the cluster version
git-svn-id: https://hyracks.googlecode.com/svn/branches/fullstack_genomix@2956 123451ca-8445-de46-9d55-352943316053
diff --git a/genomix/genomix-hadoop/actual/conf.xml b/genomix/genomix-hadoop/actual/conf.xml
deleted file mode 100755
index 8d2522e..0000000
--- a/genomix/genomix-hadoop/actual/conf.xml
+++ /dev/null
@@ -1,179 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><configuration>
-<property><name>fs.s3n.impl</name><value>org.apache.hadoop.fs.s3native.NativeS3FileSystem</value></property>
-<property><name>mapred.task.cache.levels</name><value>2</value></property>
-<property><name>hadoop.tmp.dir</name><value>/tmp/hadoop-${user.name}</value></property>
-<property><name>hadoop.native.lib</name><value>true</value></property>
-<property><name>map.sort.class</name><value>org.apache.hadoop.util.QuickSort</value></property>
-<property><name>dfs.namenode.decommission.nodes.per.interval</name><value>5</value></property>
-<property><name>dfs.https.need.client.auth</name><value>false</value></property>
-<property><name>ipc.client.idlethreshold</name><value>4000</value></property>
-<property><name>mapred.system.dir</name><value>${hadoop.tmp.dir}/mapred/system</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.hours</name><value>0</value></property>
-<property><name>dfs.namenode.logging.level</name><value>info</value></property>
-<property><name>dfs.datanode.address</name><value>127.0.0.1:0</value></property>
-<property><name>io.skip.checksum.errors</name><value>false</value></property>
-<property><name>fs.default.name</name><value>hdfs://localhost:49270</value></property>
-<property><name>mapred.child.tmp</name><value>./tmp</value></property>
-<property><name>fs.har.impl.disable.cache</name><value>true</value></property>
-<property><name>dfs.safemode.threshold.pct</name><value>0.999f</value></property>
-<property><name>mapred.skip.reduce.max.skip.groups</name><value>0</value></property>
-<property><name>dfs.namenode.handler.count</name><value>10</value></property>
-<property><name>dfs.blockreport.initialDelay</name><value>0</value></property>
-<property><name>mapred.jobtracker.instrumentation</name><value>org.apache.hadoop.mapred.JobTrackerMetricsInst</value></property>
-<property><name>mapred.tasktracker.dns.nameserver</name><value>default</value></property>
-<property><name>io.sort.factor</name><value>10</value></property>
-<property><name>mapred.task.timeout</name><value>600000</value></property>
-<property><name>mapred.max.tracker.failures</name><value>4</value></property>
-<property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>
-<property><name>fs.hdfs.impl</name><value>org.apache.hadoop.hdfs.DistributedFileSystem</value></property>
-<property><name>mapred.queue.default.acl-administer-jobs</name><value>*</value></property>
-<property><name>mapred.queue.default.acl-submit-job</name><value>*</value></property>
-<property><name>mapred.skip.map.auto.incr.proc.count</name><value>true</value></property>
-<property><name>io.mapfile.bloom.size</name><value>1048576</value></property>
-<property><name>dfs.safemode.extension</name><value>0</value></property>
-<property><name>tasktracker.http.threads</name><value>40</value></property>
-<property><name>mapred.job.shuffle.merge.percent</name><value>0.66</value></property>
-<property><name>fs.ftp.impl</name><value>org.apache.hadoop.fs.ftp.FTPFileSystem</value></property>
-<property><name>mapred.output.compress</name><value>false</value></property>
-<property><name>io.bytes.per.checksum</name><value>512</value></property>
-<property><name>topology.node.switch.mapping.impl</name><value>org.apache.hadoop.net.StaticMapping</value></property>
-<property><name>dfs.https.server.keystore.resource</name><value>ssl-server.xml</value></property>
-<property><name>mapred.reduce.slowstart.completed.maps</name><value>0.05</value></property>
-<property><name>mapred.reduce.max.attempts</name><value>4</value></property>
-<property><name>fs.ramfs.impl</name><value>org.apache.hadoop.fs.InMemoryFileSystem</value></property>
-<property><name>dfs.name.edits.dir</name><value>${dfs.name.dir}</value></property>
-<property><name>mapred.skip.map.max.skip.records</name><value>0</value></property>
-<property><name>hadoop.job.ugi</name><value>hadoop,staff,everyone,localaccounts</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.dir</name><value>/jobtracker/jobsInfo</value></property>
-<property><name>dfs.block.size</name><value>67108864</value></property>
-<property><name>fs.s3.buffer.dir</name><value>${hadoop.tmp.dir}/s3</value></property>
-<property><name>job.end.retry.attempts</name><value>0</value></property>
-<property><name>fs.file.impl</name><value>org.apache.hadoop.fs.LocalFileSystem</value></property>
-<property><name>mapred.local.dir.minspacestart</name><value>0</value></property>
-<property><name>mapred.output.compression.type</name><value>RECORD</value></property>
-<property><name>dfs.datanode.ipc.address</name><value>127.0.0.1:0</value></property>
-<property><name>dfs.permissions</name><value>true</value></property>
-<property><name>topology.script.number.args</name><value>100</value></property>
-<property><name>io.mapfile.bloom.error.rate</name><value>0.005</value></property>
-<property><name>mapred.max.tracker.blacklists</name><value>4</value></property>
-<property><name>mapred.task.profile.maps</name><value>0-2</value></property>
-<property><name>dfs.datanode.https.address</name><value>0.0.0.0:50475</value></property>
-<property><name>mapred.userlog.retain.hours</name><value>24</value></property>
-<property><name>dfs.secondary.http.address</name><value>0.0.0.0:50090</value></property>
-<property><name>dfs.replication.max</name><value>512</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
-<property><name>hadoop.security.authorization</name><value>false</value></property>
-<property><name>local.cache.size</name><value>10737418240</value></property>
-<property><name>mapred.min.split.size</name><value>0</value></property>
-<property><name>mapred.map.tasks</name><value>2</value></property>
-<property><name>mapred.child.java.opts</name><value>-Xmx200m</value></property>
-<property><name>dfs.https.client.keystore.resource</name><value>ssl-client.xml</value></property>
-<property><name>dfs.namenode.startup</name><value>REGULAR</value></property>
-<property><name>mapred.job.queue.name</name><value>default</value></property>
-<property><name>dfs.https.address</name><value>0.0.0.0:50470</value></property>
-<property><name>dfs.balance.bandwidthPerSec</name><value>1048576</value></property>
-<property><name>ipc.server.listen.queue.size</name><value>128</value></property>
-<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
-<property><name>job.end.retry.interval</name><value>30000</value></property>
-<property><name>mapred.skip.attempts.to.start.skipping</name><value>2</value></property>
-<property><name>fs.checkpoint.dir</name><value>build/test/data/dfs/namesecondary1,build/test/data/dfs/namesecondary2</value></property>
-<property><name>mapred.reduce.tasks</name><value>1</value></property>
-<property><name>mapred.merge.recordsBeforeProgress</name><value>10000</value></property>
-<property><name>mapred.userlog.limit.kb</name><value>0</value></property>
-<property><name>dfs.max.objects</name><value>0</value></property>
-<property><name>webinterface.private.actions</name><value>false</value></property>
-<property><name>io.sort.spill.percent</name><value>0.80</value></property>
-<property><name>mapred.job.shuffle.input.buffer.percent</name><value>0.70</value></property>
-<property><name>dfs.datanode.dns.nameserver</name><value>default</value></property>
-<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
-<property><name>hadoop.util.hash.type</name><value>murmur</value></property>
-<property><name>dfs.blockreport.intervalMsec</name><value>3600000</value></property>
-<property><name>mapred.map.max.attempts</name><value>4</value></property>
-<property><name>dfs.client.block.write.retries</name><value>3</value></property>
-<property><name>mapred.job.tracker.handler.count</name><value>10</value></property>
-<property><name>mapred.tasktracker.expiry.interval</name><value>600000</value></property>
-<property><name>dfs.https.enable</name><value>false</value></property>
-<property><name>mapred.jobtracker.maxtasks.per.job</name><value>-1</value></property>
-<property><name>mapred.jobtracker.job.history.block.size</name><value>3145728</value></property>
-<property><name>keep.failed.task.files</name><value>false</value></property>
-<property><name>ipc.client.tcpnodelay</name><value>false</value></property>
-<property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
-<property><name>mapred.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>io.map.index.skip</name><value>0</value></property>
-<property><name>ipc.server.tcpnodelay</name><value>false</value></property>
-<property><name>dfs.default.chunk.view.size</name><value>32768</value></property>
-<property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>mapred.reduce.tasks.speculative.execution</name><value>true</value></property>
-<property><name>dfs.datanode.du.reserved</name><value>0</value></property>
-<property><name>fs.checkpoint.period</name><value>3600</value></property>
-<property><name>dfs.web.ugi</name><value>webuser,webgroup</value></property>
-<property><name>mapred.job.reuse.jvm.num.tasks</name><value>1</value></property>
-<property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
-<property><name>dfs.df.interval</name><value>60000</value></property>
-<property><name>dfs.data.dir</name><value>${hadoop.tmp.dir}/dfs/data</value></property>
-<property><name>fs.s3.maxRetries</name><value>4</value></property>
-<property><name>dfs.datanode.dns.interface</name><value>default</value></property>
-<property><name>dfs.support.append</name><value>false</value></property>
-<property><name>dfs.permissions.supergroup</name><value>supergroup</value></property>
-<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
-<property><name>fs.hftp.impl</name><value>org.apache.hadoop.hdfs.HftpFileSystem</value></property>
-<property><name>fs.trash.interval</name><value>0</value></property>
-<property><name>fs.s3.sleepTimeSeconds</name><value>10</value></property>
-<property><name>dfs.replication.min</name><value>1</value></property>
-<property><name>mapred.submit.replication</name><value>10</value></property>
-<property><name>fs.har.impl</name><value>org.apache.hadoop.fs.HarFileSystem</value></property>
-<property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
-<property><name>dfs.namenode.decommission.interval</name><value>3</value></property>
-<property><name>dfs.http.address</name><value>localhost:49271</value></property>
-<property><name>dfs.heartbeat.interval</name><value>3</value></property>
-<property><name>mapred.job.tracker</name><value>local</value></property>
-<property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
-<property><name>dfs.name.dir</name><value>build/test/data/dfs/name1,build/test/data/dfs/name2</value></property>
-<property><name>mapred.line.input.format.linespermap</name><value>1</value></property>
-<property><name>mapred.jobtracker.taskScheduler</name><value>org.apache.hadoop.mapred.JobQueueTaskScheduler</value></property>
-<property><name>mapred.tasktracker.instrumentation</name><value>org.apache.hadoop.mapred.TaskTrackerMetricsInst</value></property>
-<property><name>dfs.datanode.http.address</name><value>127.0.0.1:0</value></property>
-<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
-<property><name>mapred.local.dir.minspacekill</name><value>0</value></property>
-<property><name>dfs.replication.interval</name><value>3</value></property>
-<property><name>io.sort.record.percent</name><value>0.05</value></property>
-<property><name>fs.kfs.impl</name><value>org.apache.hadoop.fs.kfs.KosmosFileSystem</value></property>
-<property><name>mapred.temp.dir</name><value>${hadoop.tmp.dir}/mapred/temp</value></property>
-<property><name>mapred.tasktracker.reduce.tasks.maximum</name><value>2</value></property>
-<property><name>dfs.replication</name><value>2</value></property>
-<property><name>fs.checkpoint.edits.dir</name><value>${fs.checkpoint.dir}</value></property>
-<property><name>mapred.job.reduce.input.buffer.percent</name><value>0.0</value></property>
-<property><name>mapred.tasktracker.indexcache.mb</name><value>10</value></property>
-<property><name>hadoop.logfile.count</name><value>10</value></property>
-<property><name>mapred.skip.reduce.auto.incr.proc.count</name><value>true</value></property>
-<property><name>io.seqfile.compress.blocksize</name><value>1000000</value></property>
-<property><name>fs.s3.block.size</name><value>67108864</value></property>
-<property><name>mapred.tasktracker.taskmemorymanager.monitoring-interval</name><value>5000</value></property>
-<property><name>mapred.acls.enabled</name><value>false</value></property>
-<property><name>mapred.queue.names</name><value>default</value></property>
-<property><name>dfs.access.time.precision</name><value>3600000</value></property>
-<property><name>fs.hsftp.impl</name><value>org.apache.hadoop.hdfs.HsftpFileSystem</value></property>
-<property><name>mapred.task.tracker.http.address</name><value>0.0.0.0:50060</value></property>
-<property><name>mapred.reduce.parallel.copies</name><value>5</value></property>
-<property><name>io.seqfile.lazydecompress</name><value>true</value></property>
-<property><name>io.sort.mb</name><value>100</value></property>
-<property><name>ipc.client.connection.maxidletime</name><value>10000</value></property>
-<property><name>mapred.compress.map.output</name><value>false</value></property>
-<property><name>mapred.task.tracker.report.address</name><value>127.0.0.1:0</value></property>
-<property><name>ipc.client.kill.max</name><value>10</value></property>
-<property><name>ipc.client.connect.max.retries</name><value>10</value></property>
-<property><name>fs.s3.impl</name><value>org.apache.hadoop.fs.s3.S3FileSystem</value></property>
-<property><name>mapred.job.tracker.http.address</name><value>0.0.0.0:50030</value></property>
-<property><name>io.file.buffer.size</name><value>4096</value></property>
-<property><name>mapred.jobtracker.restart.recover</name><value>false</value></property>
-<property><name>io.serializations</name><value>org.apache.hadoop.io.serializer.WritableSerialization</value></property>
-<property><name>dfs.datanode.handler.count</name><value>3</value></property>
-<property><name>mapred.reduce.copy.backoff</name><value>300</value></property>
-<property><name>mapred.task.profile</name><value>false</value></property>
-<property><name>dfs.replication.considerLoad</name><value>true</value></property>
-<property><name>jobclient.output.filter</name><value>FAILED</value></property>
-<property><name>mapred.tasktracker.map.tasks.maximum</name><value>2</value></property>
-<property><name>io.compression.codecs</name><value>org.apache.hadoop.io.compress.DefaultCodec,org.apache.hadoop.io.compress.GzipCodec,org.apache.hadoop.io.compress.BZip2Codec</value></property>
-<property><name>fs.checkpoint.size</name><value>67108864</value></property>
-</configuration>
\ No newline at end of file
diff --git a/genomix/genomix-hadoop/actual/result2/.part-00000.crc b/genomix/genomix-hadoop/actual/result2/.part-00000.crc
deleted file mode 100755
index d254c47..0000000
--- a/genomix/genomix-hadoop/actual/result2/.part-00000.crc
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-hadoop/actual/result2/part-00000 b/genomix/genomix-hadoop/actual/result2/part-00000
deleted file mode 100755
index 4c44896..0000000
--- a/genomix/genomix-hadoop/actual/result2/part-00000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java
index a72d740..42b8309 100755
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java
@@ -17,11 +17,6 @@
import java.io.IOException;
import java.util.Iterator;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.IntWritable;
-import org.apache.hadoop.io.LongWritable;
-import org.apache.hadoop.io.VLongWritable;
import org.apache.hadoop.mapred.MapReduceBase;
import org.apache.hadoop.mapred.OutputCollector;
import org.apache.hadoop.mapred.Reducer;
@@ -30,13 +25,14 @@
/**
* This class implement the combiner operator of Mapreduce model
*/
+@SuppressWarnings("deprecation")
public class GenomixCombiner extends MapReduceBase implements
- Reducer<ValueBytesWritable, ValueWritable, ValueBytesWritable, ValueWritable> {
- public ValueWritable vaWriter = new ValueWritable();
+ Reducer<KmerBytesWritable, AdjacentWritable, KmerBytesWritable, AdjacentWritable> {
+ public AdjacentWritable vaWriter = new AdjacentWritable();
@Override
- public void reduce(ValueBytesWritable key, Iterator<ValueWritable> values,
- OutputCollector<ValueBytesWritable, ValueWritable> output, Reporter reporter) throws IOException {
+ public void reduce(KmerBytesWritable key, Iterator<AdjacentWritable> values,
+ OutputCollector<KmerBytesWritable, AdjacentWritable> output, Reporter reporter) throws IOException {
byte groupByAdjList = 0;
int count = 0;
byte bytCount = 0;
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java
index 4699a7d..575c923 100755
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java
@@ -16,23 +16,14 @@
package edu.uci.ics.graphbuilding;
import java.io.IOException;
-
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.IntWritable;
-import org.apache.hadoop.io.LongWritable;
-import org.apache.hadoop.io.SequenceFile.CompressionType;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.io.VLongWritable;
-import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.FileInputFormat;
import org.apache.hadoop.mapred.FileOutputFormat;
import org.apache.hadoop.mapred.JobClient;
import org.apache.hadoop.mapred.JobConf;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.hadoop.mapred.TextInputFormat;
-import org.apache.hadoop.mapred.TextOutputFormat;
import org.kohsuke.args4j.CmdLineParser;
import org.kohsuke.args4j.Option;
@@ -70,13 +61,13 @@
conf.setReducerClass(GenomixReducer.class);
conf.setCombinerClass(GenomixCombiner.class);
- conf.setMapOutputKeyClass(ValueBytesWritable.class);
- conf.setMapOutputValueClass(ValueWritable.class);
+ conf.setMapOutputKeyClass(KmerBytesWritable.class);
+ conf.setMapOutputValueClass(AdjacentWritable.class);
conf.setInputFormat(TextInputFormat.class);
conf.setOutputFormat(SequenceFileOutputFormat.class);
- conf.setOutputKeyClass(ValueBytesWritable.class);
- conf.setOutputValueClass(ValueWritable.class);
+ conf.setOutputKeyClass(KmerBytesWritable.class);
+ conf.setOutputValueClass(AdjacentWritable.class);
FileInputFormat.setInputPaths(conf, new Path(inputPath));
FileOutputFormat.setOutputPath(conf, new Path(outputPath));
conf.setNumReduceTasks(numReducers);
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java
index d711114..77772e2 100755
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java
@@ -18,8 +18,6 @@
import java.io.IOException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-
-//import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.JobConf;
@@ -33,7 +31,7 @@
*/
@SuppressWarnings("deprecation")
public class GenomixMapper extends MapReduceBase implements
- Mapper<LongWritable, Text, ValueBytesWritable, ValueWritable> {
+ Mapper<LongWritable, Text, KmerBytesWritable, AdjacentWritable> {
public class CurrenByte {
public byte curByte;
@@ -41,8 +39,8 @@
}
public static int KMER_SIZE;
- public ValueWritable outputAdjList = new ValueWritable();
- public ValueBytesWritable outputKmer = new ValueBytesWritable();
+ public AdjacentWritable outputAdjList = new AdjacentWritable();
+ public KmerBytesWritable outputKmer = new KmerBytesWritable();
@Override
public void configure(JobConf job) {
@@ -91,7 +89,7 @@
C 01000000 64
T 10000000 128*/
@Override
- public void map(LongWritable key, Text value, OutputCollector<ValueBytesWritable, ValueWritable> output,
+ public void map(LongWritable key, Text value, OutputCollector<KmerBytesWritable, AdjacentWritable> output,
Reporter reporter) throws IOException {
/* A 00
G 01
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java
index 951f7b1..167e756 100755
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java
@@ -16,11 +16,6 @@
import java.io.IOException;
import java.util.Iterator;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.IntWritable;
-import org.apache.hadoop.io.LongWritable;
-import org.apache.hadoop.io.VLongWritable;
import org.apache.hadoop.mapred.MapReduceBase;
import org.apache.hadoop.mapred.OutputCollector;
import org.apache.hadoop.mapred.Reducer;
@@ -29,19 +24,20 @@
/**
* This class implement reducer operator of mapreduce model
*/
+@SuppressWarnings("deprecation")
public class GenomixReducer extends MapReduceBase implements
- Reducer<ValueBytesWritable, ValueWritable, ValueBytesWritable, ValueWritable> {
- ValueWritable valWriter = new ValueWritable();
+ Reducer<KmerBytesWritable, AdjacentWritable, KmerBytesWritable, AdjacentWritable> {
+ AdjacentWritable valWriter = new AdjacentWritable();
@Override
- public void reduce(ValueBytesWritable key, Iterator<ValueWritable> values,
- OutputCollector<ValueBytesWritable, ValueWritable> output, Reporter reporter) throws IOException {
+ public void reduce(KmerBytesWritable key, Iterator<AdjacentWritable> values,
+ OutputCollector<KmerBytesWritable, AdjacentWritable> output, Reporter reporter) throws IOException {
byte groupByAdjList = 0;
int count = 0;
byte bytCount = 0;
while (values.hasNext()) {
//Merge By the all adjacent Nodes;
- ValueWritable geneValue = values.next();
+ AdjacentWritable geneValue = values.next();
groupByAdjList = (byte) (groupByAdjList | geneValue.getFirst());
count = count + (int) geneValue.getSecond();
}
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java
index 3b6c377..ac2d773 100755
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java
@@ -46,12 +46,12 @@
public class GraphBuildingTest {
private static final String ACTUAL_RESULT_DIR = "actual";
+ @SuppressWarnings("deprecation")
private JobConf conf = new JobConf();
private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
private static final String DATA_PATH = "data/webmap/text.txt";
private static final String HDFS_PATH = "/webmap";
private static final String RESULT_PATH = "/result2";
- private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR + RESULT_PATH + "/part-00000";
private static final String EXPECTED_PATH = "expected/result2";
private static final String TEST_SOURCE_DIR = "testactual/source.txt";
@@ -59,6 +59,7 @@
private MiniMRCluster mrCluster;
private FileSystem dfs;
+ @SuppressWarnings("resource")
@Test
public void test() throws Exception {
FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
@@ -72,8 +73,8 @@
SequenceFile.Reader reader = null;
Path path = new Path(RESULT_PATH + "/part-00000");
reader = new SequenceFile.Reader(dfs, path, conf);
- ValueBytesWritable key = (ValueBytesWritable) ReflectionUtils.newInstance(reader.getKeyClass(), conf);
- ValueWritable value = (ValueWritable) ReflectionUtils.newInstance(reader.getValueClass(), conf);
+ KmerBytesWritable key = (KmerBytesWritable) ReflectionUtils.newInstance(reader.getKeyClass(), conf);
+ AdjacentWritable value = (AdjacentWritable) ReflectionUtils.newInstance(reader.getValueClass(), conf);
File filePathTo = new File(TEST_SOURCE_DIR);
BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
while (reader.next(key, value)) {