Update plugins (#92)

* Update plugins to latest versions * Formatting
disq-bio · Mar 8, 2019 · a17266d · a17266d
1 parent 6b61a9b
commit a17266d
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Showing 8 changed files with 15 additions and 26 deletions.
diff --git a/pom.xml b/pom.xml
@@ -157,7 +157,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-enforcer-plugin</artifactId>
-                <version>1.4.1</version>
+                <version>3.0.0-M2</version>
                 <executions>
                     <execution>
                         <id>enforce-versions</id>
@@ -182,7 +182,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
-                <version>3.0.0-M1</version>
+                <version>3.0.0-M3</version>
             </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
@@ -207,7 +207,7 @@
                 <!-- If this fails the build, type 'mvn fmt:format' from the command line to reformat code. -->
                 <groupId>com.coveo</groupId>
                 <artifactId>fmt-maven-plugin</artifactId>
-                <version>2.5.1</version>
+                <version>2.8</version>
                 <executions>
                     <execution>
                         <goals>
@@ -248,7 +248,7 @@
             <plugin>
                 <groupId>org.jacoco</groupId>
                 <artifactId>jacoco-maven-plugin</artifactId>
-                <version>0.8.1</version>
+                <version>0.8.3</version>
                 <executions>
                     <execution>
                         <id>jacoco-initialize</id>
@@ -268,7 +268,7 @@
             <plugin>
                 <groupId>com.github.spotbugs</groupId>
                 <artifactId>spotbugs-maven-plugin</artifactId>
-                <version>3.1.5</version>
+                <version>3.1.10</version>
                 <configuration>
                     <excludeFilterFile>src/build/conf/spotbugs-exclude.xml</excludeFilterFile>
                     <onlyAnalyze>org.disq_bio.disq.-</onlyAnalyze>
@@ -285,7 +285,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-failsafe-plugin</artifactId>
-                <version>3.0.0-M1</version>
+                <version>3.0.0-M3</version>
                 <executions>
                     <execution>
                         <goals>

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
@@ -152,8 +152,7 @@ public void concat(Configuration conf, List<String> parts, String path) throws I
   static void concat(List<String> 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
@@ -83,8 +83,7 @@ public void mergeParts(
     try (OutputStream out = fileSystemWrapper.create(conf, outputFile)) {
       IndexMerger<I> indexMerger = newIndexMerger(out, partLengths.get(i++));
       List<Callable<I>> callables =
-          filteredParts
-              .stream()
+          filteredParts.stream()
               .map(part -> (Callable<I>) () -> readIndex(conf, part, header))
               .collect(Collectors.toList());
       for (Future<I> 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
@@ -42,8 +42,7 @@ public void mergeParts(
       Configuration conf, List<FileSystemWrapper.FileStatus> fileStatuses, String outputFile)
       throws IOException {
     List<String> 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
@@ -40,8 +40,7 @@ public static <T extends Locatable> 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
@@ -106,14 +106,11 @@ public void save(
     }
 
     List<FileSystemWrapper.FileStatus> bamParts =
-        fileSystemWrapper
-            .listDirectoryStatus(conf, tempPartsDirectory)
-            .stream()
+        fileSystemWrapper.listDirectoryStatus(conf, tempPartsDirectory).stream()
             .filter(fs -> new HiddenFileFilter().test(fs.getPath()))
             .collect(Collectors.toList());
     List<Long> 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
@@ -93,9 +93,7 @@ protected JavaRDD<PathChunk> getPathChunks(
     Map<String, NavigableSet<Long>> pathToContainerOffsets = new LinkedHashMap<>();
     if (fileSystemWrapper.isDirectory(conf, path)) {
       List<FileSystemWrapper.FileStatus> 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
@@ -103,14 +103,12 @@ public void save(
     }
 
     List<FileSystemWrapper.FileStatus> vcfParts =
-        fileSystemWrapper
-            .listDirectoryStatus(jsc.hadoopConfiguration(), tempPartsDirectory)
+        fileSystemWrapper.listDirectoryStatus(jsc.hadoopConfiguration(), tempPartsDirectory)
             .stream()
             .filter(fs -> new HiddenFileFilter().test(fs.getPath()))
             .collect(Collectors.toList());
     List<Long> partLengths =
-        vcfParts
-            .stream()
+        vcfParts.stream()
             .mapToLong(FileSystemWrapper.FileStatus::getLength)
             .boxed()
             .collect(Collectors.toList());