Allow the ability to specify a custom temp directory

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

@@ -7,35 +7,41 @@
 import java.io.File;
 import java.io.IOException;
 import java.nio.channels.FileChannel;
+import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
 import java.util.ArrayList;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
-
 public class TempFileService {
 
     private static final Logger logger = Logger.getLogger(TempFileService.class.getName());
 
-    private final ArrayList<Pair<File, FileChannel>> tempFiles;
-
-    public TempFileService(){
-        tempFiles = new ArrayList<>();
+    private final ArrayList<Pair<File, FileChannel>> tempFiles = new ArrayList<>();
+    private final Path tempDir;
+
+    public TempFileService() {
+        this.tempDir = null;
+    }
+
+    public TempFileService(final Path tempDir) {
+        this.tempDir = tempDir;
     }
-
-    public File createTempFile(String prefix, String suffix) throws IOException {
-        File f = File.createTempFile(prefix, suffix);
+
+    public File createTempFile(final String prefix,
+                               final String suffix) throws IOException {
+        File f = File.createTempFile(prefix, suffix, toFileOrNull(tempDir));
         FileChannel fileChannel = FileChannel.open(
                 f.toPath(),
                 StandardOpenOption.READ,
                 StandardOpenOption.WRITE,
                 StandardOpenOption.CREATE
         );
         tempFiles.add(new ImmutablePair<>(f, fileChannel));
-        return(f);
+        return f;
     }
-    
-    public void deleteRCallerTempFiles(){
+
+    public void deleteRCallerTempFiles() {
         for (Pair<File, FileChannel> tempFileAndChannel : tempFiles) {
             var fileChannel = tempFileAndChannel.getRight();
             var tempFile = tempFileAndChannel.getLeft();
@@ -66,4 +72,8 @@ public File createControlFile() {
             throw new ExecutionException("Can not create a temporary file for storing the R results: " + e.getMessage());
         }
     }
-}
+
+    private File toFileOrNull(final Path tempDir) {
+        return tempDir == null ? null : tempDir.toFile();
+    }
+}

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

@@ -18,7 +18,6 @@
 import static java.lang.String.join;
 import static java.lang.System.currentTimeMillis;
 
-
 public class RCaller {
 
     private static final Logger logger = Logger.getLogger(RCaller.class.getName());
@@ -40,14 +39,13 @@ protected RCaller(RCode rCode,
                    RStreamHandler rOutput,
                    RStreamHandler rError,
                    MessageSaver messageSaver,
-                   TempFileService tempFileService,
                    RCallerOptions rCallerOptions) {
         this.rCode = rCode;
         this.parser = parser;
         this.rOutput = rOutput;
         this.rError = rError;
         this.errorMessageSaver = messageSaver;
-        this.tempFileService = tempFileService;
+        this.tempFileService = rCode.getTempFileService();
         this.rCallerOptions = rCallerOptions;
 
         this.rError.addEventHandler(errorMessageSaver);
@@ -60,7 +58,12 @@ protected RCaller(RCode rCode,
      */
     public static RCaller create() {
         RCallerOptions rCallerOptions = RCallerOptions.create();
-        return new RCaller(RCode.create(), ROutputParser.create(rCallerOptions), new RStreamHandler(null, "Output"), new RStreamHandler(null, "Error"), new MessageSaver(), new TempFileService(), rCallerOptions);
+        return new RCaller(RCode.create(),
+                ROutputParser.create(rCallerOptions),
+                new RStreamHandler(null, "Output"),
+                new RStreamHandler(null, "Error"),
+                new MessageSaver(),
+                rCallerOptions);
     }
 
     /***
@@ -69,8 +72,13 @@ public static RCaller create() {
      * @param rCallerOptions given startup options
      * @return RCaller object
      */
-    public static RCaller create(RCallerOptions rCallerOptions) {
-        return new RCaller(RCode.create(rCallerOptions), ROutputParser.create(rCallerOptions), new RStreamHandler(null, "Output"), new RStreamHandler(null, "Error"), new MessageSaver(), new TempFileService(), rCallerOptions);
+    public static RCaller create(final RCallerOptions rCallerOptions) {
+        return new RCaller(RCode.create(rCallerOptions),
+                ROutputParser.create(rCallerOptions),
+                new RStreamHandler(null, "Output"),
+                new RStreamHandler(null, "Error"),
+                new MessageSaver(),
+                rCallerOptions);
     }
 
     /**
@@ -80,11 +88,16 @@ public static RCaller create(RCallerOptions rCallerOptions) {
      * @param rCallerOptions given startup object
      * @return RCaller object
      */
-    public static RCaller create(RCode rcode, RCallerOptions rCallerOptions) {
-        return new RCaller(rcode, ROutputParser.create(rCallerOptions), new RStreamHandler(null, "Output"), new RStreamHandler(null, "Error"), new MessageSaver(), new TempFileService(), rCallerOptions);
+    public static RCaller create(final RCode rcode,
+                                 final RCallerOptions rCallerOptions) {
+        return new RCaller(rcode,
+                ROutputParser.create(rCallerOptions),
+                new RStreamHandler(null, "Output"),
+                new RStreamHandler(null, "Error"),
+                new MessageSaver(),
+                rCallerOptions);
     }
 
-
     /**
      * Stops the threads that are emptying the output and error streams of the
      * live but idle R process. If R is still working, this may cause it to

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

@@ -10,48 +10,140 @@
 
 import javax.swing.*;
 import java.io.*;
+import java.nio.file.Path;
 
 public class RCode {
 
-    private StringBuilder code;
-    private TempFileService tempFileService = null;
+    private StringBuilder code = new StringBuilder();
+    private final TempFileService tempFileService;
     private final RCallerOptions rCallerOptions;
 
-
     private RCode() {
-        this.code = new StringBuilder();
-        rCallerOptions = RCallerOptions.create();
+        this.rCallerOptions = RCallerOptions.create();
+        this.tempFileService = new TempFileService();
+    }
+
+    private RCode(Path tempDir) {
+        this.rCallerOptions = RCallerOptions.create();
+        this.tempFileService = new TempFileService(tempDir);
     }
 
     private RCode(RCallerOptions rCallerOptions) {
-        this.code = new StringBuilder();
         this.rCallerOptions = rCallerOptions;
+        this.tempFileService = new TempFileService();
     }
 
+    private RCode(Path tempDir,
+                  RCallerOptions rCallerOptions) {
+        this.rCallerOptions = rCallerOptions;
+        this.tempFileService = new TempFileService(tempDir);
+    }
+
+    /**
+     * Static factory creator for the default object
+     *
+     * @return default RCode object
+     */
     public static RCode create() {
         RCode rCode = new RCode();
         rCode.clear();
         return rCode;
     }
 
+    /**
+     * Static factory creator with given temporary file directory
+     *
+     * @param tempDir the directory to use to store temporary files
+     * @return RCode object
+     */
+    public static RCode create(Path tempDir) {
+        RCode rCode = new RCode(tempDir);
+        rCode.clear();
+        return rCode;
+    }
+
+    /**
+     * Static factory creator with given string buffer
+     *
+     * @param stringBuffer the string buffer used for holding R code
+     * @return RCode object
+     */
     public static RCode create(StringBuffer stringBuffer) {
         RCode rCode = RCode.create();
         rCode.getCode().append(stringBuffer.toString());
         return rCode;
     }
 
+    /**
+     * Static factory creator with given temporary file directory and string buffer
+     *
+     * @param tempDir the directory to use to store temporary files
+     * @param stringBuffer the string buffer used for holding R code
+     * @return RCode object
+     */
+    public static RCode create(Path tempDir,
+                               StringBuffer stringBuffer) {
+        RCode rCode = RCode.create(tempDir);
+        rCode.getCode().append(stringBuffer.toString());
+        return rCode;
+    }
+
+    /**
+     * Static factory creator with given startup options
+     *
+     * @param rCallerOptions given startup object
+     * @return RCode object
+     */
     public static RCode create(RCallerOptions rCallerOptions) {
         RCode rCode = new RCode(rCallerOptions);
         rCode.clear();
         return rCode;
     }
 
-    public static RCode create(StringBuffer stringBuffer, RCallerOptions rCallerOptions) {
+    /**
+     * Static factory creator with given temporary file directory and startup options
+     *
+     * @param tempDir the directory to use to store temporary files
+     * @param rCallerOptions given startup object
+     * @return RCode object
+     */
+    public static RCode create(Path tempDir,
+                               RCallerOptions rCallerOptions) {
+        RCode rCode = new RCode(tempDir, rCallerOptions);
+        rCode.clear();
+        return rCode;
+    }
+
+    /**
+     * Static factory creator with given string buffer and startup options
+     *
+     * @param stringBuffer the string buffer used for holding R code
+     * @param rCallerOptions given startup object
+     * @return RCode object
+     */
+    public static RCode create(StringBuffer stringBuffer,
+                               RCallerOptions rCallerOptions) {
         RCode rCode = RCode.create(rCallerOptions);
         rCode.getCode().append(stringBuffer.toString());
         return rCode;
     }
 
+    /**
+     * Static factory creator with given temporary file directory and string buffer and startup options
+     *
+     * @param tempDir the directory to use to store temporary files
+     * @param stringBuffer the string buffer used for holding R code
+     * @param rCallerOptions given startup object
+     * @return RCode object
+     */
+    public static RCode create(Path tempDir,
+                               StringBuffer stringBuffer,
+                               RCallerOptions rCallerOptions) {
+        RCode rCode = RCode.create(tempDir, rCallerOptions);
+        rCode.getCode().append(stringBuffer.toString());
+        return rCode;
+    }
+
     public void setCode(StringBuffer sb) {
         this.code = new StringBuilder();
         clear();
@@ -68,6 +160,10 @@ public StringBuilder getCode() {
         return (this.code);
     }
 
+    public TempFileService getTempFileService() {
+        return tempFileService;
+    }
+
     public final void clear() {
         this.code.setLength(0);
         addRCode(RCodeIO.getInterprocessDependencies(rCallerOptions));
@@ -171,17 +267,14 @@ public void addString(String name, String value){
     }
 
     public void addDataFrame(String name, DataFrame dataFrame) {
-        RCodeUtils.addDataFrame(code, name, dataFrame);
+        RCodeUtils.addDataFrame(code, name, dataFrame, tempFileService);
     }
 
     public File startPlot() throws IOException {
         return (startPlot(GraphicsType.png));
     }
 
     public File startPlot(GraphicsType type) throws IOException {
-        if(tempFileService == null){
-            tempFileService = new TempFileService();
-        }
         //File f = File.createTempFile("RPlot", "." + type.name());
         File f = tempFileService.createTempFile("RPlot", "." + type.name());
         switch (type) {
@@ -227,9 +320,7 @@ public void R_source(String sourceFile) {
     }
 
     public void deleteTempFiles(){
-        if (tempFileService != null){
-            tempFileService.deleteRCallerTempFiles();   
-        }
+        tempFileService.deleteRCallerTempFiles();
     }
 
     @Override

RCaller/src/main/java/com/github/rcaller/util/RCodeUtils.java

@@ -1,6 +1,7 @@
 package com.github.rcaller.util;
 
 import com.github.rcaller.JavaObject;
+import com.github.rcaller.TempFileService;
 import com.github.rcaller.datatypes.DataFrame;
 import com.github.rcaller.exception.ExecutionException;
 import com.github.rcaller.io.CSVFileWriter;
@@ -201,21 +202,25 @@ public static void addRespectToType(StringBuilder rCode, String name, Object o,
                 throw new ExecutionException("Cannot convert Java object " + o.toString() + " in type of " + o.getClass().getCanonicalName() + " to R code due to " + iae.toString());
             }
         }
-
     }
 
     public static void addDataFrame(StringBuilder rCode, String name, DataFrame dataFrame) {
+        addDataFrame(rCode, name, dataFrame, null);
+    }
+
+    public static void addDataFrame(StringBuilder rCode, String name, DataFrame dataFrame, TempFileService tempFileService) {
+        if (tempFileService == null) {
+            tempFileService = new TempFileService();
+        }
         try {
-            File file = File.createTempFile("dataFrame", ".csv");
+            File file = tempFileService.createTempFile("dataFrame", ".csv");
             try (CSVFileWriter csvFileWriter = CSVFileWriter.create(file)) {
                 csvFileWriter.writeDataFrameToFile(dataFrame);
             }
             rCode.append(name).append(" <- read.csv(\"").append(Globals.getSystemSpecificRPathParameter(file)).append("\")\n");
-
         } catch (IOException e) {
             Logger.getLogger(RCodeUtils.class.getName()).log(Level.WARNING, "Couldn't export data frame to csv-file!", e.getStackTrace());
         }
-
     }
 
     public static void addResourceScript(StringBuilder rCode, String name) {