Changeset 412

Timestamp:

06/22/10 17:30:16 (20 months ago)

Author:

rodche

Message:

Modified and temporarily disabled biomart (was down) tests; buildsystem.Measure was duplicated in the bridgedb.rdb and bridgedb modules, so it's now only in org.bridgedb (arc/main/ - to be accessible by other modules's tests)

Location:

trunk

Files:

• org.bridgedb.rdb (modified) (1 prop)
• org.bridgedb.rdb/test/buildsystem (deleted)
• org.bridgedb.rdb/test/org/bridgedb/rdb/Test2.java (modified) (1 diff)
• org.bridgedb.rdb/test/org/bridgedb/rdb/TestStack.java (modified) (1 diff)
• org.bridgedb.server (modified) (1 prop)
• org.bridgedb.webservice.biomart/test/org/bridgedb/webservice/biomart/TestBiomart.java (modified) (4 diffs)
• org.bridgedb/src/buildsystem (moved) (moved from trunk/org.bridgedb/test/buildsystem)

trunk/org.bridgedb.rdb/test/org/bridgedb/rdb/Test2.java

@@ -33 +33 @@
 import org.bridgedb.rdb.SimpleGdb;
 import org.bridgedb.rdb.SimpleGdbFactory;
+import org.junit.Ignore;
 
+//@Ignore
 public class Test2 extends TestCase 
 {

trunk/org.bridgedb.rdb/test/org/bridgedb/rdb/TestStack.java

@@ -13 +13 @@
 import org.bridgedb.Xref;
 import org.bridgedb.bio.BioDataSource;
+import org.junit.Ignore;
 
 import junit.framework.TestCase;
 
+//@Ignore
 public class TestStack extends TestCase
 {

trunk/org.bridgedb.webservice.biomart/test/org/bridgedb/webservice/biomart/TestBiomart.java

@@ -23 +23 @@
 import org.bridgedb.IDMapperException;
 import org.bridgedb.Xref;
-import org.bridgedb.webservice.biomart.util.BiomartClient;
-//import buildsystem.Measure;
 
-import java.io.File;
 import java.io.IOException;
-import java.net.MalformedURLException;
 
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
 
-import junit.framework.TestCase;
-
-import org.bridgedb.webservice.biomart.*;
+import org.junit.Ignore;
+import org.junit.Test;
+import static org.junit.Assert.*;
 
 /**
  * Test identifier mapping using Biomart web service.
  */
-public class TestBiomart extends TestCase
+@Ignore //uncomment if biomart service is down again...
+public class TestBiomart // do not need to extend TestCase
 {
         // disabled test, because it takes several minutes to run
+        //@Test
     public void _testBiomartStub() throws IOException, IDMapperException {
         BiomartStub biomartStub = BiomartStub.getInstance();
@@ -86 +81 @@
     }
 
-    public void testBioMartConnector() throws IOException, IDMapperException
+    @Test
+    public void testBioMartConnector() throws IOException, IDMapperException, ClassNotFoundException
     {
-//        BiomartStub biomartStub = BiomartStub.getInstance();
-//        Map<String, Database> reg = null;
-//        try {
-//            reg = biomartStub.getRegistry();
-//        } catch (Exception e) {
-//            e.printStackTrace();
-//        }
-//        Set<Database> dbs = new HashSet(reg.size());
-//         for (Database db : reg.values()) {
-//             //if (db.visible()) {
-//                 dbs.add(db);
-//             //}
-//                System.out.println (db.getName());
-//         }
+    /*
+        BiomartStub biomartStub = BiomartStub.getInstance();
+        Map<String, Database> reg = null;
+        try {
+            reg = biomartStub.getRegistry();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+        Set<Database> dbs = new HashSet(reg.size());
+         for (Database db : reg.values()) {
+             //if (db.visible()) {
+                 dbs.add(db);
+             //}
+                System.out.println (db.getName());
+         }
         //BiomartStub biomartStub = BiomartStub.getInstance();
 
         //Set<Dataset> datasets = new HashSet(biomartStub.getAvailableDatasets("ensembl"));
+    */
 
-        IDMapperBiomart mapper = new IDMapperBiomart("ensembl", "hsapiens_gene_ensembl");
+        IDMapperBiomart mapper = new IDMapperBiomart("ensembl", "hsapiens_gene_ensembl");
+        //Class.forName("org.bridgedb.webservice.biomart.IDMapperBiomart");
+        //IDMapper mapper = BridgeDb.connect ("idmapper-biomart:http://www.biomart.org/biomart/martservice?mart=ensembl&dataset=hsapiens_gene_ensembl");
                 Set<DataSource> dest = mapper.getCapabilities().getSupportedTgtDataSources(); 
                  
@@ -117 +117 @@
     }
 
+    @Test
     public void testBioMartConnector2() throws IOException, IDMapperException, ClassNotFoundException
     {
                 Class.forName("org.bridgedb.webservice.biomart.IDMapperBiomart");
                 
-                 //IDMapperBiomart mapper = new IDMapperBiomart("hsapiens_gene_ensembl");
                 IDMapper mapper = BridgeDb.connect ("idmapper-biomart:http://www.biomart.org/biomart/martservice?mart=ensembl&dataset=hsapiens_gene_ensembl");
                 Set<DataSource> dest = mapper.getCapabilities().getSupportedTgtDataSources(); 
@@ -155 +155 @@
     }
     
+    
+    @Test
     public void testBioMartMapping() throws IOException, IDMapperException, ClassNotFoundException
     {
-        Class.forName("org.bridgedb.webservice.biomart.IDMapperBiomart");
+       Class.forName("org.bridgedb.webservice.biomart.IDMapperBiomart");
         
-        //IDMapperBiomart mapper = new IDMapperBiomart("hsapiens_gene_ensembl");
        IDMapper mapper = BridgeDb.connect ("idmapper-biomart:http://www.biomart.org/biomart/martservice?mart=ensembl&dataset=hsapiens_gene_ensembl");