Add S3Handle using minio 5.0.0

.travis.yml

@@ -10,7 +10,6 @@ cache:
 jdk:
   - oraclejdk10
   - oraclejdk8
-  - openjdk7
 
 matrix:
   fast_finish: true

pom.xml

@@ -101,6 +101,11 @@
   </distributionManagement>
 
   <dependencies>
+    <dependency>
+     <groupId>io.minio</groupId>
+     <artifactId>minio</artifactId>
+     <version>5.0.0</version>
+    </dependency>
     <dependency>
      <groupId>com.esotericsoftware.kryo</groupId>
      <artifactId>kryo</artifactId>

src/main/java/loci/common/Location.java

@@ -37,9 +37,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
+import java.net.*;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Iterator;
@@ -93,8 +91,9 @@ protected class ListingsResult {
 
   // -- Fields --
 
-  private boolean isURL = true;
+  private boolean isURL = false;
   private URL url;
+  private URI uri;
   private File file;
 
   // -- Constructors --
@@ -107,22 +106,7 @@ protected class ListingsResult {
    * @see #getMappedFile(String)
    */
   public Location(String pathname) {
-    LOGGER.trace("Location({})", pathname);
-    if (pathname.contains("://")) {
-      // Avoid expensive exception handling in case when path is
-      // obviously not an URL
-      try {
-        url = new URL(getMappedId(pathname));
-      }
-      catch (MalformedURLException e) {
-        LOGGER.trace("Location is not a URL", e);
-        isURL = false;
-      }
-    } else {
-      LOGGER.trace("Location is not a URL");
-      isURL = false;
-    }
-    if (!isURL) file = new File(getMappedId(pathname));
+    this((String) null, pathname);
   }
 
   /**
@@ -145,7 +129,41 @@ public Location(File file) {
    * @param child the relative path name
    */
   public Location(String parent, String child) {
-    this(parent + File.separator + child);
+    LOGGER.trace("Location({}, {})", parent, child);
+
+    String mapped = null;
+    String pathname = null;
+
+    // First handle possible URIs
+    if (child != null && child.contains("://")) {
+      // Avoid expensive exception handling in case when path is
+      // obviously not an URL
+      try {
+        mapped = getMappedId(child);
+        pathname = child;
+        uri = new URI(mapped);
+        isURL = true;
+        url = uri.toURL();
+      }
+      catch (URISyntaxException | MalformedURLException e) {
+        // TODO: this should possibly throw
+        // possibly leaves url null
+      }
+    }
+
+    // If not a URI, then deal with relative vs. absolute paths
+    if (pathname == null) {
+      if (parent != null) {
+        // TODO: in some cases child here may be null
+        pathname = parent + File.separator + child;
+      } else {
+        pathname = child;
+      }
+      mapped = getMappedId(pathname);
+    }
+
+    if (!isURL) file = new File(mapped);
+
   }
 
   /**
@@ -395,7 +413,10 @@ public static IRandomAccess getHandle(String id, boolean writable,
       LOGGER.trace("no handle was mapped for this ID");
       String mapId = getMappedId(id);
 
-      if (id.startsWith("http://") || id.startsWith("https://")) {
+      if (id.startsWith("s3://")) {
+        handle = new S3Handle(mapId);
+      }
+      else if (id.startsWith("http://") || id.startsWith("https://")) {
         handle = new URLHandle(mapId);
       }
       else if (allowArchiveHandles && ZipHandle.isZipFile(mapId)) {
@@ -464,6 +485,17 @@ public String[] list(boolean noHiddenFiles) {
     final List<String> files = new ArrayList<String>();
     if (isURL) {
       try {
+        if (url == null) {
+          // Likely s3
+          if (!exists()) {
+            return null;
+          }
+          if (uri.toString().endsWith("/")) {
+            return new String[0];
+          } else {
+            return null;
+          }
+        }
         URLConnection c = url.openConnection();
         InputStream is = c.getInputStream();
         boolean foundEnd = false;
@@ -539,7 +571,8 @@ public String[] list(boolean noHiddenFiles) {
    */
   public boolean canRead() {
     LOGGER.trace("canRead()");
-    return isURL ? (isDirectory() || isFile() || exists()) : file.canRead();
+    // Note: isFile calls exist
+    return isURL ? (isDirectory() || isFile()) : file.canRead();
   }
 
   /**
@@ -642,7 +675,9 @@ public boolean exists() {
     LOGGER.trace("exists()");
     if (isURL) {
       try {
-        url.getContent();
+        // TODO: existence should almost certainly be cached.
+        IRandomAccess handle = getHandle(uri.toString());
+        handle.length();
         return true;
       }
       catch (IOException e) {
@@ -675,7 +710,7 @@ public Location getAbsoluteFile() {
    */
   public String getAbsolutePath() {
     LOGGER.trace("getAbsolutePath()");
-    return isURL ? url.toExternalForm() : file.getAbsolutePath();
+    return isURL ? uri.normalize().toString() : file.getAbsolutePath();
   }
 
   /**
@@ -715,9 +750,8 @@ public String getCanonicalPath() throws IOException {
   public String getName() {
     LOGGER.trace("getName()");
     if (isURL) {
-      String name = url.getFile();
-      name = name.substring(name.lastIndexOf("/") + 1);
-      return name;
+      // TODO: we should just store new File(uri) in file
+      return  new File(uri.getPath()).getName();
     }
     return file.getName();
   }
@@ -757,7 +791,7 @@ public Location getParentFile() {
    * @see java.io.File#getPath()
    */
   public String getPath() {
-    return isURL ? url.getHost() + url.getPath() : file.getPath();
+    return isURL ? uri.getHost() + uri.getPath() : file.getPath();
   }
 
   /**
@@ -769,7 +803,7 @@ public String getPath() {
    */
   public boolean isAbsolute() {
     LOGGER.trace("isAbsolute()");
-    return isURL ? true : file.isAbsolute();
+    return isURL ? uri.isAbsolute() : file.isAbsolute();
   }
 
   /**
@@ -781,8 +815,13 @@ public boolean isAbsolute() {
   public boolean isDirectory() {
     LOGGER.trace("isDirectory()");
     if (isURL) {
-      String[] list = list();
-      return list != null;
+      if ("s3".equals(uri.getScheme())) {
+        return uri.toString().endsWith("/") && exists();
+      } else {
+        // TODO: this should be removed as well.
+        String[] list = list();
+        return list != null;
+      }
     }
     return file.isDirectory();
   }
@@ -829,7 +868,11 @@ public long lastModified() {
     LOGGER.trace("lastModified()");
     if (isURL) {
       try {
-        return url.openConnection().getLastModified();
+        if (url != null) {
+          return url.openConnection().getLastModified();
+        } else {
+          return 0;
+        }
       }
       catch (IOException e) {
         LOGGER.trace("Could not determine URL's last modification time", e);
@@ -908,7 +951,7 @@ public URL toURL() throws MalformedURLException {
    */
   @Override
   public String toString() {
-    return isURL ? url.toString() : file.toString();
+    return isURL ? uri.toString() : file.toString();
   }
 
 }