use java.util.logging instead of apache commons logging
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/config/GenomixJobConf.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/config/GenomixJobConf.java
index 7652f5a..e907ac7 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/config/GenomixJobConf.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/config/GenomixJobConf.java
@@ -43,13 +43,19 @@
public class GenomixJobConf extends JobConf {
static {
- /*
- * Prefer logging.properties from the following four places (in order):
- * 1. the passed in system property "java.util.logging.config.file"
- * 2. ${app.home}/conf/logging.properties
- * 3. src/main/resources/conf/logging.properties
- * 4. src/test/resources/conf/logging.properties
- */
+ loadLoggingFile();
+ }
+
+ /**
+ * Utility to catch logging.properties when they aren't set using JVM parameters.
+ *
+ * Prefer logging.properties from the following four places (in order):
+ * 1. the passed in system property "java.util.logging.config.file" (if it exists, we won't change anything)
+ * 2. ${app.home}/conf/logging.properties
+ * 3. src/main/resources/conf/logging.properties
+ * 4. src/test/resources/conf/logging.properties
+ */
+ private static void loadLoggingFile() {
if (System.getProperty("java.util.logging.config.file") == null) {
String logBasePath = new File("src/main/resources/conf/logging.properties").isFile() ? "src/main/resources" : "src/test/resources";
String logProperties = System.getProperty("app.home", logBasePath) + "/conf/logging.properties";
@@ -60,7 +66,6 @@
}
}
}
-
/* The following section ties together command-line options with a global JobConf
* Each variable has an annotated, command-line Option which is private here but
diff --git a/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java b/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
index 5485eb5..65b23d9 100644
--- a/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
+++ b/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
@@ -18,15 +18,11 @@
import java.io.DataOutputStream;
import java.io.File;
import java.io.FileOutputStream;
-import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
-import java.util.Properties;
+import java.util.logging.Logger;
import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.mapred.FileInputFormat;
@@ -41,7 +37,6 @@
import edu.uci.ics.genomix.minicluster.GenomixClusterManager.ClusterType;
import edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat;
import edu.uci.ics.genomix.pregelix.format.P2InitialGraphCleanInputFormat;
-import edu.uci.ics.genomix.pregelix.operator.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeRemoveVertex;
import edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.P1ForPathMergeVertex;
@@ -52,7 +47,6 @@
import edu.uci.ics.genomix.pregelix.operator.splitrepeat.SplitRepeatVertex;
import edu.uci.ics.genomix.pregelix.operator.tipremove.TipRemoveVertex;
import edu.uci.ics.genomix.pregelix.operator.unrolltandemrepeat.UnrollTandemRepeat;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.hyracks.api.exceptions.HyracksException;
import edu.uci.ics.pregelix.api.job.PregelixJob;
import edu.uci.ics.pregelix.api.util.BspUtils;
@@ -62,7 +56,7 @@
*/
public class GenomixDriver {
- private static final Log LOG = LogFactory.getLog(GenomixDriver.class);
+ private static final Logger LOG = Logger.getLogger(GenomixDriver.class.getName());
private static final String HADOOP_CONF = "hadoop.conf.xml";
private String prevOutput;
private String curOutput;
diff --git a/genomix/genomix-driver/src/test/java/edu/uci/ics/genomix/driver/realtests/SingleLongReadCreateTool.java b/genomix/genomix-driver/src/test/java/edu/uci/ics/genomix/driver/realtests/SingleLongReadCreateTool.java
index fa75808..43c4d65 100644
--- a/genomix/genomix-driver/src/test/java/edu/uci/ics/genomix/driver/realtests/SingleLongReadCreateTool.java
+++ b/genomix/genomix-driver/src/test/java/edu/uci/ics/genomix/driver/realtests/SingleLongReadCreateTool.java
@@ -4,11 +4,13 @@
import java.io.IOException;
import java.util.HashSet;
import java.util.Random;
+import java.util.logging.Logger;
import org.apache.commons.io.FileUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
+import edu.uci.ics.genomix.driver.GenomixDriver;
import edu.uci.ics.genomix.hyracks.graph.driver.Driver;
import edu.uci.ics.genomix.type.KmerBytesWritable;
@@ -19,7 +21,7 @@
* target path: relative path: longreadfortest
*/
private static final char[] symbols = new char[4];
- private static final Log LOG = LogFactory.getLog(Driver.class);
+ private static final Logger LOG = Logger.getLogger(Driver.class.getName());
static {
symbols[0] = 'A';
symbols[1] = 'C';
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/ReadsKeyValueParserFactory.java
index 1287083..5ae4651 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/ReadsKeyValueParserFactory.java
@@ -17,6 +17,7 @@
import java.io.IOException;
import java.nio.ByteBuffer;
+import java.util.logging.Logger;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@@ -47,7 +48,7 @@
public class ReadsKeyValueParserFactory implements IKeyValueParserFactory<LongWritable, Text> {
private static final long serialVersionUID = 1L;
- private static final Log LOG = LogFactory.getLog(ReadsKeyValueParserFactory.class);
+ private static final Logger LOG = Logger.getLogger(ReadsKeyValueParserFactory.class.getName());
public static final int OutputKmerField = 0;
public static final int OutputNodeField = 1;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/aggregators/MergeKmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/aggregators/MergeKmerAggregateFactory.java
index 50243f9..3cb0354 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/aggregators/MergeKmerAggregateFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/aggregators/MergeKmerAggregateFactory.java
@@ -17,6 +17,7 @@
import java.io.DataOutput;
import java.io.IOException;
+import java.util.logging.Logger;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@@ -35,7 +36,7 @@
public class MergeKmerAggregateFactory implements IAggregatorDescriptorFactory {
private static final long serialVersionUID = 1L;
- private static final Log LOG = LogFactory.getLog(MergeKmerAggregateFactory.class);
+ private static final Logger LOG = Logger.getLogger(MergeKmerAggregateFactory.class.getName());
private final int kmerSize;
@@ -111,7 +112,7 @@
NodeWritable localUniNode = (NodeWritable) state.state;
try {
if (localUniNode.getSerializedLength() > frameSize / 2) {
- LOG.warn("MergeKmer: output data kmerByteSize is too big: " + localUniNode.getSerializedLength());
+ LOG.warning("MergeKmer: output data kmerByteSize is too big: " + localUniNode.getSerializedLength());
}
fieldOutput.write(localUniNode.marshalToByteArray(), 0, localUniNode.getSerializedLength());
tupleBuilder.addFieldEndOffset();
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/driver/Driver.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/driver/Driver.java
index 7d0655a..ae76da3 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/driver/Driver.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/driver/Driver.java
@@ -22,9 +22,8 @@
import java.util.EnumSet;
import java.util.List;
import java.util.Map;
+import java.util.logging.Logger;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.mapred.FileInputFormat;
@@ -54,7 +53,7 @@
BUILD_UNMERGED_GRAPH,
}
- private static final Log LOG = LogFactory.getLog(Driver.class);
+ private static final Logger LOG = Logger.getLogger(Driver.class.getName());
private JobGen jobGen;
private boolean profiling;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/job/JobGenBrujinGraph.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/job/JobGenBrujinGraph.java
index 4e1add3..bf13da8 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/job/JobGenBrujinGraph.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/job/JobGenBrujinGraph.java
@@ -17,6 +17,7 @@
import java.io.IOException;
import java.util.Map;
+import java.util.logging.Logger;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@@ -26,6 +27,7 @@
import org.apache.hadoop.mapred.lib.NLineInputFormat;
import edu.uci.ics.genomix.config.GenomixJobConf;
+import edu.uci.ics.genomix.driver.GenomixDriver;
import edu.uci.ics.genomix.hyracks.data.accessors.KmerHashPartitioncomputerFactory;
import edu.uci.ics.genomix.hyracks.data.accessors.KmerNormarlizedComputerFactory;
import edu.uci.ics.genomix.hyracks.data.primitive.KmerPointable;
@@ -79,7 +81,7 @@
}
protected ConfFactory hadoopJobConfFactory;
- protected static final Log LOG = LogFactory.getLog(JobGenBrujinGraph.class);
+ private static final Logger LOG = Logger.getLogger(JobGenBrujinGraph.class.getName());
private static final int DEFAULT_FRAME_LIMIT = 4096;
private static final int DEFAULT_FRAME_SIZE = 65535;
protected String[] ncNodeNames;
@@ -93,7 +95,7 @@
protected OutputFormat outputFormat;
protected void logDebug(String status) {
- LOG.debug(status + " nc nodes:" + ncNodeNames.length);
+ LOG.fine(status + " nc nodes:" + ncNodeNames.length);
}
public JobGenBrujinGraph(GenomixJobConf job, Scheduler scheduler, final Map<String, NodeControllerInfo> ncMap,