From 04e1be91062083b62170bcd4480d1f2823292ffd Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Fri, 13 Apr 2012 11:44:08 -0400
Subject: [PATCH] Better handling of Mongo errors + exceptions

---
 .../sting/gatk/walkers/InsertRODsWalker.java         | 12 ++++++++----
 .../gatk/walkers/variantutils/SelectVariants.java    | 10 +++++++---
 2 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java
index 6faba48eb..2a46031eb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java
@@ -16,6 +16,7 @@ import org.broadinstitute.sting.commandline.RodBinding;
 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.exceptions.StingException;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
@@ -42,8 +43,7 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
     private String RODFileName;
 
     @Override
-    public void initialize()
-    {
+    public void initialize() {
         try {
             mongo = new Mongo(MONGO_HOST, MONGO_PORT);
             DB mongoDb = mongo.getDB(MONGO_DB_NAME);
@@ -64,8 +64,12 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
             // set up primary key
             mongoCollection.ensureIndex(new BasicDBObject("location", 1).append("sample", 1).append("sourceROD", 1).append("alleles", 1), new BasicDBObject("unique", 1));
         }
-        catch (MongoException e) {}
-        catch (java.net.UnknownHostException e) {}
+        catch (MongoException e) {
+            throw e;
+        }
+        catch (java.net.UnknownHostException e) {
+            throw new StingException(e.getMessage(), e);
+        }
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 1d4f8745e..5183930e0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -39,6 +39,7 @@ 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.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.variantcontext.*;
@@ -461,9 +462,12 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             DB mongoDb = mongo.getDB(MONGO_DB_NAME);
             mongoCollection = mongoDb.getCollection(MONGO_VC_COLLECTION);
         }
-        catch (MongoException e) {}
-        catch (java.net.UnknownHostException e) {}
-
+        catch (MongoException e) {
+            throw e;
+        }
+        catch (java.net.UnknownHostException e) {
+            throw new StingException(e.getMessage(), e);
+        }
     }
 
     /**