Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix
diff --git a/genomix/genomix-hadoop/pom.xml b/genomix/genomix-hadoop/pom.xml
index 8ca2fa3..f305c49 100755
--- a/genomix/genomix-hadoop/pom.xml
+++ b/genomix/genomix-hadoop/pom.xml
@@ -160,6 +160,8 @@
<groupId>edu.uci.ics.hyracks</groupId>
<artifactId>genomix-hyracks</artifactId>
<version>0.2.6-SNAPSHOT</version>
+ <type>test-jar</type>
+ <scope>test</scope>
</dependency>
<dependency>
<groupId>edu.uci.ics.hyracks</groupId>
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
index 87627e1..3a98573 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
@@ -40,7 +40,7 @@
private static final String HDFS_INPUT_PATH = "/webmap";
private static final String HDFS_OUTPUT_PATH = "/webmap_result";
- private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + "/merged.txt";
+ private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + "/Tips4.txt";
private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";;
private MiniDFSCluster dfsCluster;
diff --git a/genomix/genomix-hyracks/src/test/resources/HighSplitRepeatResult.txt b/genomix/genomix-hyracks/src/test/resources/HighSplitRepeatResult.txt
new file mode 100755
index 0000000..dc4395d
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/HighSplitRepeatResult.txt
@@ -0,0 +1,6 @@
+{[(1-0_0)] [] [] [] [GCC] CCA 1.0x}
+{[(2-0_0)] [GCC] [] [] [] CGC 1.0x}
+{[(3-0_0)] [] [CCG] [] [GCC] CCG 2.0x}
+{[(2-0_0),(3-0_0),(1-0_0)] [CCG,CCA] [AGG] [] [AGC,CGC] GCC 3.0x}
+{[(1-0_0)] [GCC] [] [] [] AGC 1.0x}
+{[(2-0_0)] [] [GCC] [] [] AGG 1.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/LowSplitRepeatResult.txt b/genomix/genomix-hyracks/src/test/resources/LowSplitRepeatResult.txt
new file mode 100755
index 0000000..f8df8bb
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/LowSplitRepeatResult.txt
@@ -0,0 +1,6 @@
+{[(1-0_0)] [] [] [] [GCC] CCA 1.0x}
+{[(2-0_0)] [] [] [] [GCC] CCG 1.0x}
+{[(2-0_0),(3-0_0),(1-0_0)] [CCG,CCA] [AGG] [] [AGC] GCC 3.0x}
+{[(2-0_0),(1-0_0)] [GCC] [] [] [] AGC 2.0x}
+{[(3-0_0)] [AGG] [] [] [] AAG 1.0x}
+{[(3-0_0)] [] [GCC] [] [AAG] AGG 1.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/MidSplitRepeatResult.txt b/genomix/genomix-hyracks/src/test/resources/MidSplitRepeatResult.txt
new file mode 100755
index 0000000..dc4395d
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/MidSplitRepeatResult.txt
@@ -0,0 +1,6 @@
+{[(1-0_0)] [] [] [] [GCC] CCA 1.0x}
+{[(2-0_0)] [GCC] [] [] [] CGC 1.0x}
+{[(3-0_0)] [] [CCG] [] [GCC] CCG 2.0x}
+{[(2-0_0),(3-0_0),(1-0_0)] [CCG,CCA] [AGG] [] [AGC,CGC] GCC 3.0x}
+{[(1-0_0)] [GCC] [] [] [] AGC 1.0x}
+{[(2-0_0)] [] [GCC] [] [] AGG 1.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/Tips1Result.txt b/genomix/genomix-hyracks/src/test/resources/Tips1Result.txt
new file mode 100755
index 0000000..3f04844
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/Tips1Result.txt
@@ -0,0 +1,7 @@
+{[(1-0_0)] [] [] [] [GCC] CCA 1.0x}
+{[(1-0_0)] [AGC] [] [] [] CAG 1.0x}
+{[(2-0_0)] [] [ACG] [] [GCC] CCG 1.0x}
+{[(2-0_0)] [] [] [ACG] [] GTA 1.0x}
+{[(2-0_0),(1-0_0)] [CCG,CCA] [] [] [AGC] GCC 2.0x}
+{[(1-0_0)] [GCC] [] [] [CAG] AGC 1.0x}
+{[(2-0_0)] [] [CCG] [GTA] [] ACG 1.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/Tips2Result.txt b/genomix/genomix-hyracks/src/test/resources/Tips2Result.txt
new file mode 100755
index 0000000..322cc70
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/Tips2Result.txt
@@ -0,0 +1,7 @@
+{[(2-0_0)] [GAA] [] [CGC] [] CGA 1.0x}
+{[(2-0_0),(1-0_0)] [GCC] [AGC] [CGA] [] CGC 2.0x}
+{[(1-0_0)] [AGC] [] [] [ACA] CAG 1.0x}
+{[(2-0_0)] [] [] [] [CGA] GAA 1.0x}
+{[(2-0_0)] [] [] [] [CGC] GCC 1.0x}
+{[(1-0_0)] [CAG] [] [] [] ACA 1.0x}
+{[(1-0_0)] [] [CGC] [] [CAG] AGC 1.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/Tips3Result.txt b/genomix/genomix-hyracks/src/test/resources/Tips3Result.txt
new file mode 100755
index 0000000..d37d70c
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/Tips3Result.txt
@@ -0,0 +1,5 @@
+{[(2-0_0)] [] [] [] [GCC] CCA 1.0x}
+{[(2-0_0),(1-0_0)] [AGC] [] [] [] CAG 2.0x}
+{[(2-0_0),(1-0_0)] [CCA] [AGG] [] [AGC] GCC 2.0x}
+{[(2-0_0),(1-0_0)] [GCC] [] [] [CAG] AGC 2.0x}
+{[(1-0_0)] [] [GCC] [] [] AGG 1.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/Tips4Result.txt b/genomix/genomix-hyracks/src/test/resources/Tips4Result.txt
new file mode 100755
index 0000000..de3a226
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/Tips4Result.txt
@@ -0,0 +1,4 @@
+{[(2-0_0),(1-0_0)] [AGG] [] [] [] CAG 2.0x}
+{[(1-0_0)] [] [] [GCC] [] GCA 1.0x}
+{[(2-0_0),(1-0_0)] [] [AGG] [GCC,GCA] [] GCC 3.0x}
+{[(2-0_0),(1-0_0)] [] [GCC] [] [CAG] AGG 2.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result2 b/genomix/genomix-hyracks/src/test/resources/expected/result2
deleted file mode 100755
index 9296453..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result2
+++ /dev/null
@@ -1,4 +0,0 @@
-AATAG |A 5
-AGAAG T| 5
-ATAGA A|A 5
-TAGAA A|G 5
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_after_generateNode b/genomix/genomix-hyracks/src/test/resources/expected/result_after_generateNode
deleted file mode 100644
index 9334b95..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_after_generateNode
+++ /dev/null
@@ -1,14 +0,0 @@
-((1,1) [(1,3)] [] [] [] AATAGA)
-((1,3) [(6,1),(1,4)] [] [] [(1,1)] TAGAA)
-((1,4) [(6,2)] [] [] [(1,3)] AGAAG)
-((2,1) [] [] [] [] AATAGCTT)
-((3,1) [(3,3)] [] [] [] AATAGA)
-((3,3) [(6,1),(3,4)] [] [] [(3,1)] TAGAA)
-((3,4) [(6,2)] [] [] [(3,3)] AGAAG)
-((4,1) [] [] [] [] AATAGCTT)
-((5,1) [(5,3)] [] [] [] AATAGA)
-((5,3) [(6,1),(5,4)] [] [] [(5,1)] TAGAA)
-((5,4) [(6,2)] [] [] [(5,3)] AGAAG)
-((6,1) [(6,2)] [] [] [(5,3),(3,3),(1,3)] AGAAG)
-((6,2) [(6,3)] [] [] [(1,4),(3,4),(5,4),(6,1)] GAAGA)
-((6,3) [] [] [] [(6,2)] AAGAAG)
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_after_initial_read b/genomix/genomix-hyracks/src/test/resources/expected/result_after_initial_read
deleted file mode 100644
index 3502e95..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_after_initial_read
+++ /dev/null
@@ -1,48 +0,0 @@
-AAGAA (6,3)
-AAGCT (2,-4)
-AAGCT (4,-4)
-AATAG (1,1)
-AATAG (2,1)
-AATAG (3,1)
-AATAG (4,1)
-AATAG (5,1)
-AGAAG (1,4)
-AGAAG (3,4)
-AGAAG (5,4)
-AGAAG (6,1)
-AGAAG (6,4)
-AGCTA (2,-3)
-AGCTA (4,-3)
-AGCTT (2,4)
-AGCTT (4,4)
-ATAGA (1,2)
-ATAGA (3,2)
-ATAGA (5,2)
-ATAGC (2,2)
-ATAGC (4,2)
-CTATT (1,-1)
-CTATT (2,-1)
-CTATT (3,-1)
-CTATT (4,-1)
-CTATT (5,-1)
-CTTCT (1,-4)
-CTTCT (3,-4)
-CTTCT (5,-4)
-CTTCT (6,-1)
-CTTCT (6,-4)
-GAAGA (6,2)
-GCTAT (2,-2)
-GCTAT (4,-2)
-TAGAA (1,3)
-TAGAA (3,3)
-TAGAA (5,3)
-TAGCT (2,3)
-TAGCT (4,3)
-TCTAT (1,-2)
-TCTAT (3,-2)
-TCTAT (5,-2)
-TCTTC (6,-2)
-TTCTA (1,-3)
-TTCTA (3,-3)
-TTCTA (5,-3)
-TTCTT (6,-3)
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_after_kmer2readId b/genomix/genomix-hyracks/src/test/resources/expected/result_after_kmer2readId
deleted file mode 100644
index b52a848..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_after_kmer2readId
+++ /dev/null
@@ -1,48 +0,0 @@
-1 -1 []
-1 -2 []
-1 -3 []
-1 -4 [(6,-1)]
-1 1 [] AATAG
-1 2 [] ATAGA
-1 3 [] TAGAA
-1 4 [(6,1)] AGAAG
-2 -1 []
-2 -2 []
-2 -3 []
-2 -4 []
-2 1 [] AATAG
-2 2 [] ATAGC
-2 3 [] TAGCT
-2 4 [] AGCTT
-3 -1 []
-3 -2 []
-3 -3 []
-3 -4 [(6,-1)]
-3 1 [] AATAG
-3 2 [] ATAGA
-3 3 [] TAGAA
-3 4 [(6,1)] AGAAG
-4 -1 []
-4 -2 []
-4 -3 []
-4 -4 []
-4 1 [] AATAG
-4 2 [] ATAGC
-4 3 [] TAGCT
-4 4 [] AGCTT
-5 -1 []
-5 -2 []
-5 -3 []
-5 -4 [(6,-1)]
-5 1 [] AATAG
-5 2 [] ATAGA
-5 3 [] TAGAA
-5 4 [(6,1)] AGAAG
-6 -1 [(1,-4),(3,-4),(5,-4)]
-6 -2 []
-6 -3 []
-6 -4 []
-6 1 [(1,4),(3,4),(5,4)] AGAAG
-6 2 [] GAAGA
-6 3 [] AAGAA
-6 4 [] AGAAG
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_after_kmerAggregate b/genomix/genomix-hyracks/src/test/resources/expected/result_after_kmerAggregate
deleted file mode 100644
index 9035f33..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_after_kmerAggregate
+++ /dev/null
@@ -1,18 +0,0 @@
-AAGAA [(6,3)]
-AAGCT [(2,-4),(4,-4)]
-AATAG [(1,1),(2,1),(3,1),(4,1),(5,1)]
-AGAAG [(1,4),(3,4),(5,4),(6,1),(6,4)]
-AGCTA [(2,-3),(4,-3)]
-AGCTT [(2,4),(4,4)]
-ATAGA [(1,2),(3,2),(5,2)]
-ATAGC [(2,2),(4,2)]
-CTATT [(1,-1),(2,-1),(3,-1),(4,-1),(5,-1)]
-CTTCT [(1,-4),(3,-4),(5,-4),(6,-1),(6,-4)]
-GAAGA [(6,2)]
-GCTAT [(2,-2),(4,-2)]
-TAGAA [(1,3),(3,3),(5,3)]
-TAGCT [(2,3),(4,3)]
-TCTAT [(1,-2),(3,-2),(5,-2)]
-TCTTC [(6,-2)]
-TTCTA [(1,-3),(3,-3),(5,-3)]
-TTCTT [(6,-3)]
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_after_readIDAggreage b/genomix/genomix-hyracks/src/test/resources/expected/result_after_readIDAggreage
deleted file mode 100644
index 2cc283d..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_after_readIDAggreage
+++ /dev/null
@@ -1,6 +0,0 @@
-1 1 [] AATAG -1 [] 2 [] ATAGA -2 [] 3 [] TAGAA -3 [] 4 [(6,1)] AGAAG -4 [(6,-1)]
-2 1 [] AATAG -1 [] 2 [] ATAGC -2 [] 3 [] TAGCT -3 [] 4 [] AGCTT -4 []
-3 1 [] AATAG -1 [] 2 [] ATAGA -2 [] 3 [] TAGAA -3 [] 4 [(6,1)] AGAAG -4 [(6,-1)]
-4 1 [] AATAG -1 [] 2 [] ATAGC -2 [] 3 [] TAGCT -3 [] 4 [] AGCTT -4 []
-5 1 [] AATAG -1 [] 2 [] ATAGA -2 [] 3 [] TAGAA -3 [] 4 [(6,1)] AGAAG -4 [(6,-1)]
-6 1 [(3,4),(1,4),(5,4)] AGAAG -1 [(1,-4),(3,-4),(5,-4)] 2 [] GAAGA -2 [] 3 [] AAGAA -3 [] 4 [] AGAAG -4 []
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_reverse b/genomix/genomix-hyracks/src/test/resources/expected/result_reverse
deleted file mode 100644
index cf2712d..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_reverse
+++ /dev/null
@@ -1,8 +0,0 @@
-AAGAT G|A 5
-AATAG |A 5
-AGAAG T| 5
-AGATA A|A 5
-ATAGA A|A 5
-GAAGA |T 5
-GATAA A| 5
-TAGAA A|G 5
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_unmerged b/genomix/genomix-hyracks/src/test/resources/expected/result_unmerged
deleted file mode 100644
index f617779..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_unmerged
+++ /dev/null
@@ -1,24 +0,0 @@
-((1,1) [(1,2)] [] [] [] AATAG)
-((1,2) [(1,3)] [] [] [(1,1)] ATAGA)
-((1,3) [(6,1),(1,4)] [] [] [(1,2)] TAGAA)
-((1,4) [(6,2)] [] [] [(1,3)] AGAAG)
-((2,1) [(2,2)] [] [] [] AATAG)
-((2,2) [(2,3)] [] [] [(2,1)] ATAGC)
-((2,3) [(2,4)] [] [] [(2,2)] TAGCT)
-((2,4) [] [] [] [(2,3)] AGCTT)
-((3,1) [(3,2)] [] [] [] AATAG)
-((3,2) [(3,3)] [] [] [(3,1)] ATAGA)
-((3,3) [(6,1),(3,4)] [] [] [(3,2)] TAGAA)
-((3,4) [(6,2)] [] [] [(3,3)] AGAAG)
-((4,1) [(4,2)] [] [] [] AATAG)
-((4,2) [(4,3)] [] [] [(4,1)] ATAGC)
-((4,3) [(4,4)] [] [] [(4,2)] TAGCT)
-((4,4) [] [] [] [(4,3)] AGCTT)
-((5,1) [(5,2)] [] [] [] AATAG)
-((5,2) [(5,3)] [] [] [(5,1)] ATAGA)
-((5,3) [(6,1),(5,4)] [] [] [(5,2)] TAGAA)
-((5,4) [(6,2)] [] [] [(5,3)] AGAAG)
-((6,1) [(6,2)] [] [] [(1,3),(3,3),(5,3)] AGAAG)
-((6,2) [(6,3)] [] [] [(3,4),(1,4),(5,4),(6,1)] GAAGA)
-((6,3) [(6,4)] [] [] [(6,2)] AAGAA)
-((6,4) [] [] [] [(6,3)] AGAAG)
diff --git a/genomix/genomix-pregelix/pom.xml b/genomix/genomix-pregelix/pom.xml
index f609d3b..95227c5 100644
--- a/genomix/genomix-pregelix/pom.xml
+++ b/genomix/genomix-pregelix/pom.xml
@@ -1,60 +1,61 @@
<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <groupId>edu.uci.ics.pregelix</groupId>
- <artifactId>genomix-pregelix</artifactId>
- <packaging>jar</packaging>
- <version>0.2.6-SNAPSHOT</version>
- <name>genomix-pregelix</name>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>edu.uci.ics.pregelix</groupId>
+ <artifactId>genomix-pregelix</artifactId>
+ <packaging>jar</packaging>
+ <version>0.2.6-SNAPSHOT</version>
+ <name>genomix-pregelix</name>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
- <profiles>
- <profile>
- <id>macosx</id>
- <activation>
- <os>
- <name>mac os x</name>
- </os>
- <jdk>1.7</jdk>
- </activation>
- <properties>
- <jvm.extraargs>-Djava.nio.channels.spi.SelectorProvider=sun.nio.ch.KQueueSelectorProvider</jvm.extraargs>
- </properties>
- </profile>
- </profiles>
+ <profiles>
+ <profile>
+ <id>macosx</id>
+ <activation>
+ <os>
+ <name>mac os x</name>
+ </os>
+ <jdk>1.7</jdk>
+ </activation>
+ <properties>
+ <jvm.extraargs>-Djava.nio.channels.spi.SelectorProvider=sun.nio.ch.KQueueSelectorProvider</jvm.extraargs>
+ </properties>
+ </profile>
+ </profiles>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-compiler-plugin</artifactId>
- <version>2.0.2</version>
- <configuration>
- <source>1.7</source>
- <target>1.7</target>
- <fork>true</fork>
- </configuration>
- </plugin>
- <plugin>
- <artifactId>maven-assembly-plugin</artifactId>
- <configuration>
- <descriptorRefs>
- <descriptorRef>jar-with-dependencies</descriptorRef>
- </descriptorRefs>
- </configuration>
- <executions>
- <execution>
- <id>make-my-jar-with-dependencies</id>
- <phase>package</phase>
- <goals>
- <goal>single</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <version>2.0.2</version>
+ <configuration>
+ <source>1.7</source>
+ <target>1.7</target>
+ <fork>true</fork>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <descriptorRefs>
+ <descriptorRef>jar-with-dependencies</descriptorRef>
+ </descriptorRefs>
+ </configuration>
+ <executions>
+ <execution>
+ <id>make-my-jar-with-dependencies</id>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>appassembler-maven-plugin</artifactId>
@@ -78,207 +79,207 @@
</execution>
</executions>
</plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-surefire-plugin</artifactId>
- <version>2.7.2</version>
- <configuration>
- <forkMode>pertest</forkMode>
- <argLine>-enableassertions -Xmx2047m -Dfile.encoding=UTF-8
- -Djava.util.logging.config.file=src/test/resources/logging.properties</argLine>
- <includes>
- <include>**/*TestSuite.java</include>
- <include>**/*Test.java</include>
- </includes>
- </configuration>
- </plugin>
- <plugin>
- <artifactId>maven-clean-plugin</artifactId>
- <configuration>
- <filesets>
- <fileset>
- <directory>.</directory>
- <includes>
- <include>teststore*</include>
- <include>edu*</include>
- <include>actual*</include>
- <include>build*</include>
- <include>expect*</include>
- <include>ClusterController*</include>
- <include>edu.uci.*</include>
- </includes>
- </fileset>
- </filesets>
- </configuration>
- </plugin>
- </plugins>
- </build>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>2.7.2</version>
+ <configuration>
+ <forkMode>pertest</forkMode>
+ <argLine>-enableassertions -Xmx2047m -Dfile.encoding=UTF-8
+ -Djava.util.logging.config.file=src/test/resources/logging.properties</argLine>
+ <includes>
+ <include>**/*TestSuite.java</include>
+ <include>**/*Test.java</include>
+ </includes>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-clean-plugin</artifactId>
+ <configuration>
+ <filesets>
+ <fileset>
+ <directory>.</directory>
+ <includes>
+ <include>teststore*</include>
+ <include>edu*</include>
+ <include>actual*</include>
+ <include>build*</include>
+ <include>expect*</include>
+ <include>ClusterController*</include>
+ <include>edu.uci.*</include>
+ </includes>
+ </fileset>
+ </filesets>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
- <dependencies>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>4.8.1</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>pregelix-core</artifactId>
- <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>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-dataflow-std</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-api</artifactId>
- <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>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-data-std</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-control-cc</artifactId>
- <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>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>com.kenai.nbpwr</groupId>
- <artifactId>org-apache-commons-io</artifactId>
- <version>1.3.1-201002241208</version>
- <type>nbm</type>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks.examples</groupId>
- <artifactId>hyracks-integration-tests</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-ipc</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>org.apache.hadoop</groupId>
- <artifactId>hadoop-core</artifactId>
- <version>0.20.2</version>
- </dependency>
- <dependency>
- <groupId>org.apache.hadoop</groupId>
- <artifactId>hadoop-test</artifactId>
- <version>0.20.2</version>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-hdfs-core</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>hyracks-hdfs-core</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>test-jar</type>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>genomix-hyracks</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>genomix-hadoop</artifactId>
- <version>0.2.6-SNAPSHOT</version>
- <type>jar</type>
- <scope>compile</scope>
- </dependency>
- </dependencies>
+ <dependencies>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.8.1</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>pregelix-core</artifactId>
+ <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>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-dataflow-std</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-api</artifactId>
+ <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>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-data-std</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-control-cc</artifactId>
+ <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>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>com.kenai.nbpwr</groupId>
+ <artifactId>org-apache-commons-io</artifactId>
+ <version>1.3.1-201002241208</version>
+ <type>nbm</type>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks.examples</groupId>
+ <artifactId>hyracks-integration-tests</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-ipc</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.hadoop</groupId>
+ <artifactId>hadoop-core</artifactId>
+ <version>0.20.2</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.hadoop</groupId>
+ <artifactId>hadoop-test</artifactId>
+ <version>0.20.2</version>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-hdfs-core</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>hyracks-hdfs-core</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>test-jar</type>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>genomix-hyracks</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>edu.uci.ics.hyracks</groupId>
+ <artifactId>genomix-hadoop</artifactId>
+ <version>0.2.6-SNAPSHOT</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ </dependencies>
- <scm>
- <connection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</connection>
- <developerConnection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</developerConnection>
- <url>http://code.google.com/p/hyracks/source/browse/#svn/trunk/fullstack/pregelix</url>
- </scm>
+ <scm>
+ <connection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</connection>
+ <developerConnection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</developerConnection>
+ <url>http://code.google.com/p/hyracks/source/browse/#svn/trunk/fullstack/pregelix</url>
+ </scm>
- <distributionManagement>
- <repository>
- <id>hyracks-releases</id>
- <url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-releases/</url>
- </repository>
- <snapshotRepository>
- <id>hyracks-snapshots</id>
- <url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-snapshots/</url>
- </snapshotRepository>
- </distributionManagement>
+ <distributionManagement>
+ <repository>
+ <id>hyracks-releases</id>
+ <url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-releases/</url>
+ </repository>
+ <snapshotRepository>
+ <id>hyracks-snapshots</id>
+ <url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-snapshots/</url>
+ </snapshotRepository>
+ </distributionManagement>
- <reporting>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-changelog-plugin</artifactId>
- </plugin>
- </plugins>
- </reporting>
+ <reporting>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-changelog-plugin</artifactId>
+ </plugin>
+ </plugins>
+ </reporting>
- <repositories>
- <repository>
- <id>hyracks-public</id>
- <url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
- </repository>
- <repository>
- <id>jboss-public</id>
- <url>https://repository.jboss.org/nexus/content/groups/public/</url>
- </repository>
- </repositories>
+ <repositories>
+ <repository>
+ <id>hyracks-public</id>
+ <url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
+ </repository>
+ <repository>
+ <id>jboss-public</id>
+ <url>https://repository.jboss.org/nexus/content/groups/public/</url>
+ </repository>
+ </repositories>
- <pluginRepositories>
- <pluginRepository>
- <id>hyracks-public</id>
- <url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
- <releases>
- <updatePolicy>always</updatePolicy>
- </releases>
- </pluginRepository>
- </pluginRepositories>
+ <pluginRepositories>
+ <pluginRepository>
+ <id>hyracks-public</id>
+ <url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
+ <releases>
+ <updatePolicy>always</updatePolicy>
+ </releases>
+ </pluginRepository>
+ </pluginRepositories>
</project>