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

r215 - in trunk/src: main/java/org/nuiton/j2r/jni main/java/org/nuiton/j2r/net main/java/org/nuiton/j2r/types test/java/org/nuiton/j2r
by jcouteau＠users.nuiton.org 14 May '10

14 May '10

Author: jcouteau Date: 2010-05-14 11:23:03 +0200 (Fri, 14 May 2010) New Revision: 215 Url: http://nuiton.org/repositories/revision/nuiton-j2r/215 Log: Fix NPE when getting list with anonymous elements Modified: trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java trunk/src/main/java/org/nuiton/j2r/types/RList.java trunk/src/test/java/org/nuiton/j2r/JNITest.java trunk/src/test/java/org/nuiton/j2r/ListTest.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 2010-05-09 12:34:27 UTC (rev 214) +++ trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java 2010-05-14 09:23:03 UTC (rev 215) @@ -25,11 +25,6 @@ package org.nuiton.j2r.jni; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.LinkedList; -import java.util.List; - import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.j2r.REngine; @@ -41,6 +36,11 @@ import org.rosuda.JRI.REXP; import org.rosuda.JRI.Rengine; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.LinkedList; +import java.util.List; + /** * RJniEngine.java * @@ -300,21 +300,40 @@ protected RList convertToRList(REXP rexp){ RList temp = new RList(this); List<Object> data = new ArrayList<Object>(); + + //get the names of the list objects + REXP attrNames = rexp.getAttribute(RInstructions.ATTRIBUTE_NAMES); + String[] names = {}; + if (attrNames != null) { + names = attrNames.asStringArray(); + } + org.rosuda.JRI.RList dataList = rexp.asList(); - for (int i = 0; i < dataList.keys().length; i++) { + + //Use this because do not have a size() or length() method, cannot use + // the keys size (elements might not have keys) and RList do not throw + // out of bound exception if going to far. + Boolean flag = true; + int index = 0; + + while (flag) { //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); + REXP tempREXP = dataList.at(index); + + if (tempREXP == null) { + flag = false; + } else { + Object convertedREXP = convertResult(tempREXP); + //add this object to the data list. + data.add(convertedREXP); + index++; + } } //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, ""); + temp = new RList(names, data, this, ""); } catch (RException re) { //don't propagate the error as it is normal. Log it for debug. if (log.isDebugEnabled()) { Modified: trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java 2010-05-09 12:34:27 UTC (rev 214) +++ trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java 2010-05-14 09:23:03 UTC (rev 215) @@ -32,11 +32,6 @@ */ package org.nuiton.j2r.net; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.LinkedList; -import java.util.List; - import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.j2r.REngine; @@ -44,12 +39,17 @@ import org.nuiton.j2r.RException; import org.nuiton.j2r.RInstructions; import org.nuiton.j2r.types.RDataFrame; +import org.nuiton.j2r.types.RList; import org.rosuda.REngine.REXP; import org.rosuda.REngine.REXPMismatchException; -import org.nuiton.j2r.types.RList; import org.rosuda.REngine.Rserve.RConnection; import org.rosuda.REngine.Rserve.RserveException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.LinkedList; +import java.util.List; + /** * This class represents the network engine to access R. By default, it tries to * connect on address 127.0.0.1 and port 6311. Meanwhile, it is possible to @@ -318,7 +318,16 @@ protected RList convertToRList (REXP rexp) throws REXPMismatchException { RList temp = new RList(this); List<Object> data = new ArrayList<Object>(); + + //get the names of the list objects + REXP attrNames = rexp.getAttribute(RInstructions.ATTRIBUTE_NAMES); + String[] names = {}; + if (attrNames!=null){ + names = attrNames.asStrings(); + } + 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. @@ -328,13 +337,11 @@ data.add(convertedREXP); } - //Create a new dataframe with the names, row.names and data + //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).asStrings(), - data, this, ""); + temp = new RList(names, data, this, ""); } catch (RException re) { //don't propagate the error as it is normal. Log it for debug. if (log.isDebugEnabled()) { Modified: trunk/src/main/java/org/nuiton/j2r/types/RList.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-05-09 12:34:27 UTC (rev 214) +++ trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-05-14 09:23:03 UTC (rev 215) @@ -319,11 +319,13 @@ * x coordinates (between 0 and size-1) * @return the Object located at the [x] coordinate * @throws RException - * if no variable name has been given to the list + * if no variable name has been given to the list and tries to + * retrieve data from R */ public Object get(int x) throws RException { checkX(x); if (engine.isAutoCommit()) { + checkVariable(); Object returnObject = engine.eval(String.format( RInstructions.GET_LIST_ITEM, this.variable, x + 1)); if (returnObject instanceof String) { Modified: trunk/src/test/java/org/nuiton/j2r/JNITest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/JNITest.java 2010-05-09 12:34:27 UTC (rev 214) +++ trunk/src/test/java/org/nuiton/j2r/JNITest.java 2010-05-14 09:23:03 UTC (rev 215) @@ -35,17 +35,6 @@ * par : */ package org.nuiton.j2r; -import static org.nuiton.j2r.TestConstants.S_NB_LOOPS; -import static org.nuiton.j2r.TestConstants.S_OP; -import static org.nuiton.j2r.TestConstants.S_T_MAX; -import static org.nuiton.j2r.TestConstants.V_MAX; -import static org.nuiton.j2r.TestConstants.V_NB_LOOPS; -import static org.nuiton.j2r.TestConstants.V_OP_A; -import static org.nuiton.j2r.TestConstants.V_OP_AB; -import static org.nuiton.j2r.TestConstants.V_OP_B; -import static org.nuiton.j2r.TestConstants.V_OP_R; -import java.io.File; - import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.junit.After; @@ -55,6 +44,10 @@ import org.nuiton.j2r.types.RDataFrame; import org.nuiton.j2r.types.RList; +import java.io.File; + +import static org.nuiton.j2r.TestConstants.*; + public class JNITest { private static Log log = LogFactory.getLog(JNITest.class); @@ -405,4 +398,20 @@ Assert.fail("Error should not have been thrown : " + npe); } } + + @Test + public void testListWithNullNames() throws Exception { + RList b= new RList(engine); + try { + b = (RList)engine.eval("b<-list(\"a\",\"b\")"); + b.setVariable("b"); + } catch (NullPointerException npe) { + npe.printStackTrace(); + Assert.fail("Error should not have been thrown : " + npe); + } + + Assert.assertEquals("a",b.get(0)); + Assert.assertEquals("b", b.get(1)); + + } } // JNITest Modified: trunk/src/test/java/org/nuiton/j2r/ListTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/ListTest.java 2010-05-09 12:34:27 UTC (rev 214) +++ trunk/src/test/java/org/nuiton/j2r/ListTest.java 2010-05-14 09:23:03 UTC (rev 215) @@ -25,13 +25,6 @@ package org.nuiton.j2r; -import static org.junit.Assert.assertEquals; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.junit.After; @@ -40,6 +33,13 @@ import org.junit.Test; import org.nuiton.j2r.types.RList; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import static org.junit.Assert.assertEquals; + public class ListTest { private static Log log = LogFactory.getLog(DataframeTest.class); @@ -922,4 +922,8 @@ engine.setAutoCommit(true); } + + + + } Modified: trunk/src/test/java/org/nuiton/j2r/NetTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-05-09 12:34:27 UTC (rev 214) +++ trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-05-14 09:23:03 UTC (rev 215) @@ -359,4 +359,19 @@ Assert.fail("Error should not have been thrown : " + npe); } } + + @Test + public void testListWithNullNames() throws Exception { + RList b = new RList(engine); + try { + b = (RList) engine.eval("b<-list(\"b\",\"a\")"); + b.setVariable("b"); + } catch (NullPointerException npe) { + Assert.fail("Error should not have been thrown : " + npe); + } + + Assert.assertEquals("b", b.get(0)); + Assert.assertEquals("a", b.get(1)); + + } } // NetTest

1 0

r214 - trunk
by tchemit＠users.nuiton.org 09 May '10

09 May '10

Author: tchemit Date: 2010-05-09 14:34:27 +0200 (Sun, 09 May 2010) New Revision: 214 Url: http://nuiton.org/repositories/revision/nuiton-j2r/214 Log: Utilisation de mavenpom4redmine 2.1.4 Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2010-04-29 05:44:38 UTC (rev 213) +++ trunk/pom.xml 2010-05-09 12:34:27 UTC (rev 214) @@ -34,7 +34,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmine</artifactId> - <version>2.1.3</version> + <version>2.1.4</version> </parent> <artifactId>nuiton-j2r</artifactId>

1 0

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>

1 0

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{ engine.voidEval("SensitivityBiomassY3<-c(2.179694924446179E7,2.179468496519559E7,2.1818736174725175E7,2.1816429067949396E7,2.1800098718126506E7,2.1838067907599747E7,2.183569971088971E7,2.1833313097146016E7,2.185719149559428E7,2.1854762634011697E7,2.185231549094628E7,2.187610838662306E7,2.187361928018277E7,2.1871112026349083E7,2.189482001091965E7,2.1892271074663457E7,2.1889704123663016E7,2.1913327781288046E7,2.1910719425357413E7,2.1908093185913157E7,2.193163309335182E7,2.192896572306039E7,2.1926280599087697E7,2.1949737325799696E7,2.1964830419511076E7,2.1944267732381735E7,2.1967641840627935E7,2.196485763859664E7,2.1962055938437656E7,2.198534798337946E7,2.198250595466467E7,2.19796465535838E7,2.2002857083381277E7,2.1999957614685252E7,2.1997040898068156E7,2.2020170453976974E7,2.2017213927520543E7,2.201424027629076E7,2.201424027629076E7,2.2007088929931033E7,2.1999922487316884E7,2.197681420767298E7,2.196962074430254E7,2.1962412278355762E7,2.1939244418647803E7,2.19320089340683E7,2.1924758538858987E7,2.1901530675850462E7,2.1894253260547817E7,2.1886961024817027E7,2.186367272884308E7,2.1856353467938498E7,2.1849019475049105E7,2.182567030993665E7,2.181830928313515E7,2.1810933611020483E7,2.1787523134007405E7,2.178012041554803E7,2.1772703136661157E7,2.1749230898314577E7,2.1749758710004635E7,2.1734327738178723E7,2.171079328231229E7,2.1703307381126277E7,2.1695807083871227E7,2.167220994746149E7,2.1664682544012114E7,2.1657140823937435E7,2.1633480537039224E7,2.162591168317374E7,2.161832859028344E7,2.1594604675944276E7,2.158699441777762E7,2.157936999632849E7,2.1555581970502105E7,2.1547930348361045E7,2.155103621183836E7,2.152717169457966E7,2.1530236120902758E7,2.153328412702021E7,2.1509330625330385E7,2.1512336892940816E7,2.1515326604867205E7,2.1491283471099153E7,2.1494231139260102E7,2.1497162114652816E7,2.147302869279387E7,2.14759173151992E7,2.147878910612182E7,2.1454564731677204E7,2.1457393856367446E7,2.1462383791402113E7,2.1435890009080574E7,2.143865917835912E7,2.1441411233736E7,2.1417002926115625E7,2.141971167646219E7,2.1424717356960263E7,2.1397901863381278E7,2.1400549725365438E7,2.140318018420746E7,2.137858518066629E7,2.1381171678860184E7,2.1383740626669012E7,2.135905121665088E7,2.1361575869539354E7,2.1364082823016256E7,2.1339298288600616E7,2.1341760608492017E7,2.1344205078135047E7,2.1319324692060333E7,2.1321724184994433E7,2.132410567500613E7,2.132410567500613E7,2.1331536055398986E7,2.133895052044593E7,2.1363853672607094E7,2.137123650604985E7,2.137860336066902E7,2.140343328441597E7,2.1410768581059605E7,2.1418087833224125E7,2.1442845113907605E7,2.1450132877092432E7,2.1457404527983494E7,2.148208974251862E7,2.1489329968841057E7,2.1496554012913797E7,2.1521167729882605E7,2.1528360409261446E7,2.1535536834311184E7,2.1560079614063937E7,2.156722472980476E7,2.1563254271749333E7,2.1598825911786724E7,2.1605923440646578E7,2.1613004564718306E7,2.1637407118662428E7,2.1644457030912723E7,2.1651490460029803E7,2.167582370941422E7,2.1682825968903817E7,2.1689811664860353E7,2.171407613809878E7,2.1721030702315085E7,2.172796862056064E7,2.1752164838324733E7,2.1759071658455327E7,2.1765961748155564E7,2.1790090223469418E7,2.179694924446179E7,2.180379144855871E7,2.182785268689249E7,2.18346638475134E7,2.184145810278461E7,2.1865452602147E7,2.1872215835041337E7,2.1878962072157502E7,2.1902890323187094E7,2.1909605554935444E7,2.191630369851899E7,2.1940166184574656E7,2.1946833335751027E7,2.1953483304432537E7,2.1977280501682773E7,2.198389948690986E7,2.1990501193384256E7,2.20142335708955E7,2.2020804298901647E7,2.20273576499835E7,2.205102566980741E7,2.205754804348026E7,2.2064052940158665E7,2.20876570574184E7,2.2094130973859813E7,2.2100587311352342E7,2.2124127974327955E7,2.2130553324907117E7,2.2136960992712937E7,2.2160438642925616E7,2.2166815313332282E7,2.2173174195284456E7,2.2196589267580014E7,2.2202917137875687E7,2.2209227112193614E7,2.2232580034824714E7,2.2238858979494706E7,2.2245119918834776E7,2.2245119918834776E7,2.2247156092664756E7,2.2249172537482113E7,2.222580215006561E7,2.2227776978241052E7,2.2229731947289977E7,2.2206281851083208E7,2.2208194947734725E7,2.221008805387345E7,2.2186557726205546E7,2.2188408701148424E7,2.219023955290159E7,2.2166628464420535E7,2.2168416923091725E7,2.217018512458671E7,2.2146492739166215E7,2.2148218282559495E7,2.214992343346224E7,2.2126149208107647E7,2.212781143270992E7,2.21294531281596E7,2.21055965129125E7,2.21071950106372E7,2.21087728411807E7,2.2084833279022325E7,2.208636763714323E7,2.2087881188668158E7,2.2063858115421828E7,2.2065327916506168E7,2.2066776770173687E7,2.2042669614405714E7,2.2044074436245814E7,2.2045458168422367E7,2.2021266351342022E7,2.2022605766886715E7,2.2023923949074898E7,2.1999646884433046E7,2.200092046171817E7,2.1995009663381506E7,2.1970654681075428E7,2.196470853722463E7,2.195874261494959E7,2.1934317104578134E7,2.1928315823420756E7,2.1922294864394967E7,2.1897798306555357E7,2.1891741970889103E7,2.1885666055779688E7,2.1861097923225783E7,2.1854986609282427E7,2.1848855812173687E7,2.1824215569718488E7,2.1818049347101532E7,2.1811863735432312E7,2.1787150839849222E7,2.1780929771470487E7,2.177468940597102E7,2.174990330589387E7,2.174362744790923E7,2.1737332382536206E7,2.1712472518358346E7,2.1706141920103204E7,2.1699792201974563E7,2.167485800574659E7,2.1668472709669497E7,2.1662068378999148E7,2.163705927432551E7,2.1630619315921858E7,2.162416040595164E7,2.159907580788612E7,2.1592581215630468E7,2.1586067752563022E7,2.1560907067502897E7,2.1554357862780496E7,2.154778986571032E7,2.154778986571032E7,2.1546318044922113E7,2.1544825743281327E7,2.1569967765090413E7,2.1568428834061984E7,2.156686958059507E7,2.1591916967334844E7,2.159031142387256E7,2.158868571459585E7,2.1613639174591307E7,2.1611967510410193E7,2.161027583527415E7,2.1635136067757037E7,2.1633398768567167E7,2.163164161154166E7,2.165640930677329E7,2.165460685236462E7,2.1652784691524632E7,2.167746053091718E7,2.1675593395243883E7,2.1673706702852983E7,2.169829135908928E7,2.169636001035316E7,2.1694409252946746E7,2.1718903390098736E7,2.171690829083134E7,2.1714893929297917E7,2.1739298202943414E7,2.173723981008732E7,2.173516229975055E7,2.1759477357088927E7,2.1757356122077797E7,2.1755215912775498E7,2.1779442392741513E7,2.1777258761579778E7,2.178652675221615E7,2.1799194831120383E7,2.179694924446179E7,2.1210710366918586E7,2.0627838516436625E7,2.0073198124600604E7,2.0549043683745503E7,2.117617571938369E7,2.183569971088971E7,2.251575186207285E7,2.3202940491524644E7,2.3925578765007686E7,2.3793188782694403E7,2.3138942654097542E7,2.2516415708366465E7,2.1910735239279598E7,2.1308393153166354E7,2.0735369629764337E7,2.062075197238507E7,2.1249415366315708E7,2.1910719425357413E7,2.259259256512906E7,2.3281412413469028E7,2.4005949681793142E7,2.4574434204009376E7,2.3898455248209067E7,2.3255404417702474E7,2.262975868639601E7,2.200742405102502E7,2.1415521959997784E7,2.083963435585132E7,2.131951539029141E7,2.198250595466467E7,2.2666103736809526E7,2.3356464740940552E7,2.408279910221071E7,2.4831709742932335E7,2.4678545581240475E7,2.4014418717275385E7,2.336827049681634E7,2.2701638689529963E7,2.208683280168035E7,2.1488775533901934E7,2.1311501623371568E7,2.196962074430254E7,2.2648053985047437E7,2.3288386059390273E7,2.4007555430756032E7,2.474892353613376E7,2.5265224263798002E7,2.4580599089304656E7,2.391463458979512E7,2.3207892262497313E7,2.2579298145611316E7,2.1967830705018844E7,2.131877140228872E7,2.181830928313515E7,2.249157157422271E7,2.3126786933162935E7,2.3840438079766467E7,2.457610205488776E7,2.5270239604048863E7,2.5124739696302816E7,2.4443945095785588E7,2.3721312789605163E7,2.3078729441986065E7,2.2453656465589404E7,2.1790012717726383E7,2.1664682544012114E7,2.2332706673176605E7,2.2962731499231942E7,2.3670793068546023E7,2.440067947692717E7,2.508909057246626E7,2.567639023587526E7,2.498055401716986E7,2.424178659806919E7,2.358501525826246E7,2.2874950937338676E7,2.2198548154310785E7,2.1530236120902758E7,2.1965503936487645E7,2.2584629567022495E7,2.320849669835539E7,2.384970751062438E7,2.45221053058604E7,2.5199807825752024E7,2.497663210108002E7,2.4237269925320312E7,2.350704443679568E7,2.2798810309156775E7,2.2123949376097146E7,2.1457393856367446E7,2.1267154434465587E7,2.186632936271173E7,2.2470263114487886E7,2.309098302604801E7,2.3741694406832688E7,2.4397726677086536E7,2.4891263455218945E7,2.415364079136865E7,2.3425395629407085E7,2.2719097290006068E7,2.204587078549588E7,2.1381171678860184E7,2.073900458098361E7,2.1166832797286097E7,2.175135042538578E7,2.235211102801546E7,2.2981695918150727E7,2.361661976445475E7,2.4269194166454904E7,2.4066108134309478E7,2.3339955269476753E7,2.2635701478342265E7,2.1989961404597342E7,2.1331536055398986E7,2.0692815253972054E7,2.0567634415260237E7,2.1140548759382922E7,2.1729519249264557E7,2.239368387026964E7,2.3017741380537957E7,2.365929520573126E7,2.4206701581383433E7,2.348135733257032E7,2.2777736161977123E7,2.2153147761613276E7,2.1490754107489396E7,2.084539277225918E7,2.0273814573353328E7,2.068819355156516E7,2.1264457718227006E7,2.191411528874908E7,2.2524699062038783E7,2.315239814183554E7,2.3859881227222998E7,2.3652744106745705E7,2.2943451323818333E7,2.231358810227405E7,2.1644457030912723E7,2.0995380304288536E7,2.041902359479725E7,2.0241553740604583E7,2.080528000864457E7,2.1440642248132315E7,2.2037931744211115E7,2.265196079778825E7,2.334386505298643E7,2.382125038917487E7,2.3106368725026328E7,2.2471315736226093E7,2.179694924446179E7,2.114280859614047E7,2.0561751071342427E7,1.9944682760952137E7,2.0350159569657844E7,2.0973412533695985E7,2.155759032627611E7,2.2158137251554392E7,2.283469632473654E7,2.3470999338094838E7,2.3266517442576505E7,2.262635851712963E7,2.1946833335751027E7,2.1287703290811926E7,2.0702021560467873E7,2.0080279995467488E7,1.990513870532304E7,2.051255252742858E7,2.1083803801994085E7,2.1671059161511026E7,2.2332508169542134E7,2.2954719241943117E7,2.34239211469535E7,2.277873906946373E7,2.2094130973859813E7,2.1430085140456423E7,2.0839854889200248E7,2.021350938890342E7,1.9605976414660845E7,2.0058169000206765E7,2.061668109380032E7,2.1190837643538114E7,2.1837412735002644E7,2.244573693600014E7,2.3071107465361953E7,2.2928475004387636E7,2.2238858979494706E7,2.156997020837422E7,2.0953327634262163E7,2.031928213123918E7,1.9704409478000913E7,1.9541523597534645E7,2.008178918447587E7,2.063708154184719E7,2.1222097881208595E7,2.1782167960600212E7,2.2412409214834034E7,2.288129069845474E7,2.2188408701148424E7,2.15164929188283E7,2.0878899065220114E7,2.0246637990616675E7,1.9633509009368904E7,1.9051741734870337E7,1.943691348751304E7,1.9974288495292652E7,2.054031454051603E7,2.1108353968718503E7,2.1692195304523874E7,2.2307045752282713E7,2.21071950106372E7,2.14372382543343E7,2.080136258699364E7,2.0170976443629496E7,1.9559679007026408E7,1.8979519529000968E7,1.8809283014624868E7,1.93292166557891E7,1.9876754569292802E7,2.0426347190258507E7,2.0991225086705297E7,2.1585975945808336E7,2.2022605766886715E7,2.1354706270342696E7,2.072063602091685E7,2.0092217646871667E7,1.9547542072900824E7,1.8967197285597503E7,1.845315493151521E7,1.88885315004027E7,1.9423221602180608E7,2.0026269354807056E7,2.0648023852639187E7,2.123254141631277E7,2.1891741970889103E7,2.1766843919877376E7,2.11202361159165E7,2.0547498003043916E7,1.9990375859496813E7,1.9396653734149992E7,1.8870873471726857E7,1.8763303218098205E7,1.9293827317314055E7,1.9892377693907846E7,2.050948101367075E7,2.1089394951270908E7,2.174362744790923E7,2.2256048212515533E7,2.1594636798160095E7,2.1008919924772583E7,2.0439176253408026E7,1.9831872060683697E7,1.929418962356003E7,1.877116511955032E7,1.9161829949933916E7,1.9755805516186837E7,2.036817790478417E7,2.0943401537336618E7,2.1592581215630468E7,2.226186697834365E7,2.207520884537028E7,2.150042212522819E7,2.0893799125253893E7,2.0296482026974823E7,1.975080361854921E7,1.9219878954244867E7,1.9103331447423942E7,1.969971166041202E7,2.0314695355330423E7,2.0936715189178452E7,2.159031142387256E7,2.2264295589739572E7,2.278023273354139E7,2.2167399452806022E7,2.1571145688384026E7,2.0978751356566936E7,2.0414621112687685E7,1.9865747259597294E7,1.9320301685983643E7,1.977913755335712E7,2.039610798916919E7,2.1019920570274755E7,2.1675593395243883E7,2.235170388479439E7,2.3035350368316166E7,2.2908356203498308E7,2.2292060248826306E7,2.1679592173124865E7,2.109651200763306E7,2.0529204331880063E7,1.996529365701334E7,1.985533137222209E7,2.047419246080403E7,2.1099708315389667E7,2.1757356122077797E7,2.2435488309007194E7,2.3120953305239443E7,2.366944962251461E7,2.303257115592817E7,2.239949051917674E7,2.179694924446179E7,2.1582800974755637E7,2.132220069552558E7,2.11185307878848E7,2.1300085123832006E7,2.1489528672464654E7,2.1736105267599385E7,2.198861916011158E7,2.2193554178466234E7,2.2457935854459632E7,2.2412186365163937E7,2.213057294206349E7,2.1907952140411254E7,2.169068649422258E7,2.142664453126697E7,2.122005824647036E7,2.118128447617866E7,2.1367566254266616E7,2.161075181662697E7,2.1859762569234636E7,2.206122758866795E7,2.2321875708625615E7,2.2525810552501842E7,2.2239737444893744E7,2.2013925463701107E7,2.1793570223308872E7,2.152613268334539E7,2.1316657773628376E7,2.1112096708960515E7,2.1240944809821565E7,2.148073900218816E7,2.1726247176682107E7,2.192426483120831E7,2.2181182026772894E7,2.244441874563338E7,2.2343965586001858E7,2.2114989687818263E7,2.189157217722438E7,2.1657826684049536E7,2.1481861134108696E7,2.1310252383222595E7,2.1291347515805926E7,2.1566643386439852E7,2.184848374525294E7,2.212099677165949E7,2.2416407281501427E7,2.2719070295959707E7,2.2948119668591738E7,2.274961574759145E7,2.2556164993357025E7,2.23512613904517E7,2.2167552537808113E7,2.1988405842782084E7,2.1797702239891656E7,2.2020726285927694E7,2.2306401811247114E7,2.258232341259566E7,2.2881670928634193E7,2.3188326435314238E7,2.3485266775847882E7,2.3476131980370786E7,2.3274195584546782E7,2.306036373905514E7,2.2868626133802254E7,2.268166433271607E7,2.2482696884429052E7,2.2477917896325614E7,2.276739128485571E7,2.30466605563571E7,2.3349903694826085E7,2.3660508278237984E7,2.396093157217119E7,2.4218903733917497E7,2.400817095216517E7,2.3785073969811365E7,2.3585015258262463E7,2.331744627757713E7,2.3110555462957747E7,2.2854656147084348E7,2.3015747009194948E7,2.329569902877019E7,2.352682183843316E7,2.3763595550652813E7,2.4062787877269357E7,2.4312045364394195E7,2.422605003323576E7,2.3998389588862572E7,2.3720508444658138E7,2.344921021315164E7,2.323879969201972E7,2.2979398848798577E7,2.2908514230288062E7,2.317843503805836E7,2.3406229476741273E7,2.363956721378428E7,2.393468756390962E7,2.4180270050182305E7,2.4363700074971378E7,2.4132154914224472E7,2.3850425399392366E7,2.3575403674530827E7,2.336145454882542E7,2.3098559659378957E7,2.284173125333958E7,2.3055480880316418E7,2.3279914564995393E7,2.3509783969288055E7,2.380077829850311E7,2.404265337521539E7,2.4290565645753462E7,2.4260010642767034E7,2.397444172413691E7,2.3695706229231913E7,2.344269054528998E7,2.314165334501904E7,2.2847617039811883E7,2.2753802012594562E7,2.293840026763693E7,2.312765269094679E7,2.3340650997364912E7,2.3539855804151304E7,2.3744215648609586E7,2.3906272591229875E7,2.358672878959545E7,2.3274896029086925E7,2.2989060548060637E7,2.2691627934628997E7,2.2401151307133447E7,2.213521218864193E7,2.2233697486671917E7,2.243673498704297E7,2.2640960988426235E7,2.2840282445538927E7,2.3027808515149347E7,2.3247410698483635E7,2.312776918021058E7,2.28196915866069E7,2.2537018610587217E7,2.236588221206764E7,2.195639121440947E7,2.1693499155164544E7,2.158564929535018E7,2.1759558502130054E7,2.1955324631112434E7,2.213832390612545E7,2.2326030617057707E7,2.2536488275080547E7,2.2670694454728946E7,2.2366430382259358E7,2.208699936159411E7,2.179694924446181E7,2.1513758481920857E7,2.125398523455025E7,2.0983612842204567E7,2.109628427519062E7,2.128389504203701E7,2.1459210724855714E7,2.163902271099347E7,2.1840666883719392E7,2.20300919715181E7,2.191552349058341E7,2.1639406437831394E7,2.1353121527253184E7,2.1073644505494516E7,2.0817054812208567E7,2.0550302057201367E7,2.0447032525084432E7,2.0626784465038262E7,2.079468773941211E7,2.0966884332654934E7,2.1160037325478908E7,2.134141261153796E7,2.1467352175718762E7,2.1194614044124752E7,2.0912135723046537E7,2.0636411887780488E7,2.038306384233572E7,2.011996627976353E7,1.9862964308494963E7,1.998406758446474E7,2.014482325506297E7,2.0309677182599295E7,2.0494652542036593E7,2.0668267840910804E7,2.0846422601373654E7,2.0752968445634652E7,2.0474332543329127E7,2.0202395902872443E7,1.9986682536912356E7,1.9760783130720664E7,1.954012785927571E7,1.9522960082094874E7,1.9712048810959406E7,1.9905695371214602E7,2.015416369746075E7,2.0357915944941416E7,2.057028078195899E7,2.0774294803816352E7,2.0528646016777497E7,2.0288910016423583E7,2.0104803904727656E7,1.987573241675546E7,1.965200603795866E7,1.948178428520774E7,1.961812604291848E7,1.9809037937128045E7,2.0054303216014933E7,2.0255131313945077E7,2.046092617504088E7,2.0723211319667727E7,2.064888077648577E7,2.0405765289619416E7,2.0218535995389506E7,1.9986293836112317E7,1.9759498533282418E7,1.9586432159852266E7,1.9519652120447874E7,1.970780474520424E7,1.9949825653636657E7,2.0147705058135226E7,2.0350455509476036E7,2.060917061217219E7,2.076448699013356E7,2.0517994842178896E7,2.032762600569117E7,2.0094532572243024E7,1.992826566491457E7,1.9751750631704066E7,1.959596157545169E7,1.979762799759906E7,2.003872797416884E7,2.030269428304801E7,2.0573039811826043E7,2.0832368015315235E7,2.111591827455593E7,2.1108926062609725E7,2.091082189492144E7,2.0735169770109635E7,2.0563940105959684E7,2.037967933771062E7,2.021699863297404E7,2.021385253589832E7,2.0457917553273804E7,2.0725379982846912E7,2.099926924265825E7,2.126168137899885E7,2.1548867561324272E7,2.1782102633357514E7,2.157531083889262E7,2.139190792954339E7,2.1213135769972038E7,2.1020838240174975E7,2.0851016532201312E7,2.068537553775501E7,2.087914392806134E7,2.1150053600132417E7,2.1427435630355682E7,2.1692855929514192E7,2.1983622377098937E7,2.228156314295964E7,2.2253718670445587E7,2.2062286164065335E7,2.1875700901274793E7,2.16421155231462E7,2.1432541076814383E7,2.12279161177933E7,2.11406015194917E7,2.138029925476085E7,2.162567378947092E7,2.182469883557617E7,2.2081413149714403E7,2.234440567100169E7,2.249678298707227E7,2.226712223265128E7,2.204307246241817E7,2.177224617969986E7,2.1559367015092243E7,2.1351538647396944E7,2.109796385286568E7,2.1280348766236868E7,2.152256335771631E7,2.171838083469002E7,2.19717253498737E7,2.223123375820159E7,2.2443167564732175E7,2.2399210234947044E7,2.217165957284462E7,2.1896949965474334E7,2.1680795126377612E7,2.146979246769457E7,2.121268092757171E7,2.1174895022551663E7,2.1413937683383066E7,2.1606560535874575E7,2.1856524594306666E7,2.2112538879026916E7,2.2320964295446754E7,2.252591870060584E7,2.2294895699372217E7,2.2016351148507055E7,2.179694924446179E7,2.2331824429699514E7,2.2855433361901157E7,2.3404487214268394E7,2.294142103956324E7,2.2324441999097317E7,2.1736105267599385E7,2.1157628653165985E7,2.0571940996573642E7,2.001321950420239E7,2.012001521949783E7,2.0610767161002416E7,2.1125120342784844E7,2.164651010639106E7,2.2156678383773886E7,2.2691918664613448E7,2.2805112652218632E7,2.219354176321105E7,2.161075181662697E7,2.1037735985237803E7,2.0457219288610935E7,1.9903793747161057E7,1.9488637544425823E7,1.9966665391087614E7,2.0467920301008943E7,2.0976050836749885E7,2.1473027341601636E7,2.199468580517517E7,2.2523424240659732E7,2.205791439697501E7,2.148073900218816E7,2.0913250056273438E7,2.033798567507657E7,1.978991846894483E7,1.9251159123297397E7,1.9337016475624252E7,1.982539976317407E7,2.0320500278302457E7,2.0840234256234802E7,2.1385944860698376E7,2.194030469414052E7,2.210590277779634E7,2.1566643386439852E7,2.1035276284650847E7,2.052916558712231E7,2.0012885688423205E7,1.9504240212668225E7,1.914597245636108E7,1.966564970768373E7,2.019365888132567E7,2.0747578982121963E7,2.129296337826814E7,2.1846984486465834E7,2.2428472535802145E7,2.20207262859277E7,2.1481059856196947E7,2.0966801053767882E7,2.044242611337692E7,1.9925785984183084E7,1.9445287866034742E7,1.9569464602423172E7,2.0097071911044825E7,2.0650197120948106E7,2.1195143034974054E7,2.174871092095583E7,2.2329323898903012E7,2.247791789632563E7,2.1929942224403653E7,2.1407504349966824E7,2.0875024935201477E7,2.0350380737533808E7,1.9849734706027746E7,1.946867528159764E7,1.9995768957046025E7,2.0547974113317214E7,2.1092364920947142E7,2.166394686541127E7,2.226314941013937E7,2.2854656147084344E7,2.2458540272984866E7,2.1944900002136175E7,2.14203655338795E7,2.090289713492715E7,2.0408796196330402E7,1.990484878917003E7,2.006108299669223E7,2.0634694427358806E7,2.120175864847823E7,2.1778463552713715E7,2.2382616792808183E7,2.2979398848798577E7,2.315131943473774E7,2.2624412031072915E7,2.2086607573908266E7,2.1556030220523257E7,2.1049134932153124E7,2.0532394305307217E7,2.0155591800375476E7,2.0733841117966734E7,2.130586365490205E7,2.188760285404254E7,2.2496595819886178E7,2.3098559659378957E7,2.3710626159261644E7,2.3317646387790464E7,2.2766369623098884E7,2.222248331524084E7,2.1702572233762216E7,2.1172843463076215E7,2.0650291112794127E7,2.082750676368124E7,2.1404392701349508E7,2.1991069029673535E7,2.2570531369717266E7,2.314165334501904E7,2.3721248524592787E7,2.384361141338243E7,2.324742537082883E7,2.2660365518774025E7,2.2065367969340097E7,2.1496636553747363E7,2.0936717628245063E7,2.0504862578794934E7,2.1043720865348622E7,2.1590676545610815E7,2.212863152921111E7,2.269162793462899E7,2.3262996016340885E7,2.382431088401486E7,2.337519266281572E7,2.2787036963065572E7,2.2190511690875802E7,2.1620748035310674E7,2.105982235960949E7,2.0491385644285306E7,2.061950674156031E7,2.1158520148774885E7,2.168839965714183E7,2.224325053139479E7,2.2806371268771283E7,2.3359296776102714E7,2.349720266248471E7,2.290809018288732E7,2.231018627306776E7,2.1739523735758387E7,2.1177722084197752E7,2.060801683057323E7,2.019737896084555E7,2.0728438400004502E7,2.1250255491423395E7,2.179694924446179E7,2.2351810845186867E7,2.2896361415497024E7,2.34673816862853E7,2.3023658536161214E7,2.2424519877953082E7,2.1853086965165038E7,2.1290535352017526E7,2.071969638585591E7,2.0175002659378543E7,2.03008146798796E7,2.0814588591157842E7,2.1353121527253184E7,2.1901198553444345E7,2.2435916535651654E7,2.299846519089168E7,2.3133874006937698E7,2.2533639436262306E7,2.196155994087558E7,2.1398379756241336E7,2.0831880676123228E7,2.0281258428302288E7,1.9876004085683852E7,2.0381759861590605E7,2.0912135723046537E7,2.145047510584317E7,2.19783439218411E7,2.250403067372545E7,2.3094738815524373E7,2.2637670594426885E7,2.206506373089962E7,2.1501371873062074E7,2.092865113588225E7,2.0382899411775194E7,1.984574849092129E7,1.9952103012631103E7,2.0474332543329116E7,2.1004423430395804E7,2.1560931405266024E7,2.214531691178439E7,2.2739694435204152E7,2.293183714702572E7,2.2392468378613237E7,2.1860316289117955E7,2.1353463074323934E7,2.083509649568674E7,2.032373871512065E7,1.9968283859677758E7,2.052864601677749E7,2.10986999234755E7,2.1696853675125007E7,2.2287125819984794E7,2.288748409851376E7,2.3517699057573907E7,2.3110838351093642E7,2.256465697425747E7,2.204419087489216E7,2.1512127255885277E7,2.09872383735701E7,2.048655364123707E7,2.0648880776485767E7,2.122458291883902E7,2.182827231603412E7,2.24243705563821E7,2.3030647473853115E7,2.3666655701840118E7,2.3845490098184697E7,2.3285031169750787E7,2.2750687572362773E7,2.2204684529074334E7,2.166602485979557E7,2.115597872152922E7,2.076448699013355E7,2.134577305876403E7,2.195491375186435E7,2.2556769890430007E7,2.3147282149450656E7,2.376620284426716E7,2.4375786394523405E7,2.3931872915482566E7,2.3363614362415303E7,2.278476306724695E7,2.2214436631114103E7,2.166992274332534E7,2.111720637510088E7,2.1262608405934777E7,2.1850997058493238E7,2.2431386797166683E7,2.3020909338318553E7,2.363834581164402E7,2.424687907733571E7,2.440641797253779E7,2.3829612158466004E7,2.3242349369345333E7,2.2663715094404805E7,2.211097304843052E7,2.1548867561324283E7,2.113448349320343E7,2.1721362444207337E7,2.2300655419081565E7,2.2889054497973528E7,2.3504857204500623E7,2.4112200705898315E7,2.472897408636128E7,2.4297366495217163E7,2.3701711277208768E7,2.3114787944667332E7,2.2553810127248496E7,2.1983622377098937E7,2.1421880205984302E7,2.158639021257613E7,2.216445036005833E7,2.2751587222834248E7,2.3330198176623296E7,2.3899141443574466E7,2.4475790187439345E7,2.4580038347294193E7,2.3944009003179368E7,2.331848771734921E7,2.2685904040408395E7,2.2081413149714403E7,2.1487028738378E7,2.1025001579972226E7,2.155823036015128E7,2.2098775932078365E7,2.262913248602956E7,2.318410728953877E7,2.3746616648948003E7,2.429784782814121E7,2.381848647603142E7,2.3198415705305327E7,2.257092092866275E7,2.1971725349873707E7,2.1382556244578436E7,2.078680346996282E7,2.0898066861377403E7,2.1425185257755164E7,2.194210317579236E7,2.248332025721476E7,2.3031903414525803E7,2.3569200583172016E7,2.3687145499773234E7,2.307262263082037E7,2.2450332590421747E7,2.1856524594306674E7,2.1272660891316224E7,2.068189171160841E7,2.0251656789155245E7,2.076555837714624E7,2.126927413321792E7,2.179694924446179E7,2.213116718552735E7,2.246018275214548E7,2.2793386737650182E7,2.251754579935805E7,2.215442388523303E7,2.178854077274378E7,2.1427126685079534E7,2.106157904802944E7,2.0701138214833025E7,2.0773944912109643E7,2.1101465426650804E7,2.1433100464210358E7,2.1764271340060156E7,2.2090015665627636E7,2.2420165109055676E7,2.249132869478557E7,2.2126750183904264E7,2.1767738629090924E7,2.1409186884565722E7,2.1046228244790338E7,2.0688662432563096E7,2.0417344641128927E7,2.074161267764567E7,2.1070184959778205E7,2.1398291111033108E7,2.172076722500235E7,2.2047845484131202E7,2.2374457080896217E7,2.2097893441498995E7,2.1741786556917153E7,2.1386142993088838E7,2.1025830190565377E7,2.067118393968909E7,2.0317001890927445E7,2.0382995002645098E7,2.0708489133795545E7,2.1033515559888493E7,2.136340525201984E7,2.169840487685392E7,2.2033265214395232E7,2.211925454959629E7,2.1776092924952056E7,2.1433050145102777E7,2.1095258360241335E7,2.075235486570361E7,2.040957221310045E7,2.0156420587720197E7,2.0491160162338886E7,2.082575581621871E7,2.1165220453865502E7,2.1499588426140405E7,2.183381015811834E7,2.217306550422337E7,2.191476188237164E7,2.1571952981072295E7,2.123416105086194E7,2.0891507074234065E7,2.054897992897586E7,2.0211169587614678E7,2.0291543958151996E7,2.062546395185741E7,2.0963922971693087E7,2.1297595905977003E7,2.1631115351925932E7,2.196932265075469E7,2.2049149449651577E7,2.1706620175496623E7,2.136885960794005E7,2.1026501555585966E7,2.0684276589569606E7,2.0346531168816715E7,2.0088890876042236E7,2.042207015433829E7,2.075945285553371E7,2.1092364920947142E7,2.1443512902899195E7,2.1799591715697154E7,2.215164384132646E7,2.190919700394338E7,2.1591572878593247E7,2.1266333167743467E7,2.0940659486331966E7,2.0618667809263937E7,2.029657380496712E7,2.038977321780365E7,2.0746703971546523E7,2.1100039606520064E7,2.145379603664496E7,2.1812170196025584E7,2.2292064789759554E7,2.2265949129802387E7,2.1942508824345823E7,2.1614412967304908E7,2.1285886423563544E7,2.096080944025547E7,2.063134218494296E7,2.0387105571562193E7,2.074629946264688E7,2.110219114480961E7,2.145849802944873E7,2.181909587151287E7,2.217627453315524E7,2.25338665516033E7,2.2293329929795306E7,2.1962403947523773E7,2.1631051027927198E7,2.1302894012890726E7,2.0970611448442176E7,2.0637903342391748E7,2.0740233324627433E7,2.1098618786468294E7,2.1457413259454835E7,2.181305404475645E7,2.21653663667723E7,2.2517853759280954E7,2.2606843724317852E7,2.2266409759461284E7,2.192577389687896E7,2.1581245687123094E7,2.1240246186690632E7,2.0899047650914412E7,2.0640782981424157E7,2.0993243544121888E7,2.134587434832578E7,2.169479966535781E7,2.204768539415516E7,2.2400738881680105E7,2.274981089827507E7,2.249513555151646E7,2.2153435522500593E7,2.180748526212628E7,2.146544446275548E7,2.112321306551354E7,2.077684967631617E7,2.0869057477606162E7,2.122222567971505E7,2.1571385156871144E7,2.1924789693298157E7,2.2278354977550384E7,2.2627623389205378E7,2.2720265686633166E7,2.2377576254602447E7,2.203028430628418E7,2.168727610950106E7,2.1344085418163724E7,2.099642788218404E7,2.0740069206834726E7,2.10937215858802E7,2.144307838962735E7,2.179694924446179E7,2.215097412810185E7,2.2500403515029244E7,2.2854640304381732E7,2.259826496351339E7,2.2249708890561175E7,2.1905804502854098E7,2.1561725399713792E7,2.121284956437676E7,2.0868480202648208E7,2.0960618156792175E7,2.13101369141091E7,2.16644236455553E7,2.2018857969948325E7,2.236841433045245E7,2.272304367552804E7,2.2815570534137573E7,2.246582517992849E7,2.212109319241742E7,2.1776193954069816E7,2.1426172998139642E7,2.1081003572337553E7,2.082316155138529E7,2.117280830940476E7,2.152746246234586E7,2.188225804706417E7,2.223190875838836E7,2.258688315926801E7,2.2941996945590645E7,2.267869938466166E7,2.233320585050489E7,2.198755222497734E7,2.1636456734349225E7,2.1290552214313257E7,2.0944489880218506E7,2.103133052028953E7,2.138630556724513E7,2.1741416151269894E7,2.2102177878745247E7,2.2468860631676275E7,2.2836038310408268E7,2.2945687236781634E7,2.2612719279902168E7,2.2273677288560297E7,2.1942267253234595E7,2.1604923806593705E7,2.1267085001947533E7,2.1022105600575626E7,2.1390359289542053E7,2.175910576245078E7,2.2133588608280737E7,2.250502508749301E7,2.2873682908682838E7,2.3249900756728288E7,2.299963321810378E7,2.266013122351906E7,2.232527884072038E7,2.1984691646895032E7,2.1643610560785435E7,2.130687473488357E7,2.1410768581059605E7,2.1782602188130923E7,2.2159884271906532E7,2.253276093273297E7,2.290612601370952E7,2.3285112231117953E7,2.3390658086396478E7,2.3047920674569204E7,2.2709619831580997E7,2.2365803662953384E7,2.202149548465024E7,2.168132727280335E7,2.1425968280136056E7,2.180084296539032E7,2.2180865188004896E7,2.2556769890430007E7,2.2911765048773307E7,2.3271371750394486E7,2.362602129252303E7,2.334940506752772E7,2.2987459560247686E7,2.262092478740898E7,2.22545672732479E7,2.189275834365621E7,2.1526664734883662E7,2.1610979452846672E7,2.196960664655238E7,2.2323770905053537E7,2.267772897583815E7,2.30359135106662E7,2.338950404252862E7,2.3473080167829003E7,2.311140404908859E7,2.2745457342557747E7,2.2387986861214887E7,2.2018193155184593E7,2.1652713020338293E7,2.1377239824947886E7,2.173441405058799E7,2.2087475718837444E7,2.244032285623016E7,2.2797004950716525E7,2.314946176159337E7,2.3501701224178124E7,2.3230032301504742E7,2.286472783809281E7,2.2499614754180383E7,2.2138458506287802E7,2.177364708122389E7,2.140902958136632E7,2.1495936912840076E7,2.1847819703758527E7,2.2199479275088135E7,2.2547232634178057E7,2.2890908920416724E7,2.3234133341663122E7,2.3305089715198282E7,2.2933609691497754E7,2.256256812860144E7,2.2188170320348766E7,2.1818049347101532E7,2.144836871900218E7,2.1164369664856385E7,2.1506519057850003E7,2.1848214021155674E7,2.2185491404237065E7,2.2526194797414433E7,2.2866442538502313E7,2.3202003165464114E7,2.292174846684657E7,2.2553380916979983E7,2.218133086477366E7,2.181390146857249E7,2.1446918157622144E7,2.107638224904164E7,2.1150988251362223E7,2.148969345387186E7,2.182372039746341E7,2.2161423890132982E7,2.2498668436132073E7,2.283095666766323E7,2.2903932219217736E7,2.2538300661784396E7,2.2168673288001645E7,2.180399590267255E7,2.1439769739313908E7,2.1071694686412726E7,2.0795805064918812E7,2.1131495475113433E7,2.14622695284985E7)"); - 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