May 2009 - Nuiton-j2r-commits - mailman.cloud.codelutin.com

[LutinJ2R-commits] r81 - /
by tchemit＠users.labs.libre-entreprise.org May 16, 2009

May 16, 2009

Author: tchemit Date: 2009-05-16 15:43:07 +0000 (Sat, 16 May 2009) New Revision: 81 Added: nuiton-j2r/ Log: dettach project for nuiton Copied: nuiton-j2r (from rev 80, lutinj2r)

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[LutinJ2R-commits] r80 - in lutinj2r/trunk/src/main/java/org/codelutin/j2r: jni net
by jcouteau＠users.labs.libre-entreprise.org May 12, 2009

May 12, 2009

Author: jcouteau Date: 2009-05-12 08:11:31 +0000 (Tue, 12 May 2009) New Revision: 80 Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/jni/RJniEngine.java lutinj2r/trunk/src/main/java/org/codelutin/j2r/net/RNetEngine.java Log: Should fix setwd() bug under windows Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/jni/RJniEngine.java =================================================================== --- lutinj2r/trunk/src/main/java/org/codelutin/j2r/jni/RJniEngine.java 2009-05-04 19:07:48 UTC (rev 79) +++ lutinj2r/trunk/src/main/java/org/codelutin/j2r/jni/RJniEngine.java 2009-05-12 08:11:31 UTC (rev 80) @@ -78,7 +78,7 @@ public Object eval(String expr) throws RException { REXP result = null; try { - log.debug(expr); + log.info(expr); result = engine.eval(expr); } catch (Exception eee) { throw new RException("Unable to evaluate the R expression " @@ -181,6 +181,7 @@ // 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); @@ -219,7 +220,7 @@ * @throws RException */ public void setwd(File directory) throws RException { - voidEval("setwd(\"" + directory.getAbsolutePath() + "\")"); + voidEval("setwd(\"" + directory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); } /** Modified: lutinj2r/trunk/src/main/java/org/codelutin/j2r/net/RNetEngine.java =================================================================== --- lutinj2r/trunk/src/main/java/org/codelutin/j2r/net/RNetEngine.java 2009-05-04 19:07:48 UTC (rev 79) +++ lutinj2r/trunk/src/main/java/org/codelutin/j2r/net/RNetEngine.java 2009-05-12 08:11:31 UTC (rev 80) @@ -255,7 +255,7 @@ * @throws RException */ public void setwd(File directory) throws RException { - voidEval("setwd(\"" + directory.getAbsolutePath() + "\")"); + voidEval("setwd(\"" + directory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); } /**

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[LutinJ2R-commits] r79 - lutinj2r/trunk/src/main/resources
by chatellier＠users.labs.libre-entreprise.org May 4, 2009

May 4, 2009

Author: chatellier Date: 2009-05-04 19:07:48 +0000 (Mon, 04 May 2009) New Revision: 79 Added: lutinj2r/trunk/src/main/resources/rJava.txt Modified: lutinj2r/trunk/src/main/resources/jri.dll Log: Update jri.dll Modified: lutinj2r/trunk/src/main/resources/jri.dll =================================================================== (Binary files differ) Added: lutinj2r/trunk/src/main/resources/rJava.txt =================================================================== --- lutinj2r/trunk/src/main/resources/rJava.txt (rev 0) +++ lutinj2r/trunk/src/main/resources/rJava.txt 2009-05-04 19:07:48 UTC (rev 79) @@ -0,0 +1,12 @@ +Windows +------- +http://cran.r-project.org/bin/windows/contrib/2.10/rJava_0.6-2.zip + +Linux +----- +http://www.rforge.net/rJava/files/ + + ./configure + make + +

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[LutinJ2R-commits] r78 - lutinj2r/trunk
by chatellier＠users.labs.libre-entreprise.org May 4, 2009

May 4, 2009

Author: chatellier Date: 2009-05-04 17:41:30 +0000 (Mon, 04 May 2009) New Revision: 78 Modified: lutinj2r/trunk/pom.xml Log: Fix scm values. Update lutin project. Modified: lutinj2r/trunk/pom.xml =================================================================== --- lutinj2r/trunk/pom.xml 2009-05-04 15:58:12 UTC (rev 77) +++ lutinj2r/trunk/pom.xml 2009-05-04 17:41:30 UTC (rev 78) @@ -9,7 +9,7 @@ <parent> <groupId>org.codelutin</groupId> <artifactId>lutinproject</artifactId> - <version>3.4</version> + <version>3.5</version> </parent> <artifactId>lutinj2r</artifactId> @@ -120,9 +120,9 @@ </build> <scm> - <connection>scm:svn:svn://anonymous@labs.libre-entreprise.org/svnroot/lutinj2r/lutinj2r/trunk</connection> - <developerConnection>scm:svn:svn+ssh://chatellier@labs.libre-entreprise.org/svnroot/lutinj2r/lutinj2r/trunk</developerConnection> - <url>http://labs.libre-entreprise.org/plugins/scmsvn/viewcvs.php/lutinj2r/trunk/…</url> + <connection>${maven.scm.connection}</connection> + <developerConnection>${maven.scm.developerConnection}</developerConnection> + <url>${maven.scm.url}</url> </scm>

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[LutinJ2R-commits] r77 - lutinj2r/trunk
by chatellier＠users.labs.libre-entreprise.org May 4, 2009

May 4, 2009

Author: chatellier Date: 2009-05-04 15:58:12 +0000 (Mon, 04 May 2009) New Revision: 77 Modified: lutinj2r/trunk/pom.xml Log: [maven-release-plugin] prepare for next development iteration Modified: lutinj2r/trunk/pom.xml =================================================================== --- lutinj2r/trunk/pom.xml 2009-05-04 15:58:09 UTC (rev 76) +++ lutinj2r/trunk/pom.xml 2009-05-04 15:58:12 UTC (rev 77) @@ -13,7 +13,7 @@ </parent> <artifactId>lutinj2r</artifactId> - <version>0.4</version> + <version>0.5-SNAPSHOT</version> <dependencies>

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[LutinJ2R-commits] r76 - in lutinj2r/tags: . lutinj2r-0.4
by chatellier＠users.labs.libre-entreprise.org May 4, 2009

May 4, 2009

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 May 4, 2009

May 4, 2009

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 May 3, 2009

May 3, 2009

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 May 1, 2009

May 1, 2009

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

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[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 May 1, 2009

May 1, 2009

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()); + } + } + }

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