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Posted to reviews@spark.apache.org by ProtD <gi...@git.apache.org> on 2017/08/07 17:42:16 UTC
[GitHub] spark pull request #18872: [MLlib] Fix writing LibSVM
GitHub user ProtD opened a pull request:
https://github.com/apache/spark/pull/18872
[MLlib] Fix writing LibSVM
## What changes were proposed in this pull request?
Check the option "numFeatures" only when reading LibSVM, not when writing. When writing, Spark was raising an exception. After the change it will ignore the option completely. @liancheng @HyukjinKwon
(Maybe the usage should be forbidden when writing, in a major version change?).
## How was this patch tested?
Manual test, that loading and writing LibSVM files work fine, both with and without the numFeatures option.
Please review http://spark.apache.org/contributing.html before opening a pull request.
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/ProtD/spark master
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/18872.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #18872
----
commit 3b43de07ea43b341aa782d629dff1e5da970916f
Author: Jan Vrsovsky <ja...@firma.seznam.cz>
Date: 2017-08-07T16:24:11Z
check numFeatures only when reading LibSVM -- not when writing
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[GitHub] spark pull request #18872: [SPARK-21723][ML] Fix writing LibSVM (key not fou...
Posted by WeichenXu123 <gi...@git.apache.org>.
Github user WeichenXu123 commented on a diff in the pull request:
https://github.com/apache/spark/pull/18872#discussion_r133081682
--- Diff: mllib/src/test/scala/org/apache/spark/ml/source/libsvm/LibSVMRelationSuite.scala ---
@@ -109,14 +112,15 @@ class LibSVMRelationSuite extends SparkFunSuite with MLlibTestSparkContext {
test("write libsvm data and read it again") {
val df = spark.read.format("libsvm").load(path)
val tempDir2 = new File(tempDir, "read_write_test")
--- End diff --
I suggest the temp dir name to be `Identifiable.randomUID("read_write_test")`. Avoid conflicts with other parallel running tests.
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM (key not found: numFeatures)
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18872
**[Test build #80508 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80508/testReport)** for PR 18872 at commit [`b86bb44`](https://github.com/apache/spark/commit/b86bb446581e057637e9639eeda5d046ce0b57fa).
* This patch **fails Scala style tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM (key not found: numFeatures)
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/18872
Merged build finished. Test PASSed.
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[GitHub] spark pull request #18872: [SPARK-21723][ML] Fix writing LibSVM (key not fou...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/18872
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM (key not found: numFeatures)
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18872
**[Test build #80508 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80508/testReport)** for PR 18872 at commit [`b86bb44`](https://github.com/apache/spark/commit/b86bb446581e057637e9639eeda5d046ce0b57fa).
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[GitHub] spark pull request #18872: [SPARK-21723][ML] Fix writing LibSVM (key not fou...
Posted by ProtD <gi...@git.apache.org>.
Github user ProtD commented on a diff in the pull request:
https://github.com/apache/spark/pull/18872#discussion_r133150156
--- Diff: mllib/src/test/scala/org/apache/spark/ml/source/libsvm/LibSVMRelationSuite.scala ---
@@ -109,14 +112,15 @@ class LibSVMRelationSuite extends SparkFunSuite with MLlibTestSparkContext {
test("write libsvm data and read it again") {
val df = spark.read.format("libsvm").load(path)
val tempDir2 = new File(tempDir, "read_write_test")
--- End diff --
`Utils.createTempDir` seems to be a nicer way. The directory is automatically deleted when VM shuts down, so I believe no manual cleanup (cf. comment lower) is needed.
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[GitHub] spark issue #18872: [SPARK-21723][ML] Fix writing LibSVM (key not found: num...
Posted by ProtD <gi...@git.apache.org>.
Github user ProtD commented on the issue:
https://github.com/apache/spark/pull/18872
@srowen Ok, I created and linked a JIRA.
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[GitHub] spark issue #18872: [SPARK-21723][ML] Fix writing LibSVM (key not found: num...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18872
**[Test build #80676 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80676/testReport)** for PR 18872 at commit [`7530f00`](https://github.com/apache/spark/commit/7530f0029bfac609b2ee19bce54977f1cf993ba3).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark pull request #18872: [MLlib] Fix writing LibSVM (key not found: numFea...
Posted by ProtD <gi...@git.apache.org>.
Github user ProtD commented on a diff in the pull request:
https://github.com/apache/spark/pull/18872#discussion_r132671477
--- Diff: mllib/src/test/scala/org/apache/spark/ml/source/libsvm/LibSVMRelationSuite.scala ---
@@ -126,6 +130,29 @@ class LibSVMRelationSuite extends SparkFunSuite with MLlibTestSparkContext {
}
}
+ test("write libsvm data from scratch and read it again") {
+ val rawData = new java.util.ArrayList[Row]()
+ rawData.add(Row(1.0, Vectors.sparse(3, Seq((0, 2.0), (1, 3.0)))))
+ rawData.add(Row(4.0, Vectors.sparse(3, Seq((0, 5.0), (2, 6.0)))))
+
--- End diff --
Fixed.
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[GitHub] spark pull request #18872: [MLlib] Fix writing LibSVM (key not found: numFea...
Posted by srowen <gi...@git.apache.org>.
Github user srowen commented on a diff in the pull request:
https://github.com/apache/spark/pull/18872#discussion_r132647596
--- Diff: mllib/src/test/scala/org/apache/spark/ml/source/libsvm/LibSVMRelationSuite.scala ---
@@ -126,6 +130,29 @@ class LibSVMRelationSuite extends SparkFunSuite with MLlibTestSparkContext {
}
}
+ test("write libsvm data from scratch and read it again") {
+ val rawData = new java.util.ArrayList[Row]()
+ rawData.add(Row(1.0, Vectors.sparse(3, Seq((0, 2.0), (1, 3.0)))))
+ rawData.add(Row(4.0, Vectors.sparse(3, Seq((0, 5.0), (2, 6.0)))))
+
--- End diff --
Subtle: it didn't like the whitespace on this line
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM (key not found: numFeatures)
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/18872
Merged build finished. Test FAILed.
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM (key not found: numFeatures)
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18872
**[Test build #80533 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80533/testReport)** for PR 18872 at commit [`38da77d`](https://github.com/apache/spark/commit/38da77dda5edf82f33fc0702154ef3989bae559d).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM (key not found: numFeatures)
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18872
**[Test build #80533 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80533/testReport)** for PR 18872 at commit [`38da77d`](https://github.com/apache/spark/commit/38da77dda5edf82f33fc0702154ef3989bae559d).
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[GitHub] spark issue #18872: [SPARK-21723][ML] Fix writing LibSVM (key not found: num...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18872
**[Test build #80676 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80676/testReport)** for PR 18872 at commit [`7530f00`](https://github.com/apache/spark/commit/7530f0029bfac609b2ee19bce54977f1cf993ba3).
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[GitHub] spark pull request #18872: [SPARK-21723][ML] Fix writing LibSVM (key not fou...
Posted by srowen <gi...@git.apache.org>.
Github user srowen commented on a diff in the pull request:
https://github.com/apache/spark/pull/18872#discussion_r133135541
--- Diff: mllib/src/test/scala/org/apache/spark/ml/source/libsvm/LibSVMRelationSuite.scala ---
@@ -109,14 +112,15 @@ class LibSVMRelationSuite extends SparkFunSuite with MLlibTestSparkContext {
test("write libsvm data and read it again") {
val df = spark.read.format("libsvm").load(path)
val tempDir2 = new File(tempDir, "read_write_test")
--- End diff --
Use `Utils.createTempDir`
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM
Posted by ProtD <gi...@git.apache.org>.
Github user ProtD commented on the issue:
https://github.com/apache/spark/pull/18872
@srowen It worked in v2.0, but was broken probably in v2.2.0 by b3d39620c563e5f6a32a4082aa3908e1009c17d2. Current unit tests check writing only for dataframes which were previously read from a LibSVM format, not general ones. (And I guess people don't write LibSVMs very often - that may be why nobody has reported it.)
@WeichenXu123 Yes, good idea, will do it!
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM (key not found: numFeatures)
Posted by srowen <gi...@git.apache.org>.
Github user srowen commented on the issue:
https://github.com/apache/spark/pull/18872
@ProtD this needs a JIRA or else needs to be linked to whatever one you opened, in the title
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/18872
Can one of the admins verify this patch?
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM
Posted by ProtD <gi...@git.apache.org>.
Github user ProtD commented on the issue:
https://github.com/apache/spark/pull/18872
To reproduce the bug on v2.2 and v2.3:
```scala
import org.apache.spark.ml.linalg.Vectors
val rawData = Seq((1.0, Vectors.sparse(3, Seq((0, 2.0), (1, 3.0)))),
(4.0, Vectors.sparse(3, Seq((0, 5.0), (2, 6.0)))))
val dfTemp = spark.sparkContext.parallelize(rawData).toDF("label", "features")
dfTemp.coalesce(1).write.format("libsvm").save("...filename...")
```
This causes `java.util.NoSuchElementException: key not found: numFeatures`.
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[GitHub] spark pull request #18872: [SPARK-21723][ML] Fix writing LibSVM (key not fou...
Posted by WeichenXu123 <gi...@git.apache.org>.
Github user WeichenXu123 commented on a diff in the pull request:
https://github.com/apache/spark/pull/18872#discussion_r133082255
--- Diff: mllib/src/test/scala/org/apache/spark/ml/source/libsvm/LibSVMRelationSuite.scala ---
@@ -109,14 +112,15 @@ class LibSVMRelationSuite extends SparkFunSuite with MLlibTestSparkContext {
test("write libsvm data and read it again") {
val df = spark.read.format("libsvm").load(path)
val tempDir2 = new File(tempDir, "read_write_test")
- val writepath = tempDir2.toURI.toString
+ val writePath = tempDir2.toURI.toString
// TODO: Remove requirement to coalesce by supporting multiple reads.
- df.coalesce(1).write.format("libsvm").mode(SaveMode.Overwrite).save(writepath)
+ df.coalesce(1).write.format("libsvm").mode(SaveMode.Overwrite).save(writePath)
- val df2 = spark.read.format("libsvm").load(writepath)
+ val df2 = spark.read.format("libsvm").load(writePath)
val row1 = df2.first()
val v = row1.getAs[SparseVector](1)
assert(v == Vectors.sparse(6, Seq((0, 1.0), (2, 2.0), (4, 3.0))))
+ Utils.deleteRecursively(tempDir2)
--- End diff --
You can remove this cleanup I think. The test framework will clean temp dir automatically I think.
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[GitHub] spark pull request #18872: [SPARK-21723][ML] Fix writing LibSVM (key not fou...
Posted by WeichenXu123 <gi...@git.apache.org>.
Github user WeichenXu123 commented on a diff in the pull request:
https://github.com/apache/spark/pull/18872#discussion_r133081995
--- Diff: mllib/src/test/scala/org/apache/spark/ml/source/libsvm/LibSVMRelationSuite.scala ---
@@ -109,14 +112,15 @@ class LibSVMRelationSuite extends SparkFunSuite with MLlibTestSparkContext {
test("write libsvm data and read it again") {
val df = spark.read.format("libsvm").load(path)
val tempDir2 = new File(tempDir, "read_write_test")
- val writepath = tempDir2.toURI.toString
+ val writePath = tempDir2.toURI.toString
--- End diff --
use `tempDir2.getPath`
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM
Posted by srowen <gi...@git.apache.org>.
Github user srowen commented on the issue:
https://github.com/apache/spark/pull/18872
Better title please?
See http://spark.apache.org/contributing.html
How does this work at all now?
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[GitHub] spark issue #18872: [SPARK-21723][ML] Fix writing LibSVM (key not found: num...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/18872
Merged build finished. Test PASSed.
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[GitHub] spark issue #18872: [SPARK-21723][ML] Fix writing LibSVM (key not found: num...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/18872
Test PASSed.
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM (key not found: numFeatures)
Posted by ProtD <gi...@git.apache.org>.
Github user ProtD commented on the issue:
https://github.com/apache/spark/pull/18872
I added the unit test, please review.
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM (key not found: numFeatures)
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/18872
Test FAILed.
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Test FAILed.
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM (key not found: numFeatures)
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/18872
Test PASSed.
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Test PASSed.
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[GitHub] spark issue #18872: [MLlib] Fix writing LibSVM (key not found: numFeatures)
Posted by HyukjinKwon <gi...@git.apache.org>.
Github user HyukjinKwon commented on the issue:
https://github.com/apache/spark/pull/18872
ok to test
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