Move MongoDB connection handling to a separate class

public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java

@@ -8,7 +8,8 @@ package org.broadinstitute.sting.gatk.walkers;
  * To change this template use File | Settings | File Templates.
  */
 
-import com.mongodb.*;
+import com.mongodb.BasicDBObject;
+import com.mongodb.DBCollection;
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
@@ -17,7 +18,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.db.MongoDB;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
@@ -35,55 +36,36 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
     @Output
     PrintStream out;
 
-    private final static String MONGO_HOST = "gsa4.broadinstitute.org";
-    private final static Integer MONGO_PORT = 43054;
-    private final static String MONGO_DB_NAME = "bjorn";
-    private final static String MONGO_ATTRIBUTES_COLLECTION = "attributes";
-    private final static String MONGO_SAMPLES_COLLECTION = "samples";
-
-    protected Mongo mongo;
-    protected DBCollection mongoAttributes;
-    protected DBCollection mongoSamples;
 
     private String RODFileName;
 
     @Override
     public void initialize() {
-        try {
+        DBCollection mongoAttributes = MongoDB.getAttributesCollection();
-            mongo = new Mongo(MONGO_HOST, MONGO_PORT);
+        DBCollection mongoSamples = MongoDB.getSamplesCollection();
-            DB mongoDb = mongo.getDB(MONGO_DB_NAME);
-            mongoAttributes = mongoDb.getCollection(MONGO_ATTRIBUTES_COLLECTION);
-            mongoSamples = mongoDb.getCollection(MONGO_SAMPLES_COLLECTION);
 
-            RODFileName = input.getSource();
+        RODFileName = input.getSource();
-            int lastSep = RODFileName.lastIndexOf(File.separator);
+        int lastSep = RODFileName.lastIndexOf(File.separator);
-            RODFileName = RODFileName.substring(lastSep + 1);
+        RODFileName = RODFileName.substring(lastSep + 1);
 
-            // set up indices
+        // set up indices
 
-            mongoAttributes.ensureIndex("location");
+        mongoAttributes.ensureIndex("location");
-            mongoAttributes.ensureIndex("sourceROD");
+        mongoAttributes.ensureIndex("sourceROD");
-            mongoAttributes.ensureIndex("contig");
+        mongoAttributes.ensureIndex("contig");
-            mongoAttributes.ensureIndex("start");
+        mongoAttributes.ensureIndex("start");
-            mongoAttributes.ensureIndex("stop");
+        mongoAttributes.ensureIndex("stop");
 
-            mongoSamples.ensureIndex("location");
+        mongoSamples.ensureIndex("location");
-            mongoSamples.ensureIndex("sample");
+        mongoSamples.ensureIndex("sample");
-            mongoSamples.ensureIndex("sourceROD");
+        mongoSamples.ensureIndex("sourceROD");
-            mongoSamples.ensureIndex("contig");
+        mongoSamples.ensureIndex("contig");
-            mongoSamples.ensureIndex("start");
+        mongoSamples.ensureIndex("start");
-            mongoSamples.ensureIndex("stop");
+        mongoSamples.ensureIndex("stop");
 
-            // set up primary keys
+        // set up primary keys
-            mongoAttributes.ensureIndex(new BasicDBObject("location", 1).append("sourceROD", 1).append("alleles", 1), new BasicDBObject("unique", 1));
+        mongoAttributes.ensureIndex(new BasicDBObject("location", 1).append("sourceROD", 1).append("alleles", 1), new BasicDBObject("unique", 1));
-            mongoSamples.ensureIndex(new BasicDBObject("location", 1).append("sourceROD", 1).append("alleles", 1).append("sample", 1), new BasicDBObject("unique", 1));
+        mongoSamples.ensureIndex(new BasicDBObject("location", 1).append("sourceROD", 1).append("alleles", 1).append("sample", 1), new BasicDBObject("unique", 1));
-        }
-        catch (MongoException e) {
-            throw e;
-        }
-        catch (java.net.UnknownHostException e) {
-            throw new StingException(e.getMessage(), e);
-        }
     }
 
     /**
@@ -104,6 +86,9 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
+        DBCollection mongoAttributes = MongoDB.getAttributesCollection();
+        DBCollection mongoSamples = MongoDB.getSamplesCollection();
+
         for ( Feature feature : tracker.getValues(Feature.class, context.getLocation()) ) {
             if ( feature instanceof VariantContext ) {
                 VariantContext vc = (VariantContext) feature;
@@ -131,6 +116,6 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
     }
 
     public void onTraversalDone(Integer result) {
-        mongo.close();
+        MongoDB.close();
     }
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -24,7 +24,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import com.mongodb.*;
+import com.mongodb.BasicDBList;
+import com.mongodb.BasicDBObject;
+import com.mongodb.DBCursor;
+import com.mongodb.DBObject;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
@@ -39,7 +42,7 @@ import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.db.MongoDB;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.variantcontext.*;
@@ -349,16 +352,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
     private Set<String> IDsToKeep = null;
 
-    private final static String MONGO_HOST = "gsa4.broadinstitute.org";
-    private final static Integer MONGO_PORT = 43054;
-    private final static String MONGO_DB_NAME = "bjorn";
-    private final static String MONGO_ATTRIBUTES_COLLECTION = "attributes";
-    private final static String MONGO_SAMPLES_COLLECTION = "samples";
-
-    protected Mongo mongo;
-    protected DBCollection mongoAttributes;
-    protected DBCollection mongoSamples;
-
     /**
      * Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
      */
@@ -458,19 +451,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
                 throw new UserException.CouldNotReadInputFile(rsIDFile, e);
             }
         }
-
-        try {
-            mongo = new Mongo(MONGO_HOST, MONGO_PORT);
-            DB mongoDb = mongo.getDB(MONGO_DB_NAME);
-            mongoAttributes = mongoDb.getCollection(MONGO_ATTRIBUTES_COLLECTION);
-            mongoSamples = mongoDb.getCollection(MONGO_SAMPLES_COLLECTION);
-        }
-        catch (MongoException e) {
-            throw e;
-        }
-        catch (java.net.UnknownHostException e) {
-            throw new StingException(e.getMessage(), e);
-        }
     }
 
     /**
@@ -571,8 +551,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         query.put("start", start);
         // can't know stop location for deletions from reference
 
-        DBCursor attributesCursor = mongoAttributes.find(query);
+        DBCursor attributesCursor = MongoDB.getAttributesCollection().find(query);
-        DBCursor samplesCursor = mongoSamples.find(query);
+        DBCursor samplesCursor = MongoDB.getSamplesCollection().find(query);
 
         Map<Pair<String,List<Allele>>,VariantContextBuilder> attributesFromDB = new HashMap<Pair<String,List<Allele>>,VariantContextBuilder>();
 
@@ -841,7 +821,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     }
 
     public void onTraversalDone(Integer result) {
-        mongo.close();
+        MongoDB.close();
+
         logger.info(result + " records processed.");
 
         if (SELECT_RANDOM_NUMBER) {

public/java/src/org/broadinstitute/sting/utils/db/MongoDB.java

@@ -0,0 +1,52 @@
+package org.broadinstitute.sting.utils.db;
+
+import com.mongodb.DB;
+import com.mongodb.DBCollection;
+import com.mongodb.Mongo;
+import org.broadinstitute.sting.utils.exceptions.StingException;
+
+import java.net.UnknownHostException;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: thibault
+ * Date: 4/26/12
+ * Time: 3:01 PM
+ * Handles Mongo DB connections
+ */
+final public class MongoDB {
+    private final static String MONGO_HOST = "gsa4.broadinstitute.org";
+    private final static Integer MONGO_PORT = 43054;
+    private final static String MONGO_DB_NAME = "bjorn";
+    private final static String MONGO_ATTRIBUTES_COLLECTION = "attributes";
+    private final static String MONGO_SAMPLES_COLLECTION = "samples";
+
+    protected Mongo mongo;
+    protected DBCollection mongoAttributes;
+    protected DBCollection mongoSamples;
+
+    final private static MongoDB INSTANCE = new MongoDB();
+
+    public static DBCollection getAttributesCollection() {
+        return INSTANCE.mongoAttributes;
+    }
+
+    public static DBCollection getSamplesCollection() {
+        return INSTANCE.mongoSamples;
+    }
+
+    public static void close() {
+        INSTANCE.mongo.close();
+    }
+
+    private MongoDB() {
+        try {
+            mongo = new Mongo(MONGO_HOST, MONGO_PORT);
+            DB mongoDb = mongo.getDB(MONGO_DB_NAME);
+            mongoAttributes = mongoDb.getCollection(MONGO_ATTRIBUTES_COLLECTION);
+            mongoSamples = mongoDb.getCollection(MONGO_SAMPLES_COLLECTION);
+        } catch (UnknownHostException e) {
+            throw new StingException(e.getMessage(), e);
+        }
+    }
+}

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java

@@ -1,11 +1,9 @@
 package org.broadinstitute.sting.utils.variantcontext;
 
-import com.mongodb.BasicDBList;
 import com.mongodb.BasicDBObject;
 import org.broad.tribble.Feature;
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.util.ParsingUtils;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;