feature: get ready for update

pom.xml - define UTF8 as encoding, add copy dependend jars
refactoring - extract problematic inner classes

haas-imagej-client/pom.xml

-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<parent>
@@ -60,16 +61,16 @@
 	<properties>
 		<license.licenseName>${license.base.licenseName}</license.licenseName>
 		<license.copyrightOwners>${license.base.copyrightOwners}</license.copyrightOwners>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 	</properties>
-	
-	
+
 	<dependencies>
 		<dependency>
 			<groupId>net.imagej</groupId>
 			<artifactId>imagej</artifactId>
 			<scope>provided</scope>
 		</dependency>
-		
+
 		<dependency>
 			<groupId>cz.it4i.fiji</groupId>
 			<artifactId>haas-java-client</artifactId>
@@ -90,10 +91,21 @@
 
 		<!-- https://mvnrepository.com/artifact/org.yaml/snakeyaml -->
 		<dependency>
-		    <groupId>org.yaml</groupId>
-		    <artifactId>snakeyaml</artifactId>
-		    <version>1.19</version>
+			<groupId>org.yaml</groupId>
+			<artifactId>snakeyaml</artifactId>
+			<version>1.19</version>
 		</dependency>
-
 	</dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<configuration>
+					<source>1.8</source>
+					<target>1.8</target>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
 </project>

haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/FutureValueUpdater.java

+package cz.it4i.fiji.haas.ui;
+
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.Executor;
+
+import cz.it4i.fiji.haas.ui.TableCellAdapter.TableCellUpdater;
+import javafx.scene.control.TableCell;
+
+public class FutureValueUpdater<S, T, U extends CompletableFuture<T>> implements TableCellUpdater<S, U> {
+
+	private final TableCellUpdater<S, T> inner;
+	private final Executor executor;
+
+	public FutureValueUpdater(TableCellUpdater<S, T> inner, Executor exec) {
+		this.inner = inner;
+		this.executor = exec;
+	}
+
+	@Override
+	public void accept(TableCell<?, ?> cell, U value, boolean empty) {
+		if (value != null) {
+			if (!value.isDone()) {
+				inner.accept(cell, null, empty);
+			}
+			value.thenAcceptAsync(val -> {
+				inner.accept(cell, val, empty);
+			}, executor);
+		} else {
+			inner.accept(cell, null, empty);
+		}
+	}
+}
\ No newline at end of file

haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/JavaFXRoutines.java

@@ -2,7 +2,6 @@ package cz.it4i.fiji.haas.ui;
 
 import java.io.IOException;
 import java.util.concurrent.Callable;
-import java.util.concurrent.CompletableFuture;
 import java.util.concurrent.Executor;
 import java.util.function.Consumer;
 import java.util.function.Function;
@@ -11,11 +10,9 @@ import java.util.function.Predicate;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import cz.it4i.fiji.haas.ui.JavaFXRoutines.TableCellAdapter.TableCellUpdater;
 import javafx.application.Platform;
 import javafx.beans.value.ObservableValue;
 import javafx.fxml.FXMLLoader;
-import javafx.scene.control.TableCell;
 import javafx.scene.control.TableColumn;
 import javafx.scene.control.TableView;
 
@@ -23,63 +20,6 @@ public interface JavaFXRoutines {
 
 	Logger log = LoggerFactory.getLogger(cz.it4i.fiji.haas.ui.CloseableControl.class);
 
-	static public class TableCellAdapter<S, T> extends TableCell<S, T> {
-		public interface TableCellUpdater<A, B> {
-			void accept(TableCell<?, ?> cell, B value, boolean empty);
-		}
-
-		private final TableCellUpdater<S, T> updater;
-
-		public TableCellAdapter(TableCellUpdater<S, T> updater) {
-			this.updater = updater;
-		}
-
-		@Override
-		protected void updateItem(T item, boolean empty) {
-			if(empty) {
-				this.setText("");
-			} else {
-				updater.accept(this, item, empty);
-			}
-		}
-	}
-
-	static public class FutureValueUpdater<S, T, U extends CompletableFuture<T>> implements TableCellUpdater<S, U> {
-
-		private final TableCellUpdater<S, T> inner;
-		private final Executor executor;
-
-		public FutureValueUpdater(TableCellUpdater<S, T> inner, Executor exec) {
-			this.inner = inner;
-			this.executor = exec;
-		}
-
-		@Override
-		public void accept(TableCell<?, ?> cell, U value, boolean empty) {
-			if (value != null) {
-				if (!value.isDone()) {
-					inner.accept(cell, null, empty);
-				}
-				value.thenAcceptAsync(val -> {
-					inner.accept(cell, val, empty);
-				}, executor);
-			} else {
-				inner.accept(cell, null, empty);
-			}
-		}
-	}
-
-	static public class StringValueUpdater<S> implements TableCellUpdater<S, String> {
-		@Override
-		public void accept(TableCell<?, ?> cell, String value, boolean empty) {
-			if (value != null) {
-				cell.setText(value);
-			} else if (!empty) {
-				cell.setText("N/A");
-			}
-		}
-	}
-
 	static void initRootAndController(String string, Object parent) {
 		initRootAndController(string, parent, false);
 	}

haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/StringValueUpdater.java

+package cz.it4i.fiji.haas.ui;
+
+import cz.it4i.fiji.haas.ui.TableCellAdapter.TableCellUpdater;
+import javafx.scene.control.TableCell;
+
+public class StringValueUpdater<S> implements TableCellUpdater<S, String> {
+	@Override
+	public void accept(TableCell<?, ?> cell, String value, boolean empty) {
+		if (value != null) {
+			cell.setText(value);
+		} else if (!empty) {
+			cell.setText("N/A");
+		}
+	}
+}
\ No newline at end of file

haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/TableCellAdapter.java

+package cz.it4i.fiji.haas.ui;
+
+import javafx.scene.control.TableCell;
+
+public class TableCellAdapter<S, T> extends TableCell<S, T> {
+	public interface TableCellUpdater<A, B> {
+		void accept(TableCell<?, ?> cell, B value, boolean empty);
+	}
+
+	private final TableCellAdapter.TableCellUpdater<S, T> updater;
+
+	public TableCellAdapter(TableCellAdapter.TableCellUpdater<S, T> updater) {
+		this.updater = updater;
+	}
+
+	@Override
+	protected void updateItem(T item, boolean empty) {
+		if(empty) {
+			this.setText("");
+		} else {
+			updater.accept(this, item, empty);
+		}
+	}
+}
\ No newline at end of file

haas-java-client/pom.xml

@@ -6,6 +6,9 @@
 	<version>0.0.2-SNAPSHOT</version>
 	<name>HaaS library for Java</name>
 	<packaging>jar</packaging>
+	<properties>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+	</properties>
 	<build>
 		<plugins>
 			<plugin>
@@ -19,6 +22,7 @@
 			</plugin>
 			<plugin>
 		      <artifactId>maven-source-plugin</artifactId>
+		      <version>3.0.1</version>
 		      <executions>
 		        <execution>
 		          <id>attach-sources</id>
@@ -42,8 +46,7 @@
 			<artifactId>java-scpclient</artifactId>
 			<version>0.0.1-SNAPSHOT</version>
 		</dependency>
-		<!-- https://mvnrepository.com/artifact/org.apache.axis2/axis2 -->
-
+		
 		<!-- https://mvnrepository.com/artifact/javax.activation/activation -->
 		<dependency>
 			<groupId>javax.activation</groupId>
@@ -74,8 +77,6 @@
 			<artifactId>jaxrpc</artifactId>
 			<version>1.1</version>
 		</dependency>
-		<!-- https://mvnrepository.com/artifact/javax.xml/saaj-api -->
-		<!-- https://mvnrepository.com/artifact/javax.xml/saaj-api -->
 		<!-- https://mvnrepository.com/artifact/javax.xml.soap/saaj-api -->
 		<dependency>
 			<groupId>javax.xml.soap</groupId>

haas-spim-benchmark/pom.xml

-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<parent>
@@ -59,13 +60,14 @@
 		<system>None</system>
 	</ciManagement>
 
-	
+
 
 	<properties>
 		<license.licenseName>${license.base.licenseName}</license.licenseName>
 		<license.copyrightOwners>${license.base.copyrightOwners}</license.copyrightOwners>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 	</properties>
-	
+
 	<dependencies>
 		<dependency>
 			<groupId>net.imagej</groupId>
@@ -78,14 +80,14 @@
 			<artifactId>haas-imagej-client</artifactId>
 			<version>0.0.1-SNAPSHOT</version>
 		</dependency>
-		
+
 		<!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
 		<dependency>
-		    <groupId>commons-io</groupId>
-		    <artifactId>commons-io</artifactId>
-		    <version>2.6</version>
+			<groupId>commons-io</groupId>
+			<artifactId>commons-io</artifactId>
+			<version>2.6</version>
 		</dependency>
-				
+
 		<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
 		<dependency>
 			<groupId>org.slf4j</groupId>
@@ -103,21 +105,13 @@
 	<build>
 		<plugins>
 			<plugin>
-				<artifactId>maven-assembly-plugin</artifactId>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-dependency-plugin</artifactId>
 				<configuration>
-					<descriptorRefs>
-						<descriptorRef>jar-with-dependencies</descriptorRef>
-					</descriptorRefs>
+					<outputDirectory>
+						${project.build.directory}/jars
+					</outputDirectory>
 				</configuration>
-				<executions>
-					<execution>
-						<id>make-assembly</id>
-						<phase>package</phase>
-						<goals>
-							<goal>single</goal>
-						</goals>
-					</execution>
-				</executions>
 			</plugin>
 
 		</plugins>

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIMControl.java

@@ -28,11 +28,14 @@ import org.slf4j.LoggerFactory;
 import cz.it4i.fiji.haas.UploadingFileFromResource;
 import cz.it4i.fiji.haas.ui.CloseableControl;
 import cz.it4i.fiji.haas.ui.DummyProgress;
+import cz.it4i.fiji.haas.ui.FutureValueUpdater;
 import cz.it4i.fiji.haas.ui.InitiableControl;
 import cz.it4i.fiji.haas.ui.JavaFXRoutines;
 import cz.it4i.fiji.haas.ui.ModalDialogs;
 import cz.it4i.fiji.haas.ui.ProgressDialog;
 import cz.it4i.fiji.haas.ui.ShellRoutines;
+import cz.it4i.fiji.haas.ui.StringValueUpdater;
+import cz.it4i.fiji.haas.ui.TableCellAdapter;
 import cz.it4i.fiji.haas.ui.TableViewContextMenu;
 import cz.it4i.fiji.haas_java_client.JobState;
 import cz.it4i.fiji.haas_java_client.UploadingFile;
@@ -323,9 +326,9 @@ public class BenchmarkSPIMControl extends BorderPane implements CloseableControl
 	private void setCellValueFactoryCompletable(int index, Function<BenchmarkJob, CompletableFuture<String>> mapper) {
 		JavaFXRoutines.setCellValueFactory(jobs, index, mapper);
 		((TableColumn<ObservableBenchmarkJob, CompletableFuture<String>>) jobs.getColumns().get(index)).setCellFactory(
-				column -> new JavaFXRoutines.TableCellAdapter<ObservableBenchmarkJob, CompletableFuture<String>>(
-						new JavaFXRoutines.FutureValueUpdater<ObservableBenchmarkJob, String, CompletableFuture<String>>(
-								new JavaFXRoutines.StringValueUpdater<ObservableBenchmarkJob>(), executorServiceFX)));
+				column -> new TableCellAdapter<ObservableBenchmarkJob, CompletableFuture<String>>(
+						new FutureValueUpdater<ObservableBenchmarkJob, String, CompletableFuture<String>>(
+								new StringValueUpdater<ObservableBenchmarkJob>(), executorServiceFX)));
 	}
 
 	private interface P_JobAction {

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/SPIMPipelineProgressViewController.java

@@ -23,6 +23,7 @@ import cz.it4i.fiji.haas.ui.CloseableControl;
 import cz.it4i.fiji.haas.ui.InitiableControl;
 import cz.it4i.fiji.haas.ui.JavaFXRoutines;
 import cz.it4i.fiji.haas.ui.ModalDialogs;
+import cz.it4i.fiji.haas.ui.TableCellAdapter;
 import cz.it4i.fiji.haas.ui.TableViewContextMenu;
 import cz.it4i.fiji.haas_java_client.JobState;
 import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.BenchmarkJob;
@@ -208,7 +209,7 @@ public class SPIMPipelineProgressViewController extends BorderPane implements Cl
 			}
 		});
 		((TableColumn<ObservableValue<Task>, TaskComputation>) this.tasks.getColumns().get(index))
-				.setCellFactory(column -> new JavaFXRoutines.TableCellAdapter<>((cell, val, empty) -> {
+				.setCellFactory(column -> new TableCellAdapter<>((cell, val, empty) -> {
 					if (val == null || empty) {
 						cell.setText(EMPTY_VALUE);
 						cell.setStyle("");

haas-spim-benchmark/src/main/resources/configuration.properties.template

-USER_NAME=
-PASSWORD=
-EMAIL=
-PHONE=
\ No newline at end of file

java-scpclient/pom.xml

@@ -7,6 +7,9 @@
 	<version>0.0.1-SNAPSHOT</version>
 	<name>Scp client library for Java</name>
 	<packaging>jar</packaging>
+	<properties>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+	</properties>
 	<build>
 		<plugins>
 			<plugin>