Remove apache commons io

build.gradle

@@ -15,6 +15,10 @@ repositories {
     mavenCentral()
 }
 
+configurations.all {
+    exclude group: 'commons-io'
+}
+
 java {
     sourceCompatibility = JavaVersion.VERSION_1_8
     targetCompatibility = JavaVersion.VERSION_1_8

src/main/java/org/openmicroscopy/shoola/agents/fsimporter/util/ChecksumTableRenderer.java

@@ -27,6 +27,7 @@
 //Java imports
 import java.awt.Color;
 import java.awt.Component;
+import java.nio.file.Paths;
 import javax.swing.Icon;
 import javax.swing.JTable;
 import javax.swing.SwingConstants;
@@ -35,7 +36,6 @@
 //Third-party libraries
 
 //Application-internal dependencies
-import org.apache.commons.io.FilenameUtils;
 import org.openmicroscopy.shoola.util.ui.UIUtilities;
 
 /**
@@ -107,7 +107,7 @@ public Component getTableCellRendererComponent(JTable table, Object value,
 					setText(v.substring(0, MAX_CHARACTERS));
 				else setText(v);
 			} else {
-				setText(FilenameUtils.getName(v));
+				setText(Paths.get(v).getFileName().toString());
 			}
 		}
 		return this;

src/main/java/org/openmicroscopy/shoola/agents/fsimporter/util/FileImportComponent.java

@@ -61,7 +61,6 @@
 import omero.cmd.CmdCallbackI;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.io.FileUtils;
 import org.jdesktop.swingx.JXBusyLabel;
 import org.jdesktop.swingx.JXTaskPane;
 import org.openmicroscopy.shoola.agents.events.importer.BrowseContainer;
@@ -80,6 +79,7 @@
 import org.openmicroscopy.shoola.env.data.util.Status;
 import org.openmicroscopy.shoola.env.data.util.StatusLabel;
 import org.openmicroscopy.shoola.env.event.EventBus;
+import org.openmicroscopy.shoola.util.file.IOUtil;
 import org.openmicroscopy.shoola.util.file.ImportErrorObject;
 import org.openmicroscopy.shoola.util.ui.UIUtilities;
 
@@ -363,7 +363,7 @@ private void formatResultTooltip()
 			}
 		}
 		buf.append("<b>Size: </b>");
-		buf.append(FileUtils.byteCountToDisplaySize(status.getSizeUpload()));
+		buf.append(IOUtil.byteCountToDisplaySize(status.getSizeUpload()));
 		buf.append("<br>");
 		buf.append("<b>Group: </b>");
 		buf.append(importable.getGroup().getName());

src/main/java/org/openmicroscopy/shoola/agents/fsimporter/view/ImporterModel.java

@@ -20,9 +20,12 @@
  */
 package org.openmicroscopy.shoola.agents.fsimporter.view;
 
+import com.google.common.io.MoreFiles;
 import ij.ImagePlus;
 
 import java.io.File;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.text.SimpleDateFormat;
 import java.nio.file.Files;
 import java.util.Collection;
@@ -39,7 +42,6 @@
 import omero.model.ImageI;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.io.FilenameUtils;
 import org.openmicroscopy.shoola.agents.fsimporter.AnnotationDataLoader;
 import org.openmicroscopy.shoola.agents.fsimporter.DataLoader;
 import org.openmicroscopy.shoola.agents.fsimporter.DataObjectCreator;
@@ -203,7 +205,7 @@ private GroupData getGroup(long groupId)
 	/** 
 	 * Creates a new instance.
 	 *
-	 * @param groupID The id to the group selected for the current user.
+	 * @param groupId The id to the group selected for the current user.
 	 * @param displayMode Group/Experimenter view.
 	 */
 	ImporterModel(long groupId, int displayMode)
@@ -214,7 +216,7 @@ private GroupData getGroup(long groupId)
 	/** 
 	 * Creates a new instance.
 	 *
-	 * @param groupID The id to the group selected for the current user.
+	 * @param groupId The id to the group selected for the current user.
 	 * @param master Pass <code>true</code> if the importer is used a stand-alone
 	 * application, <code>false</code> otherwise.
 	 * @param displayMode Group/Experimenter view.
@@ -381,7 +383,7 @@ void importCompleted(int loaderID)
 	/**
 	 * Sets the collection of the existing tags.
 	 * 
-	 * @param The value to set.
+	 * @param tags The value to set.
 	 */
 	void setTags(Collection tags)
 	{ 
@@ -739,11 +741,11 @@ private File createFile(String imageName)
                 fileName = object.getTableName();
             }
             if (CommonsLangUtils.isBlank(fileName)) {
-                name = "ImageJ-"+FilenameUtils.getBaseName(
-                    FilenameUtils.removeExtension(imageName))+"-Results-";
+				Path baseName = Paths.get(imageName).getFileName();
+                name = "ImageJ-"+MoreFiles.getNameWithoutExtension(baseName)+"-Results-";
                 name += new SimpleDateFormat("yyyy-MM-dd").format(new Date());
             } else {
-                name = FilenameUtils.removeExtension(fileName);
+                name = MoreFiles.getNameWithoutExtension(Paths.get(fileName));
             }
 
             name += ".csv";

src/main/java/org/openmicroscopy/shoola/agents/fsimporter/view/ImporterUIElement.java

@@ -59,7 +59,6 @@
 import omero.gateway.model.TagAnnotationData;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.io.FileUtils;
 import org.jdesktop.swingx.JXBusyLabel;
 import org.openmicroscopy.shoola.agents.fsimporter.IconManager;
 import org.openmicroscopy.shoola.agents.fsimporter.ImporterAgent;
@@ -75,6 +74,7 @@
 import org.openmicroscopy.shoola.env.data.model.ImportableObject;
 import org.openmicroscopy.shoola.env.ui.UserNotifier;
 import org.openmicroscopy.shoola.util.CommonsLangUtils;
+import org.openmicroscopy.shoola.util.file.IOUtil;
 import org.openmicroscopy.shoola.util.file.ImportErrorObject;
 import org.openmicroscopy.shoola.util.ui.ClosableTabbedPaneComponent;
 import org.openmicroscopy.shoola.util.ui.RotationIcon;
@@ -517,7 +517,7 @@ void setNumberOfImport()
     JPanel buildHeader()
     {
         sizeLabel = UIUtilities.createComponent(null);
-        sizeLabel.setText(FileUtils.byteCountToDisplaySize(sizeImport));
+        sizeLabel.setText(IOUtil.byteCountToDisplaySize(sizeImport));
         reportLabel = UIUtilities.setTextFont("Report:", Font.BOLD);
         importSizeLabel = UIUtilities.setTextFont("Import Size:", Font.BOLD);
 
@@ -638,7 +638,7 @@ Object uploadComplete(FileImportComponentI c, Object result) {
         if (file.isFile()) {
             countUploaded++;
             sizeImport += c.getImportSize();
-            sizeLabel.setText(FileUtils.byteCountToDisplaySize(sizeImport));
+            sizeLabel.setText(IOUtil.byteCountToDisplaySize(sizeImport));
             // handle error that occurred during the scanning or upload.
             // Check that the result has not been set.
             // if (!c.hasResult()) {
@@ -718,7 +718,7 @@ void setImportResult(FileImportComponentI fc, Object result) {
             if (fc.hasUploadFailed()) {
                 countUploadFailure++;
                 sizeImport -= fc.getImportSize();
-                sizeLabel.setText(FileUtils.byteCountToDisplaySize(sizeImport));
+                sizeLabel.setText(IOUtil.byteCountToDisplaySize(sizeImport));
             }
             if (fc.hasImportFailed())
                 countFailure++;

src/main/java/org/openmicroscopy/shoola/agents/imviewer/util/saver/ImgSaver.java

@@ -34,13 +34,14 @@
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
 import java.util.Iterator;
 import java.util.List;
 import java.util.regex.Pattern;
 import javax.swing.JDialog;
 import javax.swing.JFrame;
 
-import org.apache.commons.io.FileUtils;
 import org.openmicroscopy.shoola.agents.imviewer.ImViewerAgent;
 import org.openmicroscopy.shoola.agents.imviewer.util.ImagePaintingFactory;
 import org.openmicroscopy.shoola.agents.imviewer.view.ImViewer;
@@ -486,7 +487,7 @@ void saveImage(boolean init)
         	String name = uiDelegate.getSelectedFilePath();
 
         	// make sure the parent directory paths all exist
-        	FileUtils.forceMkdir(new File(name).getParentFile());
+            Files.createDirectories(Paths.get(new File(name).getParentFile().toURI()));
 
             if (imageComponents == null) {
                 if (mainImage == null) return;

src/main/java/org/openmicroscopy/shoola/agents/imviewer/view/ImViewerModel.java

@@ -28,6 +28,7 @@
 import java.awt.Rectangle;
 import java.awt.Toolkit;
 import java.awt.image.BufferedImage;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -38,13 +39,13 @@
 import java.util.List;
 import java.util.Map;
 
+import com.google.common.io.MoreFiles;
 import omero.model.Length;
 import omero.model.LengthI;
 import omero.model.PlaneInfo;
 import omero.model.enums.UnitsLength;
 import omero.romio.PlaneDef;
 
-import org.apache.commons.io.FilenameUtils;
 import org.openmicroscopy.shoola.agents.events.iviewer.CopyRndSettings;
 import org.openmicroscopy.shoola.agents.imviewer.AcquisitionDataLoader;
 import org.openmicroscopy.shoola.agents.imviewer.BirdEyeLoader;
@@ -2199,7 +2200,7 @@ void fireImageProjection(int startZ, int endZ, int stepping, int type,
 	 * @return See above.
 	 */
 	private String combineFilenameWith(String projectName, String imageName) {
-		String extension = FilenameUtils.getExtension(imageName);
+		String extension = MoreFiles.getFileExtension(Paths.get(imageName));
 
 		StringBuilder nameBuilder = new StringBuilder();
 		nameBuilder.append(projectName);

src/main/java/org/openmicroscopy/shoola/agents/metadata/editor/OriginalMetadataComponent.java

@@ -30,6 +30,7 @@
 import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.LinkedHashMap;
@@ -49,8 +50,8 @@
 import javax.swing.JToolBar;
 import javax.swing.table.DefaultTableModel;
 
+import com.google.common.io.MoreFiles;
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.io.FilenameUtils;
 import org.openmicroscopy.shoola.util.CommonsLangUtils;
 import org.jdesktop.swingx.JXBusyLabel;
 import org.jdesktop.swingx.JXTable;
@@ -121,7 +122,7 @@ private void download()
         if (data != null) name = data.getFileName();
         else {
             ImageData img = model.getImage();
-            name = FilenameUtils.removeExtension(img.getName());
+            name = MoreFiles.getNameWithoutExtension(Paths.get(img.getName()));
         }
         chooser.setSelectedFileFull(name);
         chooser.setApproveButtonText("Download");

src/main/java/org/openmicroscopy/shoola/agents/treeviewer/view/ToolBar.java

@@ -39,6 +39,7 @@
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.beans.PropertyChangeListenerProxy;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -69,7 +70,6 @@
 import javax.swing.border.BevelBorder;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.io.FilenameUtils;
 import org.jdesktop.swingx.JXBusyLabel;
 import org.openmicroscopy.shoola.agents.treeviewer.IconManager;
 import org.openmicroscopy.shoola.agents.treeviewer.TreeViewerAgent;
@@ -1015,7 +1015,7 @@ public void actionPerformed(ActionEvent e) {
                 value = "";
                 path = so.getPath();
                 if (path != null && path.length() > 1) {
-                    sep = FilenameUtils.getPrefix(path);
+                    sep = Paths.get(path).getRoot().toString();
                     if (path.startsWith(sep))
                         path = path.substring(1, path.length());
                     values = UIUtilities.splitString(path);
@@ -1036,7 +1036,7 @@ public void actionPerformed(ActionEvent e) {
                 so = i.next();
                 path = so.getPath();
                 if (path != null) {
-                    sep = FilenameUtils.getPrefix(path);
+                    sep = Paths.get(path).getRoot().toString();
                     if (path.startsWith(sep))
                         path = path.substring(1, path.length());
                     values = UIUtilities.splitString(path);

src/main/java/org/openmicroscopy/shoola/agents/treeviewer/view/TreeViewerFactory.java

@@ -27,6 +27,7 @@
 import java.io.File;
 import java.io.FileReader;
 import java.io.FileWriter;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -42,7 +43,6 @@
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
 
-import org.apache.commons.io.FilenameUtils;
 import org.openmicroscopy.shoola.agents.events.SaveData;
 import org.openmicroscopy.shoola.agents.treeviewer.TreeViewerAgent;
 import org.openmicroscopy.shoola.env.Agent;
@@ -442,7 +442,7 @@ private void readExternalApplications()
 
 		Environment env = (Environment) 
 		TreeViewerAgent.getRegistry().lookup(LookupNames.ENV);
-		String name = FilenameUtils.concat(env.getOmeroHome(),FILE_NAME);
+		String name = Paths.get(env.getOmeroHome(), FILE_NAME).toString();
 
 		File f = new File(name);
 		if (!f.exists()) return;

src/main/java/org/openmicroscopy/shoola/env/Container.java

@@ -23,12 +23,13 @@
 package org.openmicroscopy.shoola.env;
 
 import java.io.File;
+import java.nio.file.Paths;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 
-import org.apache.commons.io.FilenameUtils;
+import com.google.common.io.MoreFiles;
 import org.openmicroscopy.shoola.util.CommonsLangUtils;
 import org.openmicroscopy.shoola.env.config.AgentInfo;
 import org.openmicroscopy.shoola.env.config.Registry;
@@ -247,12 +248,13 @@ private Container(String home, String configFile, String pluginDir)
 	private Container(String home, String configFile, String pluginDir, List<String> cmdLineArgs)
 		throws StartupException
 	{
-	    if (CommonsLangUtils.isBlank(configFile) || !FilenameUtils.isExtension(configFile, "xml")) {
+	    if (CommonsLangUtils.isBlank(configFile) ||
+				!MoreFiles.getFileExtension(Paths.get(configFile)).toLowerCase().equals("xml")) {
 			configFile = CONFIG_FILE;
 		}
 		this.configFile = configFile;
 
-        if (CommonsLangUtils.isBlank(FilenameUtils.getPath(home))) {
+        if (CommonsLangUtils.isBlank(home)) {
         	home = System.getProperty("user.dir");
 		}
         File f = new File(home);
@@ -465,7 +467,7 @@ public void exit()
 	 * plug-in. Those plug-in will have an UI entry.
 	 * @param pluginDir  Path to the plugin directory. Used in plugin mode only.
 	 * @return A reference to the newly created singleton Container.
-	 * @throws Throws a startup exception if the application cannot be used as
+	 * @throws StartupException Throws a startup exception if the application cannot be used as
 	 * a plugin due to missing dependencies.
 	 */
 	public static Container startupInPluginMode(String home, String configFile,
@@ -493,7 +495,7 @@ public static Container startupInPluginMode(String home, String configFile,
      * @param plugin Pass positive value. See {@link LookupNames} for supported
      * plug-in. Those plug-in will have an UI entry.
      * @return A reference to the newly created singleton Container.
-     * @throws Throws a startup exception if the application cannot be used as 
+     * @throws StartupException Throws a startup exception if the application cannot be used as
      * a plugin due to missing dependencies.
      */
     public static Container startupInPluginMode(String home, String configFile,
@@ -522,7 +524,7 @@ public static Container startupInPluginMode(String home, String configFile,
 	 * plug-in. Those plug-in will have an UI entry.
 	 * @param listener Listens to <code>ConnectedEvent</code>.
 	 * @return A reference to the newly created singleton Container.
-	 * @throws Throws a startup exception if the application cannot be used as
+	 * @throws StartupException Throws a startup exception if the application cannot be used as
 	 * a plugin due to missing dependencies.
 	 */
 	public static Container startupInPluginMode(String home, String configFile,
@@ -552,7 +554,7 @@ public static Container startupInPluginMode(String home, String configFile,
      * plug-in. Those plug-in will have an UI entry.
      * @param listener Listens to <code>ConnectedEvent</code>.
      * @return A reference to the newly created singleton Container.
-     * @throws Throws a startup exception if the application cannot be used as 
+     * @throws StartupException Throws a startup exception if the application cannot be used as
      * a plugin due to missing dependencies.
      */
     public static Container startupInPluginMode(String home, String configFile,
@@ -637,7 +639,7 @@ public static Container startupInPluginMode(String home, String configFile,
      * @param plugin Pass positive value. See {@link LookupNames} for supported
      * plug-in. Those plug-in will have an UI entry.
      * @return A reference to the newly created singleton Container.
-     * @throws Throws a startup exception if the application cannot be used as 
+     * @throws StartupException Throws a startup exception if the application cannot be used as
      * a plugin due to missing dependencies.
      */
     public static Container startupInHeadlessMode(String home,
@@ -695,7 +697,7 @@ public void eventFired(AgentEvent e) {
      *              empty, then the user directory is assumed.
      * @param configFile The configuration file.
      * @return A reference to the newly created singleton Container.
-     * @throws Throws a startup exception if the application cannot be used as 
+     * @throws StartupException Throws a startup exception if the application cannot be used as
      * a plugin due to missing dependencies.
      */
     public static Container startupInHeadlessMode(String home, String configFile