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Fix shard ordering bug on some filesystems. #138

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Fix shard ordering bug on some filesystems. #138

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404515f
Fix shard ordering bug on some filesystems.
lbergelson May 29, 2020
370c7fc
Improve read tests to check for content/order instead of just number …
lbergelson Jun 2, 2020
cb1b269
fix formatting
lbergelson Jun 3, 2020
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2 changes: 1 addition & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

<groupId>org.disq-bio</groupId>
<artifactId>disq</artifactId>
<version>0.3.7-SNAPSHOT</version>
<version>0.3.7-bugfix-SNAPSHOT</version>

@heuermh heuermh Jun 2, 2020

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This change isn't necessary for this pull request -- versioning will be handled by the Maven release plugin on the next release cycle.

@lbergelson lbergelson Jun 2, 2020

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Woops! That's funny, I literally told @tedsharpe the same thing on his last PR and then I did it myself...

<name>Disq</name>
<description>A library for manipulating bioinformatics sequencing formats in Apache Spark.</description>
<url>https://github.com/disq-bio/disq</url>
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14 changes: 14 additions & 0 deletions src/main/java/org/disq_bio/disq/impl/file/FileSplitInputFormat.java
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Expand Up @@ -26,7 +26,11 @@
package org.disq_bio.disq.impl.file;

import java.io.IOException;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.mapreduce.InputSplit;
import org.apache.hadoop.mapreduce.JobContext;
import org.apache.hadoop.mapreduce.RecordReader;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
Expand Down Expand Up @@ -84,4 +88,14 @@ public RecordReader<Void, FileSplit> createRecordReader(
InputSplit split, TaskAttemptContext context) {
return new FileSplitRecordReader();
}

/**
* We override this method because super.listStatus returns files in an effectively random order
* on some filesystems. This breaks ordering assumptions and results in data corruption. We sort
* the results here in order to guarantee part files are returned in numeric order.
*/
@Override
protected List<FileStatus> listStatus(final JobContext job) throws IOException {
return super.listStatus(job).stream().sorted().collect(Collectors.toList());
}
}