

@@ -14,13 +14,13 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package de.cebitec.common.dbxref;
+package de.cebitec.common.dbxref.impl;
 
 /**
  *
  * @author Lukas Jelonek {@literal <ljelonek at cebitec.uni-bielefeld.de>}
  */
-public class DbXrefParserException extends RuntimeException {
+class DbXrefParserException extends RuntimeException {
 
     /**
      * Creates a new instance of

src/main/java/de/cebitec/common/dbxref/DbXrefResourceException.java → src/main/java/de/cebitec/common/dbxref/impl/DbXrefResourceException.java

@@ -14,7 +14,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package de.cebitec.common.dbxref;
+package de.cebitec.common.dbxref.impl;
 
 /**
  *

src/main/java/de/cebitec/common/dbxref/api/GenericResource.java → src/main/java/de/cebitec/common/dbxref/impl/GenericResource.java

@@ -14,9 +14,11 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package de.cebitec.common.dbxref.api;
+package de.cebitec.common.dbxref.impl;
 
 import com.google.common.base.Preconditions;
+import de.cebitec.common.dbxref.api.DbXRef;
+import de.cebitec.common.dbxref.api.Resource;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.HttpURLConnection;

src/main/java/de/cebitec/common/dbxref/providers/CompositeProvider.java

@@ -42,6 +42,8 @@ public class CompositeProvider implements DbXRefResolver {
         Gson gson = new Gson();
         InputStream is = this.getClass().getResourceAsStream("providers.json");
         InputStreamReader isr = new InputStreamReader(is);
+        
+        @SuppressWarnings("unchecked")
         List<Map<String, List<String>>> fromJson = gson.fromJson(isr, List.class);
         for (Map<String, List<String>> entry : fromJson) {
             GenericDbXRefProvider.ResolverData data = new GenericDbXRefProvider.ResolverData();

src/main/java/de/cebitec/common/dbxref/providers/GenericDbXRefProvider.java

@@ -19,7 +19,7 @@ package de.cebitec.common.dbxref.providers;
 import com.google.common.collect.LinkedHashMultimap;
 import com.google.common.collect.Lists;
 import de.cebitec.common.dbxref.api.DbXRef;
-import de.cebitec.common.dbxref.api.GenericResource;
+import de.cebitec.common.dbxref.impl.GenericResource;
 import de.cebitec.common.dbxref.api.Resource;
 import de.cebitec.common.dbxref.api.Resource.Type;
 import de.cebitec.common.dbxref.spi.DbXRefResolver;

src/main/java/de/cebitec/common/dbxref/providers/HttpProvider.java

@@ -16,9 +16,9 @@
  */
 package de.cebitec.common.dbxref.providers;
 
-import de.cebitec.common.dbxref.DbXrefResourceException;
+import de.cebitec.common.dbxref.impl.DbXrefResourceException;
 import de.cebitec.common.dbxref.api.DbXRef;
-import de.cebitec.common.dbxref.api.GenericResource;
+import de.cebitec.common.dbxref.impl.GenericResource;
 import de.cebitec.common.dbxref.spi.DbXRefResolver;
 import de.cebitec.common.dbxref.api.Resource;
 import java.net.URI;

src/test/java/de/cebitec/common/dbxref/DbXRefResourceRegistryTest.java → src/test/java/de/cebitec/common/dbxref/impl/DbXRefResourceRegistryTest.java

@@ -14,7 +14,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package de.cebitec.common.dbxref;
+package de.cebitec.common.dbxref.impl;
 
 import de.cebitec.common.dbxref.persistence.SimpleDbXRef;
 import de.cebitec.common.dbxref.api.Resource;
@@ -28,7 +28,7 @@ import static org.junit.Assert.*;
  * @author cb
  */
 public class DbXRefResourceRegistryTest {
-    
+
     public DbXRefResourceRegistryTest() {
     }
 
@@ -37,9 +37,10 @@ public class DbXRefResourceRegistryTest {
      */
     @Test
     public void testResolve_DbXRef() {
-         DbXRef validGI = new SimpleDbXRef("GI", "731497");
-        Iterable<? extends DbXRefResolver> resolvers = DbXRefResourceRegistry.getDefault().getResolvers();
+        DbXRef validGI = new SimpleDbXRef("GI", "731497");
+        DbXRefResourceRegistry registry = new DbXRefResourceRegistry();
+        Iterable<? extends DbXRefResolver> resolvers = registry.getResolvers();
         System.out.println("resolvers = " + resolvers);
-         Iterable<? extends Resource> resources = DbXRefResourceRegistry.getDefault().resolve(validGI);
+        Iterable<? extends Resource> resources = registry.resolve(validGI);
     }
 }

src/test/java/de/cebitec/common/dbxref/DbXRefServiceRegisteredTest.java → src/test/java/de/cebitec/common/dbxref/impl/DbXRefServiceRegisteredTest.java

@@ -14,8 +14,9 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package de.cebitec.common.dbxref;
+package de.cebitec.common.dbxref.impl;
 
+import de.cebitec.common.dbxref.api.DbXRefService;
 import java.util.ServiceLoader;
 import org.junit.Test;
 import static org.junit.Assert.*;

src/test/java/de/cebitec/common/dbxref/DbXrefParserTest.java → src/test/java/de/cebitec/common/dbxref/impl/DbXrefParserTest.java

@@ -14,7 +14,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package de.cebitec.common.dbxref;
+package de.cebitec.common.dbxref.impl;
 
 import de.cebitec.common.dbxref.api.DbXRef;
 import org.junit.Test;

src/test/java/de/cebitec/common/dbxref/persistence/PersistenceTest.java

@@ -16,7 +16,6 @@
  */
 package de.cebitec.common.dbxref.persistence;
 
-import de.cebitec.common.dbxref.DbXrefParser;
 import de.cebitec.common.dbxref.api.DbXRef;
 import javax.persistence.EntityManager;
 import javax.persistence.EntityManagerFactory;
@@ -35,8 +34,7 @@ public class PersistenceTest {
         EntityManagerFactory emf = Persistence.createEntityManagerFactory("DbXRefTest");
         EntityManager em = emf.createEntityManager();
 
-        DbXrefParser p = new DbXrefParser();
-        DbXRef parse = p.parse("GO:0000001");
+        DbXRef parse = new SimpleDbXRef("GO", "0000001");
         EntityTransaction transaction = em.getTransaction();
         transaction.begin();
         em.persist(parse);

src/test/java/de/cebitec/common/dbxref/providers/ValidResourceAvailableTest.java

@@ -16,8 +16,8 @@
  */
 package de.cebitec.common.dbxref.providers;
 
-import de.cebitec.common.dbxref.DbXrefParser;
 import de.cebitec.common.dbxref.api.DbXRef;
+import de.cebitec.common.dbxref.api.DbXRefService;
 import de.cebitec.common.dbxref.api.Resource;
 import de.cebitec.common.dbxref.spi.DbXRefResolver;
 import java.util.Arrays;
@@ -64,7 +64,7 @@ public class ValidResourceAvailableTest {
 
     public ValidResourceAvailableTest(DbXRefResolver provider, String dbxref) {
         this.provider = provider;
-        this.dbxref = new DbXrefParser().parse(dbxref);
+        this.dbxref = DbXRefService.getInstance().create(dbxref);
     }
 
     @Test