Remove tests using MRUnit (whose old API doesn't work with MultipleOutputs)
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/TestPathNodeInitial.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/TestPathNodeInitial.java
deleted file mode 100644
index f24fdc1..0000000
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/TestPathNodeInitial.java
+++ /dev/null
@@ -1,60 +0,0 @@
-package edu.uci.ics.genomix.hadoop.pmcommon;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.io.NullWritable;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapred.SequenceFileOutputFormat;
-import org.apache.hadoop.mapred.lib.MultipleOutputs;
-import org.apache.hadoop.mrunit.MapDriver;
-import org.apache.hadoop.mrunit.ReduceDriver;
-import org.junit.Test;
-
-import edu.uci.ics.genomix.hadoop.graphclean.mergepaths.h3.MergePathsH3.MergeMessageFlag;
-import edu.uci.ics.genomix.hadoop.pmcommon.NodeWithFlagWritable;
-import edu.uci.ics.genomix.hadoop.pmcommon.PathNodeInitial;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.NodeWritable;
-import edu.uci.ics.genomix.type.PositionListWritable;
-import edu.uci.ics.genomix.type.PositionWritable;
-
-@SuppressWarnings("deprecation")
-public class TestPathNodeInitial {
- PositionWritable posn1 = new PositionWritable(0, (byte) 1);
- PositionWritable posn2 = new PositionWritable(1, (byte) 1);
- PositionWritable posn3 = new PositionWritable(2, (byte) 1);
- PositionWritable posn4 = new PositionWritable(3, (byte) 1);
- PositionWritable posn5 = new PositionWritable(5, (byte) 1);
- String kmerString = "ATGCA";
- KmerBytesWritable kmer = new KmerBytesWritable(kmerString.length(), kmerString);
- JobConf conf = new JobConf();
- MultipleOutputs mos = new MultipleOutputs(conf);
-
- {
- conf.set("sizeKmer", String.valueOf(kmerString.length()));
- }
-
-// @Test
- public void testNoNeighbors() throws IOException {
- NodeWritable noNeighborNode = new NodeWritable(posn1, new PositionListWritable(), new PositionListWritable(),
- new PositionListWritable(), new PositionListWritable(), kmer);
- NodeWithFlagWritable output = new NodeWithFlagWritable((byte) (MergeMessageFlag.MSG_SELF | MergeMessageFlag.IS_COMPLETE), noNeighborNode);
- // test mapper
- new MapDriver<NodeWritable, NullWritable, PositionWritable, NodeWithFlagWritable>()
- .withMapper(new PathNodeInitial.PathNodeInitialMapper())
- .withConfiguration(conf)
- .withInput(noNeighborNode, NullWritable.get())
- .withOutput(posn1, output)
- .runTest();
- // test reducer
-// MultipleOutputs.addNamedOutput(conf, "complete", SequenceFileOutputFormat.class, PositionWritable.class, MessageWritableNodeWithFlag.class);
- new ReduceDriver<PositionWritable, NodeWithFlagWritable, PositionWritable, NodeWithFlagWritable>()
- .withReducer(new PathNodeInitial.PathNodeInitialReducer())
- .withConfiguration(conf)
- .withInput(posn1, Arrays.asList(output))
- .runTest();
- }
-}