Merge pull request #6 from broadinstitute/ks_impl

More impl

alfre-v0-bom/pom.xml

@@ -12,7 +12,6 @@
     <maven.compiler.source>1.8</maven.compiler.source>
     <maven.compiler.target>1.8</maven.compiler.target>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <junit.jupiter.version>5.3.1</junit.jupiter.version>
     <slf4j.version>1.7.25</slf4j.version>
   </properties>
 
@@ -30,18 +29,8 @@
       </dependency>
       <dependency>
         <groupId>org.junit.jupiter</groupId>
-        <artifactId>junit-jupiter-api</artifactId>
-        <version>${junit.jupiter.version}</version>
-      </dependency>
-      <dependency>
-        <groupId>org.junit.jupiter</groupId>
-        <artifactId>junit-jupiter-params</artifactId>
-        <version>${junit.jupiter.version}</version>
-      </dependency>
-      <dependency>
-        <groupId>org.junit.jupiter</groupId>
-        <artifactId>junit-jupiter-engine</artifactId>
-        <version>${junit.jupiter.version}</version>
+        <artifactId>junit-jupiter</artifactId>
+        <version>5.4.0</version>
       </dependency>
       <dependency>
         <groupId>org.mockito</groupId>

alfre-v0-cli/pom.xml

@@ -43,17 +43,7 @@
     </dependency>
     <dependency>
       <groupId>org.junit.jupiter</groupId>
-      <artifactId>junit-jupiter-api</artifactId>
-      <scope>test</scope>
-    </dependency>
-    <dependency>
-      <groupId>org.junit.jupiter</groupId>
-      <artifactId>junit-jupiter-params</artifactId>
-      <scope>test</scope>
-    </dependency>
-    <dependency>
-      <groupId>org.junit.jupiter</groupId>
-      <artifactId>junit-jupiter-engine</artifactId>
+      <artifactId>junit-jupiter</artifactId>
       <scope>test</scope>
     </dependency>
     <dependency>

alfre-v0-cli/src/main/java/alfre/v0/cli/MainRunner.java

@@ -70,12 +70,12 @@ private static boolean runLsPath(final LsOptions lsOptions, final Path path) {
         final String[] columns = {
           String.valueOf(attributes.size()),
           String.valueOf(attributes.lastModifiedTime()),
-          CloudPaths.showAbsolute(path),
+          CloudPaths.toAbsoluteString(path),
           attributes.fileHash() == null ? "" : attributes.fileHash(),
         };
         System.out.println(String.join("\t", columns));
       } else {
-        System.out.println(CloudPaths.showAbsolute(path));
+        System.out.println(CloudPaths.toAbsoluteString(path));
       }
       return false;
     } catch (final Exception exception) {
@@ -102,7 +102,7 @@ private static boolean runCpPath(
         System.out.println(
             String.format(
                 "%s -> %s",
-                CloudPaths.showAbsolute(sourcePath), CloudPaths.showAbsolute(targetPath)));
+                CloudPaths.toAbsoluteString(sourcePath), CloudPaths.toAbsoluteString(targetPath)));
       }
       if (cpOptions.isDoModifications()) {
         final Path parent = targetPath.getParent();
@@ -132,7 +132,7 @@ private static boolean runRmFile(final RmOptions rmOptions, final String filePat
   private static boolean runRmPath(final RmOptions rmOptions, final Path path) {
     try {
       if (!rmOptions.isDoModifications() || rmOptions.getVerbosity() == Verbosity.VERBOSE) {
-        System.out.println(CloudPaths.showAbsolute(path));
+        System.out.println(CloudPaths.toAbsoluteString(path));
       }
       if (rmOptions.isDoModifications()) {
         Files.deleteIfExists(path);

alfre-v0-spi/pom.xml

@@ -30,17 +30,7 @@
   <dependencies>
     <dependency>
       <groupId>org.junit.jupiter</groupId>
-      <artifactId>junit-jupiter-api</artifactId>
-      <scope>test</scope>
-    </dependency>
-    <dependency>
-      <groupId>org.junit.jupiter</groupId>
-      <artifactId>junit-jupiter-params</artifactId>
-      <scope>test</scope>
-    </dependency>
-    <dependency>
-      <groupId>org.junit.jupiter</groupId>
-      <artifactId>junit-jupiter-engine</artifactId>
+      <artifactId>junit-jupiter</artifactId>
       <scope>test</scope>
     </dependency>
     <dependency>

alfre-v0-spi/src/main/java/alfre/v0/spi/CloudFileProvider.java

@@ -3,7 +3,9 @@
 import java.nio.channels.ReadableByteChannel;
 import java.nio.channels.WritableByteChannel;
 import java.nio.file.CopyOption;
+import java.nio.file.LinkOption;
 import java.nio.file.OpenOption;
+import java.nio.file.Path;
 import java.util.Collection;
 import java.util.Optional;
 
@@ -45,4 +47,11 @@ WritableByteChannel write(
 
   Optional<CloudRegularFileAttributes> fileAttributes(CloudPath<CloudHostT> cloudPath)
       throws Exception;
+
+  @SuppressWarnings({"unused", "RedundantThrows"})
+  default Path toRealPath(
+      final CloudPath<CloudHostT> cloudPath, final Collection<? extends LinkOption> options)
+      throws Exception {
+    return cloudPath.toAbsolutePath();
+  }
 }

alfre-v0-spi/src/main/java/alfre/v0/spi/CloudFileSystemProvider.java

@@ -252,14 +252,14 @@ public <A extends BasicFileAttributes> A readAttributes(
       return (A) attributes;
     }
 
-    final CloudFileSystem<CloudHostT> fileSystem = cloudPath.getFileSystem();
-    final CloudFileProvider<CloudHostT> fileProvider = fileSystem.getFileProvider();
-    final CloudRetry retry = fileSystem.getRetry();
-
     if (checkDirectoryExists(cloudPath)) {
       return (A) CloudPseudoDirectoryAttributes.INSTANCE;
     } else {
       try {
+        final CloudFileSystem<CloudHostT> fileSystem = cloudPath.getFileSystem();
+        final CloudFileProvider<CloudHostT> fileProvider = fileSystem.getFileProvider();
+        final CloudRetry retry = fileSystem.getRetry();
+
         return (A)
             retry
                 .runWithRetries(() -> fileProvider.fileAttributes(cloudPath))
@@ -282,6 +282,25 @@ public void setAttribute(
     throw new UnsupportedOperationException();
   }
 
+  /**
+   * Returns the <em>real</em> path of an existing file.
+   *
+   * @see Path#toRealPath(java.nio.file.LinkOption...)
+   */
+  public Path toRealPath(final CloudPath<CloudHostT> cloudPath, final LinkOption... options)
+      throws IOException {
+    try {
+      final CloudFileSystem<CloudHostT> fileSystem = cloudPath.getFileSystem();
+      final CloudFileProvider<CloudHostT> fileProvider = fileSystem.getFileProvider();
+      final CloudRetry retry = fileSystem.getRetry();
+      final Collection<LinkOption> optionsCollection = Arrays.asList(options);
+
+      return retry.runWithRetries(() -> fileProvider.toRealPath(cloudPath, optionsCollection));
+    } catch (final CloudRetryException cloudRetryException) {
+      throw cloudRetryException.getCauseIoException();
+    }
+  }
+
   private boolean checkDirectoryExists(final CloudPath<CloudHostT> cloudPath) throws IOException {
     try {
       final CloudFileSystem<CloudHostT> fileSystem = cloudPath.getFileSystem();

alfre-v0-spi/src/main/java/alfre/v0/spi/CloudPath.java

@@ -1,6 +1,7 @@
 package alfre.v0.spi;
 
 import java.io.File;
+import java.io.IOException;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.nio.file.LinkOption;
@@ -234,8 +235,8 @@ public CloudPath<CloudHostT> toAbsolutePath() {
   }
 
   @Override
-  public CloudPath<CloudHostT> toRealPath(final LinkOption... options) {
-    return toAbsolutePath();
+  public Path toRealPath(final LinkOption... options) throws IOException {
+    return this.fileSystem.provider().toRealPath(this, options);
   }
 
   @Override

alfre-v0-test/pom.xml

@@ -30,17 +30,7 @@
   <dependencies>
     <dependency>
       <groupId>org.junit.jupiter</groupId>
-      <artifactId>junit-jupiter-api</artifactId>
-      <scope>test</scope>
-    </dependency>
-    <dependency>
-      <groupId>org.junit.jupiter</groupId>
-      <artifactId>junit-jupiter-params</artifactId>
-      <scope>test</scope>
-    </dependency>
-    <dependency>
-      <groupId>org.junit.jupiter</groupId>
-      <artifactId>junit-jupiter-engine</artifactId>
+      <artifactId>junit-jupiter</artifactId>
       <scope>test</scope>
     </dependency>
     <dependency>

alfre-v0-util/src/main/java/alfre/v0/util/CloudFiles.java

@@ -19,7 +19,7 @@ public static Stream<Path> listRegularFiles(final Path path) throws IOException
   /** Lists all files under a path. */
   public static Stream<PathPair> relativeFiles(final Path sourcePath, final Path targetPath)
       throws IOException {
-    return relativeFiles(sourcePath, targetPath, CloudPaths::showRelative);
+    return relativeFiles(sourcePath, targetPath, CloudPaths::toRelativeString);
   }
 
   /** Returns all regular files under sourcePath mapped relatively to targetPath. */

alfre-v0-util/src/main/java/alfre/v0/util/CloudPaths.java

@@ -11,10 +11,9 @@
 public class CloudPaths {
 
   /**
-   * Parses a path in a way reciprocal with
-   * [[cloud.nio.util.CloudNioPaths#showAbsolute(java.nio.file.Path)]].
+   * Parses a path in a way reciprocal with {@link #toAbsoluteString toAbsoluteString}.
    *
-   * @see alfre.v0.util.CloudPaths#showAbsolute(java.nio.file.Path)
+   * @see alfre.v0.util.CloudPaths#toAbsoluteString(java.nio.file.Path)
    * @see alfre.v0.spi.CloudPath#getUriAsString()
    */
   public static Path get(final String filePath) {
@@ -34,13 +33,13 @@ public static Path get(final String filePath) {
   }
 
   /**
-   * Return a path in a way reciprocal with [[cloud.nio.util.CloudNioPaths#get]].
+   * Return a path in a way reciprocal with {@link alfre.v0.util.CloudPaths#get get}.
    *
    * @see alfre.v0.util.CloudPaths#get(java.lang.String)
-   * @see alfre.v0.util.CloudPaths#showRelative(java.nio.file.Path)
+   * @see alfre.v0.util.CloudPaths#toRelativeString(java.nio.file.Path)
    * @see alfre.v0.spi.CloudPath#getUriAsString()
    */
-  public static String showAbsolute(final Path path) {
+  public static String toAbsoluteString(final Path path) {
     Objects.requireNonNull(path, "path is null");
     if (path instanceof CloudPath<?>) {
       final CloudPath<?> cloudPath = (CloudPath<?>) path;
@@ -51,14 +50,16 @@ public static String showAbsolute(final Path path) {
   }
 
   /**
-   * When the path is relative returns a relative path in a way reciprocal with resolve. If the path
-   * is absolute then it is returned as relative but including the host/bucket.
+   * When the path is relative returns a relative path in a way reciprocal with {@link
+   * java.nio.file.Path#resolve resolve}.
    *
-   * @see alfre.v0.util.CloudPaths#showAbsolute(java.nio.file.Path)
+   * <p>If the path is absolute then it is returned as relative but including the host/bucket.
+   *
+   * @see alfre.v0.util.CloudPaths#toAbsoluteString(java.nio.file.Path)
    * @see java.nio.file.Path#resolve(java.nio.file.Path)
    * @see alfre.v0.spi.CloudPath#getUriAsString()
    */
-  public static String showRelative(final Path path) {
+  public static String toRelativeString(final Path path) {
     Objects.requireNonNull(path, "path is null");
     if (path instanceof CloudPath<?>) {
       final CloudPath<?> cloudPath = (CloudPath<?>) path;