Replace Minio dependency with a service

src/main/java/loci/common/S3Handle.java

@@ -40,15 +40,14 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.security.InvalidKeyException;
-import java.security.NoSuchAlgorithmException;
 import java.util.regex.Pattern;
 
-import io.minio.MinioClient;
-import io.minio.errors.MinioException;
-import io.minio.ObjectStat;
-import org.xmlpull.v1.XmlPullParserException;
+import loci.common.services.DependencyException;
+import loci.common.services.S3ClientService;
+import loci.common.services.S3ClientServiceException;
+import loci.common.services.S3ClientStat;
 
+import loci.common.services.ServiceFactory;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -103,11 +102,11 @@ class DelayedObjectNotFound extends IOException {
   /** remaining path, or key, for this accessed resource */
   private final String path;
 
-  /** Minio client */
-  private MinioClient s3Client;
+  /** S3 client */
+  private S3ClientService s3Client;
 
   /** Remote file stat */
-  private ObjectStat stat;
+  private S3ClientStat stat;
 
   /** Is this a directory (currently only buckets are considered directories */
   private boolean isBucket;
@@ -228,11 +227,7 @@ else if (scheme.startsWith("s3+")) {
       try {
         this.initialize();
       }
-      catch (
-        MinioException |
-        InvalidKeyException |
-        NoSuchAlgorithmException |
-        XmlPullParserException e) {
+      catch (S3ClientServiceException e) {
         this.objectNotFound = e;
         LOGGER.debug("Object not found: [{}] {}", this, e);
       }
@@ -245,32 +240,33 @@ else if (scheme.startsWith("s3+")) {
    * @throws IOException if there was an error connecting to the server
    */
   protected void connect() throws IOException {
+    final String appName = "Bio-Formats";
+    // TODO: Replace "dev" with a version
+    final String appVersion = "dev";
     try {
-      s3Client = new MinioClient(server, port, accessKey, secretKey);
-      // TODO: Replace "dev" with a version
-      s3Client.setAppInfo("Bio-Formats", "dev");
+      ServiceFactory factory = new ServiceFactory();
+      s3Client = factory.getInstance(S3ClientService.class);
+      s3Client.initialize(server, port, accessKey, secretKey, appName, appVersion);
     }
-    catch (MinioException e) {
+    catch (S3ClientServiceException e) {
       throw new IOException(String.format(
               "Failed to connect: %s", this), e);
     }
+    catch (DependencyException e) {
+      throw new IOException(String.format(
+          "S3 requires additional dependencies: %s", this), e);
+    }
     LOGGER.trace("connected: server:{} port:{}", server, port);
   }
 
   /**
    * Check bucket or object exists
    * @throws IOException if unable to get the object
-   * @throws MinioException if unable to get the object
-   * @throws InvalidKeyException if unable to get the object
-   * @throws NoSuchAlgorithmException if unable to get the object
-   * @throws XmlPullParserException if unable to get the object
+   * @throws S3ClientServiceException if unable to get the object
    */
   protected void initialize() throws
       IOException,
-      MinioException,
-      InvalidKeyException,
-      NoSuchAlgorithmException,
-      XmlPullParserException {
+      S3ClientServiceException {
     if (path == null) {
       isBucket = s3Client.bucketExists(bucket);
     }
@@ -347,16 +343,11 @@ protected void downloadObject(Path destination) throws HandleException, IOExcept
     if (path == null) {
       throw new HandleException("Download path=null not allowed");
     }
+    Files.createDirectories(destination.getParent());
     try {
-      Files.createDirectories(destination.getParent());
       s3Client.getObject(bucket, path, destination.toString());
     }
-    catch (
-      IOException |
-      InvalidKeyException |
-      MinioException |
-      NoSuchAlgorithmException |
-      XmlPullParserException e) {
+    catch (S3ClientServiceException e) {
         throw new HandleException("Download failed " + toString(), e);
       }
   }
@@ -437,11 +428,7 @@ protected void resetStream(long offset) throws IOException {
       fp = offset;
       mark = offset;
       }
-      catch (
-        InvalidKeyException |
-        MinioException |
-        NoSuchAlgorithmException |
-        XmlPullParserException e) {
+      catch (S3ClientServiceException e) {
         throw new IOException(String.format(
               "failed to load s3: %s\n\t%s", uri, this), e);
     }

src/main/java/loci/common/services/S3ClientService.java

@@ -0,0 +1,97 @@
+/*
+ * #%L
+ * S3 client service
+ * %%
+ * Copyright (C) 2019 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package loci.common.services;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+/**
+ * An S3 client
+ */
+public interface S3ClientService extends Service {
+
+  /**
+   * Initialise the S3 client
+   * @param server servername
+   * @param port port
+   * @param accessKey access key
+   * @param secretKey secret key
+   * @param appName user agent application name
+   * @param appVersion user agent application version
+   * @throws S3ClientServiceException if an S3 error occurred
+   */
+  void initialize(String server, int port, String accessKey, String secretKey,
+                  String appName, String appVersion)
+      throws S3ClientServiceException;
+
+  /**
+   * Check whether a bucket exists
+   * @param bucket Bucket name
+   * @return true if bucket exists
+   * @throws S3ClientServiceException if an S3 error occurred
+   * @throws IOException if an S3 error occurred
+   */
+  boolean bucketExists(String bucket) throws S3ClientServiceException, IOException;
+
+  /**
+   * Stat the object
+   * @param bucket Bucket name
+   * @param object Object path
+   * @return S3ClientStat object
+   * @throws S3ClientServiceException if an S3 error occurred
+   * @throws IOException if an S3 error occurred
+   */
+  S3ClientStat statObject(String bucket, String object) throws S3ClientServiceException, IOException;
+
+  /**
+   * Read an object
+   * @param bucket Bucket name
+   * @param object Object path
+   * @param offset Start reading at this offset
+   * @return InputStream to the object
+   * @throws S3ClientServiceException if an S3 error occurred
+   * @throws IOException if an S3 error occurred
+   */
+  InputStream getObject(String bucket, String object, long offset) throws S3ClientServiceException, IOException;
+
+  /**
+   * Download an object
+   * @param bucket Bucket name
+   * @param object Object path
+   * @param filename Destination file
+   * @throws S3ClientServiceException if an S3 error occurred
+   * @throws IOException if an S3 error occurred
+   */
+  void getObject(String bucket, String object, String filename) throws S3ClientServiceException, IOException;
+
+}

src/main/java/loci/common/services/S3ClientServiceException.java

@@ -0,0 +1,67 @@
+/*
+ * #%L
+ * S3 client stat object
+ * %%
+ * Copyright (C) 2019 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package loci.common.services;
+
+/**
+ * Exception thrown when internal error specific to the S3 client is raised
+ */
+public class S3ClientServiceException extends ServiceException
+{
+  /**
+   * Constructor.
+   * @param message Error message.
+   */
+  public S3ClientServiceException(String message)
+  {
+    super(message);
+  }
+
+  /**
+   * Constructor.
+   * @param message Error message. 
+   * @param cause Upstream exception.
+   */
+  public S3ClientServiceException(String message, Throwable cause)
+  {
+    super(message, cause);
+  }
+
+  /**
+   * Constructor.
+   * @param cause Upstream exception.
+   */
+  public S3ClientServiceException(Throwable cause)
+  {
+    super(cause);
+  }
+}