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[LutinJ2R-commits] r76 - in lutinj2r/tags: . lutinj2r-0.4
by chatellier＠users.labs.libre-entreprise.org 04 May '09

04 May '09

Author: chatellier Date: 2009-05-04 15:58:09 +0000 (Mon, 04 May 2009) New Revision: 76 Added: lutinj2r/tags/lutinj2r-0.4/ lutinj2r/tags/lutinj2r-0.4/pom.xml Removed: lutinj2r/tags/lutinj2r-0.4/pom.xml Log: [maven-release-plugin] copy for tag lutinj2r-0.4 Copied: lutinj2r/tags/lutinj2r-0.4 (from rev 74, lutinj2r/trunk) Deleted: lutinj2r/tags/lutinj2r-0.4/pom.xml =================================================================== --- lutinj2r/trunk/pom.xml 2009-05-03 09:18:40 UTC (rev 74) +++ lutinj2r/tags/lutinj2r-0.4/pom.xml 2009-05-04 15:58:09 UTC (rev 76) @@ -1,190 +0,0 @@ -<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> - - <modelVersion>4.0.0</modelVersion> - -  -  -  - - <parent> - <groupId>org.codelutin</groupId> - <artifactId>lutinproject</artifactId> - <version>3.4</version> - </parent> - - <artifactId>lutinj2r</artifactId> - <version>0.4-SNAPSHOT</version> - - <dependencies> -  - <dependency> - <groupId>externallib</groupId> - <artifactId>JRI</artifactId> - <version>0.7-0</version> - <scope>compile</scope> - </dependency> - <dependency> - <groupId>externallib</groupId> - <artifactId>REngine</artifactId> - <version>0.6-0</version> - <scope>compile</scope> - </dependency> - <dependency> - <groupId>externallib</groupId> - <artifactId>Rserve</artifactId> - <version>0.6-0</version> - <scope>compile</scope> - </dependency> - </dependencies> - -  -  -  - - <name>Lutin Java-2-R library</name> - <description>Librairie permettant d'utiliser R en Java, que ce soit par le - Network ou en JNI. - </description> - <inceptionYear>2006</inceptionYear> - -  -  -  - - <packaging>jar</packaging> - - <properties> -  - <labs.id>109</labs.id> - - <labs.project>lutinj2r</labs.project> - -  - <maven.test.skip>true</maven.test.skip> - -  -  - </properties> - - <build> - <defaultGoal>install</defaultGoal> - - <plugins> - -  - <plugin> - <groupId>org.codelutin</groupId> - <artifactId>maven-jrst-plugin</artifactId> - <version>0.8.4</version> - <configuration> - <defaultLocale>fr</defaultLocale> - </configuration> - <executions> - <execution> - <goals> - <goal>jrst</goal> - </goals> - </execution> - </executions> - </plugin> - </plugins> - - <pluginManagement> - <plugins> - <plugin> - <artifactId>maven-assembly-plugin</artifactId> - <configuration> - <descriptors> - <descriptor>src/main/assembly/deps.xml</descriptor> - <descriptor>src/main/assembly/full.xml</descriptor> - </descriptors> - <attach>false</attach> - </configuration> - <executions> - <execution> - <id>create-assembly</id> - <goals> - <goal>single</goal> - </goals> - </execution> - </executions> - </plugin> - </plugins> - </pluginManagement> - - </build> - - <scm> - <connection>${maven.scm.connection}</connection> - <developerConnection>${maven.scm.developerConnection}</developerConnection> - <url>${maven.scm.url}</url> - </scm> - -  - <repositories> - <repository> - <id>codelutin-repository</id> - <name>CodeLutinRepository</name> - <url>http://lutinbuilder.labs.libre-entreprise.org/maven2</url> - <snapshots> - <enabled>true</enabled> - <checksumPolicy>warn</checksumPolicy> - </snapshots> - <releases> - <enabled>true</enabled> - <checksumPolicy>warn</checksumPolicy> - </releases> - </repository> - </repositories> - - <profiles> - <profile> - <id>release-profile</id> - <activation> - <property> - <name>performRelease</name> - <value>true</value> - </property> - </activation> - <build> - <plugins> - -  - <plugin> - <artifactId>maven-assembly-plugin</artifactId> - <executions> - <execution> - <id>create-assembly</id> - <phase>package</phase> - </execution> - </executions> - </plugin> - -  - <plugin> - <groupId>org.codelutin</groupId> - <artifactId>maven-license-switcher-plugin</artifactId> - <version>0.6</version> - <executions> - <execution> - <id>attach-licenses</id> - <goals> - <goal>license</goal> - <goal>third-party</goal> - </goals> - </execution> - </executions> - </plugin> - - </plugins> - - </build> - </profile> - </profiles> - -</project> \ No newline at end of file Copied: lutinj2r/tags/lutinj2r-0.4/pom.xml (from rev 75, lutinj2r/trunk/pom.xml) =================================================================== --- lutinj2r/tags/lutinj2r-0.4/pom.xml (rev 0) +++ lutinj2r/tags/lutinj2r-0.4/pom.xml 2009-05-04 15:58:09 UTC (rev 76) @@ -0,0 +1,190 @@ +<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> + + <modelVersion>4.0.0</modelVersion> + +  +  +  + + <parent> + <groupId>org.codelutin</groupId> + <artifactId>lutinproject</artifactId> + <version>3.4</version> + </parent> + + <artifactId>lutinj2r</artifactId> + <version>0.4</version> + + <dependencies> +  + <dependency> + <groupId>externallib</groupId> + <artifactId>JRI</artifactId> + <version>0.7-0</version> + <scope>compile</scope> + </dependency> + <dependency> + <groupId>externallib</groupId> + <artifactId>REngine</artifactId> + <version>0.6-0</version> + <scope>compile</scope> + </dependency> + <dependency> + <groupId>externallib</groupId> + <artifactId>Rserve</artifactId> + <version>0.6-0</version> + <scope>compile</scope> + </dependency> + </dependencies> + +  +  +  + + <name>Lutin Java-2-R library</name> + <description>Librairie permettant d'utiliser R en Java, que ce soit par le + Network ou en JNI. + </description> + <inceptionYear>2006</inceptionYear> + +  +  +  + + <packaging>jar</packaging> + + <properties> +  + <labs.id>109</labs.id> + + <labs.project>lutinj2r</labs.project> + +  + <maven.test.skip>true</maven.test.skip> + +  +  + </properties> + + <build> + <defaultGoal>install</defaultGoal> + + <plugins> + +  + <plugin> + <groupId>org.codelutin</groupId> + <artifactId>maven-jrst-plugin</artifactId> + <version>0.8.4</version> + <configuration> + <defaultLocale>fr</defaultLocale> + </configuration> + <executions> + <execution> + <goals> + <goal>jrst</goal> + </goals> + </execution> + </executions> + </plugin> + </plugins> + + <pluginManagement> + <plugins> + <plugin> + <artifactId>maven-assembly-plugin</artifactId> + <configuration> + <descriptors> + <descriptor>src/main/assembly/deps.xml</descriptor> + <descriptor>src/main/assembly/full.xml</descriptor> + </descriptors> + <attach>false</attach> + </configuration> + <executions> + <execution> + <id>create-assembly</id> + <goals> + <goal>single</goal> + </goals> + </execution> + </executions> + </plugin> + </plugins> + </pluginManagement> + + </build> + + <scm> + <connection>scm:svn:svn://anonymous@labs.libre-entreprise.org/svnroot/lutinj2r/lutinj2r/tags/lutinj2r-0.4</connection> + <developerConnection>scm:svn:svn+ssh://chatellier@labs.libre-entreprise.org/svnroot/lutinj2r/lutinj2r/tags/lutinj2r-0.4</developerConnection> + <url>http://labs.libre-entreprise.org/plugins/scmsvn/viewcvs.php/lutinj2r/tags/l…</url> + </scm> + +  + <repositories> + <repository> + <id>codelutin-repository</id> + <name>CodeLutinRepository</name> + <url>http://lutinbuilder.labs.libre-entreprise.org/maven2</url> + <snapshots> + <enabled>true</enabled> + <checksumPolicy>warn</checksumPolicy> + </snapshots> + <releases> + <enabled>true</enabled> + <checksumPolicy>warn</checksumPolicy> + </releases> + </repository> + </repositories> + + <profiles> + <profile> + <id>release-profile</id> + <activation> + <property> + <name>performRelease</name> + <value>true</value> + </property> + </activation> + <build> + <plugins> + +  + <plugin> + <artifactId>maven-assembly-plugin</artifactId> + <executions> + <execution> + <id>create-assembly</id> + <phase>package</phase> + </execution> + </executions> + </plugin> + +  + <plugin> + <groupId>org.codelutin</groupId> + <artifactId>maven-license-switcher-plugin</artifactId> + <version>0.6</version> + <executions> + <execution> + <id>attach-licenses</id> + <goals> + <goal>license</goal> + <goal>third-party</goal> + </goals> + </execution> + </executions> + </plugin> + + </plugins> + + </build> + </profile> + </profiles> + +</project> \ No newline at end of file

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[LutinJ2R-commits] r75 - lutinj2r/trunk
by chatellier＠users.labs.libre-entreprise.org 04 May '09

04 May '09

Author: chatellier Date: 2009-05-04 15:58:05 +0000 (Mon, 04 May 2009) New Revision: 75 Modified: lutinj2r/trunk/pom.xml Log: [maven-release-plugin] prepare release lutinj2r-0.4 Modified: lutinj2r/trunk/pom.xml =================================================================== --- lutinj2r/trunk/pom.xml 2009-05-03 09:18:40 UTC (rev 74) +++ lutinj2r/trunk/pom.xml 2009-05-04 15:58:05 UTC (rev 75) @@ -13,7 +13,7 @@ </parent> <artifactId>lutinj2r</artifactId> - <version>0.4-SNAPSHOT</version> + <version>0.4</version> <dependencies>

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[LutinJ2R-commits] r74 - in lutinj2r/trunk/src: main/java/org/codelutin/j2r/types test/java/org/codelutin/j2r
by jcouteau＠users.labs.libre-entreprise.org 03 May '09

03 May '09

Author: jcouteau Date: 2009-05-03 09:18:40 +0000 (Sun, 03 May 2009) New Revision: 74 Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java Log: Add csv import/export to dataframes Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java =================================================================== --- lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java 2009-05-01 09:47:16 UTC (rev 73) +++ lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java 2009-05-03 09:18:40 UTC (rev 74) @@ -1,5 +1,27 @@ +/* *##% Lutin Java-2-R library + * Copyright (C) 2006 - 2008 CodeLutin + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Lesser Public License for more details. + * + * You should have received a copy of the GNU General Lesser Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/lgpl-3.0.html>. ##%*/ + package org.codelutin.j2r.types; +import java.io.BufferedReader; +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileReader; +import java.io.FileWriter; import java.io.Serializable; import java.util.HashMap; import java.util.Set; @@ -128,7 +150,7 @@ public void setData(Vector<Vector<? extends Serializable>> data, REngine engine) throws RException { this.data = data; - if(checkConsistency()==false){ + if (checkConsistency() == false) { throw new RException("A dimension is wrong on the dataframe"); } } @@ -219,7 +241,7 @@ Vector<Serializable> thisColumn = new Vector<Serializable>(); for (int j = 0; j < vectorlength; j++) { thisColumn.add((Serializable) engine.eval(this.variable + "[" - + (i + 1) + "," + (j + 1) + "]")); + + (j + 1) + "," + (i + 1) + "]")); } data.add(thisColumn); } @@ -236,8 +258,8 @@ + this.variable + ")$" + key + ")"); attributes.put(key, attribute); } - - if(checkConsistency()==false){ + + if (checkConsistency() == false) { throw new RException("A dimension is wrong on the dataframe"); } @@ -428,4 +450,276 @@ return true; } + public void exportCsv(File outputFile, boolean rowNames, boolean names) { + try { + BufferedWriter file = new BufferedWriter(new FileWriter(outputFile)); + + if (names) { + if (rowNames) { + file.write(";"); + } + for (int i = 0; i < this.names.size(); i++) { + file.write(this.names.get(i) + ";"); + } + file.newLine(); + } + + for (int i = 0; i < this.data.get(0).size(); i++) { + if (rowNames) { + file.write(this.rowNames.get(i) + ";"); + } + for (int j = 0; j < this.data.size(); j++) { + file.write(this.data.get(j).get(i) + ";"); + } + file.newLine(); + } + file.close(); + } catch (Exception e) { + e.printStackTrace(); + } + + } + + /** + * Import a dataframe form a csv file. The dataframe will contain Strings. + * Use this method if you don't know the type of data that is in the csv + * file. + * + * @param inputFile + * Csv file to import. + * @param rowNames + * Does the csv file contains names of the rows. + * @param names + * Does the csv file contain names of the columns. + */ + public void importCsv(File inputFile, boolean rowNames, boolean names) { + String tmp; + Integer dataSize = 0; + try { + + BufferedReader first = new BufferedReader(new FileReader(inputFile)); + tmp = first.readLine(); + String[] splitted = tmp.split("\\;"); + if (rowNames) { + dataSize = splitted.length - 1; + } else { + dataSize = splitted.length; + } + + BufferedReader br = new BufferedReader(new FileReader(inputFile)); + if (this.data != null) { + this.data.clear(); + } + if (rowNames) { + if (this.rowNames != null) { + this.rowNames.clear(); + } + } + if (names) { + if (this.names != null) { + this.names.clear(); + } + tmp = br.readLine(); + splitted = tmp.split("\\;"); + for (int i = 1; i < splitted.length; i++) { + this.names.add(splitted[i]); + } + } + + Vector<Vector<? extends Serializable>> data = new Vector<Vector<? extends Serializable>>(); + + for (int i = 0; i < dataSize; i++) { + Vector<Serializable> vector = new Vector<Serializable>(); + data.add(vector); + } + + while ((tmp = br.readLine()) != null) { + splitted = tmp.split("\\;"); + int index = 0; + if (rowNames) { + this.rowNames.add(splitted[0]); + index = 1; + } + for (int i = 0 + index; i < splitted.length; i++) { + ((Vector<Serializable>) data.get(i - index)) + .add((Serializable) splitted[i]); + } + } + br.close(); + this.data = data; + } catch (Exception e) { + e.printStackTrace(); + } + } + + /** + * Import a dataframe form a csv file. The dataframe will contain Objects of + * the same class than importType. Use this method if you know the type of + * data that is in the csv file. + * + * @param inputFile + * Csv file to import. + * @param rowNames + * Does the csv file contains names of the rows. + * @param names + * Does the csv file contain names of the columns. + * @param importType + * Object of the class of the data imported (all the data have + * the same type). (Supported types : String, Double and Integer) + */ + public void importCsv(File inputFile, boolean rowNames, boolean names, + Object importType) { + String tmp; + Integer dataSize = 0; + try { + + BufferedReader first = new BufferedReader(new FileReader(inputFile)); + tmp = first.readLine(); + String[] splitted = tmp.split("\\;"); + if (rowNames) { + dataSize = splitted.length - 1; + } else { + dataSize = splitted.length; + } + + BufferedReader br = new BufferedReader(new FileReader(inputFile)); + if (this.data != null) { + this.data.clear(); + } + if (rowNames) { + if (this.rowNames != null) { + this.rowNames.clear(); + } + } + if (names) { + if (this.names != null) { + this.names.clear(); + } + tmp = br.readLine(); + splitted = tmp.split("\\;"); + for (int i = 1; i < splitted.length; i++) { + this.names.add(splitted[i]); + } + } + + Vector<Vector<? extends Serializable>> data = new Vector<Vector<? extends Serializable>>(); + + for (int i = 0; i < dataSize; i++) { + Vector<Serializable> vector = new Vector<Serializable>(); + data.add(vector); + } + + while ((tmp = br.readLine()) != null) { + splitted = tmp.split("\\;"); + int index = 0; + if (rowNames) { + this.rowNames.add(splitted[0]); + index = 1; + } + for (int i = 0 + index; i < splitted.length; i++) { + if (importType instanceof String) { + ((Vector<Serializable>) data.get(i - index)) + .add((Serializable) splitted[i]); + } else if (importType instanceof Double) { + ((Vector<Serializable>) data.get(i - index)).add(Double + .valueOf(splitted[i])); + } else if (importType instanceof Integer) { + ((Vector<Serializable>) data.get(i - index)) + .add(Integer.valueOf(splitted[i])); + } + } + } + br.close(); + this.data = data; + } catch (Exception e) { + e.printStackTrace(); + } + } + + /** + * Import a dataframe form a csv file. The dataframe will contain Objects of + * the same class than each element of importTypes (one element = one + * column). Use this method if you know the type of data that is in the csv + * file. + * + * @param inputFile + * Csv file to import. + * @param rowNames + * Does the csv file contains names of the rows. + * @param names + * Does the csv file contain names of the columns. + * @param importTypes + * Vector of Object of the class of the data imported (the Vector + * match the data type of the columns). (Supported types : + * String, Double and Integer) + */ + public void importCsv(File inputFile, boolean rowNames, boolean names, + Vector<Object> importTypes) { + String tmp; + Integer dataSize = 0; + try { + + BufferedReader first = new BufferedReader(new FileReader(inputFile)); + tmp = first.readLine(); + String[] splitted = tmp.split("\\;"); + if (rowNames) { + dataSize = splitted.length - 1; + } else { + dataSize = splitted.length; + } + + BufferedReader br = new BufferedReader(new FileReader(inputFile)); + if (this.data != null) { + this.data.clear(); + } + if (rowNames) { + if (this.rowNames != null) { + this.rowNames.clear(); + } + } + if (names) { + if (this.names != null) { + this.names.clear(); + } + tmp = br.readLine(); + splitted = tmp.split("\\;"); + for (int i = 1; i < splitted.length; i++) { + this.names.add(splitted[i]); + } + } + + Vector<Vector<? extends Serializable>> data = new Vector<Vector<? extends Serializable>>(); + + for (int i = 0; i < dataSize; i++) { + Vector<Serializable> vector = new Vector<Serializable>(); + data.add(vector); + } + + while ((tmp = br.readLine()) != null) { + splitted = tmp.split("\\;"); + int index = 0; + if (rowNames) { + this.rowNames.add(splitted[0]); + index = 1; + } + for (int i = 0 + index; i < splitted.length; i++) { + if (importTypes.get(i - index) instanceof String) { + ((Vector<Serializable>) data.get(i - index)) + .add((Serializable) splitted[i]); + } else if (importTypes.get(i - index) instanceof Double) { + ((Vector<Serializable>) data.get(i - index)).add(Double + .valueOf(splitted[i])); + } else if (importTypes.get(i - index) instanceof Integer) { + ((Vector<Serializable>) data.get(i - index)) + .add(Integer.valueOf(splitted[i])); + } + } + } + br.close(); + this.data = data; + } catch (Exception e) { + e.printStackTrace(); + } + } + } Modified: lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java =================================================================== --- lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java 2009-05-01 09:47:16 UTC (rev 73) +++ lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java 2009-05-03 09:18:40 UTC (rev 74) @@ -17,6 +17,7 @@ package org.codelutin.j2r; +import java.io.File; import java.io.Serializable; import java.util.HashMap; import java.util.Vector; @@ -166,15 +167,22 @@ dataframe2.getFrom("test", engine); //Test data - Assert.assertEquals(new Double(3.0), (Double) engine.eval("test[1,1]")); - Assert.assertEquals(new Double(4.5), (Double) engine.eval("test[2,1]")); Assert - .assertEquals(new Double(0.01), (Double) engine - .eval("test[3,1]")); - Assert.assertEquals(new Double(1.0), (Double) engine.eval("test[1,2]")); - Assert.assertEquals(new Double(5555555555555555555555.0), - (Double) engine.eval("test[2,2]")); - Assert.assertEquals(new Double(3.0), (Double) engine.eval("test[3,2]")); + .assertEquals(new Double(3.0), dataframe2.getData().get(0).get( + 0)); + Assert + .assertEquals(new Double(4.5), dataframe2.getData().get(0).get( + 1)); + Assert.assertEquals(new Double(0.01), dataframe2.getData().get(0) + .get(2)); + Assert + .assertEquals(new Double(1.0), dataframe2.getData().get(1).get( + 0)); + Assert.assertEquals(new Double(5555555555555555555555.0), dataframe2 + .getData().get(1).get(1)); + Assert + .assertEquals(new Double(3.0), dataframe2.getData().get(1).get( + 2)); //Test names Assert.assertEquals("column1", dataframe2.getNames().get(0)); Assert.assertEquals("column2", dataframe2.getNames().get(1)); @@ -285,4 +293,168 @@ } } + @Test + public void testImportExportCsv() throws Exception { + + //Test import with same type for each column. + + Vector<String> names = new Vector<String>(); + names.add("column1"); + names.add("column2"); + + Vector<String> rowNames = new Vector<String>(); + rowNames.add("row 1"); + rowNames.add("row 2"); + rowNames.add("row 3"); + + Vector<Double> column1 = new Vector<Double>(); + column1.add(3.0); + column1.add(4.5); + column1.add(0.01); + + Vector<Double> column2 = new Vector<Double>(); + column2.add(1.0); + column2.add(5555555555555555555555.0); + column2.add(3.0); + + Vector<Vector<? extends Serializable>> data = new Vector<Vector<? extends Serializable>>(); + data.add(column1); + data.add(column2); + + RDataFrame testDataFrame = new RDataFrame(); + try { + testDataFrame = new RDataFrame(names, rowNames, data, engine, + "test"); + } catch (RException eee) { + Assert.fail(); + } + testDataFrame.exportCsv(new File("/tmp/test.csv"), true, true); + + RDataFrame dataframe2 = new RDataFrame(); + dataframe2.importCsv(new File("/tmp/test.csv"), true, true, new Double( + 3.0)); + + //Test data + Assert + .assertEquals(new Double(3.0), dataframe2.getData().get(0).get( + 0)); + Assert + .assertEquals(new Double(4.5), dataframe2.getData().get(0).get( + 1)); + Assert.assertEquals(new Double(0.01), dataframe2.getData().get(0) + .get(2)); + Assert + .assertEquals(new Double(1.0), dataframe2.getData().get(1).get( + 0)); + Assert.assertEquals(new Double(5555555555555555555555.0), dataframe2 + .getData().get(1).get(1)); + Assert + .assertEquals(new Double(3.0), dataframe2.getData().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 different types for each column + + names = new Vector<String>(); + names.add("column1"); + names.add("column3"); + names.add("column4"); + + rowNames = new Vector<String>(); + rowNames.add("row 1"); + rowNames.add("row 2"); + rowNames.add("row 3"); + + column1 = new Vector<Double>(); + column1.add(3.0); + column1.add(4.5); + column1.add(0.01); + + Vector<Integer> column3 = new Vector<Integer>(); + column3.add(1); + column3.add(5); + column3.add(3); + + Vector<String> column4 = new Vector<String>(); + column4.add("bla"); + column4.add("blabla"); + column4.add("blablabla"); + + data = new Vector<Vector<? extends Serializable>>(); + data.add(column1); + data.add(column3); + data.add(column4); + + Vector<Object> types = new Vector<Object>(); + types.add(new Double(4.0)); + types.add(new Integer(4)); + types.add(new String()); + + testDataFrame = new RDataFrame(); + try { + testDataFrame = new RDataFrame(names, rowNames, data, engine, + "test"); + } catch (RException eee) { + Assert.fail(); + } + testDataFrame.exportCsv(new File("/tmp/test.csv"), true, true); + + RDataFrame dataframe3 = new RDataFrame(); + dataframe3.importCsv(new File("/tmp/test.csv"), true, true, types); + + //Test data + Assert + .assertEquals(new Double(3.0), dataframe3.getData().get(0).get( + 0)); + Assert + .assertEquals(new Double(4.5), dataframe3.getData().get(0).get( + 1)); + Assert.assertEquals(new Double(0.01), dataframe3.getData().get(0) + .get(2)); + Assert.assertEquals(new Integer(1), dataframe3.getData().get(1).get(0)); + Assert.assertEquals(new Integer(5), dataframe3.getData().get(1).get(1)); + Assert.assertEquals(new Integer(3), dataframe3.getData().get(1).get(2)); + Assert.assertEquals("bla", dataframe3.getData().get(2).get(0)); + Assert.assertEquals("blabla", dataframe3.getData().get(2).get(1)); + Assert.assertEquals("blablabla", dataframe3.getData().get(2).get(2)); + //Test names + Assert.assertEquals("column1", dataframe3.getNames().get(0)); + Assert.assertEquals("column3", dataframe3.getNames().get(1)); + Assert.assertEquals("column4", dataframe3.getNames().get(2)); + //Test row names + Assert.assertEquals("row 1", dataframe3.getRowNames().get(0)); + Assert.assertEquals("row 2", dataframe3.getRowNames().get(1)); + Assert.assertEquals("row 3", dataframe3.getRowNames().get(2)); + + //Test import without precision on type + + RDataFrame dataframe4 = new RDataFrame(); + dataframe4.importCsv(new File("/tmp/test.csv"), true, true); + + //Test data + Assert.assertEquals("3.0", dataframe4.getData().get(0).get(0)); + Assert.assertEquals("4.5", dataframe4.getData().get(0).get(1)); + Assert.assertEquals("0.01", dataframe4.getData().get(0).get(2)); + Assert.assertEquals("1", dataframe4.getData().get(1).get(0)); + Assert.assertEquals("5", dataframe4.getData().get(1).get(1)); + Assert.assertEquals("3", dataframe4.getData().get(1).get(2)); + Assert.assertEquals("bla", dataframe4.getData().get(2).get(0)); + Assert.assertEquals("blabla", dataframe4.getData().get(2).get(1)); + Assert.assertEquals("blablabla", dataframe4.getData().get(2).get(2)); + //Test names + Assert.assertEquals("column1", dataframe4.getNames().get(0)); + Assert.assertEquals("column3", dataframe4.getNames().get(1)); + Assert.assertEquals("column4", dataframe4.getNames().get(2)); + //Test row names + Assert.assertEquals("row 1", dataframe4.getRowNames().get(0)); + Assert.assertEquals("row 2", dataframe4.getRowNames().get(1)); + Assert.assertEquals("row 3", dataframe4.getRowNames().get(2)); + } + }

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[LutinJ2R-commits] r73 - lutinj2r/trunk/src/site/rst
by jcouteau＠users.labs.libre-entreprise.org 01 May '09

01 May '09

Author: jcouteau Date: 2009-05-01 09:47:16 +0000 (Fri, 01 May 2009) New Revision: 73 Modified: lutinj2r/trunk/src/site/rst/installation.rst Log: Adding installation precisions for Windows on website. Modified: lutinj2r/trunk/src/site/rst/installation.rst =================================================================== --- lutinj2r/trunk/src/site/rst/installation.rst 2009-05-01 09:43:50 UTC (rev 72) +++ lutinj2r/trunk/src/site/rst/installation.rst 2009-05-01 09:47:16 UTC (rev 73) @@ -76,7 +76,11 @@ La compilation effectuée, un fichier a été généré, dont le nom est propre à la plateforme (libjri.so, jri.dll, ...). Il ne reste plus qu'à configurer le système comme indiqué à l'étape suivante. +Des versions précompilées des librairies sont disponibles (http://lutinj2r.labs.libre-entreprise.org/libsys/) +Site web de JRI : http://www.rforge.net/JRI/ + + Configuration ============= @@ -120,9 +124,9 @@ Quelque soit la plateforme, il faut positionner des variables d'environnement. -- R_HOME : doit pointer sur le dossier d'installation de R (soit /usr/lib/R sous Linux ou C:\Program Files\R\R-2.3.1 sous Windows ou ...) +- R_HOME : doit pointer sur le dossier d'installation de R (soit /usr/lib/R sous Linux ou C:\Program Files\R\R-(version) sous Windows ou ...) - LD_LIBRARY_PATH : doit pointer sur le dossier lib contenu dans R_HOME (soit R_HOME/lib/ sous Linux ou R_HOME\lib sous Windows ou ...) - +- PATH (pour Windows) : doit pointer sur le dossier d'installation de R (C:\Program Files\R\R-(version) ou ...) (en fait sur le dossier contenant la librairie R.dll) Il faut ensuite copier la librairie (libjri.so ou jri.dll ou ...) dans le dossier LD_LIBRARY_PATH @@ -151,3 +155,10 @@ Rserve.exe dans le dossier d'installation de R (par défaut : C:\Program Files\R\R-2.3.1\bin) + +A noter que vous pouvez aussi lancer Rserve à partir de R : + +:: + + library(Rserve) + Rserve() \ No newline at end of file

1 0

[LutinJ2R-commits] r72 - in lutinj2r/trunk/src: main/java/org/codelutin/j2r/types test/java/org/codelutin/j2r
by jcouteau＠users.labs.libre-entreprise.org 01 May '09

01 May '09

Author: jcouteau Date: 2009-05-01 09:43:50 +0000 (Fri, 01 May 2009) New Revision: 72 Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java Log: Adding data checking in data.frames Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java =================================================================== --- lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java 2009-05-01 08:14:19 UTC (rev 71) +++ lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java 2009-05-01 09:43:50 UTC (rev 72) @@ -2,7 +2,6 @@ import java.io.Serializable; import java.util.HashMap; -import java.util.Iterator; import java.util.Set; import java.util.Vector; @@ -38,6 +37,9 @@ this.rowNames = rowNames; this.data = (Vector<Vector<? extends Serializable>>) data; this.variable = variable; + if (checkConsistency() == false) { + throw new RException("A dimension is wrong on the dataframe"); + } } /** @@ -66,6 +68,9 @@ public void setNames(Vector<String> names, REngine engine) throws RException { this.names = names; + if (checkConsistency() == false) { + throw new RException("A dimension is wrong on the dataframe"); + } } /** @@ -93,6 +98,9 @@ public void setRowNames(Vector<String> rowNames, REngine engine) throws RException { this.rowNames = rowNames; + if (checkConsistency() == false) { + throw new RException("A dimension is wrong on the dataframe"); + } } /** @@ -120,6 +128,9 @@ public void setData(Vector<Vector<? extends Serializable>> data, REngine engine) throws RException { this.data = data; + if(checkConsistency()==false){ + throw new RException("A dimension is wrong on the dataframe"); + } } /** @@ -225,6 +236,10 @@ + this.variable + ")$" + key + ")"); attributes.put(key, attribute); } + + if(checkConsistency()==false){ + throw new RException("A dimension is wrong on the dataframe"); + } } @@ -388,6 +403,29 @@ } } - //TODO check data consistency. + /** + * Method to check data consistency + * + * @return true if data is consistent (no dimensions error), false if there + * is a dimension error. + */ + public boolean checkConsistency() { + Integer rowNameslength = rowNames.size(); + Integer namesLength = names.size(); + Integer dataLength = data.size(); + Integer datavectorLength = data.get(0).size(); + if (rowNameslength != datavectorLength) { + return false; + } + if (namesLength != dataLength) { + return false; + } + for (int i = 0; i < dataLength; i++) { + if (data.get(i).size() != datavectorLength) { + return false; + } + } + return true; + } } Modified: lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java =================================================================== --- lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java 2009-05-01 08:14:19 UTC (rev 71) +++ lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java 2009-05-01 09:43:50 UTC (rev 72) @@ -80,8 +80,13 @@ attributes.put("attr1", "\"this is an attribute\""); attributes.put("attr2", "\"this is another attribute\""); - RDataFrame testDataFrame = new RDataFrame(names, rowNames, data, - engine, "test"); + RDataFrame testDataFrame = new RDataFrame(); + try { + testDataFrame = new RDataFrame(names, rowNames, data, engine, + "test"); + } catch (RException eee) { + Assert.fail(); + } testDataFrame.setAttributes(attributes); testDataFrame.commit(engine); @@ -147,8 +152,13 @@ attributes.put("attr1", "\"this is an attribute\""); attributes.put("attr2", "\"this is another attribute\""); - RDataFrame testDataFrame = new RDataFrame(names, rowNames, data, - engine, "test"); + RDataFrame testDataFrame = new RDataFrame(); + try { + testDataFrame = new RDataFrame(names, rowNames, data, engine, + "test"); + } catch (RException eee) { + Assert.fail(); + } testDataFrame.setAttributes(attributes); testDataFrame.commit(engine); @@ -179,4 +189,100 @@ .getAttribute("attr2")); } + @Test + public void testDataFrameWrongDimensions() throws Exception { + //Test wrong names size + Vector<String> names = new Vector<String>(); + names.add("column1"); + + Vector<String> rowNames = new Vector<String>(); + rowNames.add("row 1"); + rowNames.add("row 2"); + rowNames.add("row 3"); + + Vector<Double> column1 = new Vector<Double>(); + column1.add(3.0); + column1.add(4.5); + column1.add(0.01); + + Vector<Double> column2 = new Vector<Double>(); + column2.add(1.0); + column2.add(5555555555555555555555.0); + column2.add(3.0); + + Vector<Vector<? extends Serializable>> data = new Vector<Vector<? extends Serializable>>(); + data.add(column1); + data.add(column2); + + try { + RDataFrame testDataFrame = new RDataFrame(names, rowNames, data, + engine, "test"); + } catch (RException eee) { + Assert.assertEquals("A dimension is wrong on the dataframe", eee + .getMessage()); + } + + //Test wrong row names size + names = new Vector<String>(); + names.add("column1"); + names.add("column2"); + + rowNames = new Vector<String>(); + rowNames.add("row 1"); + rowNames.add("row 2"); + + column1 = new Vector<Double>(); + column1.add(3.0); + column1.add(4.5); + column1.add(0.01); + + column2 = new Vector<Double>(); + column2.add(1.0); + column2.add(5555555555555555555555.0); + column2.add(3.0); + + data = new Vector<Vector<? extends Serializable>>(); + data.add(column1); + data.add(column2); + + try { + RDataFrame testDataFrame = new RDataFrame(names, rowNames, data, + engine, "test"); + } catch (RException eee) { + Assert.assertEquals("A dimension is wrong on the dataframe", eee + .getMessage()); + } + + //Test wrong data size + names = new Vector<String>(); + names.add("column1"); + names.add("column2"); + + rowNames = new Vector<String>(); + rowNames.add("row 1"); + rowNames.add("row 2"); + rowNames.add("row 3"); + + column1 = new Vector<Double>(); + column1.add(3.0); + column1.add(4.5); + column1.add(0.01); + + column2 = new Vector<Double>(); + column2.add(1.0); + column2.add(5555555555555555555555.0); + + data = new Vector<Vector<? extends Serializable>>(); + data.add(column1); + data.add(column2); + + try { + RDataFrame testDataFrame = new RDataFrame(names, rowNames, data, + engine, "test"); + } catch (RException eee) { + Assert.assertEquals("A dimension is wrong on the dataframe", eee + .getMessage()); + } + } + }

1 0

[LutinJ2R-commits] r71 - in lutinj2r/trunk/src: main/java/org/codelutin/j2r/types test/java/org/codelutin/j2r
by jcouteau＠users.labs.libre-entreprise.org 01 May '09

01 May '09

Author: jcouteau Date: 2009-05-01 08:14:19 +0000 (Fri, 01 May 2009) New Revision: 71 Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java Log: Adding attributes management to data.frames Changing the R/Java update process. Now need to be expressed. Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java =================================================================== --- lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java 2009-04-30 12:10:02 UTC (rev 70) +++ lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java 2009-05-01 08:14:19 UTC (rev 71) @@ -1,6 +1,9 @@ package org.codelutin.j2r.types; import java.io.Serializable; +import java.util.HashMap; +import java.util.Iterator; +import java.util.Set; import java.util.Vector; import org.codelutin.j2r.REngine; @@ -8,10 +11,16 @@ public class RDataFrame { + //Vector containing the names of the data.frame vectors private Vector<String> names; + //Vector containing the names of the rows of the data.frame vectors private Vector<String> rowNames; + //Vector containing the vectors of the data.frame private Vector<Vector<? extends Serializable>> data; + //Name of the data.frame in R private String variable; + //Attributes of the data.frame under a map -> name : R expression + private HashMap<String, String> attributes; public RDataFrame() { super(); @@ -29,12 +38,11 @@ this.rowNames = rowNames; this.data = (Vector<Vector<? extends Serializable>>) data; this.variable = variable; - assignTo(variable, engine); } /** * Method to get the names of the vectors of the R data.frame (there is no - * synchronizing with R, use the synchro() method to synchronize data with R + * synchronizing with R, use the update() method to synchronize data with R * before using this method if you think data may have changed. * * @return a vector of strings containing the names of each vector of the R @@ -45,8 +53,8 @@ } /** - * Method to assign names of the vectors of the R data.frame (the names will - * then be synchronized with R) + * Method to assign names of the vectors of the R data.frame (there is no + * synchronizing with R, use the commit() method to send data to R. * * @param names * a vector containing the names of the vector of the R @@ -58,12 +66,11 @@ public void setNames(Vector<String> names, REngine engine) throws RException { this.names = names; - assignNames(engine); } /** * Method to get the names of the rows of the R data.frame (there is no - * synchronizing with R, use the synchro() method to synchronize data with R + * synchronizing with R, use the update() method to synchronize data with R * before using this method if you think data may have changed. * * @return a vector of strings containing the names of each row of the R @@ -74,8 +81,8 @@ } /** - * Method to assign names of the rows of the R data.frame (the names will - * then be synchronized with R) + * Method to assign names of the rows of the R data.frame (there is no + * synchronizing with R, use the commit() method to send data to R. * * @param rowNames * a vector containing the names of the rows of the R data.frame @@ -86,12 +93,11 @@ public void setRowNames(Vector<String> rowNames, REngine engine) throws RException { this.rowNames = rowNames; - assignRowNames(engine); } /** * Method to get the vectors of the R data.frame (there is no synchronizing - * with R, use the synchro() method to synchronize data with R before using + * with R, use the update() method to synchronize data with R before using * this method if you think data may have changed. * * @return a Vector containing the vectors of the R data.frame @@ -101,8 +107,8 @@ } /** - * Method to assign the data of the R data.frame (the data will then be - * synchronized with R) + * 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. * * @param data * a Vector of Vectors, containing each vector of the R @@ -114,7 +120,6 @@ public void setData(Vector<Vector<? extends Serializable>> data, REngine engine) throws RException { this.data = data; - assignData(engine); } /** @@ -127,12 +132,24 @@ * @throws RException */ public void assignTo(String variable, REngine engine) throws RException { + this.variable = variable; + commit(engine); - this.variable = variable; + } + + /** + * Method to commit changes made to the data.frame in java and send them to + * R. + * + * @param engine + * a REngine where the R session is located. + * @throws RException + */ + public void commit(REngine engine) throws RException { assignData(engine); assignRowNames(engine); assignNames(engine); - + assignAttributes(engine); } /** @@ -146,20 +163,42 @@ */ public void getFrom(String variable, REngine engine) throws RException { this.variable = variable; - rowNames.clear(); - names.clear(); - data.clear(); + if (rowNames != null) { + rowNames.clear(); + } else { + rowNames = new Vector<String>(); + } + if (names != null) { + names.clear(); + } else { + names = new Vector<String>(); + } + if (data != null) { + data.clear(); + } else { + data = new Vector<Vector<? extends Serializable>>(); + } + if (attributes != null) { + attributes.clear(); + } else { + attributes = new HashMap<String, String>(); + } + + //update row names String[] rowNamesArray = (String[]) engine.eval("row.names(" + this.variable + ")"); for (int i = 0; i < rowNamesArray.length; i++) { rowNames.add(rowNamesArray[i]); } + + //update names String[] namesArray = (String[]) engine.eval("names(" + this.variable + ")"); for (int i = 0; i < namesArray.length; i++) { names.add(namesArray[i]); } + //update data Integer dataframelength = (Integer) engine.eval("length(" + this.variable + ")"); @@ -174,6 +213,19 @@ data.add(thisColumn); } + //update attributes + Integer attributeslength = (Integer) engine.eval("length(attributes(" + + this.variable + "))"); + + for (int i = 0; i < attributeslength; i++) { + String key = (String) engine.eval("names(attributes(" + + this.variable + "))[" + (i + 1) + "]"); + + String attribute = (String) engine.eval("toString(attributes(" + + this.variable + ")$" + key + ")"); + attributes.put(key, attribute); + } + } /** @@ -184,7 +236,7 @@ * a REngine where the R session is located. * @throws RException */ - public void check(REngine engine) throws RException { + public void update(REngine engine) throws RException { getFrom(variable, engine); } @@ -245,10 +297,97 @@ engine.voidEval(dataframe); } - //TODO method set attributes, get attributes + /** + * Assign a value to an attribute in R. + * + * @param engine + * a REngine where the R session is located. + * @param attribute + * the attribute name + * @param value + * the value to be assigned (this is a R expression, String may + * be rounded with escaped quote like : \"this is a R string\" ). + * @throws RException + */ + private void assignAttribute(REngine engine, String attribute, String value) + throws RException { + engine.voidEval("attr(" + this.variable + ",\"" + attribute + "\")<-" + + value); + } - //TODO method add attribute, remove attribute + /** + * Assign all the attributes in R. + * + * @param engine + * a REngine where the R session is located. + * @throws RException + */ + private void assignAttributes(REngine engine) throws RException { + if (attributes != null) { + Set<String> keyset = attributes.keySet(); + String[] keys = keyset.toArray(new String[0]); + for (int i = 0; i < keys.length; i++) { + assignAttribute(engine, keys[i], attributes.get(keys[i])); + } + } + } + /** + * Method to set all the attributes of the data.frame (there is no + * synchronizing with R, use the commit() method to send data to R. + * + * @param attributes + * a Map containing the attributes (key) and values (value) + * (values are a R expression, String may be rounded with escaped + * quote like : \"this is a R string\" ). + */ + public void setAttributes(HashMap<String, String> attributes) { + this.attributes = attributes; + } + + /** + * Method to get all the attributes of the data.frame (there is no + * synchronizing with R, use the update() method to synchronize data with R + * before using this method if you think data may have changed. + * + * @return a Map containing the attributes (key) and values (value) + */ + public HashMap<String, String> getAttributes() { + return this.attributes; + } + + /** + * Method to get the value of an attribute (there is no synchronizing with + * R, use the update() method to synchronize data with R before using this + * method if you think data may have changed. + * + * @param attribute + * name of the attribute + * @return + */ + public String getAttribute(String attribute) { + return attributes.get(attribute); + } + + /** + * Method to set the value of an attribute (there is no synchronizing with + * R, use the commit() method to send data to R. + * + * @param attribute + * name of the attribute + * @param value + * the value to be set (this is a R expression, String may be + * rounded with escaped quote like : \"this is a R string\" ). + */ + public void setAttribute(String attribute, String value) { + if (attributes.containsKey(attribute)) { + attributes.remove(attribute); + attributes.put(attribute, value); + } else { + attributes.put(attribute, value); + } + } + //TODO check data consistency. } Modified: lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java =================================================================== --- lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java 2009-04-30 12:10:02 UTC (rev 70) +++ lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java 2009-05-01 08:14:19 UTC (rev 71) @@ -18,6 +18,7 @@ package org.codelutin.j2r; import java.io.Serializable; +import java.util.HashMap; import java.util.Vector; import org.apache.commons.logging.Log; @@ -75,8 +76,15 @@ data.add(column1); data.add(column2); + HashMap<String, String> attributes = new HashMap<String, String>(); + attributes.put("attr1", "\"this is an attribute\""); + attributes.put("attr2", "\"this is another attribute\""); + RDataFrame testDataFrame = new RDataFrame(names, rowNames, data, engine, "test"); + testDataFrame.setAttributes(attributes); + testDataFrame.commit(engine); + //Test data Assert.assertEquals(new Double(3.0), (Double) engine.eval("test[1,1]")); Assert.assertEquals(new Double(4.5), (Double) engine.eval("test[2,1]")); @@ -100,8 +108,14 @@ Assert .assertEquals("row 3", (String) engine .eval("row.names(test)[3]")); + + //Test attributes + Assert.assertEquals("this is an attribute", (String) engine + .eval("attr(test,\"attr1\")")); + Assert.assertEquals("this is another attribute", (String) engine + .eval("attr(test,\"attr2\")")); } - + @Test public void testGetDataFrame() throws Exception { //This test is also a test for all the setters... @@ -129,10 +143,18 @@ data.add(column1); data.add(column2); + HashMap<String, String> attributes = new HashMap<String, String>(); + attributes.put("attr1", "\"this is an attribute\""); + attributes.put("attr2", "\"this is another attribute\""); + RDataFrame testDataFrame = new RDataFrame(names, rowNames, data, engine, "test"); + testDataFrame.setAttributes(attributes); + testDataFrame.commit(engine); + RDataFrame dataframe2 = new RDataFrame(); dataframe2.getFrom("test", engine); + //Test data Assert.assertEquals(new Double(3.0), (Double) engine.eval("test[1,1]")); Assert.assertEquals(new Double(4.5), (Double) engine.eval("test[2,1]")); @@ -147,12 +169,14 @@ 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)); + 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 attributes + Assert.assertEquals("this is an attribute", dataframe2 + .getAttribute("attr1")); + Assert.assertEquals("this is another attribute", dataframe2 + .getAttribute("attr2")); } }

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[LutinJ2R-commits] r70 - in lutinj2r/trunk/src: main/java/org/codelutin/j2r main/java/org/codelutin/j2r/types test/java/org/codelutin/j2r
by jcouteau＠users.labs.libre-entreprise.org 30 Apr '09

30 Apr '09

Author: jcouteau Date: 2009-04-30 12:10:02 +0000 (Thu, 30 Apr 2009) New Revision: 70 Added: lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/ lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java Log: Adding data.frame data type + tests. Added: lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java =================================================================== --- lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java (rev 0) +++ lutinj2r/trunk/src/main/java/org/codelutin/j2r/types/RDataFrame.java 2009-04-30 12:10:02 UTC (rev 70) @@ -0,0 +1,254 @@ +package org.codelutin.j2r.types; + +import java.io.Serializable; +import java.util.Vector; + +import org.codelutin.j2r.REngine; +import org.codelutin.j2r.RException; + +public class RDataFrame { + + private Vector<String> names; + private Vector<String> rowNames; + private Vector<Vector<? extends Serializable>> data; + private String variable; + + public RDataFrame() { + super(); + this.names = new Vector<String>(); + this.rowNames = new Vector<String>(); + this.data = new Vector<Vector<? extends Serializable>>(); + this.variable = ""; + } + + public RDataFrame(Vector<String> names, Vector<String> rowNames, + Vector<Vector<? extends Serializable>> data, REngine engine, + String variable) throws RException { + super(); + this.names = names; + this.rowNames = rowNames; + this.data = (Vector<Vector<? extends Serializable>>) data; + this.variable = variable; + assignTo(variable, engine); + } + + /** + * Method to get the names of the vectors of the R data.frame (there is no + * synchronizing with R, use the synchro() method to synchronize data with R + * before using this method if you think data may have changed. + * + * @return a vector of strings containing the names of each vector of the R + * data.frame + */ + public Vector<String> getNames() { + return names; + } + + /** + * Method to assign names of the vectors of the R data.frame (the names will + * then be synchronized with R) + * + * @param names + * a vector containing the names of the vector of the R + * data.frame + * @param engine + * a REngine where the R session is located. + * @throws RException + */ + public void setNames(Vector<String> names, REngine engine) + throws RException { + this.names = names; + assignNames(engine); + } + + /** + * Method to get the names of the rows of the R data.frame (there is no + * synchronizing with R, use the synchro() method to synchronize data with R + * before using this method if you think data may have changed. + * + * @return a vector of strings containing the names of each row of the R + * data.frame + */ + public Vector<String> getRowNames() { + return rowNames; + } + + /** + * Method to assign names of the rows of the R data.frame (the names will + * then be synchronized with R) + * + * @param rowNames + * a vector containing the names of the rows of the R data.frame + * @param engine + * a REngine where the R session is located. + * @throws RException + */ + public void setRowNames(Vector<String> rowNames, REngine engine) + throws RException { + this.rowNames = rowNames; + assignRowNames(engine); + } + + /** + * Method to get the vectors of the R data.frame (there is no synchronizing + * with R, use the synchro() method to synchronize data with R before using + * this method if you think data may have changed. + * + * @return a Vector containing the vectors of the R data.frame + */ + public Vector<Vector<? extends Serializable>> getData() { + return data; + } + + /** + * Method to assign the data of the R data.frame (the data will then be + * synchronized with R) + * + * @param data + * a Vector of Vectors, containing each vector of the R + * data.frame + * @param engine + * a REngine where the R session is located. + * @throws RException + */ + public void setData(Vector<Vector<? extends Serializable>> data, + REngine engine) throws RException { + this.data = data; + assignData(engine); + } + + /** + * Method to assign this data.frame to a variable in R. + * + * @param variable + * name of the variable + * @param engine + * a REngine where the R session is located. + * @throws RException + */ + public void assignTo(String variable, REngine engine) throws RException { + + this.variable = variable; + assignData(engine); + assignRowNames(engine); + assignNames(engine); + + } + + /** + * Method to get a data.frame from a variable in R. + * + * @param variable + * name of the data.frame in R + * @param engine + * a REngine where the R session is located. + * @throws RException + */ + public void getFrom(String variable, REngine engine) throws RException { + this.variable = variable; + rowNames.clear(); + names.clear(); + data.clear(); + String[] rowNamesArray = (String[]) engine.eval("row.names(" + + this.variable + ")"); + for (int i = 0; i < rowNamesArray.length; i++) { + rowNames.add(rowNamesArray[i]); + } + String[] namesArray = (String[]) engine.eval("names(" + this.variable + + ")"); + for (int i = 0; i < namesArray.length; i++) { + names.add(namesArray[i]); + } + + Integer dataframelength = (Integer) engine.eval("length(" + + this.variable + ")"); + + for (int i = 0; i < dataframelength; i++) { + Integer vectorlength = (Integer) engine.eval("length(" + + this.variable + "[," + (i + 1) + "])"); + Vector<Serializable> thisColumn = new Vector<Serializable>(); + for (int j = 0; j < vectorlength; j++) { + thisColumn.add((Serializable) engine.eval(this.variable + "[" + + (i + 1) + "," + (j + 1) + "]")); + } + data.add(thisColumn); + } + + } + + /** + * Synchronization with R method. This method updates the content of the + * data.frame from R. All local changes are lost. + * + * @param engine + * a REngine where the R session is located. + * @throws RException + */ + public void check(REngine engine) throws RException { + getFrom(variable, engine); + } + + /** + * Send names changes to R + * + * @param engine + * @throws RException + */ + private void assignNames(REngine engine) throws RException { + String vectorNames = "names(" + this.variable + ")<-c("; + for (int i = 0; i < names.size(); i++) { + vectorNames = vectorNames + "\"" + names.get(i) + "\"" + ","; + } + vectorNames = vectorNames.substring(0, vectorNames.length() - 1) + ")"; + engine.voidEval(vectorNames); + } + + /** + * Send row names changes to R + * + * @param engine + * a REngine where the R session is located. + * @throws RException + */ + private void assignRowNames(REngine engine) throws RException { + String vectorRowNames = "row.names(" + this.variable + ")<-c("; + for (int i = 0; i < rowNames.size(); i++) { + vectorRowNames = vectorRowNames + "\"" + rowNames.get(i) + "\"" + + ","; + } + vectorRowNames = vectorRowNames.substring(0, + vectorRowNames.length() - 1) + + ")"; + engine.voidEval(vectorRowNames); + } + + /** + * Send data changes to R + * + * @param engine + * a REngine where the R session is located. + * @throws RException + */ + private void assignData(REngine engine) throws RException { + String dataframe = variable + "<-data.frame("; + for (int i = 0; i < data.size(); i++) { + dataframe = dataframe + "data" + i + ","; + String datai = "data" + i + "<-c("; + for (int j = 0; j < data.get(i).size(); j++) { + datai = datai + data.get(i).get(j) + ","; + } + datai = datai.substring(0, datai.length() - 1) + ")"; + engine.voidEval(datai); + + } + dataframe = dataframe.substring(0, dataframe.length() - 1) + ")"; + engine.voidEval(dataframe); + } + + //TODO method set attributes, get attributes + + //TODO method add attribute, remove attribute + + //TODO check data consistency. + +} Added: lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java =================================================================== --- lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java (rev 0) +++ lutinj2r/trunk/src/test/java/org/codelutin/j2r/DataframeTest.java 2009-04-30 12:10:02 UTC (rev 70) @@ -0,0 +1,158 @@ +/* *##% Lutin Java-2-R library + * Copyright (C) 2006 - 2008 CodeLutin + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Lesser Public License for more details. + * + * You should have received a copy of the GNU General Lesser Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/lgpl-3.0.html>. ##%*/ + +package org.codelutin.j2r; + +import java.io.Serializable; +import java.util.Vector; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.j2r.types.RDataFrame; +import org.junit.After; +import org.junit.Assert; +import org.junit.Before; +import org.junit.Test; + +public class DataframeTest { + + private static Log log = LogFactory.getLog(DataframeTest.class); + + private REngine engine; + + @Before + public void setUp() throws Exception { + LutinTimer init = new LutinTimer(); + init.startTiming(); + if (engine == null) { + engine = new RProxy(); + } + } + + @After + public void tearDown() throws Exception { + engine.terminate(); + } + + @Test + public void testDataFrameCreation() throws Exception { + //This test is also a test for all the setters... + //they work the same way and use the same internal methods. + Vector<String> names = new Vector<String>(); + names.add("column1"); + names.add("column2"); + + Vector<String> rowNames = new Vector<String>(); + rowNames.add("row 1"); + rowNames.add("row 2"); + rowNames.add("row 3"); + + Vector<Double> column1 = new Vector<Double>(); + column1.add(3.0); + column1.add(4.5); + column1.add(0.01); + + Vector<Double> column2 = new Vector<Double>(); + column2.add(1.0); + column2.add(5555555555555555555555.0); + column2.add(3.0); + + Vector<Vector<? extends Serializable>> data = new Vector<Vector<? extends Serializable>>(); + data.add(column1); + data.add(column2); + + RDataFrame testDataFrame = new RDataFrame(names, rowNames, data, + engine, "test"); + //Test data + Assert.assertEquals(new Double(3.0), (Double) engine.eval("test[1,1]")); + Assert.assertEquals(new Double(4.5), (Double) engine.eval("test[2,1]")); + Assert + .assertEquals(new Double(0.01), (Double) engine + .eval("test[3,1]")); + Assert.assertEquals(new Double(1.0), (Double) engine.eval("test[1,2]")); + Assert.assertEquals(new Double(5555555555555555555555.0), + (Double) engine.eval("test[2,2]")); + Assert.assertEquals(new Double(3.0), (Double) engine.eval("test[3,2]")); + //Test names + Assert.assertEquals("column1", (String) engine.eval("names(test)[1]")); + Assert.assertEquals("column2", (String) engine.eval("names(test)[2]")); + //Test row names + Assert + .assertEquals("row 1", (String) engine + .eval("row.names(test)[1]")); + Assert + .assertEquals("row 2", (String) engine + .eval("row.names(test)[2]")); + Assert + .assertEquals("row 3", (String) engine + .eval("row.names(test)[3]")); + } + + @Test + public void testGetDataFrame() throws Exception { + //This test is also a test for all the setters... + //they work the same way and use the same internal methods. + Vector<String> names = new Vector<String>(); + names.add("column1"); + names.add("column2"); + + Vector<String> rowNames = new Vector<String>(); + rowNames.add("row 1"); + rowNames.add("row 2"); + rowNames.add("row 3"); + + Vector<Double> column1 = new Vector<Double>(); + column1.add(3.0); + column1.add(4.5); + column1.add(0.01); + + Vector<Double> column2 = new Vector<Double>(); + column2.add(1.0); + column2.add(5555555555555555555555.0); + column2.add(3.0); + + Vector<Vector<? extends Serializable>> data = new Vector<Vector<? extends Serializable>>(); + data.add(column1); + data.add(column2); + + RDataFrame testDataFrame = new RDataFrame(names, rowNames, data, + engine, "test"); + RDataFrame dataframe2 = new RDataFrame(); + dataframe2.getFrom("test", engine); + //Test data + Assert.assertEquals(new Double(3.0), (Double) engine.eval("test[1,1]")); + Assert.assertEquals(new Double(4.5), (Double) engine.eval("test[2,1]")); + Assert + .assertEquals(new Double(0.01), (Double) engine + .eval("test[3,1]")); + Assert.assertEquals(new Double(1.0), (Double) engine.eval("test[1,2]")); + Assert.assertEquals(new Double(5555555555555555555555.0), + (Double) engine.eval("test[2,2]")); + Assert.assertEquals(new Double(3.0), (Double) engine.eval("test[3,2]")); + //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)); + } + +}

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[LutinJ2R-commits] r69 - in lutinj2r/trunk/src: main/java/org/codelutin/j2r main/java/org/codelutin/j2r/jni main/java/org/codelutin/j2r/net test/java/org/codelutin/j2r
by jcouteau＠users.labs.libre-entreprise.org 29 Apr '09

29 Apr '09

Author: jcouteau Date: 2009-04-29 14:43:55 +0000 (Wed, 29 Apr 2009) New Revision: 69 Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/REngine.java lutinj2r/trunk/src/main/java/org/codelutin/j2r/RProxy.java lutinj2r/trunk/src/main/java/org/codelutin/j2r/jni/RJniEngine.java lutinj2r/trunk/src/main/java/org/codelutin/j2r/net/RNetEngine.java lutinj2r/trunk/src/test/java/org/codelutin/j2r/JNITest.java lutinj2r/trunk/src/test/java/org/codelutin/j2r/NetTest.java Log: Adding copy, move, list all objects and clear session capability Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/REngine.java =================================================================== --- lutinj2r/trunk/src/main/java/org/codelutin/j2r/REngine.java 2009-04-28 18:42:55 UTC (rev 68) +++ lutinj2r/trunk/src/main/java/org/codelutin/j2r/REngine.java 2009-04-29 14:43:55 UTC (rev 69) @@ -30,6 +30,7 @@ package org.codelutin.j2r; import java.io.File; +import java.util.List; /** * Cette interface est le point commun entre les differentes technologies @@ -37,114 +38,171 @@ */ public interface REngine { - /** + /** * Effectue l'initialisation du moteur. Les parametres sont passes par les * options de JVM, -D... - * @return true/false pour indiquer si l'initialisation a pu se faire sans - * encombre - */ - public boolean init(); + * + * @return true/false pour indiquer si l'initialisation a pu se faire sans + * encombre + */ + public boolean init(); - /** - * Delegue a R le traitement passe en parametre. - * @param expr l'expression a evaluer - * @return La valeur renvoyee par la commande - * @throws RException - */ - public Object eval(String expr) throws RException; + /** + * Delegue a R le traitement passe en parametre. + * + * @param expr + * l'expression a evaluer + * @return La valeur renvoyee par la commande + * @throws RException + */ + public Object eval(String expr) throws RException; /** * Effectue un eval mais sans retour de resultat. Quand c'est possible cela * permet donc de na pas consommer du temps de transfert et conversion de R * a Java. - * @param expr l'expression a evaluer - * @throws RException + * + * @param expr + * l'expression a evaluer + * @throws RException */ public void voidEval(String expr) throws RException; - /** + /** * Met fin a l'utilisation de l'engine - * @throws RException - */ - public void terminate() throws RException; - - /** + * + * @throws RException + */ + public void terminate() throws RException; + + /** * Load .RData file located in directory * - * @param directory directory where the .RData file is located + * @param directory + * directory where the .RData file is located * @throws RException */ - public void loadRData(File directory) throws RException; - + public void loadRData(File directory) throws RException; + /** * Save the session in a .RData file in directory * - * @param directory where the .RData file will be saved + * @param directory + * where the .RData file will be saved * @throws RException */ public void saveRData(File directory) throws RException; - + /** * Set the R working directory - * @param directory to set + * + * @param directory + * to set * @throws RException */ public void setwd(File directory) throws RException; - + /** * Get the actual R session working directory * * @return a File that is the actual R session working directory * @throws RException */ - + public File getwd() throws RException; - + /** * Use the dput R instruction to store the content of a R object to a file. * The file created will be in the working directory * - * @param rObject name of the R object to save - * @param outputFileName name of the file to save + * @param rObject + * name of the R object to save + * @param outputFileName + * name of the file to save * @throws RException */ public void dput(String rObject, String outputFileName) throws RException; - - + /** - * Use the dget rInstruction to store the content of a file (created with the dput instruction) into a R object. - * The file used have to be in the working directory + * Use the dget rInstruction to store the content of a file (created with + * the dput instruction) into a R object. The file used have to be in the + * working directory * - * @param rObject name of the R object created - * @param inputFileName name of the file to load + * @param rObject + * name of the R object created + * @param inputFileName + * name of the file to load * @throws RException */ public void dget(String rObject, String inputFileName) throws RException; - + /** * Use the dput R instruction to store the content of a R object to a file. * - * @param rObject R object to save - * @param outputFileName the file to save + * @param rObject + * R object to save + * @param outputFileName + * the file to save * @throws RException */ public void dput(String rObject, File outputFile) throws RException; - - + /** - * Use the dget rInstruction to store the content of a file (created with the dput instruction) into a R object. + * Use the dget rInstruction to store the content of a file (created with + * the dput instruction) into a R object. * - * @param rObject name of the R object created - * @param inputFile file to load + * @param rObject + * name of the R object created + * @param inputFile + * file to load * @throws RException */ public void dget(String rObject, File inputFile) throws RException; - + /** * Remove a R object from the actual session - * @param rObject to be removed from the session + * + * @param rObject + * to be removed from the session * @throws RException */ - public void remove (String rObject) throws RException; + public void remove(String rObject) throws RException; + /** + * Make a copy of an object and remove the old one. + * + * @param inputObject + * the object to be copied and deleted + * @param outputObject + * the object to be created + * @throws RException + */ + public void mv(String inputObject, String outputObject) throws RException; + + /** + * Copy an object. + * + * @param inputObject + * the object to be copied + * @param outputObject + * the object to be created + * @throws RException + */ + public void cp(String inputObject, String outputObject) throws RException; + + /** + * List all R object present in the actual session + * + * @return a list containing the name of all the R objects in the R session. + * @throws RException + */ + public String[] ls() throws RException; + + /** + * Remove all the objects present in the actual R session. + * + * @throws RException + */ + public void clearSession() throws RException; + } //RJniEngine Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/RProxy.java =================================================================== --- lutinj2r/trunk/src/main/java/org/codelutin/j2r/RProxy.java 2009-04-28 18:42:55 UTC (rev 68) +++ lutinj2r/trunk/src/main/java/org/codelutin/j2r/RProxy.java 2009-04-29 14:43:55 UTC (rev 69) @@ -41,21 +41,21 @@ * l'implatation choisie. La detection est basee sur l'option de demarrage de la * JVM : * <ul> - * <li><code>-DR.type=net</code></li> - * <li><code>-DR.type=jni</code></li> - * <li><code>-DR.type=...</code></li> + * <li><code>-DR.type=net</code></li> + * <li><code>-DR.type=jni</code></li> + * <li><code>-DR.type=...</code></li> * </ul> * Il est possible de parametrer la solution network, pour cela, voir la * documentation de {@link org.codelutin.j2r.net.RNetEngine} */ public class RProxy implements REngine { - private Log log = LogFactory.getLog(RProxy.class); + private Log log = LogFactory.getLog(RProxy.class); - private REngine engine; + private REngine engine; public RProxy() { - init(); + init(); } private boolean init(String RType) { @@ -64,255 +64,312 @@ RType = "net"; } if (RType.startsWith("net")) { - initSucceded = initOnNet(); - if (!initSucceded) { - if (log.isErrorEnabled()) { - log.error("Initialization of R with Network failed, trying JNI"); - } - initSucceded = initOnJNI(); - } + initSucceded = initOnNet(); + if (!initSucceded) { + if (log.isErrorEnabled()) { + log + .error("Initialization of R with Network failed, trying JNI"); + } + initSucceded = initOnJNI(); + } } else if ("jni".equalsIgnoreCase(RType)) { - initSucceded = initOnJNI(); - if (!initSucceded) { - if (log.isErrorEnabled()) { - log.error("Initialization of R over JNI failed, trying with Network"); - } - initSucceded = initOnNet(); - } + initSucceded = initOnJNI(); + if (!initSucceded) { + if (log.isErrorEnabled()) { + log + .error("Initialization of R over JNI failed, trying with Network"); + } + initSucceded = initOnNet(); + } } else if (log.isErrorEnabled()) { - log.error("Invalid type specified : " + RType); + log.error("Invalid type specified : " + RType); } return initSucceded; } private boolean initOnJNI() { - if (log.isInfoEnabled()) { - log.info("Trying to initialize the R Proxy over JNI"); - } - RJniEngine newEngine = new RJniEngine(); - if (newEngine.init()) { - engine = newEngine; - return true; - } - return false; + if (log.isInfoEnabled()) { + log.info("Trying to initialize the R Proxy over JNI"); + } + RJniEngine newEngine = new RJniEngine(); + if (newEngine.init()) { + engine = newEngine; + return true; + } + return false; } private boolean initOnNet() { - if (log.isInfoEnabled()) { - log.info("Trying to initialize the R Proxy with Network"); - } - RNetEngine newEngine = new RNetEngine(); - if (newEngine.init()) { - engine = newEngine; - return true; - } - return false; + if (log.isInfoEnabled()) { + log.info("Trying to initialize the R Proxy with Network"); + } + RNetEngine newEngine = new RNetEngine(); + if (newEngine.init()) { + engine = newEngine; + return true; + } + return false; } - /* (non-Javadoc) - * @see org.codelutin.R.REngine#eval(java.lang.String) - */ - public Object eval(String expr) throws RException { - if (engine == null) { - log.fatal("The R Proxy is not initialized. An error probably " + - "occured during the initialization."); - return null; - } - return engine.eval(expr); - } + /* (non-Javadoc) + * @see org.codelutin.R.REngine#eval(java.lang.String) + */ + public Object eval(String expr) throws RException { + if (engine == null) { + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); + return null; + } + return engine.eval(expr); + } - /* (non-Javadoc) - * @see org.codelutin.j2r.REngine#init() - */ - public boolean init() { + /* (non-Javadoc) + * @see org.codelutin.j2r.REngine#init() + */ + public boolean init() { String RType = System.getProperty("R.type"); if (RType == null || "".equals(RType)) { - log.warn("No R type specified.\nusage:\n\tjava -DR.type=net ...\n" + - "or\n\tjava -DR.type=jni ...\n\nConsidering network type"); - RType = "net"; + log + .warn("No R type specified.\nusage:\n\tjava -DR.type=net ...\n" + + "or\n\tjava -DR.type=jni ...\n\nConsidering network type"); + RType = "net"; } if (!init(RType)) { - if (log.isFatalEnabled()) { - log.fatal("The initializing of R failed."); - } - return false; + if (log.isFatalEnabled()) { + log.fatal("The initializing of R failed."); + } + return false; } - return true; - } + return true; + } - /* (non-Javadoc) - * @see org.codelutin.j2r.REngine#terminate() - */ - public void terminate() throws RException { - if (engine == null) { - log.fatal("The R Proxy is not initialized. An error probably " + - "occured during the initialization."); - } else { - engine.terminate(); - } - } + /* (non-Javadoc) + * @see org.codelutin.j2r.REngine#terminate() + */ + public void terminate() throws RException { + if (engine == null) { + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); + } else { + engine.terminate(); + } + } /* (non-Javadoc) * @see org.codelutin.j2r.REngine#voidEval(java.lang.String) */ public void voidEval(String expr) throws RException { if (engine == null) { - log.fatal("The R Proxy is not initialized. An error probably " + - "occured during the initialization."); + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); return; } engine.voidEval(expr); } - + /** * Load .RData file located in directory * - * @param directory directory where the .RData file is located + * @param directory + * directory where the .RData file is located * @throws RException */ public void loadRData(File directory) throws RException { if (engine == null) { - log.fatal("The R Proxy is not initialized. An error probably " + - "occured during the initialization."); + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); return; } engine.setwd(directory); engine.voidEval("load(\".RData\")"); } - + /** * Save the session in a .RData file in directory * - * @param directory where the .RData file will be saved + * @param directory + * where the .RData file will be saved * @throws RException */ - public void saveRData(File directory) throws RException{ + public void saveRData(File directory) throws RException { if (engine == null) { - log.fatal("The R Proxy is not initialized. An error probably " + - "occured during the initialization."); + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); return; } engine.setwd(directory); engine.voidEval("save.image()"); } - + /** * Set the R working directory - * @param directory to set + * + * @param directory + * to set * @throws RException */ public void setwd(File directory) throws RException { if (engine == null) { - log.fatal("The R Proxy is not initialized. An error probably " + - "occured during the initialization."); + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); return; } - engine.voidEval("setwd(\""+directory.getAbsolutePath() + "\")"); + engine.voidEval("setwd(\"" + directory.getAbsolutePath() + "\")"); } - + /** * Get the actual R session working directory * - * @return a File that is the actual R session working directory, null if the engine is not initialized + * @return a File that is the actual R session working directory, null if + * the engine is not initialized * @throws RException */ - + public File getwd() throws RException { if (engine == null) { - log.fatal("The R Proxy is not initialized. An error probably " + - "occured during the initialization."); + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); return null; } - String directory = (String)engine.eval("getwd()"); + String directory = (String) engine.eval("getwd()"); return new File(directory); } - + /** * Use the dput R instruction to store the content of a R object to a file. * The file created will be in the working directory * - * @param rObject name of the R object to save - * @param outputFileName name of the file to save + * @param rObject + * name of the R object to save + * @param outputFileName + * name of the file to save * @throws RException */ public void dput(String rObject, String outputFileName) throws RException { if (engine == null) { - log.fatal("The R Proxy is not initialized. An error probably " + - "occured during the initialization."); + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); return; } String rInstruction = "dput(%s,file=\"%s\")"; engine.voidEval(String.format(rInstruction, rObject, outputFileName)); } - - + /** - * Use the dget rInstruction to store the content of a file (created with the dput instruction) into a R object. - * The file used have to be in the working directory + * Use the dget rInstruction to store the content of a file (created with + * the dput instruction) into a R object. The file used have to be in the + * working directory * - * @param rObject name of the R object created - * @param inputFileName name of the file to load + * @param rObject + * name of the R object created + * @param inputFileName + * name of the file to load * @throws RException */ public void dget(String rObject, String inputFileName) throws RException { if (engine == null) { - log.fatal("The R Proxy is not initialized. An error probably " + - "occured during the initialization."); + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); return; } String rInstruction = "%s <- dget(\"%s\")"; engine.voidEval(String.format(rInstruction, rObject, inputFileName)); - + } - + /** * Use the dput R instruction to store the content of a R object to a file. * - * @param rObject R object to save - * @param outputFileName the file to save + * @param rObject + * R object to save + * @param outputFileName + * the file to save * @throws RException */ public void dput(String rObject, File outputFile) throws RException { if (engine == null) { - log.fatal("The R Proxy is not initialized. An error probably " + - "occured during the initialization."); + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); return; } File workingdir = getwd(); engine.setwd(outputFile.getParentFile()); String rInstruction = "dput(%s,file=\"%s\")"; - engine.voidEval(String.format(rInstruction, rObject, outputFile.getName())); + engine.voidEval(String.format(rInstruction, rObject, outputFile + .getName())); setwd(workingdir); } - - + /** - * Use the dget rInstruction to store the content of a file (created with the dput instruction) into a R object. + * Use the dget rInstruction to store the content of a file (created with + * the dput instruction) into a R object. * - * @param rObject name of the R object created - * @param inputFile file to load + * @param rObject + * name of the R object created + * @param inputFile + * file to load * @throws RException */ public void dget(String rObject, File inputFile) throws RException { if (engine == null) { - log.fatal("The R Proxy is not initialized. An error probably " + - "occured during the initialization."); + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); return; } File workingdir = getwd(); engine.setwd(inputFile.getParentFile()); String rInstruction = "%s <- dget(\"%s\")"; - engine.voidEval(String.format(rInstruction, rObject, inputFile.getName())); - setwd(workingdir); + engine.voidEval(String.format(rInstruction, rObject, inputFile + .getName())); + setwd(workingdir); } - + public void remove(String rObject) throws RException { if (engine == null) { - log.fatal("The R Proxy is not initialized. An error probably " + - "occured during the initialization."); + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); return; } engine.remove(rObject); } + public void mv(String inputObject, String outputObject) throws RException { + if (engine == null) { + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); + return; + } + engine.mv(inputObject, outputObject); + + } + + public void cp(String inputObject, String outputObject) throws RException { + if (engine == null) { + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); + return; + } + engine.cp(inputObject, outputObject); + + } + + public String[] ls() throws RException { + if (engine == null) { + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); + return null; + } + return engine.ls(); + } + + public void clearSession() throws RException { + if (engine == null) { + log.fatal("The R Proxy is not initialized. An error probably " + + "occured during the initialization."); + return; + } + engine.clearSession(); + + } + } //RProxy Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/jni/RJniEngine.java =================================================================== --- lutinj2r/trunk/src/main/java/org/codelutin/j2r/jni/RJniEngine.java 2009-04-28 18:42:55 UTC (rev 68) +++ lutinj2r/trunk/src/main/java/org/codelutin/j2r/jni/RJniEngine.java 2009-04-29 14:43:55 UTC (rev 69) @@ -78,7 +78,7 @@ public Object eval(String expr) throws RException { REXP result = null; try { - log.info(expr); + log.debug(expr); result = engine.eval(expr); } catch (Exception eee) { throw new RException("Unable to evaluate the R expression " @@ -102,7 +102,7 @@ result = rexp.asString(); break; case REXP.XT_INT: - result = (Integer)rexp.asInt(); + result = (Integer) rexp.asInt(); break; case REXP.XT_ARRAY_INT: result = rexp.asIntArray(); @@ -120,7 +120,6 @@ break; case REXP.XT_BOOL: result = rexp.asBool().isTRUE(); - log.info(result); break; case REXP.XT_DOUBLE: result = rexp.asDoubleArray(); @@ -151,6 +150,9 @@ case REXP.XT_VECTOR: result = rexp.asVector(); break; + case 34: + result = rexp.asStringArray(); + break; default: log.error("Unknown return type [" + type + "] " + "on : " + rexp.toString()); @@ -179,7 +181,6 @@ // voidEval is not really supproted by JRI, we just discard the result // conversion try { - log.info(expr); engine.eval(expr); } catch (Exception eee) { throw new RException("An error occured while voidEval on JNI", eee); @@ -304,4 +305,28 @@ voidEval("remove(" + rObject + ")"); } + public void mv(String inputObject, String outputObject) throws RException { + cp(inputObject, outputObject); + remove(inputObject); + + } + + public void cp(String inputObject, String outputObject) throws RException { + voidEval(outputObject + "<-" + inputObject); + + } + + public String[] ls() throws RException { + String[] Robjects = (String[]) eval("ls()"); + return Robjects; + } + + public void clearSession() throws RException { + String[] Robjects = ls(); + for (int i = 0; i < Robjects.length; i++) { + remove(Robjects[i]); + } + + } + } // RJniEngine Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/net/RNetEngine.java =================================================================== --- lutinj2r/trunk/src/main/java/org/codelutin/j2r/net/RNetEngine.java 2009-04-28 18:42:55 UTC (rev 68) +++ lutinj2r/trunk/src/main/java/org/codelutin/j2r/net/RNetEngine.java 2009-04-29 14:43:55 UTC (rev 69) @@ -30,6 +30,7 @@ package org.codelutin.j2r.net; import java.io.File; +import java.util.List; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -40,7 +41,6 @@ import org.rosuda.REngine.Rserve.RConnection; import org.rosuda.REngine.Rserve.RserveException; - /** * Cette classe represente le moteur reseau pour acceder a R. Par defaut, il * essaye de se connecter a l'adresse 127.0.0.1 sur le port 6311. Cependant, il @@ -53,252 +53,262 @@ */ public class RNetEngine implements REngine { - public static final int DEFAULT_PORT = 6311; - public static final String DEFAULT_HOST = "127.0.0.1"; + public static final int DEFAULT_PORT = 6311; + public static final String DEFAULT_HOST = "127.0.0.1"; - private Log log = LogFactory.getLog(RNetEngine.class); + private Log log = LogFactory.getLog(RNetEngine.class); - private RConnection conn; + private RConnection conn; - /* - * (non-Javadoc) - * - * @see org.codelutin.j2r.REngine#init() - */ - public boolean init() { - String typeProp = System.getProperty("R.type", "net"); - int urlPos = typeProp.indexOf("net://"); - String host = null; - String portAsString = null; - if (urlPos != -1) { - String url = typeProp.substring(urlPos + 6); - int commaPos = url.indexOf(":"); - if (commaPos != -1) { - host = url.substring(0, commaPos); - portAsString = url.substring(commaPos + 1); - } else { - host = url; - } - } - if (host == null || "".equals(host)) { - host = DEFAULT_HOST; - } - int port = DEFAULT_PORT; - if (portAsString != null) { - try { - port = Integer.parseInt(portAsString); - } catch (NumberFormatException nfe) { - if (log.isWarnEnabled()) { - log.warn("Bad port format " + portAsString - + ", using default" + " port : " + port); - } - } - } - return init(host, port); - } + /* + * (non-Javadoc) + * + * @see org.codelutin.j2r.REngine#init() + */ + public boolean init() { + String typeProp = System.getProperty("R.type", "net"); + int urlPos = typeProp.indexOf("net://"); + String host = null; + String portAsString = null; + if (urlPos != -1) { + String url = typeProp.substring(urlPos + 6); + int commaPos = url.indexOf(":"); + if (commaPos != -1) { + host = url.substring(0, commaPos); + portAsString = url.substring(commaPos + 1); + } else { + host = url; + } + } + if (host == null || "".equals(host)) { + host = DEFAULT_HOST; + } + int port = DEFAULT_PORT; + if (portAsString != null) { + try { + port = Integer.parseInt(portAsString); + } catch (NumberFormatException nfe) { + if (log.isWarnEnabled()) { + log.warn("Bad port format " + portAsString + + ", using default" + " port : " + port); + } + } + } + return init(host, port); + } - public boolean init(String host, int port) { - if (log.isInfoEnabled()) { - log.info("Trying to connect to the Rserve on '" + host + ":" + port - + "'"); - } - try { - conn = new RConnection(host, port); - } catch (RserveException e) { - log.error("Unable to establish a connection to the R server. " - + "Maybe you forgot to start it. " - + "Try using the command \"R CMD Rserve\"."); - e.printStackTrace(); - return false; - } - return conn.isConnected(); - } + public boolean init(String host, int port) { + if (log.isInfoEnabled()) { + log.info("Trying to connect to the Rserve on '" + host + ":" + port + + "'"); + } + try { + conn = new RConnection(host, port); + } catch (RserveException e) { + log.error("Unable to establish a connection to the R server. " + + "Maybe you forgot to start it. " + + "Try using the command \"R CMD Rserve\"."); + e.printStackTrace(); + return false; + } + return conn.isConnected(); + } - /* - * (non-Javadoc) - * - * @see org.codelutin.R.REngine#eval(java.lang.String) - */ - public Object eval(String expr) throws RException { - REXP result = null; - try { - log.info(expr); - result = conn.eval(expr); - } catch (RserveException e) { - throw new RException("An error occured during the eval method", e); - } - return convertResult(result); - } + /* + * (non-Javadoc) + * + * @see org.codelutin.R.REngine#eval(java.lang.String) + */ + public Object eval(String expr) throws RException { + REXP result = null; + try { + log.debug(expr); + result = conn.eval(expr); + } catch (RserveException e) { + throw new RException("An error occured during the eval method", e); + } + return convertResult(result); + } - private Object convertResult(REXP rexp) { - if (rexp == null) { - log.debug("Null returned"); - return null; - } - if (log.isDebugEnabled()) { - log.debug("Converting : " + rexp.toString()); - } + private Object convertResult(REXP rexp) { + if (rexp == null) { + log.debug("Null returned"); + return null; + } + if (log.isDebugEnabled()) { + log.debug("Converting : " + rexp.toString()); + } - Object result = null; + Object result = null; - try { + try { - if (rexp.isInteger()) { - result = rexp.asIntegers(); - int[] intarray = (int[]) result; - if (intarray.length == 1) { - result = intarray[0]; - } - } + if (rexp.isInteger()) { + result = rexp.asIntegers(); + int[] intarray = (int[]) result; + if (intarray.length == 1) { + result = intarray[0]; + } + } - else if (rexp.isFactor()) { - result = rexp.asFactor(); - } + else if (rexp.isFactor()) { + result = rexp.asFactor(); + } - else if (rexp.isNumeric()) { - result = rexp.asDoubles(); - double[] doublearray = (double[]) result; - if (doublearray.length == 1) { - result = doublearray[0]; - } - } - - else if (rexp.isString()) { - result = rexp.asStrings(); - String[] stringArray = (String[]) result; - if (stringArray.length == 1) { - result = stringArray[0]; - } - - } - - else if (rexp.isLogical()) { - result = rexp.asStrings(); - String[] strings = ((String [])result); - Boolean[] stringArray = new Boolean[strings.length]; - for (int i=0;i<((String [])result).length;i++){ - stringArray[i]=Boolean.parseBoolean(strings[i]); - } - if (stringArray.length == 1) { - result = (Boolean)stringArray[0]; - } - else {result = (Boolean[])stringArray;} - } - - else if (rexp.isNull()) { - return null; - } + else if (rexp.isNumeric()) { + result = rexp.asDoubles(); + double[] doublearray = (double[]) result; + if (doublearray.length == 1) { + result = doublearray[0]; + } + } - else { - log.error("Unknown return type on : " + rexp.toString()); - } - } catch (REXPMismatchException e) { - e.printStackTrace(); - } - return result; - } + else if (rexp.isString()) { + result = rexp.asStrings(); + String[] stringArray = (String[]) result; + if (stringArray.length == 1) { + result = stringArray[0]; + } - /* - * (non-Javadoc) - * - * @see org.codelutin.j2r.REngine#terminate() - */ - public void terminate() throws RException { - if (conn != null && conn.isConnected()) { - conn.close(); - } - } + } - /* - * (non-Javadoc) - * - * @see org.codelutin.j2r.REngine#voidEval(java.lang.String) - */ - public void voidEval(String expr) throws RException { - try { - log.info(expr); - conn.voidEval(expr); - } catch (RserveException rse) { - throw new RException("An error occured while voidEval on net", rse); - } - } - - /** + else if (rexp.isLogical()) { + result = rexp.asStrings(); + String[] strings = ((String[]) result); + Boolean[] stringArray = new Boolean[strings.length]; + for (int i = 0; i < ((String[]) result).length; i++) { + stringArray[i] = Boolean.parseBoolean(strings[i]); + } + if (stringArray.length == 1) { + result = (Boolean) stringArray[0]; + } else { + result = (Boolean[]) stringArray; + } + } + + else if (rexp.isNull()) { + return null; + } + + else { + log.error("Unknown return type on : " + rexp.toString()); + } + } catch (REXPMismatchException e) { + e.printStackTrace(); + } + return result; + } + + /* + * (non-Javadoc) + * + * @see org.codelutin.j2r.REngine#terminate() + */ + public void terminate() throws RException { + if (conn != null && conn.isConnected()) { + conn.close(); + } + } + + /* + * (non-Javadoc) + * + * @see org.codelutin.j2r.REngine#voidEval(java.lang.String) + */ + public void voidEval(String expr) throws RException { + try { + conn.voidEval(expr); + } catch (RserveException rse) { + throw new RException("An error occured while voidEval on net", rse); + } + } + + /** * Load .RData file located in directory * - * @param directory directory where the .RData file is located + * @param directory + * directory where the .RData file is located * @throws RException */ public void loadRData(File directory) throws RException { setwd(directory); voidEval("load(\".RData\")"); } - + /** * Save the session in a .RData file in directory * - * @param directory where the .RData file will be saved + * @param directory + * where the .RData file will be saved * @throws RException */ - public void saveRData(File directory) throws RException{ + public void saveRData(File directory) throws RException { setwd(directory); voidEval("save.image()"); } - + /** * Set the R working directory - * @param directory to set + * + * @param directory + * to set * @throws RException */ public void setwd(File directory) throws RException { - voidEval("setwd(\""+directory.getAbsolutePath() + "\")"); + voidEval("setwd(\"" + directory.getAbsolutePath() + "\")"); } - + /** * Get the actual R session working directory * * @return a File that is the actual R session working directory * @throws RException */ - + public File getwd() throws RException { - String directory = (String)eval("getwd()"); + String directory = (String) eval("getwd()"); return new File(directory); } - + /** * Use the dput R instruction to store the content of a R object to a file. * The file created will be in the working directory * - * @param rObject name of the R object to save - * @param outputFileName name of the file to save + * @param rObject + * name of the R object to save + * @param outputFileName + * name of the file to save * @throws RException */ public void dput(String rObject, String outputFileName) throws RException { String rInstruction = "dput(%s,file=\"%s\")"; voidEval(String.format(rInstruction, rObject, outputFileName)); } - - + /** - * Use the dget rInstruction to store the content of a file (created with the dput instruction) into a R object. - * The file used have to be in the working directory + * Use the dget rInstruction to store the content of a file (created with + * the dput instruction) into a R object. The file used have to be in the + * working directory * - * @param rObject name of the R object created - * @param inputFileName name of the file to load + * @param rObject + * name of the R object created + * @param inputFileName + * name of the file to load * @throws RException */ public void dget(String rObject, String inputFileName) throws RException { String rInstruction = "%s <- dget(\"%s\")"; voidEval(String.format(rInstruction, rObject, inputFileName)); - + } - + /** * Use the dput R instruction to store the content of a R object to a file. * - * @param rObject R object to save - * @param outputFileName the file to save + * @param rObject + * R object to save + * @param outputFileName + * the file to save * @throws RException */ public void dput(String rObject, File outputFile) throws RException { @@ -308,13 +318,15 @@ voidEval(String.format(rInstruction, rObject, outputFile.getName())); setwd(workingdir); } - - + /** - * Use the dget rInstruction to store the content of a file (created with the dput instruction) into a R object. + * Use the dget rInstruction to store the content of a file (created with + * the dput instruction) into a R object. * - * @param rObject name of the R object created - * @param inputFile file to load + * @param rObject + * name of the R object created + * @param inputFile + * file to load * @throws RException */ public void dget(String rObject, File inputFile) throws RException { @@ -322,11 +334,35 @@ setwd(inputFile.getParentFile()); String rInstruction = "%s <- dget(\"%s\")"; voidEval(String.format(rInstruction, rObject, inputFile.getName())); - setwd(workingdir); + setwd(workingdir); } - - public void remove (String rObject) throws RException { - voidEval("remove("+rObject+")"); + + public void remove(String rObject) throws RException { + voidEval("remove(" + rObject + ")"); } + public void mv(String inputObject, String outputObject) throws RException { + cp(inputObject, outputObject); + remove(inputObject); + + } + + public void cp(String inputObject, String outputObject) throws RException { + voidEval(outputObject + "<-" + inputObject); + + } + + public String[] ls() throws RException { + String[] Robjects = (String[]) eval("ls()"); + return Robjects; + } + + public void clearSession() throws RException { + String[] Robjects = ls(); + for (int i = 0; i < Robjects.length; i++) { + remove(Robjects[i]); + } + + } + } // RNetEngine Modified: lutinj2r/trunk/src/test/java/org/codelutin/j2r/JNITest.java =================================================================== --- lutinj2r/trunk/src/test/java/org/codelutin/j2r/JNITest.java 2009-04-28 18:42:55 UTC (rev 68) +++ lutinj2r/trunk/src/test/java/org/codelutin/j2r/JNITest.java 2009-04-29 14:43:55 UTC (rev 69) @@ -255,5 +255,31 @@ engine.remove("a"); Assert.assertNull(engine.eval("a")); } + + @Test + public void testMvCp() throws Exception { + //Test only mv as mv uses cp. + engine.voidEval("a<-5.0"); + engine.remove("b"); + engine.mv("a", "b"); + Assert.assertEquals(new Double(5.0), engine.eval("b")); + Assert.assertFalse((Boolean) engine.eval("exists(\"a\")")); + } + + @Test + public void testLsClearSession() throws Exception { + //Test only ClearSession as it uses ls + engine.voidEval("a<-5.0"); + engine.voidEval("b<-5.0"); + engine.voidEval("d<-5.0"); + engine.voidEval("e<-5.0"); + engine.voidEval("f<-5.0"); + engine.clearSession(); + Assert.assertFalse((Boolean) engine.eval("exists(\"a\")")); + Assert.assertFalse((Boolean) engine.eval("exists(\"b\")")); + Assert.assertFalse((Boolean) engine.eval("exists(\"d\")")); + Assert.assertFalse((Boolean) engine.eval("exists(\"e\")")); + Assert.assertFalse((Boolean) engine.eval("exists(\"f\")")); + } } // JNITest Modified: lutinj2r/trunk/src/test/java/org/codelutin/j2r/NetTest.java =================================================================== --- lutinj2r/trunk/src/test/java/org/codelutin/j2r/NetTest.java 2009-04-28 18:42:55 UTC (rev 68) +++ lutinj2r/trunk/src/test/java/org/codelutin/j2r/NetTest.java 2009-04-29 14:43:55 UTC (rev 69) @@ -49,129 +49,130 @@ public class NetTest { - private static Log log = LogFactory.getLog(NetTest.class); + private static Log log = LogFactory.getLog(NetTest.class); - private REngine engine; - private String savedRType; + private REngine engine; + private String savedRType; - @Before - public void setUp() throws Exception { - LutinTimer init = new LutinTimer(); - init.startTiming(); - savedRType = System.getProperty("R.type", ""); - System.setProperty("R.type", "net://:6311"); - if (engine == null) { - engine = new RProxy(); - } - if (log.isInfoEnabled()) { - log.info("net init: " + init.endTiming() + "ms"); - } - } + @Before + public void setUp() throws Exception { + LutinTimer init = new LutinTimer(); + init.startTiming(); + savedRType = System.getProperty("R.type", ""); + System.setProperty("R.type", "net://:6311"); + if (engine == null) { + engine = new RProxy(); + } + if (log.isInfoEnabled()) { + log.info("net init: " + init.endTiming() + "ms"); + } + } - @After - public void tearDown() throws Exception { - engine.terminate(); - System.setProperty("R.type", savedRType); - } + @After + public void tearDown() throws Exception { + engine.terminate(); + System.setProperty("R.type", savedRType); + } - @Test - public void testDouble() throws Exception { - Assert.assertEquals(5.0, engine.eval("5.0")); - engine.voidEval("t<-sin(0)"); - double d = (Double) engine.eval("t"); - Assert.assertEquals(0.0, d, 0); - } + @Test + public void testDouble() throws Exception { + Assert.assertEquals(5.0, engine.eval("5.0")); + engine.voidEval("t<-sin(0)"); + double d = (Double) engine.eval("t"); + Assert.assertEquals(0.0, d, 0); + } - @Test - public void testIntArray() throws Exception { - Object result = engine.eval("5:10"); - Assert.assertNotNull(result); - Assert.assertEquals(int[].class, result.getClass()); - int[] intArray = (int[]) result; - Assert.assertEquals(6, intArray.length); - for (int i = 5; i < 11; i++) { - Assert.assertEquals(i, intArray[i - 5]); - } - } + @Test + public void testIntArray() throws Exception { + Object result = engine.eval("5:10"); + Assert.assertNotNull(result); + Assert.assertEquals(int[].class, result.getClass()); + int[] intArray = (int[]) result; + Assert.assertEquals(6, intArray.length); + for (int i = 5; i < 11; i++) { + Assert.assertEquals(i, intArray[i - 5]); + } + } - @Test - public void testSimpleOp() throws Exception { - LutinTimer t = new LutinTimer(); - for (int loop = 0; loop < S_NB_LOOPS; loop++) { - engine.voidEval("t<-0"); - t.startTiming(); - engine.voidEval(S_OP); - t.endTiming(); - double d = (Double) engine.eval("t"); - Assert.assertEquals((double) S_T_MAX, d, 0); - } - double[] results = t.computeResults(); - System.err.println("[SO]min: " + results[0]); - System.err.println("[SO]avg: " + results[1]); - System.err.println("[SO]max: " + results[2]); - System.err.println("[SO]etype: " + results[3]); - } + @Test + public void testSimpleOp() throws Exception { + LutinTimer t = new LutinTimer(); + for (int loop = 0; loop < S_NB_LOOPS; loop++) { + engine.voidEval("t<-0"); + t.startTiming(); + engine.voidEval(S_OP); + t.endTiming(); + double d = (Double) engine.eval("t"); + Assert.assertEquals((double) S_T_MAX, d, 0); + } + double[] results = t.computeResults(); + System.err.println("[SO]min: " + results[0]); + System.err.println("[SO]avg: " + results[1]); + System.err.println("[SO]max: " + results[2]); + System.err.println("[SO]etype: " + results[3]); + } - @Test - public void testVector() throws Exception { - LutinTimer t = new LutinTimer(); - for (int loop = 0; loop < V_NB_LOOPS; loop++) { - t.startTiming(); - engine.voidEval(V_OP_A); - engine.voidEval(V_OP_B); - double[] r = (double[]) engine.eval(V_OP_AB); - t.endTiming(); - Assert.assertEquals(V_MAX, r.length); - } - double[] results = t.computeResults(); - System.err.println("[V]min: " + results[0]); - System.err.println("[V]avg: " + results[1]); - System.err.println("[V]max: " + results[2]); - System.err.println("[V]etype: " + results[3]); - } + @Test + public void testVector() throws Exception { + LutinTimer t = new LutinTimer(); + for (int loop = 0; loop < V_NB_LOOPS; loop++) { + t.startTiming(); + engine.voidEval(V_OP_A); + engine.voidEval(V_OP_B); + double[] r = (double[]) engine.eval(V_OP_AB); + t.endTiming(); + Assert.assertEquals(V_MAX, r.length); + } + double[] results = t.computeResults(); + System.err.println("[V]min: " + results[0]); + System.err.println("[V]avg: " + results[1]); + System.err.println("[V]max: " + results[2]); + System.err.println("[V]etype: " + results[3]); + } - @Test - public void testString() throws Exception { - engine.voidEval("a<-\"testing string\""); - String testString = (String) engine.eval("a"); - Assert.assertEquals("testing string", testString); - } + @Test + public void testString() throws Exception { + engine.voidEval("a<-\"testing string\""); + String testString = (String) engine.eval("a"); + Assert.assertEquals("testing string", testString); + } - @Test - public void testInt() throws Exception { - engine.voidEval("a<-as.integer(5)"); - Integer testInteger = (Integer) engine.eval("a"); - Integer toCompare = 5; - Assert.assertEquals(toCompare, testInteger); - } + @Test + public void testInt() throws Exception { + engine.voidEval("a<-as.integer(5)"); + Integer testInteger = (Integer) engine.eval("a"); + Integer toCompare = 5; + Assert.assertEquals(toCompare, testInteger); + } - @Test - public void testBool() throws Exception { - engine.voidEval("a<-TRUE"); - engine.voidEval("b<-FALSE"); - Boolean testA = (Boolean) engine.eval("a"); - Boolean testB = (Boolean) engine.eval("b"); - Assert.assertTrue(testA); - Assert.assertFalse(testB); - } + @Test + public void testBool() throws Exception { + engine.voidEval("a<-TRUE"); + engine.voidEval("b<-FALSE"); + Boolean testA = (Boolean) engine.eval("a"); + Boolean testB = (Boolean) engine.eval("b"); + Assert.assertTrue(testA); + Assert.assertFalse(testB); + } - @Test - public void testArrayBool() throws Exception { - engine.voidEval("a<-c(TRUE,FALSE,TRUE)"); - Boolean[] testBoolArray = (Boolean[]) engine.eval("a"); - Assert.assertTrue(testBoolArray[0]); - Assert.assertFalse(testBoolArray[1]); - Assert.assertTrue(testBoolArray[2]); - } - - @Test + @Test + public void testArrayBool() throws Exception { + engine.voidEval("a<-c(TRUE,FALSE,TRUE)"); + Boolean[] testBoolArray = (Boolean[]) engine.eval("a"); + Assert.assertTrue(testBoolArray[0]); + Assert.assertFalse(testBoolArray[1]); + Assert.assertTrue(testBoolArray[2]); + } + + @Test public void testWorkingDirectory() throws Exception { File workingDirectory = new File("/tmp"); engine.setwd(workingDirectory); File testWorkingDirectory = engine.getwd(); - Assert.assertEquals(workingDirectory.getAbsolutePath(), testWorkingDirectory.getAbsolutePath()); + Assert.assertEquals(workingDirectory.getAbsolutePath(), + testWorkingDirectory.getAbsolutePath()); } - + @Test public void testRData() throws Exception { File workingdir = new File("/tmp"); @@ -179,46 +180,73 @@ engine.saveRData(workingdir); engine.remove("a"); engine.loadRData(workingdir); - Double testDouble = (Double)engine.eval("a"); - Double compareTo = new Double (5.0); + Double testDouble = (Double) engine.eval("a"); + Double compareTo = new Double(5.0); Assert.assertEquals(compareTo, testDouble); } - + @Test public void testDputDget() throws Exception { File workingdir = new File("/tmp"); File testingFile = new File("/tmp/testfile"); - + // test method using the workingdir engine.voidEval("a<-5.0"); engine.setwd(workingdir); engine.dput("a", "testDputDgetfile"); engine.remove("a"); engine.dget("a", "testDputDgetfile"); - Double testDouble = (Double)engine.eval("a"); - Double compareTo = new Double (5.0); + Double testDouble = (Double) engine.eval("a"); + Double compareTo = new Double(5.0); Assert.assertEquals(compareTo, testDouble); - - workingdir= new File("/"); + + workingdir = new File("/"); //test method using absolute path engine.setwd(workingdir); engine.voidEval("a<-6.0"); - engine.dput("a",testingFile); + engine.dput("a", testingFile); engine.remove("a"); engine.dget("a", testingFile); - Double testDouble2 = (Double)engine.eval("a"); - Double compareTo2 = new Double (6.0); + Double testDouble2 = (Double) engine.eval("a"); + Double compareTo2 = new Double(6.0); Assert.assertEquals(compareTo2, testDouble2); File testWorkingDirectory = engine.getwd(); - Assert.assertEquals(workingdir.getAbsolutePath(), testWorkingDirectory.getAbsolutePath()); + Assert.assertEquals(workingdir.getAbsolutePath(), testWorkingDirectory + .getAbsolutePath()); } - + @Test public void testRemove() throws Exception { engine.voidEval("a<-6.0"); - Assert.assertEquals(new Double(6.0),engine.eval("a")); + Assert.assertEquals(new Double(6.0), engine.eval("a")); engine.remove("a"); - Assert.assertFalse((Boolean)engine.eval("exists(\"a\")")); + Assert.assertFalse((Boolean) engine.eval("exists(\"a\")")); } + + @Test + public void testMvCp() throws Exception { + //Test only mv as mv uses cp. + engine.voidEval("a<-5.0"); + engine.remove("b"); + engine.mv("a", "b"); + Assert.assertEquals(new Double(5.0), engine.eval("b")); + Assert.assertFalse((Boolean) engine.eval("exists(\"a\")")); + } + + @Test + public void testLsClearSession() throws Exception { + //Test only ClearSession as it uses ls + engine.voidEval("a<-5.0"); + engine.voidEval("b<-5.0"); + engine.voidEval("d<-5.0"); + engine.voidEval("e<-5.0"); + engine.voidEval("f<-5.0"); + engine.clearSession(); + Assert.assertFalse((Boolean) engine.eval("exists(\"a\")")); + Assert.assertFalse((Boolean) engine.eval("exists(\"b\")")); + Assert.assertFalse((Boolean) engine.eval("exists(\"d\")")); + Assert.assertFalse((Boolean) engine.eval("exists(\"e\")")); + Assert.assertFalse((Boolean) engine.eval("exists(\"f\")")); + } } // NetTest

1 0

[LutinJ2R-commits] r68 - lutinj2r/trunk/src/test/java/org/codelutin/j2r
by jcouteau＠users.labs.libre-entreprise.org 28 Apr '09

28 Apr '09

Author: jcouteau Date: 2009-04-28 18:42:55 +0000 (Tue, 28 Apr 2009) New Revision: 68 Modified: lutinj2r/trunk/src/test/java/org/codelutin/j2r/NetTest.java Log: Fixed integer test on Net engine Modified: lutinj2r/trunk/src/test/java/org/codelutin/j2r/NetTest.java =================================================================== --- lutinj2r/trunk/src/test/java/org/codelutin/j2r/NetTest.java 2009-04-28 16:25:41 UTC (rev 67) +++ lutinj2r/trunk/src/test/java/org/codelutin/j2r/NetTest.java 2009-04-28 18:42:55 UTC (rev 68) @@ -137,13 +137,13 @@ Assert.assertEquals("testing string", testString); } - /*@Test + @Test public void testInt() throws Exception { - engine.voidEval("a<-5"); + engine.voidEval("a<-as.integer(5)"); Integer testInteger = (Integer) engine.eval("a"); Integer toCompare = 5; Assert.assertEquals(toCompare, testInteger); - }*/ + } @Test public void testBool() throws Exception {

1 0

[LutinJ2R-commits] r67 - in lutinj2r/trunk/src: main/java/org/codelutin/j2r/jni test/java/org/codelutin/j2r
by jcouteau＠users.labs.libre-entreprise.org 28 Apr '09

28 Apr '09

Author: jcouteau Date: 2009-04-28 16:25:41 +0000 (Tue, 28 Apr 2009) New Revision: 67 Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/jni/RJniEngine.java lutinj2r/trunk/src/test/java/org/codelutin/j2r/JNITest.java Log: Adding Boolean management to JRIEngine Fixed Integer tests Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/jni/RJniEngine.java =================================================================== --- lutinj2r/trunk/src/main/java/org/codelutin/j2r/jni/RJniEngine.java 2009-04-28 15:42:01 UTC (rev 66) +++ lutinj2r/trunk/src/main/java/org/codelutin/j2r/jni/RJniEngine.java 2009-04-28 16:25:41 UTC (rev 67) @@ -26,7 +26,6 @@ import org.rosuda.JRI.REXP; import org.rosuda.JRI.Rengine; - /** * RJniEngine.java * @@ -39,212 +38,240 @@ */ public class RJniEngine implements REngine { - private Log log = LogFactory.getLog(RJniEngine.class); + private Log log = LogFactory.getLog(RJniEngine.class); - /** - * Le Rengine est fait pour tourner en static - */ - private static Rengine engine; + /** + * Le Rengine est fait pour tourner en static + */ + private static Rengine engine; - /* - * (non-Javadoc) - * - * @see org.codelutin.j2r.REngine#init() - */ - public boolean init() { - if (engine == null) { - try { - String[] args = { "--no-save" }; - engine = new Rengine(args, false, null); - if (!engine.waitForR()) { - if (log.isErrorEnabled()) { - log.error("Cannot load the R engine"); - } - return false; - } - } catch (Throwable twable) { - log.error("An error occured during R/JNI initialization.", - twable); - return false; - } - } - return true; - } + /* + * (non-Javadoc) + * + * @see org.codelutin.j2r.REngine#init() + */ + public boolean init() { + if (engine == null) { + try { + String[] args = { "--no-save" }; + engine = new Rengine(args, false, null); + if (!engine.waitForR()) { + if (log.isErrorEnabled()) { + log.error("Cannot load the R engine"); + } + return false; + } + } catch (Throwable twable) { + log.error("An error occured during R/JNI initialization.", + twable); + return false; + } + } + return true; + } - /* - * (non-Javadoc) - * - * @see org.codelutin.R.REngine#eval(java.lang.String) - */ - public Object eval(String expr) throws RException { - REXP result = null; - try { - log.info(expr); - result = engine.eval(expr); - } catch (Exception eee) { - throw new RException("Unable to evaluate the R expression " - + "over JNI", eee); - } - return convertResult(result); - } + /* + * (non-Javadoc) + * + * @see org.codelutin.R.REngine#eval(java.lang.String) + */ + public Object eval(String expr) throws RException { + REXP result = null; + try { + log.info(expr); + result = engine.eval(expr); + } catch (Exception eee) { + throw new RException("Unable to evaluate the R expression " + + "over JNI", eee); + } + return convertResult(result); + } - private Object convertResult(REXP rexp) { - if (rexp == null) { - log.debug("Null returned"); - return null; - } - if (log.isDebugEnabled()) { - log.debug("Converting : " + rexp.toString()); - } - int type = rexp.getType(); - Object result = null; - switch (type) { - case REXP.XT_STR: - result = rexp.asString(); - break; - /*case REXP.XT_INT: + private Object convertResult(REXP rexp) { + if (rexp == null) { + log.debug("Null returned"); + return null; + } + if (log.isDebugEnabled()) { + log.debug("Converting : " + rexp.toString()); + } + int type = rexp.getType(); + Object result = null; + switch (type) { + case REXP.XT_STR: + result = rexp.asString(); + break; + case REXP.XT_INT: result = (Integer)rexp.asInt(); - break;*/ - case REXP.XT_ARRAY_INT: + break; + case REXP.XT_ARRAY_INT: result = rexp.asIntArray(); int[] intarray = (int[]) result; if (intarray.length == 1) { - result = (Integer)intarray[0]; + result = (Integer) intarray[0]; } break; - case REXP.XT_ARRAY_DOUBLE: - result = rexp.asDoubleArray(); - double[] doublearray = (double[]) result; - if (doublearray.length == 1) { - result = doublearray[0]; - } - break; - case REXP.XT_BOOL: - result = rexp.asBool().isTRUE(); - break; - case REXP.XT_DOUBLE: - result = rexp.asDoubleArray(); - double[] doublearray2 = (double[]) result; - result = doublearray2[0]; - /*case REXP.XT_NULL: - result = null;*/ - /*case REXP.XT_ARRAY_BOOL: - result = rexp.asIntArray(); - boolean[] booleanarray = (boolean[]) result; - result = booleanarray;*/ - case REXP.XT_VECTOR: - result = rexp.asVector(); - default: - log.error("Unknown return type [" + type + "] " + "on : " - + rexp.toString()); - } - return result; - } + case REXP.XT_ARRAY_DOUBLE: + result = rexp.asDoubleArray(); + double[] doublearray = (double[]) result; + if (doublearray.length == 1) { + result = doublearray[0]; + } + break; + case REXP.XT_BOOL: + result = rexp.asBool().isTRUE(); + log.info(result); + break; + case REXP.XT_DOUBLE: + result = rexp.asDoubleArray(); + double[] doublearray2 = (double[]) result; + result = doublearray2[0]; + break; + case REXP.XT_NULL: + result = null; + break; + case 37: + result = rexp.asIntArray(); + int[] integers = ((int[]) result); + Boolean[] booleanArray = new Boolean[integers.length]; + for (int i = 0; i < integers.length; i++) { + if (integers[i] == 1) { + booleanArray[i] = Boolean.TRUE; + } else { + booleanArray[i] = Boolean.FALSE; + } + } + if (booleanArray.length == 1) { + result = booleanArray[0]; + } else { + result = booleanArray; + } - /* - * (non-Javadoc) - * - * @see org.codelutin.j2r.REngine#terminate() - */ - public void terminate() { - if (engine.isAlive()) { - engine.end(); - } - } + break; + case REXP.XT_VECTOR: + result = rexp.asVector(); + break; + default: + log.error("Unknown return type [" + type + "] " + "on : " + + rexp.toString()); + break; + } + return result; + } - /* - * (non-Javadoc) - * - * @see org.codelutin.j2r.REngine#voidEval(java.lang.String) - */ - public void voidEval(String expr) throws RException { - // voidEval is not really supproted by JRI, we just discard the result - // conversion - try { - log.info(expr); - engine.eval(expr); - } catch (Exception eee) { - throw new RException("An error occured while voidEval on JNI", eee); - } - } - - - /** - * Load .RData file located in directory - * - * @param directory directory where the .RData file is located - * @throws RException - */ - public void loadRData(File directory) throws RException { - setwd(directory); + /* + * (non-Javadoc) + * + * @see org.codelutin.j2r.REngine#terminate() + */ + public void terminate() { + if (engine.isAlive()) { + engine.end(); + } + } + + /* + * (non-Javadoc) + * + * @see org.codelutin.j2r.REngine#voidEval(java.lang.String) + */ + public void voidEval(String expr) throws RException { + // voidEval is not really supproted by JRI, we just discard the result + // conversion + try { + log.info(expr); + engine.eval(expr); + } catch (Exception eee) { + throw new RException("An error occured while voidEval on JNI", eee); + } + } + + /** + * Load .RData file located in directory + * + * @param directory + * directory where the .RData file is located + * @throws RException + */ + public void loadRData(File directory) throws RException { + setwd(directory); voidEval("load(\".RData\")"); - } - - /** - * Save the session in a .RData file in directory - * - * @param directory where the .RData file will be saved - * @throws RException - */ - public void saveRData(File directory) throws RException{ - setwd(directory); + } + + /** + * Save the session in a .RData file in directory + * + * @param directory + * where the .RData file will be saved + * @throws RException + */ + public void saveRData(File directory) throws RException { + setwd(directory); voidEval("save.image()"); - } - - /** - * Set the R working directory - * @param directory to set - * @throws RException - */ - public void setwd(File directory) throws RException { - voidEval("setwd(\""+directory.getAbsolutePath() + "\")"); - } - - /** - * Get the actual R session working directory - * - * @return a File that is the actual R session working directory - * @throws RException - */ - + } + + /** + * Set the R working directory + * + * @param directory + * to set + * @throws RException + */ + public void setwd(File directory) throws RException { + voidEval("setwd(\"" + directory.getAbsolutePath() + "\")"); + } + + /** + * Get the actual R session working directory + * + * @return a File that is the actual R session working directory + * @throws RException + */ + public File getwd() throws RException { - String directory = (String)eval("getwd()"); + String directory = (String) eval("getwd()"); return new File(directory); } - + /** * Use the dput R instruction to store the content of a R object to a file. * The file created will be in the working directory * - * @param rObject name of the R object to save - * @param outputFileName name of the file to save + * @param rObject + * name of the R object to save + * @param outputFileName + * name of the file to save * @throws RException */ public void dput(String rObject, String outputFileName) throws RException { String rInstruction = "dput(%s,file=\"%s\")"; voidEval(String.format(rInstruction, rObject, outputFileName)); } - - + /** - * Use the dget rInstruction to store the content of a file (created with the dput instruction) into a R object. - * The file used have to be in the working directory + * Use the dget rInstruction to store the content of a file (created with + * the dput instruction) into a R object. The file used have to be in the + * working directory * - * @param rObject name of the R object created - * @param inputFileName name of the file to load + * @param rObject + * name of the R object created + * @param inputFileName + * name of the file to load * @throws RException */ public void dget(String rObject, String inputFileName) throws RException { String rInstruction = "%s <- dget(\"%s\")"; voidEval(String.format(rInstruction, rObject, inputFileName)); - + } - + /** * Use the dput R instruction to store the content of a R object to a file. * - * @param rObject R object to save - * @param outputFileName the file to save + * @param rObject + * R object to save + * @param outputFileName + * the file to save * @throws RException */ public void dput(String rObject, File outputFile) throws RException { @@ -254,13 +281,15 @@ voidEval(String.format(rInstruction, rObject, outputFile.getName())); setwd(workingdir); } - - + /** - * Use the dget rInstruction to store the content of a file (created with the dput instruction) into a R object. + * Use the dget rInstruction to store the content of a file (created with + * the dput instruction) into a R object. * - * @param rObject name of the R object created - * @param inputFile file to load + * @param rObject + * name of the R object created + * @param inputFile + * file to load * @throws RException */ public void dget(String rObject, File inputFile) throws RException { @@ -268,11 +297,11 @@ setwd(inputFile.getParentFile()); String rInstruction = "%s <- dget(\"%s\")"; voidEval(String.format(rInstruction, rObject, inputFile.getName())); - setwd(workingdir); + setwd(workingdir); } - - public void remove (String rObject) throws RException { - voidEval("remove("+rObject+")"); + + public void remove(String rObject) throws RException { + voidEval("remove(" + rObject + ")"); } } // RJniEngine Modified: lutinj2r/trunk/src/test/java/org/codelutin/j2r/JNITest.java =================================================================== --- lutinj2r/trunk/src/test/java/org/codelutin/j2r/JNITest.java 2009-04-28 15:42:01 UTC (rev 66) +++ lutinj2r/trunk/src/test/java/org/codelutin/j2r/JNITest.java 2009-04-28 16:25:41 UTC (rev 67) @@ -84,17 +84,6 @@ } @Test - public void testIntArray() throws Exception { - Object result = engine.eval("5:10"); - Assert.assertEquals(int[].class, result.getClass()); - int[] intArray = (int[]) result; - Assert.assertEquals(6, intArray.length); - for (int i = 5; i < 11; i++) { - Assert.assertEquals(i, intArray[i - 5]); - } - } - - @Test public void testDoubleArray() throws Exception { Object result = engine.eval("5.5:10.5"); Assert.assertEquals(double[].class, result.getClass()); @@ -150,15 +139,27 @@ Assert.assertEquals("testing string", testString); } - /*@Test + @Test public void testInt() throws Exception { - engine.voidEval("a<-5"); + engine.voidEval("a<-as.integer(5)"); Integer testInteger = (Integer) engine.eval("a"); Integer toCompare = 5; Assert.assertEquals(toCompare, testInteger); - }*/ + } + + @Test + public void testIntArray() throws Exception { + engine.voidEval("a<-as.integer(5)"); + engine.voidEval("b<-as.integer(6)"); + engine.voidEval("z<-c(a,b)"); + int[] testIntArray = (int[]) engine.eval("z"); + int toCompare1 = 5; + Assert.assertEquals(toCompare1, testIntArray[0]); + int toCompare2 = 6; + Assert.assertEquals(toCompare2, testIntArray[1]); + } - /* @Test + @Test public void testBool() throws Exception { engine.voidEval("a<-TRUE"); engine.voidEval("b<-FALSE"); @@ -166,16 +167,16 @@ Boolean testB = (Boolean) engine.eval("b"); Assert.assertTrue(testA); Assert.assertFalse(testB); - }*/ + } - /* @Test + @Test public void testArrayBool() throws Exception { engine.voidEval("a<-c(TRUE,FALSE,TRUE)"); Boolean[] testBoolArray = (Boolean[]) engine.eval("a"); Assert.assertTrue(testBoolArray[0]); Assert.assertFalse(testBoolArray[1]); Assert.assertTrue(testBoolArray[2]); - }*/ + } /*@Test public void testDataFrame() throws Exception {

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