Author: echatellier Date: 2017-03-17 10:57:57 +0100 (Fri, 17 Mar 2017) New Revision: 4406 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4406 Log: Mise ?\195?\160 jour des libs Retrait des deprecated (commons-io) Modified: trunk/pom.xml trunk/src/main/java/fr/ifremer/isisfish/actions/ExportAction.java trunk/src/main/java/fr/ifremer/isisfish/actions/ImportAction.java trunk/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java trunk/src/main/java/fr/ifremer/isisfish/actions/ValidateSimulationAction.java trunk/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java trunk/src/main/java/fr/ifremer/isisfish/datastore/RegionStorage.java trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java trunk/src/main/java/fr/ifremer/isisfish/logging/console/LogMail.java trunk/src/main/java/fr/ifremer/isisfish/mexico/MexicoHelper.java trunk/src/main/java/fr/ifremer/isisfish/mexico/export/RegionExportFactorXML.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityAnalysis.java trunk/src/main/java/fr/ifremer/isisfish/ui/logging/LoggingFrame.java trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivitySecondPassHandler.java trunk/src/main/java/fr/ifremer/isisfish/util/EvaluatorHelper.java trunk/src/main/java/fr/ifremer/isisfish/util/RUtil.java trunk/src/main/resources/i18n/isis-fish_fr_FR.properties trunk/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java trunk/src/test/java/fr/ifremer/isisfish/IsisFishMiscTest.java trunk/src/test/java/fr/ifremer/isisfish/datastore/ScriptStorageTest.java trunk/src/test/java/fr/ifremer/isisfish/logging/RegionChangeLoggerTest.java trunk/src/test/java/fr/ifremer/isisfish/logging/SimulationLoggerUtilTest.java trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java trunk/src/test/java/fr/ifremer/isisfish/mexico/export/RegionExplorerTest.java trunk/src/test/java/fr/ifremer/isisfish/util/CompileHelperTest.java trunk/src/test/java/fr/ifremer/isisfish/vcs/VCSSVNTest.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/pom.xml 2017-03-17 09:57:57 UTC (rev 4406) @@ -104,7 +104,7 @@ <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-widgets</artifactId> - <version>${nuitonWidgetsVersion}</version> + <version>1.1.1</version> <scope>compile</scope> </dependency> @@ -229,7 +229,7 @@ <dependency> <groupId>org.slf4j</groupId> <artifactId>slf4j-api</artifactId> - <version>1.7.24</version> + <version>1.7.25</version> <scope>runtime</scope> </dependency> @@ -561,11 +561,9 @@ <!-- Dependencies version --> <jaxxVersion>2.41</jaxxVersion> - <eugeneVersion>2.14</eugeneVersion> <topiaVersion>2.12-SNAPSHOT</topiaVersion> - <hibernateVersion>5.1.4.Final</hibernateVersion> + <hibernateVersion>5.1.5.Final</hibernateVersion> <nuitonI18nVersion>3.6.3</nuitonI18nVersion> - <nuitonWidgetsVersion>1.1.1</nuitonWidgetsVersion> <redmine.releaseFiles>target/isis-fish-${project.version}-bin.zip</redmine.releaseFiles> <skipPostRelease>false</skipPostRelease> @@ -615,7 +613,7 @@ <plugin> <groupId>org.nuiton.eugene</groupId> <artifactId>eugene-maven-plugin</artifactId> - <version>${eugeneVersion}</version> + <version>2.14</version> </plugin> <plugin> Modified: trunk/src/main/java/fr/ifremer/isisfish/actions/ExportAction.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/actions/ExportAction.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/actions/ExportAction.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -28,6 +28,7 @@ import static org.nuiton.i18n.I18n.t; import java.io.File; +import java.nio.charset.StandardCharsets; import java.util.ArrayList; import java.util.Iterator; import java.util.List; @@ -202,7 +203,7 @@ throw new IllegalArgumentException(t("could not found %s", name)); } String content = storage.getContent(); - FileUtils.writeStringToFile(file, content); + FileUtils.writeStringToFile(file, content, StandardCharsets.UTF_8); } @Step(IsisConfig.STEP_AFTER_INIT_VCS) @@ -215,7 +216,7 @@ throw new IllegalArgumentException(t("could not found %s", name)); } String content = storage.getContent(); - FileUtils.writeStringToFile(file, content); + FileUtils.writeStringToFile(file, content, StandardCharsets.UTF_8); } @Step(IsisConfig.STEP_AFTER_INIT_VCS) @@ -228,7 +229,7 @@ throw new IllegalArgumentException(t("could not found %s", name)); } String content = storage.getContent(); - FileUtils.writeStringToFile(file, content); + FileUtils.writeStringToFile(file, content, StandardCharsets.UTF_8); } @Step(IsisConfig.STEP_AFTER_INIT_VCS) @@ -241,7 +242,7 @@ throw new IllegalArgumentException(t("could not found %s", name)); } String content = storage.getContent(); - FileUtils.writeStringToFile(file, content); + FileUtils.writeStringToFile(file, content, StandardCharsets.UTF_8); } @Step(IsisConfig.STEP_AFTER_INIT_VCS) @@ -254,7 +255,7 @@ throw new IllegalArgumentException(t("could not found %s", name)); } String content = storage.getContent(); - FileUtils.writeStringToFile(file, content); + FileUtils.writeStringToFile(file, content, StandardCharsets.UTF_8); } @Step(IsisConfig.STEP_AFTER_INIT_VCS) @@ -267,7 +268,7 @@ throw new IllegalArgumentException(t("could not found %s", name)); } String content = storage.getContent(); - FileUtils.writeStringToFile(file, content); + FileUtils.writeStringToFile(file, content, StandardCharsets.UTF_8); } } Modified: trunk/src/main/java/fr/ifremer/isisfish/actions/ImportAction.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/actions/ImportAction.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/actions/ImportAction.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -28,6 +28,7 @@ import static org.nuiton.i18n.I18n.t; import java.io.File; +import java.nio.charset.StandardCharsets; import org.apache.commons.io.FileUtils; @@ -64,7 +65,7 @@ if(!force && storage.exists()) { throw new IllegalArgumentException(t("destination already exists %s use \'force\' argument to force overwrite", storage.getFile())); } - String content = FileUtils.readFileToString(file); + String content = FileUtils.readFileToString(file, StandardCharsets.UTF_8); storage.setContent(content); } @@ -74,7 +75,7 @@ if(!force && storage.exists()) { throw new IllegalArgumentException(t("destination already exists %s use \'force\' argument to force overwrite", storage.getFile())); } - String content = FileUtils.readFileToString(file); + String content = FileUtils.readFileToString(file, StandardCharsets.UTF_8); storage.setContent(content); } @@ -84,7 +85,7 @@ if(!force && storage.exists()) { throw new IllegalArgumentException(t("destination already exists %s use \'force\' argument to force overwrite", storage.getFile())); } - String content = FileUtils.readFileToString(file); + String content = FileUtils.readFileToString(file, StandardCharsets.UTF_8); storage.setContent(content); } @@ -94,7 +95,7 @@ if(!force && storage.exists()) { throw new IllegalArgumentException(t("destination already exists %s use \'force\' argument to force overwrite", storage.getFile())); } - String content = FileUtils.readFileToString(file); + String content = FileUtils.readFileToString(file, StandardCharsets.UTF_8); storage.setContent(content); } @@ -104,7 +105,7 @@ if(!force && storage.exists()) { throw new IllegalArgumentException(t("destination already exists %s use \'force\' argument to force overwrite", storage.getFile())); } - String content = FileUtils.readFileToString(file); + String content = FileUtils.readFileToString(file, StandardCharsets.UTF_8); storage.setContent(content); } @@ -117,7 +118,7 @@ if(!force && storage.exists()) { throw new IllegalArgumentException(t("destination already exists %s use \'force\' argument to force overwrite", storage.getFile())); } - String content = FileUtils.readFileToString(file); + String content = FileUtils.readFileToString(file, StandardCharsets.UTF_8); storage.setContent(content); } Modified: trunk/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -29,6 +29,7 @@ import java.io.File; import java.io.FileInputStream; +import java.nio.charset.StandardCharsets; import java.util.Properties; import org.apache.commons.io.FileUtils; @@ -140,7 +141,7 @@ //simulation.getStorage().closeContext(); String generatedPrescriptContent = null; if (simulationPrescript != null && simulationPrescript.canRead()) { - generatedPrescriptContent = FileUtils.readFileToString(simulationPrescript); + generatedPrescriptContent = FileUtils.readFileToString(simulationPrescript, StandardCharsets.UTF_8); } SimulationControl control = new SimulationControl(name); @@ -220,7 +221,7 @@ //simulation.getStorage().closeContext(); String generatedPrescriptContent = null; if (simulationPrescript != null && simulationPrescript.canRead()) { - generatedPrescriptContent = FileUtils.readFileToString(simulationPrescript); + generatedPrescriptContent = FileUtils.readFileToString(simulationPrescript, StandardCharsets.UTF_8); } SimulationControl control = new SimulationControl(name); Modified: trunk/src/main/java/fr/ifremer/isisfish/actions/ValidateSimulationAction.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/actions/ValidateSimulationAction.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/actions/ValidateSimulationAction.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -41,6 +41,7 @@ import org.nuiton.math.matrix.MatrixND; import java.io.File; +import java.nio.charset.StandardCharsets; import java.text.SimpleDateFormat; import java.util.Date; import java.util.List; @@ -125,7 +126,7 @@ //simulation.getStorage().closeContext(); String generatedPrescriptContent = null; if (simulationPrescript != null && simulationPrescript.canRead()) { - generatedPrescriptContent = FileUtils.readFileToString(simulationPrescript); + generatedPrescriptContent = FileUtils.readFileToString(simulationPrescript, StandardCharsets.UTF_8); } SimulationControl control = new SimulationControl(name); Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -27,6 +27,7 @@ import java.io.File; import java.io.IOException; +import java.nio.charset.StandardCharsets; import java.util.Collections; import java.util.List; @@ -194,7 +195,7 @@ content = ""; } else { try { - content = FileUtils.readFileToString(getFile()); + content = FileUtils.readFileToString(getFile(), StandardCharsets.UTF_8); lastContentUpdate = System.nanoTime(); lastContentLength = getFile().length(); } catch (IOException eee) { Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/RegionStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/RegionStorage.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/RegionStorage.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -44,6 +44,7 @@ import java.io.File; import java.io.IOException; +import java.nio.charset.StandardCharsets; import java.text.MessageFormat; import java.util.ArrayList; import java.util.Date; @@ -106,7 +107,7 @@ public String getCommentForNextCommit() throws IOException { commentForNextCommitFile.createNewFile(); String result; - result = FileUtils.readFileToString(commentForNextCommitFile); + result = FileUtils.readFileToString(commentForNextCommitFile, StandardCharsets.UTF_8); return result; } @@ -116,7 +117,7 @@ */ public void setCommentForNextCommit(String commentForNextCommit) throws IOException { commentForNextCommitFile.createNewFile(); - FileUtils.writeStringToFile(commentForNextCommitFile, commentForNextCommit); + FileUtils.writeStringToFile(commentForNextCommitFile, commentForNextCommit, StandardCharsets.UTF_8); } /** @@ -124,7 +125,7 @@ * must be used in user application after commit */ public void clearCommentForNextCommit() { - String date = DateFormatUtils.ISO_DATETIME_FORMAT.format(new Date()); + String date = DateFormatUtils.ISO_8601_EXTENDED_DATETIME_FORMAT.format(new Date()); File dest = new File(commentForNextCommitFile, date); commentForNextCommitFile.renameTo(dest); } Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -31,6 +31,7 @@ import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; +import java.nio.charset.StandardCharsets; import java.util.ArrayList; import java.util.List; import java.util.Map; @@ -223,7 +224,7 @@ if (objective == null) { File ObjFile = getObjectiveFile(); if (file.exists()) { - String s = FileUtils.readFileToString(ObjFile); + String s = FileUtils.readFileToString(ObjFile, StandardCharsets.UTF_8); objective = Double.parseDouble(s); } } @@ -232,7 +233,7 @@ public void setObjective(double d) throws IOException { objective = d; - FileUtils.writeStringToFile(getObjectiveFile(), String.valueOf(d)); + FileUtils.writeStringToFile(getObjectiveFile(), String.valueOf(d), StandardCharsets.UTF_8); } /** Modified: trunk/src/main/java/fr/ifremer/isisfish/logging/console/LogMail.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/logging/console/LogMail.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/logging/console/LogMail.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -39,6 +39,7 @@ import java.io.InputStream; import java.io.OutputStream; import java.io.OutputStreamWriter; +import java.nio.charset.StandardCharsets; import java.util.Date; import java.util.Properties; import java.util.zip.ZipEntry; @@ -170,7 +171,7 @@ ZipOutputStream zipOutputStream = new ZipOutputStream(byteArrayOutputStream); BufferedWriter zipWriter = new BufferedWriter(new OutputStreamWriter(zipOutputStream)); zipOutputStream.putNextEntry(new ZipEntry(zipFile.getName())); - String content = FileUtils.readFileToString(zipFile); + String content = FileUtils.readFileToString(zipFile, StandardCharsets.UTF_8); zipWriter.write(content); zipWriter.flush(); Modified: trunk/src/main/java/fr/ifremer/isisfish/mexico/MexicoHelper.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/mexico/MexicoHelper.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/mexico/MexicoHelper.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -30,6 +30,7 @@ import java.io.File; import java.io.IOException; import java.lang.reflect.Method; +import java.nio.charset.StandardCharsets; import java.util.ArrayList; import java.util.List; import java.util.Properties; @@ -118,7 +119,7 @@ public static void writeDesignPlanToFile(File file, DesignPlan designPlan) { String content = getDesignPlanAsXML(designPlan); try { - FileUtils.writeStringToFile(file, content); + FileUtils.writeStringToFile(file, content, StandardCharsets.UTF_8); } catch (IOException ex) { throw new IsisFishRuntimeException("Can't export factors to xml file", ex); } Modified: trunk/src/main/java/fr/ifremer/isisfish/mexico/export/RegionExportFactorXML.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/mexico/export/RegionExportFactorXML.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/mexico/export/RegionExportFactorXML.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -27,6 +27,7 @@ import java.io.File; import java.io.IOException; +import java.nio.charset.StandardCharsets; import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.RandomStringUtils; @@ -150,7 +151,7 @@ String xml = MexicoHelper.formatXML(stringBuffer.toString()); try { - FileUtils.writeStringToFile(outputFile, xml); + FileUtils.writeStringToFile(outputFile, xml, StandardCharsets.UTF_8); } catch (IOException ex) { if (log.isErrorEnabled()) { log.error("Can't wrtie xml content to output file", ex); Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -34,6 +34,7 @@ import java.io.InputStream; import java.io.StringWriter; import java.io.Writer; +import java.nio.charset.StandardCharsets; import java.rmi.RemoteException; import java.util.HashMap; import java.util.List; @@ -395,7 +396,7 @@ if (md5ControlFile != null) { control.setText(t("isisfish.simulation.remote.message.downloadresults")); - String md5sum = FileUtils.readFileToString(md5ControlFile); + String md5sum = FileUtils.readFileToString(md5ControlFile, StandardCharsets.UTF_8); if (log.isDebugEnabled()) { log.debug("MD5 Control file have been downloaded : " + md5ControlFile.getAbsolutePath()); @@ -616,7 +617,7 @@ try { // use usefull readLines from commons-io - List<String> contents = FileUtils.readLines(publicKey); + List<String> contents = FileUtils.readLines(publicKey, StandardCharsets.UTF_8); // only one line if (contents != null && contents.size() == 1) { Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityAnalysis.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityAnalysis.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityAnalysis.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -29,6 +29,7 @@ import java.io.File; import java.io.IOException; +import java.nio.charset.StandardCharsets; import java.util.Collection; import java.util.List; import java.util.Map; @@ -375,7 +376,7 @@ String simulResult = ""; try { - simulResult = FileUtils.readFileToString(importFile); + simulResult = FileUtils.readFileToString(importFile, StandardCharsets.UTF_8); } catch (IOException ioe) { log.error("An error occured trying to read a result file : ", ioe); } Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/logging/LoggingFrame.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/logging/LoggingFrame.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/logging/LoggingFrame.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -27,6 +27,7 @@ import java.awt.Frame; import java.io.File; import java.io.IOException; +import java.nio.charset.StandardCharsets; import javax.swing.JFrame; import javax.swing.JMenu; @@ -82,7 +83,7 @@ SimulationStorage storage = SimulationStorage.getSimulation(simulationName); File logFile = new File(storage.getSimulationLogFile()); - String content = FileUtils.readFileToString(logFile); + String content = FileUtils.readFileToString(logFile, StandardCharsets.UTF_8); editor.setText(content); } } Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivitySecondPassHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivitySecondPassHandler.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivitySecondPassHandler.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -25,6 +25,7 @@ import java.awt.event.ActionEvent; import java.io.File; import java.io.IOException; +import java.nio.charset.StandardCharsets; import java.util.ArrayList; import java.util.List; import java.util.SortedMap; @@ -123,7 +124,7 @@ for(File file : files) { content += "Fichier " + file.getName() + "\n"; content += "------------------------------\n"; - content += FileUtils.readFileToString(file) + "\n"; + content += FileUtils.readFileToString(file, StandardCharsets.UTF_8) + "\n"; content += "\n"; } sensitivitySecondPassUI.textAreaSensitivitySecondpassResult.setText(content); Modified: trunk/src/main/java/fr/ifremer/isisfish/util/EvaluatorHelper.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/EvaluatorHelper.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/util/EvaluatorHelper.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -31,6 +31,7 @@ import java.io.IOException; import java.io.PrintWriter; import java.lang.reflect.Method; +import java.nio.charset.StandardCharsets; import java.util.ArrayList; import java.util.Collections; import java.util.List; @@ -84,7 +85,7 @@ // on verifie dans le fichier if (fileCheckSum.exists()) { try { - result = FileUtils.readFileToString(fileCheckSum); + result = FileUtils.readFileToString(fileCheckSum, StandardCharsets.UTF_8); } catch (IOException eee) { log.info("Can't read old checkSum: " + fileCheckSum, eee); } @@ -107,7 +108,7 @@ // on est pas dans une simulation // on ecrit dans le fichier try { - FileUtils.writeStringToFile(fileCheckSum, hashcode); + FileUtils.writeStringToFile(fileCheckSum, hashcode, StandardCharsets.UTF_8); } catch (IOException eee) { log.info("Can't write checkSum: " + fileCheckSum, eee); } Modified: trunk/src/main/java/fr/ifremer/isisfish/util/RUtil.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/RUtil.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/java/fr/ifremer/isisfish/util/RUtil.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -29,6 +29,7 @@ import java.io.IOException; import java.io.InputStream; import java.lang.reflect.Field; +import java.nio.charset.StandardCharsets; import java.util.List; import org.apache.commons.io.IOUtils; @@ -66,7 +67,7 @@ // R trouvé, mais la commande R a échoué InputStream err = process.getErrorStream(); if (log.isErrorEnabled()) { - log.error("Can't call Rscript : " + IOUtils.toString(err)); + log.error("Can't call Rscript : " + IOUtils.toString(err, StandardCharsets.UTF_8)); } } } catch (IOException ex) { @@ -88,7 +89,7 @@ * @throws IOException */ protected static void parseRscriptOutput(InputStream is) throws IOException { - List<String> output = IOUtils.readLines(is); + List<String> output = IOUtils.readLines(is, StandardCharsets.UTF_8); // 1 lignes = commande OK, mais rJava n'est pas installé // 2 lignes = commande OK et rJava est installé Modified: trunk/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2017-03-17 09:57:57 UTC (rev 4406) @@ -1,3 +1,4 @@ +%s\ has\ a\ discrete\ domain,\ this\ is\ not\ acceptable\ for\ this\ method.= %s\ has\ a\ non\ uniform\ distribution,\ this\ is\ not\ acceptable\ for\ this\ method.= Add\ to\ default\ queue= Analyse\ plan\ error,\ too\ many\ simulation\ for\ %s\ \:\ %s= Modified: trunk/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -152,7 +152,7 @@ * @return freemarker {@link Configuration} */ protected static Configuration getFreemarkerConfiguration() { - Configuration freemarkerConfiguration = new Configuration(); + Configuration freemarkerConfiguration = new Configuration(Configuration.VERSION_2_3_25); // needed to overwrite "Defaults to default system encoding." // fix encoding issue on some systems @@ -162,7 +162,7 @@ ClassTemplateLoader templateLoader = new ClassTemplateLoader(AbstractIsisFishTest.class, "/"); freemarkerConfiguration.setTemplateLoader(templateLoader); - freemarkerConfiguration.setObjectWrapper(new BeansWrapper()); + freemarkerConfiguration.setObjectWrapper(new BeansWrapper(Configuration.VERSION_2_3_25)); return freemarkerConfiguration; } Modified: trunk/src/test/java/fr/ifremer/isisfish/IsisFishMiscTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/IsisFishMiscTest.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/test/java/fr/ifremer/isisfish/IsisFishMiscTest.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -27,6 +27,7 @@ import java.io.File; import java.io.IOException; +import java.nio.charset.StandardCharsets; import org.apache.commons.io.FileUtils; import org.junit.Assert; @@ -55,7 +56,7 @@ File batFile = new File("src" + File.separator + "main" + File.separator + "assembly" + File.separator + "isisfish.bat"); batFile = batFile.getAbsoluteFile(); // for maven - String content = FileUtils.readFileToString(batFile); + String content = FileUtils.readFileToString(batFile, StandardCharsets.UTF_8); System.out.println(content); String[] lines = content.split("\n"); Modified: trunk/src/test/java/fr/ifremer/isisfish/datastore/ScriptStorageTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/datastore/ScriptStorageTest.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/test/java/fr/ifremer/isisfish/datastore/ScriptStorageTest.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -27,6 +27,7 @@ import java.io.StringWriter; import java.io.Writer; +import java.nio.charset.StandardCharsets; import java.util.Date; import java.util.HashMap; import java.util.Map; @@ -84,7 +85,7 @@ //System.out.println("Content: '" + script.getContent() + "'"); Assert.assertEquals(content1, script.getContent()); - FileUtils.writeStringToFile(script.getFile(), content2); + FileUtils.writeStringToFile(script.getFile(), content2, StandardCharsets.UTF_8); //System.out.println("Content: '" + script.getContent() + "'"); Assert.assertEquals(content2, script.getContent()); } finally { Modified: trunk/src/test/java/fr/ifremer/isisfish/logging/RegionChangeLoggerTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/logging/RegionChangeLoggerTest.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/test/java/fr/ifremer/isisfish/logging/RegionChangeLoggerTest.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -24,10 +24,9 @@ * Test que les evenements sur les entités existantes sont bien logués. * * @throws IOException si le fichier ne peux pas être lu - * @throws StorageException */ @Test - public void testLoggingOnExistingEntities() throws IOException, StorageException { + public void testLoggingOnExistingEntities() throws IOException { RegionStorage regionStorage = RegionStorage.getRegion("BaseMotosICA"); TopiaContext storage = regionStorage.getStorage(); TopiaContext topiaContext = storage.beginTransaction(); @@ -58,7 +57,7 @@ */ @Test public void testLoggingOnNewEntities() throws IOException, StorageException { - RegionStorage regionStorage = RegionStorage.getRegion("BaseMotosICA"); + RegionStorage regionStorage = RegionStorage.create("test"); TopiaContext storage = regionStorage.getStorage(); TopiaContext topiaContext = storage.beginTransaction(); RegionChangeLogger regionChangeLogger = new RegionChangeLogger(regionStorage, topiaContext); Modified: trunk/src/test/java/fr/ifremer/isisfish/logging/SimulationLoggerUtilTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/logging/SimulationLoggerUtilTest.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/test/java/fr/ifremer/isisfish/logging/SimulationLoggerUtilTest.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -26,6 +26,7 @@ package fr.ifremer.isisfish.logging; import java.io.File; +import java.nio.charset.StandardCharsets; import java.util.ArrayList; import java.util.List; @@ -116,7 +117,7 @@ File logFile = new File(loggerFile); - String logFileContent = FileUtils.readFileToString(logFile); + String logFileContent = FileUtils.readFileToString(logFile, StandardCharsets.UTF_8); log.info("++ File content ----------------------------------------------------------"); for (Object o : logFileContent.split("\n")) { @@ -207,7 +208,7 @@ File logFile = new File(loggerFile); - String logFileContent = FileUtils.readFileToString(logFile); + String logFileContent = FileUtils.readFileToString(logFile, StandardCharsets.UTF_8); log.info("++ File content ----------------------------------------------------------"); for (Object o : logFileContent.split("\n")) { Modified: trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -29,6 +29,7 @@ import java.io.IOException; import java.io.StringReader; import java.net.URL; +import java.nio.charset.StandardCharsets; import java.util.Arrays; import java.util.Date; import java.util.List; @@ -489,7 +490,7 @@ String content = MexicoHelper.getDesignPlanAsXML(testDesignPlan); File tempFile = File.createTempFile("testdesignplan", ".xml"); tempFile.deleteOnExit(); - FileUtils.writeStringToFile(tempFile, content); + FileUtils.writeStringToFile(tempFile, content, StandardCharsets.UTF_8); // test to read it and get content DesignPlan plan = MexicoHelper.getDesignPlanFromXML(tempFile, null); @@ -528,7 +529,7 @@ File tempFile = File.createTempFile("testdesignplan", ".xml"); tempFile.deleteOnExit(); - FileUtils.writeStringToFile(tempFile, content); + FileUtils.writeStringToFile(tempFile, content, StandardCharsets.UTF_8); // test to read it and get content DesignPlan plan = MexicoHelper.getDesignPlanFromXML(tempFile, null); Modified: trunk/src/test/java/fr/ifremer/isisfish/mexico/export/RegionExplorerTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/mexico/export/RegionExplorerTest.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/test/java/fr/ifremer/isisfish/mexico/export/RegionExplorerTest.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -27,6 +27,7 @@ import java.io.File; import java.io.IOException; +import java.nio.charset.StandardCharsets; import org.apache.commons.io.FileUtils; import org.apache.commons.logging.Log; @@ -79,7 +80,7 @@ // explore region (export as xml) RegionExplorer explorer = new RegionExplorer(); explorer.explore(fisheryRegion, xmlFactorExport); - String xmlExport = FileUtils.readFileToString(file); + String xmlExport = FileUtils.readFileToString(file, StandardCharsets.UTF_8); if (log.isDebugEnabled()) { log.debug("Export xml is : \n" + xmlExport); @@ -123,7 +124,7 @@ // explore region (export as xml) RegionExplorer explorer = new RegionExplorer(); explorer.explore(fisheryRegion, xmlFactorExport); - String xmlExport = FileUtils.readFileToString(file); + String xmlExport = FileUtils.readFileToString(file, StandardCharsets.UTF_8); // test that all sensitivity properties appear in xml content // entity part and property part must appear in factors names Modified: trunk/src/test/java/fr/ifremer/isisfish/util/CompileHelperTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/util/CompileHelperTest.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/test/java/fr/ifremer/isisfish/util/CompileHelperTest.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -29,6 +29,7 @@ import java.io.IOException; import java.net.URL; import java.net.URLClassLoader; +import java.nio.charset.StandardCharsets; import java.util.ArrayList; import java.util.Collections; import java.util.List; @@ -109,7 +110,7 @@ File f = File.createTempFile("testCompile", ".java", getTestDirectory()); String filename = FileUtil.basename(f, ".java"); String code = getFirstClassContent(filename); - FileUtils.writeStringToFile(f, code); + FileUtils.writeStringToFile(f, code, StandardCharsets.UTF_8); List<File> classpath = new ArrayList<>(); classpath.add(f.getParentFile()); @@ -143,12 +144,12 @@ File fA = File.createTempFile("testCompileA", ".java", getTestDirectory()); String filenameA = FileUtil.basename(fA, ".java"); String codeA = getFirstClassContent(filenameA); - FileUtils.writeStringToFile(fA, codeA); + FileUtils.writeStringToFile(fA, codeA, StandardCharsets.UTF_8); File fB = File.createTempFile("testCompileB", ".java", getTestDirectory()); String filenameB = FileUtil.basename(fB, ".java"); String codeB = getSecondClassContent(filenameB, filenameA); - FileUtils.writeStringToFile(fB, codeB); + FileUtils.writeStringToFile(fB, codeB, StandardCharsets.UTF_8); File dest = new File(fB.getParentFile(), "testCompile"); Modified: trunk/src/test/java/fr/ifremer/isisfish/vcs/VCSSVNTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/vcs/VCSSVNTest.java 2017-03-17 09:15:03 UTC (rev 4405) +++ trunk/src/test/java/fr/ifremer/isisfish/vcs/VCSSVNTest.java 2017-03-17 09:57:57 UTC (rev 4406) @@ -51,6 +51,7 @@ import java.io.File; import java.io.IOException; +import java.nio.charset.StandardCharsets; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; @@ -128,7 +129,7 @@ new File(template, "scripts").mkdirs(); FileUtils.writeStringToFile(new File(template, "scripts" + File.separator - + "version.txt"), FILECONTENTTAG); + + "version.txt"), FILECONTENTTAG, StandardCharsets.UTF_8); // creation du repo pour les tests SVNRepositoryFactory.createLocalRepository(remoteRepo, false, true); @@ -298,12 +299,12 @@ File version = new File(vcs.getLocalRepository(), "scripts" + File.separator + "version.txt"); Assert.assertTrue(version.exists()); - Assert.assertEquals(FILECONTENTTAG, FileUtils.readFileToString(version)); + Assert.assertEquals(FILECONTENTTAG, FileUtils.readFileToString(version, StandardCharsets.UTF_8)); // modification du fichier version.txt - FileUtils.writeStringToFile(version, FILECONTENTTRUNK); + FileUtils.writeStringToFile(version, FILECONTENTTRUNK, StandardCharsets.UTF_8); vcs.commit(null, "modif du fichier version"); - Assert.assertEquals(FILECONTENTTRUNK, FileUtils.readFileToString(version)); + Assert.assertEquals(FILECONTENTTRUNK, FileUtils.readFileToString(version, StandardCharsets.UTF_8)); // recuperation de DemoRegion File demo = new File(vcs.getLocalRepository(), "regions" @@ -318,13 +319,13 @@ // ajout d'un fichier sur le trunk avant passage sur le tag File fileToAdd = new File(vcs.getLocalRepository(), "newfile.txt"); String lecontent = "Le nouveau fichier"; - FileUtils.writeStringToFile(fileToAdd, lecontent); + FileUtils.writeStringToFile(fileToAdd, lecontent, StandardCharsets.UTF_8); vcs.add(Arrays.asList(fileToAdd), "ajout d'un fichier"); // test switchTag vcs.setTag(Versions.valueOf("3.1.0")); Assert.assertTrue(vcs.getTag().startsWith("/tags/3.1.0")); - Assert.assertEquals(FILECONTENTTAG, FileUtils.readFileToString(version)); + Assert.assertEquals(FILECONTENTTAG, FileUtils.readFileToString(version, StandardCharsets.UTF_8)); Assert.assertTrue(demo.exists()); // recherche du status des fichiers @@ -341,7 +342,7 @@ Assert.assertTrue(map.containsKey(newfileAdded)); // modif dans repo trunk de version pour qu'il y ait un conflit - FileUtils.writeStringToFile(fileVersion, "Le nouveau content de version"); + FileUtils.writeStringToFile(fileVersion, "Le nouveau content de version", StandardCharsets.UTF_8); // update global du repo trunk List<File> conflictFile = trunk.update(null, true); @@ -352,7 +353,7 @@ Assert.assertTrue(conflictFile.contains(fileVersion)); File fileAdded = new File(trunk.getLocalRepository(), "newfile.txt"); - Assert.assertEquals(lecontent, FileUtils.readFileToString(fileAdded)); + Assert.assertEquals(lecontent, FileUtils.readFileToString(fileAdded, StandardCharsets.UTF_8)); Assert.assertFalse(fileDeleted.exists()); // recherche du status des fichiers en remote, il ne doit plus y avoir de diff @@ -397,7 +398,7 @@ // now, make a modification, on LOCAL repo File firstFile = new File(vcs.getLocalRepository() + File.separator + "scripts" + File.separator + "version.txt"); - FileUtils.writeStringToFile(firstFile, "Version 3.2.1"); + FileUtils.writeStringToFile(firstFile, "Version 3.2.1", StandardCharsets.UTF_8); List<File> files = Collections.singletonList(firstFile); @@ -462,8 +463,8 @@ vcs.checkout(null, true); // now, make a modification, on LOCAL repo - FileUtils.writeStringToFile(firstFile, "version 3.2.1"); - FileUtils.writeStringToFile(secondFile, "name = test1"); + FileUtils.writeStringToFile(firstFile, "version 3.2.1", StandardCharsets.UTF_8); + FileUtils.writeStringToFile(secondFile, "name = test1", StandardCharsets.UTF_8); SVNClientManager svnManager = SVNClientManager.newInstance(); svnManager.getWCClient().doAdd(secondFile, // File path true, // boolean force @@ -504,7 +505,7 @@ vcs.checkout(null, true); // now, make a modification, on LOCAL repo - FileUtils.writeStringToFile(firstFile, "Version 3.2.1"); + FileUtils.writeStringToFile(firstFile, "Version 3.2.1", StandardCharsets.UTF_8); String result = vcs.getDiff(firstFile); @@ -860,7 +861,7 @@ // modif on local repo File file = new File(vcs.getLocalRepository() + File.separator + "test.txt"); - FileUtils.writeStringToFile(file, "name = test1"); + FileUtils.writeStringToFile(file, "name = test1", StandardCharsets.UTF_8); SVNClientManager svnManager = SVNClientManager.newInstance(); svnManager.getWCClient().doAdd(file, // File path true, // boolean force @@ -934,7 +935,7 @@ // modif on local repo File file = new File(vcs.getLocalRepository() + File.separator + "test.txt"); - FileUtils.writeStringToFile(file, "name = test1"); + FileUtils.writeStringToFile(file, "name = test1", StandardCharsets.UTF_8); SVNClientManager svnManager = SVNClientManager.newInstance(); svnManager.getWCClient().doAdd(file, // File path true, // boolean force @@ -1009,7 +1010,7 @@ // modif on remote repo File file = new File(vcs.getLocalRepository(), "scripts" + File.separator + "version.txt"); - FileUtils.writeStringToFile(file, "aaaaaz"); + FileUtils.writeStringToFile(file, "aaaaaz", StandardCharsets.UTF_8); SVNClientManager svnManager = SVNClientManager.newInstance(); SVNCommitInfo rev = svnManager.getCommitClient().doCommit( new File[] { file },// File[] paths, @@ -1079,7 +1080,7 @@ // modif on remote repo File file = new File(vcs.getLocalRepository(), "scripts" + File.separator + "version.txt"); - FileUtils.writeStringToFile(file, "aaaaaz"); + FileUtils.writeStringToFile(file, "aaaaaz", StandardCharsets.UTF_8); SVNClientManager svnManager = SVNClientManager.newInstance(); SVNCommitInfo rev = svnManager.getCommitClient().doCommit( new File[] { file },// File[] paths, @@ -1108,7 +1109,7 @@ // modify one file File file2 = new File(vcs.getLocalRepository(), "scripts" + File.separator + "version.txt"); - FileUtils.writeStringToFile(file2, "oooooo"); + FileUtils.writeStringToFile(file2, "oooooo", StandardCharsets.UTF_8); // try to update... List<File> filesInConflict = vcs.update(null, true); @@ -1145,7 +1146,7 @@ // modif on remote repo on tag :) File file = new File(vcs.getLocalRepository(), "scripts" + File.separator + "version.txt"); - FileUtils.writeStringToFile(file, "aaaaaz"); + FileUtils.writeStringToFile(file, "aaaaaz", StandardCharsets.UTF_8); SVNClientManager svnManager = SVNClientManager.newInstance(); SVNCommitInfo rev = svnManager.getCommitClient().doCommit( new File[] { file },// File[] paths, @@ -1166,7 +1167,7 @@ // modify one file File file2 = new File(vcs.getLocalRepository(), "scripts" + File.separator + "version.txt"); - FileUtils.writeStringToFile(file2, "oooooo"); + FileUtils.writeStringToFile(file2, "oooooo", StandardCharsets.UTF_8); // try to update... List<File> filesInConflict = vcs.setTag(Versions.valueOf("3.1.0")); @@ -1203,7 +1204,7 @@ // modif on remote repo File file = new File(vcs.getLocalRepository(), "scripts" + File.separator + "version.txt"); - FileUtils.writeStringToFile(file, "aaaaaz"); + FileUtils.writeStringToFile(file, "aaaaaz", StandardCharsets.UTF_8); SVNClientManager svnManager = SVNClientManager.newInstance(); SVNCommitInfo rev = svnManager.getCommitClient().doCommit( new File[] { file },// File[] paths, @@ -1232,7 +1233,7 @@ // modify one file File file2 = new File(vcs.getLocalRepository(), "scripts" + File.separator + "version.txt"); - FileUtils.writeStringToFile(file2, "oooooo"); + FileUtils.writeStringToFile(file2, "oooooo", StandardCharsets.UTF_8); // try to update... List<File> filesInConflict = vcs.checkFileStatus(); @@ -1272,7 +1273,7 @@ // modif on remote repo File file = new File(vcs.getLocalRepository(), "scripts" + File.separator + "version.txt"); - FileUtils.writeStringToFile(file, "modified content"); + FileUtils.writeStringToFile(file, "modified content", StandardCharsets.UTF_8); Assert.assertEquals(Status.STATUS_MODIFIED, vcs.getLocalStatus(file)); }