April 2010 - Nuiton-j2r-commits - mailman.cloud.codelutin.com

r213 - trunk
by tchemit＠users.nuiton.org 29 Apr '10

29 Apr '10

Author: tchemit Date: 2010-04-29 07:44:38 +0200 (Thu, 29 Apr 2010) New Revision: 213 Log: Utilisation de mavenpom4redmine 2.1.3 Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2010-04-22 16:27:14 UTC (rev 212) +++ trunk/pom.xml 2010-04-29 05:44:38 UTC (rev 213) @@ -34,7 +34,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmine</artifactId> - <version>2.1.2</version> + <version>2.1.3</version> </parent> <artifactId>nuiton-j2r</artifactId>

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r212 - in trunk/src: main/java/org/nuiton/j2r/jni main/java/org/nuiton/j2r/net test/java/org/nuiton/j2r
by jcouteau＠users.nuiton.org 22 Apr '10

22 Apr '10

Author: jcouteau Date: 2010-04-22 18:27:14 +0200 (Thu, 22 Apr 2010) New Revision: 212 Log: Come back to primitive types use, simplify convert methods Modified: trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java trunk/src/test/java/org/nuiton/j2r/JNITest.java trunk/src/test/java/org/nuiton/j2r/NetTest.java Modified: trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java 2010-04-22 09:29:23 UTC (rev 211) +++ trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java 2010-04-22 16:27:14 UTC (rev 212) @@ -145,7 +145,7 @@ * * @return the java object corresponding to the R expression. */ - private Object convertResult(REXP rexp) { + protected Object convertResult(REXP rexp) { if (rexp == null) { log.debug("Null returned"); return null; @@ -166,11 +166,7 @@ break; case REXP.XT_ARRAY_INT: int[] array = rexp.asIntArray(); - Integer[] bigArray = new Integer[array.length]; - for (int i = 0; i < array.length; i++) { - bigArray[i] = array[i]; - } - result = bigArray; + result = array; //Check if only one integer, return an integer. if (array.length == 1) { result = array[0]; @@ -178,15 +174,11 @@ break; case REXP.XT_ARRAY_DOUBLE: //if double array, return the rexp as double array. - double[] doublearray = rexp.asDoubleArray(); - Double[] bigdoublearray = new Double[doublearray.length]; - for (int i = 0; i < doublearray.length; i++) { - bigdoublearray[i] = doublearray[i]; - } - result = bigdoublearray; + double[] doubleArray = rexp.asDoubleArray(); + result = doubleArray; //Check if only one double, return a double. - if (doublearray.length == 1) { - result = doublearray[0]; + if (doubleArray.length == 1) { + result = doubleArray[0]; } break; case REXP.XT_BOOL: @@ -241,62 +233,9 @@ //get REXP asList to successfully detect lists. org.rosuda.JRI.RList list = rexp.asList(); if (klass.equals(RInstructions.CLASS_DATAFRAME)) { - - //if rexp is a data.frame - RDataFrame temp; - - //create the data list. - List<List<?>> data = new ArrayList<List<?>>(); - //get rexp as a list (data.frame is a list of vectors) - for (int i = 0; i < list.keys().length; i++) { - //for each vector, create a list and fill it with the - //content of the vector. - List<Object> templist; - REXP tempREXP = list.at(i); - Object[] convertedREXP = (Object[]) convertResult( - tempREXP); - templist = Arrays.asList(convertedREXP); - //add this list to the data list. - data.add(templist); - - } - //Create a new dataframe with the names, row.names and data - //gotten from rexp. It has no variable name so throws a - //RException. - - temp = new RDataFrame(this, rexp.getAttribute( - RInstructions.ATTRIBUTE_NAMES).asStringArray(), - rexp.getAttribute(RInstructions.ATTRIBUTE_ROWNAMES).asStringArray(), - data, ""); - result = temp; + result = convertToDataFrame(rexp); } else if (list != null) { - RList temp = new RList(this); - List<Object> data = new ArrayList<Object>(); - org.rosuda.JRI.RList dataList = rexp.asList(); - for (int i = 0; i < dataList.keys().length; i++) { - //for each object of the list, convert it to java. - REXP tempREXP = dataList.at(i); - Object convertedREXP = convertResult( - tempREXP); - //add this object to the data list. - data.add(convertedREXP); - - } - //Create a new list with the names and data - //gotten from rexp. It has no variable name so throws a - //RException. - try { - temp = new RList( - rexp.getAttribute(RInstructions.ATTRIBUTE_NAMES).asStringArray(), - data, this, ""); - } catch (RException re) { - //don't propagate the error as it is normal. Log it for debug. - if (log.isDebugEnabled()) { - log.debug( - "Converting REXP to RList. Creating list without variable name"); - } - } - result = temp; + result = convertToRList(rexp); } else { rexp.asVector(); } @@ -311,6 +250,82 @@ return result; } + protected RDataFrame convertToDataFrame(REXP rexp){ + + org.rosuda.JRI.RList list = rexp.asList(); + + RDataFrame temp; + + //create the data list. + List<List<?>> data = new ArrayList<List<?>>(); + //get rexp as a list (data.frame is a list of vectors) + for (int i = 0; i < list.keys().length; i++) { + //for each vector, create a list and fill it with the + //content of the vector. + List<Object> templist = new ArrayList<Object>(); + REXP tempREXP = list.at(i); + Object convertedREXP = convertResult(tempREXP); + if (convertedREXP instanceof int[]){ + for(int value:(int[])convertedREXP){ + templist.add(value); + } + } + if (convertedREXP instanceof double[]){ + for(double value:(double[])convertedREXP){ + templist.add(value); + } + } + if (convertedREXP instanceof String[]){ + templist.addAll(Arrays.asList((String[])convertedREXP)); + } + if (convertedREXP instanceof Boolean[]){ + templist.addAll(Arrays.asList((Boolean[])convertedREXP)); + } + + //add this list to the data list. + data.add(templist); + + } + //Create a new dataframe with the names, row.names and data + //gotten from rexp. It has no variable name so throws a + //RException. + + temp = new RDataFrame(this, rexp.getAttribute( + RInstructions.ATTRIBUTE_NAMES).asStringArray(), + rexp.getAttribute(RInstructions.ATTRIBUTE_ROWNAMES).asStringArray(), + data, ""); + return temp; + } + + protected RList convertToRList(REXP rexp){ + RList temp = new RList(this); + List<Object> data = new ArrayList<Object>(); + org.rosuda.JRI.RList dataList = rexp.asList(); + for (int i = 0; i < dataList.keys().length; i++) { + //for each object of the list, convert it to java. + REXP tempREXP = dataList.at(i); + Object convertedREXP = convertResult(tempREXP); + //add this object to the data list. + data.add(convertedREXP); + } + //Create a new list with the names and data + //gotten from rexp. It has no variable name so throws a + //RException. + try { + temp = new RList( + rexp.getAttribute(RInstructions.ATTRIBUTE_NAMES).asStringArray(), + data, this, ""); + } catch (RException re) { + //don't propagate the error as it is normal. Log it for debug. + if (log.isDebugEnabled()) { + log.debug( + "Converting REXP to RList. Creating list without variable name"); + } + } + + return temp; + } + /** * Terminate the R connection. * Modified: trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java 2010-04-22 09:29:23 UTC (rev 211) +++ trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java 2010-04-22 16:27:14 UTC (rev 212) @@ -152,7 +152,7 @@ */ @Override public Object eval(String expr) throws RException { - REXP result = null; + REXP result; try { //Encapsulate the R expression to get back the R error message //if thrown. @@ -204,15 +204,11 @@ //true if rexp is an integer or an integer array. //get rexp as an integer array int[] array = rexp.asIntegers(); - Integer[] bigArray = new Integer[array.length]; - for (int i = 0; i < array.length; i++) { - bigArray[i] = (Integer) array[i]; - } - result = bigArray; + result = array; //if the size of the array is 1, then return the integer alone. //else return the integer array. if (array.length == 1) { - result = (Integer) array[0]; + result = array[0]; } } else if (rexp.isFactor()) { //if rexp is a factor, return it as a RFactor. @@ -220,17 +216,13 @@ } else if (rexp.isNumeric()) { //true if rexp is a double or a double array. //get rexp as a double array - double[] doublearray = rexp.asDoubles(); - Double[] bigDoubleArray = new Double[doublearray.length]; - for (int i = 0; i < doublearray.length; i++) { - bigDoubleArray[i] = (Double) doublearray[i]; - } - result = bigDoubleArray; + double[] doubleArray = rexp.asDoubles(); + result = doubleArray; //if the size of the array is 1, then return the double alone. //else return the double array. - if (doublearray.length == 1) { - result = (Double) doublearray[0]; + if (doubleArray.length == 1) { + result = doubleArray[0]; } } else if (rexp.isString()) { //true if rexp is a string or a string array. @@ -263,61 +255,9 @@ //if rexp contains a null R expression return null; } else if (rexp.inherits(RInstructions.CLASS_DATAFRAME)) { - //if rexp is a data.frame - RDataFrame temp = new RDataFrame((REngine) this); - - //create the data list. - List<List<? extends Object>> data = - new ArrayList<List<? extends Object>>(); - //get rexp as a list (data.frame is a list of vectors) - org.rosuda.REngine.RList dataList = rexp.asList(); - for (int i = 0; i < dataList.size(); i++) { - //for each vector, create a list and fill it with the - //content of the vector. - List<Object> templist = new ArrayList<Object>(); - REXP tempREXP = dataList.at(i); - Object[] convertedREXP = (Object[]) convertResult(tempREXP); - templist = Arrays.asList(convertedREXP); - //add this list to the data list. - data.add(templist); - - } - //Create a new dataframe with the names, row.names and data - //gotten from rexp. It has no variable name so throws a - //RException. - temp = new RDataFrame((REngine) this, rexp.getAttribute( - RInstructions.ATTRIBUTE_NAMES).asStrings(), - rexp.getAttribute(RInstructions.ATTRIBUTE_ROWNAMES).asStrings(), - data, ""); - result = temp; + result = convertToRDataFrame(rexp); } else if (rexp.isList()) { - RList temp = new RList((REngine) this); - List<Object> data = new ArrayList<Object>(); - org.rosuda.REngine.RList dataList = rexp.asList(); - for (int i = 0; i < dataList.size(); i++) { - //for each vector, create a list and fill it with the - //content of the vector. - REXP tempREXP = dataList.at(i); - Object convertedREXP = convertResult(tempREXP); - //add this list to the data list. - data.add(convertedREXP); - - } - //Create a new dataframe with the names, row.names and data - //gotten from rexp. It has no variable name so throws a - //RException. - try { - temp = new RList(rexp.getAttribute( - RInstructions.ATTRIBUTE_NAMES).asStrings(), - data, (REngine) this, ""); - } catch (RException re) { - //don't propagate the error as it is normal. Log it for debug. - if (log.isDebugEnabled()) { - log.debug( - "Converting REXP to RList. Creating list without variable name"); - } - } - result = temp; + result = convertToRList(rexp); } else { //if the type is not supported. log.error("Unknown return type on : " + rexp.toString()); @@ -329,6 +269,82 @@ return result; } + protected RDataFrame convertToRDataFrame (REXP rexp) throws REXPMismatchException { + //if rexp is a data.frame + RDataFrame temp; + + //create the data list. + List<List<?>> data = new ArrayList<List<?>>(); + + //get rexp as a list (data.frame is a list of vectors) + org.rosuda.REngine.RList dataList = rexp.asList(); + + for (int i = 0; i < dataList.size(); i++) { + //for each vector, create a list and fill it with the + //content of the vector. + List<Object> templist = new ArrayList<Object>(); + REXP tempREXP = dataList.at(i); + Object convertedREXP = convertResult(tempREXP); + if (convertedREXP instanceof int[]){ + for(int value:(int[])convertedREXP){ + templist.add(value); + } + } + if (convertedREXP instanceof double[]){ + for(double value:(double[])convertedREXP){ + templist.add(value); + } + } + if (convertedREXP instanceof String[]){ + templist.addAll(Arrays.asList((String[])convertedREXP)); + } + if (convertedREXP instanceof Boolean[]){ + templist.addAll(Arrays.asList((Boolean[])convertedREXP)); + } + //add this list to the data list. + data.add(templist); + } + + //Create a new dataframe with the names, row.names and data + //gotten from rexp. It has no variable name so throws a + //RException. + temp = new RDataFrame(this, rexp.getAttribute( + RInstructions.ATTRIBUTE_NAMES).asStrings(), + rexp.getAttribute(RInstructions.ATTRIBUTE_ROWNAMES).asStrings(), + data, ""); + return temp; + } + + protected RList convertToRList (REXP rexp) throws REXPMismatchException { + RList temp = new RList(this); + List<Object> data = new ArrayList<Object>(); + org.rosuda.REngine.RList dataList = rexp.asList(); + for (int i = 0; i < dataList.size(); i++) { + //for each vector, create a list and fill it with the + //content of the vector. + REXP tempREXP = dataList.at(i); + Object convertedREXP = convertResult(tempREXP); + //add this list to the data list. + data.add(convertedREXP); + + } + //Create a new dataframe with the names, row.names and data + //gotten from rexp. It has no variable name so throws a + //RException. + try { + temp = new RList(rexp.getAttribute( + RInstructions.ATTRIBUTE_NAMES).asStrings(), + data, this, ""); + } catch (RException re) { + //don't propagate the error as it is normal. Log it for debug. + if (log.isDebugEnabled()) { + log.debug( + "Converting REXP to RList. Creating list without variable name"); + } + } + return temp; + } + /** * Terminate the connection with the server. * @@ -395,10 +411,8 @@ */ @Override public void commit() throws RException { - for (int i = 0; i < rInstructions.size(); i++) { - //run all methods stored in the list. - String expr = rInstructions.get(i); - voidEval(expr); + for (String instruction:rInstructions) { + voidEval(instruction); } //clear the list. rInstructions = new LinkedList<String>(); Modified: trunk/src/test/java/org/nuiton/j2r/JNITest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/JNITest.java 2010-04-22 09:29:23 UTC (rev 211) +++ trunk/src/test/java/org/nuiton/j2r/JNITest.java 2010-04-22 16:27:14 UTC (rev 212) @@ -92,8 +92,8 @@ @Test public void testDoubleArray() throws Exception { Object result = engine.eval("5.5:10.5"); - Assert.assertEquals(Double[].class, result.getClass()); - Double[] doubleArray = (Double[]) result; + Assert.assertEquals(double[].class, result.getClass()); + double[] doubleArray = (double[]) result; Assert.assertEquals(6, doubleArray.length); for (int i = 5; i < 11; i++) { double d = i + 0.5; @@ -127,7 +127,7 @@ t.startTiming(); engine.voidEval(V_OP_A); engine.voidEval(V_OP_B); - Double[] r = (Double[]) engine.eval(V_OP_AB); + double[] r = (double[]) engine.eval(V_OP_AB); t.endTiming(); Assert.assertEquals(V_MAX, r.length); } @@ -158,11 +158,9 @@ engine.voidEval("a<-as.integer(5)"); engine.voidEval("b<-as.integer(6)"); engine.voidEval("z<-c(a,b)"); - Integer[] testIntArray = (Integer[]) engine.eval("z"); - Integer toCompare1 = 5; - Assert.assertEquals(toCompare1, testIntArray[0]); - Integer toCompare2 = 6; - Assert.assertEquals(toCompare2, testIntArray[1]); + int[] testIntArray = (int[]) engine.eval("z"); + Assert.assertEquals(5, testIntArray[0]); + Assert.assertEquals(6, testIntArray[1]); } @Test @@ -184,27 +182,7 @@ Assert.assertTrue(testBoolArray[2]); } - /*@Test - public void testDataFrame() throws Exception { - engine.voidEval("X1<-data.frame(matrix(runif(5*100),nrow=100))"); - Assert.assertTrue(engine.eval("X1") instanceof Vector); - Assert.assertEquals(((Vector<REXP>) engine.eval("X1")).size(), 5); - Assert.assertEquals(((Vector<REXP>) engine.eval("X1")).get(0) - .asDoubleArray().length, 100); - - } @Test - public void testSobol() throws Exception { - engine.voidEval("library(sensitivity)"); - engine.voidEval("setwd(\"/home/couteau/isis-export/as__2009-04-07-17-36\")"); - engine.voidEval("a<-fast99(model=NULL,factors=c(2), n=17,M=1, q = \"qunif\", q.arg=list(min=0,max=1))"); - engine.voidEval("dput(a,file=\".fast99\")"); - Assert.assertTrue(engine.eval("a$X") instanceof Vector); - Assert.assertEquals(((Integer) engine.eval("length(a$X[,1])")).intValue(), 34); - - - }*/ - @Test public void testWorkingDirectory() throws Exception { //test linux paths @@ -216,8 +194,8 @@ //test windows paths File tempFile = File.createTempFile("test","", new File(System.getProperty("java.io.tmpdir"))); - tempFile.delete(); - tempFile.mkdirs(); + Boolean tempBoolean = tempFile.delete(); + tempBoolean = tempFile.mkdirs(); workingDirectory = new File(System.getProperty("java.io.tmpdir") + "\\" + tempFile.getName()); engine.setwd(workingDirectory); @@ -415,7 +393,7 @@ @Test public void testLongLines() throws Exception{ 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- Double[] test = (Double[])engine.eval("SensitivityBiomassY3"); + double[] test = (double[])engine.eval("SensitivityBiomassY3"); Assert.assertEquals(1500, test.length); } Modified: trunk/src/test/java/org/nuiton/j2r/NetTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-04-22 09:29:23 UTC (rev 211) +++ trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-04-22 16:27:14 UTC (rev 212) @@ -92,10 +92,10 @@ public void testIntArray() throws Exception { Object result = engine.eval("5:10"); Assert.assertNotNull(result); - Assert.assertEquals(Integer[].class, result.getClass()); - Integer[] intArray = (Integer[]) result; + Assert.assertEquals(int[].class, result.getClass()); + int[] intArray = (int[]) result; Assert.assertEquals(6, intArray.length); - for (Integer i = 5; i < 11; i++) { + for (int i = 5; i < 11; i++) { Assert.assertEquals(i, intArray[i - 5]); } } @@ -125,7 +125,7 @@ t.startTiming(); engine.voidEval(V_OP_A); engine.voidEval(V_OP_B); - Double[] r = (Double[]) engine.eval(V_OP_AB); + double[] r = (double[]) engine.eval(V_OP_AB); t.endTiming(); Assert.assertEquals(V_MAX, r.length); }

1 0

r211 - trunk
by tchemit＠users.nuiton.org 22 Apr '10

22 Apr '10

Author: tchemit Date: 2010-04-22 11:29:23 +0200 (Thu, 22 Apr 2010) New Revision: 211 Log: improve release profiles Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2010-04-21 15:08:21 UTC (rev 210) +++ trunk/pom.xml 2010-04-22 09:29:23 UTC (rev 211) @@ -136,8 +136,10 @@ </scm> <profiles> + +  <profile> - <id>release-profile</id> + <id>release-assembly-profile</id> <activation> <property> <name>performRelease</name>

1 0

r210 - in trunk/src: main/java/org/nuiton/j2r/jni main/java/org/nuiton/j2r/types test/java/org/nuiton/j2r
by jcouteau＠users.nuiton.org 21 Apr '10

21 Apr '10

Author: jcouteau Date: 2010-04-21 17:08:21 +0200 (Wed, 21 Apr 2010) New Revision: 210 Log: Simplify code Modified: trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java trunk/src/test/java/org/nuiton/j2r/DataframeTest.java Modified: trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java 2010-04-21 09:59:36 UTC (rev 209) +++ trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java 2010-04-21 15:08:21 UTC (rev 210) @@ -119,7 +119,7 @@ */ @Override public Object eval(String expr) throws RException { - REXP result = null; + REXP result; if (log.isDebugEnabled()) { log.debug(String.format(RInstructions.RTRY, expr)); } @@ -162,18 +162,18 @@ break; case REXP.XT_INT: //if integer, return the rexp as integer - result = (Integer) rexp.asInt(); + result = rexp.asInt(); break; case REXP.XT_ARRAY_INT: int[] array = rexp.asIntArray(); Integer[] bigArray = new Integer[array.length]; for (int i = 0; i < array.length; i++) { - bigArray[i] = (Integer) array[i]; + bigArray[i] = array[i]; } result = bigArray; //Check if only one integer, return an integer. if (array.length == 1) { - result = (Integer) array[0]; + result = array[0]; } break; case REXP.XT_ARRAY_DOUBLE: @@ -181,7 +181,7 @@ double[] doublearray = rexp.asDoubleArray(); Double[] bigdoublearray = new Double[doublearray.length]; for (int i = 0; i < doublearray.length; i++) { - bigdoublearray[i] = (Double) doublearray[i]; + bigdoublearray[i] = doublearray[i]; } result = bigdoublearray; //Check if only one double, return a double. @@ -198,7 +198,7 @@ //Get a double array result = rexp.asDoubleArray(); //return only the first element. - result = (Double) ((double[]) result)[0]; + result = ((double[]) result)[0]; break; case REXP.XT_NULL: //if null return null @@ -243,18 +243,16 @@ if (klass.equals(RInstructions.CLASS_DATAFRAME)) { //if rexp is a data.frame - RDataFrame temp = new RDataFrame((REngine) this); + RDataFrame temp; //create the data list. - List<List<? extends Object>> data = - new ArrayList<List<? extends Object>>(); + List<List<?>> data = new ArrayList<List<?>>(); //get rexp as a list (data.frame is a list of vectors) - org.rosuda.JRI.RList dataList = rexp.asList(); - for (int i = 0; i < dataList.keys().length; i++) { + for (int i = 0; i < list.keys().length; i++) { //for each vector, create a list and fill it with the //content of the vector. - List<Object> templist = new ArrayList<Object>(); - REXP tempREXP = dataList.at(i); + List<Object> templist; + REXP tempREXP = list.at(i); Object[] convertedREXP = (Object[]) convertResult( tempREXP); templist = Arrays.asList(convertedREXP); @@ -265,13 +263,14 @@ //Create a new dataframe with the names, row.names and data //gotten from rexp. It has no variable name so throws a //RException. - temp = new RDataFrame((REngine) this, rexp.getAttribute( + + temp = new RDataFrame(this, rexp.getAttribute( RInstructions.ATTRIBUTE_NAMES).asStringArray(), rexp.getAttribute(RInstructions.ATTRIBUTE_ROWNAMES).asStringArray(), data, ""); result = temp; } else if (list != null) { - RList temp = new RList((REngine) this); + RList temp = new RList(this); List<Object> data = new ArrayList<Object>(); org.rosuda.JRI.RList dataList = rexp.asList(); for (int i = 0; i < dataList.keys().length; i++) { @@ -289,7 +288,7 @@ try { temp = new RList( rexp.getAttribute(RInstructions.ATTRIBUTE_NAMES).asStringArray(), - data, (REngine) this, ""); + data, this, ""); } catch (RException re) { //don't propagate the error as it is normal. Log it for debug. if (log.isDebugEnabled()) { @@ -371,10 +370,9 @@ */ @Override public void commit() throws RException { - for (int i = 0; i < rInstructions.size(); i++) { + for (String expr:rInstructions) { //Send one by one, all the Rinstructions stored, beginning by //the first one stored - String expr = rInstructions.get(i); engine.eval(expr); } //Clean the list of R instructions Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-21 09:59:36 UTC (rev 209) +++ trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-21 15:08:21 UTC (rev 210) @@ -31,7 +31,6 @@ import java.io.FileReader; import java.io.FileWriter; import java.io.IOException; -import java.io.Serializable; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; @@ -537,23 +536,13 @@ public Object get(int x, int y) throws RException { checkX(x); checkY(y); - if ((engine.isAutoCommit())&&(this.variable!=null)&&(!this.variable.isEmpty())) { + if (engine.isAutoCommit()) { + checkVariable(); Object returnObject = engine.eval(String.format( RInstructions.GET_DATAFRAME_ITEM, this.variable, y + 1, x + 1)); - if (returnObject instanceof String) { - ((ArrayList<String>) this.data.get(x)).set(y, - (String) returnObject); - } else if (returnObject instanceof Double) { - ((ArrayList<Double>) this.data.get(x)).set(y, - (Double) returnObject); - } else if (returnObject instanceof Integer) { - ((ArrayList<Integer>) this.data.get(x)).set(y, - (Integer) returnObject); - } else if (returnObject instanceof Boolean) { - ((ArrayList<Boolean>) this.data.get(x)).set(y, - (Boolean) returnObject); - } + + ((ArrayList<Object>) this.data.get(x)).set(y,returnObject); } return this.data.get(x).get(y); } @@ -579,6 +568,8 @@ return data; } + initData(rowNumber, columnNumber); + try { for(int i=0;i<columnNumber;i++){ for(int j=0;j<rowNumber;j++){ @@ -594,6 +585,20 @@ return data; } + private void initData(int rowNumber, int columnNumber){ + + + this.data = new ArrayList<List<?>>(); + + for (int i=0;i<columnNumber;i++){ + List<Object> column = new ArrayList<Object>(); + for(int j=0;j<rowNumber;j++){ + column.add(new Object()); + } + this.data.add(column); + } + } + /** * Method to assign the data of the R data.frame (there is no synchronizing * with R, use the commit() method to send data to R. @@ -619,68 +624,23 @@ public void getFrom(String variable) throws RException { this.variable = variable; if (engine.isAutoCommit()) { - if (rowNames != null) { - rowNames.clear(); - } else { - rowNames = new ArrayList<String>(); - } - if (names != null) { - names.clear(); - } else { - names = new ArrayList<String>(); - } - if (data != null) { - data.clear(); - } else { - data = new ArrayList<List<?>>(); - } - if (attributes != null) { - attributes.clear(); - } else { - attributes = new HashMap<String, Object>(); - } - //update row names - String[] rowNamesArray = (String[]) engine.eval(String.format( - RInstructions.GET_ROW_NAMES, this.variable)); - rowNames.addAll(Arrays.asList(rowNamesArray)); + rowNames.clear(); + names.clear(); + data.clear(); + attributes.clear(); - //update names - String[] namesArray = (String[]) engine.eval(String.format( - RInstructions.GET_NAMES, this.variable)); - names.addAll(Arrays.asList(namesArray)); - //update data - Integer dataframelength = (Integer) engine.eval(String.format( - RInstructions.LENGTH, this.variable)); + getData(); - for (int i = 0; i < dataframelength; i++) { - Integer arrayListLength = (Integer) engine.eval(String.format( - RInstructions.LENGTH_COLUMN, this.variable, i + 1)); - ArrayList<Serializable> thisColumn = - new ArrayList<Serializable>(); - for (int j = 0; j < arrayListLength; j++) { - thisColumn.add((Serializable) engine.eval(String.format( - RInstructions.GET_DATAFRAME_ITEM, this.variable, - j + 1, i + 1))); - } - data.add(thisColumn); + //update row names + getRowNames(); - } + //update names + getNames(); //update attributes - Integer attributeslength = (Integer) engine.eval(String.format( - RInstructions.LENGTH_ATTRIBUTES, this.variable)); - - for (int i = 0; - i < attributeslength; i++) { - String key = (String) engine.eval(String.format( - RInstructions.GET_ATTRIBUTE_NAME, this.variable, i + 1)); - - String attribute = (String) engine.eval("toString(" + String.format( - RInstructions.GET_ATTRIBUTE, this.variable, key) + ")"); - attributes.put(key, attribute); - } + getAttributes(); } } @@ -814,21 +774,11 @@ dataSize = splitted.length; } - //if data has already been initialized, clear it. - if (this.data != null) { - this.data.clear(); - } + //clear data, rowNames and names + this.data.clear(); + this.rowNames.clear(); + this.names.clear(); - //Clear rowNames - if ((this.rowNames != null)) { - this.rowNames.clear(); - } - - //if names has already been initialized, clear it. - if (this.names != null) { - this.names.clear(); - } - if (names) { //if names are present in the file, parse the first line to get //the names. Modified: trunk/src/test/java/org/nuiton/j2r/DataframeTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/DataframeTest.java 2010-04-21 09:59:36 UTC (rev 209) +++ trunk/src/test/java/org/nuiton/j2r/DataframeTest.java 2010-04-21 15:08:21 UTC (rev 210) @@ -786,6 +786,23 @@ dataframe2.importCsv(new File("/tmp/test.csv"), true, true, 3.0); dataframe2.setVariable("a"); + List<List<?>> data2 = dataframe2.getData(); + + //Test data + Assert.assertEquals(3.0, data2.get(0).get(0)); + Assert.assertEquals(4.5, data2.get(0).get(1)); + Assert.assertEquals(0.01, data2.get(0).get(2)); + Assert.assertEquals(1.0, data2.get(1).get(0)); + Assert.assertEquals(5555555555555555555555.0, data2.get(1).get(1)); + Assert.assertEquals(3.0, data2.get(1).get(2)); + //Test names + Assert.assertEquals("column1", dataframe2.getNames().get(0)); + Assert.assertEquals("column2", dataframe2.getNames().get(1)); + //Test row names + Assert.assertEquals("row 1", dataframe2.getRowNames().get(0)); + Assert.assertEquals("row 2", dataframe2.getRowNames().get(1)); + Assert.assertEquals("row 3", dataframe2.getRowNames().get(2)); + //Test import with same type for each column (String). names = new ArrayList<String>();

1 0

r209 - trunk/src/main/java/org/nuiton/j2r/types
by jcouteau＠users.nuiton.org 21 Apr '10

21 Apr '10

Author: jcouteau Date: 2010-04-21 11:59:36 +0200 (Wed, 21 Apr 2010) New Revision: 209 Log: Add toString method to RList Simplify set(x,y) methods for RDataFrame Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java trunk/src/main/java/org/nuiton/j2r/types/RList.java Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-21 07:56:37 UTC (rev 208) +++ trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-21 09:59:36 UTC (rev 209) @@ -417,20 +417,41 @@ * if no variable name has been given to the data.frame or the * data type is not allowed at this location. */ - public void set(int x, int y, Object data) throws RException { + public void set(int x, int y, Double data) throws RException { checkVariable(); checkX(x); checkY(y); try { - if (this.data.get(x).get(y) instanceof Double) { - ((ArrayList<Double>) this.data.get(x)).set(y, (Double) data); + if (this.data.get(x).get(y) instanceof Double){ + //set the value in the data.frame + ((ArrayList<Double>) this.data.get(x)).set(y, data); + + //send the value to REngine engine.voidEval(String.format(RInstructions.SET_DATAFRAME_ITEM, - this.variable, y + 1, - x + 1, - data)); - } else if (this.data.get(x).get(y) instanceof Boolean) { - ((ArrayList<Boolean>) this.data.get(x)).set(y, (Boolean) data); - if ((Boolean) data) { + this.variable, y + 1, x + 1, data)); + } else { + throw new RException( + "The data.frame does not accept this type on those coordinates : " + + data.getClass()); + } + } catch (ClassCastException eee) { + throw new RException( + "The data.frame does not accept this type on those coordinates : " + + data.getClass(), eee); + } + } + + public void set(int x, int y, Boolean data) throws RException { + checkVariable(); + checkX(x); + checkY(y); + try { + if (this.data.get(x).get(y) instanceof Boolean){ + //set the value in the data.frame + ((ArrayList<Boolean>) this.data.get(x)).set(y, data); + + //send the value to REngine + if (data) { engine.voidEval(String.format( RInstructions.SET_DATAFRAME_ITEM, this.variable, y + 1, x + 1, RInstructions.TRUE)); @@ -439,26 +460,65 @@ RInstructions.SET_DATAFRAME_ITEM, this.variable, y + 1, x + 1, RInstructions.FALSE)); } - } else if (this.data.get(x).get(y) instanceof String) { - ((ArrayList<String>) this.data.get(x)).set(y, (String) data); + } else { + throw new RException( + "The data.frame does not accept this type on those coordinates : " + + data.getClass()); + } + } catch (ClassCastException eee) { + throw new RException( + "The data.frame does not accept this type on those coordinates : " + + data.getClass(), eee); + } + } + + public void set(int x, int y, String data) throws RException { + checkVariable(); + checkX(x); + checkY(y); + try { + if (this.data.get(x).get(y) instanceof String){ + //set the value in the data.frame + ((ArrayList<String>) this.data.get(x)).set(y, data); + + //send the value to REngine engine.voidEval(String.format(RInstructions.SET_DATAFRAME_ITEM, this.variable, y + 1, x + 1, "\"" + data + "\"")); - } else if (this.data.get(x).get(y) instanceof Integer) { - ((ArrayList<Integer>) this.data.get(x)).set(y, (Integer) data); + } else { + throw new RException( + "The data.frame does not accept this type on those coordinates : " + + data.getClass()); + } + } catch (ClassCastException eee) { + throw new RException( + "The data.frame does not accept this type on those coordinates : " + + data.getClass(), eee); + } + } + + public void set(int x, int y, Integer data) throws RException { + checkVariable(); + checkX(x); + checkY(y); + try { + if (this.data.get(x).get(y) instanceof Integer){ + //set the value in the data.frame + ((ArrayList<Integer>) this.data.get(x)).set(y, data); + + //send the value to REngine engine.voidEval(String.format(RInstructions.SET_DATAFRAME_ITEM, this.variable, y + 1, x + 1, String.format( - RInstructions.AS_INTEGER, data))); + RInstructions.AS_INTEGER, data))); } else { - throw new ArrayStoreException( + throw new RException( "The data.frame does not accept this type on those coordinates : " + - data.getClass()); + data.getClass()); } - } catch (ClassCastException cce) { + } catch (ClassCastException eee) { throw new RException( "The data.frame does not accept this type on those coordinates : " + - data.getClass(), cce); + data.getClass(), eee); } - } /** @@ -899,10 +959,8 @@ Integer numberOfLines = 0; //Calculate the number of lines to display - if (!this.data.isEmpty()) { - if (!this.data.get(0).isEmpty()){ + if ((!this.data.isEmpty()) &&(!this.data.get(0).isEmpty())){ numberOfLines = this.data.get(0).size(); - } } if (displayNames){ numberOfLines += 1; Modified: trunk/src/main/java/org/nuiton/j2r/types/RList.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-21 07:56:37 UTC (rev 208) +++ trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-21 09:59:36 UTC (rev 209) @@ -141,25 +141,7 @@ String returnString = this.variable + "<-list("; if ((this.data != null) && (!(this.data.isEmpty()))) { for (int i = 0; i < data.size(); i++) { - if (!(this.names.isEmpty())) { - returnString += this.names.get(i) + "="; - } - if (data.get(i) instanceof String) { - returnString += "\"" + data.get(i) + "\","; - } else if ((data.get(i) instanceof Boolean) && - ((Boolean) data.get(i))) { - returnString += RInstructions.TRUE + ","; - } else if ((data.get(i) instanceof Boolean) && - (!(Boolean) data.get(i))) { - returnString += RInstructions.FALSE + ","; - } else if (data.get(i) instanceof Integer) { - returnString += String.format(RInstructions.AS_INTEGER, - data.get(i)) + ","; - } else if (data.get(i) instanceof REXP) { - returnString += ((REXP) (data.get(i))).toRString() + ","; - } else { - returnString += data.get(i) + ","; - } + returnString += toRString(i); } returnString = returnString.substring(0, returnString.length() - 1); } @@ -173,6 +155,38 @@ } /** + * Create the R instruction for element at index i + * @param i index + * @return the corresponding R instruction + * @throws RException if an error occur creating R instruction for REXPs + */ + private String toRString(int i) throws RException { + String returnString=""; + + Object obj = data.get(i); + + if (!(this.names.isEmpty())) { + returnString += this.names.get(i) + "="; + } + + if (obj instanceof String) { + returnString += "\"" + obj + "\","; + } else if ((obj instanceof Boolean) && ((Boolean) obj)) { + returnString += RInstructions.TRUE + ","; + } else if ((obj instanceof Boolean) && (!(Boolean)obj)) { + returnString += RInstructions.FALSE + ","; + } else if (obj instanceof Integer) { + returnString += String.format(RInstructions.AS_INTEGER, obj) + ","; + } else if (obj instanceof REXP) { + returnString += ((REXP)obj).toRString() + ","; + } else { + returnString += obj + ","; + } + + return returnString; + } + + /** * Method to set the xth object of the list to a value. * * @param x

1 0

r208 - trunk/src/main/java/org/nuiton/j2r/types
by jcouteau＠users.nuiton.org 21 Apr '10

21 Apr '10

Author: jcouteau Date: 2010-04-21 09:56:37 +0200 (Wed, 21 Apr 2010) New Revision: 208 Log: Add toString method on RList, almost looks like in R Modified: trunk/src/main/java/org/nuiton/j2r/types/RList.java Modified: trunk/src/main/java/org/nuiton/j2r/types/RList.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-20 13:07:38 UTC (rev 207) +++ trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-21 07:56:37 UTC (rev 208) @@ -411,4 +411,24 @@ x, this.data.size())); } } + + @Override + public String toString(){ + + String returnString=""; + + for(int i=0;i<this.data.size();i++){ + + //display the index + if( (names!=null) && (!names.isEmpty()) && (names.get(i)!=null)){ + returnString += "[[" + names.get(i) + "]]\n"; + } else { + returnString += "[[" + i + "]]\n"; + } + + //display the item at index i + returnString += this.data.get(i) + "\n\n"; + } + return returnString; + } }

1 0

r207 - trunk
by tchemit＠users.nuiton.org 20 Apr '10

20 Apr '10

Author: tchemit Date: 2010-04-20 15:07:38 +0200 (Tue, 20 Apr 2010) New Revision: 207 Log: Utilisation de mavenpom4redmine 2.1.2 Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2010-04-19 15:28:31 UTC (rev 206) +++ trunk/pom.xml 2010-04-20 13:07:38 UTC (rev 207) @@ -34,7 +34,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmine</artifactId> - <version>2.1.1</version> + <version>2.1.2</version> </parent> <artifactId>nuiton-j2r</artifactId>

1 0

r206 - trunk/src/main/java/org/nuiton/j2r/types
by jcouteau＠users.nuiton.org 19 Apr '10

19 Apr '10

Author: jcouteau Date: 2010-04-19 17:28:31 +0200 (Mon, 19 Apr 2010) New Revision: 206 Log: Remove a system.out.println() Modified: trunk/src/main/java/org/nuiton/j2r/types/RList.java Modified: trunk/src/main/java/org/nuiton/j2r/types/RList.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-19 14:44:30 UTC (rev 205) +++ trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-19 15:28:31 UTC (rev 206) @@ -165,10 +165,10 @@ } returnString += ")"; + if (log.isDebugEnabled()){ + log.debug(returnString); + } - - System.out.println(returnString); - return returnString; }

1 0

r205 - trunk/src/main/java/org/nuiton/j2r/types
by jcouteau＠users.nuiton.org 19 Apr '10

19 Apr '10

Author: jcouteau Date: 2010-04-19 16:44:30 +0200 (Mon, 19 Apr 2010) New Revision: 205 Log: Deal with autocommit mode in DataFrame getData() method Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-19 13:20:43 UTC (rev 204) +++ trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-19 14:44:30 UTC (rev 205) @@ -499,13 +499,38 @@ } /** - * Method to get the ArrayLists of the R data.frame (there is no - * synchronizing with R). + * Method to get the ArrayLists of the R data.frame. Synchronize with R only + * if in autocommit mode and variable set. * - * @return a ArrayList containing the ArrayLists of the R data.frame + * @return the data of the data.frame */ public List<List<?>> getData() { - //TODO JC manage the autocommit mode here. + if (this.engine.isAutoCommit()){ + + int rowNumber; + int columnNumber; + + try { + checkVariable(); + int[] dim = dim(); + rowNumber = dim[0]; + columnNumber = dim[1]; + } catch (RException eee) { + return data; + } + + try { + for(int i=0;i<columnNumber;i++){ + for(int j=0;j<rowNumber;j++){ + get(i,j); + } + } + + } catch (RException eee) { + log.error("An error occurred while trying to contact R"); + } + + } return data; }

1 0

r204 - in trunk/src: main/java/org/nuiton/j2r/types test/java/org/nuiton/j2r
by jcouteau＠users.nuiton.org 19 Apr '10

19 Apr '10

Author: jcouteau Date: 2010-04-19 15:20:43 +0200 (Mon, 19 Apr 2010) New Revision: 204 Log: Improve attributes management Modified: trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java trunk/src/test/java/org/nuiton/j2r/ListTest.java Modified: trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java 2010-04-19 10:50:13 UTC (rev 203) +++ trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java 2010-04-19 13:20:43 UTC (rev 204) @@ -25,10 +25,8 @@ package org.nuiton.j2r.types; -import java.util.Arrays; -import java.util.List; -import java.util.Map; -import java.util.Set; +import java.util.*; + import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.j2r.REngine; @@ -65,54 +63,9 @@ @Override public void setAttributes(Map<String, Object> attributes) throws RException { - //TODO JC should be useful to test the validity of attributes before assigning it. - this.attributes = attributes; - - if ((this.attributes != null) && (!this.attributes.isEmpty())) { - Set<String> keyset = attributes.keySet(); - for (String key : keyset) { - //foreach type of attribute, adapt the R instruction. - if (this.attributes.get(key) instanceof String) { - engine.eval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, key, - "\"" + this.attributes.get(key) + "\"")); - //String, value between quotes - } else if (this.attributes.get(key) instanceof Double) { - engine.eval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, - key, this.attributes.get(key))); - } else if (this.attributes.get(key) instanceof Integer) { - engine.eval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, - key, String.format(RInstructions.AS_INTEGER, - this.attributes.get(key)))); - //Integer, value formated by the R function : as.integer() - } else if (this.attributes.get(key) instanceof Boolean) { - if ((Boolean) this.attributes.get(key)) { - engine.eval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, - key, RInstructions.TRUE)); - //Boolean true replaced by TRUE - } else { - engine.eval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, - key, RInstructions.FALSE)); - //Boolean false replaced by REPLACE - } - } else if (this.attributes.get(key) instanceof REXP) { - engine.eval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, - key, - ((REXP) this.attributes.get(key)).toRString())); - //REXP replaced by the result of their toRString() method. - } else { - if (log.isWarnEnabled()) { - log.warn("This attribute is not valid : " + key + - " ; " + this.attributes.get(key) + - ". It will not be sent to R"); - //if the attribute is not recognised. - } - } + if (attributes!=null){ + for(Map.Entry<String, Object> entry : attributes.entrySet()){ + setAttribute(entry.getKey(),entry.getValue()); } } } @@ -166,7 +119,7 @@ if (returnedAttribute != null) { if (attributes.containsKey(attribute)) { //if the attribute already exists, remove it first (or you - //will have too times the same attribubte with different + //will have too times the same attribute with different //values) attributes.remove(attribute); attributes.put(attribute, returnedAttribute); @@ -186,45 +139,63 @@ /** {@inheritDoc} */ @Override public void setAttribute(String attribute, Object value) throws RException { - //variable to check if the attribute is valid before setting it. - boolean isOK = false; if (value instanceof String) { - isOK = true; - engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, attribute, "\"" + value + "\"")); - //if String, between quotes + setAttribute(attribute, (String)value); } else if (value instanceof Double) { - isOK = true; - engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, attribute, value)); + setAttribute(attribute, (Double)value); } else if (value instanceof Integer) { - isOK = true; - engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, attribute, String.format( - RInstructions.AS_INTEGER, value))); - //If integer in the R function : as.integer() + setAttribute(attribute, (Integer)value); } else if (value instanceof Boolean) { - isOK = true; - //R boolean is upper case - engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, attribute, value.toString().toUpperCase())); + setAttribute(attribute,(Boolean)value); } else if (value instanceof REXP) { - isOK = true; - engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, attribute, ((REXP) value).toRString())); - //if REXP, use its method toRString() + setAttribute(attribute, (REXP)value); } else { log.warn("This attribute is not valid : " + attribute + " ; " + value + ". It will not be processed"); } - //if attribute is valid, out it in the attribute list. - if (isOK) { - if (attributes.containsKey(attribute)) { - attributes.remove(attribute); - attributes.put(attribute, value); - } else { - attributes.put(attribute, value); - } + } + + public void setAttribute(String attribute, Double value) throws RException { + engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, + this.variable, attribute, value)); + putAttributeInData(attribute,value); + } + + public void setAttribute(String attribute, Integer value) throws RException { + //If integer in the R function : as.integer() + engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, + this.variable, attribute, String.format( + RInstructions.AS_INTEGER, value))); + putAttributeInData(attribute,value); + } + + public void setAttribute(String attribute, Boolean value) throws RException { + //R boolean is upper case + engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, + this.variable, attribute, value.toString().toUpperCase())); + putAttributeInData(attribute,value); + } + + public void setAttribute(String attribute, String value) throws RException { + //if String, between quotes + engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, + this.variable, attribute, "\"" + value + "\"")); + putAttributeInData(attribute,value); + } + + public void setAttribute(String attribute, REXP value) throws RException { + //if REXP, use its method toRString() + engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, + this.variable, attribute, value.toRString())); + putAttributeInData(attribute,value); + } + + private void putAttributeInData(String attribute, Object value){ + if (attributes.containsKey(attribute)) { + attributes.remove(attribute); + attributes.put(attribute, value); + } else { + attributes.put(attribute, value); } } Modified: trunk/src/test/java/org/nuiton/j2r/ListTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/ListTest.java 2010-04-19 10:50:13 UTC (rev 203) +++ trunk/src/test/java/org/nuiton/j2r/ListTest.java 2010-04-19 13:20:43 UTC (rev 204) @@ -134,8 +134,7 @@ assertEquals("c", list1.getNames().get(2)); assertEquals("d", list1.getNames().get(3)); - engine - .voidEval("a<-list(a=as.integer(1),b=\"toto\",c=3.6,d=TRUE,e=FALSE)"); + engine.voidEval("a<-list(a=as.integer(1),b=\"toto\",c=3.6,d=TRUE,e=FALSE)"); try { list1.getNames(); Assert.fail("Error was not thrown although it should have been");

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