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Better handling of Mongo errors + exceptions

This commit is contained in:
Joel Thibault 2012-04-13 11:44:08 -04:00
parent ca737479cf
commit 04e1be9106
2 changed files with 15 additions and 7 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java
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@ -16,6 +16,7 @@ import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File; import java.io.File;
@ -42,8 +43,7 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
private String RODFileName; private String RODFileName;
@Override @Override
public void initialize() public void initialize() {
{
try { try {
mongo = new Mongo(MONGO_HOST, MONGO_PORT); mongo = new Mongo(MONGO_HOST, MONGO_PORT);
DB mongoDb = mongo.getDB(MONGO_DB_NAME); DB mongoDb = mongo.getDB(MONGO_DB_NAME);
@ -64,8 +64,12 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
// set up primary key // set up primary key
mongoCollection.ensureIndex(new BasicDBObject("location", 1).append("sample", 1).append("sourceROD", 1).append("alleles", 1), new BasicDBObject("unique", 1)); mongoCollection.ensureIndex(new BasicDBObject("location", 1).append("sample", 1).append("sourceROD", 1).append("alleles", 1), new BasicDBObject("unique", 1));
} }
catch (MongoException e) {} catch (MongoException e) {
catch (java.net.UnknownHostException e) {} throw e;
}
catch (java.net.UnknownHostException e) {
throw new StingException(e.getMessage(), e);
}
} }
/** /**

10
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -39,6 +39,7 @@ import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.collections.Pair; 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.exceptions.UserException;
import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.variantcontext.*; 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); DB mongoDb = mongo.getDB(MONGO_DB_NAME);
mongoCollection = mongoDb.getCollection(MONGO_VC_COLLECTION); mongoCollection = mongoDb.getCollection(MONGO_VC_COLLECTION);
} }
catch (MongoException e) {} catch (MongoException e) {
catch (java.net.UnknownHostException e) {} throw e;
}
catch (java.net.UnknownHostException e) {
throw new StingException(e.getMessage(), e);
}
} }
/** /**