public code v1

plugins/afryca.ase.engine.R/src/afryca/ase/engine/R/R.java

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+package afryca.ase.engine.R;
+
+import javax.script.ScriptException;
+
+import org.rosuda.JRI.Rengine;
+
+import afryca.ase.engine.IEngine;
+
+/**
+ * R engine for ASE
+ * 
+ * @author Sinbad²
+ * @version 3.0
+ */
+public class R implements IEngine {
+	
+	public static final String ID = "R"; //$NON-NLS-1$
+
+	private Rengine rengine;
+	private String name;
+
+	private R() {
+		super();
+		name = ID;
+		rengine = null;
+	}
+
+	/**
+	 * Build R engine
+	 * 
+	 * @param rengine
+	 *            JRI Rengine
+	 */
+	public R(Rengine rengine) {
+		this();
+		assert rengine != null;
+		this.rengine = rengine;
+	}
+	
+	@Override
+	public String getName() {
+		return name;
+	}
+
+	@Override
+	public Object getEngine() {
+		return rengine;
+	}
+	
+	@Override
+	public Object eval(String script) throws ScriptException {
+		return rengine.eval(script);
+	}
+
+	@Override
+	public void end() {
+		rengine.end();
+	}
+
+}

plugins/afryca.ase.engine.R/src/afryca/ase/engine/R/l10n/Messages.java

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+package afryca.ase.engine.R.l10n;
+
+/**
+ * Localization messages
+ * 
+ * @author Sinbad²
+ * @version 3.0
+ */
+public class Messages {
+	public String invalid_jri;
+	public String invalid_jri_version;
+	public String invalid_r_home;
+	public String r_home_not_setted;
+	public String r_manual_linux;
+	public String r_manual_windows;
+}

plugins/afryca.ase.engine.R/src/afryca/ase/engine/R/l10n/Messages.properties

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+invalid_jri=Invalid JRI
+invalid_jri_version=Invalid JRI version
+invalid_r_home=Invalid R_HOME
+r_home_not_setted=R_HOME not setted
+r_manual_linux=R configuration for AFRYCA\
+\n\n\
+1 - Open R\
+\n\n\
+2 - Set R_HOME environment var. Execute in R the following command:\
+\n\
+\tR.home()\
+\n\
+\tSet the return at system environment var R_HOME (without '"' character).\
+\n\n\
+3 - Optional - Install rJava (if it is not installed yet)\
+\n\
+\tinstall.packages("rJava")\
+\n\n\
+4 - Set JRI value in afryca.ini. Execute in R the following command:\
+\n\
+\tsystem.file("jri",package="rJava")\
+\n\
+\tModify the REPLACE value in afryca.ini with the previous value\
+\n\
+\t(without '"' character) adding a final '/' character.
+r_manual_windows=Configuring R for AFRYCA\
+\n\n\
+1 - Open Rgui.exe with administrator permissions\
+\n\n\
+2 - set the environment variable R_HOME. Execute the command in Rgui:\
+\n\
+\tR.home()\
+\n\
+\tEstablish the value for the variable R_HOME (without the signs '"').\
+\n\n\
+3 - Add the path R_HOME\\bin[\\x64] to the PATH environment variable.\
+\n\n\
+4 - Optional - Install rJava (if it is not already installed)\
+\n\
+\tinstall.packages ("rJava")\
+\n\n\
+5 - Optional - Install Rsolnp (if it is not already installed)\
+\n\
+\tinstall.packages ("Rsolnp")\
+\n\n\
+6 - Execute the command in Rgui:\
+\n\tsystem.file ("jri", package = "rJava")\
+\n\
+\tAdd to the PATH variable the previous value\\[x64]\
+\n\n\
+7 - set JRI in file afryca.ini. Execute the command in Rgui:\
+\n\
+\tsystem.file ("jri", package = "rJava")\
+\n\
+\tModify the REPLACE value of afryca.ini with this value.\
+\n\
+\tIf you are using 64-bit binaries add /x64 to the previous value\
+\n\
+\t (is usually the name of this directory ...).\
+\n\
+\tC: / Users /.../rJava/jri -> C: / Users /.../ jri / x64

plugins/afryca.ase.engine.R/src/afryca/ase/engine/R/l10n/Messages_es.properties

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+invalid_jri=JRI inválido
+invalid_jri_version=Versión de JRI inválida
+invalid_r_home=Variable de entorno ''R_HOME'' inválida
+r_home_not_setted=Variable de entorno ''R_HOME'' no establecida
+r_manual_linux=Configuración de R para AFRYCA\
+\n\n\
+1 - Abrir R\
+\n\n\
+2 - Establecer la variable de entorno R_HOME. Ejecutar en R el comando:\
+\n\
+\tR.home()\
+\n\
+\tEstablecer el valor para la variable R_HOME (sin los signos '"').\
+\n\n\
+3 - Opcional - Instalar rJava (si aún no está instalado)\
+\n\
+\tinstall.packages("rJava")\
+\n\n\
+4 - Establecer JRI en afryca.ini. Ejecutar en R el comando:\
+\n\
+\tsystem.file("jri",package="rJava")\
+\n\
+\tModificar el valor REPLACE de afryca.ini con este valor\
+\n\
+\t(sin los signos '"') añadiendo al final el signo '/'.
+r_manual_windows=Configuración de R para AFRYCA\
+\n\n\
+1 - Abrir Rgui.exe\
+\n\n\
+2 - Establecer la variable de entorno R_HOME. Ejecutar en Rgui el comando:\
+\n\
+\tR.home()\
+\n\
+\tEstablecer el valor para la variable R_HOME (sin los signos '"').\
+\n\n\
+3 - Añadir Rcmd.exe al PATH (<R_HOME>\\bin[\\x64]).\
+\n\n\
+4 - Opcional - Instalar rJava (si aún no está instalado)\
+\n\
+\tinstall.packages("rJava")\
+\n\n\
+5 - Establecer JRI en afryca.ini. Ejecutar en Rgui el comando:\
+\n\
+\tsystem.file("jri",package="rJava")\
+\n\
+\tModificar el valor REPLACE de afryca.ini con este valor.\
+\n\
+\tSi está usando los binarios de 64 bits añada /x64 al valor anterior\
+\n\
+\t(es habitualmente el nombre de este directorio...).\
+\n\
+\tC:/Users /.../rJava/jri -> C:/Users/.../jri/x64

plugins/afryca.ase.engine.R/src/afryca/ase/engine/R/provider/IREngineProvider.java

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+package afryca.ase.engine.R.provider;
+
+import afryca.ase.engine.IEngine;
+
+/**
+ * R engine provider interface
+ * 
+ * @author Sinbad²
+ * @version 3.0
+ */
+public interface IREngineProvider {
+	
+	public static final String R = "R"; //$NON-NLS-1$
+	public static final String R_STATUS = "R_STATUS"; //$NON-NLS-1$
+	public static final String R_MANUAL = "R_MANUAL"; //$NON-NLS-1$
+	public static final String R_VERSION = "R_VERSION";
+	public static final String R_PATHS = "R_PATHS"; //$NON-NLS-1$
+
+	/**
+	 * Return R engine instance
+	 * 
+	 * @return R engine instance
+	 */
+	IEngine getEngine();
+}

plugins/afryca.ase.engine.R/src/afryca/ase/engine/R/provider/internal/REngineDefaultProvider.java

@@ -0,0 +1,187 @@
+package afryca.ase.engine.R.provider.internal;
+
+import java.io.File;
+import java.text.MessageFormat;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.annotation.PostConstruct;
+import javax.inject.Inject;
+
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.core.runtime.IStatus;
+import org.eclipse.core.runtime.Platform;
+import org.eclipse.core.runtime.Status;
+import org.eclipse.core.runtime.jobs.Job;
+import org.eclipse.e4.core.contexts.IEclipseContext;
+import org.eclipse.e4.core.services.nls.Translation;
+import org.rosuda.JRI.Rengine;
+
+import afryca.ase.engine.IEngine;
+import afryca.ase.engine.R.R;
+import afryca.ase.engine.R.l10n.Messages;
+import afryca.ase.engine.R.provider.IREngineProvider;
+
+/**
+ * R engine default provider
+ * 
+ * @author Sinbad²
+ * @version 3.0
+ */
+public class REngineDefaultProvider implements IREngineProvider {
+
+	private static final String VERSION = "--vanilla"; //$NON-NLS-1$
+
+	private static final String JRI_IGNORE_FLAG = "jri.ignore.ule"; //$NON-NLS-1$
+	private static final String JRI_IGNORE_FLAG_VALUE = "yes"; //$NON-NLS-1$
+
+	private static final String R_HOME = "R_HOME"; //$NON-NLS-1$
+	private static final String BINARIES_DIRECTORY = "bin"; //$NON-NLS-1$
+	private static final String LIBRARIES_DIRECTORY = "library"; //$NON-NLS-1$
+
+	private static final String R_VERSION_CMD = "R.version.string"; //$NON-NLS-1$
+	private static final String R_JRI_CMD = "system.file(\"jri\",package=\"rJava\")"; //$NON-NLS-1$
+
+	@Inject
+	@Translation
+	private Messages messages;
+
+	@Inject
+	private IEclipseContext context;
+
+	private IEclipseContext topContext;
+
+	private R engine;
+	
+	private Job job;
+
+	@PostConstruct
+	private void initialize() {
+		getTopContext();
+		saveRConfigurationInstructions();
+		saveRStatus();
+		createEngineJob(R);
+	}
+
+	private void getTopContext() {
+		IEclipseContext parent = context;
+		do {
+			topContext = parent;
+			parent = topContext.getParent();
+		} while (parent != null);
+	}
+
+	private void saveRConfigurationInstructions() {
+		topContext.set(R_MANUAL, getOSManual());
+	}
+
+	private String getOSManual() {
+		return Platform.OS_LINUX.equals(Platform.getOS())
+				? messages.r_manual_linux
+				: messages.r_manual_windows;
+	}
+
+	@Override
+	public IEngine getEngine() {
+		try {
+			job.join();
+		} catch (InterruptedException e) {
+			// Nothing to do
+		}
+		return (afryca.ase.engine.IEngine) topContext.get(R);
+	}
+
+	private void saveRStatus() {
+		String status = checkDependenciesStatus();
+		topContext.set(R_STATUS, status);
+	}
+
+	private String checkDependenciesStatus() {
+		System.setProperty(JRI_IGNORE_FLAG, JRI_IGNORE_FLAG_VALUE);
+		try {
+			if (!Rengine.jriLoaded) {
+				return messages.invalid_jri;
+			}
+			if (!Rengine.versionCheck()) {
+				return messages.invalid_jri_version;
+			}
+			if (System.getenv(R_HOME) == null) {
+				return messages.r_home_not_setted;
+			}
+			if (!validateR_HOME()) {
+				return messages.invalid_r_home;
+			}
+		} catch (UnsatisfiedLinkError error) {
+			return messages.invalid_jri;
+		}
+		return null;
+	}
+
+	private boolean validateR_HOME() {
+		String home = System.getenv(R_HOME);
+		File dir = new File(home);
+		if (!dir.exists()) {
+			return false;
+		}
+		if (!dir.canRead()) {
+			return false;
+		}
+		if (!dir.isDirectory()) {
+			return false;
+		}
+		List<String> files = Arrays.asList(dir.list());
+		if (!files.contains(BINARIES_DIRECTORY) || !files.contains(LIBRARIES_DIRECTORY)) {
+			return false;
+		}
+		return true;
+	}
+	
+	private void createEngineJob(String scriptName) {
+		job = new Job(scriptName) {
+			@Override
+			protected IStatus run(IProgressMonitor monitor) {
+				createEngine();
+				return (topContext.get(scriptName) != null)
+						? Status.OK_STATUS
+						: Status.CANCEL_STATUS;
+			}
+		};
+		job.schedule();
+	}
+
+	private void createEngine() {
+		Rengine rengine = getRengine();
+		topContext.set(R, (rengine != null)
+				? new R(rengine)
+				: null);
+	}
+
+	private Rengine getRengine() {
+		Rengine result = null;
+		if (topContext.get(R_STATUS) == null) {
+			result = new Rengine(new String[] { VERSION }, false, null);
+			if (!result.waitForR()) {
+				result = null;
+			} else {
+				String rVersion = result.eval(R_VERSION_CMD).asString();
+				String rJRI = result.eval(R_JRI_CMD).asString();
+				String rHome = System.getenv(R_HOME);
+				topContext.set(R_VERSION, rVersion);
+				topContext.set(
+						R_PATHS,
+						MessageFormat.format(
+								"{0}\n\nJRI:\n{1}\n\nR_HOME:\n{2}", //$NON-NLS-1$
+								rVersion,
+								rJRI,
+								rHome));
+			}
+		}
+		return result;
+	}
+
+	public void end() {
+		if (engine != null) {
+			engine.end();
+		}
+	}
+}

plugins/afryca.ase.engine.R/src/afryca/ase/engine/R/provider/internal/REngineProviderContextFunction.java

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+package afryca.ase.engine.R.provider.internal;
+
+import org.eclipse.e4.core.contexts.ContextFunction;
+import org.eclipse.e4.core.contexts.ContextInjectionFactory;
+import org.eclipse.e4.core.contexts.IEclipseContext;
+import org.eclipse.e4.ui.model.application.MApplication;
+
+import afryca.ase.engine.R.provider.IREngineProvider;
+
+/**
+ * R engine provider context function
+ * 
+ * @author Sinbad²
+ * @version 3.0
+ */
+public class REngineProviderContextFunction extends ContextFunction {
+	@Override
+	public Object compute(IEclipseContext context, String contextKey) {
+		IREngineProvider rEngineProvider = ContextInjectionFactory.make(REngineDefaultProvider.class,
+				context);
+		MApplication application = context.get(MApplication.class);
+		IEclipseContext applicationContext = application.getContext();
+		applicationContext.set(IREngineProvider.class, rEngineProvider);
+		return rEngineProvider;
+	}
+
+}