TryCatch disable by default, 4.0.0 release

Author: Kopilov

RCaller/build.gradle

@@ -8,7 +8,7 @@ repositories {
 }
 
 group = 'com.github.jbytecode'
-version = '4.0.0-SNAPSHOT'
+version = '4.0.0'
 description = 'RCaller is a software library which simplifies performing data analysis and statistical calculations in Java using R. The details are hidden from users including transferring data between platforms, function calls, and retrieving results.'
 
 dependencies {

RCaller/pom.xml

@@ -3,7 +3,7 @@
 
     <groupId>com.github.jbytecode</groupId>
     <artifactId>RCaller</artifactId>
-    <version>4.0.0-SNAPSHOT</version>
+    <version>4.0.0</version>
     <packaging>jar</packaging>
 
     <name>RCaller</name>

RCaller/src/main/java/benchmark/PassingArraysAndMatrices.java

@@ -53,7 +53,7 @@ private final static double[][] generateRandomMatrix(int n, int m) {
 
     public static void main(String[] args) {
 
-        performSimulation(/* size of vector */ 10, 10 /* times */ , SimType.Vector);
+        performSimulation(/* size of vector */ 2, 100 /* times */ , SimType.Vector);
 
     }
 
@@ -77,7 +77,7 @@ public static void performSimulation(int VectorSize, int SimCount, SimType type)
                 code.addRCode("result <- t(randommatrix)");
             }
             caller.setRCode(code);
-            caller.runAndReturnResultOnline("result");
+            caller.runAndReturnResultOnline("result", false);
             /* return variable is not handled */ caller.getParser().getAsDoubleArray("result");
             elapsed[simulations] = (int) System.currentTimeMillis() - timeStart;
 

RCaller/src/main/java/com/github/rcaller/rstuff/RCaller.java

@@ -278,11 +278,30 @@ private void runRCode() throws ExecutionException {
      * re-used by invoking this method again. When you are done with this
      * process, you must explicitly stop it.
      *
+     * If R raises an error, it is ignored. For throwing them in Java, use
+     * {@link #runAndReturnResultOnline(String, boolean)} with addTryCatch=true
+     *
      * @see #stopStreamConsumers()
      * @param var The R variable to return
      * @throws ExecutionException if R cannot be started
      */
     public void runAndReturnResultOnline(String var) throws ExecutionException {
+        runAndReturnResultOnline(var, false);
+    }
+
+    /**
+     * Runs the current code in the existing R instance (or in a new one) and
+     * returns the R variable "var". The R process is kept alive and can be
+     * re-used by invoking this method again. When you are done with this
+     * process, you must explicitly stop it.
+     *
+     * @since 4.0.0
+     * @see #stopStreamConsumers()
+     * @param var The R variable to return
+     * @param addTryCatch wrap original R code to tryCatch function (can impact performance)
+     * @throws ExecutionException if R cannot be started or raise error inside while addTryCatch parameter is true
+     */
+    public void runAndReturnResultOnline(String var, boolean addTryCatch) throws ExecutionException {
         rCallerOptions.resetRetries();
         boolean done = false;
         do {
@@ -323,7 +342,13 @@ public void runAndReturnResultOnline(String var) throws ExecutionException {
             }
 
             try {
-                var script = rCode.toTryCatchScript(errorFile) + rCode.createEndSignalCode(resultReadyControlFile);
+                String script;
+                if (addTryCatch) {
+                    script = rCode.toTryCatchScript(errorFile);
+                } else {
+                    script = rCode.toString();
+                }
+                script += rCode.createEndSignalCode(resultReadyControlFile);
                 rInput.write(script.getBytes(Globals.standardCharset));
                 rInput.flush();
             } catch (IOException e) {

RCaller/src/main/java/com/github/rcaller/rstuff/RCode.java

@@ -267,8 +267,8 @@ public String toString() {
     /**
      * Wrap current code to standard tryCatch function.
      * Error handler saves details to errorOutputFile if the error occurs.
-     * @param errorOutputFile
-     * @return
+     * @param errorOutputFile file to save error if it occurs
+     * @return generated script to be evaluated
      */
     String toTryCatchScript(File errorOutputFile) {
         //Using code snippet "An improved “error handler”" with withCallingHandlers nested in tryCatch

RCaller/src/main/resources/arrow_bridge.R

@@ -28,7 +28,6 @@ send_element_by_arrow <- function(obj, name, stream) {
     if (length(dim(obj)) > 2) {
       #3- and more-D arrays are not supported
       stop(paste(length(dim(obj)), "-D arrays are not supported"))
-      #TODO add try-catch support on toplevel
     }
     #1-D array and empty matrix can be converted to Vector
     dim(obj) <- c()

RCaller/src/test/java/com/github/rcaller/RunOnlineTest.java

@@ -216,7 +216,7 @@ public void exceptionCatchTest() {
         RCaller rcaller = RCaller.create();
         RCode code = rcaller.getRCode();
         code.addRCode("a <- log(\"not a number\")");
-        rcaller.runAndReturnResultOnline("a");
+        rcaller.runAndReturnResultOnline("a", true);
     }
 
     @Test
@@ -234,7 +234,7 @@ public void rHaltedTest() {
             rcaller.runAndReturnResultOnline("a");
         } catch (ExecutionException ex) {
             Logger.getLogger(RunOnlineTest.class.getName()).log(Level.SEVERE, ex.getMessage());
-            if (ex.getMessage().contains("R code throw an error:")) {
+            if (ex.getMessage().contains("R process died, stderr:")) {
                 exceptionThrown = true;
             }
             rcaller.stopRCallerOnline();