Merge branch 'fullstack_genomix' of https://code.google.com/p/hyracks into fullstack_genomix
diff --git a/.gitignore b/.gitignore
index 4a4cb4b..31c9fc1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,4 +13,4 @@
derby.log
hadoop-conf-tmp
metastore_db
-teststore
\ No newline at end of file
+teststore
diff --git a/algebricks/algebricks-common/pom.xml b/algebricks/algebricks-common/pom.xml
index 8311b8a..0e840fa 100644
--- a/algebricks/algebricks-common/pom.xml
+++ b/algebricks/algebricks-common/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,7 +27,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
diff --git a/algebricks/algebricks-compiler/pom.xml b/algebricks/algebricks-compiler/pom.xml
index 74a8ef7..2f78812 100644
--- a/algebricks/algebricks-compiler/pom.xml
+++ b/algebricks/algebricks-compiler/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,12 +27,12 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-rewriter</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-core</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
diff --git a/algebricks/algebricks-core/pom.xml b/algebricks/algebricks-core/pom.xml
index dc2ddd0..11b03ee 100644
--- a/algebricks/algebricks-core/pom.xml
+++ b/algebricks/algebricks-core/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,27 +27,27 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-rtree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-runtime</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
diff --git a/algebricks/algebricks-data/pom.xml b/algebricks/algebricks-data/pom.xml
index 1b6646f..1ca1557 100644
--- a/algebricks/algebricks-data/pom.xml
+++ b/algebricks/algebricks-data/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,12 +27,12 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
diff --git a/algebricks/algebricks-examples/piglet-example/pom.xml b/algebricks/algebricks-examples/piglet-example/pom.xml
index 7294979..4b101d7 100644
--- a/algebricks/algebricks-examples/piglet-example/pom.xml
+++ b/algebricks/algebricks-examples/piglet-example/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-examples</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -89,7 +89,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-compiler</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>junit</groupId>
diff --git a/algebricks/algebricks-examples/pom.xml b/algebricks/algebricks-examples/pom.xml
index b19150c..a02379d 100644
--- a/algebricks/algebricks-examples/pom.xml
+++ b/algebricks/algebricks-examples/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<modules>
diff --git a/algebricks/algebricks-rewriter/pom.xml b/algebricks/algebricks-rewriter/pom.xml
index 172d7b8..9fd5aac 100644
--- a/algebricks/algebricks-rewriter/pom.xml
+++ b/algebricks/algebricks-rewriter/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,7 +27,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-core</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
diff --git a/algebricks/algebricks-runtime/pom.xml b/algebricks/algebricks-runtime/pom.xml
index bdb8c0f..a2ad833 100644
--- a/algebricks/algebricks-runtime/pom.xml
+++ b/algebricks/algebricks-runtime/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,27 +27,27 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-rtree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-data</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
diff --git a/algebricks/algebricks-tests/pom.xml b/algebricks/algebricks-tests/pom.xml
index 02b7c45..031dfbe 100644
--- a/algebricks/algebricks-tests/pom.xml
+++ b/algebricks/algebricks-tests/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -85,7 +85,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-compiler</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>junit</groupId>
@@ -96,17 +96,17 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
diff --git a/algebricks/pom.xml b/algebricks/pom.xml
index d7c871a..e1abc89 100644
--- a/algebricks/pom.xml
+++ b/algebricks/pom.xml
@@ -2,7 +2,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<packaging>pom</packaging>
<name>algebricks</name>
diff --git a/genomix/genomix-data/pom.xml b/genomix/genomix-data/pom.xml
index 4faf4a3..2dd44bb 100644
--- a/genomix/genomix-data/pom.xml
+++ b/genomix/genomix-data/pom.xml
@@ -8,7 +8,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>genomix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<properties>
diff --git a/genomix/genomix-hadoop/actual1/conf.xml b/genomix/genomix-hadoop/actual1/conf.xml
deleted file mode 100644
index 506913d..0000000
--- a/genomix/genomix-hadoop/actual1/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:61115</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:61116</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/actual1/result1/.part-00000.crc b/genomix/genomix-hadoop/actual1/result1/.part-00000.crc
deleted file mode 100644
index 3422e04..0000000
--- a/genomix/genomix-hadoop/actual1/result1/.part-00000.crc
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-hadoop/actual1/result1/part-00000 b/genomix/genomix-hadoop/actual1/result1/part-00000
deleted file mode 100755
index c21f5f6..0000000
--- a/genomix/genomix-hadoop/actual1/result1/part-00000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-hadoop/actual2/conf.xml b/genomix/genomix-hadoop/actual2/conf.xml
deleted file mode 100644
index ff11b9e..0000000
--- a/genomix/genomix-hadoop/actual2/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:61195</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:61196</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/actual2/result2/.part-00000.crc b/genomix/genomix-hadoop/actual2/result2/.part-00000.crc
deleted file mode 100644
index 3f8c2c5..0000000
--- a/genomix/genomix-hadoop/actual2/result2/.part-00000.crc
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-hadoop/actual2/result2/part-00000 b/genomix/genomix-hadoop/actual2/result2/part-00000
deleted file mode 100755
index ea3e875..0000000
--- a/genomix/genomix-hadoop/actual2/result2/part-00000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-hadoop/actual3/complete2/.complete2-r-00000.crc b/genomix/genomix-hadoop/actual3/complete2/.complete2-r-00000.crc
deleted file mode 100644
index b0b2753..0000000
--- a/genomix/genomix-hadoop/actual3/complete2/.complete2-r-00000.crc
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-hadoop/actual3/complete2/complete2-r-00000 b/genomix/genomix-hadoop/actual3/complete2/complete2-r-00000
deleted file mode 100755
index d3d3667..0000000
--- a/genomix/genomix-hadoop/actual3/complete2/complete2-r-00000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-hadoop/actual3/conf.xml b/genomix/genomix-hadoop/actual3/conf.xml
deleted file mode 100644
index 16a0edc..0000000
--- a/genomix/genomix-hadoop/actual3/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:62106</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:62107</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/actual5/conf.xml b/genomix/genomix-hadoop/actual5/conf.xml
deleted file mode 100644
index d19b061..0000000
--- a/genomix/genomix-hadoop/actual5/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:58289</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:58290</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/actual5/result5/.part-00000.crc b/genomix/genomix-hadoop/actual5/result5/.part-00000.crc
deleted file mode 100644
index dafaae3..0000000
--- a/genomix/genomix-hadoop/actual5/result5/.part-00000.crc
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-hadoop/actual5/result5/part-00000 b/genomix/genomix-hadoop/actual5/result5/part-00000
deleted file mode 100755
index deeff28..0000000
--- a/genomix/genomix-hadoop/actual5/result5/part-00000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-hadoop/compare/result1/comparesource.txt b/genomix/genomix-hadoop/compare/result1/comparesource.txt
deleted file mode 100644
index ba52008..0000000
--- a/genomix/genomix-hadoop/compare/result1/comparesource.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-GCA ACT|T 3
-AGC |A 1
-CGC T|AT 2
-TGC |A 1
-ATC C|G 2
-TCG A|C 2
-CAT G|C 2
-GCT C| 1
diff --git a/genomix/genomix-hadoop/compare/result2/comparesource.txt b/genomix/genomix-hadoop/compare/result2/comparesource.txt
deleted file mode 100644
index db55a38..0000000
--- a/genomix/genomix-hadoop/compare/result2/comparesource.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-GCA -72
-AGC 1
-CGC -119
-TGC 1
-ATC 36
-TCG 18
-CAT 66
-GCT 32
diff --git a/genomix/genomix-hadoop/compare/result3/comparesource.txt b/genomix/genomix-hadoop/compare/result3/comparesource.txt
deleted file mode 100644
index 5f9dd78..0000000
--- a/genomix/genomix-hadoop/compare/result3/comparesource.txt
+++ /dev/null
@@ -1 +0,0 @@
-02 71 66 1
diff --git a/genomix/genomix-hadoop/compare/result5/comparesource.txt b/genomix/genomix-hadoop/compare/result5/comparesource.txt
deleted file mode 100644
index 6f4bd5e..0000000
--- a/genomix/genomix-hadoop/compare/result5/comparesource.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-GCA AT|T 2
-AGC |A 1
-TGC |A 1
diff --git a/genomix/genomix-hadoop/data/.DS_Store b/genomix/genomix-hadoop/data/.DS_Store
new file mode 100644
index 0000000..07f4ca0
--- /dev/null
+++ b/genomix/genomix-hadoop/data/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/data/webmap/.DS_Store b/genomix/genomix-hadoop/data/webmap/.DS_Store
new file mode 100644
index 0000000..17172c4
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/data/webmap/BridgePath b/genomix/genomix-hadoop/data/webmap/BridgePath
new file mode 100644
index 0000000..0717611
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/BridgePath
@@ -0,0 +1,2 @@
+TTTCCACTCCGTG
+TTTCCACCCCGTG
\ No newline at end of file
diff --git a/genomix/genomix-hadoop/data/webmap/CyclePath b/genomix/genomix-hadoop/data/webmap/CyclePath
new file mode 100644
index 0000000..04080f4
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/CyclePath
@@ -0,0 +1 @@
+GCAACTTCATCAACT
\ No newline at end of file
diff --git a/genomix/genomix-hadoop/data/webmap/SimplePath b/genomix/genomix-hadoop/data/webmap/SimplePath
new file mode 100644
index 0000000..80c03af
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/SimplePath
@@ -0,0 +1,3 @@
+ATATCGCATC
+AAGACAGCAC
+GCGGCAAGAA
diff --git a/genomix/genomix-hadoop/data/webmap/SinglePath b/genomix/genomix-hadoop/data/webmap/SinglePath
new file mode 100644
index 0000000..56ef5f8
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/SinglePath
@@ -0,0 +1 @@
+AGACAACAGT
diff --git a/genomix/genomix-hadoop/data/webmap/TreePath b/genomix/genomix-hadoop/data/webmap/TreePath
new file mode 100644
index 0000000..f3c13ce
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/TreePath
@@ -0,0 +1,3 @@
+GGCCTGGCTATCCC
+GGCCTCAGTAACTAAAC
+GGCCTCAGTACGCCCGG
\ No newline at end of file
diff --git a/genomix/genomix-hadoop/data/webmap/simplePath~ b/genomix/genomix-hadoop/data/webmap/simplePath~
new file mode 100644
index 0000000..6615392
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/simplePath~
@@ -0,0 +1 @@
+AGCATGCTATAT
diff --git a/genomix/genomix-hadoop/data/webmap/text.txt b/genomix/genomix-hadoop/data/webmap/text.txt
deleted file mode 100755
index c6cd7fe..0000000
--- a/genomix/genomix-hadoop/data/webmap/text.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-@625E1AAXX100810:1:100:10000:10271/1
-AATAGAAGATCGAT
-+
-EDBDB?BEEEDGGEGGGDGGGA>DG@GGD;GD@DG@F?<B<BFFD?
diff --git a/genomix/genomix-hadoop/pom.xml b/genomix/genomix-hadoop/pom.xml
index f791f5b..fe83c3c 100755
--- a/genomix/genomix-hadoop/pom.xml
+++ b/genomix/genomix-hadoop/pom.xml
@@ -8,7 +8,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>genomix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<properties>
@@ -22,8 +22,9 @@
<artifactId>maven-compiler-plugin</artifactId>
<version>2.0.2</version>
<configuration>
- <source>1.6</source>
- <target>1.6</target>
+ <source>1.7</source>
+ <target>1.7</target>
+ <fork>true</fork>
</configuration>
</plugin>
<plugin>
@@ -151,7 +152,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>genomix-data</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/genomix/genomix-hadoop/src/.DS_Store b/genomix/genomix-hadoop/src/.DS_Store
new file mode 100644
index 0000000..e0bf627
--- /dev/null
+++ b/genomix/genomix-hadoop/src/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/.DS_Store b/genomix/genomix-hadoop/src/main/.DS_Store
new file mode 100644
index 0000000..325c6de
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/.DS_Store b/genomix/genomix-hadoop/src/main/java/.DS_Store
new file mode 100644
index 0000000..dd6c872
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/edu/.DS_Store b/genomix/genomix-hadoop/src/main/java/edu/.DS_Store
new file mode 100644
index 0000000..5e0c641
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/.DS_Store b/genomix/genomix-hadoop/src/main/java/edu/uci/.DS_Store
new file mode 100644
index 0000000..4f27e83
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/.DS_Store b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/.DS_Store
new file mode 100644
index 0000000..8f46380
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/.DS_Store b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/.DS_Store
new file mode 100644
index 0000000..f5eb144
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/.DS_Store b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/.DS_Store
new file mode 100644
index 0000000..f9e3926
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathDriver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathDriver.java
index cfdf8d5..36c12ae 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathDriver.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathDriver.java
@@ -23,12 +23,15 @@
import org.apache.hadoop.mapred.JobConf;
import org.apache.hadoop.mapred.SequenceFileInputFormat;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.hadoop.mapred.TextOutputFormat;
import org.apache.hadoop.mapred.lib.MultipleOutputs;
import org.apache.hadoop.mapred.lib.MultipleSequenceFileOutputFormat;
+import org.apache.hadoop.mapred.lib.MultipleTextOutputFormat;
import org.kohsuke.args4j.CmdLineParser;
import org.kohsuke.args4j.Option;
import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
@SuppressWarnings("deprecation")
public class MergePathDriver {
@@ -74,7 +77,7 @@
conf.setInputFormat(SequenceFileInputFormat.class);
conf.setOutputFormat(SequenceFileOutputFormat.class);
- conf.setOutputKeyClass(KmerBytesWritable.class);
+ conf.setOutputKeyClass(VKmerBytesWritable.class);
conf.setOutputValueClass(MergePathValueWritable.class);
FileInputFormat.setInputPaths(conf, new Path(inputPath));
@@ -83,8 +86,9 @@
FileSystem dfs = FileSystem.get(conf);
dfs.delete(new Path(inputPath + "-step1"), true);
JobClient.runJob(conf);
+ int iMerge = 0;
/*----------------------------------------------------------------------*/
- for(int iMerge = 0; iMerge < mergeRound; iMerge ++){
+ for(iMerge = 0; iMerge < mergeRound; iMerge ++){
conf = new JobConf(MergePathDriver.class);
conf.setInt("sizeKmer", sizeKmer);
@@ -98,24 +102,23 @@
conf.setMapperClass(MergePathMapper.class);
conf.setReducerClass(MergePathReducer.class);
- conf.setMapOutputKeyClass(KmerBytesWritable.class);
+ conf.setMapOutputKeyClass(VKmerBytesWritable.class);
conf.setMapOutputValueClass(MergePathValueWritable.class);
conf.setInputFormat(SequenceFileInputFormat.class);
- conf.setOutputFormat(MultipleSequenceFileOutputFormat.class);
String uncomplete = "uncomplete" + iMerge;
String complete = "complete" + iMerge;
MultipleOutputs.addNamedOutput(conf, uncomplete,
- MergePathMultiSeqOutputFormat.class, KmerBytesWritable.class,
+ MergePathMultiSeqOutputFormat.class, VKmerBytesWritable.class,
MergePathValueWritable.class);
MultipleOutputs.addNamedOutput(conf, complete,
- MergePathMultiSeqOutputFormat.class, KmerBytesWritable.class,
+ MergePathMultiSeqOutputFormat.class, VKmerBytesWritable.class,
MergePathValueWritable.class);
- conf.setOutputKeyClass(KmerBytesWritable.class);
+ conf.setOutputKeyClass(VKmerBytesWritable.class);
conf.setOutputValueClass(MergePathValueWritable.class);
FileInputFormat.setInputPaths(conf, new Path(inputPath + "-step1"));
@@ -127,6 +130,46 @@
dfs.rename(new Path(outputPath + "/" + uncomplete), new Path(inputPath + "-step1"));
dfs.rename(new Path(outputPath + "/" + complete), new Path(mergeResultPath + "/" + complete));
}
+ /*----------------------------------------*/
+ conf = new JobConf(MergePathDriver.class);
+ conf.setInt("sizeKmer", sizeKmer);
+ conf.setInt("iMerge", iMerge);
+
+ if (defaultConfPath != null) {
+ conf.addResource(new Path(defaultConfPath));
+ }
+ conf.setJobName("Path Merge");
+
+ conf.setMapperClass(MergePathMapper.class);
+ conf.setReducerClass(MergePathReducer.class);
+
+ conf.setMapOutputKeyClass(VKmerBytesWritable.class);
+ conf.setMapOutputValueClass(MergePathValueWritable.class);
+
+ conf.setInputFormat(SequenceFileInputFormat.class);
+
+ String uncomplete = "uncomplete" + iMerge;
+ String complete = "complete" + iMerge;
+
+ MultipleOutputs.addNamedOutput(conf, uncomplete,
+ MergePathMultiSeqOutputFormat.class, VKmerBytesWritable.class,
+ MergePathValueWritable.class);
+
+ MultipleOutputs.addNamedOutput(conf, complete,
+ MergePathMultiSeqOutputFormat.class, VKmerBytesWritable.class,
+ MergePathValueWritable.class);
+
+ conf.setOutputKeyClass(VKmerBytesWritable.class);
+ conf.setOutputValueClass(MergePathValueWritable.class);
+
+ FileInputFormat.setInputPaths(conf, new Path(inputPath + "-step1"));
+ FileOutputFormat.setOutputPath(conf, new Path(outputPath));
+ conf.setNumReduceTasks(numReducers);
+ dfs.delete(new Path(outputPath), true);
+ JobClient.runJob(conf);
+ dfs.delete(new Path(inputPath + "-step1"), true);
+ dfs.rename(new Path(outputPath + "/" + uncomplete), new Path(inputPath + "-step1"));
+ dfs.rename(new Path(outputPath + "/" + complete), new Path(mergeResultPath + "/" + complete));
}
public static void main(String[] args) throws Exception {
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java
index c3255f2..0c7dcc1 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java
@@ -20,32 +20,31 @@
import org.apache.hadoop.mapred.Mapper;
import org.apache.hadoop.mapred.OutputCollector;
import org.apache.hadoop.mapred.Reporter;
-
import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
@SuppressWarnings("deprecation")
public class MergePathMapper extends MapReduceBase implements
- Mapper<KmerBytesWritable, MergePathValueWritable, KmerBytesWritable, MergePathValueWritable> {
+ Mapper<VKmerBytesWritable, MergePathValueWritable, VKmerBytesWritable, MergePathValueWritable> {
private int KMER_SIZE;
private VKmerBytesWritableFactory outputKmerFactory;
- private MergePathValueWritable outputAdjList;
+ private MergePathValueWritable outputValue;
private VKmerBytesWritable tmpKmer;
private VKmerBytesWritable outputKmer;
+
public void configure(JobConf job) {
KMER_SIZE = job.getInt("sizeKmer", 0);
outputKmerFactory = new VKmerBytesWritableFactory(KMER_SIZE);
- outputAdjList = new MergePathValueWritable();
+ outputValue = new MergePathValueWritable();
tmpKmer = new VKmerBytesWritable(KMER_SIZE);
outputKmer = new VKmerBytesWritable(KMER_SIZE);
}
@Override
- public void map(KmerBytesWritable key, MergePathValueWritable value,
- OutputCollector<KmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
+ public void map(VKmerBytesWritable key, MergePathValueWritable value,
+ OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
byte precursor = (byte) 0xF0;
byte succeed = (byte) 0x0F;
@@ -54,19 +53,18 @@
precursor = (byte) (precursor & adjBitMap);
precursor = (byte) ((precursor & 0xff) >> 4);
succeed = (byte) (succeed & adjBitMap);
-
- if (bitFlag == 1) {
+ if (bitFlag == 1) {
byte succeedCode = GeneCode.getGeneCodeFromBitMap(succeed);
tmpKmer.set(outputKmerFactory.getLastKmerFromChain(KMER_SIZE, key));
outputKmer.set(outputKmerFactory.shiftKmerWithNextCode(tmpKmer, succeedCode));
-
- KmerBytesWritable mergedKmer = outputKmerFactory.getFirstKmerFromChain(value.getKmerSize()
- - (KMER_SIZE - 1), value.getKmer());
- outputAdjList.set(mergedKmer, adjBitMap, bitFlag);
- output.collect(outputKmer, outputAdjList);
+
+ tmpKmer.set(outputKmerFactory.getFirstKmerFromChain(key.getKmerLength() - (KMER_SIZE - 1), key));
+ outputValue.set(adjBitMap, bitFlag, tmpKmer);
+ output.collect(outputKmer, outputValue);
} else {
- outputAdjList.set(value);
- output.collect(key, outputAdjList);
+ outputKmer.set(key);
+ outputValue.set(value);
+ output.collect(key, outputValue);
}
}
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMultiSeqOutputFormat.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMultiSeqOutputFormat.java
index 64fbb91..bd4cd2a 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMultiSeqOutputFormat.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMultiSeqOutputFormat.java
@@ -17,9 +17,10 @@
import java.io.File;
import org.apache.hadoop.io.BytesWritable;
import org.apache.hadoop.mapred.lib.MultipleSequenceFileOutputFormat;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
-public class MergePathMultiSeqOutputFormat extends MultipleSequenceFileOutputFormat<BytesWritable, MergePathValueWritable>{
+public class MergePathMultiSeqOutputFormat extends MultipleSequenceFileOutputFormat<VKmerBytesWritable, MergePathValueWritable>{
@Override
protected String generateLeafFileName(String name) {
// TODO Auto-generated method stub System.out.println(name);
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java
index cead0e8..52abc1c 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java
@@ -22,19 +22,18 @@
import org.apache.hadoop.mapred.Reducer;
import org.apache.hadoop.mapred.Reporter;
import org.apache.hadoop.mapred.lib.MultipleOutputs;
-
-import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
@SuppressWarnings("deprecation")
public class MergePathReducer extends MapReduceBase implements
- Reducer<KmerBytesWritable, MergePathValueWritable, KmerBytesWritable, MergePathValueWritable> {
+ Reducer<VKmerBytesWritable, MergePathValueWritable, VKmerBytesWritable, MergePathValueWritable> {
private VKmerBytesWritableFactory kmerFactory;
private VKmerBytesWritable outputKmer;
private VKmerBytesWritable tmpKmer;
private int KMER_SIZE;
- private MergePathValueWritable outputAdjList;
+ private MergePathValueWritable outputValue;
+ private MergePathValueWritable tmpOutputValue;
MultipleOutputs mos = null;
private int I_MERGE;
@@ -42,7 +41,8 @@
mos = new MultipleOutputs(job);
I_MERGE = Integer.parseInt(job.get("iMerge"));
KMER_SIZE = job.getInt("sizeKmer", 0);
- outputAdjList = new MergePathValueWritable();
+ outputValue = new MergePathValueWritable();
+ tmpOutputValue = new MergePathValueWritable();
kmerFactory = new VKmerBytesWritableFactory(KMER_SIZE);
outputKmer = new VKmerBytesWritable(KMER_SIZE);
tmpKmer = new VKmerBytesWritable(KMER_SIZE);
@@ -50,55 +50,87 @@
@SuppressWarnings("unchecked")
@Override
- public void reduce(KmerBytesWritable key, Iterator<MergePathValueWritable> values,
- OutputCollector<KmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
- outputAdjList = values.next();
-
-
+ public void reduce(VKmerBytesWritable key, Iterator<MergePathValueWritable> values,
+ OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
+ outputValue = values.next();
if (values.hasNext() == true) {
-
- if (outputAdjList.getFlag() == 1) {
- byte adjBitMap = outputAdjList.getAdjBitMap();
- byte bitFlag = outputAdjList.getFlag();
- outputKmer.set(kmerFactory.mergeTwoKmer(outputAdjList.getKmer(), key));
-
- outputAdjList = values.next();
- byte nextAdj = outputAdjList.getAdjBitMap();
+ if (outputValue.getFlag() != 1) {
+ byte nextAdj = outputValue.getAdjBitMap();
byte succeed = (byte) 0x0F;
succeed = (byte) (succeed & nextAdj);
+
+ outputValue = values.next();
+ byte adjBitMap = outputValue.getAdjBitMap();
+ byte flag = outputValue.getFlag();
+ if (outputValue.getKmerLength() != 0)
+ outputKmer.set(kmerFactory.mergeTwoKmer(outputValue.getKmer(), key));
+ else
+ outputKmer.set(key);
+
adjBitMap = (byte) (adjBitMap & 0xF0);
adjBitMap = (byte) (adjBitMap | succeed);
- outputAdjList.set(null, 0, 0, adjBitMap, bitFlag, KMER_SIZE + outputAdjList.getKmerSize());
-
- mos.getCollector("uncomplete" + I_MERGE, reporter).collect(outputKmer, outputAdjList);
+ outputValue.set(adjBitMap, flag, null);
+ mos.getCollector("uncomplete" + I_MERGE, reporter).collect(outputKmer, outputValue);
} else {
- byte nextAdj = outputAdjList.getAdjBitMap();
- byte succeed = (byte) 0x0F;
- succeed = (byte) (succeed & nextAdj);
- outputAdjList = values.next();
- byte adjBitMap = outputAdjList.getAdjBitMap();
- byte flag = outputAdjList.getFlag();
- int kmerSize = outputAdjList.getKmerSize();
-
- outputKmer.set(kmerFactory.mergeTwoKmer(outputAdjList.getKmer(), key));
- adjBitMap = (byte) (adjBitMap & 0xF0);
- adjBitMap = (byte) (adjBitMap | succeed);
- outputAdjList.set(null, 0, 0, adjBitMap, flag, KMER_SIZE + kmerSize);
+ tmpOutputValue.set(outputValue);
+ byte tmpAdjMap = tmpOutputValue.getAdjBitMap();
- mos.getCollector("uncomplete" + I_MERGE, reporter).collect(outputKmer, outputAdjList);
+ outputValue = values.next();
+ if (outputValue.getFlag() != 1) {
+ if (tmpOutputValue.getKmerLength() != 0)
+ outputKmer.set(kmerFactory.mergeTwoKmer(tmpOutputValue.getKmer(), key));
+ else
+ outputKmer.set(key);
+
+ byte nextAdj = outputValue.getAdjBitMap();
+ byte succeed = (byte) 0x0F;
+ succeed = (byte) (succeed & nextAdj);
+ tmpAdjMap = (byte) (tmpAdjMap & 0xF0);
+ tmpAdjMap = (byte) (tmpAdjMap | succeed);
+ outputValue.set(tmpAdjMap, tmpOutputValue.getFlag(), null);
+ mos.getCollector("uncomplete" + I_MERGE, reporter).collect(outputKmer, outputValue);
+ } else {
+
+ tmpKmer.set(kmerFactory.getFirstKmerFromChain(KMER_SIZE - 1, key));
+ if (tmpOutputValue.getKmerLength() != 0)
+ outputKmer.set(kmerFactory.mergeTwoKmer(tmpOutputValue.getKmer(), tmpKmer));
+ else
+ outputKmer.set(tmpKmer);
+ tmpOutputValue.set(tmpAdjMap, tmpOutputValue.getFlag(), null);
+ mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, tmpOutputValue);
+
+ tmpKmer.set(kmerFactory.getFirstKmerFromChain(KMER_SIZE - 1, key));
+ if (outputValue.getKmerLength() != 0)
+ outputKmer.set(kmerFactory.mergeTwoKmer(outputValue.getKmer(), tmpKmer));
+ else
+ outputKmer.set(tmpKmer);
+ outputValue.set(outputValue.getAdjBitMap(), outputValue.getFlag(), null);
+ mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, outputValue);
+
+ while (values.hasNext()) {
+ outputValue = values.next();
+ tmpKmer.set(kmerFactory.getFirstKmerFromChain(KMER_SIZE - 1, key));
+ if (outputValue.getKmerLength() != 0)
+ outputKmer.set(kmerFactory.mergeTwoKmer(outputValue.getKmer(), tmpKmer));
+ else
+ outputKmer.set(tmpKmer);
+ outputValue.set(outputValue.getAdjBitMap(), outputValue.getFlag(), null);
+ mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, outputValue);
+ }
+ }
}
} else {
- if (outputAdjList.getFlag() != 0) {
- byte adjBitMap = outputAdjList.getAdjBitMap();
- byte flag = outputAdjList.getFlag();
- int kmerSize = outputAdjList.getKmerSize();
-
+ if (outputValue.getFlag() != 0) {
tmpKmer.set(kmerFactory.getFirstKmerFromChain(KMER_SIZE - 1, key));
- outputKmer.set(kmerFactory.mergeTwoKmer(outputAdjList.getKmer(), tmpKmer));
- outputAdjList.set(null, 0, 0, adjBitMap, flag, KMER_SIZE + kmerSize);
- mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, outputAdjList);
+ if (outputValue.getKmerLength() != 0)
+ outputKmer.set(kmerFactory.mergeTwoKmer(outputValue.getKmer(), tmpKmer));
+ else
+ outputKmer.set(tmpKmer);
+ outputValue.set(outputValue.getAdjBitMap(), outputValue.getFlag(), null);
+ mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, outputValue);
+
} else
- mos.getCollector("uncomplete" + I_MERGE, reporter).collect(key, outputAdjList);
+ mos.getCollector("uncomplete" + I_MERGE, reporter).collect(key, outputValue);
}
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathValueWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathValueWritable.java
index c5ff116..9686c18 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathValueWritable.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathValueWritable.java
@@ -28,115 +28,53 @@
public class MergePathValueWritable extends BinaryComparable implements WritableComparable<BinaryComparable> {
private static final byte[] EMPTY_BYTES = {};
- private int size;
- private byte[] bytes;
-
private byte adjBitMap;
private byte flag;
- private int kmerSize;
-
private VKmerBytesWritable kmer;
public MergePathValueWritable() {
- this((byte) 0, (byte) 0, (byte) 0, EMPTY_BYTES);
+ this((byte) 0, (byte) 0, 0, EMPTY_BYTES);
}
- public MergePathValueWritable(byte adjBitMap, byte flag, byte kmerSize, byte[] bytes) {
+ public MergePathValueWritable(byte adjBitMap, byte flag, int kmerSize, byte[] bytes) {
this.adjBitMap = adjBitMap;
this.flag = flag;
- this.kmerSize = kmerSize;
-
- this.bytes = bytes;
- this.size = bytes.length;
- this.kmer = new VKmerBytesWritable(kmerSize);
+ this.kmer = new VKmerBytesWritable(kmerSize, bytes);
kmer.set(bytes, 0, bytes.length);
}
- public void setSize(int size) {
- if (size > getCapacity()) {
- setCapacity(size * 3 / 2);
- }
- this.size = size;
+ public void set(MergePathValueWritable right) {
+ set(right.getAdjBitMap(), right.getFlag(), right.getKmer());
}
- public int getCapacity() {
- return bytes.length;
- }
-
- public void setCapacity(int new_cap) {
- if (new_cap != getCapacity()) {
- byte[] new_data = new byte[new_cap];
- if (new_cap < size) {
- size = new_cap;
- }
- if (size != 0) {
- System.arraycopy(bytes, 0, new_data, 0, size);
- }
- bytes = new_data;
- }
- }
-
- public void set(MergePathValueWritable newData) {
- set(newData.bytes, 0, newData.size, newData.adjBitMap, newData.flag, newData.kmerSize);
- }
-
- public void set(KmerBytesWritable mergedKmer, byte adjBitMap, byte bitFlag) {
- set(mergedKmer.getBytes(),0,mergedKmer.getLength(), adjBitMap, bitFlag, mergedKmer.getKmerLength());
- }
-
- public void set(byte[] newData, int offset, int length, byte adjBitMap, byte flag, int kmerSize) {
- setSize(0);
- if (length != 0) {
- setSize(length);
- System.arraycopy(newData, offset, bytes, 0, size);
- kmer.set(kmerSize, newData, offset, length);
- }
- this.adjBitMap = adjBitMap;
- this.flag = flag;
- this.kmerSize = kmerSize;
- }
-
- public KmerBytesWritable getKmer(){
- if (size != 0){
- return kmer;
- }
- return null;
+ public void set(byte adjBitMap, byte flag, VKmerBytesWritable kmer) {
+ this.kmer.set(kmer);
+ this.adjBitMap = adjBitMap;
+ this.flag = flag;
}
@Override
public void readFields(DataInput arg0) throws IOException {
// TODO Auto-generated method stub
- setSize(0); // clear the old data
- setSize(arg0.readInt());
- if(size != 0){
- arg0.readFully(bytes, 0, size);
- kmer.set(bytes,0,size);
- }
+ kmer.readFields(arg0);
adjBitMap = arg0.readByte();
flag = arg0.readByte();
- kmerSize = arg0.readInt();
}
@Override
public void write(DataOutput arg0) throws IOException {
// TODO Auto-generated method stub
- arg0.writeInt(size);
- arg0.write(bytes, 0, size);
+
+ kmer.write(arg0);
arg0.writeByte(adjBitMap);
arg0.writeByte(flag);
- arg0.writeInt(kmerSize);
}
- @Override
- public byte[] getBytes() {
- // TODO Auto-generated method stub
- return bytes;
- }
-
- @Override
- public int getLength() {
- // TODO Auto-generated method stub
- return size;
+ public VKmerBytesWritable getKmer() {
+ if (kmer.getLength() != 0) {
+ return kmer;
+ }
+ return null;
}
public byte getAdjBitMap() {
@@ -147,26 +85,26 @@
return this.flag;
}
- public int getKmerSize() {
- return this.kmerSize;
- }
-
public String toString() {
- StringBuffer sb = new StringBuffer(3 * size);
- for (int idx = 0; idx < size; idx++) {
- // if not the first, put a blank separator in
- if (idx != 0) {
- sb.append(' ');
- }
- String num = Integer.toHexString(0xff & bytes[idx]);
- // if it is only one digit, add a leading 0.
- if (num.length() < 2) {
- sb.append('0');
- }
- sb.append(num);
- }
- return GeneCode.getSymbolFromBitMap(adjBitMap) + '\t' + String.valueOf(flag) + '\t' + sb.toString();
+ return GeneCode.getSymbolFromBitMap(adjBitMap) + '\t' + String.valueOf(flag);
}
-
+ @Override
+ public byte[] getBytes() {
+ // TODO Auto-generated method stub
+ if (kmer.getLength() != 0) {
+ return kmer.getBytes();
+ } else
+ return null;
+
+ }
+
+ public int getKmerLength() {
+ return kmer.getKmerLength();
+ }
+
+ @Override
+ public int getLength() {
+ return kmer.getLength();
+ }
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java
index ae824e7..1058fda 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java
@@ -22,8 +22,8 @@
import org.apache.hadoop.mapred.Mapper;
import org.apache.hadoop.mapred.OutputCollector;
import org.apache.hadoop.mapred.Reporter;
-
import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.GeneCode;
@SuppressWarnings("deprecation")
public class SNodeInitialMapper extends MapReduceBase implements
@@ -97,43 +97,36 @@
@Override
public void map(KmerBytesWritable key, ByteWritable value,
OutputCollector<KmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
-
byte precursor = (byte) 0xF0;
byte succeed = (byte) 0x0F;
byte adjBitMap = value.get();
- byte flag = (byte) 0;
+ byte bitFlag = (byte) 0;
precursor = (byte) (precursor & adjBitMap);
precursor = (byte) ((precursor & 0xff) >> 4);
succeed = (byte) (succeed & adjBitMap);
boolean inDegree = measureDegree(precursor);
boolean outDegree = measureDegree(succeed);
- byte initial = 0;
- if (inDegree == true && outDegree == false) {
- flag = (byte) 2;
- switch (succeed) {
- case 1:
- initial = (byte) 0x00;
- break;
- case 2:
- initial = (byte) 0x01;
- break;
- case 4:
- initial = (byte) 0x02;
- break;
- case 8:
- initial = (byte) 0x03;
- break;
- }
- outputKmer.set(key);
- outputKmer.shiftKmerWithNextCode(initial);
- adjBitMap = (byte) (adjBitMap & 0xF0);
- outputAdjList.set(null, 0, 0, adjBitMap, flag, KMER_SIZE);
- output.collect(outputKmer, outputAdjList);
- }
if (inDegree == false && outDegree == false) {
outputKmer.set(key);
- outputAdjList.set(null, 0, 0, adjBitMap, flag, KMER_SIZE);
+ bitFlag = (byte) 2;
+ outputAdjList.set(adjBitMap, bitFlag, null);///~~~~~kmersize----->0
output.collect(outputKmer, outputAdjList);
}
+ else{
+ for(int i = 0 ; i < 4; i ++){
+ byte temp = 0x01;
+ byte shiftedCode = 0;
+ temp = (byte)(temp << i);
+ temp = (byte) (succeed & temp);
+ if(temp != 0 ){
+ byte succeedCode = GeneCode.getGeneCodeFromBitMap(temp);
+ shiftedCode = key.shiftKmerWithNextCode(succeedCode);
+ outputKmer.set(key);
+ outputAdjList.set((byte)0, bitFlag, null);
+ output.collect(outputKmer, outputAdjList);
+ key.shiftKmerWithPreCode(shiftedCode);
+ }
+ }
+ }
}
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialReducer.java
index 734abd6..07cc32f 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialReducer.java
@@ -16,50 +16,51 @@
import java.io.IOException;
import java.util.Iterator;
-
import org.apache.hadoop.mapred.MapReduceBase;
import org.apache.hadoop.mapred.OutputCollector;
import org.apache.hadoop.mapred.Reducer;
import org.apache.hadoop.mapred.Reporter;
-
import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
@SuppressWarnings("deprecation")
public class SNodeInitialReducer extends MapReduceBase implements
- Reducer<KmerBytesWritable, MergePathValueWritable, KmerBytesWritable, MergePathValueWritable> {
- private MergePathValueWritable outputAdjList = new MergePathValueWritable();
+ Reducer<KmerBytesWritable, MergePathValueWritable, VKmerBytesWritable, MergePathValueWritable> {
+ private VKmerBytesWritable outputKmer = new VKmerBytesWritable();
+ private MergePathValueWritable outputValue = new MergePathValueWritable();
+
@Override
public void reduce(KmerBytesWritable key, Iterator<MergePathValueWritable> values,
- OutputCollector<KmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
- outputAdjList = values.next();
+ OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
+ outputKmer.set(key);
+ outputValue = values.next();
if (values.hasNext() == true) {
- if (outputAdjList.getFlag() != 2) {
- byte adjBitMap = outputAdjList.getAdjBitMap();
- int kmerSize = outputAdjList.getKmerSize();
+ if (outputValue.getFlag() == 2) {
byte bitFlag = 1;
- outputAdjList.set(null, 0, 0, adjBitMap, bitFlag, kmerSize);
- output.collect(key, outputAdjList);
-
+ outputValue.set(outputValue.getAdjBitMap(), bitFlag, null);///outputValue.getKmerLength()
+ output.collect(outputKmer, outputValue);
} else {
boolean flag = false;
while (values.hasNext()) {
- outputAdjList = values.next();
- if (outputAdjList.getFlag() != 2) {
+ outputValue = values.next();
+ if (outputValue.getFlag() == 2) {
flag = true;
break;
}
}
if (flag == true) {
- byte adjBitMap = outputAdjList.getAdjBitMap();
- int kmerSize = outputAdjList.getKmerSize();
byte bitFlag = 1;
- outputAdjList.set(null, 0, 0, adjBitMap, bitFlag, kmerSize);
- output.collect(key, outputAdjList);
+ outputValue.set(outputValue.getAdjBitMap(), bitFlag, null);
+ output.collect(outputKmer, outputValue);
}
}
} else {
- output.collect(key, outputAdjList);
+ if (outputValue.getFlag() == 2) {
+ byte bitFlag = 0;
+ outputValue.set(outputValue.getAdjBitMap(), bitFlag, null);
+ output.collect(outputKmer, outputValue);
+ }
}
}
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/.DS_Store b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/.DS_Store
new file mode 100644
index 0000000..7c4ae29
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/ENodeInitialReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/ENodeInitialReducer.java
new file mode 100644
index 0000000..1f9bc82
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/ENodeInitialReducer.java
@@ -0,0 +1,58 @@
+package edu.uci.ics.pathmergingh2;
+
+import java.io.IOException;
+import java.util.Iterator;
+import org.apache.hadoop.io.BytesWritable;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reducer;
+import org.apache.hadoop.mapred.Reporter;
+import edu.uci.ics.genomix.type.KmerUtil;
+
+@SuppressWarnings("deprecation")
+public class ENodeInitialReducer extends MapReduceBase implements
+ Reducer<BytesWritable, MergePathValueWritable, BytesWritable, MergePathValueWritable> {
+ public BytesWritable outputKmer = new BytesWritable();
+ public MergePathValueWritable outputAdjList = new MergePathValueWritable();
+
+ @Override
+ public void reduce(BytesWritable key, Iterator<MergePathValueWritable> values,
+ OutputCollector<BytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
+ outputAdjList = values.next();
+ outputKmer.set(key);
+ if (values.hasNext() == true) {
+ byte bitFlag = outputAdjList.getFlag();
+ bitFlag = (byte) (bitFlag & 0xFE);
+ if (bitFlag == 2) {
+ bitFlag = (byte) (0x80 | outputAdjList.getFlag());
+ outputAdjList.set(outputAdjList.getAdjBitMap(), bitFlag, null);
+ output.collect(outputKmer, outputAdjList);
+
+ } else {
+ boolean flag = false;
+ while (values.hasNext()) {
+ outputAdjList = values.next();
+ if (outputAdjList.getFlag() == 2) {
+ flag = true;
+ break;
+ }
+ }
+ if (flag == true) {
+ bitFlag = (byte) (0x80 | outputAdjList.getFlag());
+ outputAdjList.set(outputAdjList.getAdjBitMap(), bitFlag, null);
+ output.collect(outputKmer, outputAdjList);
+ }
+ }
+ } else {
+ byte bitFlag = outputAdjList.getFlag();
+ bitFlag = (byte) (bitFlag & 0xFE);
+ if (bitFlag == 2) {
+ bitFlag = 0;
+ outputAdjList.set(outputAdjList.getAdjBitMap(), bitFlag, null);
+ output.collect(outputKmer, outputAdjList);
+ }
+ }
+ }
+}
+
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Driver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Driver.java
new file mode 100644
index 0000000..58849e2
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Driver.java
@@ -0,0 +1,166 @@
+package edu.uci.ics.pathmergingh2;
+
+import java.io.IOException;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+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.SequenceFileInputFormat;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.hadoop.mapred.TextOutputFormat;
+import org.apache.hadoop.mapred.lib.MultipleOutputs;
+import org.apache.hadoop.mapred.lib.MultipleSequenceFileOutputFormat;
+import org.apache.hadoop.mapred.lib.MultipleTextOutputFormat;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.Option;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+
+
+@SuppressWarnings("deprecation")
+public class MergePathH2Driver {
+
+ private static class Options {
+ @Option(name = "-inputpath", usage = "the input path", required = true)
+ public String inputPath;
+
+ @Option(name = "-outputpath", usage = "the output path", required = true)
+ public String outputPath;
+
+ @Option(name = "-mergeresultpath", usage = "the merging results path", required = true)
+ public String mergeResultPath;
+
+ @Option(name = "-num-reducers", usage = "the number of reducers", required = true)
+ public int numReducers;
+
+ @Option(name = "-kmer-size", usage = "the size of kmer", required = true)
+ public int sizeKmer;
+
+ @Option(name = "-merge-rounds", usage = "the while rounds of merging", required = true)
+ public int mergeRound;
+
+ }
+
+
+ public void run(String inputPath, String outputPath, String mergeResultPath, int numReducers, int sizeKmer, int mergeRound, String defaultConfPath)
+ throws IOException{
+
+ JobConf conf = new JobConf(MergePathH2Driver.class);
+ conf.setInt("sizeKmer", sizeKmer);
+
+ if (defaultConfPath != null) {
+ conf.addResource(new Path(defaultConfPath));
+ }
+ conf.setJobName("Initial Path-Starting-Points Table");
+ conf.setMapperClass(SNodeInitialMapper.class);
+ conf.setReducerClass(SNodeInitialReducer.class);
+
+ conf.setMapOutputKeyClass(KmerBytesWritable.class);
+ conf.setMapOutputValueClass(MergePathValueWritable.class);
+
+ conf.setInputFormat(SequenceFileInputFormat.class);
+ conf.setOutputFormat(SequenceFileOutputFormat.class);
+
+ conf.setOutputKeyClass(VKmerBytesWritable.class);
+ conf.setOutputValueClass(MergePathValueWritable.class);
+
+ FileInputFormat.setInputPaths(conf, new Path(inputPath));
+ FileOutputFormat.setOutputPath(conf, new Path(inputPath + "-step1"));
+ conf.setNumReduceTasks(numReducers);
+ FileSystem dfs = FileSystem.get(conf);
+ dfs.delete(new Path(inputPath + "-step1"), true);
+ JobClient.runJob(conf);
+ int iMerge = 0;
+/*----------------------------------------------------------------------*/
+ for(iMerge = 0; iMerge < mergeRound; iMerge ++){
+ conf = new JobConf(MergePathH2Driver.class);
+ conf.setInt("sizeKmer", sizeKmer);
+ conf.setInt("iMerge", iMerge);
+
+ if (defaultConfPath != null) {
+ conf.addResource(new Path(defaultConfPath));
+ }
+ conf.setJobName("Path Merge");
+
+ conf.setMapperClass(MergePathH2Mapper.class);
+ conf.setReducerClass(MergePathH2Reducer.class);
+
+ conf.setMapOutputKeyClass(VKmerBytesWritable.class);
+ conf.setMapOutputValueClass(MergePathValueWritable.class);
+
+ conf.setInputFormat(SequenceFileInputFormat.class);
+
+ String uncomplete = "uncomplete" + iMerge;
+ String complete = "complete" + iMerge;
+
+ MultipleOutputs.addNamedOutput(conf, uncomplete,
+ MergePathMultiSeqOutputFormat.class, VKmerBytesWritable.class,
+ MergePathValueWritable.class);
+
+ MultipleOutputs.addNamedOutput(conf, complete,
+ MergePathMultiTextOutputFormat.class, VKmerBytesWritable.class,
+ MergePathValueWritable.class);
+
+ conf.setOutputKeyClass(VKmerBytesWritable.class);
+ conf.setOutputValueClass(MergePathValueWritable.class);
+
+ FileInputFormat.setInputPaths(conf, new Path(inputPath + "-step1"));
+ FileOutputFormat.setOutputPath(conf, new Path(outputPath));
+ conf.setNumReduceTasks(numReducers);
+ dfs.delete(new Path(outputPath), true);
+ JobClient.runJob(conf);
+ dfs.delete(new Path(inputPath + "-step1"), true);
+ dfs.rename(new Path(outputPath + "/" + uncomplete), new Path(inputPath + "-step1"));
+ dfs.rename(new Path(outputPath + "/" + complete), new Path(mergeResultPath + "/" + complete));
+ }
+ conf = new JobConf(MergePathH2Driver.class);
+ conf.setInt("sizeKmer", sizeKmer);
+ conf.setInt("iMerge", iMerge);
+
+ if (defaultConfPath != null) {
+ conf.addResource(new Path(defaultConfPath));
+ }
+ conf.setJobName("Path Merge");
+
+ conf.setMapperClass(MergePathH2Mapper.class);
+ conf.setReducerClass(MergePathH2Reducer.class);
+
+ conf.setMapOutputKeyClass(VKmerBytesWritable.class);
+ conf.setMapOutputValueClass(MergePathValueWritable.class);
+
+ conf.setInputFormat(SequenceFileInputFormat.class);
+
+ String uncomplete = "uncomplete" + iMerge;
+ String complete = "complete" + iMerge;
+
+ MultipleOutputs.addNamedOutput(conf, uncomplete,
+ MergePathMultiTextOutputFormat.class, VKmerBytesWritable.class,
+ MergePathValueWritable.class);
+
+ MultipleOutputs.addNamedOutput(conf, complete,
+ MergePathMultiTextOutputFormat.class, VKmerBytesWritable.class,
+ MergePathValueWritable.class);
+
+ conf.setOutputKeyClass(VKmerBytesWritable.class);
+ conf.setOutputValueClass(MergePathValueWritable.class);
+
+ FileInputFormat.setInputPaths(conf, new Path(inputPath + "-step1"));
+ FileOutputFormat.setOutputPath(conf, new Path(outputPath));
+ conf.setNumReduceTasks(numReducers);
+ dfs.delete(new Path(outputPath), true);
+ JobClient.runJob(conf);
+ dfs.delete(new Path(inputPath + "-step1"), true);
+ dfs.rename(new Path(outputPath + "/" + uncomplete), new Path(inputPath + "-step1"));
+ dfs.rename(new Path(outputPath + "/" + complete), new Path(mergeResultPath + "/" + complete));
+ }
+
+ public static void main(String[] args) throws Exception {
+ Options options = new Options();
+ CmdLineParser parser = new CmdLineParser(options);
+ parser.parseArgument(args);
+ MergePathH2Driver driver = new MergePathH2Driver();
+ driver.run(options.inputPath, options.outputPath, options.mergeResultPath, options.numReducers, options.sizeKmer, options.mergeRound, null);
+ }
+}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Mapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Mapper.java
new file mode 100644
index 0000000..6ea9dd3
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Mapper.java
@@ -0,0 +1,87 @@
+package edu.uci.ics.pathmergingh2;
+
+import java.io.IOException;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hadoop.mapred.Mapper;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+import edu.uci.ics.genomix.type.GeneCode;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
+
+@SuppressWarnings("deprecation")
+public class MergePathH2Mapper extends MapReduceBase implements
+ Mapper<VKmerBytesWritable, MergePathValueWritable, VKmerBytesWritable, MergePathValueWritable> {
+
+ private int KMER_SIZE;
+ private VKmerBytesWritableFactory outputKmerFactory;
+ private MergePathValueWritable outputValue;
+ private VKmerBytesWritable tmpKmer;
+ private VKmerBytesWritable outputKmer;
+
+ public void configure(JobConf job) {
+ KMER_SIZE = job.getInt("sizeKmer", 0);
+ outputKmerFactory = new VKmerBytesWritableFactory(KMER_SIZE);
+ outputValue = new MergePathValueWritable();
+ tmpKmer = new VKmerBytesWritable(KMER_SIZE);
+ outputKmer = new VKmerBytesWritable(KMER_SIZE);
+ }
+
+ @Override
+ public void map(VKmerBytesWritable key, MergePathValueWritable value,
+ OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
+ byte precursor = (byte) 0xF0;
+ byte succeed = (byte) 0x0F;
+ byte adjBitMap = value.getAdjBitMap();
+ byte bitFlag = value.getFlag();
+ precursor = (byte) (precursor & adjBitMap);
+ precursor = (byte) ((precursor & 0xff) >> 4);
+ succeed = (byte) (succeed & adjBitMap);
+ byte bitStartEnd = (byte) (0x81 & bitFlag);
+
+ switch (bitStartEnd) {
+ case (byte) 0x01:
+ byte succeedCode = GeneCode.getGeneCodeFromBitMap(succeed);
+ tmpKmer.set(outputKmerFactory.getLastKmerFromChain(KMER_SIZE, key));
+ outputKmer.set(outputKmerFactory.shiftKmerWithNextCode(tmpKmer, succeedCode));
+
+ tmpKmer.set(outputKmerFactory.getFirstKmerFromChain(key.getKmerLength() - (KMER_SIZE - 1), key));
+ bitFlag = (byte) (bitFlag | 0x08);
+ outputValue.set(adjBitMap, bitFlag, tmpKmer);
+ output.collect(outputKmer, outputValue);
+ break;
+ case (byte) 0x80:
+ tmpKmer.set(outputKmerFactory.getFirstKmerFromChain(KMER_SIZE, key));
+ outputKmer.set(tmpKmer);
+ tmpKmer.set(outputKmerFactory.getLastKmerFromChain(key.getKmerLength() - KMER_SIZE, key));
+ bitFlag = (byte) (bitFlag | 0x10);
+ outputValue.set(adjBitMap, bitFlag, tmpKmer);
+ output.collect(outputKmer, outputValue);
+ break;
+ case (byte) 0x00:
+ succeedCode = GeneCode.getGeneCodeFromBitMap(succeed);
+ tmpKmer.set(outputKmerFactory.getLastKmerFromChain(KMER_SIZE, key));
+ outputKmer.set(outputKmerFactory.shiftKmerWithNextCode(tmpKmer, succeedCode));
+
+ tmpKmer.set(outputKmerFactory.getFirstKmerFromChain(key.getKmerLength() - (KMER_SIZE - 1), key));
+ bitFlag = (byte) (bitFlag | 0x08);
+ outputValue.set(adjBitMap, bitFlag, tmpKmer);
+ output.collect(outputKmer, outputValue);
+
+ bitFlag = (byte) (bitFlag & 0xF7);
+ tmpKmer.set(outputKmerFactory.getFirstKmerFromChain(KMER_SIZE, key));
+ outputKmer.set(tmpKmer);
+ tmpKmer.set(outputKmerFactory.getLastKmerFromChain(key.getKmerLength() - KMER_SIZE, key));
+ bitFlag = (byte) (bitFlag | 0x10);
+ outputValue.set(adjBitMap, bitFlag, tmpKmer);
+ output.collect(outputKmer, outputValue);
+ break;
+ case (byte) 0x81:
+ outputKmer.set(key);
+ outputValue.set(adjBitMap, bitFlag, null);
+ output.collect(outputKmer, outputValue);
+ break;
+ }
+ }
+}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Reducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Reducer.java
new file mode 100644
index 0000000..ad8b3c2
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Reducer.java
@@ -0,0 +1,119 @@
+package edu.uci.ics.pathmergingh2;
+
+import java.io.IOException;
+import java.util.Iterator;
+
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reducer;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hadoop.mapred.lib.MultipleOutputs;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
+
+@SuppressWarnings("deprecation")
+public class MergePathH2Reducer extends MapReduceBase implements
+ Reducer<VKmerBytesWritable, MergePathValueWritable, VKmerBytesWritable, MergePathValueWritable> {
+ private VKmerBytesWritableFactory kmerFactory;
+ private VKmerBytesWritable outputKmer;
+ private VKmerBytesWritable tmpKmer1;
+ private VKmerBytesWritable tmpKmer2;
+ private int KMER_SIZE;
+ private MergePathValueWritable outputValue;
+ private MergePathValueWritable tmpOutputValue;
+
+ MultipleOutputs mos = null;
+ private int I_MERGE;
+
+ public void configure(JobConf job) {
+ mos = new MultipleOutputs(job);
+ I_MERGE = Integer.parseInt(job.get("iMerge"));
+ KMER_SIZE = job.getInt("sizeKmer", 0);
+ outputValue = new MergePathValueWritable();
+ tmpOutputValue = new MergePathValueWritable();
+ kmerFactory = new VKmerBytesWritableFactory(KMER_SIZE);
+ outputKmer = new VKmerBytesWritable(KMER_SIZE);
+ tmpKmer1 = new VKmerBytesWritable(KMER_SIZE);
+ tmpKmer2 = new VKmerBytesWritable(KMER_SIZE);
+ }
+
+ @SuppressWarnings("unchecked")
+ public void reduce(VKmerBytesWritable key, Iterator<MergePathValueWritable> values,
+ OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
+ outputValue = values.next();
+ outputKmer.set(key);
+ if (values.hasNext() == true) {
+ byte bitFlag = outputValue.getFlag();
+ byte bitStartEnd = (byte) (0x81 & bitFlag);
+ byte bitPosiNegative = (byte) (0x18 & bitFlag);
+ byte succeed = (byte) 0x0F;
+ switch (bitPosiNegative) {
+ case (byte) 0x08:
+ if (outputValue.getKmerLength() != 0)
+ tmpKmer1.set(kmerFactory.mergeTwoKmer(outputValue.getKmer(), key));
+ else
+ tmpKmer1.set(key);
+ byte adjBitMap = outputValue.getAdjBitMap();
+ outputValue = values.next();
+ bitStartEnd = (byte) (0x81 & outputValue.getFlag());
+ if (bitStartEnd == (byte) 0x80) {
+ if (outputValue.getKmerLength() != 0)
+ tmpKmer2.set(kmerFactory.mergeTwoKmer(key, outputValue.getKmer()));
+ else
+ tmpKmer2.set(key);
+ byte tmpFlag = (byte) 0x80;
+ tmpOutputValue.set(outputValue.getAdjBitMap(), outputValue.getFlag(), null);
+ mos.getCollector("uncomplete" + I_MERGE, reporter).collect(tmpKmer2, tmpOutputValue);
+ }
+ if (outputValue.getKmerLength() != 0)
+ outputKmer.set(kmerFactory.mergeTwoKmer(tmpKmer1, outputValue.getKmer()));
+ else
+ outputKmer.set(tmpKmer1);
+ succeed = (byte) (succeed & outputValue.getAdjBitMap());
+ adjBitMap = (byte) (adjBitMap & 0xF0);
+ adjBitMap = (byte) (adjBitMap | succeed);
+ byte outputFlag = (byte) (0x81 & bitFlag);
+ outputFlag = (byte) (outputFlag | ((byte) 0x81 & outputValue.getFlag()));
+ outputValue.set(adjBitMap, outputFlag, null);
+ mos.getCollector("uncomplete" + I_MERGE, reporter).collect(outputKmer, outputValue);
+ break;
+ case (byte) 0x10:
+ if (outputValue.getKmerLength() != 0)
+ tmpKmer1.set(kmerFactory.mergeTwoKmer(key, outputValue.getKmer()));
+ else
+ tmpKmer1.set(key);
+ if (bitStartEnd == (byte) 0x80) {
+ byte tmpFlag = (byte) 0x80;
+ tmpOutputValue.set(outputValue.getAdjBitMap(), tmpFlag, null);
+ mos.getCollector("uncomplete" + I_MERGE, reporter).collect(tmpKmer1, tmpOutputValue);
+ }
+ succeed = (byte) (succeed & outputValue.getAdjBitMap());
+ outputValue = values.next();
+ if (outputValue.getKmerLength() != 0)
+ outputKmer.set(kmerFactory.mergeTwoKmer(outputValue.getKmer(), tmpKmer1));
+ else
+ outputKmer.set(tmpKmer1);
+ adjBitMap = outputValue.getAdjBitMap();
+ adjBitMap = (byte) (adjBitMap & 0xF0);
+ adjBitMap = (byte) (adjBitMap | succeed);
+ outputFlag = (byte) (0x81 & bitFlag);
+ outputFlag = (byte) (outputFlag | ((byte) 0x81 & outputValue.getFlag()));
+ outputValue.set(adjBitMap, outputFlag, null);
+ mos.getCollector("uncomplete" + I_MERGE, reporter).collect(outputKmer, outputValue);
+ break;
+ }
+ } else {
+ byte bitFlag = outputValue.getFlag();
+ byte bitStartEnd = (byte) (0x81 & bitFlag);
+ if (bitStartEnd == (byte) 0x81) {
+ outputKmer.set(key);
+ mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, outputValue);
+ }
+ }
+ }
+ public void close() throws IOException {
+ // TODO Auto-generated method stub
+ mos.close();
+ }
+}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathMultiSeqOutputFormat.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathMultiSeqOutputFormat.java
new file mode 100644
index 0000000..5e6f008
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathMultiSeqOutputFormat.java
@@ -0,0 +1,31 @@
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.uci.ics.pathmergingh2;
+
+import java.io.File;
+import org.apache.hadoop.io.BytesWritable;
+import org.apache.hadoop.mapred.lib.MultipleSequenceFileOutputFormat;
+
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+
+
+public class MergePathMultiSeqOutputFormat extends MultipleSequenceFileOutputFormat<VKmerBytesWritable, MergePathValueWritable>{
+ @Override
+ protected String generateLeafFileName(String name) {
+ // TODO Auto-generated method stub System.out.println(name);
+ String[] names = name.split("-");
+ return names[0] + File.separator + name;
+ }
+}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathMultiTextOutputFormat.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathMultiTextOutputFormat.java
new file mode 100644
index 0000000..d6176e2
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathMultiTextOutputFormat.java
@@ -0,0 +1,28 @@
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.uci.ics.pathmergingh2;
+
+import java.io.File;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.lib.MultipleTextOutputFormat;
+
+public class MergePathMultiTextOutputFormat extends MultipleTextOutputFormat<Text, Text>{
+ @Override
+ protected String generateLeafFileName(String name) {
+ // TODO Auto-generated method stub System.out.println(name);
+ String[] names = name.split("-");
+ return names[0] + File.separator + name;
+ }
+}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathValueWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathValueWritable.java
new file mode 100644
index 0000000..2f1869d
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathValueWritable.java
@@ -0,0 +1,115 @@
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.uci.ics.pathmergingh2;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+
+import org.apache.hadoop.io.BinaryComparable;
+import org.apache.hadoop.io.WritableComparable;
+
+import edu.uci.ics.genomix.type.GeneCode;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+
+public class MergePathValueWritable extends BinaryComparable implements WritableComparable<BinaryComparable> {
+
+ private static final byte[] EMPTY_BYTES = {};
+ private byte adjBitMap;
+ private byte flag;
+ private VKmerBytesWritable kmer;
+
+ public MergePathValueWritable() {
+ this((byte) 0, (byte) 0, 0, EMPTY_BYTES);
+ }
+
+ public MergePathValueWritable(int k) {
+ this.adjBitMap = 0;
+ this.flag = 0;
+ this.kmer = new VKmerBytesWritable(k);
+ }
+
+ public MergePathValueWritable(byte adjBitMap, byte flag, int kmerSize, byte[] bytes) {
+ this.adjBitMap = adjBitMap;
+ this.flag = flag;
+ this.kmer = new VKmerBytesWritable(kmerSize, bytes);
+ kmer.set(bytes, 0, bytes.length);
+ }
+
+ public void set(MergePathValueWritable right) {
+ set(right.getAdjBitMap(), right.getFlag(), right.getKmer());
+ }
+
+ public void set(byte adjBitMap, byte flag, VKmerBytesWritable kmer) {
+ this.kmer.set(kmer);
+ this.adjBitMap = adjBitMap;
+ this.flag = flag;
+ }
+
+ @Override
+ public void readFields(DataInput arg0) throws IOException {
+ // TODO Auto-generated method stub
+ kmer.readFields(arg0);
+ adjBitMap = arg0.readByte();
+ flag = arg0.readByte();
+ }
+
+ @Override
+ public void write(DataOutput arg0) throws IOException {
+ // TODO Auto-generated method stub
+
+ kmer.write(arg0);
+ arg0.writeByte(adjBitMap);
+ arg0.writeByte(flag);
+ }
+
+ public VKmerBytesWritable getKmer() {
+ if (kmer.getLength() != 0) {
+ return kmer;
+ }
+ return null;
+ }
+
+ public byte getAdjBitMap() {
+ return this.adjBitMap;
+ }
+
+ public byte getFlag() {
+ return this.flag;
+ }
+
+ public String toString() {
+ return GeneCode.getSymbolFromBitMap(adjBitMap) + '\t' + String.valueOf(flag);
+ }
+
+ @Override
+ public byte[] getBytes() {
+ // TODO Auto-generated method stub
+ if (kmer.getLength() != 0) {
+ return kmer.getBytes();
+ } else
+ return null;
+
+ }
+
+ public int getKmerLength() {
+ return kmer.getKmerLength();
+ }
+
+ @Override
+ public int getLength() {
+ return kmer.getLength();
+ }
+}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialMapper.java
new file mode 100644
index 0000000..4c05dac
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialMapper.java
@@ -0,0 +1,141 @@
+package edu.uci.ics.pathmergingh2;
+
+import java.io.IOException;
+import org.apache.hadoop.io.ByteWritable;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hadoop.mapred.Mapper;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+import edu.uci.ics.genomix.type.GeneCode;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+
+@SuppressWarnings("deprecation")
+public class SNodeInitialMapper extends MapReduceBase implements
+ Mapper<KmerBytesWritable, ByteWritable, KmerBytesWritable, MergePathValueWritable> {
+
+ public int KMER_SIZE;
+ public KmerBytesWritable outputKmer;
+ public MergePathValueWritable outputAdjList;
+
+ public void configure(JobConf job) {
+ KMER_SIZE = Integer.parseInt(job.get("sizeKmer"));
+ outputKmer = new KmerBytesWritable(KMER_SIZE);
+ outputAdjList = new MergePathValueWritable();
+ }
+
+ boolean measureDegree(byte adjacent) {
+ boolean result = true;
+ switch (adjacent) {
+ case 0:
+ result = true;
+ break;
+ case 1:
+ result = false;
+ break;
+ case 2:
+ result = false;
+ break;
+ case 3:
+ result = true;
+ break;
+ case 4:
+ result = false;
+ break;
+ case 5:
+ result = true;
+ break;
+ case 6:
+ result = true;
+ break;
+ case 7:
+ result = true;
+ break;
+ case 8:
+ result = false;
+ break;
+ case 9:
+ result = true;
+ break;
+ case 10:
+ result = true;
+ break;
+ case 11:
+ result = true;
+ break;
+ case 12:
+ result = true;
+ break;
+ case 13:
+ result = true;
+ break;
+ case 14:
+ result = true;
+ break;
+ case 15:
+ result = true;
+ break;
+ }
+ return result;
+ }
+
+ @Override
+ public void map(KmerBytesWritable key, ByteWritable value,
+ OutputCollector<KmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
+ byte precursor = (byte) 0xF0;
+ byte succeed = (byte) 0x0F;
+ byte adjBitMap = value.get();
+ byte bitFlag = (byte) 0;
+ precursor = (byte) (precursor & adjBitMap);
+ precursor = (byte) ((precursor & 0xff) >> 4);
+ succeed = (byte) (succeed & adjBitMap);
+ boolean inDegree = measureDegree(precursor);
+ boolean outDegree = measureDegree(succeed);
+ if (key.toString().equals("CGC")) {
+ int a = 2;
+ int b = a;
+ }
+ if (key.toString().equals("TCG")) {
+ int a = 2;
+ int b = a;
+ }
+ if (inDegree == false && outDegree == false) {
+ outputKmer.set(key);
+ System.out.println(outputKmer.hashCode());
+ bitFlag = (byte) 2;
+ outputAdjList.set(adjBitMap, bitFlag, null);
+ output.collect(outputKmer, outputAdjList);
+ } else {
+ for (int i = 0; i < 4; i++) {
+ byte temp = (byte) 0x01;
+ byte shiftedCode = 0;
+ temp = (byte) (temp << i);
+ temp = (byte) (precursor & temp);
+ if (temp != 0) {
+ byte precurCode = GeneCode.getGeneCodeFromBitMap(temp);
+ shiftedCode = key.shiftKmerWithPreCode(precurCode);
+ outputKmer.set(key);
+ bitFlag = (byte) 0x80;
+ outputAdjList.set((byte) 0, bitFlag, null);
+ output.collect(outputKmer, outputAdjList);
+ key.shiftKmerWithNextCode(shiftedCode);
+ }
+ }
+ for (int i = 0; i < 4; i++) {
+ byte temp = (byte) 0x01;
+ byte shiftedCode = 0;
+ temp = (byte) (temp << i);
+ temp = (byte) (succeed & temp);
+ if (temp != 0) {
+ byte succeedCode = GeneCode.getGeneCodeFromBitMap(temp);
+ shiftedCode = key.shiftKmerWithNextCode(succeedCode);
+ outputKmer.set(key);
+ bitFlag = (byte) 0x01;
+ outputAdjList.set((byte) 0, bitFlag, null);
+ output.collect(outputKmer, outputAdjList);
+ key.shiftKmerWithPreCode(shiftedCode);
+ }
+ }
+ }
+ }
+}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialReducer.java
new file mode 100644
index 0000000..7fd7a2e
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialReducer.java
@@ -0,0 +1,80 @@
+package edu.uci.ics.pathmergingh2;
+
+import java.io.IOException;
+import java.util.Iterator;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reducer;
+import org.apache.hadoop.mapred.Reporter;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+
+@SuppressWarnings("deprecation")
+public class SNodeInitialReducer extends MapReduceBase implements
+ Reducer<KmerBytesWritable, MergePathValueWritable, VKmerBytesWritable, MergePathValueWritable> {
+ private VKmerBytesWritable outputKmer = new VKmerBytesWritable();
+ private MergePathValueWritable outputValue = new MergePathValueWritable();
+
+ @Override
+ public void reduce(KmerBytesWritable key, Iterator<MergePathValueWritable> values,
+ OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
+ outputKmer.set(key);
+ outputValue = values.next();
+ byte startFlag = 0x00;
+ byte endFlag = 0x00;
+ byte targetPointFlag = 0x00;
+ byte targetAdjList = 0x00;
+ byte outputFlag = 0x00;
+ if(key.toString().equals("TCG")){
+ int a = 2;
+ int b = a;
+ }
+ if (values.hasNext() == true) {
+ switch (outputValue.getFlag()) {
+ case (byte) 0x01:
+ startFlag = (byte) 0x01;
+ break;
+ case (byte) 0x80:
+ endFlag = (byte) 0x80;
+ break;
+ case (byte) 0x02:
+ targetPointFlag = (byte) 0x02;
+ targetAdjList = outputValue.getAdjBitMap();
+ break;
+ }
+ while (values.hasNext()) {
+ outputValue = values.next();
+ switch (outputValue.getFlag()) {
+ case (byte) 0x01:
+ startFlag = (byte) 0x01;
+ break;
+ case (byte) 0x80:
+ endFlag = (byte) 0x80;
+ break;
+ case (byte) 0x02:
+ targetPointFlag = (byte) 0x02;
+ targetAdjList = outputValue.getAdjBitMap();
+ break;
+ }
+ if(startFlag != (byte) 0x00 && endFlag!= (byte) 0x00 && targetPointFlag != (byte) 0x00)
+ break;
+ }
+ if(targetPointFlag == (byte) 0x02) {
+ if(startFlag == (byte) 0x01) {
+ outputFlag = (byte) (outputFlag | startFlag);
+ }
+ if(endFlag == (byte) 0x80) {
+ outputFlag = (byte) (outputFlag | endFlag);
+ }
+ outputValue.set(targetAdjList, outputFlag, null);
+ output.collect(outputKmer, outputValue);
+ }
+ } else {
+ if (outputValue.getFlag() == 2) {
+ byte bitFlag = 0;
+ outputValue.set(outputValue.getAdjBitMap(), bitFlag, null);
+ output.collect(outputKmer, outputValue);
+ }
+ }
+ }
+}
diff --git a/genomix/genomix-hadoop/src/test/.DS_Store b/genomix/genomix-hadoop/src/test/.DS_Store
new file mode 100644
index 0000000..bfe14e8
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/test/java/.DS_Store b/genomix/genomix-hadoop/src/test/java/.DS_Store
new file mode 100644
index 0000000..fb3684c
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/java/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/test/java/edu/.DS_Store b/genomix/genomix-hadoop/src/test/java/edu/.DS_Store
new file mode 100644
index 0000000..f50e64b
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/java/edu/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/.DS_Store b/genomix/genomix-hadoop/src/test/java/edu/uci/.DS_Store
new file mode 100644
index 0000000..9aea623
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/.DS_Store b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/.DS_Store
new file mode 100644
index 0000000..64f18c4
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/.DS_Store
Binary files differ
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 44af11b..97b861c 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
@@ -32,6 +32,7 @@
import org.apache.hadoop.util.ReflectionUtils;
import org.junit.Test;
+import edu.uci.ics.genomix.type.GeneCode;
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.KmerCountValue;
import edu.uci.ics.utils.TestUtils;
@@ -45,13 +46,14 @@
private static final String COMPARE_DIR = "compare";
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/Test.txt";
+ private static final String DATA_PATH = "data/webmap/BridgePath";
private static final String HDFS_PATH = "/webmap";
private static final String RESULT_PATH = "/result1";
private static final String EXPECTED_PATH = "expected/result1";
private static final String TEST_SOURCE_DIR = COMPARE_DIR + RESULT_PATH + "/comparesource.txt";
private static final int COUNT_REDUCER = 4;
- private static final int SIZE_KMER = 3;
+ private static final int SIZE_KMER = 5;
+ private static final String GRAPHVIZ = "Graphviz/GenomixSource.txt";
private MiniDFSCluster dfsCluster;
private MiniMRCluster mrCluster;
@@ -76,15 +78,35 @@
KmerCountValue value = (KmerCountValue) ReflectionUtils.newInstance(reader.getValueClass(), conf);
File filePathTo = new File(TEST_SOURCE_DIR);
BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
+ File GraphViz = new File(GRAPHVIZ);
+ BufferedWriter bw2 = new BufferedWriter(new FileWriter(GraphViz));
while (reader.next(key, value)) {
+ byte succeed = (byte) 0x0F;
+ byte adjBitMap = value.getAdjBitMap();
+ succeed = (byte) (succeed & adjBitMap);
+ byte shiftedCode = 0;
+ for(int i = 0 ; i < 4; i ++){
+ byte temp = 0x01;
+ temp = (byte)(temp << i);
+ temp = (byte) (succeed & temp);
+ if(temp != 0 ){
+ bw2.write(key.toString());
+ bw2.newLine();
+ byte succeedCode = GeneCode.getGeneCodeFromBitMap(temp);
+ shiftedCode = key.shiftKmerWithNextCode(succeedCode);
+ bw2.write(key.toString());
+ bw2.newLine();
+ key.shiftKmerWithPreCode(shiftedCode);
+ }
+ }
bw.write(key.toString() + "\t" + value.toString());
- bw.newLine();
+ bw.newLine();
}
bw.close();
dumpResult();
- TestUtils.compareWithResult(new File(TEST_SOURCE_DIR), new File(EXPECTED_PATH));
+// TestUtils.compareWithResult(new File(TEST_SOURCE_DIR), new File(EXPECTED_PATH));
cleanupHadoop();
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmerging/MergePathTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmerging/MergePathTest.java
index 95a9785..5e6e51e 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmerging/MergePathTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmerging/MergePathTest.java
@@ -18,6 +18,7 @@
import org.junit.Test;
import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.utils.TestUtils;
@SuppressWarnings("deprecation")
@@ -33,7 +34,7 @@
private static final String RESULT_PATH = "/result3";
private static final String EXPECTED_PATH = "expected/result3";
private static final String TEST_SOURCE_DIR = COMPARE_DIR + RESULT_PATH + "/comparesource.txt";
- private static final int COUNT_REDUCER = 4;
+ private static final int COUNT_REDUCER = 1;
private static final int SIZE_KMER = 3;
private MiniDFSCluster dfsCluster;
@@ -48,12 +49,13 @@
startHadoop();
MergePathDriver tldriver = new MergePathDriver();
- tldriver.run(HDFS_PATH, RESULT_PATH, HDFA_PATH_DATA, COUNT_REDUCER, SIZE_KMER, 3, HADOOP_CONF_PATH);
-
- SequenceFile.Reader reader = null;
- Path path = new Path(HDFA_PATH_DATA + "/complete2" + "/complete2-r-00000");
+ tldriver.run(HDFS_PATH, RESULT_PATH, HDFA_PATH_DATA, COUNT_REDUCER, SIZE_KMER, 1, HADOOP_CONF_PATH);
+
+/* SequenceFile.Reader reader = null;
+ Path path = new Path(RESULT_PATH + "/part-00000");
+// Path path = new Path(RESULT_PATH + "/uncomplete0" + "/uncomplete0-r-00000");
reader = new SequenceFile.Reader(dfs, path, conf);
- KmerBytesWritable key = (KmerBytesWritable) ReflectionUtils.newInstance(reader.getKeyClass(), conf);
+ VKmerBytesWritable key = (VKmerBytesWritable) ReflectionUtils.newInstance(reader.getKeyClass(), conf);
MergePathValueWritable value = (MergePathValueWritable) ReflectionUtils.newInstance(reader.getValueClass(), conf);
File filePathTo = new File(TEST_SOURCE_DIR);
BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
@@ -61,10 +63,10 @@
bw.write(key.toString() + "\t" + value.getAdjBitMap() + "\t" + value.getFlag());
bw.newLine();
}
- bw.close();
-
+ bw.close();*/
dumpResult();
- TestUtils.compareWithResult(new File(TEST_SOURCE_DIR), new File(EXPECTED_PATH));
+
+// TestUtils.compareWithResult(new File(TEST_SOURCE_DIR), new File(EXPECTED_PATH));
cleanupHadoop();
@@ -96,7 +98,8 @@
}
private void dumpResult() throws IOException {
- Path src = new Path(HDFA_PATH_DATA + "/" + "complete2");
+// Path src = new Path(HDFA_PATH_DATA + "/" + "complete2");
+ Path src = new Path(RESULT_PATH);
Path dest = new Path(ACTUAL_RESULT_DIR + "/");
dfs.copyToLocalFile(src, dest);
}
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmergingh2/MergePathH2Test.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmergingh2/MergePathH2Test.java
new file mode 100644
index 0000000..ff15299
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmergingh2/MergePathH2Test.java
@@ -0,0 +1,105 @@
+package edu.uci.ics.pathmergingh2;
+
+import java.io.BufferedWriter;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileWriter;
+import java.io.IOException;
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.hdfs.MiniDFSCluster;
+import org.apache.hadoop.io.SequenceFile;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MiniMRCluster;
+import org.apache.hadoop.util.ReflectionUtils;
+import org.junit.Test;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.utils.TestUtils;
+
+@SuppressWarnings("deprecation")
+public class MergePathH2Test {
+ private static final String ACTUAL_RESULT_DIR = "actual4";
+ private static final String COMPARE_DIR = "compare";
+ 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 = "actual2" + "/result2" + "/part-00000";
+ private static final String HDFS_PATH = "/webmap";
+ private static final String HDFA_PATH_DATA = "/webmapdata";
+
+ private static final String RESULT_PATH = "/result4";
+ private static final String EXPECTED_PATH = "expected/result4";
+ private static final String TEST_SOURCE_DIR = COMPARE_DIR + RESULT_PATH + "/comparesource.txt";
+ private static final int COUNT_REDUCER = 1;
+ private static final int SIZE_KMER = 3;
+
+ private MiniDFSCluster dfsCluster;
+ private MiniMRCluster mrCluster;
+ private FileSystem dfs;
+
+ @SuppressWarnings("resource")
+ @Test
+ public void test() throws Exception {
+ FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
+ FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
+ startHadoop();
+
+ MergePathH2Driver tldriver = new MergePathH2Driver();
+ tldriver.run(HDFS_PATH, RESULT_PATH, HDFA_PATH_DATA, COUNT_REDUCER, SIZE_KMER, 1, HADOOP_CONF_PATH);
+
+/* SequenceFile.Reader reader = null;
+// Path path = new Path(RESULT_PATH + "/part-00000");
+ Path path = new Path(RESULT_PATH + "/uncomplete0" + "/uncomplete0-r-00000");
+ reader = new SequenceFile.Reader(dfs, path, conf);
+ VKmerBytesWritable key = (VKmerBytesWritable) ReflectionUtils.newInstance(reader.getKeyClass(), conf);
+ MergePathValueWritable value = (MergePathValueWritable) ReflectionUtils.newInstance(reader.getValueClass(), conf);
+ File filePathTo = new File(TEST_SOURCE_DIR);
+ BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
+ while (reader.next(key, value)) {
+ bw.write(key.toString() + "\t" + value.getAdjBitMap() + "\t" + value.getFlag());
+ bw.newLine();
+ }
+ bw.close();*/
+// dumpResult();
+
+// TestUtils.compareWithResult(new File(TEST_SOURCE_DIR), new File(EXPECTED_PATH));
+
+ cleanupHadoop();
+
+ }
+ private void startHadoop() throws IOException {
+ FileSystem lfs = FileSystem.getLocal(new Configuration());
+ lfs.delete(new Path("build"), true);
+ System.setProperty("hadoop.log.dir", "logs");
+ dfsCluster = new MiniDFSCluster(conf, 2, true, null);
+ dfs = dfsCluster.getFileSystem();
+ mrCluster = new MiniMRCluster(4, dfs.getUri().toString(), 2);
+
+ Path src = new Path(DATA_PATH);
+ Path dest = new Path(HDFS_PATH + "/");
+ dfs.mkdirs(dest);
+ dfs.copyFromLocalFile(src, dest);
+ Path data = new Path(HDFA_PATH_DATA + "/");
+ dfs.mkdirs(data);
+
+ DataOutputStream confOutput = new DataOutputStream(new FileOutputStream(new File(HADOOP_CONF_PATH)));
+ conf.writeXml(confOutput);
+ confOutput.flush();
+ confOutput.close();
+ }
+
+ private void cleanupHadoop() throws IOException {
+ mrCluster.shutdown();
+ dfsCluster.shutdown();
+ }
+
+ private void dumpResult() throws IOException {
+// Path src = new Path(HDFA_PATH_DATA + "/" + "complete2");
+ Path src = new Path(RESULT_PATH);
+ Path dest = new Path(ACTUAL_RESULT_DIR + "/");
+ dfs.copyToLocalFile(src, dest);
+ }
+}
\ No newline at end of file
diff --git a/genomix/genomix-hadoop/testactual/source.txt b/genomix/genomix-hadoop/testactual/source.txt
deleted file mode 100644
index aa7a107..0000000
--- a/genomix/genomix-hadoop/testactual/source.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-ATAGAAGATCGA A|T 1
-AATAGAAGATCG |A 1
-TAGAAGATCGAT A| 1
diff --git a/genomix/genomix-hyracks/pom.xml b/genomix/genomix-hyracks/pom.xml
index b246a0e..ca5cb61 100644
--- a/genomix/genomix-hyracks/pom.xml
+++ b/genomix/genomix-hyracks/pom.xml
@@ -8,7 +8,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>genomix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<properties>
@@ -175,40 +175,40 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
@@ -222,13 +222,13 @@
<dependency>
<groupId>edu.uci.ics.hyracks.examples</groupId>
<artifactId>hyracks-integration-tests</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-ipc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
@@ -245,19 +245,19 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-hdfs-core</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-hdfs-core</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>genomix-data</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/genomix/genomix-pregelix/pom.xml b/genomix/genomix-pregelix/pom.xml
index 4a810b7..854335f 100644
--- a/genomix/genomix-pregelix/pom.xml
+++ b/genomix/genomix-pregelix/pom.xml
@@ -4,7 +4,7 @@
<groupId>edu.uci.ics.pregelix</groupId>
<artifactId>genomix-pregelix</artifactId>
<packaging>jar</packaging>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<name>genomix-pregelix</name>
<properties>
@@ -124,14 +124,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-core</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>genomix-data</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hivesterix/hivesterix-common/pom.xml b/hivesterix/hivesterix-common/pom.xml
index bf0ec0a..2dbb788 100644
--- a/hivesterix/hivesterix-common/pom.xml
+++ b/hivesterix/hivesterix-common/pom.xml
@@ -7,7 +7,7 @@
<parent>
<artifactId>hivesterix</artifactId>
<groupId>edu.uci.ics.hyracks</groupId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -30,21 +30,21 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-compiler</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-hdfs-core</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hivesterix/hivesterix-dist/pom.xml b/hivesterix/hivesterix-dist/pom.xml
index aef0320..5f4c46b 100644
--- a/hivesterix/hivesterix-dist/pom.xml
+++ b/hivesterix/hivesterix-dist/pom.xml
@@ -2,13 +2,13 @@
<modelVersion>4.0.0</modelVersion>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix-dist</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<name>hivesterix-dist</name>
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<dependencies>
@@ -276,14 +276,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix-translator</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix-optimizer</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
@@ -297,21 +297,21 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-compiler</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hivesterix/hivesterix-dist/src/main/resources/conf/cluster.properties b/hivesterix/hivesterix-dist/src/main/resources/conf/cluster.properties
index 2d2401a..056cce4 100644
--- a/hivesterix/hivesterix-dist/src/main/resources/conf/cluster.properties
+++ b/hivesterix/hivesterix-dist/src/main/resources/conf/cluster.properties
@@ -4,9 +4,6 @@
#The CC port for Hyracks cluster management
CC_CLUSTERPORT=1099
-#The directory of hyracks binaries
-HYRACKS_HOME=../../../../hyracks
-
#The tmp directory for cc to install jars
CCTMP_DIR=/tmp/t1
@@ -29,9 +26,11 @@
FRAME_SIZE=65536
#CC JAVA_OPTS
-CCJAVA_OPTS="-Xdebug -Xrunjdwp:transport=dt_socket,address=7001,server=y,suspend=n -Xmx1g -Djava.util.logging.config.file=logging.properties"
+CCJAVA_OPTS="-Xmx1g -Djava.util.logging.config.file=logging.properties"
+# debug option: CCJAVA_OPTS="-Xdebug -Xrunjdwp:transport=dt_socket,address=7001,server=y,suspend=n -Xmx1g -Djava.util.logging.config.file=logging.properties"
# Yourkit option: -agentpath:/grid/0/dev/vborkar/tools/yjp-10.0.4/bin/linux-x86-64/libyjpagent.so=port=20001"
#NC JAVA_OPTS
-NCJAVA_OPTS="-Xdebug -Xrunjdwp:transport=dt_socket,address=7002,server=y,suspend=n -Xmx1g -Djava.util.logging.config.file=logging.properties"
-
+NCJAVA_OPTS="-Xmx1g -Djava.util.logging.config.file=logging.properties"
+# debug option: NCJAVA_OPTS="-Xdebug -Xrunjdwp:transport=dt_socket,address=7002,server=y,suspend=n -Xmx1g -Djava.util.logging.config.file=logging.properties"
+# Yourkit option: -agentpath:/grid/0/dev/vborkar/tools/yjp-10.0.4/bin/linux-x86-64/libyjpagent.so=port=20001"
diff --git a/hivesterix/hivesterix-dist/src/main/resources/scripts/getip.sh b/hivesterix/hivesterix-dist/src/main/resources/scripts/getip.sh
index 8c9ae76..1b44d09 100755
--- a/hivesterix/hivesterix-dist/src/main/resources/scripts/getip.sh
+++ b/hivesterix/hivesterix-dist/src/main/resources/scripts/getip.sh
@@ -1,3 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
#get the OS
OS_NAME=`uname -a|awk '{print $1}'`
LINUX_OS='Linux'
@@ -6,10 +24,10 @@
then
#Get IP Address
IPADDR=`/sbin/ifconfig eth0 | grep "inet " | awk '{print $2}' | cut -f 2 -d ':'`
- if [ "$IPADDR" = "" ]
+ if [ "$IPADDR" = "" ]
then
- IPADDR=`/sbin/ifconfig em1 | grep "inet " | awk '{print $2}' | cut -f 2 -d ':'`
- fi
+ IPADDR=`/sbin/ifconfig em1 | grep "inet " | awk '{print $2}' | cut -f 2 -d ':'`
+ fi
if [ "$IPADDR" = "" ]
then
IPADDR=`/sbin/ifconfig lo | grep "inet " | awk '{print $2}' | cut -f 2 -d ':'`
diff --git a/hivesterix/hivesterix-dist/src/main/resources/scripts/hive b/hivesterix/hivesterix-dist/src/main/resources/scripts/hive
index f98f340..38a9e33 100755
--- a/hivesterix/hivesterix-dist/src/main/resources/scripts/hive
+++ b/hivesterix/hivesterix-dist/src/main/resources/scripts/hive
@@ -81,7 +81,7 @@
exit 3;
fi
-CLASSPATH=${CLASSPATH}:${HIVE_LIB}/a-hive-path.jar
+CLASSPATH=${CLASSPATH}:${HIVE_LIB}/a-hive-patch.jar
for f in ${HIVE_LIB}/*.jar; do
CLASSPATH=${CLASSPATH}:$f;
diff --git a/hivesterix/hivesterix-dist/src/main/resources/scripts/hivesterixcc b/hivesterix/hivesterix-dist/src/main/resources/scripts/hivesterixcc
new file mode 100755
index 0000000..d2adffd
--- /dev/null
+++ b/hivesterix/hivesterix-dist/src/main/resources/scripts/hivesterixcc
@@ -0,0 +1,122 @@
+#!/bin/sh
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
+# resolve links - $0 may be a softlink
+PRG="$0"
+
+while [ -h "$PRG" ]; do
+ ls=`ls -ld "$PRG"`
+ link=`expr "$ls" : '.*-> \(.*\)$'`
+ if expr "$link" : '/.*' > /dev/null; then
+ PRG="$link"
+ else
+ PRG=`dirname "$PRG"`/"$link"
+ fi
+done
+
+PRGDIR=`dirname "$PRG"`
+BASEDIR=`cd "$PRGDIR/.." >/dev/null; pwd`
+
+
+
+# OS specific support. $var _must_ be set to either true or false.
+cygwin=false;
+darwin=false;
+case "`uname`" in
+ CYGWIN*) cygwin=true ;;
+ Darwin*) darwin=true
+ if [ -z "$JAVA_VERSION" ] ; then
+ JAVA_VERSION="CurrentJDK"
+ else
+ echo "Using Java version: $JAVA_VERSION"
+ fi
+ if [ -z "$JAVA_HOME" ] ; then
+ JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/${JAVA_VERSION}/Home
+ fi
+ ;;
+esac
+
+if [ -z "$JAVA_HOME" ] ; then
+ if [ -r /etc/gentoo-release ] ; then
+ JAVA_HOME=`java-config --jre-home`
+ fi
+fi
+
+# For Cygwin, ensure paths are in UNIX format before anything is touched
+if $cygwin ; then
+ [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
+ [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --unix "$CLASSPATH"`
+fi
+
+# If a specific java binary isn't specified search for the standard 'java' binary
+if [ -z "$JAVACMD" ] ; then
+ if [ -n "$JAVA_HOME" ] ; then
+ if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+ # IBM's JDK on AIX uses strange locations for the executables
+ JAVACMD="$JAVA_HOME/jre/sh/java"
+ else
+ JAVACMD="$JAVA_HOME/bin/java"
+ fi
+ else
+ JAVACMD=`which java`
+ fi
+fi
+
+if [ ! -x "$JAVACMD" ] ; then
+ echo "Error: JAVA_HOME is not defined correctly." 1>&2
+ echo " We cannot execute $JAVACMD" 1>&2
+ exit 1
+fi
+
+if [ -z "$REPO" ]
+then
+ REPO="$BASEDIR"/lib
+fi
+
+CLASSPATH=$CLASSPATH_PREFIX:"$HADOOP_HOME"/conf:/etc/hadoop/conf:"$BASEDIR"/etc:$1
+
+#add the desired hive patch
+CLASSPATH=${CLASSPATH}:${REPO}/a-hive-patch.jar
+
+#add the desired jetty jar
+for f in ${REPO}/servlet-api-3*.jar; do
+ CLASSPATH=${CLASSPATH}:$f;
+done
+
+for f in ${REPO}/*.jar; do
+ CLASSPATH=${CLASSPATH}:$f;
+done
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin; then
+ [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --windows "$CLASSPATH"`
+ [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
+ [ -n "$HOME" ] && HOME=`cygpath --path --windows "$HOME"`
+ [ -n "$BASEDIR" ] && BASEDIR=`cygpath --path --windows "$BASEDIR"`
+ [ -n "$REPO" ] && REPO=`cygpath --path --windows "$REPO"`
+fi
+
+exec "$JAVACMD" $JAVA_OPTS \
+ -classpath "$CLASSPATH" \
+ -Dapp.name="hivesterixcc" \
+ -Dapp.pid="$$" \
+ -Dapp.repo="$REPO" \
+ -Dapp.home="$BASEDIR" \
+ -Dbasedir="$BASEDIR" \
+ edu.uci.ics.hyracks.control.cc.CCDriver \
+ "$@"
diff --git a/hivesterix/hivesterix-dist/src/main/resources/scripts/hivesterixnc b/hivesterix/hivesterix-dist/src/main/resources/scripts/hivesterixnc
new file mode 100755
index 0000000..40f3ec6
--- /dev/null
+++ b/hivesterix/hivesterix-dist/src/main/resources/scripts/hivesterixnc
@@ -0,0 +1,117 @@
+#!/bin/sh
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
+# resolve links - $0 may be a softlink
+PRG="$0"
+
+while [ -h "$PRG" ]; do
+ ls=`ls -ld "$PRG"`
+ link=`expr "$ls" : '.*-> \(.*\)$'`
+ if expr "$link" : '/.*' > /dev/null; then
+ PRG="$link"
+ else
+ PRG=`dirname "$PRG"`/"$link"
+ fi
+done
+
+PRGDIR=`dirname "$PRG"`
+BASEDIR=`cd "$PRGDIR/.." >/dev/null; pwd`
+
+
+
+# OS specific support. $var _must_ be set to either true or false.
+cygwin=false;
+darwin=false;
+case "`uname`" in
+ CYGWIN*) cygwin=true ;;
+ Darwin*) darwin=true
+ if [ -z "$JAVA_VERSION" ] ; then
+ JAVA_VERSION="CurrentJDK"
+ else
+ echo "Using Java version: $JAVA_VERSION"
+ fi
+ if [ -z "$JAVA_HOME" ] ; then
+ JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/${JAVA_VERSION}/Home
+ fi
+ ;;
+esac
+
+if [ -z "$JAVA_HOME" ] ; then
+ if [ -r /etc/gentoo-release ] ; then
+ JAVA_HOME=`java-config --jre-home`
+ fi
+fi
+
+# For Cygwin, ensure paths are in UNIX format before anything is touched
+if $cygwin ; then
+ [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
+ [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --unix "$CLASSPATH"`
+fi
+
+# If a specific java binary isn't specified search for the standard 'java' binary
+if [ -z "$JAVACMD" ] ; then
+ if [ -n "$JAVA_HOME" ] ; then
+ if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+ # IBM's JDK on AIX uses strange locations for the executables
+ JAVACMD="$JAVA_HOME/jre/sh/java"
+ else
+ JAVACMD="$JAVA_HOME/bin/java"
+ fi
+ else
+ JAVACMD=`which java`
+ fi
+fi
+
+if [ ! -x "$JAVACMD" ] ; then
+ echo "Error: JAVA_HOME is not defined correctly." 1>&2
+ echo " We cannot execute $JAVACMD" 1>&2
+ exit 1
+fi
+
+if [ -z "$REPO" ]
+then
+ REPO="$BASEDIR"/lib
+fi
+
+CLASSPATH=$CLASSPATH_PREFIX:"$HADOOP_HOME"/conf:/etc/hadoop/conf:"$BASEDIR"/etc:$1
+
+#add the desired hive patch
+CLASSPATH=${CLASSPATH}:${REPO}/a-hive-patch.jar
+
+for f in ${REPO}/*.jar; do
+ CLASSPATH=${CLASSPATH}:$f;
+done
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin; then
+ [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --windows "$CLASSPATH"`
+ [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
+ [ -n "$HOME" ] && HOME=`cygpath --path --windows "$HOME"`2
+ [ -n "$BASEDIR" ] && BASEDIR=`cygpath --path --windows "$BASEDIR"`
+ [ -n "$REPO" ] && REPO=`cygpath --path --windows "$REPO"`
+fi
+
+exec "$JAVACMD" $JAVA_OPTS \
+ -classpath "$CLASSPATH" \
+ -Dapp.name="hivesterixnc" \
+ -Dapp.pid="$$" \
+ -Dapp.repo="$REPO" \
+ -Dapp.home="$BASEDIR" \
+ -Dbasedir="$BASEDIR" \
+ edu.uci.ics.hyracks.control.nc.NCDriver \
+ "$@"
diff --git a/hivesterix/hivesterix-dist/src/main/resources/scripts/startAllNCs.sh b/hivesterix/hivesterix-dist/src/main/resources/scripts/startAllNCs.sh
index d30da26..34a318d 100644
--- a/hivesterix/hivesterix-dist/src/main/resources/scripts/startAllNCs.sh
+++ b/hivesterix/hivesterix-dist/src/main/resources/scripts/startAllNCs.sh
@@ -1,6 +1,24 @@
-PREGELIX_PATH=`pwd`
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
+HIVESTERIX_PATH=`pwd`
for i in `cat conf/slaves`
do
- ssh $i "cd ${PREGELIX_PATH}; export JAVA_HOME=${JAVA_HOME}; bin/startnc.sh"
+ ssh $i "cd ${HIVESTERIX_PATH}; export JAVA_HOME=${JAVA_HOME}; bin/startnc.sh"
done
diff --git a/hivesterix/hivesterix-dist/src/main/resources/scripts/startCluster.sh b/hivesterix/hivesterix-dist/src/main/resources/scripts/startCluster.sh
index 6aa9161..cddf9a4 100644
--- a/hivesterix/hivesterix-dist/src/main/resources/scripts/startCluster.sh
+++ b/hivesterix/hivesterix-dist/src/main/resources/scripts/startCluster.sh
@@ -1,19 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
bin/startcc.sh
sleep 5
bin/startAllNCs.sh
-
-. conf/cluster.properties
-# do we need to specify the version somewhere?
-hyrackcmd=`ls ${HYRACKS_HOME}/hyracks-cli/target/hyracks-cli-*-binary-assembly/bin/hyrackscli`
-# find zip file
-appzip=`ls $PWD/../hivesterix-dist-*-binary-assembly.zip`
-
-[ -f $hyrackcmd ] || { echo "Hyracks commandline is missing"; exit -1;}
-[ -f $appzip ] || { echo "Genomix binary-assembly.zip is missing"; exit -1;}
-
-CCHOST_NAME=`cat conf/master`
-
-IPADDR=`bin/getip.sh`
-echo "connect to \"${IPADDR}:${CC_CLIENTPORT}\"; create application hivesterix \"$appzip\";" | $hyrackcmd
-echo ""
-
diff --git a/hivesterix/hivesterix-dist/src/main/resources/scripts/startDebugNc.sh b/hivesterix/hivesterix-dist/src/main/resources/scripts/startDebugNc.sh
index fe6cf27..cab8bb3 100755
--- a/hivesterix/hivesterix-dist/src/main/resources/scripts/startDebugNc.sh
+++ b/hivesterix/hivesterix-dist/src/main/resources/scripts/startDebugNc.sh
@@ -1,3 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
hostname
#Get the IP address of the cc
@@ -40,11 +58,11 @@
#Set JAVA_OPTS
export JAVA_OPTS=$NCJAVA_OPTS2
-cd $HYRACKS_HOME
-HYRACKS_HOME=`pwd`
+HIVESTERIX_HOME=`pwd`
#Enter the temp dir
cd $NCTMP_DIR2
#Launch hyracks nc
-$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyracksnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS2}" &> $NCLOGS_DIR2/$NODEID.log &
+#echo ${HIVESTERIX_HOME}/bin/hivesterixnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -result-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS}"
+${HIVESTERIX_HOME}/bin/hivesterixnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -result-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS2}" &> $NCLOGS_DIR2/$NODEID.log &
diff --git a/hivesterix/hivesterix-dist/src/main/resources/scripts/startcc.sh b/hivesterix/hivesterix-dist/src/main/resources/scripts/startcc.sh
index 484ecac..213b9eb 100644
--- a/hivesterix/hivesterix-dist/src/main/resources/scripts/startcc.sh
+++ b/hivesterix/hivesterix-dist/src/main/resources/scripts/startcc.sh
@@ -1,4 +1,21 @@
#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
hostname
#Import cluster properties
@@ -20,12 +37,15 @@
export JAVA_HOME=$JAVA_HOME
export JAVA_OPTS=$CCJAVA_OPTS
-#Launch hyracks cc script
-chmod -R 755 $HYRACKS_HOME
+HIVESTERIX_HOME=`pwd`
+
+#Enter the temp dir
+cd $CCTMP_DIR
+
if [ -f "conf/topology.xml" ]; then
#Launch hyracks cc script with topology
-$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyrackscc -client-net-ip-address $CCHOST -cluster-net-ip-address $CCHOST -client-net-port $CC_CLIENTPORT -cluster-net-port $CC_CLUSTERPORT -max-heartbeat-lapse-periods 999999 -default-max-job-attempts 0 -job-history-size 0 -cluster-topology "conf/topology.xml" &> $CCLOGS_DIR/cc.log &
+${HIVESTERIX_HOME}/bin/hivesterixcc -client-net-ip-address $CCHOST -cluster-net-ip-address $CCHOST -client-net-port $CC_CLIENTPORT -cluster-net-port $CC_CLUSTERPORT -max-heartbeat-lapse-periods 999999 -default-max-job-attempts 0 -job-history-size 0 -cluster-topology "conf/topology.xml" &> $CCLOGS_DIR/cc.log &
else
#Launch hyracks cc script without toplogy
-$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyrackscc -client-net-ip-address $CCHOST -cluster-net-ip-address $CCHOST -client-net-port $CC_CLIENTPORT -cluster-net-port $CC_CLUSTERPORT -max-heartbeat-lapse-periods 999999 -default-max-job-attempts 0 -job-history-size 0 &> $CCLOGS_DIR/cc.log &
+${HIVESTERIX_HOME}/bin/hivesterixcc -client-net-ip-address $CCHOST -cluster-net-ip-address $CCHOST -client-net-port $CC_CLIENTPORT -cluster-net-port $CC_CLUSTERPORT -max-heartbeat-lapse-periods 999999 -default-max-job-attempts 0 -job-history-size 0 &> $CCLOGS_DIR/cc.log &
fi
diff --git a/hivesterix/hivesterix-dist/src/main/resources/scripts/startnc.sh b/hivesterix/hivesterix-dist/src/main/resources/scripts/startnc.sh
index 23a4c36..904858d 100644
--- a/hivesterix/hivesterix-dist/src/main/resources/scripts/startnc.sh
+++ b/hivesterix/hivesterix-dist/src/main/resources/scripts/startnc.sh
@@ -1,3 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
hostname
MY_NAME=`hostname`
@@ -39,11 +57,11 @@
#Set JAVA_OPTS
export JAVA_OPTS=$NCJAVA_OPTS
-cd $HYRACKS_HOME
-HYRACKS_HOME=`pwd`
+HIVESTERIX_HOME=`pwd`
#Enter the temp dir
cd $NCTMP_DIR
#Launch hyracks nc
-$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyracksnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -result-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS}" &> $NCLOGS_DIR/$NODEID.log &
+#echo ${HIVESTERIX_HOME}/bin/hivesterixnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -result-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS}"
+${HIVESTERIX_HOME}/bin/hivesterixnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -result-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS}" &> $NCLOGS_DIR/$NODEID.log &
diff --git a/hivesterix/hivesterix-dist/src/main/resources/scripts/stopAllNCs.sh b/hivesterix/hivesterix-dist/src/main/resources/scripts/stopAllNCs.sh
index 12367c1..456ff68 100644
--- a/hivesterix/hivesterix-dist/src/main/resources/scripts/stopAllNCs.sh
+++ b/hivesterix/hivesterix-dist/src/main/resources/scripts/stopAllNCs.sh
@@ -1,6 +1,24 @@
-PREGELIX_PATH=`pwd`
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
+HIVESTERIX_PATH=`pwd`
for i in `cat conf/slaves`
do
- ssh $i "cd ${PREGELIX_PATH}; bin/stopnc.sh"
+ ssh $i "cd ${HIVESTERIX_PATH}; bin/stopnc.sh"
done
diff --git a/hivesterix/hivesterix-dist/src/main/resources/scripts/stopCluster.sh b/hivesterix/hivesterix-dist/src/main/resources/scripts/stopCluster.sh
index 4889934..6b829aa 100644
--- a/hivesterix/hivesterix-dist/src/main/resources/scripts/stopCluster.sh
+++ b/hivesterix/hivesterix-dist/src/main/resources/scripts/stopCluster.sh
@@ -1,3 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
bin/stopAllNCs.sh
sleep 2
bin/stopcc.sh
diff --git a/hivesterix/hivesterix-dist/src/main/resources/scripts/stopcc.sh b/hivesterix/hivesterix-dist/src/main/resources/scripts/stopcc.sh
index c2f525a..d7f78a8 100644
--- a/hivesterix/hivesterix-dist/src/main/resources/scripts/stopcc.sh
+++ b/hivesterix/hivesterix-dist/src/main/resources/scripts/stopcc.sh
@@ -1,8 +1,37 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
hostname
. conf/cluster.properties
#Kill process
-PID=`ps -ef|grep ${USER}|grep java|grep hyracks|awk '{print $2}'`
+#Kill process
+PID=`ps -ef|grep ${USER}|grep java|grep 'Dapp.name=hivesterixcc'|awk '{print $2}'`
+
+if [ "$PID" == "" ]; then
+ PID=`ps -ef|grep ${USER}|grep java|grep 'hyracks'|awk '{print $2}'`
+fi
+
+if [ "$PID" == "" ]; then
+ USERID=`id | sed 's/^uid=//;s/(.*$//'`
+ PID=`ps -ef|grep ${USERID}|grep java|grep 'Dapp.name=hivesterixcc'|awk '{print $2}'`
+fi
+
echo $PID
kill -9 $PID
diff --git a/hivesterix/hivesterix-dist/src/main/resources/scripts/stopnc.sh b/hivesterix/hivesterix-dist/src/main/resources/scripts/stopnc.sh
index 35c4794..5dc4ccd 100644
--- a/hivesterix/hivesterix-dist/src/main/resources/scripts/stopnc.sh
+++ b/hivesterix/hivesterix-dist/src/main/resources/scripts/stopnc.sh
@@ -1,8 +1,26 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
hostname
. conf/cluster.properties
#Kill process
-PID=`ps -ef|grep ${USER}|grep java|grep 'Dapp.name=hyracksnc'|awk '{print $2}'`
+PID=`ps -ef|grep ${USER}|grep java|grep 'Dapp.name=hivesterixnc'|awk '{print $2}'`
if [ "$PID" == "" ]; then
PID=`ps -ef|grep ${USER}|grep java|grep 'hyracks'|awk '{print $2}'`
@@ -10,7 +28,7 @@
if [ "$PID" == "" ]; then
USERID=`id | sed 's/^uid=//;s/(.*$//'`
- PID=`ps -ef|grep ${USERID}|grep java|grep 'Dapp.name=hyracksnc'|awk '{print $2}'`
+ PID=`ps -ef|grep ${USERID}|grep java|grep 'Dapp.name=hivesterixnc'|awk '{print $2}'`
fi
echo $PID
diff --git a/hivesterix/hivesterix-optimizer/pom.xml b/hivesterix/hivesterix-optimizer/pom.xml
index 77a5d53..55d6adf 100644
--- a/hivesterix/hivesterix-optimizer/pom.xml
+++ b/hivesterix/hivesterix-optimizer/pom.xml
@@ -4,7 +4,7 @@
<parent>
<artifactId>hivesterix</artifactId>
<groupId>edu.uci.ics.hyracks</groupId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<artifactId>hivesterix-optimizer</artifactId>
@@ -30,14 +30,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix-translator</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hivesterix/hivesterix-runtime/pom.xml b/hivesterix/hivesterix-runtime/pom.xml
index fc55273..18b8f62 100644
--- a/hivesterix/hivesterix-runtime/pom.xml
+++ b/hivesterix/hivesterix-runtime/pom.xml
@@ -2,13 +2,13 @@
<modelVersion>4.0.0</modelVersion>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix-runtime</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<name>hivesterix-runtime</name>
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<dependencies>
@@ -276,35 +276,35 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-compiler</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix-serde</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hivesterix/hivesterix-serde/pom.xml b/hivesterix/hivesterix-serde/pom.xml
index 72c9cc9..bf5a9b8 100644
--- a/hivesterix/hivesterix-serde/pom.xml
+++ b/hivesterix/hivesterix-serde/pom.xml
@@ -4,7 +4,7 @@
<parent>
<artifactId>hivesterix</artifactId>
<groupId>edu.uci.ics.hyracks</groupId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<artifactId>hivesterix-serde</artifactId>
@@ -44,14 +44,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-compiler</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hivesterix/hivesterix-translator/pom.xml b/hivesterix/hivesterix-translator/pom.xml
index e7ad3ed..7bcbb85 100644
--- a/hivesterix/hivesterix-translator/pom.xml
+++ b/hivesterix/hivesterix-translator/pom.xml
@@ -7,7 +7,7 @@
<parent>
<artifactId>hivesterix</artifactId>
<groupId>edu.uci.ics.hyracks</groupId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -37,21 +37,21 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>algebricks-compiler</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix-runtime</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hivesterix/pom.xml b/hivesterix/pom.xml
index 6ae37b5..3a212ec 100644
--- a/hivesterix/pom.xml
+++ b/hivesterix/pom.xml
@@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hivesterix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<packaging>pom</packaging>
<name>hivesterix</name>
diff --git a/hyracks/hyracks-api/pom.xml b/hyracks/hyracks-api/pom.xml
index 45421e1..04a64c1 100644
--- a/hyracks/hyracks-api/pom.xml
+++ b/hyracks/hyracks-api/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -47,7 +47,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-ipc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
diff --git a/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/client/HyracksConnection.java b/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/client/HyracksConnection.java
index eb25b70..6af8dd9 100644
--- a/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/client/HyracksConnection.java
+++ b/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/client/HyracksConnection.java
@@ -123,10 +123,12 @@
@Override
public DeploymentId deployBinary(List<String> jars) throws Exception {
+ /** generate a deployment id */
DeploymentId deploymentId = new DeploymentId(UUID.randomUUID().toString());
List<URL> binaryURLs = new ArrayList<URL>();
if (jars != null && jars.size() > 0) {
HttpClient hc = new DefaultHttpClient();
+ /** upload jars through a http client one-by-one to the CC server */
for (String jar : jars) {
int slashIndex = jar.lastIndexOf('/');
String fileName = jar.substring(slashIndex + 1);
@@ -139,11 +141,14 @@
response.getEntity().consumeContent();
}
if (response.getStatusLine().getStatusCode() != 200) {
+ hci.unDeployBinary(deploymentId);
throw new HyracksException(response.getStatusLine().toString());
}
+ /** add the uploaded URL address into the URLs of jars to be deployed at NCs */
binaryURLs.add(new URL(url));
}
}
+ /**deploy the URLs to the CC and NCs*/
hci.deployBinary(binaryURLs, deploymentId);
return deploymentId;
}
diff --git a/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/client/IHyracksClientConnection.java b/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/client/IHyracksClientConnection.java
index 37bbdfa..41b07d7 100644
--- a/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/client/IHyracksClientConnection.java
+++ b/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/client/IHyracksClientConnection.java
@@ -168,4 +168,4 @@
public JobId startJob(DeploymentId deploymentId, IActivityClusterGraphGeneratorFactory acggf,
EnumSet<JobFlag> jobFlags) throws Exception;
-}
\ No newline at end of file
+}
diff --git a/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/deployment/DeploymentId.java b/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/deployment/DeploymentId.java
index b642bc7..8d8d728 100644
--- a/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/deployment/DeploymentId.java
+++ b/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/deployment/DeploymentId.java
@@ -1,7 +1,28 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
package edu.uci.ics.hyracks.api.deployment;
import java.io.Serializable;
+/**
+ * The representation of a deployment id
+ *
+ * @author yingyib
+ *
+ */
public class DeploymentId implements Serializable {
private static final long serialVersionUID = 1L;
diff --git a/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/job/IJobSerializerDeserializer.java b/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/job/IJobSerializerDeserializer.java
index d402cd3..a105953 100644
--- a/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/job/IJobSerializerDeserializer.java
+++ b/hyracks/hyracks-api/src/main/java/edu/uci/ics/hyracks/api/job/IJobSerializerDeserializer.java
@@ -21,14 +21,49 @@
import edu.uci.ics.hyracks.api.exceptions.HyracksException;
+/**
+ * The serializer/deserializer/classloader interface for job/task information such as job specifications, activity graphs and so on.
+ *
+ * @author yingyib
+ */
public interface IJobSerializerDeserializer {
+ /**
+ * Deserialize the bytes to an object
+ *
+ * @param bytes
+ * the binary content of an object
+ * @return the deserialized object
+ * @throws HyracksException
+ */
public Object deserialize(byte[] bytes) throws HyracksException;
- public byte[] serialize(Serializable job) throws HyracksException;
+ /**
+ * Serialize a object into bytes
+ *
+ * @param object
+ * a Serializable Java object
+ * @return
+ * the byte array which contains the binary content of the input object
+ * @throws HyracksException
+ */
+ public byte[] serialize(Serializable object) throws HyracksException;
+ /**
+ * Load a class by its name
+ *
+ * @param className
+ * the name of the class
+ * @return
+ * @throws HyracksException
+ */
public Class<?> loadClass(String className) throws HyracksException;
+ /**
+ *
+ * @param binaryURLs
+ * @throws HyracksException
+ */
public void addClassPathURLs(List<URL> binaryURLs) throws HyracksException;
public ClassLoader getClassLoader() throws HyracksException;
diff --git a/hyracks/hyracks-client/pom.xml b/hyracks/hyracks-client/pom.xml
index 4febc6e..76a2659 100644
--- a/hyracks/hyracks-client/pom.xml
+++ b/hyracks/hyracks-client/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -25,22 +25,22 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-net</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-comm</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
diff --git a/hyracks/hyracks-comm/pom.xml b/hyracks/hyracks-comm/pom.xml
index 647faa6..036e507 100644
--- a/hyracks/hyracks-comm/pom.xml
+++ b/hyracks/hyracks-comm/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -25,12 +25,12 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-net</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
diff --git a/hyracks/hyracks-control/hyracks-control-cc/pom.xml b/hyracks/hyracks-control/hyracks-control-cc/pom.xml
index 2af1a85..7782346 100644
--- a/hyracks/hyracks-control/hyracks-control-cc/pom.xml
+++ b/hyracks/hyracks-control/hyracks-control-cc/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -26,7 +26,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/web/ApplicationInstallationHandler.java b/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/web/ApplicationInstallationHandler.java
index 0236c4b..35165de 100755
--- a/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/web/ApplicationInstallationHandler.java
+++ b/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/web/ApplicationInstallationHandler.java
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2010 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* you may obtain a copy of the License from
diff --git a/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/web/WebServer.java b/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/web/WebServer.java
index c32cb97..cd7a684 100644
--- a/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/web/WebServer.java
+++ b/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/web/WebServer.java
@@ -71,6 +71,7 @@
addHandler(createAdminConsoleHandler());
addHandler(createStaticResourcesHandler());
+ /** the service of uploading/downloading deployment jars */
handler = new ContextHandler("/applications");
handler.setHandler(new ApplicationInstallationHandler(ccs));
addHandler(handler);
diff --git a/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/work/CliDeployBinaryWork.java b/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/work/CliDeployBinaryWork.java
index fa44633..1a889f8 100644
--- a/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/work/CliDeployBinaryWork.java
+++ b/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/work/CliDeployBinaryWork.java
@@ -30,6 +30,14 @@
import edu.uci.ics.hyracks.control.common.work.IPCResponder;
import edu.uci.ics.hyracks.control.common.work.SynchronizableWork;
+/***
+ * This is the work happens on the CC for a dynamic deployment.
+ * It first deploys the jar to CC application context.
+ * Then, it remotely calls each NC service to deploy the jars listed as http URLs.
+ * NOTE: in current implementation, a user cannot deploy with the same deployment id simultaneously.
+ *
+ * @author yingyib
+ */
public class CliDeployBinaryWork extends SynchronizableWork {
private ClusterControllerService ccs;
@@ -67,6 +75,8 @@
nodeIds.add(nc);
}
final DeploymentRun dRun = new DeploymentRun(nodeIds);
+
+ /** The following call prevents a user to deploy with the same deployment id simultaneously. */
ccs.addDeploymentRun(deploymentId, dRun);
/***
diff --git a/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/work/CliUnDeployBinaryWork.java b/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/work/CliUnDeployBinaryWork.java
index 8e429c9..d54444c 100644
--- a/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/work/CliUnDeployBinaryWork.java
+++ b/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/work/CliUnDeployBinaryWork.java
@@ -28,6 +28,14 @@
import edu.uci.ics.hyracks.control.common.work.IPCResponder;
import edu.uci.ics.hyracks.control.common.work.SynchronizableWork;
+/***
+ * This is the work happens on the CC for an undeployment.
+ * It first undeploys the jar to CC application context by giving it a deployment id.
+ * Then, it remotely calls each NC service to undeploy by giving them a deployment id.
+ * NOTE: in current implementation, a user cannot undeploy with the same deployment id simultaneously.
+ *
+ * @author yingyib
+ */
public class CliUnDeployBinaryWork extends SynchronizableWork {
private ClusterControllerService ccs;
@@ -63,6 +71,8 @@
nodeIds.add(nc);
}
final DeploymentRun dRun = new DeploymentRun(nodeIds);
+
+ /** The following call prevents a user to undeploy with the same deployment id simultaneously. */
ccs.addDeploymentRun(deploymentId, dRun);
/***
diff --git a/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/work/NotifyDeployBinaryWork.java b/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/work/NotifyDeployBinaryWork.java
index 903cad3..c4c8873 100644
--- a/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/work/NotifyDeployBinaryWork.java
+++ b/hyracks/hyracks-control/hyracks-control-cc/src/main/java/edu/uci/ics/hyracks/control/cc/work/NotifyDeployBinaryWork.java
@@ -21,6 +21,11 @@
import edu.uci.ics.hyracks.control.common.deployment.DeploymentStatus;
import edu.uci.ics.hyracks.control.common.work.AbstractWork;
+/***
+ * This is the work happens on the CC when CC gets a deployment or undeployment notification status message from one NC.
+ *
+ * @author yingyib
+ */
public class NotifyDeployBinaryWork extends AbstractWork {
private final ClusterControllerService ccs;
@@ -39,7 +44,7 @@
@Override
public void run() {
- // notify that one NC is deployed
+ /** triggered remotely by a NC to notify that the NC is deployed */
DeploymentRun dRun = ccs.getDeploymentRun(deploymentId);
dRun.notifyDeploymentStatus(nodeId, deploymentStatus);
}
diff --git a/hyracks/hyracks-control/hyracks-control-common/pom.xml b/hyracks/hyracks-control/hyracks-control-common/pom.xml
index 4ffb716..15e2840 100644
--- a/hyracks/hyracks-control/hyracks-control-common/pom.xml
+++ b/hyracks/hyracks-control/hyracks-control-common/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,7 +27,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/ClassLoaderJobSerializerDeserializer.java b/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/ClassLoaderJobSerializerDeserializer.java
index 894f59b..3a35c25 100644
--- a/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/ClassLoaderJobSerializerDeserializer.java
+++ b/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/ClassLoaderJobSerializerDeserializer.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
package edu.uci.ics.hyracks.control.common.deployment;
import java.io.Serializable;
@@ -12,6 +27,12 @@
import edu.uci.ics.hyracks.api.job.IJobSerializerDeserializer;
import edu.uci.ics.hyracks.api.util.JavaSerializationUtils;
+/**
+ * This is the IJobSerializerDeserializer implementation for jobs with dynamic deployed jars.
+ *
+ * @author yingyib
+ *
+ */
public class ClassLoaderJobSerializerDeserializer implements IJobSerializerDeserializer {
private URLClassLoader classLoader;
diff --git a/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/DeploymentRun.java b/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/DeploymentRun.java
index 519905c..84cfbb1 100644
--- a/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/DeploymentRun.java
+++ b/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/DeploymentRun.java
@@ -1,8 +1,29 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
package edu.uci.ics.hyracks.control.common.deployment;
import java.util.Set;
import java.util.TreeSet;
+/**
+ * The class maintain the status of a deployment process and the states
+ * of all slave machines involved in the deployment.
+ *
+ * @author yingyib
+ */
public class DeploymentRun implements IDeploymentStatusConditionVariable {
private DeploymentStatus deploymentStatus = DeploymentStatus.FAIL;
@@ -12,10 +33,22 @@
deploymentNodeIds.addAll(nodeIds);
}
+ /**
+ * One notify the deployment status
+ *
+ * @param nodeId
+ * @param status
+ */
public synchronized void notifyDeploymentStatus(String nodeId, DeploymentStatus status) {
- deploymentNodeIds.remove(nodeId);
- if (deploymentNodeIds.size() == 0) {
- deploymentStatus = DeploymentStatus.SUCCEED;
+ if (status == DeploymentStatus.SUCCEED) {
+ deploymentNodeIds.remove(nodeId);
+ if (deploymentNodeIds.size() == 0) {
+ deploymentStatus = DeploymentStatus.SUCCEED;
+ notifyAll();
+ }
+ } else {
+ deploymentNodeIds.clear();
+ deploymentStatus = DeploymentStatus.FAIL;
notifyAll();
}
}
diff --git a/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/DeploymentStatus.java b/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/DeploymentStatus.java
index 3690518..4ba50b7 100644
--- a/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/DeploymentStatus.java
+++ b/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/DeploymentStatus.java
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2010 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* you may obtain a copy of the License from
diff --git a/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/DeploymentUtils.java b/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/DeploymentUtils.java
index 715db96..0677e2e 100644
--- a/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/DeploymentUtils.java
+++ b/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/DeploymentUtils.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
package edu.uci.ics.hyracks.control.common.deployment;
import java.io.File;
@@ -23,10 +38,24 @@
import edu.uci.ics.hyracks.api.util.JavaSerializationUtils;
import edu.uci.ics.hyracks.control.common.context.ServerContext;
+/**
+ * A utility class which is in charge of the actual work of deployments.
+ *
+ * @author yingyib
+ */
public class DeploymentUtils {
private static final String DEPLOYMENT = "applications";
+ /**
+ * undeploy an existing deployment
+ *
+ * @param deploymentId
+ * the deployment id
+ * @param container
+ * @param ctx
+ * @throws HyracksException
+ */
public static void undeploy(DeploymentId deploymentId, IJobSerializerDeserializerContainer container,
ServerContext ctx) throws HyracksException {
container.removeJobSerializerDeserializer(deploymentId);
@@ -43,6 +72,21 @@
}
}
+ /**
+ * Deploying jars in NC or CC
+ *
+ * @param deploymentId
+ * the deployment id
+ * @param urls
+ * the jar URLs
+ * @param container
+ * the container of serailizer/deserializer
+ * @param ctx
+ * the ServerContext
+ * @param isNC
+ * true is NC/false is CC
+ * @throws HyracksException
+ */
public static void deploy(DeploymentId deploymentId, List<URL> urls, IJobSerializerDeserializerContainer container,
ServerContext ctx, boolean isNC) throws HyracksException {
IJobSerializerDeserializer jobSerDe = container.getJobSerializerDeerializer(deploymentId);
@@ -56,6 +100,17 @@
jobSerDe.addClassPathURLs(downloadURLs(urls, deploymentDir, isNC));
}
+ /**
+ * Deserialize bytes to an object according to a specific deployment
+ *
+ * @param bytes
+ * the bytes to be deserialized
+ * @param deploymentId
+ * the deployment id
+ * @param appCtx
+ * @return the deserialized object
+ * @throws HyracksException
+ */
public static Object deserialize(byte[] bytes, DeploymentId deploymentId, IApplicationContext appCtx)
throws HyracksException {
try {
@@ -69,6 +124,15 @@
}
}
+ /**
+ * Load a class from its class name
+ *
+ * @param className
+ * @param deploymentId
+ * @param appCtx
+ * @return the loaded class
+ * @throws HyracksException
+ */
public static Class<?> loadClass(String className, DeploymentId deploymentId, IApplicationContext appCtx)
throws HyracksException {
try {
@@ -83,6 +147,14 @@
}
}
+ /**
+ * Get the classloader of a specific deployment
+ *
+ * @param deploymentId
+ * @param appCtx
+ * @return
+ * @throws HyracksException
+ */
public static ClassLoader getClassLoader(DeploymentId deploymentId, IApplicationContext appCtx)
throws HyracksException {
try {
@@ -96,6 +168,18 @@
}
}
+ /**
+ * Download remote Http URLs and return the stored local file URLs
+ *
+ * @param urls
+ * the remote Http URLs
+ * @param deploymentDir
+ * the deployment jar storage directory
+ * @param isNC
+ * true is NC/false is CC
+ * @return a list of local file URLs
+ * @throws HyracksException
+ */
private static List<URL> downloadURLs(List<URL> urls, String deploymentDir, boolean isNC) throws HyracksException {
try {
List<URL> downloadedFileURLs = new ArrayList<URL>();
diff --git a/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/IDeploymentStatusConditionVariable.java b/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/IDeploymentStatusConditionVariable.java
index 06e398e..771baaa 100644
--- a/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/IDeploymentStatusConditionVariable.java
+++ b/hyracks/hyracks-control/hyracks-control-common/src/main/java/edu/uci/ics/hyracks/control/common/deployment/IDeploymentStatusConditionVariable.java
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2010 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* you may obtain a copy of the License from
@@ -15,7 +15,18 @@
package edu.uci.ics.hyracks.control.common.deployment;
+/**
+ * The conditional variable interface for deployment
+ *
+ * @author yingyib
+ */
public interface IDeploymentStatusConditionVariable {
+ /**
+ * synchronously wait the deployment to complete
+ *
+ * @return the deployment status
+ * @throws Exception
+ */
public DeploymentStatus waitForCompletion() throws Exception;
}
diff --git a/hyracks/hyracks-control/hyracks-control-nc/pom.xml b/hyracks/hyracks-control/hyracks-control-nc/pom.xml
index ad83d86..f554523 100644
--- a/hyracks/hyracks-control/hyracks-control-nc/pom.xml
+++ b/hyracks/hyracks-control/hyracks-control-nc/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -26,19 +26,19 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-net</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-comm</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
<reporting>
diff --git a/hyracks/hyracks-control/hyracks-control-nc/src/main/java/edu/uci/ics/hyracks/control/nc/work/DeployBinaryWork.java b/hyracks/hyracks-control/hyracks-control-nc/src/main/java/edu/uci/ics/hyracks/control/nc/work/DeployBinaryWork.java
index 4f613a1..e5f1bc1 100644
--- a/hyracks/hyracks-control/hyracks-control-nc/src/main/java/edu/uci/ics/hyracks/control/nc/work/DeployBinaryWork.java
+++ b/hyracks/hyracks-control/hyracks-control-nc/src/main/java/edu/uci/ics/hyracks/control/nc/work/DeployBinaryWork.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
package edu.uci.ics.hyracks.control.nc.work;
import java.net.URL;
@@ -10,6 +25,12 @@
import edu.uci.ics.hyracks.control.common.work.AbstractWork;
import edu.uci.ics.hyracks.control.nc.NodeControllerService;
+/**
+ * Deploy binary work that happens at each NC
+ *
+ * @author yingyib
+ *
+ */
public class DeployBinaryWork extends AbstractWork {
private DeploymentId deploymentId;
@@ -24,11 +45,18 @@
@Override
public void run() {
+ DeploymentStatus status;
try {
DeploymentUtils.deploy(deploymentId, binaryURLs, ncs.getApplicationContext()
.getJobSerializerDeserializerContainer(), ncs.getServerContext(), true);
+ status = DeploymentStatus.SUCCEED;
+ } catch (Exception e) {
+ status = DeploymentStatus.FAIL;
+ e.printStackTrace();
+ }
+ try {
IClusterController ccs = ncs.getClusterController();
- ccs.notifyDeployBinary(deploymentId, ncs.getId(), DeploymentStatus.SUCCEED);
+ ccs.notifyDeployBinary(deploymentId, ncs.getId(), status);
} catch (Exception e) {
throw new RuntimeException(e);
}
diff --git a/hyracks/hyracks-control/hyracks-control-nc/src/main/java/edu/uci/ics/hyracks/control/nc/work/UnDeployBinaryWork.java b/hyracks/hyracks-control/hyracks-control-nc/src/main/java/edu/uci/ics/hyracks/control/nc/work/UnDeployBinaryWork.java
index bd77fb5..605d63f 100644
--- a/hyracks/hyracks-control/hyracks-control-nc/src/main/java/edu/uci/ics/hyracks/control/nc/work/UnDeployBinaryWork.java
+++ b/hyracks/hyracks-control/hyracks-control-nc/src/main/java/edu/uci/ics/hyracks/control/nc/work/UnDeployBinaryWork.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
package edu.uci.ics.hyracks.control.nc.work;
import edu.uci.ics.hyracks.api.deployment.DeploymentId;
@@ -7,6 +22,11 @@
import edu.uci.ics.hyracks.control.common.work.AbstractWork;
import edu.uci.ics.hyracks.control.nc.NodeControllerService;
+/**
+ * undeploy binaries regarding to a deployment id
+ *
+ * @author yingyib
+ */
public class UnDeployBinaryWork extends AbstractWork {
private DeploymentId deploymentId;
@@ -19,11 +39,17 @@
@Override
public void run() {
+ DeploymentStatus status;
try {
DeploymentUtils.undeploy(deploymentId, ncs.getApplicationContext().getJobSerializerDeserializerContainer(),
ncs.getServerContext());
+ status = DeploymentStatus.SUCCEED;
+ } catch (Exception e) {
+ status = DeploymentStatus.FAIL;
+ }
+ try {
IClusterController ccs = ncs.getClusterController();
- ccs.notifyDeployBinary(deploymentId, ncs.getId(), DeploymentStatus.SUCCEED);
+ ccs.notifyDeployBinary(deploymentId, ncs.getId(), status);
} catch (Exception e) {
throw new RuntimeException(e);
}
diff --git a/hyracks/hyracks-control/pom.xml b/hyracks/hyracks-control/pom.xml
index 5696ffe..9141bf5 100644
--- a/hyracks/hyracks-control/pom.xml
+++ b/hyracks/hyracks-control/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<modules>
diff --git a/hyracks/hyracks-data/hyracks-data-std/pom.xml b/hyracks/hyracks-data/hyracks-data-std/pom.xml
index 9152d0d..b71548a 100644
--- a/hyracks/hyracks-data/hyracks-data-std/pom.xml
+++ b/hyracks/hyracks-data/hyracks-data-std/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,7 +27,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
diff --git a/hyracks/hyracks-data/pom.xml b/hyracks/hyracks-data/pom.xml
index 2af86c9..0df5325 100644
--- a/hyracks/hyracks-data/pom.xml
+++ b/hyracks/hyracks-data/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<modules>
diff --git a/hyracks/hyracks-dataflow-common/pom.xml b/hyracks/hyracks-dataflow-common/pom.xml
index 4afb088..a87336d 100644
--- a/hyracks/hyracks-dataflow-common/pom.xml
+++ b/hyracks/hyracks-dataflow-common/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -26,14 +26,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
diff --git a/hyracks/hyracks-dataflow-hadoop/pom.xml b/hyracks/hyracks-dataflow-hadoop/pom.xml
index 3947387..657f6db 100644
--- a/hyracks/hyracks-dataflow-hadoop/pom.xml
+++ b/hyracks/hyracks-dataflow-hadoop/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -26,14 +26,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
@@ -53,7 +53,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
</dependencies>
diff --git a/hyracks/hyracks-dataflow-std/pom.xml b/hyracks/hyracks-dataflow-std/pom.xml
index db4f452..56046f7 100644
--- a/hyracks/hyracks-dataflow-std/pom.xml
+++ b/hyracks/hyracks-dataflow-std/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,14 +27,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-dist/pom.xml b/hyracks/hyracks-dist/pom.xml
index d600fd8..2dcd0ed 100755
--- a/hyracks/hyracks-dist/pom.xml
+++ b/hyracks/hyracks-dist/pom.xml
@@ -4,7 +4,7 @@
<parent>
<artifactId>hyracks</artifactId>
<groupId>edu.uci.ics.hyracks</groupId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<artifactId>hyracks-dist</artifactId>
diff --git a/hyracks/hyracks-documentation/pom.xml b/hyracks/hyracks-documentation/pom.xml
index 6473cc8..958bd71 100644
--- a/hyracks/hyracks-documentation/pom.xml
+++ b/hyracks/hyracks-documentation/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
diff --git a/hyracks/hyracks-examples/btree-example/btreeclient/pom.xml b/hyracks/hyracks-examples/btree-example/btreeclient/pom.xml
index f7698be..b2c1779 100644
--- a/hyracks/hyracks-examples/btree-example/btreeclient/pom.xml
+++ b/hyracks/hyracks-examples/btree-example/btreeclient/pom.xml
@@ -6,26 +6,26 @@
<parent>
<groupId>edu.uci.ics.hyracks.examples</groupId>
<artifactId>btree-example</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<dependencies>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks.examples.btree</groupId>
<artifactId>btreehelper</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-examples/btree-example/btreehelper/pom.xml b/hyracks/hyracks-examples/btree-example/btreehelper/pom.xml
index 637612d..b394a88 100644
--- a/hyracks/hyracks-examples/btree-example/btreehelper/pom.xml
+++ b/hyracks/hyracks-examples/btree-example/btreehelper/pom.xml
@@ -6,32 +6,32 @@
<parent>
<groupId>edu.uci.ics.hyracks.examples</groupId>
<artifactId>btree-example</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<dependencies>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
<build>
diff --git a/hyracks/hyracks-examples/btree-example/btreeserver/pom.xml b/hyracks/hyracks-examples/btree-example/btreeserver/pom.xml
index ead4e89..c70578e 100644
--- a/hyracks/hyracks-examples/btree-example/btreeserver/pom.xml
+++ b/hyracks/hyracks-examples/btree-example/btreeserver/pom.xml
@@ -2,13 +2,13 @@
<modelVersion>4.0.0</modelVersion>
<groupId>edu.uci.ics.hyracks.examples.btree</groupId>
<artifactId>btreeserver</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<name>btreeserver</name>
<parent>
<groupId>edu.uci.ics.hyracks.examples</groupId>
<artifactId>btree-example</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -63,20 +63,20 @@
<dependency>
<groupId>edu.uci.ics.hyracks.examples.btree</groupId>
<artifactId>btreehelper</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-examples/btree-example/pom.xml b/hyracks/hyracks-examples/btree-example/pom.xml
index ce0a486..7332d0e 100644
--- a/hyracks/hyracks-examples/btree-example/pom.xml
+++ b/hyracks/hyracks-examples/btree-example/pom.xml
@@ -8,7 +8,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-examples</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<modules>
diff --git a/hyracks/hyracks-examples/hadoop-compat-example/hadoopcompatclient/pom.xml b/hyracks/hyracks-examples/hadoop-compat-example/hadoopcompatclient/pom.xml
index e618295..acf2dbf 100644
--- a/hyracks/hyracks-examples/hadoop-compat-example/hadoopcompatclient/pom.xml
+++ b/hyracks/hyracks-examples/hadoop-compat-example/hadoopcompatclient/pom.xml
@@ -7,20 +7,20 @@
<parent>
<groupId>edu.uci.ics.hyracks.examples</groupId>
<artifactId>hadoop-compat-example</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<dependencies>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks.examples.compat</groupId>
<artifactId>hadoopcompathelper</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-examples/hadoop-compat-example/hadoopcompathelper/pom.xml b/hyracks/hyracks-examples/hadoop-compat-example/hadoopcompathelper/pom.xml
index 5f7f072..94f43df 100644
--- a/hyracks/hyracks-examples/hadoop-compat-example/hadoopcompathelper/pom.xml
+++ b/hyracks/hyracks-examples/hadoop-compat-example/hadoopcompathelper/pom.xml
@@ -7,20 +7,20 @@
<parent>
<groupId>edu.uci.ics.hyracks.examples</groupId>
<artifactId>hadoop-compat-example</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<dependencies>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
</dependencies>
diff --git a/hyracks/hyracks-examples/hadoop-compat-example/hadoopcompatserver/pom.xml b/hyracks/hyracks-examples/hadoop-compat-example/hadoopcompatserver/pom.xml
index 6536606..e545663 100644
--- a/hyracks/hyracks-examples/hadoop-compat-example/hadoopcompatserver/pom.xml
+++ b/hyracks/hyracks-examples/hadoop-compat-example/hadoopcompatserver/pom.xml
@@ -2,13 +2,13 @@
<modelVersion>4.0.0</modelVersion>
<groupId>edu.uci.ics.hyracks.examples.compat</groupId>
<artifactId>hadoopcompatserver</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<name>hadoopcompatserver</name>
<parent>
<groupId>edu.uci.ics.hyracks.examples</groupId>
<artifactId>hadoop-compat-example</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -60,7 +60,7 @@
<plugin>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-virtualcluster-maven-plugin</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<configuration>
<hyracksServerHome>${basedir}/target/hadoopcompatserver-${project.version}-binary-assembly</hyracksServerHome>
<jvmOptions>${jvm.extraargs}</jvmOptions>
@@ -136,27 +136,27 @@
<dependency>
<groupId>edu.uci.ics.hyracks.examples.compat</groupId>
<artifactId>hadoopcompathelper</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks.examples.compat</groupId>
<artifactId>hadoopcompatclient</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>test</scope>
</dependency>
diff --git a/hyracks/hyracks-examples/hadoop-compat-example/pom.xml b/hyracks/hyracks-examples/hadoop-compat-example/pom.xml
index 980e800..e927a1c 100644
--- a/hyracks/hyracks-examples/hadoop-compat-example/pom.xml
+++ b/hyracks/hyracks-examples/hadoop-compat-example/pom.xml
@@ -8,7 +8,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-examples</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<modules>
@@ -29,7 +29,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-hadoop-compat</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-examples/hyracks-integration-tests/pom.xml b/hyracks/hyracks-examples/hyracks-integration-tests/pom.xml
index 7c38b13..08ff5e2 100644
--- a/hyracks/hyracks-examples/hyracks-integration-tests/pom.xml
+++ b/hyracks/hyracks-examples/hyracks-integration-tests/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-examples</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
<plugins>
@@ -32,75 +32,75 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-rtree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-lsm-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-lsm-rtree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-lsm-invertedindex</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-test-support</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-client</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-examples/pom.xml b/hyracks/hyracks-examples/pom.xml
index a47cb9c..6159b49 100644
--- a/hyracks/hyracks-examples/pom.xml
+++ b/hyracks/hyracks-examples/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<modules>
diff --git a/hyracks/hyracks-examples/text-example/pom.xml b/hyracks/hyracks-examples/text-example/pom.xml
index ee75f31..54aa3be 100644
--- a/hyracks/hyracks-examples/text-example/pom.xml
+++ b/hyracks/hyracks-examples/text-example/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-examples</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<modules>
diff --git a/hyracks/hyracks-examples/text-example/textclient/pom.xml b/hyracks/hyracks-examples/text-example/textclient/pom.xml
index 7bf1c44..b2b7dbb 100644
--- a/hyracks/hyracks-examples/text-example/textclient/pom.xml
+++ b/hyracks/hyracks-examples/text-example/textclient/pom.xml
@@ -6,20 +6,20 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>text-example</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<dependencies>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>texthelper</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-examples/text-example/texthelper/pom.xml b/hyracks/hyracks-examples/text-example/texthelper/pom.xml
index c948242..c20ba88 100644
--- a/hyracks/hyracks-examples/text-example/texthelper/pom.xml
+++ b/hyracks/hyracks-examples/text-example/texthelper/pom.xml
@@ -6,26 +6,26 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>text-example</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<dependencies>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
<build>
diff --git a/hyracks/hyracks-examples/text-example/textserver/pom.xml b/hyracks/hyracks-examples/text-example/textserver/pom.xml
index d409203..0ee6e0a 100644
--- a/hyracks/hyracks-examples/text-example/textserver/pom.xml
+++ b/hyracks/hyracks-examples/text-example/textserver/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>text-example</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -59,7 +59,7 @@
<plugin>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-virtualcluster-maven-plugin</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<configuration>
<hyracksServerHome>${basedir}/target/textserver-${project.version}-binary-assembly</hyracksServerHome>
<jvmOptions>${jvm.extraargs}</jvmOptions>
@@ -135,27 +135,27 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>texthelper</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>textclient</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>test</scope>
</dependency>
diff --git a/hyracks/hyracks-examples/tpch-example/pom.xml b/hyracks/hyracks-examples/tpch-example/pom.xml
index f8acd8d..68577a0 100644
--- a/hyracks/hyracks-examples/tpch-example/pom.xml
+++ b/hyracks/hyracks-examples/tpch-example/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-examples</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<modules>
diff --git a/hyracks/hyracks-examples/tpch-example/tpchclient/pom.xml b/hyracks/hyracks-examples/tpch-example/tpchclient/pom.xml
index 9f08f0c..127d0f1 100644
--- a/hyracks/hyracks-examples/tpch-example/tpchclient/pom.xml
+++ b/hyracks/hyracks-examples/tpch-example/tpchclient/pom.xml
@@ -5,20 +5,20 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>tpch-example</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<dependencies>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
<build>
diff --git a/hyracks/hyracks-examples/tpch-example/tpchserver/pom.xml b/hyracks/hyracks-examples/tpch-example/tpchserver/pom.xml
index 6b97078..fb45c3b 100644
--- a/hyracks/hyracks-examples/tpch-example/tpchserver/pom.xml
+++ b/hyracks/hyracks-examples/tpch-example/tpchserver/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>tpch-example</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -62,25 +62,25 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-hadoop-compat/pom.xml b/hyracks/hyracks-hadoop-compat/pom.xml
index 88082af..f9b1b3a 100644
--- a/hyracks/hyracks-hadoop-compat/pom.xml
+++ b/hyracks/hyracks-hadoop-compat/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -80,7 +80,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-hadoop</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-hdfs/hyracks-hdfs-0.20.2/pom.xml b/hyracks/hyracks-hdfs/hyracks-hdfs-0.20.2/pom.xml
index dd26f1e..39f064f 100644
--- a/hyracks/hyracks-hdfs/hyracks-hdfs-0.20.2/pom.xml
+++ b/hyracks/hyracks-hdfs/hyracks-hdfs-0.20.2/pom.xml
@@ -6,7 +6,7 @@
<parent>
<artifactId>hyracks-hdfs</artifactId>
<groupId>edu.uci.ics.hyracks</groupId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -98,7 +98,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-hdfs/hyracks-hdfs-0.23.1/pom.xml b/hyracks/hyracks-hdfs/hyracks-hdfs-0.23.1/pom.xml
index d0f11eb..fd8b1c5 100644
--- a/hyracks/hyracks-hdfs/hyracks-hdfs-0.23.1/pom.xml
+++ b/hyracks/hyracks-hdfs/hyracks-hdfs-0.23.1/pom.xml
@@ -6,7 +6,7 @@
<parent>
<artifactId>hyracks-hdfs</artifactId>
<groupId>edu.uci.ics.hyracks</groupId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
<plugins>
@@ -202,7 +202,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-hdfs/hyracks-hdfs-core/pom.xml b/hyracks/hyracks-hdfs/hyracks-hdfs-core/pom.xml
index 5de9f37..bec0d34 100644
--- a/hyracks/hyracks-hdfs/hyracks-hdfs-core/pom.xml
+++ b/hyracks/hyracks-hdfs/hyracks-hdfs-core/pom.xml
@@ -7,7 +7,7 @@
<parent>
<artifactId>hyracks-hdfs</artifactId>
<groupId>edu.uci.ics.hyracks</groupId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -191,31 +191,31 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>test</scope>
</dependency>
<dependency>
diff --git a/hyracks/hyracks-hdfs/pom.xml b/hyracks/hyracks-hdfs/pom.xml
index e3ada06..b8cb5fe 100644
--- a/hyracks/hyracks-hdfs/pom.xml
+++ b/hyracks/hyracks-hdfs/pom.xml
@@ -8,7 +8,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<modules>
diff --git a/hyracks/hyracks-ipc/pom.xml b/hyracks/hyracks-ipc/pom.xml
index 1368e20..d76aa56 100644
--- a/hyracks/hyracks-ipc/pom.xml
+++ b/hyracks/hyracks-ipc/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
diff --git a/hyracks/hyracks-maven-plugins/hyracks-virtualcluster-maven-plugin/pom.xml b/hyracks/hyracks-maven-plugins/hyracks-virtualcluster-maven-plugin/pom.xml
index c0a9c45..3a84622 100644
--- a/hyracks/hyracks-maven-plugins/hyracks-virtualcluster-maven-plugin/pom.xml
+++ b/hyracks/hyracks-maven-plugins/hyracks-virtualcluster-maven-plugin/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-maven-plugins</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
diff --git a/hyracks/hyracks-maven-plugins/pom.xml b/hyracks/hyracks-maven-plugins/pom.xml
index 08bbb2c..39338e7 100644
--- a/hyracks/hyracks-maven-plugins/pom.xml
+++ b/hyracks/hyracks-maven-plugins/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<dependencies>
diff --git a/hyracks/hyracks-net/pom.xml b/hyracks/hyracks-net/pom.xml
index 9dde9a1..b82a88a 100644
--- a/hyracks/hyracks-net/pom.xml
+++ b/hyracks/hyracks-net/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
diff --git a/hyracks/hyracks-server/pom.xml b/hyracks/hyracks-server/pom.xml
index e32b658..bdf8db6 100644
--- a/hyracks/hyracks-server/pom.xml
+++ b/hyracks/hyracks-server/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -74,14 +74,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-storage-am-bloomfilter/pom.xml b/hyracks/hyracks-storage-am-bloomfilter/pom.xml
index 76c64d8..3c3f14b 100644
--- a/hyracks/hyracks-storage-am-bloomfilter/pom.xml
+++ b/hyracks/hyracks-storage-am-bloomfilter/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -25,7 +25,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-storage-am-btree/pom.xml b/hyracks/hyracks-storage-am-btree/pom.xml
index 201d597..a337609 100644
--- a/hyracks/hyracks-storage-am-btree/pom.xml
+++ b/hyracks/hyracks-storage-am-btree/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,28 +27,28 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-storage-am-common/pom.xml b/hyracks/hyracks-storage-am-common/pom.xml
index 0175467..2a537a1 100644
--- a/hyracks/hyracks-storage-am-common/pom.xml
+++ b/hyracks/hyracks-storage-am-common/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,28 +27,28 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-storage-am-common/src/main/java/edu/uci/ics/hyracks/storage/am/common/api/ISearchOperationCallback.java b/hyracks/hyracks-storage-am-common/src/main/java/edu/uci/ics/hyracks/storage/am/common/api/ISearchOperationCallback.java
index b62bbcb..62d5054 100644
--- a/hyracks/hyracks-storage-am-common/src/main/java/edu/uci/ics/hyracks/storage/am/common/api/ISearchOperationCallback.java
+++ b/hyracks/hyracks-storage-am-common/src/main/java/edu/uci/ics/hyracks/storage/am/common/api/ISearchOperationCallback.java
@@ -42,4 +42,14 @@
* @param tuple the tuple that was previously reconciled
*/
public void cancel(ITupleReference tuple) throws HyracksDataException;
+
+ /**
+ * This method is only called on a tuple that was reconciled on, and found after
+ * retraversing. This method allows an opportunity to do some subsequent action that was
+ * taken in {@link #reconcile(ITupleReference))}.
+ *
+ * @param tuple
+ * the tuple that was previously reconciled
+ */
+ public void complete(ITupleReference tuple) throws HyracksDataException;
}
diff --git a/hyracks/hyracks-storage-am-common/src/main/java/edu/uci/ics/hyracks/storage/am/common/impls/NoOpOperationCallback.java b/hyracks/hyracks-storage-am-common/src/main/java/edu/uci/ics/hyracks/storage/am/common/impls/NoOpOperationCallback.java
index 6fc8dcf..8178101 100644
--- a/hyracks/hyracks-storage-am-common/src/main/java/edu/uci/ics/hyracks/storage/am/common/impls/NoOpOperationCallback.java
+++ b/hyracks/hyracks-storage-am-common/src/main/java/edu/uci/ics/hyracks/storage/am/common/impls/NoOpOperationCallback.java
@@ -15,6 +15,7 @@
package edu.uci.ics.hyracks.storage.am.common.impls;
+import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
import edu.uci.ics.hyracks.dataflow.common.data.accessors.ITupleReference;
import edu.uci.ics.hyracks.storage.am.common.api.IModificationOperationCallback;
import edu.uci.ics.hyracks.storage.am.common.api.ISearchOperationCallback;
@@ -49,4 +50,9 @@
public void cancel(ITupleReference tuple) {
// Do nothing.
}
+
+ @Override
+ public void complete(ITupleReference tuple) throws HyracksDataException {
+ // Do nothing.
+ }
}
diff --git a/hyracks/hyracks-storage-am-lsm-btree/pom.xml b/hyracks/hyracks-storage-am-lsm-btree/pom.xml
index 6c4ffd3..29c2ab3 100644
--- a/hyracks/hyracks-storage-am-lsm-btree/pom.xml
+++ b/hyracks/hyracks-storage-am-lsm-btree/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -25,21 +25,21 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-bloomfilter</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-lsm-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/impls/LSMBTreePointSearchCursor.java b/hyracks/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/impls/LSMBTreePointSearchCursor.java
index 0204833..5736200 100644
--- a/hyracks/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/impls/LSMBTreePointSearchCursor.java
+++ b/hyracks/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/impls/LSMBTreePointSearchCursor.java
@@ -91,6 +91,7 @@
// retraverse
memBTreeAccessor.search(rangeCursors[i], predicate);
+ searchCallback.complete(predicate.getLowKey());
if (rangeCursors[i].hasNext()) {
rangeCursors[i].next();
if (((ILSMTreeTupleReference) rangeCursors[i].getTuple()).isAntimatter()) {
@@ -108,6 +109,7 @@
} else {
frameTuple = rangeCursors[i].getTuple();
searchCallback.reconcile(frameTuple);
+ searchCallback.complete(frameTuple);
foundTuple = true;
return true;
}
diff --git a/hyracks/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/impls/LSMBTreeRangeSearchCursor.java b/hyracks/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/impls/LSMBTreeRangeSearchCursor.java
index 4255dbf..2923c53 100644
--- a/hyracks/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/impls/LSMBTreeRangeSearchCursor.java
+++ b/hyracks/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/impls/LSMBTreeRangeSearchCursor.java
@@ -101,14 +101,20 @@
searchCallback.reconcile(copyTuple);
} else {
searchCallback.reconcile(checkElement.getTuple());
+ searchCallback.complete(checkElement.getTuple());
}
// retraverse
reusablePred.setLowKey(copyTuple, true);
memBTreeAccessor.search(rangeCursors[0], reusablePred);
- pushIntoPriorityQueue(inMemElement);
- if (cmp.compare(copyTuple, inMemElement.getTuple()) != 0) {
- searchCallback.cancel(copyTuple);
- continue;
+ boolean isNotExhaustedCursor = pushIntoPriorityQueue(inMemElement);
+
+ if (checkElement.getCursorIndex() == 0) {
+ if (!isNotExhaustedCursor || cmp.compare(copyTuple, inMemElement.getTuple()) != 0) {
+ searchCallback.complete(copyTuple);
+ searchCallback.cancel(copyTuple);
+ continue;
+ }
+ searchCallback.complete(copyTuple);
}
} else {
// the in-memory cursor is exhausted
@@ -211,4 +217,4 @@
initPriorityQueue();
proceed = true;
}
-}
\ No newline at end of file
+}
diff --git a/hyracks/hyracks-storage-am-lsm-common/pom.xml b/hyracks/hyracks-storage-am-lsm-common/pom.xml
index e4d2040..715ec27 100644
--- a/hyracks/hyracks-storage-am-lsm-common/pom.xml
+++ b/hyracks/hyracks-storage-am-lsm-common/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -25,21 +25,21 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-bloomfilter</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-storage-am-lsm-invertedindex/pom.xml b/hyracks/hyracks-storage-am-lsm-invertedindex/pom.xml
index 1aa5302..5a056a2 100644
--- a/hyracks/hyracks-storage-am-lsm-invertedindex/pom.xml
+++ b/hyracks/hyracks-storage-am-lsm-invertedindex/pom.xml
@@ -5,7 +5,7 @@
<parent>
<artifactId>hyracks</artifactId>
<groupId>edu.uci.ics.hyracks</groupId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
@@ -26,14 +26,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-lsm-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-storage-am-lsm-rtree/pom.xml b/hyracks/hyracks-storage-am-lsm-rtree/pom.xml
index a345ee5..f842b44 100644
--- a/hyracks/hyracks-storage-am-lsm-rtree/pom.xml
+++ b/hyracks/hyracks-storage-am-lsm-rtree/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -25,21 +25,21 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-lsm-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-rtree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-storage-am-rtree/pom.xml b/hyracks/hyracks-storage-am-rtree/pom.xml
index d73ce00..af5e922 100644
--- a/hyracks/hyracks-storage-am-rtree/pom.xml
+++ b/hyracks/hyracks-storage-am-rtree/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,21 +27,21 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-storage-common/pom.xml b/hyracks/hyracks-storage-common/pom.xml
index bde1ac4..3ee262d 100644
--- a/hyracks/hyracks-storage-common/pom.xml
+++ b/hyracks/hyracks-storage-common/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,7 +27,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-test-support/pom.xml b/hyracks/hyracks-test-support/pom.xml
index 623edc4..217a9a4 100644
--- a/hyracks/hyracks-test-support/pom.xml
+++ b/hyracks/hyracks-test-support/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -27,33 +27,33 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-rtree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-lsm-invertedindex</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-test-support/src/main/java/edu/uci/ics/hyracks/storage/am/btree/AbstractSearchOperationCallbackTest.java b/hyracks/hyracks-test-support/src/main/java/edu/uci/ics/hyracks/storage/am/btree/AbstractSearchOperationCallbackTest.java
index ffa7c9a..63e320d 100644
--- a/hyracks/hyracks-test-support/src/main/java/edu/uci/ics/hyracks/storage/am/btree/AbstractSearchOperationCallbackTest.java
+++ b/hyracks/hyracks-test-support/src/main/java/edu/uci/ics/hyracks/storage/am/btree/AbstractSearchOperationCallbackTest.java
@@ -172,6 +172,11 @@
}
}
+ @Override
+ public void complete(ITupleReference tuple) throws HyracksDataException {
+
+ }
+
}
}
diff --git a/hyracks/hyracks-test-support/src/main/java/edu/uci/ics/hyracks/storage/am/common/TestOperationCallback.java b/hyracks/hyracks-test-support/src/main/java/edu/uci/ics/hyracks/storage/am/common/TestOperationCallback.java
index 04f888b..2a803d3 100644
--- a/hyracks/hyracks-test-support/src/main/java/edu/uci/ics/hyracks/storage/am/common/TestOperationCallback.java
+++ b/hyracks/hyracks-test-support/src/main/java/edu/uci/ics/hyracks/storage/am/common/TestOperationCallback.java
@@ -2,6 +2,7 @@
import java.util.Random;
+import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
import edu.uci.ics.hyracks.dataflow.common.data.accessors.ITupleReference;
import edu.uci.ics.hyracks.storage.am.common.api.IModificationOperationCallback;
import edu.uci.ics.hyracks.storage.am.common.api.ISearchOperationCallback;
@@ -42,4 +43,9 @@
// Do nothing.
}
+ @Override
+ public void complete(ITupleReference tuple) throws HyracksDataException {
+ // Do nothing.
+ }
+
}
diff --git a/hyracks/hyracks-tests/hyracks-storage-am-bloomfilter-test/pom.xml b/hyracks/hyracks-tests/hyracks-storage-am-bloomfilter-test/pom.xml
index edf9d08..aa2238f 100644
--- a/hyracks/hyracks-tests/hyracks-storage-am-bloomfilter-test/pom.xml
+++ b/hyracks/hyracks-tests/hyracks-storage-am-bloomfilter-test/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-tests</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -32,14 +32,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-bloomfilter</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-test-support</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>test</scope>
</dependency>
diff --git a/hyracks/hyracks-tests/hyracks-storage-am-btree-test/pom.xml b/hyracks/hyracks-tests/hyracks-storage-am-btree-test/pom.xml
index bfb2d61..8e7df1d 100644
--- a/hyracks/hyracks-tests/hyracks-storage-am-btree-test/pom.xml
+++ b/hyracks/hyracks-tests/hyracks-storage-am-btree-test/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-tests</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -34,14 +34,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-test-support</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>test</scope>
</dependency>
diff --git a/hyracks/hyracks-tests/hyracks-storage-am-lsm-btree-test/pom.xml b/hyracks/hyracks-tests/hyracks-storage-am-lsm-btree-test/pom.xml
index f687212..35ab780 100644
--- a/hyracks/hyracks-tests/hyracks-storage-am-lsm-btree-test/pom.xml
+++ b/hyracks/hyracks-tests/hyracks-storage-am-lsm-btree-test/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-tests</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -25,20 +25,20 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-lsm-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-test-support</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
</dependencies>
diff --git a/hyracks/hyracks-tests/hyracks-storage-am-lsm-btree-test/src/test/java/edu/uci/ics/hyracks/storage/am/lsm/btree/LSMBTreeSearchOperationCallbackTest.java b/hyracks/hyracks-tests/hyracks-storage-am-lsm-btree-test/src/test/java/edu/uci/ics/hyracks/storage/am/lsm/btree/LSMBTreeSearchOperationCallbackTest.java
index 389c87f..41d7ae8 100644
--- a/hyracks/hyracks-tests/hyracks-storage-am-lsm-btree-test/src/test/java/edu/uci/ics/hyracks/storage/am/lsm/btree/LSMBTreeSearchOperationCallbackTest.java
+++ b/hyracks/hyracks-tests/hyracks-storage-am-lsm-btree-test/src/test/java/edu/uci/ics/hyracks/storage/am/lsm/btree/LSMBTreeSearchOperationCallbackTest.java
@@ -164,10 +164,6 @@
condition.awaitUninterruptibly();
blockOnHigh = false;
}
- expectedTupleToBeLockedValue++;
- TupleUtils.createIntegerTuple(expectedTupleToBeLockedBuilder, expectedTupleToBeLocked,
- expectedTupleToBeLockedValue);
-
}
@Override
@@ -183,6 +179,14 @@
Assert.assertTrue(found);
}
+ @Override
+ public void complete(ITupleReference tuple) throws HyracksDataException {
+ Assert.assertEquals(0, cmp.compare(SearchTask.this.expectedTupleToBeLocked, tuple));
+ expectedTupleToBeLockedValue++;
+ TupleUtils.createIntegerTuple(expectedTupleToBeLockedBuilder, expectedTupleToBeLocked,
+ expectedTupleToBeLockedValue);
+ }
+
}
}
diff --git a/hyracks/hyracks-tests/hyracks-storage-am-lsm-common-test/pom.xml b/hyracks/hyracks-tests/hyracks-storage-am-lsm-common-test/pom.xml
index 68b432b..7508f7c 100644
--- a/hyracks/hyracks-tests/hyracks-storage-am-lsm-common-test/pom.xml
+++ b/hyracks/hyracks-tests/hyracks-storage-am-lsm-common-test/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-tests</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -25,14 +25,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-lsm-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-test-support</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-tests/hyracks-storage-am-lsm-invertedindex-test/pom.xml b/hyracks/hyracks-tests/hyracks-storage-am-lsm-invertedindex-test/pom.xml
index 273b90f..be0bb6f 100644
--- a/hyracks/hyracks-tests/hyracks-storage-am-lsm-invertedindex-test/pom.xml
+++ b/hyracks/hyracks-tests/hyracks-storage-am-lsm-invertedindex-test/pom.xml
@@ -5,7 +5,7 @@
<parent>
<artifactId>hyracks-tests</artifactId>
<groupId>edu.uci.ics.hyracks</groupId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
@@ -26,21 +26,21 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-lsm-invertedindex</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-test-support</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>test</scope>
</dependency>
diff --git a/hyracks/hyracks-tests/hyracks-storage-am-lsm-rtree-test/pom.xml b/hyracks/hyracks-tests/hyracks-storage-am-lsm-rtree-test/pom.xml
index a39fd3a..95332a7 100644
--- a/hyracks/hyracks-tests/hyracks-storage-am-lsm-rtree-test/pom.xml
+++ b/hyracks/hyracks-tests/hyracks-storage-am-lsm-rtree-test/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-tests</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -25,14 +25,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-lsm-rtree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-test-support</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-tests/hyracks-storage-am-rtree-test/pom.xml b/hyracks/hyracks-tests/hyracks-storage-am-rtree-test/pom.xml
index b9b0cc3..14adffb 100644
--- a/hyracks/hyracks-tests/hyracks-storage-am-rtree-test/pom.xml
+++ b/hyracks/hyracks-tests/hyracks-storage-am-rtree-test/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-tests</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -34,14 +34,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-rtree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-test-support</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>test</scope>
</dependency>
diff --git a/hyracks/hyracks-tests/hyracks-storage-common-test/pom.xml b/hyracks/hyracks-tests/hyracks-storage-common-test/pom.xml
index 7abf086..7f69d25 100644
--- a/hyracks/hyracks-tests/hyracks-storage-common-test/pom.xml
+++ b/hyracks/hyracks-tests/hyracks-storage-common-test/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-tests</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -34,13 +34,13 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-test-support</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/hyracks/hyracks-tests/pom.xml b/hyracks/hyracks-tests/pom.xml
index 38ddadc..d61209e 100644
--- a/hyracks/hyracks-tests/pom.xml
+++ b/hyracks/hyracks-tests/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<modules>
diff --git a/hyracks/pom.xml b/hyracks/pom.xml
index 7972b10..4eccb73 100644
--- a/hyracks/pom.xml
+++ b/hyracks/pom.xml
@@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<packaging>pom</packaging>
<name>hyracks</name>
diff --git a/pom.xml b/pom.xml
index 2933182..1c20cc8 100644
--- a/pom.xml
+++ b/pom.xml
@@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>fullstack</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<packaging>pom</packaging>
<name>hyracks-ecosystem-full-stack</name>
@@ -26,9 +26,9 @@
</build>
<scm>
- <connection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack</connection>
- <developerConnection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack</developerConnection>
- <url>http://code.google.com/p/hyracks/source/browse/#svn/trunk/fullstack</url>
+ <connection>scm:git:https://vinayakb@code.google.com/p/hyracks/</connection>
+ <developerConnection>scm:git:https://vinayakb@code.google.com/p/hyracks/</developerConnection>
+ <url>https://code.google.com/p/hyracks/source/browse/</url>
</scm>
<distributionManagement>
diff --git a/pregelix/pom.xml b/pregelix/pom.xml
index 46fe7e6..bb2b336 100644
--- a/pregelix/pom.xml
+++ b/pregelix/pom.xml
@@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<packaging>pom</packaging>
<name>pregelix</name>
diff --git a/pregelix/pregelix-api/pom.xml b/pregelix/pregelix-api/pom.xml
index d8a49e0..c997ec8 100644
--- a/pregelix/pregelix-api/pom.xml
+++ b/pregelix/pregelix-api/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<properties>
@@ -68,7 +68,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
@@ -81,7 +81,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-hdfs-core</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/pregelix/pregelix-core/pom.xml b/pregelix/pregelix-core/pom.xml
index 39fc396..d229dc7 100644
--- a/pregelix/pregelix-core/pom.xml
+++ b/pregelix/pregelix-core/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
@@ -195,84 +195,84 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-dataflow</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-runtime</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
@@ -286,7 +286,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks.examples</groupId>
<artifactId>hyracks-integration-tests</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>test</scope>
</dependency>
<dependency>
@@ -306,7 +306,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-ipc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/pregelix/pregelix-core/src/main/java/edu/uci/ics/pregelix/core/driver/Driver.java b/pregelix/pregelix-core/src/main/java/edu/uci/ics/pregelix/core/driver/Driver.java
index a309529..3a344d9 100644
--- a/pregelix/pregelix-core/src/main/java/edu/uci/ics/pregelix/core/driver/Driver.java
+++ b/pregelix/pregelix-core/src/main/java/edu/uci/ics/pregelix/core/driver/Driver.java
@@ -66,7 +66,6 @@
@Override
public void runJob(PregelixJob job, Plan planChoice, String ipAddress, int port, boolean profiling)
throws HyracksException {
- DeploymentId deploymentId = null;
try {
/** add hadoop configurations */
URL hadoopCore = job.getClass().getClassLoader().getResource("core-site.xml");
@@ -116,7 +115,7 @@
for (URL url : urls)
if (url.toString().endsWith(".jar"))
jars.add(new File(url.getPath()));
- deploymentId = installApplication(jars);
+ DeploymentId deploymentId = installApplication(jars);
start = System.currentTimeMillis();
FileSystem dfs = FileSystem.get(job.getConfiguration());
diff --git a/pregelix/pregelix-core/src/main/resources/conf/cluster.properties b/pregelix/pregelix-core/src/main/resources/conf/cluster.properties
index 2d2401a..056cce4 100644
--- a/pregelix/pregelix-core/src/main/resources/conf/cluster.properties
+++ b/pregelix/pregelix-core/src/main/resources/conf/cluster.properties
@@ -4,9 +4,6 @@
#The CC port for Hyracks cluster management
CC_CLUSTERPORT=1099
-#The directory of hyracks binaries
-HYRACKS_HOME=../../../../hyracks
-
#The tmp directory for cc to install jars
CCTMP_DIR=/tmp/t1
@@ -29,9 +26,11 @@
FRAME_SIZE=65536
#CC JAVA_OPTS
-CCJAVA_OPTS="-Xdebug -Xrunjdwp:transport=dt_socket,address=7001,server=y,suspend=n -Xmx1g -Djava.util.logging.config.file=logging.properties"
+CCJAVA_OPTS="-Xmx1g -Djava.util.logging.config.file=logging.properties"
+# debug option: CCJAVA_OPTS="-Xdebug -Xrunjdwp:transport=dt_socket,address=7001,server=y,suspend=n -Xmx1g -Djava.util.logging.config.file=logging.properties"
# Yourkit option: -agentpath:/grid/0/dev/vborkar/tools/yjp-10.0.4/bin/linux-x86-64/libyjpagent.so=port=20001"
#NC JAVA_OPTS
-NCJAVA_OPTS="-Xdebug -Xrunjdwp:transport=dt_socket,address=7002,server=y,suspend=n -Xmx1g -Djava.util.logging.config.file=logging.properties"
-
+NCJAVA_OPTS="-Xmx1g -Djava.util.logging.config.file=logging.properties"
+# debug option: NCJAVA_OPTS="-Xdebug -Xrunjdwp:transport=dt_socket,address=7002,server=y,suspend=n -Xmx1g -Djava.util.logging.config.file=logging.properties"
+# Yourkit option: -agentpath:/grid/0/dev/vborkar/tools/yjp-10.0.4/bin/linux-x86-64/libyjpagent.so=port=20001"
diff --git a/pregelix/pregelix-core/src/main/resources/hyracks-deployment.properties b/pregelix/pregelix-core/src/main/resources/hyracks-deployment.properties
deleted file mode 100644
index d5d7cd0..0000000
--- a/pregelix/pregelix-core/src/main/resources/hyracks-deployment.properties
+++ /dev/null
@@ -1 +0,0 @@
-nc.bootstrap.class=edu.uci.ics.pregelix.runtime.bootstrap.NCBootstrapImpl
\ No newline at end of file
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/getip.sh b/pregelix/pregelix-core/src/main/resources/scripts/getip.sh
index a691c0f..1b44d09 100755
--- a/pregelix/pregelix-core/src/main/resources/scripts/getip.sh
+++ b/pregelix/pregelix-core/src/main/resources/scripts/getip.sh
@@ -1,3 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
#get the OS
OS_NAME=`uname -a|awk '{print $1}'`
LINUX_OS='Linux'
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/pregelix b/pregelix/pregelix-core/src/main/resources/scripts/pregelix
index b1a2f74..7232ccc 100644
--- a/pregelix/pregelix-core/src/main/resources/scripts/pregelix
+++ b/pregelix/pregelix-core/src/main/resources/scripts/pregelix
@@ -1,22 +1,20 @@
#!/bin/sh
-# ----------------------------------------------------------------------------
-# Copyright 2001-2006 The Apache Software Foundation.
#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-# ----------------------------------------------------------------------------
-#
-# Copyright (c) 2001-2006 The Apache Software Foundation. All rights
-# reserved.
# resolve links - $0 may be a softlink
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/pregelixcc b/pregelix/pregelix-core/src/main/resources/scripts/pregelixcc
index 461d76a..c1ee3f2 100755
--- a/pregelix/pregelix-core/src/main/resources/scripts/pregelixcc
+++ b/pregelix/pregelix-core/src/main/resources/scripts/pregelixcc
@@ -1,23 +1,20 @@
#!/bin/sh
-# ----------------------------------------------------------------------------
-# Copyright 2001-2006 The Apache Software Foundation.
#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-# ----------------------------------------------------------------------------
-#
-# Copyright (c) 2001-2006 The Apache Software Foundation. All rights
-# reserved.
-
# resolve links - $0 may be a softlink
PRG="$0"
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/pregelixnc b/pregelix/pregelix-core/src/main/resources/scripts/pregelixnc
index 4a6ca1f..c01b4b4 100755
--- a/pregelix/pregelix-core/src/main/resources/scripts/pregelixnc
+++ b/pregelix/pregelix-core/src/main/resources/scripts/pregelixnc
@@ -1,23 +1,20 @@
#!/bin/sh
-# ----------------------------------------------------------------------------
-# Copyright 2001-2006 The Apache Software Foundation.
#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-# ----------------------------------------------------------------------------
-#
-# Copyright (c) 2001-2006 The Apache Software Foundation. All rights
-# reserved.
-
# resolve links - $0 may be a softlink
PRG="$0"
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/startAllNCs.sh b/pregelix/pregelix-core/src/main/resources/scripts/startAllNCs.sh
index d30da26..821be00 100644
--- a/pregelix/pregelix-core/src/main/resources/scripts/startAllNCs.sh
+++ b/pregelix/pregelix-core/src/main/resources/scripts/startAllNCs.sh
@@ -1,3 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
PREGELIX_PATH=`pwd`
for i in `cat conf/slaves`
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/startCluster.sh b/pregelix/pregelix-core/src/main/resources/scripts/startCluster.sh
index a0c2063..cddf9a4 100644
--- a/pregelix/pregelix-core/src/main/resources/scripts/startCluster.sh
+++ b/pregelix/pregelix-core/src/main/resources/scripts/startCluster.sh
@@ -1,3 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
bin/startcc.sh
sleep 5
bin/startAllNCs.sh
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/startDebugNc.sh b/pregelix/pregelix-core/src/main/resources/scripts/startDebugNc.sh
index fe6cf27..bb43686 100755
--- a/pregelix/pregelix-core/src/main/resources/scripts/startDebugNc.sh
+++ b/pregelix/pregelix-core/src/main/resources/scripts/startDebugNc.sh
@@ -1,3 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
hostname
#Get the IP address of the cc
@@ -40,11 +58,11 @@
#Set JAVA_OPTS
export JAVA_OPTS=$NCJAVA_OPTS2
-cd $HYRACKS_HOME
-HYRACKS_HOME=`pwd`
+PREGELIX_HOME=`pwd`
#Enter the temp dir
cd $NCTMP_DIR2
#Launch hyracks nc
-$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyracksnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS2}" &> $NCLOGS_DIR2/$NODEID.log &
+#echo ${PREGELIX_HOME}/bin/pregelixnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -result-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS}"
+${PREGELIX_HOME}/bin/pregelixnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -result-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS2}" &> $NCLOGS_DIR2/$NODEID.log &
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/startcc.sh b/pregelix/pregelix-core/src/main/resources/scripts/startcc.sh
index 74f0987..282a6e7 100644
--- a/pregelix/pregelix-core/src/main/resources/scripts/startcc.sh
+++ b/pregelix/pregelix-core/src/main/resources/scripts/startcc.sh
@@ -1,4 +1,21 @@
#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
hostname
#Import cluster properties
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/startnc.sh b/pregelix/pregelix-core/src/main/resources/scripts/startnc.sh
index 3ab1b25..970c30b 100644
--- a/pregelix/pregelix-core/src/main/resources/scripts/startnc.sh
+++ b/pregelix/pregelix-core/src/main/resources/scripts/startnc.sh
@@ -1,3 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
hostname
MY_NAME=`hostname`
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/stopAllNCs.sh b/pregelix/pregelix-core/src/main/resources/scripts/stopAllNCs.sh
index 12367c1..dc576d1 100644
--- a/pregelix/pregelix-core/src/main/resources/scripts/stopAllNCs.sh
+++ b/pregelix/pregelix-core/src/main/resources/scripts/stopAllNCs.sh
@@ -1,3 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
PREGELIX_PATH=`pwd`
for i in `cat conf/slaves`
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/stopCluster.sh b/pregelix/pregelix-core/src/main/resources/scripts/stopCluster.sh
index 4889934..6b829aa 100644
--- a/pregelix/pregelix-core/src/main/resources/scripts/stopCluster.sh
+++ b/pregelix/pregelix-core/src/main/resources/scripts/stopCluster.sh
@@ -1,3 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
bin/stopAllNCs.sh
sleep 2
bin/stopcc.sh
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/stopcc.sh b/pregelix/pregelix-core/src/main/resources/scripts/stopcc.sh
index 84f369f..8f94fb7 100644
--- a/pregelix/pregelix-core/src/main/resources/scripts/stopcc.sh
+++ b/pregelix/pregelix-core/src/main/resources/scripts/stopcc.sh
@@ -1,3 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
hostname
. conf/cluster.properties
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/stopnc.sh b/pregelix/pregelix-core/src/main/resources/scripts/stopnc.sh
index 7a5352d..26ef089 100644
--- a/pregelix/pregelix-core/src/main/resources/scripts/stopnc.sh
+++ b/pregelix/pregelix-core/src/main/resources/scripts/stopnc.sh
@@ -1,3 +1,21 @@
+#!/bin/bash
+#
+#------------------------------------------------------------------------
+# Copyright 2009-2013 by The Regents of the University of California
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# you may obtain a copy of the License from
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+#
+
hostname
. conf/cluster.properties
@@ -9,10 +27,6 @@
fi
if [ "$PID" == "" ]; then
- PID=`ps -ef|grep ${USER}|grep java|grep 'hyracks'|awk '{print $2}'`
-fi
-
-if [ "$PID" == "" ]; then
USERID=`id | sed 's/^uid=//;s/(.*$//'`
PID=`ps -ef|grep ${USERID}|grep java|grep 'Dapp.name=pregelixnc'|awk '{print $2}'`
fi
diff --git a/pregelix/pregelix-dataflow-std-base/pom.xml b/pregelix/pregelix-dataflow-std-base/pom.xml
index 1ebc65d..1209496 100644
--- a/pregelix/pregelix-dataflow-std-base/pom.xml
+++ b/pregelix/pregelix-dataflow-std-base/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
@@ -74,14 +74,14 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/pregelix/pregelix-dataflow-std/pom.xml b/pregelix/pregelix-dataflow-std/pom.xml
index 884577e..585e82b 100644
--- a/pregelix/pregelix-dataflow-std/pom.xml
+++ b/pregelix/pregelix-dataflow-std/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
@@ -74,77 +74,77 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-dataflow-std-base</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-hdfs-core</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-ipc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/BTreeSearchFunctionUpdateOperatorNodePushable.java b/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/BTreeSearchFunctionUpdateOperatorNodePushable.java
index ff95e52..1fb5aca 100644
--- a/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/BTreeSearchFunctionUpdateOperatorNodePushable.java
+++ b/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/BTreeSearchFunctionUpdateOperatorNodePushable.java
@@ -43,7 +43,9 @@
import edu.uci.ics.pregelix.dataflow.std.base.IRecordDescriptorFactory;
import edu.uci.ics.pregelix.dataflow.std.base.IRuntimeHookFactory;
import edu.uci.ics.pregelix.dataflow.std.base.IUpdateFunctionFactory;
+import edu.uci.ics.pregelix.dataflow.util.CopyUpdateUtil;
import edu.uci.ics.pregelix.dataflow.util.FunctionProxy;
+import edu.uci.ics.pregelix.dataflow.util.SearchKeyTupleReference;
import edu.uci.ics.pregelix.dataflow.util.UpdateBuffer;
public class BTreeSearchFunctionUpdateOperatorNodePushable extends AbstractUnaryInputOperatorNodePushable {
@@ -74,6 +76,7 @@
private final FunctionProxy functionProxy;
private ArrayTupleBuilder cloneUpdateTb;
private final UpdateBuffer updateBuffer;
+ private final SearchKeyTupleReference tempTupleReference = new SearchKeyTupleReference();
public BTreeSearchFunctionUpdateOperatorNodePushable(AbstractTreeIndexOperatorDescriptor opDesc,
IHyracksTaskContext ctx, int partition, IRecordDescriptorProvider recordDescProvider, boolean isForward,
@@ -147,21 +150,8 @@
functionProxy.functionCall(tuple, cloneUpdateTb);
//doing clone update
- if (cloneUpdateTb.getSize() > 0) {
- if (!updateBuffer.appendTuple(cloneUpdateTb)) {
- //release the cursor/latch
- cursor.close();
- //batch update
- updateBuffer.updateBTree(indexAccessor);
-
- //search again
- cursor.reset();
- rangePred.setLowKey(tuple, true);
- rangePred.setHighKey(highKey, highKeyInclusive);
- indexAccessor.search(cursor, rangePred);
- }
- }
- cloneUpdateTb.reset();
+ CopyUpdateUtil.copyUpdate(tempTupleReference, tuple, updateBuffer, cloneUpdateTb, indexAccessor, cursor,
+ rangePred);
}
}
diff --git a/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/IndexNestedLoopJoinFunctionUpdateOperatorNodePushable.java b/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/IndexNestedLoopJoinFunctionUpdateOperatorNodePushable.java
index 61e4649..427ffe9 100644
--- a/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/IndexNestedLoopJoinFunctionUpdateOperatorNodePushable.java
+++ b/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/IndexNestedLoopJoinFunctionUpdateOperatorNodePushable.java
@@ -43,7 +43,9 @@
import edu.uci.ics.pregelix.dataflow.std.base.IRecordDescriptorFactory;
import edu.uci.ics.pregelix.dataflow.std.base.IRuntimeHookFactory;
import edu.uci.ics.pregelix.dataflow.std.base.IUpdateFunctionFactory;
+import edu.uci.ics.pregelix.dataflow.util.CopyUpdateUtil;
import edu.uci.ics.pregelix.dataflow.util.FunctionProxy;
+import edu.uci.ics.pregelix.dataflow.util.SearchKeyTupleReference;
import edu.uci.ics.pregelix.dataflow.util.UpdateBuffer;
public class IndexNestedLoopJoinFunctionUpdateOperatorNodePushable extends AbstractUnaryInputOperatorNodePushable {
@@ -69,6 +71,7 @@
private final FunctionProxy functionProxy;
private ArrayTupleBuilder cloneUpdateTb;
private final UpdateBuffer updateBuffer;
+ private final SearchKeyTupleReference tempTupleReference = new SearchKeyTupleReference();
public IndexNestedLoopJoinFunctionUpdateOperatorNodePushable(AbstractTreeIndexOperatorDescriptor opDesc,
IHyracksTaskContext ctx, int partition, IRecordDescriptorProvider recordDescProvider, boolean isForward,
@@ -163,21 +166,9 @@
*/
functionProxy.functionCall(leftAccessor, tIndex, tupleRef, cloneUpdateTb);
- if (cloneUpdateTb.getSize() > 0) {
- if (!updateBuffer.appendTuple(cloneUpdateTb)) {
- //release the cursor/latch
- cursor.close();
- //batch update
- updateBuffer.updateBTree(indexAccessor);
-
- //search again
- cursor.reset();
- rangePred.setLowKey(tupleRef, true);
- rangePred.setHighKey(highKey, highKeyInclusive);
- indexAccessor.search(cursor, rangePred);
- }
- }
- cloneUpdateTb.reset();
+ //doing copy update
+ CopyUpdateUtil.copyUpdate(tempTupleReference, tupleRef, updateBuffer, cloneUpdateTb, indexAccessor, cursor,
+ rangePred);
}
}
diff --git a/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/IndexNestedLoopRightOuterJoinFunctionUpdateOperatorNodePushable.java b/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/IndexNestedLoopRightOuterJoinFunctionUpdateOperatorNodePushable.java
index 5ca5382..0c13a09 100644
--- a/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/IndexNestedLoopRightOuterJoinFunctionUpdateOperatorNodePushable.java
+++ b/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/IndexNestedLoopRightOuterJoinFunctionUpdateOperatorNodePushable.java
@@ -45,7 +45,9 @@
import edu.uci.ics.pregelix.dataflow.std.base.IRecordDescriptorFactory;
import edu.uci.ics.pregelix.dataflow.std.base.IRuntimeHookFactory;
import edu.uci.ics.pregelix.dataflow.std.base.IUpdateFunctionFactory;
+import edu.uci.ics.pregelix.dataflow.util.CopyUpdateUtil;
import edu.uci.ics.pregelix.dataflow.util.FunctionProxy;
+import edu.uci.ics.pregelix.dataflow.util.SearchKeyTupleReference;
import edu.uci.ics.pregelix.dataflow.util.UpdateBuffer;
public class IndexNestedLoopRightOuterJoinFunctionUpdateOperatorNodePushable extends
@@ -79,7 +81,8 @@
private final IFrameWriter[] writers;
private final FunctionProxy functionProxy;
private ArrayTupleBuilder cloneUpdateTb;
- private UpdateBuffer updateBuffer;
+ private final UpdateBuffer updateBuffer;
+ private final SearchKeyTupleReference tempTupleReference = new SearchKeyTupleReference();
public IndexNestedLoopRightOuterJoinFunctionUpdateOperatorNodePushable(AbstractTreeIndexOperatorDescriptor opDesc,
IHyracksTaskContext ctx, int partition, IRecordDescriptorProvider recordDescProvider, boolean isForward,
@@ -184,32 +187,6 @@
}
}
- //for the join match casesos
- private void writeResults(IFrameTupleAccessor leftAccessor, int tIndex, ITupleReference frameTuple)
- throws Exception {
- /**
- * function call
- */
- functionProxy.functionCall(leftAccessor, tIndex, frameTuple, cloneUpdateTb);
-
- //doing clone update
- if (cloneUpdateTb.getSize() > 0) {
- if (!updateBuffer.appendTuple(cloneUpdateTb)) {
- //release the cursor/latch
- cursor.close();
- //batch update
- updateBuffer.updateBTree(indexAccessor);
-
- //search again and recover the cursor
- cursor.reset();
- rangePred.setLowKey(frameTuple, true);
- rangePred.setHighKey(null, true);
- indexAccessor.search(cursor, rangePred);
- }
- cloneUpdateTb.reset();
- }
- }
-
@Override
public void nextFrame(ByteBuffer buffer) throws HyracksDataException {
accessor.reset(buffer);
@@ -289,6 +266,19 @@
return lowKeySearchCmp.compare(left, right);
}
+ //for the join match casesos
+ private void writeResults(IFrameTupleAccessor leftAccessor, int tIndex, ITupleReference frameTuple)
+ throws Exception {
+ /**
+ * function call
+ */
+ functionProxy.functionCall(leftAccessor, tIndex, frameTuple, cloneUpdateTb);
+
+ //doing clone update
+ CopyUpdateUtil.copyUpdate(tempTupleReference, frameTuple, updateBuffer, cloneUpdateTb, indexAccessor, cursor,
+ rangePred);
+ }
+
/** write result for outer case */
private void writeResults(ITupleReference frameTuple) throws Exception {
/**
@@ -297,21 +287,8 @@
functionProxy.functionCall(nullTupleBuilder, frameTuple, cloneUpdateTb);
//doing clone update
- if (cloneUpdateTb.getSize() > 0) {
- if (!updateBuffer.appendTuple(cloneUpdateTb)) {
- //release the cursor/latch
- cursor.close();
- //batch update
- updateBuffer.updateBTree(indexAccessor);
-
- //search again and recover the cursor
- cursor.reset();
- rangePred.setLowKey(frameTuple, true);
- rangePred.setHighKey(null, true);
- indexAccessor.search(cursor, rangePred);
- }
- cloneUpdateTb.reset();
- }
+ CopyUpdateUtil.copyUpdate(tempTupleReference, frameTuple, updateBuffer, cloneUpdateTb, indexAccessor, cursor,
+ rangePred);
}
@Override
diff --git a/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/IndexNestedLoopSetUnionFunctionUpdateOperatorNodePushable.java b/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/IndexNestedLoopSetUnionFunctionUpdateOperatorNodePushable.java
index 160324e..1e5c2ea 100644
--- a/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/IndexNestedLoopSetUnionFunctionUpdateOperatorNodePushable.java
+++ b/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/std/IndexNestedLoopSetUnionFunctionUpdateOperatorNodePushable.java
@@ -43,7 +43,9 @@
import edu.uci.ics.pregelix.dataflow.std.base.IRecordDescriptorFactory;
import edu.uci.ics.pregelix.dataflow.std.base.IRuntimeHookFactory;
import edu.uci.ics.pregelix.dataflow.std.base.IUpdateFunctionFactory;
+import edu.uci.ics.pregelix.dataflow.util.CopyUpdateUtil;
import edu.uci.ics.pregelix.dataflow.util.FunctionProxy;
+import edu.uci.ics.pregelix.dataflow.util.SearchKeyTupleReference;
import edu.uci.ics.pregelix.dataflow.util.UpdateBuffer;
public class IndexNestedLoopSetUnionFunctionUpdateOperatorNodePushable extends AbstractUnaryInputOperatorNodePushable {
@@ -72,6 +74,7 @@
private final FunctionProxy functionProxy;
private ArrayTupleBuilder cloneUpdateTb;
private UpdateBuffer updateBuffer;
+ private final SearchKeyTupleReference tempTupleReference = new SearchKeyTupleReference();
public IndexNestedLoopSetUnionFunctionUpdateOperatorNodePushable(AbstractTreeIndexOperatorDescriptor opDesc,
IHyracksTaskContext ctx, int partition, IRecordDescriptorProvider recordDescProvider, boolean isForward,
@@ -235,21 +238,8 @@
functionProxy.functionCall(frameTuple, cloneUpdateTb);
//doing clone update
- if (cloneUpdateTb.getSize() > 0) {
- if (!updateBuffer.appendTuple(cloneUpdateTb)) {
- //release the cursor/latch
- cursor.close();
- //batch update
- updateBuffer.updateBTree(indexAccessor);
-
- //search again
- cursor.reset();
- rangePred.setLowKey(frameTuple, true);
- rangePred.setHighKey(null, true);
- indexAccessor.search(cursor, rangePred);
- }
- cloneUpdateTb.reset();
- }
+ CopyUpdateUtil.copyUpdate(tempTupleReference, frameTuple, updateBuffer, cloneUpdateTb, indexAccessor, cursor,
+ rangePred);
}
/** write the left result */
@@ -258,21 +248,8 @@
functionProxy.functionCall(leftAccessor, tIndex, frameTuple, cloneUpdateTb);
//doing clone update
- if (cloneUpdateTb.getSize() > 0) {
- if (!updateBuffer.appendTuple(cloneUpdateTb)) {
- //release the cursor/latch
- cursor.close();
- //batch update
- updateBuffer.updateBTree(indexAccessor);
-
- //search again
- cursor.reset();
- rangePred.setLowKey(frameTuple, true);
- rangePred.setHighKey(null, true);
- indexAccessor.search(cursor, rangePred);
- }
- cloneUpdateTb.reset();
- }
+ CopyUpdateUtil.copyUpdate(tempTupleReference, frameTuple, updateBuffer, cloneUpdateTb, indexAccessor, cursor,
+ rangePred);
}
@Override
diff --git a/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/util/CopyUpdateUtil.java b/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/util/CopyUpdateUtil.java
new file mode 100644
index 0000000..3f89543
--- /dev/null
+++ b/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/util/CopyUpdateUtil.java
@@ -0,0 +1,53 @@
+/*
+ * Copyright 2009-2010 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.pregelix.dataflow.util;
+
+import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
+import edu.uci.ics.hyracks.dataflow.common.comm.io.ArrayTupleBuilder;
+import edu.uci.ics.hyracks.dataflow.common.data.accessors.ITupleReference;
+import edu.uci.ics.hyracks.storage.am.btree.impls.RangePredicate;
+import edu.uci.ics.hyracks.storage.am.common.api.ITreeIndexAccessor;
+import edu.uci.ics.hyracks.storage.am.common.api.ITreeIndexCursor;
+import edu.uci.ics.hyracks.storage.am.common.api.IndexException;
+
+public class CopyUpdateUtil {
+
+ public static void copyUpdate(SearchKeyTupleReference tempTupleReference, ITupleReference frameTuple,
+ UpdateBuffer updateBuffer, ArrayTupleBuilder cloneUpdateTb, ITreeIndexAccessor indexAccessor,
+ ITreeIndexCursor cursor, RangePredicate rangePred) throws HyracksDataException, IndexException {
+ if (cloneUpdateTb.getSize() > 0) {
+ if (!updateBuffer.appendTuple(cloneUpdateTb)) {
+ tempTupleReference.reset(frameTuple.getFieldData(0), frameTuple.getFieldStart(0),
+ frameTuple.getFieldLength(0));
+ //release the cursor/latch
+ cursor.close();
+ //batch update
+ updateBuffer.updateBTree(indexAccessor);
+ //try append the to-be-updated tuple again
+ if (!updateBuffer.appendTuple(cloneUpdateTb)) {
+ throw new HyracksDataException("cannot append tuple builder!");
+ }
+ //search again and recover the cursor
+ cursor.reset();
+ rangePred.setLowKey(tempTupleReference, false);
+ rangePred.setHighKey(null, true);
+ indexAccessor.search(cursor, rangePred);
+ }
+ cloneUpdateTb.reset();
+ }
+ }
+
+}
diff --git a/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/util/SearchKeyTupleReference.java b/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/util/SearchKeyTupleReference.java
new file mode 100644
index 0000000..86fa24a
--- /dev/null
+++ b/pregelix/pregelix-dataflow-std/src/main/java/edu/uci/ics/pregelix/dataflow/util/SearchKeyTupleReference.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2009-2010 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.uci.ics.pregelix.dataflow.util;
+
+import edu.uci.ics.hyracks.dataflow.common.data.accessors.ITupleReference;
+
+public class SearchKeyTupleReference implements ITupleReference {
+
+ private byte[] copiedData;
+ private int length;
+
+ public void reset(byte[] data, int start, int len) {
+ if (copiedData == null) {
+ copiedData = new byte[len];
+ }
+ if (copiedData.length < len) {
+ copiedData = new byte[len];
+ }
+ System.arraycopy(data, start, copiedData, 0, len);
+ length = len;
+ }
+
+ @Override
+ public int getFieldCount() {
+ return 1;
+ }
+
+ @Override
+ public byte[] getFieldData(int fIdx) {
+ return copiedData;
+ }
+
+ @Override
+ public int getFieldStart(int fIdx) {
+ return 0;
+ }
+
+ @Override
+ public int getFieldLength(int fIdx) {
+ return length;
+ }
+
+}
diff --git a/pregelix/pregelix-dataflow/pom.xml b/pregelix/pregelix-dataflow/pom.xml
index 8e2be08..4c0da76 100644
--- a/pregelix/pregelix-dataflow/pom.xml
+++ b/pregelix/pregelix-dataflow/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
@@ -74,68 +74,68 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-dataflow-std-base</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-ipc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/pregelix/pregelix-dist/pom.xml b/pregelix/pregelix-dist/pom.xml
index 846ff66..0839966 100644
--- a/pregelix/pregelix-dist/pom.xml
+++ b/pregelix/pregelix-dist/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<artifactId>pregelix-dist</artifactId>
<name>pregelix-dist</name>
@@ -69,13 +69,13 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-core</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-example</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
diff --git a/pregelix/pregelix-example/pom.xml b/pregelix/pregelix-example/pom.xml
index 7ca7e5d..1d08b8c 100644
--- a/pregelix/pregelix-example/pom.xml
+++ b/pregelix/pregelix-example/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
<build>
@@ -105,7 +105,7 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-core</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
diff --git a/pregelix/pregelix-example/src/test/resources/hyracks-deployment.properties b/pregelix/pregelix-example/src/test/resources/hyracks-deployment.properties
deleted file mode 100644
index 9c42b89..0000000
--- a/pregelix/pregelix-example/src/test/resources/hyracks-deployment.properties
+++ /dev/null
@@ -1,2 +0,0 @@
-#cc.bootstrap.class=edu.uci.ics.asterix.hyracks.bootstrap.CCBootstrapImpl
-nc.bootstrap.class=edu.uci.ics.pregelix.runtime.bootstrap.NCBootstrapImpl
diff --git a/pregelix/pregelix-runtime/pom.xml b/pregelix/pregelix-runtime/pom.xml
index 2d7b20d..2b56271 100644
--- a/pregelix/pregelix-runtime/pom.xml
+++ b/pregelix/pregelix-runtime/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</parent>
@@ -74,82 +74,82 @@
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>pregelix-dataflow</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-api</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-dataflow-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-data-std</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-common</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-storage-am-btree</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-cc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-control-nc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>hyracks-ipc</artifactId>
- <version>0.2.5-SNAPSHOT</version>
+ <version>0.2.6-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>