Update google-cloud-nio to support underscores in bucket names

build.gradle

@@ -13,13 +13,15 @@ plugins {
     id 'jacoco'
     id 'application'
     id 'com.palantir.git-version' version '0.5.1'
-    id 'com.github.johnrengelman.shadow' version '5.1.0'
+    id 'com.github.johnrengelman.shadow' version '8.1.1'
     id "com.github.kt3k.coveralls" version '2.6.3'
     id "org.ajoberstar.grgit" version "5.2.0"
     id "org.ajoberstar.git-publish" version "2.1.1"
 }
 
-mainClassName = "picard.cmdline.PicardCommandLine"
+application {
+    mainClass = "picard.cmdline.PicardCommandLine"
+}
 
 repositories {
     mavenCentral()
@@ -62,7 +64,7 @@ dependencies {
     implementation('com.intel.gkl:gkl:0.8.8') {
         exclude module: 'htsjdk'
     }
-    implementation 'com.google.guava:guava:15.0'
+    implementation 'com.google.guava:guava:32.1.1-jre'
     implementation 'org.apache.commons:commons-math3:3.5'
     implementation 'org.apache.commons:commons-collections4:4.3'
     implementation 'com.github.samtools:htsjdk:' + htsjdkVersion
@@ -71,7 +73,7 @@ dependencies {
     implementation 'org.apache.logging.log4j:log4j-core:2.17.1'
     implementation 'org.openjdk.nashorn:nashorn-core:15.4'
     implementation 'org.apache.commons:commons-lang3:3.6'
-    implementation 'com.google.cloud:google-cloud-nio:0.123.25'
+    implementation 'com.google.cloud:google-cloud-nio:0.127.0'
 
     testImplementation 'org.testng:testng:6.14.3'
 }
@@ -83,8 +85,10 @@ configurations.all {
     }
 }
 
-sourceCompatibility = 1.17
-targetCompatibility = 1.17
+java {
+    sourceCompatibility = 1.17
+    targetCompatibility = 1.17
+}
 
 final isRelease = Boolean.getBoolean("release")
 final gitVersion = gitVersion().replaceAll(".dirty", "")
@@ -95,6 +99,22 @@ group = 'com.github.broadinstitute'
 
 defaultTasks 'all'
 
+distZip {
+    dependsOn 'currentJar'
+}
+
+distTar {
+    dependsOn 'currentJar'
+}
+
+startScripts {
+    dependsOn 'currentJar'
+}
+
+startShadowScripts {
+    dependsOn 'currentJar'
+}
+
 task all(dependsOn: ['jar', 'distZip', 'javadoc', 'shadowJar', 'currentJar', 'picardDoc'])
 
 // Source file names for the picard command line properties file. We select and include only one of
@@ -161,6 +181,10 @@ task picardDoc(type: Javadoc, dependsOn: ['cleanPicardDoc', classes]) {
     options.addStringOption("absolute-version", getVersion())
     options.addStringOption("build-timestamp", new Date().format("dd-mm-yyyy hh:mm:ss"))
     options.addStringOption("verbose")
+    // Avoid 'javadoc: error - invalid flag: -notimestamp'. See:
+    //   - https://github.com/gradle/gradle/issues/11898
+    //   - https://github.com/gradle/gradle/issues/11898#issuecomment-993789034
+    options.noTimestamp(false)
 }
 
 task currentJar(type: Copy){
@@ -263,13 +287,13 @@ jacocoTestReport {
     getAdditionalSourceDirs().from(sourceSets.main.allJava.srcDirs)
 
     reports {
-        xml.enabled = true // coveralls plugin depends on xml format report
-        html.enabled = true
+        xml.required = true // coveralls plugin depends on xml format report
+        html.required = true
     }
 }
 
 wrapper {
-    gradleVersion = '7.5.1'
+    gradleVersion = '8.2.1'
 }
 
 task javadocJar(type: Jar) {
@@ -362,7 +386,7 @@ publish {
 ext.htmlDir = file("build/docs/html")
 
 //update static web docs
-task copyJavadoc(dependsOn: 'javadoc', type: Copy) {
+task copyJavadoc(dependsOn: ['javadoc', 'picardDoc'], type: Copy) {
     from 'build/docs/javadoc'
     into "$htmlDir/javadoc"
 }
@@ -388,3 +412,7 @@ gitPublish {
         } 
     }
 }
+
+gitPublishCopy {
+    dependsOn 'updateGhPages', 'copyJavadoc', 'copyPicardDoc'
+}

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.2.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -205,6 +205,12 @@ set -- \
         org.gradle.wrapper.GradleWrapperMain \
         "$@"
 
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
 # Use "xargs" to parse quoted args.
 #
 # With -n1 it outputs one arg per line, with the quotes and backslashes removed.

src/test/java/picard/nio/GATKBucketUtilsTest.java

@@ -0,0 +1,29 @@
+package picard.nio;
+
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import org.testng.Assert;
+
+import java.net.URI;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+public class GATKBucketUtilsTest {
+
+    @DataProvider
+    public Object[][] getVariousPathsForPrefetching(){
+        return new Object[][]{
+                {"file:///local/file", false},
+                {"gs://abucket/bucket", true},
+                {"gs://abucket_with_underscores", true},
+        };
+    }
+
+    @Test(groups="bucket", dataProvider = "getVariousPathsForPrefetching")
+    public void testIsEligibleForPrefetching(String path, boolean isPrefetchable){
+        final URI uri = URI.create(path);
+        final Path uriPath = Paths.get(uri);
+        Assert.assertEquals(GATKBucketUtils.isEligibleForPrefetching(uriPath), isPrefetchable);
+    }
+}