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Posted to commits@systemml.apache.org by mb...@apache.org on 2016/10/08 19:15:43 UTC
[1/2] incubator-systemml git commit: [SYSTEMML-1024] Fix frame csv
write (pass non-default csv properties)
Repository: incubator-systemml
Updated Branches:
refs/heads/master 443467049 -> bb4b7b540
[SYSTEMML-1024] Fix frame csv write (pass non-default csv properties)
Project: http://git-wip-us.apache.org/repos/asf/incubator-systemml/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-systemml/commit/7525bd10
Tree: http://git-wip-us.apache.org/repos/asf/incubator-systemml/tree/7525bd10
Diff: http://git-wip-us.apache.org/repos/asf/incubator-systemml/diff/7525bd10
Branch: refs/heads/master
Commit: 7525bd107451069c13639a92b1c749b6559d6d3c
Parents: 4434670
Author: Matthias Boehm <mb...@us.ibm.com>
Authored: Fri Oct 7 18:50:05 2016 -0700
Committer: Matthias Boehm <mb...@us.ibm.com>
Committed: Sat Oct 8 12:15:00 2016 -0700
----------------------------------------------------------------------
.../apache/sysml/runtime/controlprogram/caching/FrameObject.java | 2 +-
.../sysml/runtime/instructions/cp/VariableCPInstruction.java | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-systemml/blob/7525bd10/src/main/java/org/apache/sysml/runtime/controlprogram/caching/FrameObject.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/apache/sysml/runtime/controlprogram/caching/FrameObject.java b/src/main/java/org/apache/sysml/runtime/controlprogram/caching/FrameObject.java
index effb604..d3fb74c 100644
--- a/src/main/java/org/apache/sysml/runtime/controlprogram/caching/FrameObject.java
+++ b/src/main/java/org/apache/sysml/runtime/controlprogram/caching/FrameObject.java
@@ -264,7 +264,7 @@ public class FrameObject extends CacheableData<FrameBlock>
throws IOException, DMLRuntimeException
{
OutputInfo oinfo = OutputInfo.stringToOutputInfo(ofmt);
- FrameWriter writer = FrameWriterFactory.createFrameWriter(oinfo);
+ FrameWriter writer = FrameWriterFactory.createFrameWriter(oinfo, fprop);
writer.writeFrameToHDFS(_data, fname, getNumRows(), getNumColumns());
}
http://git-wip-us.apache.org/repos/asf/incubator-systemml/blob/7525bd10/src/main/java/org/apache/sysml/runtime/instructions/cp/VariableCPInstruction.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/apache/sysml/runtime/instructions/cp/VariableCPInstruction.java b/src/main/java/org/apache/sysml/runtime/instructions/cp/VariableCPInstruction.java
index 9c45366..22b3a09 100644
--- a/src/main/java/org/apache/sysml/runtime/instructions/cp/VariableCPInstruction.java
+++ b/src/main/java/org/apache/sysml/runtime/instructions/cp/VariableCPInstruction.java
@@ -748,7 +748,7 @@ public class VariableCPInstruction extends CPInstruction
if( input1.getDataType() == DataType.SCALAR ) {
writeScalarToHDFS(ec, fname);
}
- else if( input1.getDataType() == DataType.MATRIX ){
+ else if( input1.getDataType() == DataType.MATRIX ) {
String outFmt = input3.getName();
if (outFmt.equalsIgnoreCase("matrixmarket"))
writeMMFile(ec, fname);
@@ -763,7 +763,7 @@ public class VariableCPInstruction extends CPInstruction
else if( input1.getDataType() == DataType.FRAME ) {
String outFmt = input3.getName();
FrameObject mo = ec.getFrameObject(input1.getName());
- mo.exportData(fname, outFmt);
+ mo.exportData(fname, outFmt, _formatProperties);
}
}
[2/2] incubator-systemml git commit: [SYSTEMML-1023] Fix csv line
parsing (robustness special tokens), test
Posted by mb...@apache.org.
[SYSTEMML-1023] Fix csv line parsing (robustness special tokens), test
Project: http://git-wip-us.apache.org/repos/asf/incubator-systemml/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-systemml/commit/bb4b7b54
Tree: http://git-wip-us.apache.org/repos/asf/incubator-systemml/tree/bb4b7b54
Diff: http://git-wip-us.apache.org/repos/asf/incubator-systemml/diff/bb4b7b54
Branch: refs/heads/master
Commit: bb4b7b540b2be8f5f07ed8c8f85ea873263d4462
Parents: 7525bd1
Author: Matthias Boehm <mb...@us.ibm.com>
Authored: Fri Oct 7 19:09:47 2016 -0700
Committer: Matthias Boehm <mb...@us.ibm.com>
Committed: Sat Oct 8 12:15:08 2016 -0700
----------------------------------------------------------------------
.../sysml/runtime/io/IOUtilFunctions.java | 9 +-
.../TransformFrameEncodeDecodeTest.java | 4 +-
.../TransformFrameEncodeDecodeTokenTest.java | 134 ++++
.../transform/TransformFrameEncodeDecode.dml | 5 +-
.../input/20news/20news.tfspec_recode.json | 2 +
.../transform/input/20news/20news_subset.csv | 733 +++++++++++++++++++
.../functions/transform/ZPackageSuite.java | 1 +
7 files changed, 880 insertions(+), 8 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-systemml/blob/bb4b7b54/src/main/java/org/apache/sysml/runtime/io/IOUtilFunctions.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/apache/sysml/runtime/io/IOUtilFunctions.java b/src/main/java/org/apache/sysml/runtime/io/IOUtilFunctions.java
index b2d25ec..3d41083 100644
--- a/src/main/java/org/apache/sysml/runtime/io/IOUtilFunctions.java
+++ b/src/main/java/org/apache/sysml/runtime/io/IOUtilFunctions.java
@@ -163,7 +163,8 @@ public class IOUtilFunctions
int from = 0, to = 0;
int len = str.length();
while( from < len ) { // for all tokens
- if( str.charAt(from) == CSV_QUOTE_CHAR ) {
+ if( str.charAt(from) == CSV_QUOTE_CHAR
+ && str.indexOf(CSV_QUOTE_CHAR, from+1) > 0 ) {
to = str.indexOf(CSV_QUOTE_CHAR, from+1);
// handle escaped inner quotes, e.g. "aa""a"
while( to+1 < len && str.charAt(to+1)==CSV_QUOTE_CHAR )
@@ -209,7 +210,8 @@ public class IOUtilFunctions
int len = str.length();
int pos = 0;
while( from < len ) { // for all tokens
- if( str.charAt(from) == CSV_QUOTE_CHAR ) {
+ if( str.charAt(from) == CSV_QUOTE_CHAR
+ && str.indexOf(CSV_QUOTE_CHAR, from+1) > 0 ) {
to = str.indexOf(CSV_QUOTE_CHAR, from+1);
// handle escaped inner quotes, e.g. "aa""a"
while( to+1 < len && str.charAt(to+1)==CSV_QUOTE_CHAR )
@@ -256,7 +258,8 @@ public class IOUtilFunctions
int from = 0, to = 0;
int len = str.length();
while( from < len ) { // for all tokens
- if( str.charAt(from) == CSV_QUOTE_CHAR ) {
+ if( str.charAt(from) == CSV_QUOTE_CHAR
+ && str.indexOf(CSV_QUOTE_CHAR, from+1) > 0 ) {
to = str.indexOf(CSV_QUOTE_CHAR, from+1);
// handle escaped inner quotes, e.g. "aa""a"
while( to+1 < len && str.charAt(to+1)==CSV_QUOTE_CHAR )
http://git-wip-us.apache.org/repos/asf/incubator-systemml/blob/bb4b7b54/src/test/java/org/apache/sysml/test/integration/functions/transform/TransformFrameEncodeDecodeTest.java
----------------------------------------------------------------------
diff --git a/src/test/java/org/apache/sysml/test/integration/functions/transform/TransformFrameEncodeDecodeTest.java b/src/test/java/org/apache/sysml/test/integration/functions/transform/TransformFrameEncodeDecodeTest.java
index b676989..68b434b 100644
--- a/src/test/java/org/apache/sysml/test/integration/functions/transform/TransformFrameEncodeDecodeTest.java
+++ b/src/test/java/org/apache/sysml/test/integration/functions/transform/TransformFrameEncodeDecodeTest.java
@@ -160,8 +160,8 @@ public class TransformFrameEncodeDecodeTest extends AutomatedTestBase
programArgs = new String[]{"-explain","-nvargs",
"DATA=" + HOME + "input/" + DATASET,
"TFSPEC=" + HOME + "input/" + SPEC,
- "TFDATA=" + output("tfout"),
- "OFMT=" + ofmt };
+ "TFDATA=" + output("tfout"), "SEP=,",
+ "OFMT=" + ofmt, "OSEP=\",\"" };
OptimizerUtils.ALLOW_FRAME_CSV_REBLOCK = true;
runTest(true, false, null, -1);
http://git-wip-us.apache.org/repos/asf/incubator-systemml/blob/bb4b7b54/src/test/java/org/apache/sysml/test/integration/functions/transform/TransformFrameEncodeDecodeTokenTest.java
----------------------------------------------------------------------
diff --git a/src/test/java/org/apache/sysml/test/integration/functions/transform/TransformFrameEncodeDecodeTokenTest.java b/src/test/java/org/apache/sysml/test/integration/functions/transform/TransformFrameEncodeDecodeTokenTest.java
new file mode 100644
index 0000000..fa89e28
--- /dev/null
+++ b/src/test/java/org/apache/sysml/test/integration/functions/transform/TransformFrameEncodeDecodeTokenTest.java
@@ -0,0 +1,134 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you 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
+ *
+ * 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 org.apache.sysml.test.integration.functions.transform;
+
+import org.junit.Assert;
+import org.junit.Test;
+import org.apache.sysml.api.DMLScript;
+import org.apache.sysml.api.DMLScript.RUNTIME_PLATFORM;
+import org.apache.sysml.hops.OptimizerUtils;
+import org.apache.sysml.runtime.io.FrameReader;
+import org.apache.sysml.runtime.io.FrameReaderFactory;
+import org.apache.sysml.runtime.matrix.data.CSVFileFormatProperties;
+import org.apache.sysml.runtime.matrix.data.FrameBlock;
+import org.apache.sysml.runtime.matrix.data.InputInfo;
+import org.apache.sysml.runtime.util.DataConverter;
+import org.apache.sysml.test.integration.AutomatedTestBase;
+import org.apache.sysml.test.integration.TestConfiguration;
+import org.apache.sysml.test.utils.TestUtils;
+import org.apache.sysml.utils.Statistics;
+
+/**
+ * This test is similar to TransformFrameEncodeDecode test but specifically
+ * tests for various problematic tokens such as ", ', etc.
+ *
+ */
+public class TransformFrameEncodeDecodeTokenTest extends AutomatedTestBase
+{
+ private final static String TEST_NAME1 = "TransformFrameEncodeDecode";
+ private final static String TEST_DIR = "functions/transform/";
+ private final static String TEST_CLASS_DIR = TEST_DIR + TransformFrameEncodeDecodeTokenTest.class.getSimpleName() + "/";
+
+ //dataset and transform tasks without missing values
+ private final static String DATASET1 = "20news/20news_subset.csv";
+ private final static String SPEC1 = "20news/20news.tfspec_recode.json";
+
+ @Override
+ public void setUp() {
+ TestUtils.clearAssertionInformation();
+ addTestConfiguration(TEST_NAME1, new TestConfiguration(TEST_CLASS_DIR, TEST_NAME1, new String[] { "F2" }) );
+ }
+
+ @Test
+ public void test20newsRecodeSingleNodeCSV() {
+ runTransformTest(RUNTIME_PLATFORM.SINGLE_NODE, "csv");
+ }
+
+ @Test
+ public void test20newsRecodeSparkCSV() {
+ runTransformTest(RUNTIME_PLATFORM.SPARK, "csv");
+ }
+
+ @Test
+ public void test20newsRecodeHybridCSV() {
+ runTransformTest(RUNTIME_PLATFORM.HYBRID_SPARK, "csv");
+ }
+
+ /**
+ *
+ * @param rt
+ * @param ofmt
+ * @param dataset
+ */
+ private void runTransformTest( RUNTIME_PLATFORM rt, String ofmt )
+ {
+ //set runtime platform
+ RUNTIME_PLATFORM rtold = rtplatform;
+ boolean csvReblockOld = OptimizerUtils.ALLOW_FRAME_CSV_REBLOCK;
+ rtplatform = rt;
+
+ boolean sparkConfigOld = DMLScript.USE_LOCAL_SPARK_CONFIG;
+ if( rtplatform == RUNTIME_PLATFORM.SPARK || rtplatform == RUNTIME_PLATFORM.HYBRID_SPARK)
+ DMLScript.USE_LOCAL_SPARK_CONFIG = true;
+
+ if( !ofmt.equals("csv") )
+ throw new RuntimeException("Unsupported test output format");
+
+ try
+ {
+ getAndLoadTestConfiguration(TEST_NAME1);
+
+ String HOME = SCRIPT_DIR + TEST_DIR;
+ fullDMLScriptName = HOME + TEST_NAME1 + ".dml";
+ programArgs = new String[]{"-explain","-nvargs",
+ "DATA=" + HOME + "input/" + DATASET1,
+ "TFSPEC=" + HOME + "input/" + SPEC1,
+ "TFDATA=" + output("tfout"), "SEP= ",
+ "OFMT=" + ofmt, "OSEP= " };
+
+ OptimizerUtils.ALLOW_FRAME_CSV_REBLOCK = true;
+ runTest(true, false, null, -1);
+
+ //read input/output and compare
+ FrameReader reader1 = FrameReaderFactory.createFrameReader(InputInfo.CSVInputInfo,
+ new CSVFileFormatProperties(false, " ", false));
+ FrameBlock fb1 = reader1.readFrameFromHDFS(HOME + "input/" + DATASET1, -1L, -1L);
+ FrameReader reader2 = FrameReaderFactory.createFrameReader(InputInfo.CSVInputInfo,
+ new CSVFileFormatProperties(false, " ", false));
+ FrameBlock fb2 = reader2.readFrameFromHDFS(output("tfout"), -1L, -1L);
+ String[][] R1 = DataConverter.convertToStringFrame(fb1);
+ String[][] R2 = DataConverter.convertToStringFrame(fb2);
+ TestUtils.compareFrames(R1, R2, R1.length, R1[0].length);
+
+ if( rt == RUNTIME_PLATFORM.HYBRID_SPARK ) {
+ Assert.assertEquals("Wrong number of executed Spark instructions: " +
+ Statistics.getNoOfExecutedSPInst(), new Long(2), new Long(Statistics.getNoOfExecutedSPInst()));
+ }
+ }
+ catch(Exception ex) {
+ throw new RuntimeException(ex);
+ }
+ finally {
+ rtplatform = rtold;
+ DMLScript.USE_LOCAL_SPARK_CONFIG = sparkConfigOld;
+ OptimizerUtils.ALLOW_FRAME_CSV_REBLOCK = csvReblockOld;
+ }
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-systemml/blob/bb4b7b54/src/test/scripts/functions/transform/TransformFrameEncodeDecode.dml
----------------------------------------------------------------------
diff --git a/src/test/scripts/functions/transform/TransformFrameEncodeDecode.dml b/src/test/scripts/functions/transform/TransformFrameEncodeDecode.dml
index 48c3929..0b2b6b7 100644
--- a/src/test/scripts/functions/transform/TransformFrameEncodeDecode.dml
+++ b/src/test/scripts/functions/transform/TransformFrameEncodeDecode.dml
@@ -18,8 +18,7 @@
# under the License.
#
#-------------------------------------------------------------
-
-F1 = read($DATA, data_type="frame", format="csv");
+F1 = read($DATA, data_type="frame", format="csv", sep=$SEP);
jspec = read($TFSPEC, data_type="scalar", value_type="string");
[X, M] = transformencode(target=F1, spec=jspec);
@@ -28,5 +27,5 @@ if(1==1){}
F2 = transformdecode(target=X, spec=jspec, meta=M);
-write(F2, $TFDATA, format=$OFMT);
+write(F2, $TFDATA, format=$OFMT, sep=$OSEP);
http://git-wip-us.apache.org/repos/asf/incubator-systemml/blob/bb4b7b54/src/test/scripts/functions/transform/input/20news/20news.tfspec_recode.json
----------------------------------------------------------------------
diff --git a/src/test/scripts/functions/transform/input/20news/20news.tfspec_recode.json b/src/test/scripts/functions/transform/input/20news/20news.tfspec_recode.json
new file mode 100644
index 0000000..dbe0f6b
--- /dev/null
+++ b/src/test/scripts/functions/transform/input/20news/20news.tfspec_recode.json
@@ -0,0 +1,2 @@
+{
+ "ids": true, "recode": [ 1, 2 ] }
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-systemml/blob/bb4b7b54/src/test/scripts/functions/transform/input/20news/20news_subset.csv
----------------------------------------------------------------------
diff --git a/src/test/scripts/functions/transform/input/20news/20news_subset.csv b/src/test/scripts/functions/transform/input/20news/20news_subset.csv
new file mode 100644
index 0000000..18a5c7f
--- /dev/null
+++ b/src/test/scripts/functions/transform/input/20news/20news_subset.csv
@@ -0,0 +1,733 @@
+20news-bydate-test/alt.atheism/53068 " 8
+20news-bydate-test/alt.atheism/53068 # 1
+20news-bydate-test/alt.atheism/53068 & 1
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+20news-bydate-test/alt.atheism/53068 ( 2
+20news-bydate-test/alt.atheism/53068 ) 3
+20news-bydate-test/alt.atheism/53068 , 7
+20news-bydate-test/alt.atheism/53068 . 16
+20news-bydate-test/alt.atheism/53068 12 1
+20news-bydate-test/alt.atheism/53068 153 1
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+20news-bydate-test/alt.atheism/53068 2 1
+20news-bydate-test/alt.atheism/53068 735242337 1
+20news-bydate-test/alt.atheism/53068 : 7
+20news-bydate-test/alt.atheism/53068 < 1
+20news-bydate-test/alt.atheism/53068 > 8
+20news-bydate-test/alt.atheism/53068 @ 3
+20news-bydate-test/alt.atheism/53068 AT 1
+20news-bydate-test/alt.atheism/53068 Ark 2
+20news-bydate-test/alt.atheism/53068 Atonement 1
+20news-bydate-test/alt.atheism/53068 Covenant 2
+20news-bydate-test/alt.atheism/53068 Day 1
+20news-bydate-test/alt.atheism/53068 Dean 1
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\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-systemml/blob/bb4b7b54/src/test_suites/java/org/apache/sysml/test/integration/functions/transform/ZPackageSuite.java
----------------------------------------------------------------------
diff --git a/src/test_suites/java/org/apache/sysml/test/integration/functions/transform/ZPackageSuite.java b/src/test_suites/java/org/apache/sysml/test/integration/functions/transform/ZPackageSuite.java
index 10a2518..1996b01 100644
--- a/src/test_suites/java/org/apache/sysml/test/integration/functions/transform/ZPackageSuite.java
+++ b/src/test_suites/java/org/apache/sysml/test/integration/functions/transform/ZPackageSuite.java
@@ -34,6 +34,7 @@ import org.junit.runners.Suite;
TransformFrameApplyTest.class,
TransformFrameEncodeApplyTest.class,
TransformFrameEncodeDecodeTest.class,
+ TransformFrameEncodeDecodeTokenTest.class,
TransformReadMetaTest.class,
TransformTest.class,
})