Changeset 161 for trunk/corelib/test/org/bridgedb/TestBiomart.java

Timestamp:

08/19/09 05:53:32 (3 years ago)

Author:

jgao

Message:

IDMapperBiomart refactor to clean the interface

Files:

• trunk/corelib/test/org/bridgedb/TestBiomart.java (modified) (6 diffs)

trunk/corelib/test/org/bridgedb/TestBiomart.java

@@ -17 +17 @@
 package org.bridgedb;
 
+import org.bridgedb.webservice.biomart.util.BiomartClient;
 import buildsystem.Measure;
 
@@ -30 +31 @@
 import junit.framework.TestCase;
 
-import org.bridgedb.webservice.IDMapperBiomart;
+import org.bridgedb.webservice.biomart.IDMapperBiomart;
 import org.bridgedb.webservice.biomart.*;
 
@@ -41 +42 @@
         BiomartStub biomartStub = BiomartStub.getInstance();
 
-        Map<String, Database> reg = null;
-        try {
-            reg = biomartStub.getRegistry();
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
+        Set<String> marts = biomartStub.availableMarts();
 
-        Set<Database> dbs = new HashSet(reg.size());
-        for (Database db : reg.values()) {
-            //if (db.visible()) {
-                dbs.add(db);
-            //}
-        }
-
-        for (Database db : dbs) {
-                System.out.println (db.getName());
-            Set<Dataset> datasets = new HashSet(biomartStub.getAvailableDatasets(db.getName()));
+        for (String mart : marts) {
+            System.out.println (mart);
+            Set<String> datasets = biomartStub.availableDatasets(mart);
             int nds = datasets.size();
-            for (Dataset ds : datasets) {
-                System.out.println ("\t" + ds.getName());
-                IDMapperBiomart idMapper = new IDMapperBiomart(db.getName(),ds.getName());
+            for (String ds : datasets) {
+                System.out.println ("\t" + ds);
+                IDMapperBiomart idMapper = new IDMapperBiomart(mart, ds);
                 //IDMapper idMapper = BridgeDb.connect("idmapper-biomart:dataset="+ds.getName());
                 IDMapperCapabilities cap = idMapper.getCapabilities();
@@ -83 +72 @@
         }
     }
-    
+
     public void testBioMartConnector() throws IOException, IDMapperException
     {
@@ -101 +90 @@
 //         }
         //BiomartStub biomartStub = BiomartStub.getInstance();
-        
+
         //Set<Dataset> datasets = new HashSet(biomartStub.getAvailableDatasets("ensembl"));
-        
+
          IDMapperBiomart mapper = new IDMapperBiomart("ensembl", "hsapiens_gene_ensembl");
          System.out.println("\n===Supported source data sources===");
@@ -120 +109 @@
     public void testBioMartConnector2() throws IOException, IDMapperException, ClassNotFoundException
     {
-        BiomartStub biomartStub = BiomartStub.getInstance();
         
-        Class.forName("org.bridgedb.webservice.IDMapperBiomart");
-        
-        biomartStub.getAvailableDatasets("ensembl");
+        Class.forName("org.bridgedb.webservice.biomart.IDMapperBiomart");
         
          //IDMapperBiomart mapper = new IDMapperBiomart("hsapiens_gene_ensembl");
-        IDMapper mapper = BridgeDb.connect ("idmapper-biomart:mart=ensembl&dataset=hsapiens_gene_ensembl");
+        IDMapper mapper = BridgeDb.connect ("idmapper-biomart:id-type-filter=false@http://www.biomart.org/biomart/martservice?mart=ensembl&dataset=hsapiens_gene_ensembl");
         System.out.println("\n===Supported source data sources===");
          for (DataSource ds : mapper.getCapabilities().getSupportedSrcDataSources())