April 2014 - Echobase-commits - mailman.cloud.codelutin.com

[ANN] - EchoBase 2.6 released
by codelutin.com Release Notification April 22, 2014

April 22, 2014

The EchoBase team is pleased to announce the echobase-2.6 release! The French Institute for the Exploitation of the Sea (Ifremer) has designed an open software suite for storing fisheries acoustic data and computing acoustic indicators for survey-based ecosystem monitoring. It comprises a postgreSQL database designed to store acoustic, navigation and fishing data from ecosystemic surveys (EchoBase) and a suite of R codes (EchoR) for computing fish population indicators based on Echobase data. Documentation of the project can be found here: https://doc.codelutin.com/echobase Changes ------- Changes in this version include: New features: o Données sources à extraire Issue: 4704. Thanks to Tony Chemit. Resolved by tchemit. o [Import Region] Ne pas importer les résultats *NA* Issue: 4985. Thanks to Tony Chemit. Resolved by tchemit. o Export Coser Issue: 4821. Thanks to Tony Chemit. Resolved by tchemit. o Comment rechercher un champ vide ('') avec l'outil de recherche des tables de l'interface java? Issue: 4872. Thanks to Mathieu Doray. Resolved by tchemit. Fixed Bugs: o Impossible de supprimer des données acoustiques Issue: 4947. Thanks to Tony Chemit. Resolved by tchemit. o Les données spatiales ne sont pas calculées suite à un import Issue: 4950. Thanks to Tony Chemit. Resolved by tchemit. o Les listes ne sont pas traduites Issue: 4984. Thanks to Tony Chemit. Resolved by tchemit. o Pas possible d'importer une cellule de type région avec un cellType=='Region' (alors qu'il faudrait pouvoir le faire pour le grand polygone du survey) Issue: 4888. Thanks to Mathieu Doray. Resolved by tchemit. o recherche sur addOffset dans table datametadata ne fonctionne pas Issue: 4806. Thanks to Mathieu Doray. Resolved by tchemit. Changes: o Gestion des listes d'espèces pour les indices de communauté Issue: 4703. Thanks to Tony Chemit. Resolved by mdoray. o Mise à jour des référentiels Issue: 4836. Thanks to Tony Chemit. Resolved by tchemit. Downloads --------- For a manual installation, you can download files here: http://forge.codelutin.com/projects/echobase/files * echobase-embedded-2.6.zip - http://forge.codelutin.com/attachments/download/1763 * echobase-full-2.6.war - http://forge.codelutin.com/attachments/download/1764 * echobase-referentiel-2.6.echobase - http://forge.codelutin.com/attachments/download/1765 Maven artifacts --------------- Artifacts are deployed in nuiton maven repository http://maven.nuiton.org/other-releases/ Have fun! -EchoBase team

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r1024 - in trunk: . echobase-domain echobase-services echobase-ui
by tchemit＠users.forge.codelutin.com April 22, 2014

April 22, 2014

Author: tchemit Date: 2014-04-22 23:04:45 +0200 (Tue, 22 Apr 2014) New Revision: 1024 Url: http://forge.codelutin.com/projects/echobase/repository/revisions/1024 Log: [maven-release-plugin] prepare for next development iteration Modified: trunk/echobase-domain/pom.xml trunk/echobase-services/pom.xml trunk/echobase-ui/pom.xml trunk/pom.xml Modified: trunk/echobase-domain/pom.xml =================================================================== --- trunk/echobase-domain/pom.xml 2014-04-22 21:04:39 UTC (rev 1023) +++ trunk/echobase-domain/pom.xml 2014-04-22 21:04:45 UTC (rev 1024) @@ -5,7 +5,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.6</version> + <version>2.7-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-services/pom.xml =================================================================== --- trunk/echobase-services/pom.xml 2014-04-22 21:04:39 UTC (rev 1023) +++ trunk/echobase-services/pom.xml 2014-04-22 21:04:45 UTC (rev 1024) @@ -6,7 +6,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.6</version> + <version>2.7-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-ui/pom.xml =================================================================== --- trunk/echobase-ui/pom.xml 2014-04-22 21:04:39 UTC (rev 1023) +++ trunk/echobase-ui/pom.xml 2014-04-22 21:04:45 UTC (rev 1024) @@ -7,7 +7,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.6</version> + <version>2.7-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-04-22 21:04:39 UTC (rev 1023) +++ trunk/pom.xml 2014-04-22 21:04:45 UTC (rev 1024) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.6</version> + <version>2.7-SNAPSHOT</version> <modules> <module>echobase-domain</module> @@ -84,12 +84,12 @@ </developers> <scm> - <url>https://svn.codelutin.com/repositories/browse/echobase/tags/echobase-2.6</url> + <url>https://svn.codelutin.com/repositories/browse/echobase/trunk</url> <connection> - scm:svn:https://svn.codelutin.com/echobase/tags/echobase-2.6 + scm:svn:https://svn.codelutin.com/echobase/trunk </connection> <developerConnection> - scm:svn:https://svn.codelutin.com/echobase/tags/echobase-2.6 + scm:svn:https://svn.codelutin.com/echobase/trunk </developerConnection> </scm>

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r1023 - tags
by tchemit＠users.forge.codelutin.com April 22, 2014

April 22, 2014

Author: tchemit Date: 2014-04-22 23:04:39 +0200 (Tue, 22 Apr 2014) New Revision: 1023 Url: http://forge.codelutin.com/projects/echobase/repository/revisions/1023 Log: [maven-release-plugin] copy for tag echobase-2.6 Added: tags/echobase-2.6/

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r1022 - in trunk: . echobase-domain echobase-services echobase-ui
by tchemit＠users.forge.codelutin.com April 22, 2014

April 22, 2014

Author: tchemit Date: 2014-04-22 23:04:33 +0200 (Tue, 22 Apr 2014) New Revision: 1022 Url: http://forge.codelutin.com/projects/echobase/repository/revisions/1022 Log: [maven-release-plugin] prepare release echobase-2.6 Modified: trunk/echobase-domain/pom.xml trunk/echobase-services/pom.xml trunk/echobase-ui/pom.xml trunk/pom.xml Modified: trunk/echobase-domain/pom.xml =================================================================== --- trunk/echobase-domain/pom.xml 2014-04-22 20:59:06 UTC (rev 1021) +++ trunk/echobase-domain/pom.xml 2014-04-22 21:04:33 UTC (rev 1022) @@ -5,7 +5,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.6-SNAPSHOT</version> + <version>2.6</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-services/pom.xml =================================================================== --- trunk/echobase-services/pom.xml 2014-04-22 20:59:06 UTC (rev 1021) +++ trunk/echobase-services/pom.xml 2014-04-22 21:04:33 UTC (rev 1022) @@ -6,7 +6,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.6-SNAPSHOT</version> + <version>2.6</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-ui/pom.xml =================================================================== --- trunk/echobase-ui/pom.xml 2014-04-22 20:59:06 UTC (rev 1021) +++ trunk/echobase-ui/pom.xml 2014-04-22 21:04:33 UTC (rev 1022) @@ -7,7 +7,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.6-SNAPSHOT</version> + <version>2.6</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-04-22 20:59:06 UTC (rev 1021) +++ trunk/pom.xml 2014-04-22 21:04:33 UTC (rev 1022) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.6-SNAPSHOT</version> + <version>2.6</version> <modules> <module>echobase-domain</module> @@ -84,12 +84,12 @@ </developers> <scm> - <url>https://svn.codelutin.com/repositories/browse/echobase/trunk</url> + <url>https://svn.codelutin.com/repositories/browse/echobase/tags/echobase-2.6</url> <connection> - scm:svn:https://svn.codelutin.com/echobase/trunk + scm:svn:https://svn.codelutin.com/echobase/tags/echobase-2.6 </connection> <developerConnection> - scm:svn:https://svn.codelutin.com/echobase/trunk + scm:svn:https://svn.codelutin.com/echobase/tags/echobase-2.6 </developerConnection> </scm>

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r1021 - in trunk: . echobase-domain/src/main/java/fr/ifremer/echobase/persistence/migration/workingDb echobase-domain/src/main/resources/migration echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser echobase-ui/src/license
by tchemit＠users.forge.codelutin.com April 22, 2014

April 22, 2014

Author: tchemit Date: 2014-04-22 22:59:06 +0200 (Tue, 22 Apr 2014) New Revision: 1021 Url: http://forge.codelutin.com/projects/echobase/repository/revisions/1021 Log: prepare release Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/persistence/migration/workingDb/MigrationCallBackForVersion2_6_1.java trunk/echobase-domain/src/main/resources/migration/postgis-structure-2.6.1.sql trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/SpeciesExportRow.java trunk/echobase-ui/src/license/THIRD-PARTY.properties trunk/pom.xml Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/persistence/migration/workingDb/MigrationCallBackForVersion2_6_1.java =================================================================== --- trunk/echobase-domain/src/main/java/fr/ifremer/echobase/persistence/migration/workingDb/MigrationCallBackForVersion2_6_1.java 2014-04-22 20:48:57 UTC (rev 1020) +++ trunk/echobase-domain/src/main/java/fr/ifremer/echobase/persistence/migration/workingDb/MigrationCallBackForVersion2_6_1.java 2014-04-22 20:59:06 UTC (rev 1021) @@ -1,5 +1,26 @@ package fr.ifremer.echobase.persistence.migration.workingDb; +/* + * #%L + * EchoBase :: Domain + * %% + * Copyright (C) 2011 - 2014 Ifremer, Codelutin + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero 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 Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + * #L% + */ + import fr.ifremer.echobase.entities.EchoBaseUserTopiaPersistenceContext; import fr.ifremer.echobase.io.EchoBaseIOUtil; import org.nuiton.topia.persistence.TopiaException; Modified: trunk/echobase-domain/src/main/resources/migration/postgis-structure-2.6.1.sql =================================================================== --- trunk/echobase-domain/src/main/resources/migration/postgis-structure-2.6.1.sql 2014-04-22 20:48:57 UTC (rev 1020) +++ trunk/echobase-domain/src/main/resources/migration/postgis-structure-2.6.1.sql 2014-04-22 20:59:06 UTC (rev 1021) @@ -1,3 +1,23 @@ +--- +-- #%L +-- EchoBase :: Domain +-- %% +-- Copyright (C) 2011 - 2014 Ifremer, Codelutin +-- %% +-- This program is free software: you can redistribute it and/or modify +-- it under the terms of the GNU Affero 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 Public License for more details. +-- +-- You should have received a copy of the GNU Affero General Public License +-- along with this program. If not, see <http://www.gnu.org/licenses/>. +-- #L% +--- -- -- echobase_delete_voyage trigger -- Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/SpeciesExportRow.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/SpeciesExportRow.java 2014-04-22 20:48:57 UTC (rev 1020) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/SpeciesExportRow.java 2014-04-22 20:59:06 UTC (rev 1021) @@ -1,5 +1,26 @@ package fr.ifremer.echobase.services.service.exportCoser; +/* + * #%L + * EchoBase :: Services + * %% + * Copyright (C) 2011 - 2014 Ifremer, Codelutin + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero 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 Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + * #L% + */ + import fr.ifremer.echobase.entities.references.Species; /** Modified: trunk/echobase-ui/src/license/THIRD-PARTY.properties =================================================================== --- trunk/echobase-ui/src/license/THIRD-PARTY.properties 2014-04-22 20:48:57 UTC (rev 1020) +++ trunk/echobase-ui/src/license/THIRD-PARTY.properties 2014-04-22 20:59:06 UTC (rev 1021) @@ -1,21 +1,26 @@ # Generated by org.codehaus.mojo.license.AddThirdPartyMojo #------------------------------------------------------------------------------- # Already used licenses in project : +# - AL 2.0 # - Affero General Public License (AGPL) # - Apache License 2.0 +# - Apache License, version 2.0 # - Apache Software License - Version 2.0 # - BSD License # - BSD-style license -# - CDDL + GPLv2 with classpath exception -# - CDDL/GPLv2+CE +# - CDDL # - COMMON DEVELOPMENT AND DISTRIBUTION LICENSE (CDDL) Version 1.0 # - Common Development and Distribution License # - Common Public License Version 1.0 +# - Eclipse Distribution License (EDL), Version 1.0 +# - Eclipse Public License (EPL), Version 1.0 # - Eclipse Public License - Version 1.0 +# - GNU Affero General Public License v3 # - GNU General Public License, Version 2 with the Classpath Exception -# - GNU Lesser General Public License, version 2.1 +# - GNU Lesser General Public Licence +# - GNU Lesser General Public License (LGPL), version 2.1 # - GNU Library or Lesser General Public License -# - General Public License (GPL) +# - GPLv2+CE # - Indiana University Extreme! Lab Software License, vesion 1.1.1 # - Lesser General Public License (LGPL) v 3.0 # - Lesser General Public License (LPGL) @@ -23,16 +28,15 @@ # - MIT License # - MPL 1.1 # - New BSD License +# - Public Domain # - The Apache Software License, Version 1.1 # - The Apache Software License, Version 2.0 # - The H2 License, Version 1.0 -# - license.txt #------------------------------------------------------------------------------- # Please fill the missing licenses for dependencies : # # -#Sun Dec 29 16:57:17 CET 2013 +#Tue Apr 22 22:57:39 CEST 2014 commons-primitives--commons-primitives--1.0=The Apache Software License, Version 2.0 dom4j--dom4j--1.6.1=BSD License -javassist--javassist--3.11.0.GA=The Apache Software License, Version 2.0 oro--oro--2.0.8=The Apache Software License, Version 2.0 Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-04-22 20:48:57 UTC (rev 1020) +++ trunk/pom.xml 2014-04-22 20:59:06 UTC (rev 1021) @@ -138,7 +138,7 @@  - <topiaVersion>3.0-SNAPSHOT</topiaVersion> + <topiaVersion>3.0-beta-3</topiaVersion> <nuitonUtilsVersion>3.0-rc-2</nuitonUtilsVersion> <nuitonI18nVersion>3.0</nuitonI18nVersion> <nuitonWebVersion>1.16</nuitonWebVersion>

1 0

r1020 - in trunk: . echobase-ui
by tchemit＠users.forge.codelutin.com April 22, 2014

April 22, 2014

Author: tchemit Date: 2014-04-22 22:48:57 +0200 (Tue, 22 Apr 2014) New Revision: 1020 Url: http://forge.codelutin.com/projects/echobase/repository/revisions/1020 Log: use fixed i18n coser version Modified: trunk/echobase-ui/pom.xml trunk/pom.xml Modified: trunk/echobase-ui/pom.xml =================================================================== --- trunk/echobase-ui/pom.xml 2014-04-22 20:27:38 UTC (rev 1019) +++ trunk/echobase-ui/pom.xml 2014-04-22 20:48:57 UTC (rev 1020) @@ -186,11 +186,6 @@ <version>${project.version}</version> </dependency> -  - <dependency> <groupId>org.nuiton.web</groupId> <artifactId>nuiton-struts2</artifactId> @@ -361,8 +356,7 @@ <devMode>false</devMode>  -  -  + <i18n.failsIfWarning>true</i18n.failsIfWarning> </properties> </profile> Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-04-22 20:27:38 UTC (rev 1019) +++ trunk/pom.xml 2014-04-22 20:48:57 UTC (rev 1020) @@ -185,7 +185,7 @@ <dependency> <groupId>fr.ifremer.coser</groupId> <artifactId>coser-business</artifactId> - <version>1.5-SNAPSHOT</version> + <version>1.5-alpha-3</version> </dependency>

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r1019 - in trunk: . echobase-domain/src/main/java/fr/ifremer/echobase/entities echobase-domain/src/main/java/fr/ifremer/echobase/entities/data echobase-services/src/main/java/fr/ifremer/echobase/services/service echobase-services/src/test/java/fr/ifremer/echobase/services echobase-services/src/test/java/fr/ifremer/echobase/services/service/exportdb echobase-services/src/test/java/fr/ifremer/echobase/services/service/importdata
by tchemit＠users.forge.codelutin.com April 22, 2014

April 22, 2014

Author: tchemit Date: 2014-04-22 22:27:38 +0200 (Tue, 22 Apr 2014) New Revision: 1019 Url: http://forge.codelutin.com/projects/echobase/repository/revisions/1019 Log: updates to last topia api Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/AbstractEchoBaseDao.java trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/ExportQueryTopiaDao.java trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/CategoryTopiaDao.java trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/EchotypeTopiaDao.java trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/VoyageImpl.java trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/UserDbPersistenceService.java trunk/echobase-services/src/test/java/fr/ifremer/echobase/services/EchoBaseTestServiceSupport.java trunk/echobase-services/src/test/java/fr/ifremer/echobase/services/service/exportdb/ExportDbServiceTest.java trunk/echobase-services/src/test/java/fr/ifremer/echobase/services/service/importdata/AbstractImportDataServiceIT.java trunk/pom.xml Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/AbstractEchoBaseDao.java =================================================================== --- trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/AbstractEchoBaseDao.java 2014-04-22 20:25:28 UTC (rev 1018) +++ trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/AbstractEchoBaseDao.java 2014-04-22 20:27:38 UTC (rev 1019) @@ -21,10 +21,12 @@ * #L% */ +import org.nuiton.topia.persistence.TopiaEntity; import org.nuiton.topia.persistence.TopiaNoResultException; import org.nuiton.topia.persistence.internal.AbstractTopiaDao; -import org.nuiton.topia.persistence.TopiaEntity; +import org.nuiton.topia.persistence.pager.TopiaPagerBean; +import java.util.List; import java.util.Map; /** @@ -49,4 +51,9 @@ public <K> K findAny(String hql, Map<String, Object> hqlParameters) throws TopiaNoResultException { return super.findAny(hql, hqlParameters); } + + @Override + public <K> List<K> find(String hql, Map<String, Object> hqlParameters, TopiaPagerBean pager) { + return super.find(hql, hqlParameters, pager); + } } Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/ExportQueryTopiaDao.java =================================================================== --- trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/ExportQueryTopiaDao.java 2014-04-22 20:25:28 UTC (rev 1018) +++ trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/ExportQueryTopiaDao.java 2014-04-22 20:27:38 UTC (rev 1019) @@ -26,27 +26,11 @@ public class ExportQueryTopiaDao extends AbstractExportQueryTopiaDao<ExportQuery> { public boolean isQueryExists(String queryName) throws TopiaException { - -// String hql = "SELECT COUNT(*)" + -// " FROM " + getTopiaEntityEnum().getImplementationFQN() + -// " WHERE " + ExportQuery.PROPERTY_NAME + " = :name"; -// -// boolean result = existsByQuery(hql, new String[]{"name", queryName}); -// return result; boolean result = forNameEquals(queryName).exists(); return result; } public boolean isQueryExists(String id, String queryName) throws TopiaException { - -// String hql = "SELECT COUNT(*)" + -// " FROM " + getTopiaEntityEnum().getImplementationFQN() + -// " WHERE " + ExportQuery.PROPERTY_NAME + " = :name" + -// " AND " + ExportQuery.PROPERTY_TOPIA_ID + " != :id"; -// -// boolean result = existsByQuery( -// hql, -// new String[]{"name", queryName, "id", id}); boolean result = forNameEquals(queryName). addNotEquals(ExportQuery.PROPERTY_TOPIA_ID, id). exists(); Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/CategoryTopiaDao.java =================================================================== --- trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/CategoryTopiaDao.java 2014-04-22 20:25:28 UTC (rev 1018) +++ trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/CategoryTopiaDao.java 2014-04-22 20:27:38 UTC (rev 1019) @@ -32,7 +32,6 @@ public List<Category> getCategoryUsingEchotype(Voyage voyage) throws TopiaException { String hql = "SELECT DISTINCT c FROM VoyageImpl v, CategoryImpl c WHERE " + "v = :voyage AND c.echotype in elements(v.echotype)"; -// List<Category> result = findAllByQuery(hql, "voyage", voyage); List<Category> result = forHql(hql, "voyage", voyage).findAll(); return result; } @@ -41,7 +40,6 @@ String hql = "SELECT COUNT(DISTINCT c) FROM VoyageImpl v, CategoryImpl c WHERE " + "v = :voyage AND c.echotype in elements(v.echotype)"; try { -// long result = countByQuery(hql, "voyage", voyage); Long result = findUnique(hql, TopiaUtil.convertPropertiesArrayToMap("voyage", voyage)); return result; } catch (TopiaException e) { Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/EchotypeTopiaDao.java =================================================================== --- trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/EchotypeTopiaDao.java 2014-04-22 20:25:28 UTC (rev 1018) +++ trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/EchotypeTopiaDao.java 2014-04-22 20:27:38 UTC (rev 1019) @@ -36,7 +36,6 @@ @Override public Echotype findByIdAndSpecies(Integer id, Species species) throws TopiaException { -// List<E> allById = findAllById(id); List<Echotype> allById = forIdEquals(id).findAll(); Echotype result = null; for (Echotype echotype : allById) { Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/VoyageImpl.java =================================================================== --- trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/VoyageImpl.java 2014-04-22 20:25:28 UTC (rev 1018) +++ trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/VoyageImpl.java 2014-04-22 20:27:38 UTC (rev 1019) @@ -30,7 +30,6 @@ import java.util.Collection; import java.util.Date; -import java.util.List; import java.util.Set; /** @@ -138,7 +137,7 @@ for (Transit t : transit) { Transect transect = t.getTransect(vessel); - List<Operation> operations = transect.getOperation(); + Collection<Operation> operations = transect.getOperation(); result.addAll(operations); } } Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/UserDbPersistenceService.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/UserDbPersistenceService.java 2014-04-22 20:25:28 UTC (rev 1018) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/UserDbPersistenceService.java 2014-04-22 20:27:38 UTC (rev 1019) @@ -25,7 +25,6 @@ import com.google.common.base.Optional; import com.google.common.base.Predicate; import com.google.common.collect.Iterables; -import com.google.common.collect.Lists; import com.google.common.collect.Maps; import com.google.common.collect.Sets; import fr.ifremer.echobase.EchoBaseTechnicalException; @@ -182,7 +181,7 @@ } public Cell getCellContainsResult(Result result) { - return persistenceContext.getCellDao().findContainsResult(result); + return persistenceContext.getCellDao().forResultContains(result).findAnyOrNull(); } public long countVoyageOrphanCells(final Voyage voyage) { @@ -318,7 +317,7 @@ } public DataProcessing getDataProcessingContainsCell(Cell cell) { - DataProcessing dataAcquisition = persistenceContext.getDataProcessingDao().findContainsCell(cell); + DataProcessing dataAcquisition = persistenceContext.getDataProcessingDao().forCellContains(cell).findAnyOrNull(); return dataAcquisition; } @@ -466,7 +465,7 @@ } public Operation getOperationContainsSample(Sample sample) { - Operation dataAcquisition = persistenceContext.getOperationDao().findContainsSample(sample); + Operation dataAcquisition = persistenceContext.getOperationDao().forSampleContains(sample).findAnyOrNull(); return dataAcquisition; } @@ -507,16 +506,10 @@ return persistenceContext.getResultDao().findByTopiaId(id); } - public List<Result> getResultsForMissionAndDatametadata(Mission mission, DataMetadata metas) { - // TODO - return Lists.newArrayList(); + public List<Result> getResultsForMissionAndDatametadata(Mission mission, DataMetadata dataMetadata) { + return persistenceContext.getResultDao().findAllWithMissionAndDatametadata(mission, dataMetadata); } - public Map<String, Result> getResultForCellAndMetadata(Set<String> cellIds, DataMetadata standardDeviationDataMetadata) { - // TODO - return Maps.newTreeMap(); - } - public Result createResult(Result result) { Result resultCreated = persistenceContext.getResultDao().create(result); return resultCreated; @@ -660,11 +653,11 @@ } public Transect getTransectContainsOperation(Operation operation) { - return persistenceContext.getTransectDao().findContainsOperation(operation); + return persistenceContext.getTransectDao().forOperationContains(operation).findAnyOrNull(); } public Transect getTransectContainsDataAcquisition(DataAcquisition dataAcquisition) { - return persistenceContext.getTransectDao().findContainsDataAcquisition(dataAcquisition); + return persistenceContext.getTransectDao().forDataAcquisitionContains(dataAcquisition).findAnyOrNull(); } public Transect createTransect(Transect transect) { @@ -685,7 +678,7 @@ } public Transit getTransitContainsTransect(Transect transect) { - return persistenceContext.getTransitDao().findContainsTransect(transect); + return persistenceContext.getTransitDao().forTransectContains(transect).findAnyOrNull(); } public Transit createTransit(Transit transit) { Modified: trunk/echobase-services/src/test/java/fr/ifremer/echobase/services/EchoBaseTestServiceSupport.java =================================================================== --- trunk/echobase-services/src/test/java/fr/ifremer/echobase/services/EchoBaseTestServiceSupport.java 2014-04-22 20:25:28 UTC (rev 1018) +++ trunk/echobase-services/src/test/java/fr/ifremer/echobase/services/EchoBaseTestServiceSupport.java 2014-04-22 20:27:38 UTC (rev 1019) @@ -54,6 +54,7 @@ import java.io.IOException; import java.io.InputStream; import java.util.Arrays; +import java.util.Collection; import java.util.List; import java.util.Set; import java.util.zip.GZIPInputStream; @@ -240,8 +241,8 @@ Preconditions.checkNotNull(voyageId); Voyage voyage = serviceContext.getEchoBaseUserPersistenceContext().getVoyageDao().findByTopiaId(voyageId); Preconditions.checkArgument(!voyage.isTransitEmpty()); - List<Transit> transits = voyage.getTransit(); - Transit transit = transits.get(0); + Collection<Transit> transits = voyage.getTransit(); + Transit transit = transits.iterator().next(); return transit.getTopiaId(); } Modified: trunk/echobase-services/src/test/java/fr/ifremer/echobase/services/service/exportdb/ExportDbServiceTest.java =================================================================== --- trunk/echobase-services/src/test/java/fr/ifremer/echobase/services/service/exportdb/ExportDbServiceTest.java 2014-04-22 20:25:28 UTC (rev 1018) +++ trunk/echobase-services/src/test/java/fr/ifremer/echobase/services/service/exportdb/ExportDbServiceTest.java 2014-04-22 20:27:38 UTC (rev 1019) @@ -94,7 +94,7 @@ Voyage voyage = persistenceService.getVoyage(getVoyageId()); Assert.assertNotNull(voyage); - Transect transect = voyage.getTransit().get(0).getTransect().get(0); + Transect transect = voyage.getTransit().iterator().next().getTransect().iterator().next(); Assert.assertNotNull(transect); List<AcousticInstrument> acousticInstruments = serviceContext.getEchoBaseUserPersistenceContext().getAcousticInstrumentDao().findAll(); Modified: trunk/echobase-services/src/test/java/fr/ifremer/echobase/services/service/importdata/AbstractImportDataServiceIT.java =================================================================== --- trunk/echobase-services/src/test/java/fr/ifremer/echobase/services/service/importdata/AbstractImportDataServiceIT.java 2014-04-22 20:25:28 UTC (rev 1018) +++ trunk/echobase-services/src/test/java/fr/ifremer/echobase/services/service/importdata/AbstractImportDataServiceIT.java 2014-04-22 20:27:38 UTC (rev 1019) @@ -165,7 +165,7 @@ transit = serviceContext.getEchoBaseUserPersistenceContext().getTransitDao().create(); voyage.addTransit(transit); } else { - transit = voyage.getTransit().get(0); + transit = voyage.getTransit().iterator().next(); } if (transit.isTransectEmpty()) { @@ -174,7 +174,7 @@ transect = serviceContext.getEchoBaseUserPersistenceContext().getTransectDao().create(); transit.addTransect(transect); } else { - transect = transit.getTransect().get(0); + transect = transit.getTransect().iterator().next(); } if (transect.isDataAcquisitionEmpty()) { Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-04-22 20:25:28 UTC (rev 1018) +++ trunk/pom.xml 2014-04-22 20:27:38 UTC (rev 1019) @@ -138,7 +138,7 @@  - <topiaVersion>3.0-beta-2</topiaVersion> + <topiaVersion>3.0-SNAPSHOT</topiaVersion> <nuitonUtilsVersion>3.0-rc-2</nuitonUtilsVersion> <nuitonI18nVersion>3.0</nuitonI18nVersion> <nuitonWebVersion>1.16</nuitonWebVersion> @@ -405,7 +405,7 @@ <plugin> <groupId>org.nuiton.eugene</groupId> <artifactId>eugene-maven-plugin</artifactId> - <version>2.7.4</version> + <version>2.8</version> <dependencies> <dependency> <groupId>org.nuiton.topia</groupId>

1 0

r1018 - in trunk: echobase-domain/src/main/java/fr/ifremer/echobase/entities/data echobase-domain/src/main/xmi echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser
by tchemit＠users.forge.codelutin.com April 22, 2014

April 22, 2014

Author: tchemit Date: 2014-04-22 22:25:28 +0200 (Tue, 22 Apr 2014) New Revision: 1018 Url: http://forge.codelutin.com/projects/echobase/repository/revisions/1018 Log: fixes #4821 Added: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/IndicatorExportModel.java trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/IndicatorExportRow.java Removed: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportModel.java trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportRow.java trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportModel.java trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportRow.java Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/ResultTopiaDao.java trunk/echobase-domain/src/main/xmi/echobase.properties trunk/echobase-domain/src/main/xmi/echobase.zargo trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/ExportCoserService.java Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/ResultTopiaDao.java =================================================================== --- trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/ResultTopiaDao.java 2014-04-22 15:47:09 UTC (rev 1017) +++ trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/data/ResultTopiaDao.java 2014-04-22 20:25:28 UTC (rev 1018) @@ -22,6 +22,7 @@ */ import fr.ifremer.echobase.entities.references.DataMetadata; +import fr.ifremer.echobase.entities.references.Mission; import java.util.List; import java.util.Set; @@ -31,13 +32,6 @@ public List<Result> findAllWithCategoryCellAndDataMetadata(Set<String> cellIds, DataMetadata requiredDataMetadata, List<String> categoryIds) { - -// String query = createSimpleQuery(null) + " WHERE cell.id IN :cell AND dataMetadata = :dataMetadata"; -// return findAllByQuery( -// query + " AND category.id IN :category", -// Result.PROPERTY_CELL, cellIds, -// Result.PROPERTY_DATA_METADATA, requiredDataMetadata, -// Result.PROPERTY_CATEGORY, categoryIds); return forEquals(Result.PROPERTY_DATA_METADATA, requiredDataMetadata). addTopiaIdIn(Result.PROPERTY_CELL, cellIds). addTopiaIdIn(Result.PROPERTY_CATEGORY, categoryIds). @@ -46,16 +40,15 @@ public List<Result> findAllWithNoCategoryCellAndDataMetadata(Set<String> cellIds, DataMetadata requiredDataMetadata) { - -// String query = createSimpleQuery(null) + " WHERE cell.id IN :cell AND dataMetadata = :dataMetadata"; -// return findAllByQuery( -// query + " AND category IS NULL", -// Result.PROPERTY_CELL, cellIds, -// Result.PROPERTY_DATA_METADATA, requiredDataMetadata); return forEquals(Result.PROPERTY_DATA_METADATA, requiredDataMetadata). addTopiaIdIn(Result.PROPERTY_CELL, cellIds). addNull(Result.PROPERTY_CATEGORY). findAll(); } + public List<Result> findAllWithMissionAndDatametadata(Mission mission, DataMetadata dataMetadata) { + return forEquals(Result.PROPERTY_CELL + "." + Cell.PROPERTY_VOYAGE + "." + Voyage.PROPERTY_MISSION, mission). + addEquals(Result.PROPERTY_DATA_METADATA, dataMetadata). + findAll(); + } } Modified: trunk/echobase-domain/src/main/xmi/echobase.properties =================================================================== --- trunk/echobase-domain/src/main/xmi/echobase.properties 2014-04-22 15:47:09 UTC (rev 1017) +++ trunk/echobase-domain/src/main/xmi/echobase.properties 2014-04-22 20:25:28 UTC (rev 1018) @@ -32,11 +32,11 @@ ### Ordered attributes ######################################################## ############################################################################### -fr.ifremer.echobase.entities.data.Voyage.attribute.transit.stereotype=ordered +#fr.ifremer.echobase.entities.data.Voyage.attribute.transit.stereotype=ordered fr.ifremer.echobase.entities.data.Voyage.attribute.transit.tagvalue.orderBy=startTime -fr.ifremer.echobase.entities.data.Transit.attribute.transect.stereotype=ordered +#fr.ifremer.echobase.entities.data.Transit.attribute.transect.stereotype=ordered fr.ifremer.echobase.entities.data.Transit.attribute.transect.tagvalue.orderBy=timeCoverageStart -fr.ifremer.echobase.entities.data.Transect.attribute.operation.stereotype=ordered +#fr.ifremer.echobase.entities.data.Transect.attribute.operation.stereotype=ordered fr.ifremer.echobase.entities.data.Transect.attribute.operation.tagvalue.orderBy=gearShootingStartTime ############################################################################### Modified: trunk/echobase-domain/src/main/xmi/echobase.zargo =================================================================== (Binary files differ) Deleted: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportModel.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportModel.java 2014-04-22 15:47:09 UTC (rev 1017) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportModel.java 2014-04-22 20:25:28 UTC (rev 1018) @@ -1,47 +0,0 @@ -package fr.ifremer.echobase.services.service.exportCoser; - -/* - * #%L - * EchoBase :: Services - * %% - * Copyright (C) 2011 - 2014 Ifremer, Codelutin, Chemit Tony - * %% - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU Affero 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 Public License for more details. - * - * You should have received a copy of the GNU Affero General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - * #L% - */ - -import fr.ifremer.echobase.csv.EchoBaseCsvUtil; -import org.nuiton.csv.ext.AbstractExportModel; - -/** - * Created on 3/20/14. - * - * @author Tony Chemit <chemit(a)codelutin.com> - * @since 2.6 - */ -public class CommunityIndicatorExportModel extends AbstractExportModel<CommunityIndicatorExportRow> { - - public CommunityIndicatorExportModel(char separator) { - super(separator); - newColumnForExport("Campagne", EchoBaseCsvUtil.<CommunityIndicatorExportRow, String>newBeanProperty(CommunityIndicatorExportRow.PROPERTY_MISSION_NAME)); - newColumnForExport("Indicateur", EchoBaseCsvUtil.<CommunityIndicatorExportRow, String>newBeanProperty(CommunityIndicatorExportRow.PROPERTY_INDICATOR_NAME)); - newColumnForExport("Espece", CommunityIndicatorExportRow.PROPERTY_SPECIES, EchoBaseCsvUtil.SPECIES_TO_COSER_CODE); - newColumnForExport("Strate", CommunityIndicatorExportRow.PROPERTY_STRATUM); - newColumnForExport("Annee", CommunityIndicatorExportRow.PROPERTY_DATE, EchoBaseCsvUtil.YEAR); - newColumnForExport("Estimation", CommunityIndicatorExportRow.PROPERTY_ESTIMATION); - newColumnForExport("EcartType", CommunityIndicatorExportRow.PROPERTY_STANDARD_DEVIATION); - newColumnForExport("CV", CommunityIndicatorExportRow.PROPERTY_CV); - } - -} \ No newline at end of file Deleted: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportRow.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportRow.java 2014-04-22 15:47:09 UTC (rev 1017) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportRow.java 2014-04-22 20:25:28 UTC (rev 1018) @@ -1,127 +0,0 @@ -package fr.ifremer.echobase.services.service.exportCoser; - -/* - * #%L - * EchoBase :: Services - * %% - * Copyright (C) 2011 - 2014 Ifremer, Codelutin, Chemit Tony - * %% - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU Affero 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 Public License for more details. - * - * You should have received a copy of the GNU Affero General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - * #L% - */ - -import fr.ifremer.echobase.entities.references.DataMetadata; -import fr.ifremer.echobase.entities.references.Mission; -import fr.ifremer.echobase.entities.references.Species; - -import java.util.Date; - -/** - * Created on 3/20/14. - * - * @author Tony Chemit <chemit(a)codelutin.com> - * @since 2.6 - */ -public class CommunityIndicatorExportRow { - - public static final String PROPERTY_MISSION_NAME = "mission." + Mission.PROPERTY_NAME; - - public static final String PROPERTY_INDICATOR_NAME = "indicator." + DataMetadata.PROPERTY_NAME; - - public static final String PROPERTY_SPECIES = "species"; - - public static final String PROPERTY_STRATUM = "stratum"; - - public static final String PROPERTY_DATE = "date"; - - public static final String PROPERTY_ESTIMATION = "estimation"; - - public static final String PROPERTY_STANDARD_DEVIATION = "standardDeviation"; - - public static final String PROPERTY_CV = "cv"; - - protected Mission mission; - - protected DataMetadata indicator; - - protected Species species; - - protected String stratum; - - protected Date date; - - protected float estimation; - - protected float standardDeviation; - - public Mission getMission() { - return mission; - } - - public DataMetadata getIndicator() { - return indicator; - } - - public Species getSpecies() { - return species; - } - - public String getStratum() { - return stratum; - } - - public Date getDate() { - return date; - } - - public float getEstimation() { - return estimation; - } - - public float getStandardDeviation() { - return standardDeviation; - } - - public float getCv() { - return standardDeviation / estimation; - } - - public void setMission(Mission mission) { - this.mission = mission; - } - - public void setIndicator(DataMetadata indicator) { - this.indicator = indicator; - } - - public void setSpecies(Species species) { - this.species = species; - } - - public void setStratum(String stratum) { - this.stratum = stratum; - } - - public void setDate(Date date) { - this.date = date; - } - - public void setEstimation(float estimation) { - this.estimation = estimation; - } - - public void setStandardDeviation(float standardDeviation) { - this.standardDeviation = standardDeviation; - } -} Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/ExportCoserService.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/ExportCoserService.java 2014-04-22 15:47:09 UTC (rev 1017) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/ExportCoserService.java 2014-04-22 20:25:28 UTC (rev 1018) @@ -85,8 +85,8 @@ model.setNbSteps(4 + 4 + // raw data - model.getPopulationIndicator().size() + - model.getCommunityIndicator().size()); + model.getPopulationIndicator().size() + 1 + + model.getCommunityIndicator().size() + 1); Mission mission = persistenceService.getMission(model.getMissionId()); Preconditions.checkNotNull(mission); @@ -119,10 +119,10 @@ model.incrementsProgress(); // 7 - create archive - File zipFile = generateArchive(mission, - project, - tempDirectory, - echRMapsDir); + File zipFile = generateArchive( + project, + tempDirectory, + echRMapsDir); model.setExportFile(zipFile); model.incrementsProgress(); @@ -155,8 +155,7 @@ project.setAuthor("EchoBase user: " + model.getUserName()); project.setCreationDate(serviceContext.newDate()); project.setComment("Created by Echobase application (db: " + getUserDbUrl() + ")"); - //FIXME when will publish some raw data. - project.setPubliableResult(false); + project.setPubliableResult(true); project.save(); @@ -166,8 +165,7 @@ return project; } - protected File generateArchive(Mission mission, - EchoBaseProject project, + protected File generateArchive(EchoBaseProject project, File tempDirectory, File echRMapsDir) throws IOException { @@ -184,7 +182,7 @@ } //------------------------------------------------------------------------// - //--- Extract population indicators --------------------------------------// + //--- Extract indicators -------------------------------------------------// //------------------------------------------------------------------------// protected void extractPopulationIndicators(ExportCoserConfiguration model, @@ -196,15 +194,16 @@ log.info("Generate " + exportFile); } - PopulationIndicatorExportModel exportModel = new PopulationIndicatorExportModel(getCsvSeparator()); + IndicatorExportModel exportModel = new IndicatorExportModel(getCsvSeparator()); - List<PopulationIndicatorExportRow> rows = Lists.newArrayList(); + List<IndicatorExportRow> rows = Lists.newArrayList(); Set<String> indicators = model.getPopulationIndicator(); for (String indicator : indicators) { - loadPopulationIndicatorValues(mission, indicator, rows); + loadIndicatorValues(mission, indicator, rows); + model.incrementsProgress(); } - Export<PopulationIndicatorExportRow> export = Export.newExport(exportModel, rows); + Export<IndicatorExportRow> export = Export.newExport(exportModel, rows); try { export.write(exportFile, Charsets.UTF_8); } catch (Exception e) { @@ -213,60 +212,6 @@ model.incrementsProgress(); } - protected void loadPopulationIndicatorValues(Mission mission, - String indicator, - List<PopulationIndicatorExportRow> rows) { - - if (log.isInfoEnabled()) { - log.info("Extract population indicator: " + indicator); - } - DataMetadata dataMetadata = persistenceService.getDataMetadata(indicator); - DataMetadata standardDeviationDataMetadata = - persistenceService.tryToGetDataMetadataByName(dataMetadata.getName() + "_stdev"); - - Map<String, PopulationIndicatorExportRow> rowsByCellId = Maps.newTreeMap(); - - List<Result> results = persistenceService.getResultsForMissionAndDatametadata(mission, dataMetadata); - - for (Result result : results) { - // create row - PopulationIndicatorExportRow row = new PopulationIndicatorExportRow(); - row.setMission(mission); - row.setIndicator(dataMetadata); - Species species = result.getCategory().getSpeciesCategory().getSpecies(); - row.setSpecies(species); - row.setStratum("Total"); //FIXME How to find this ? - row.setDate(new Date()); //FIXME How to find back date - row.setEstimation(Float.valueOf(result.getResultValue())); - row.setStandardDeviation(0); - if (standardDeviationDataMetadata != null) { - rowsByCellId.put(result.getCell().getTopiaId(), row); - } - } - - if (standardDeviationDataMetadata != null) { - - // find standard deviation values - - Map<String, Result> deviationResults = persistenceService.getResultForCellAndMetadata( - rowsByCellId.keySet(), standardDeviationDataMetadata); - - for (Map.Entry<String, Result> entry : deviationResults.entrySet()) { - String cellId = entry.getKey(); - Result deviationResult = entry.getValue(); - if (deviationResult != null) { - PopulationIndicatorExportRow row = rowsByCellId.get(cellId); - row.setStandardDeviation(Float.valueOf(deviationResult.getResultValue())); - } - } - } - rows.addAll(rows); - } - - //------------------------------------------------------------------------// - //--- Extract community indicators ---------------------------------------// - //------------------------------------------------------------------------// - protected void extractCommunityIndicators(ExportCoserConfiguration model, EchoBaseProject echoBaseProject, Mission mission) { @@ -276,15 +221,16 @@ if (log.isInfoEnabled()) { log.info("Generate " + exportFile); } - CommunityIndicatorExportModel exportModel = new CommunityIndicatorExportModel(getCsvSeparator()); + IndicatorExportModel exportModel = new IndicatorExportModel(getCsvSeparator()); - List<CommunityIndicatorExportRow> rows = Lists.newArrayList(); + List<IndicatorExportRow> rows = Lists.newArrayList(); Set<String> indicators = model.getCommunityIndicator(); for (String indicator : indicators) { - loadCommunityIndicatorValues(mission, indicator, rows); + loadIndicatorValues(mission, indicator, rows); + model.incrementsProgress(); } - Export<CommunityIndicatorExportRow> export = Export.newExport(exportModel, rows); + Export<IndicatorExportRow> export = Export.newExport(exportModel, rows); try { export.write(exportFile, Charsets.UTF_8); } catch (Exception e) { @@ -294,55 +240,61 @@ model.incrementsProgress(); } - protected void loadCommunityIndicatorValues(Mission mission, - String indicator, - List<CommunityIndicatorExportRow> rows) { + protected void loadIndicatorValues(Mission mission, + String indicator, + List<IndicatorExportRow> rows) { + DataMetadata dataMetadata = persistenceService.getDataMetadata(indicator); if (log.isInfoEnabled()) { - log.info("Extract community indicator: " + indicator); + log.info("Extract indicator: " + dataMetadata.getName()); } - DataMetadata dataMetadata = persistenceService.getDataMetadata(indicator); DataMetadata standardDeviationDataMetadata = persistenceService.tryToGetDataMetadataByName(dataMetadata.getName() + "_stdev"); - Map<String, CommunityIndicatorExportRow> rowsByCellId = Maps.newTreeMap(); + Map<Species, IndicatorExportRow> rowsBySpecies = Maps.newHashMap(); List<Result> results = persistenceService.getResultsForMissionAndDatametadata(mission, dataMetadata); for (Result result : results) { - // create row - CommunityIndicatorExportRow row = new CommunityIndicatorExportRow(); - row.setMission(mission); - row.setIndicator(dataMetadata); Species species = result.getCategory().getSpeciesCategory().getSpecies(); - row.setSpecies(species); - row.setStratum("Total"); //FIXME How to find this ? - row.setDate(new Date()); //FIXME How to find back date - row.setEstimation(Float.valueOf(result.getResultValue())); - row.setStandardDeviation(0); - if (standardDeviationDataMetadata != null) { - rowsByCellId.put(result.getCell().getTopiaId(), row); + IndicatorExportRow row = rowsBySpecies.get(species); + if (row == null) { + row = new IndicatorExportRow(); + rowsBySpecies.put(species, row); + row.setMission(mission); + row.setIndicator(dataMetadata); + row.setSpecies(species); + row.setStratum("Total"); + row.setDate(result.getCell().getVoyage().getEndDate()); + row.setStandardDeviation(0); } + Float resultValue = Float.valueOf(result.getResultValue()); + row.setEstimation(row.getEstimation() + resultValue); } if (standardDeviationDataMetadata != null) { // find standard deviation values - Map<String, Result> deviationResults = persistenceService.getResultForCellAndMetadata( - rowsByCellId.keySet(), standardDeviationDataMetadata); + List<Result> deviationResults = persistenceService.getResultsForMissionAndDatametadata( + mission, standardDeviationDataMetadata); - for (Map.Entry<String, Result> entry : deviationResults.entrySet()) { - String cellId = entry.getKey(); - Result deviationResult = entry.getValue(); - if (deviationResult != null) { - CommunityIndicatorExportRow row = rowsByCellId.get(cellId); - row.setStandardDeviation(Float.valueOf(deviationResult.getResultValue())); + for (Result result : deviationResults) { + Species species = result.getCategory().getSpeciesCategory().getSpecies(); + IndicatorExportRow row = rowsBySpecies.get(species); + if (row == null) { + log.warn(String.format("Could not find result for meta %s / species %s", + dataMetadata.getName(), + species.getBaracoudaCode())); + continue; } + Float resultValue = Float.valueOf(result.getResultValue()); + row.setStandardDeviation(row.getStandardDeviation() + resultValue); } } - rows.addAll(rows); + + rows.addAll(rowsBySpecies.values()); } //------------------------------------------------------------------------// Copied: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/IndicatorExportModel.java (from rev 1013, trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportModel.java) =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/IndicatorExportModel.java (rev 0) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/IndicatorExportModel.java 2014-04-22 20:25:28 UTC (rev 1018) @@ -0,0 +1,47 @@ +package fr.ifremer.echobase.services.service.exportCoser; + +/* + * #%L + * EchoBase :: Services + * %% + * Copyright (C) 2011 - 2014 Ifremer, Codelutin, Chemit Tony + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero 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 Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + * #L% + */ + +import fr.ifremer.echobase.csv.EchoBaseCsvUtil; +import org.nuiton.csv.ext.AbstractExportModel; + +/** + * Created on 3/20/14. + * + * @author Tony Chemit <chemit(a)codelutin.com> + * @since 2.6 + */ +public class IndicatorExportModel extends AbstractExportModel<IndicatorExportRow> { + + public IndicatorExportModel(char separator) { + super(separator); + newColumnForExport("Campagne", EchoBaseCsvUtil.<IndicatorExportRow, String>newBeanProperty(IndicatorExportRow.PROPERTY_MISSION_NAME)); + newColumnForExport("Indicateur", EchoBaseCsvUtil.<IndicatorExportRow, String>newBeanProperty(IndicatorExportRow.PROPERTY_INDICATOR_NAME)); + newColumnForExport("Espece", IndicatorExportRow.PROPERTY_SPECIES, EchoBaseCsvUtil.SPECIES_TO_COSER_CODE); + newColumnForExport("Strate", IndicatorExportRow.PROPERTY_STRATUM); + newColumnForExport("Annee", IndicatorExportRow.PROPERTY_DATE, EchoBaseCsvUtil.YEAR); + newColumnForExport("Estimation", IndicatorExportRow.PROPERTY_ESTIMATION, EchoBaseCsvUtil.FLOAT); + newColumnForExport("EcartType", IndicatorExportRow.PROPERTY_STANDARD_DEVIATION, EchoBaseCsvUtil.FLOAT); + newColumnForExport("CV", IndicatorExportRow.PROPERTY_CV, EchoBaseCsvUtil.FLOAT); + } + +} \ No newline at end of file Copied: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/IndicatorExportRow.java (from rev 1013, trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportRow.java) =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/IndicatorExportRow.java (rev 0) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/IndicatorExportRow.java 2014-04-22 20:25:28 UTC (rev 1018) @@ -0,0 +1,127 @@ +package fr.ifremer.echobase.services.service.exportCoser; + +/* + * #%L + * EchoBase :: Services + * %% + * Copyright (C) 2011 - 2014 Ifremer, Codelutin, Chemit Tony + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero 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 Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + * #L% + */ + +import fr.ifremer.echobase.entities.references.DataMetadata; +import fr.ifremer.echobase.entities.references.Mission; +import fr.ifremer.echobase.entities.references.Species; + +import java.util.Date; + +/** + * Created on 3/20/14. + * + * @author Tony Chemit <chemit(a)codelutin.com> + * @since 2.6 + */ +public class IndicatorExportRow { + + public static final String PROPERTY_MISSION_NAME = "mission." + Mission.PROPERTY_NAME; + + public static final String PROPERTY_INDICATOR_NAME = "indicator." + DataMetadata.PROPERTY_NAME; + + public static final String PROPERTY_SPECIES = "species"; + + public static final String PROPERTY_STRATUM = "stratum"; + + public static final String PROPERTY_DATE = "date"; + + public static final String PROPERTY_ESTIMATION = "estimation"; + + public static final String PROPERTY_STANDARD_DEVIATION = "standardDeviation"; + + public static final String PROPERTY_CV = "cv"; + + protected Mission mission; + + protected DataMetadata indicator; + + protected Species species; + + protected String stratum; + + protected Date date; + + protected float estimation; + + protected float standardDeviation; + + public Mission getMission() { + return mission; + } + + public DataMetadata getIndicator() { + return indicator; + } + + public Species getSpecies() { + return species; + } + + public String getStratum() { + return stratum; + } + + public Date getDate() { + return date; + } + + public float getEstimation() { + return estimation; + } + + public float getStandardDeviation() { + return standardDeviation; + } + + public float getCv() { + return standardDeviation / estimation; + } + + public void setMission(Mission mission) { + this.mission = mission; + } + + public void setIndicator(DataMetadata indicator) { + this.indicator = indicator; + } + + public void setSpecies(Species species) { + this.species = species; + } + + public void setStratum(String stratum) { + this.stratum = stratum; + } + + public void setDate(Date date) { + this.date = date; + } + + public void setEstimation(float estimation) { + this.estimation = estimation; + } + + public void setStandardDeviation(float standardDeviation) { + this.standardDeviation = standardDeviation; + } +} Deleted: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportModel.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportModel.java 2014-04-22 15:47:09 UTC (rev 1017) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportModel.java 2014-04-22 20:25:28 UTC (rev 1018) @@ -1,47 +0,0 @@ -package fr.ifremer.echobase.services.service.exportCoser; - -/* - * #%L - * EchoBase :: Services - * %% - * Copyright (C) 2011 - 2014 Ifremer, Codelutin, Chemit Tony - * %% - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU Affero 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 Public License for more details. - * - * You should have received a copy of the GNU Affero General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - * #L% - */ - -import fr.ifremer.echobase.csv.EchoBaseCsvUtil; -import org.nuiton.csv.ext.AbstractExportModel; - -/** - * Created on 3/20/14. - * - * @author Tony Chemit <chemit(a)codelutin.com> - * @since 2.6 - */ -public class PopulationIndicatorExportModel extends AbstractExportModel<PopulationIndicatorExportRow> { - - public PopulationIndicatorExportModel(char separator) { - super(separator); - newColumnForExport("Campagne", EchoBaseCsvUtil.<PopulationIndicatorExportRow, String>newBeanProperty(PopulationIndicatorExportRow.PROPERTY_MISSION_NAME)); - newColumnForExport("Indicateur", EchoBaseCsvUtil.<PopulationIndicatorExportRow, String>newBeanProperty(PopulationIndicatorExportRow.PROPERTY_INDICATOR_NAME)); - newColumnForExport("Espece", PopulationIndicatorExportRow.PROPERTY_SPECIES, EchoBaseCsvUtil.SPECIES_TO_COSER_CODE); - newColumnForExport("Strate", PopulationIndicatorExportRow.PROPERTY_STRATUM); - newColumnForExport("Annee", PopulationIndicatorExportRow.PROPERTY_DATE, EchoBaseCsvUtil.YEAR); - newColumnForExport("Estimation", PopulationIndicatorExportRow.PROPERTY_ESTIMATION); - newColumnForExport("EcartType", PopulationIndicatorExportRow.PROPERTY_STANDARD_DEVIATION); - newColumnForExport("CV", PopulationIndicatorExportRow.PROPERTY_CV); - } - -} \ No newline at end of file Deleted: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportRow.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportRow.java 2014-04-22 15:47:09 UTC (rev 1017) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportRow.java 2014-04-22 20:25:28 UTC (rev 1018) @@ -1,127 +0,0 @@ -package fr.ifremer.echobase.services.service.exportCoser; - -/* - * #%L - * EchoBase :: Services - * %% - * Copyright (C) 2011 - 2014 Ifremer, Codelutin, Chemit Tony - * %% - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU Affero 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 Public License for more details. - * - * You should have received a copy of the GNU Affero General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - * #L% - */ - -import fr.ifremer.echobase.entities.references.DataMetadata; -import fr.ifremer.echobase.entities.references.Mission; -import fr.ifremer.echobase.entities.references.Species; - -import java.util.Date; - -/** - * Created on 3/20/14. - * - * @author Tony Chemit <chemit(a)codelutin.com> - * @since 2.6 - */ -public class PopulationIndicatorExportRow { - - public static final String PROPERTY_MISSION_NAME = "mission." + Mission.PROPERTY_NAME; - - public static final String PROPERTY_INDICATOR_NAME = "indicator." + DataMetadata.PROPERTY_NAME; - - public static final String PROPERTY_SPECIES = "species"; - - public static final String PROPERTY_STRATUM = "stratum"; - - public static final String PROPERTY_DATE = "date"; - - public static final String PROPERTY_ESTIMATION = "estimation"; - - public static final String PROPERTY_STANDARD_DEVIATION = "standardDeviation"; - - public static final String PROPERTY_CV = "cv"; - - protected Mission mission; - - protected DataMetadata indicator; - - protected Species species; - - protected String stratum; - - protected Date date; - - protected float estimation; - - protected float standardDeviation; - - public Mission getMission() { - return mission; - } - - public DataMetadata getIndicator() { - return indicator; - } - - public Species getSpecies() { - return species; - } - - public String getStratum() { - return stratum; - } - - public Date getDate() { - return date; - } - - public float getEstimation() { - return estimation; - } - - public float getStandardDeviation() { - return standardDeviation; - } - - public float getCv() { - return standardDeviation / estimation; - } - - public void setMission(Mission mission) { - this.mission = mission; - } - - public void setIndicator(DataMetadata indicator) { - this.indicator = indicator; - } - - public void setSpecies(Species species) { - this.species = species; - } - - public void setStratum(String stratum) { - this.stratum = stratum; - } - - public void setDate(Date date) { - this.date = date; - } - - public void setEstimation(float estimation) { - this.estimation = estimation; - } - - public void setStandardDeviation(float standardDeviation) { - this.standardDeviation = standardDeviation; - } -}

1 0

r1017 - trunk/echobase-domain/src/main/data
by tchemit＠users.forge.codelutin.com April 22, 2014

April 22, 2014

Author: tchemit Date: 2014-04-22 17:47:09 +0200 (Tue, 22 Apr 2014) New Revision: 1017 Url: http://forge.codelutin.com/projects/echobase/repository/revisions/1017 Log: mise ?\195?\160 jour du r?\195?\169f?\195?\169rentiel Modified: trunk/echobase-domain/src/main/data/echobase-referentiel.echobase Modified: trunk/echobase-domain/src/main/data/echobase-referentiel.echobase =================================================================== (Binary files differ)

1 0

r1016 - in trunk: echobase-domain/src/main/java/fr/ifremer/echobase/csv echobase-domain/src/main/java/fr/ifremer/echobase/persistence echobase-services/src/main/java/fr/ifremer/echobase/services/service echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/csv
by tchemit＠users.forge.codelutin.com April 22, 2014

April 22, 2014

Author: tchemit Date: 2014-04-22 17:45:06 +0200 (Tue, 22 Apr 2014) New Revision: 1016 Url: http://forge.codelutin.com/projects/echobase/repository/revisions/1016 Log: fixes #4985 (+ use NA constant) Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/csv/EchoBaseCsvUtil.java trunk/echobase-domain/src/main/java/fr/ifremer/echobase/csv/ResultValueParser.java trunk/echobase-domain/src/main/java/fr/ifremer/echobase/persistence/EchoBaseEntityHelper.java trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/UserDbPersistenceService.java trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataSizeExportModel.java trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/AbstractImportDataService.java trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/AcousticImportConfiguration.java trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/ResultsRegionCellImportService.java trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/csv/RegionCellResultImportModel.java Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/csv/EchoBaseCsvUtil.java =================================================================== --- trunk/echobase-domain/src/main/java/fr/ifremer/echobase/csv/EchoBaseCsvUtil.java 2014-04-22 14:51:05 UTC (rev 1015) +++ trunk/echobase-domain/src/main/java/fr/ifremer/echobase/csv/EchoBaseCsvUtil.java 2014-04-22 15:45:06 UTC (rev 1016) @@ -69,13 +69,13 @@ @Override public String format(Float value) { - return value == null ? "NA" : super.format(value); + return value == null ? NA : super.format(value); } @Override protected Float parseNoneEmptyValue(String value) { Float result = null; - if (!"NA".equals(value)) { + if (!NA.equals(value)) { result = super.parseNoneEmptyValue(value); } return result; @@ -88,7 +88,7 @@ @Override protected Float parseNoneEmptyValue(String value) { Float result; - if (!"NA".equals(value)) { + if (!NA.equals(value)) { result = super.parseNoneEmptyValue(value); } else { result = defaultValue; @@ -102,13 +102,13 @@ @Override public String format(Integer value) { - return value == null ? "NA" : super.format(value); + return value == null ? NA : super.format(value); } @Override protected Integer parseNoneEmptyValue(String value) { Integer result = null; - if (!"NA".equals(value)) { + if (!NA.equals(value)) { result = super.parseNoneEmptyValue(value); } return result; @@ -132,6 +132,8 @@ public static final String DEPTH_STRATUM_ID = "depthStratumId"; + public static final String NA = "NA"; + protected EchoBaseCsvUtil() { // avoid instanciation on helper class } Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/csv/ResultValueParser.java =================================================================== --- trunk/echobase-domain/src/main/java/fr/ifremer/echobase/csv/ResultValueParser.java 2014-04-22 14:51:05 UTC (rev 1015) +++ trunk/echobase-domain/src/main/java/fr/ifremer/echobase/csv/ResultValueParser.java 2014-04-22 15:45:06 UTC (rev 1016) @@ -50,7 +50,7 @@ Result result = new ResultImpl(); result.setDataMetadata(metadata); result.setResultValue(value); - if ("NA".equals(value) && useFillValue) { + if (EchoBaseCsvUtil.NA.equals(value) && useFillValue) { // use metadata fillValue result.setResultValue(String.valueOf(metadata.getFillValue())); Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/persistence/EchoBaseEntityHelper.java =================================================================== --- trunk/echobase-domain/src/main/java/fr/ifremer/echobase/persistence/EchoBaseEntityHelper.java 2014-04-22 14:51:05 UTC (rev 1015) +++ trunk/echobase-domain/src/main/java/fr/ifremer/echobase/persistence/EchoBaseEntityHelper.java 2014-04-22 15:45:06 UTC (rev 1016) @@ -51,12 +51,6 @@ /** Logger. */ private static final Log log = LogFactory.getLog(EchoBaseEntityHelper.class); -// public static TopiaContext newTransactionFromRootContext(TopiaContext otherTx) throws TopiaException { -// TopiaContextImplementor rootContext = ((TopiaContextImplementor) otherTx).getRootContext(); -// TopiaContext tx = rootContext.beginTransaction(); -// return tx; -// } - public static void releaseApplicationContext(TopiaApplicationContext context) { if (log.isInfoEnabled()) { Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/UserDbPersistenceService.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/UserDbPersistenceService.java 2014-04-22 14:51:05 UTC (rev 1015) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/UserDbPersistenceService.java 2014-04-22 15:45:06 UTC (rev 1016) @@ -27,6 +27,7 @@ import com.google.common.collect.Iterables; import com.google.common.collect.Lists; import com.google.common.collect.Maps; +import com.google.common.collect.Sets; import fr.ifremer.echobase.EchoBaseTechnicalException; import fr.ifremer.echobase.entities.EchoBaseUserPersistenceContext; import fr.ifremer.echobase.entities.EntityModificationLog; @@ -225,9 +226,9 @@ //--- CellType -----------------------------------------------------------// //------------------------------------------------------------------------// - public List<CellType> getAllCellTypes() { + public Set<CellType> getRegionCellTypes() { List<CellType> cellTypes = persistenceContext.getCellTypeDao().findAll(); - return cellTypes; + return Sets.newHashSet(Iterables.filter(cellTypes, fr.ifremer.echobase.EchoBasePredicates.IS_REGION_CELL_TYPE)); } public CellType getCellType(String id) { Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataSizeExportModel.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataSizeExportModel.java 2014-04-22 14:51:05 UTC (rev 1015) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataSizeExportModel.java 2014-04-22 15:45:06 UTC (rev 1016) @@ -110,7 +110,7 @@ public String format(SexCategory value) { String result; if (value == null || "N".equals(value.getName())) { - result = "NA"; + result = EchoBaseCsvUtil.NA; } else { result = value.getName(); } @@ -187,7 +187,7 @@ row.setOperation(operation); row.setSpecies(species); row.setSexCategory(numberWeight.sexCategory); - row.setMaturite("NA"); + row.setMaturite(EchoBaseCsvUtil.NA); row.setLengthStep(lengthStep); row.setNumber((int) numberWeight.number); row.setWeight(numberWeight.weight); Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/AbstractImportDataService.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/AbstractImportDataService.java 2014-04-22 14:51:05 UTC (rev 1015) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/AbstractImportDataService.java 2014-04-22 15:45:06 UTC (rev 1016) @@ -42,7 +42,6 @@ import fr.ifremer.echobase.entities.references.SpeciesCategory; import fr.ifremer.echobase.io.InputFile; import fr.ifremer.echobase.services.EchoBaseServiceSupport; -import fr.ifremer.echobase.services.service.DecoratorService; import fr.ifremer.echobase.services.service.UserDbPersistenceService; import fr.ifremer.echobase.services.service.spatial.SpatialService; import org.apache.commons.lang3.StringUtils; @@ -230,13 +229,14 @@ } catch (IOException e) { throw new EchoBaseTechnicalException( "Could not close reader on file " + - inputFile.getFile(), e); + inputFile.getFile(), e + ); } } protected String getImportMessage(M configuration, InputFile inputFile) { String message = l(getLocale(), "echobase.importLabel.withFile", - getImportLabel(configuration), inputFile.getFileName()); + getImportLabel(configuration), inputFile.getFileName()); return message; } @@ -380,8 +380,9 @@ if (dataMetadata == null) { throw new ImportRuntimeException( l(locale, "echobase.importError.dataMetadata.notFound", - metadataName, - dataMetadataMap.keySet())); + metadataName, + dataMetadataMap.keySet()) + ); } result.add(dataMetadata); } @@ -407,10 +408,31 @@ String resultLabel, EchoBaseCsvFileImportResult importResult, boolean collecIds) { + addResults(row, + cell, + category, + resultLabel, + importResult, + collecIds, + true); + } + + protected void addResults(EchoBaseCsvUtil.ResultAble row, + Cell cell, + Category category, + String resultLabel, + EchoBaseCsvFileImportResult importResult, + boolean collecIds, + boolean importNAResults) { List<Result> results = row.getResult(); for (Result result : results) { + if (!importNAResults && EchoBaseCsvUtil.NA.equals(result.getResultValue())) { + + // Do not import NA results + continue; + } result.setDataQuality(row.getDataQuality()); result.setCategory(category); result.setResultLabel(resultLabel); Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/AcousticImportConfiguration.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/AcousticImportConfiguration.java 2014-04-22 14:51:05 UTC (rev 1015) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/AcousticImportConfiguration.java 2014-04-22 15:45:06 UTC (rev 1016) @@ -20,6 +20,7 @@ */ package fr.ifremer.echobase.services.service.importdata; +import fr.ifremer.echobase.csv.EchoBaseCsvUtil; import fr.ifremer.echobase.entities.ImportType; import fr.ifremer.echobase.io.InputFile; @@ -68,7 +69,7 @@ protected String soundSpeedCalculationsME70 = "(i) Equation: Mackenzie (1980), (ii) Hull-mounted thermosalinometer, (iii) surface absorption value recomputed every 30s and applied to the entire data set"; /** Manual sounderConstant. */ - protected String sounderConstant = "NA"; + protected String sounderConstant = EchoBaseCsvUtil.NA; /** Manual processingTemplate. */ protected String processingTemplate; Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/ResultsRegionCellImportService.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/ResultsRegionCellImportService.java 2014-04-22 14:51:05 UTC (rev 1015) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/ResultsRegionCellImportService.java 2014-04-22 15:45:06 UTC (rev 1016) @@ -29,7 +29,6 @@ import fr.ifremer.echobase.entities.data.Echotype; import fr.ifremer.echobase.entities.data.Voyage; import fr.ifremer.echobase.entities.references.CellType; -import fr.ifremer.echobase.entities.references.CellTypeImpl; import fr.ifremer.echobase.entities.references.DataMetadata; import fr.ifremer.echobase.entities.references.DataMetadataImpl; import fr.ifremer.echobase.entities.references.DataQuality; @@ -50,7 +49,6 @@ import java.io.Reader; import java.util.Arrays; -import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Set; @@ -97,14 +95,8 @@ InputFile inputFile = configuration.getRegionsFile(); - Set<CellType> allCellTypes = new HashSet<CellType>(persistenceService.getAllCellTypes()); + Set<CellType> allCellTypes = persistenceService.getRegionCellTypes(); - // remove some cell types (esdu, elementary, shoal) - allCellTypes.remove(persistenceService.getCellTypeById(CellTypeImpl.ELEMENTARY)); - allCellTypes.remove(persistenceService.getCellTypeById(CellTypeImpl.ESDU)); - allCellTypes.remove(persistenceService.getCellTypeById(CellTypeImpl.MAP)); - allCellTypes.remove(persistenceService.getCellTypeById(CellTypeImpl.SHOAL)); - DataMetadata dataCoordinateMeta = persistenceService.getDataMetadataByName(DataMetadataImpl.REGION_ENV_COORDINATES); DataMetadata dataSurfaceMeta = persistenceService.getDataMetadataByName(DataMetadataImpl.SURFACE); @@ -303,7 +295,7 @@ null, importResult); - addResults(row, cell, category, resultLabel, importResult, false); + addResults(row, cell, category, resultLabel, importResult, false, false); } return importResult; Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/csv/RegionCellResultImportModel.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/csv/RegionCellResultImportModel.java 2014-04-22 14:51:05 UTC (rev 1015) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/importdata/csv/RegionCellResultImportModel.java 2014-04-22 15:45:06 UTC (rev 1016) @@ -72,7 +72,7 @@ for (DataMetadata metadata : dataMetadatas) { newMandatoryColumn( metadata.getName(), - EchoBaseCsvUtil.newResultValueParser(metadata, true), + EchoBaseCsvUtil.newResultValueParser(metadata, false), EchoBaseCsvUtil.<RegionCellResultImportRow>newResultValueSetter()); } }

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