| commit | 8ed1c1f32167d89e4cc7a1be758d42dd1b1ec8d9 | [log] [tgz] |
|---|---|---|
| author | jianfeng.jia@gmail.com <jianfeng.jia@gmail.com@123451ca-8445-de46-9d55-352943316053> | Tue Jan 29 07:06:20 2013 +0000 |
| committer | jianfeng.jia@gmail.com <jianfeng.jia@gmail.com@123451ca-8445-de46-9d55-352943316053> | Tue Jan 29 07:06:20 2013 +0000 |
| tree | 703efd4aaac04b1b6107a050418d4a3d343c414c | |
| parent | 8f6b228d461e84c8d26a5b609cfc1331a8933bea [diff] |
reconstruct the code directory git-svn-id: https://hyracks.googlecode.com/svn/branches/fullstack_genomix@2737 123451ca-8445-de46-9d55-352943316053
diff --git a/genomix/HyracksCodeFormatProfile.xml b/genomix/genomix-core/HyracksCodeFormatProfile.xml similarity index 100% rename from genomix/HyracksCodeFormatProfile.xml rename to genomix/genomix-core/HyracksCodeFormatProfile.xml
diff --git a/genomix/pom.xml b/genomix/genomix-core/pom.xml similarity index 100% rename from genomix/pom.xml rename to genomix/genomix-core/pom.xml
diff --git a/genomix/src/main/assembly/binary-assembly.xml b/genomix/genomix-core/src/main/assembly/binary-assembly.xml similarity index 100% rename from genomix/src/main/assembly/binary-assembly.xml rename to genomix/genomix-core/src/main/assembly/binary-assembly.xml
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/data/normalizers/Integer64NormalizedKeyComputerFactory.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/normalizers/Integer64NormalizedKeyComputerFactory.java similarity index 100% rename from genomix/src/main/java/edu/uci/ics/genomix/data/normalizers/Integer64NormalizedKeyComputerFactory.java rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/normalizers/Integer64NormalizedKeyComputerFactory.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java similarity index 100% rename from genomix/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/data/serde/ByteSerializerDeserializer.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/serde/ByteSerializerDeserializer.java similarity index 100% rename from genomix/src/main/java/edu/uci/ics/genomix/data/serde/ByteSerializerDeserializer.java rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/serde/ByteSerializerDeserializer.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongBinaryHashFunctionFamily.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongBinaryHashFunctionFamily.java similarity index 100% rename from genomix/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongBinaryHashFunctionFamily.java rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongBinaryHashFunctionFamily.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongHashFunctionFamily.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongHashFunctionFamily.java similarity index 100% rename from genomix/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongHashFunctionFamily.java rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongHashFunctionFamily.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/ConnectorPolicyAssignmentPolicy.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/ConnectorPolicyAssignmentPolicy.java similarity index 100% rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/ConnectorPolicyAssignmentPolicy.java rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/ConnectorPolicyAssignmentPolicy.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/FileScanDescriptor.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/FileScanDescriptor.java similarity index 100% rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/FileScanDescriptor.java rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/FileScanDescriptor.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/GenKmerDescriptor.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/GenKmerDescriptor.java similarity index 100% rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/GenKmerDescriptor.java rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/GenKmerDescriptor.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/KmerSplitOperatorNodePushable.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/KmerSplitOperatorNodePushable.java similarity index 100% rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/KmerSplitOperatorNodePushable.java rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/KmerSplitOperatorNodePushable.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/SplitFrame.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/SplitFrame.java similarity index 100% rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/SplitFrame.java rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/SplitFrame.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/Tester.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/Tester.java similarity index 100% rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/Tester.java rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/Tester.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java similarity index 100% rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java similarity index 100% rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java
diff --git a/genomix/src/main/resources/conf/cluster.properties b/genomix/genomix-core/src/main/resources/conf/cluster.properties similarity index 96% rename from genomix/src/main/resources/conf/cluster.properties rename to genomix/genomix-core/src/main/resources/conf/cluster.properties index c9e87f0..5b2b757 100644 --- a/genomix/src/main/resources/conf/cluster.properties +++ b/genomix/genomix-core/src/main/resources/conf/cluster.properties
@@ -5,7 +5,7 @@ CC_CLUSTERPORT=1099 #The directory of hyracks binaries -HYRACKS_HOME="../../../hyracks" +HYRACKS_HOME="../../../../hyracks" #The tmp directory for cc to install jars CCTMP_DIR=/tmp/t1
diff --git a/genomix/src/main/resources/conf/debugnc.properties b/genomix/genomix-core/src/main/resources/conf/debugnc.properties similarity index 100% rename from genomix/src/main/resources/conf/debugnc.properties rename to genomix/genomix-core/src/main/resources/conf/debugnc.properties
diff --git a/genomix/src/main/resources/conf/master b/genomix/genomix-core/src/main/resources/conf/master similarity index 100% rename from genomix/src/main/resources/conf/master rename to genomix/genomix-core/src/main/resources/conf/master
diff --git a/genomix/src/main/resources/conf/slaves b/genomix/genomix-core/src/main/resources/conf/slaves similarity index 100% rename from genomix/src/main/resources/conf/slaves rename to genomix/genomix-core/src/main/resources/conf/slaves
diff --git a/genomix/src/main/resources/scripts/genomix b/genomix/genomix-core/src/main/resources/scripts/genomix similarity index 100% rename from genomix/src/main/resources/scripts/genomix rename to genomix/genomix-core/src/main/resources/scripts/genomix
diff --git a/genomix/src/main/resources/scripts/genomix.bat b/genomix/genomix-core/src/main/resources/scripts/genomix.bat similarity index 100% rename from genomix/src/main/resources/scripts/genomix.bat rename to genomix/genomix-core/src/main/resources/scripts/genomix.bat
diff --git a/genomix/src/main/resources/scripts/getip.sh b/genomix/genomix-core/src/main/resources/scripts/getip.sh similarity index 100% rename from genomix/src/main/resources/scripts/getip.sh rename to genomix/genomix-core/src/main/resources/scripts/getip.sh
diff --git a/genomix/src/main/resources/scripts/startAllNCs.sh b/genomix/genomix-core/src/main/resources/scripts/startAllNCs.sh similarity index 100% rename from genomix/src/main/resources/scripts/startAllNCs.sh rename to genomix/genomix-core/src/main/resources/scripts/startAllNCs.sh
diff --git a/genomix/src/main/resources/scripts/startCluster.sh b/genomix/genomix-core/src/main/resources/scripts/startCluster.sh similarity index 100% rename from genomix/src/main/resources/scripts/startCluster.sh rename to genomix/genomix-core/src/main/resources/scripts/startCluster.sh
diff --git a/genomix/src/main/resources/scripts/startDebugNc.sh b/genomix/genomix-core/src/main/resources/scripts/startDebugNc.sh similarity index 100% rename from genomix/src/main/resources/scripts/startDebugNc.sh rename to genomix/genomix-core/src/main/resources/scripts/startDebugNc.sh
diff --git a/genomix/src/main/resources/scripts/startcc.sh b/genomix/genomix-core/src/main/resources/scripts/startcc.sh similarity index 100% rename from genomix/src/main/resources/scripts/startcc.sh rename to genomix/genomix-core/src/main/resources/scripts/startcc.sh
diff --git a/genomix/src/main/resources/scripts/startnc.sh b/genomix/genomix-core/src/main/resources/scripts/startnc.sh similarity index 100% rename from genomix/src/main/resources/scripts/startnc.sh rename to genomix/genomix-core/src/main/resources/scripts/startnc.sh
diff --git a/genomix/src/main/resources/scripts/stopAllNCs.sh b/genomix/genomix-core/src/main/resources/scripts/stopAllNCs.sh similarity index 100% rename from genomix/src/main/resources/scripts/stopAllNCs.sh rename to genomix/genomix-core/src/main/resources/scripts/stopAllNCs.sh
diff --git a/genomix/src/main/resources/scripts/stopCluster.sh b/genomix/genomix-core/src/main/resources/scripts/stopCluster.sh similarity index 100% rename from genomix/src/main/resources/scripts/stopCluster.sh rename to genomix/genomix-core/src/main/resources/scripts/stopCluster.sh
diff --git a/genomix/src/main/resources/scripts/stopcc.sh b/genomix/genomix-core/src/main/resources/scripts/stopcc.sh similarity index 100% rename from genomix/src/main/resources/scripts/stopcc.sh rename to genomix/genomix-core/src/main/resources/scripts/stopcc.sh
diff --git a/genomix/src/main/resources/scripts/stopnc.sh b/genomix/genomix-core/src/main/resources/scripts/stopnc.sh similarity index 100% rename from genomix/src/main/resources/scripts/stopnc.sh rename to genomix/genomix-core/src/main/resources/scripts/stopnc.sh
diff --git a/hadoop/actual/conf.xml b/genomix/genomix-hadoop/actual/conf.xml similarity index 100% rename from hadoop/actual/conf.xml rename to genomix/genomix-hadoop/actual/conf.xml
diff --git a/hadoop/actual/result2/.part-00000.crc b/genomix/genomix-hadoop/actual/result2/.part-00000.crc similarity index 100% rename from hadoop/actual/result2/.part-00000.crc rename to genomix/genomix-hadoop/actual/result2/.part-00000.crc Binary files differ
diff --git a/hadoop/actual/result2/part-00000 b/genomix/genomix-hadoop/actual/result2/part-00000 similarity index 100% rename from hadoop/actual/result2/part-00000 rename to genomix/genomix-hadoop/actual/result2/part-00000
diff --git a/hadoop/data/webmap/text.txt b/genomix/genomix-hadoop/data/webmap/text.txt similarity index 100% rename from hadoop/data/webmap/text.txt rename to genomix/genomix-hadoop/data/webmap/text.txt
diff --git a/hadoop/expected/result2 b/genomix/genomix-hadoop/expected/result2 similarity index 100% rename from hadoop/expected/result2 rename to genomix/genomix-hadoop/expected/result2
diff --git a/hadoop/pom.xml b/genomix/genomix-hadoop/pom.xml similarity index 100% rename from hadoop/pom.xml rename to genomix/genomix-hadoop/pom.xml
diff --git a/hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java similarity index 100% rename from hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java rename to genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java
diff --git a/hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java similarity index 100% rename from hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java rename to genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java
diff --git a/hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java similarity index 100% rename from hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java rename to genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java
diff --git a/hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java similarity index 100% rename from hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java rename to genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java
diff --git a/hadoop/src/main/java/edu/uci/ics/graphbuilding/ValueWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/ValueWritable.java similarity index 100% rename from hadoop/src/main/java/edu/uci/ics/graphbuilding/ValueWritable.java rename to genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/ValueWritable.java
diff --git a/hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java similarity index 100% rename from hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java rename to genomix/genomix-hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java
diff --git a/hadoop/src/test/java/edu/uci/ics/utils/TestUtils.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/utils/TestUtils.java similarity index 100% rename from hadoop/src/test/java/edu/uci/ics/utils/TestUtils.java rename to genomix/genomix-hadoop/src/test/java/edu/uci/ics/utils/TestUtils.java