From a17266d97fc0b253fd43829d4eb0fc74b9a4dfc8 Mon Sep 17 00:00:00 2001 From: Tom White Date: Fri, 8 Mar 2019 17:11:54 +0000 Subject: [PATCH] Update plugins (#92) * Update plugins to latest versions * Formatting --- pom.xml | 12 ++++++------ .../disq/impl/file/HadoopFileSystemWrapper.java | 3 +-- .../org/disq_bio/disq/impl/file/IndexFileMerger.java | 3 +-- .../java/org/disq_bio/disq/impl/file/Merger.java | 3 +-- .../disq/impl/formats/BoundedTraversalUtil.java | 3 +-- .../org/disq_bio/disq/impl/formats/bam/BamSink.java | 7 ++----- .../disq_bio/disq/impl/formats/cram/CramSource.java | 4 +--- .../org/disq_bio/disq/impl/formats/vcf/VcfSink.java | 6 ++---- 8 files changed, 15 insertions(+), 26 deletions(-) diff --git a/pom.xml b/pom.xml index 9a77667..024e87b 100644 --- a/pom.xml +++ b/pom.xml @@ -157,7 +157,7 @@ org.apache.maven.plugins maven-enforcer-plugin - 1.4.1 + 3.0.0-M2 enforce-versions @@ -182,7 +182,7 @@ org.apache.maven.plugins maven-surefire-plugin - 3.0.0-M1 + 3.0.0-M3 org.codehaus.mojo @@ -207,7 +207,7 @@ com.coveo fmt-maven-plugin - 2.5.1 + 2.8 @@ -248,7 +248,7 @@ org.jacoco jacoco-maven-plugin - 0.8.1 + 0.8.3 jacoco-initialize @@ -268,7 +268,7 @@ com.github.spotbugs spotbugs-maven-plugin - 3.1.5 + 3.1.10 src/build/conf/spotbugs-exclude.xml org.disq_bio.disq.- @@ -285,7 +285,7 @@ org.apache.maven.plugins maven-failsafe-plugin - 3.0.0-M1 + 3.0.0-M3 diff --git a/src/main/java/org/disq_bio/disq/impl/file/HadoopFileSystemWrapper.java b/src/main/java/org/disq_bio/disq/impl/file/HadoopFileSystemWrapper.java index 682437b..357833e 100644 --- a/src/main/java/org/disq_bio/disq/impl/file/HadoopFileSystemWrapper.java +++ b/src/main/java/org/disq_bio/disq/impl/file/HadoopFileSystemWrapper.java @@ -152,8 +152,7 @@ public void concat(Configuration conf, List parts, String path) throws I static void concat(List parts, Path outputPath, FileSystem filesystem) throws IOException { org.apache.hadoop.fs.Path[] fsParts = - parts - .stream() + parts.stream() .map(Path::new) .collect(Collectors.toList()) .toArray(new org.apache.hadoop.fs.Path[parts.size()]); diff --git a/src/main/java/org/disq_bio/disq/impl/file/IndexFileMerger.java b/src/main/java/org/disq_bio/disq/impl/file/IndexFileMerger.java index 404b153..c02930a 100644 --- a/src/main/java/org/disq_bio/disq/impl/file/IndexFileMerger.java +++ b/src/main/java/org/disq_bio/disq/impl/file/IndexFileMerger.java @@ -83,8 +83,7 @@ public void mergeParts( try (OutputStream out = fileSystemWrapper.create(conf, outputFile)) { IndexMerger indexMerger = newIndexMerger(out, partLengths.get(i++)); List> callables = - filteredParts - .stream() + filteredParts.stream() .map(part -> (Callable) () -> readIndex(conf, part, header)) .collect(Collectors.toList()); for (Future futureIndex : executorService.invokeAll(callables)) { diff --git a/src/main/java/org/disq_bio/disq/impl/file/Merger.java b/src/main/java/org/disq_bio/disq/impl/file/Merger.java index 403c36e..c3cd1a7 100644 --- a/src/main/java/org/disq_bio/disq/impl/file/Merger.java +++ b/src/main/java/org/disq_bio/disq/impl/file/Merger.java @@ -42,8 +42,7 @@ public void mergeParts( Configuration conf, List fileStatuses, String outputFile) throws IOException { List parts = - fileStatuses - .stream() + fileStatuses.stream() .map(FileSystemWrapper.FileStatus::getPath) .collect(Collectors.toList()); fileSystemWrapper.concat(conf, parts, outputFile); diff --git a/src/main/java/org/disq_bio/disq/impl/formats/BoundedTraversalUtil.java b/src/main/java/org/disq_bio/disq/impl/formats/BoundedTraversalUtil.java index 14d9ff2..84ca6de 100644 --- a/src/main/java/org/disq_bio/disq/impl/formats/BoundedTraversalUtil.java +++ b/src/main/java/org/disq_bio/disq/impl/formats/BoundedTraversalUtil.java @@ -40,8 +40,7 @@ public static QueryInterval[] prepareQueryIntervals( // Convert each SimpleInterval to a QueryInterval final QueryInterval[] convertedIntervals = - rawIntervals - .stream() + rawIntervals.stream() .map( rawInterval -> convertSimpleIntervalToQueryInterval(rawInterval, sequenceDictionary)) diff --git a/src/main/java/org/disq_bio/disq/impl/formats/bam/BamSink.java b/src/main/java/org/disq_bio/disq/impl/formats/bam/BamSink.java index fa7d91a..c2f8861 100644 --- a/src/main/java/org/disq_bio/disq/impl/formats/bam/BamSink.java +++ b/src/main/java/org/disq_bio/disq/impl/formats/bam/BamSink.java @@ -106,14 +106,11 @@ public void save( } List bamParts = - fileSystemWrapper - .listDirectoryStatus(conf, tempPartsDirectory) - .stream() + fileSystemWrapper.listDirectoryStatus(conf, tempPartsDirectory).stream() .filter(fs -> new HiddenFileFilter().test(fs.getPath())) .collect(Collectors.toList()); List partLengths = - bamParts - .stream() + bamParts.stream() .mapToLong(FileSystemWrapper.FileStatus::getLength) .boxed() .collect(Collectors.toList()); diff --git a/src/main/java/org/disq_bio/disq/impl/formats/cram/CramSource.java b/src/main/java/org/disq_bio/disq/impl/formats/cram/CramSource.java index 807f6ec..889c630 100644 --- a/src/main/java/org/disq_bio/disq/impl/formats/cram/CramSource.java +++ b/src/main/java/org/disq_bio/disq/impl/formats/cram/CramSource.java @@ -93,9 +93,7 @@ protected JavaRDD getPathChunks( Map> pathToContainerOffsets = new LinkedHashMap<>(); if (fileSystemWrapper.isDirectory(conf, path)) { List statuses = - fileSystemWrapper - .listDirectoryStatus(conf, path) - .stream() + fileSystemWrapper.listDirectoryStatus(conf, path).stream() .filter(fs -> SamFormat.CRAM.fileMatches(fs.getPath())) .collect(Collectors.toList()); for (FileSystemWrapper.FileStatus status : statuses) { diff --git a/src/main/java/org/disq_bio/disq/impl/formats/vcf/VcfSink.java b/src/main/java/org/disq_bio/disq/impl/formats/vcf/VcfSink.java index f44805c..698ecdb 100644 --- a/src/main/java/org/disq_bio/disq/impl/formats/vcf/VcfSink.java +++ b/src/main/java/org/disq_bio/disq/impl/formats/vcf/VcfSink.java @@ -103,14 +103,12 @@ public void save( } List vcfParts = - fileSystemWrapper - .listDirectoryStatus(jsc.hadoopConfiguration(), tempPartsDirectory) + fileSystemWrapper.listDirectoryStatus(jsc.hadoopConfiguration(), tempPartsDirectory) .stream() .filter(fs -> new HiddenFileFilter().test(fs.getPath())) .collect(Collectors.toList()); List partLengths = - vcfParts - .stream() + vcfParts.stream() .mapToLong(FileSystemWrapper.FileStatus::getLength) .boxed() .collect(Collectors.toList());