December 2011 - Echobase-commits - mailman.cloud.codelutin.com

r208 - in trunk/echobase-ui/src/main/env: dev/resources prod/resources
by tchemit＠users.forge.codelutin.com 20 Dec '11

20 Dec '11

Author: tchemit Date: 2011-12-20 10:21:01 +0100 (Tue, 20 Dec 2011) New Revision: 208 Url: http://forge.codelutin.com/repositories/revision/echobase/208 Log: increase topia log levels Modified: trunk/echobase-ui/src/main/env/dev/resources/log4j.properties trunk/echobase-ui/src/main/env/prod/resources/log4j.properties Modified: trunk/echobase-ui/src/main/env/dev/resources/log4j.properties =================================================================== --- trunk/echobase-ui/src/main/env/dev/resources/log4j.properties 2011-12-19 23:15:41 UTC (rev 207) +++ trunk/echobase-ui/src/main/env/dev/resources/log4j.properties 2011-12-20 09:21:01 UTC (rev 208) @@ -33,5 +33,6 @@ log4j.logger.fr.ifremer.echobase=INFO log4j.logger.org.nuiton=WARN log4j.logger.org.nuiton.topia.migration=INFO +log4j.logger.org.nuiton.topia.replication=INFO log4j.logger.com.opensymphony.xwork2.util.logging.commons.CommonsLogger=ERROR log4j.logger.org.apache.struts2.util.TokenHelper=ERROR Modified: trunk/echobase-ui/src/main/env/prod/resources/log4j.properties =================================================================== --- trunk/echobase-ui/src/main/env/prod/resources/log4j.properties 2011-12-19 23:15:41 UTC (rev 207) +++ trunk/echobase-ui/src/main/env/prod/resources/log4j.properties 2011-12-20 09:21:01 UTC (rev 208) @@ -31,5 +31,6 @@ log4j.logger.fr.ifremer.echobase=INFO log4j.logger.org.nuiton.topia.migration=INFO +log4j.logger.org.nuiton.topia.replication=INFO log4j.logger.com.opensymphony.xwork2.util.logging.commons.CommonsLogger=ERROR log4j.logger.org.apache.struts2.util.TokenHelper=ERROR

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r207 - trunk/echobase-services/src/main/java/fr/ifremer/echobase/services
by tchemit＠users.forge.codelutin.com 19 Dec '11

19 Dec '11

Author: tchemit Date: 2011-12-20 00:15:41 +0100 (Tue, 20 Dec 2011) New Revision: 207 Url: http://forge.codelutin.com/repositories/revision/echobase/207 Log: fix association loading Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/DbImportService.java Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/DbImportService.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/DbImportService.java 2011-12-19 21:56:39 UTC (rev 206) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/DbImportService.java 2011-12-19 23:15:41 UTC (rev 207) @@ -271,8 +271,22 @@ ImportToMap importer = MyImportToMap.newImport(model, reader); StringBuilder builder = new StringBuilder(); + try { - String updateString = "UPDATE " + target.getContract().getSimpleName() + " SET " + source.getContract().getSimpleName() + " = '%s' WHERE topiaId ='%s';"; + String updateString; + String targetTableName = target.getContract().getSimpleName(); + String sourceTableName = source.getContract().getSimpleName(); + String table = targetTableName; + if (source == EchoBaseEntityEnum.Voyage && target == EchoBaseEntityEnum.Echotype) { + table = targetTableName + "_" + sourceTableName; + updateString = "UPDATE " + table + " SET " + sourceTableName + " = '%s' WHERE " + meta.getName() + " ='%s';"; + } else if (source == EchoBaseEntityEnum.Voyage && target == EchoBaseEntityEnum.Strata) { + table = targetTableName + "_" + source.getContract().getSimpleName(); + updateString = "UPDATE " + table + " SET " + sourceTableName + " = '%s' WHERE " + meta.getName() + " ='%s';"; + } else { + updateString = "UPDATE " + table + " SET " + sourceTableName + " = '%s' WHERE topiaId ='%s';"; + } + if (log.isDebugEnabled()) { log.debug("Will apply " + updateString); } @@ -283,7 +297,7 @@ for (String association : associations) { builder.append(String.format(updateString, topiaId, association)).append('\n'); compt++; - if (compt == 10000) { + if (compt % 10000 == 0) { // flush it getTransaction().executeSQL(builder.toString()); builder = new StringBuilder(); @@ -291,6 +305,9 @@ } csvResult.incrementsNumberUpdated(); } + if (builder.length() > 0) { + getTransaction().executeSQL(builder.toString()); + } } catch (TopiaException eee) { throw new EchoBaseTechnicalException( "Could not execute sql script", eee);

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r206 - trunk/echobase-services
by tchemit＠users.forge.codelutin.com 19 Dec '11

19 Dec '11

Author: tchemit Date: 2011-12-19 22:56:39 +0100 (Mon, 19 Dec 2011) New Revision: 206 Url: http://forge.codelutin.com/repositories/revision/echobase/206 Log: optimize dependencies Modified: trunk/echobase-services/pom.xml Modified: trunk/echobase-services/pom.xml =================================================================== --- trunk/echobase-services/pom.xml 2011-12-19 21:45:05 UTC (rev 205) +++ trunk/echobase-services/pom.xml 2011-12-19 21:56:39 UTC (rev 206) @@ -102,6 +102,11 @@ <artifactId>topia-service-replication</artifactId> </dependency> + <dependency> + <groupId>org.hibernate</groupId> + <artifactId>hibernate-core</artifactId> + </dependency> +  <dependency>

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r205 - in trunk: echobase-entities/src/main/java/fr/ifremer/echobase/entities echobase-services/src/main/java/fr/ifremer/echobase/services echobase-ui/src/main/env/dev/resources echobase-ui/src/main/env/prod/resources
by tchemit＠users.forge.codelutin.com 19 Dec '11

19 Dec '11

Author: tchemit Date: 2011-12-19 22:45:05 +0100 (Mon, 19 Dec 2011) New Revision: 205 Url: http://forge.codelutin.com/repositories/revision/echobase/205 Log: improve DbImportService Modified: trunk/echobase-entities/src/main/java/fr/ifremer/echobase/entities/EntitiesUtil.java trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/DbImportService.java trunk/echobase-ui/src/main/env/dev/resources/log4j.properties trunk/echobase-ui/src/main/env/prod/resources/log4j.properties Modified: trunk/echobase-entities/src/main/java/fr/ifremer/echobase/entities/EntitiesUtil.java =================================================================== --- trunk/echobase-entities/src/main/java/fr/ifremer/echobase/entities/EntitiesUtil.java 2011-12-19 19:18:47 UTC (rev 204) +++ trunk/echobase-entities/src/main/java/fr/ifremer/echobase/entities/EntitiesUtil.java 2011-12-19 21:45:05 UTC (rev 205) @@ -175,6 +175,8 @@ result.add(EchoBaseEntityEnum.OperationMetadata); result.add(EchoBaseEntityEnum.GearMetadata); result.add(EchoBaseEntityEnum.Gear); + result.add(EchoBaseEntityEnum.LengthAgeKey); + result.add(EchoBaseEntityEnum.LengthWeightKey); return result.toArray(new EchoBaseEntityEnum[result.size()]); } Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/DbImportService.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/DbImportService.java 2011-12-19 19:18:47 UTC (rev 204) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/DbImportService.java 2011-12-19 21:45:05 UTC (rev 205) @@ -38,6 +38,7 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.topia.TopiaException; +import org.nuiton.topia.framework.TopiaContextImplementor; import org.nuiton.topia.persistence.TopiaDAO; import org.nuiton.topia.persistence.TopiaEntity; import org.nuiton.util.StringUtil; @@ -99,10 +100,6 @@ log.warn("There is " + missingEntries.size() + "missing mandatory files " + " in import " + file + "\n" + StringUtil.join(missingEntries, "\n", false)); } - -// throw new EchoBaseTechnicalException( -// "There is some missing mandatory files " + -// missingEntries + " in import " + file); } return result; @@ -187,125 +184,120 @@ } - public <E extends TopiaEntity> void importFile(MetaFilenameAware entry, - Reader reader, - CsvImportResult csvResult) throws IOException { + public void importFile(MetaFilenameAware entry, + Reader reader, + CsvImportResult csvResult) throws IOException, TopiaException { - DbEditorService service = getDbEditorService(); - long s0; + long s0 = TimeLog.getTime(); - s0 = TimeLog.getTime(); + if (log.isInfoEnabled()) { + log.info("Will import " + entry); + } if (entry instanceof AssociationMeta) { // load a association input + importAssociationfile((AssociationMeta) entry, reader, csvResult); - AssociationMeta meta = (AssociationMeta) entry; + } else { - if (log.isInfoEnabled()) { - log.info("Will import " + meta); - } + // normal entity table import + importEntityFile((TableMeta) entry, reader, csvResult); + } - EchoBaseEntityEnum source = meta.getSource(); - EchoBaseEntityEnum target = meta.getTarget(); - timeLog.log(s0, "importFile::getTargetEntities"); -// List<TopiaEntity> targetEntities = getEntities(target); -// Map<String, TopiaEntity> targetsById = -// Maps.uniqueIndex(targetEntities, EchoBaseFunctions.TO_TOPIAID); + timeLog.log(s0, "importFile::done"); - ImportModel<Map<String, Object>> model = - EntityAssociationImportModel.newImportModel( - getConfiguration().getCsvSeparator(), - meta - ); + s0 = TimeLog.getTime(); -// EchoBaseEntityEnum sourceType = meta.getSource(); + flushTransaction(); - ImportToMap importer = MyImportToMap.newImport(model, reader); + timeLog.log(s0, "importFile::flushTransaction"); + } - s0 = TimeLog.getTime(); -// List<E> sourceEntities = getEntities(sourceType); - timeLog.log(s0, "importFile::getSourceEntities"); -// Map<String, E> sourcesById = -// Maps.uniqueIndex(sourceEntities, EchoBaseFunctions.TO_TOPIAID); - StringBuilder builder = new StringBuilder(); - try { - s0 = TimeLog.getTime(); - String updateString = "UPDATE " + target.getContract().getSimpleName() + " SET " + source.getContract().getSimpleName() + " = '%s' WHERE topiaId ='%s';"; - if (log.isInfoEnabled()) { - log.info("Will apply " + updateString); - } - int compt = 0; - for (Map<String, Object> row : importer) { - String topiaId = (String) row.get(TopiaEntity.TOPIA_ID); - String[] associations = (String[]) row.get("target"); - for (String association : associations) { - builder.append(String.format(updateString, topiaId, association)).append('\n'); - compt++; - if (compt == 10000) { - // flush it - getTransaction().executeSQL(builder.toString()); - builder = new StringBuilder(); - } - } - csvResult.incrementsNumberUpdated(); - } - timeLog.log(s0, "importFile::import"); - } catch (TopiaException eee) { - throw new EchoBaseTechnicalException( - "Could not execute sql script", eee); - } finally { + public MetaFilenameAware[] getEntries() { - importer.close(); - } + List<MetaFilenameAware> entities = Lists.newArrayList(); + List<MetaFilenameAware> associations = Lists.newArrayList(); - } else { + addEntries(entities, associations, EntitiesUtil.getReferenceTypesForCopy()); + addEntries(entities, associations, EntitiesUtil.getDataTypesforCopy()); + entities.addAll(associations); + return entities.toArray(new MetaFilenameAware[entities.size()]); + } - // normal entity table import + protected void importEntityFile(TableMeta meta, Reader reader, CsvImportResult csvResult) { - TableMeta meta = (TableMeta) entry; + ImportModel<TopiaEntity> model = getDbEditorService().buildForImport(meta); - if (log.isInfoEnabled()) { - log.info("Will import " + meta); - } + Import<TopiaEntity> importer = Import.newImport(model, reader); - ImportModel<TopiaEntity> model = service.buildForImport(meta); + try { + TopiaDAO<TopiaEntity> dao = getDAO(meta.getSource()); + for (TopiaEntity entity : importer) { - Import<TopiaEntity> importer = Import.newImport(model, reader); + TopiaEntity entityToSave = dao.create(TopiaEntity.TOPIA_ID, + entity.getTopiaId()); - try { - TopiaDAO<TopiaEntity> dao = getDAO(meta.getSource()); - s0 = TimeLog.getTime(); - for (TopiaEntity entity : importer) { + meta.copy(entity, entityToSave); - TopiaEntity entityToSave = dao.create(TopiaEntity.TOPIA_ID, - entity.getTopiaId()); + csvResult.incrementsNumberUpdated(); + } - meta.copy(entity, entityToSave); + } catch (Exception eee) { + throw new EchoBaseTechnicalException("Could not import entities of type " + meta.getSource(), eee); + } finally { - csvResult.incrementsNumberUpdated(); - } - timeLog.log(s0, "importFile::import"); - } catch (Exception eee) { - throw new EchoBaseTechnicalException("Could not import entities of type " + meta.getSource(), eee); - } finally { - - importer.close(); - } + importer.close(); } } - public MetaFilenameAware[] getEntries() { + protected void flushTransaction() throws TopiaException { + TopiaContextImplementor tx = (TopiaContextImplementor) getTransaction(); + tx.getHibernate().flush(); + } - List<MetaFilenameAware> entities = Lists.newArrayList(); - List<MetaFilenameAware> associations = Lists.newArrayList(); + protected void importAssociationfile(AssociationMeta meta, Reader reader, CsvImportResult csvResult) { + EchoBaseEntityEnum source = meta.getSource(); + EchoBaseEntityEnum target = meta.getTarget(); - addEntries(entities, associations, EntitiesUtil.getReferenceTypesForCopy()); - addEntries(entities, associations, EntitiesUtil.getDataTypesforCopy()); - entities.addAll(associations); - return entities.toArray(new MetaFilenameAware[entities.size()]); + ImportModel<Map<String, Object>> model = + EntityAssociationImportModel.newImportModel( + getConfiguration().getCsvSeparator(), + meta + ); + + ImportToMap importer = MyImportToMap.newImport(model, reader); + + StringBuilder builder = new StringBuilder(); + try { + String updateString = "UPDATE " + target.getContract().getSimpleName() + " SET " + source.getContract().getSimpleName() + " = '%s' WHERE topiaId ='%s';"; + if (log.isDebugEnabled()) { + log.debug("Will apply " + updateString); + } + int compt = 0; + for (Map<String, Object> row : importer) { + String topiaId = (String) row.get(TopiaEntity.TOPIA_ID); + String[] associations = (String[]) row.get("target"); + for (String association : associations) { + builder.append(String.format(updateString, topiaId, association)).append('\n'); + compt++; + if (compt == 10000) { + // flush it + getTransaction().executeSQL(builder.toString()); + builder = new StringBuilder(); + } + } + csvResult.incrementsNumberUpdated(); + } + } catch (TopiaException eee) { + throw new EchoBaseTechnicalException( + "Could not execute sql script", eee); + } finally { + + importer.close(); + } } protected TableMeta getTableMeta(EchoBaseEntityEnum tableName) { Modified: trunk/echobase-ui/src/main/env/dev/resources/log4j.properties =================================================================== --- trunk/echobase-ui/src/main/env/dev/resources/log4j.properties 2011-12-19 19:18:47 UTC (rev 204) +++ trunk/echobase-ui/src/main/env/dev/resources/log4j.properties 2011-12-19 21:45:05 UTC (rev 205) @@ -34,3 +34,4 @@ log4j.logger.org.nuiton=WARN log4j.logger.org.nuiton.topia.migration=INFO log4j.logger.com.opensymphony.xwork2.util.logging.commons.CommonsLogger=ERROR +log4j.logger.org.apache.struts2.util.TokenHelper=ERROR Modified: trunk/echobase-ui/src/main/env/prod/resources/log4j.properties =================================================================== --- trunk/echobase-ui/src/main/env/prod/resources/log4j.properties 2011-12-19 19:18:47 UTC (rev 204) +++ trunk/echobase-ui/src/main/env/prod/resources/log4j.properties 2011-12-19 21:45:05 UTC (rev 205) @@ -32,3 +32,4 @@ log4j.logger.fr.ifremer.echobase=INFO log4j.logger.org.nuiton.topia.migration=INFO log4j.logger.com.opensymphony.xwork2.util.logging.commons.CommonsLogger=ERROR +log4j.logger.org.apache.struts2.util.TokenHelper=ERROR

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r204 - trunk/src/doc/reunions
by tchemit＠users.forge.codelutin.com 19 Dec '11

19 Dec '11

Author: tchemit Date: 2011-12-19 20:18:47 +0100 (Mon, 19 Dec 2011) New Revision: 204 Url: http://forge.codelutin.com/repositories/revision/echobase/204 Log: update reunion CR Modified: trunk/src/doc/reunions/reunion-2011-12-19.txt Modified: trunk/src/doc/reunions/reunion-2011-12-19.txt =================================================================== --- trunk/src/doc/reunions/reunion-2011-12-19.txt 2011-12-19 19:16:34 UTC (rev 203) +++ trunk/src/doc/reunions/reunion-2011-12-19.txt 2011-12-19 19:18:47 UTC (rev 204) @@ -9,39 +9,55 @@ -------- - Revoir quelques points sur le modèle +- Discuter de l'import des nouvelles campagnes Modèle pêche ------------ -- SpeciesCategory ? -- Sample est lié à SpeciesCategory et Species ? -- LengthAgeKey ? -- WeightLengthKey ? -- BiometryScale ? +SizeCategory et SexCategory sont inversés. -Import nouvelles données ------------------------- +- SpeciesCategory On remplit la table lors de l'insertion des Samples -- Planning ? + - pour Unsorted : on utilise le code 0 de la taille (SizeCategory)? + - pour le Total et Subsample : le code taille (SizeCategory) = CATEG + - pour individual : juste Species renseignés dans SpeciesCategory. -Réalisation modèle pêche +- Sample est lié à SpeciesCategory et Species ? Non on supprime le lien vers Species. + +- LengthAgeKey ? Remplir à partir de CLE_TAILLE_AGE + +- LengthWeightKey ? et pas WeightLengthKey... A remplir depuis TAILLE_POIDS + + quand categorie = NA ou H alors utiliser 0 + + Enregistrer à nulle le numberSampled si pas de données (pas de 0) + +Supprimer entité BiometryScale + +Trouver comment mettre sur une même ligne toutes les SampleData d'un même Sample. + +TODO Voir comment corriger les problèmes d'encoding dans Libre-Office. + +- Faire un export globale de la base sur le même format que l'import de la base complête +- Lors d'un ré-import, ne pas écraser le référentiel +- Proposer à l'utilisateur le mode d'import : écraser ou pas les données. + +- Modifier Se connecter à la base : sur demo l'url est jdbc:postgresql://localhost/echobase localhost + +autoriser cette ip 134.246.53.25 sur le pg de demo + +- Ajouter une utiliser lecture seule sur la base. + +Réflechir sur comment effecuter les nouveaux import. + +Import nouvelles données ------------------------ -- Report des modifications du modèle -- Remplissage du référentiel OperationEvent -- Remplissage du référentiel SampleDataType -- Remplissage du référentiel SampleType -- Création entité BiometryScale -- Remplissage du référentiel BiometryScale -- Remplissage du référentiel SexCategory -- Remplissage du référentiel SizeCategory -- Remplissage du référentiel OperationMetadata -- Remplissage du référentiel GearMetadata -- Remplissage du référentiel Gear +- On commnce ça début janvier +- On se base sur le système déjà existant utilisé pour l'import d'une + base complête, sauf pour les clef étrangère et les associations où on utilise + non plus les identifiants techniques (topiaId) mais des clefs métiers. -- Import des opérations (depuis table STATIONS) -- Import des samples (depuis table CAPTURES/MENSURATIONS/BIOMETRIE_VALEURS) - Action ------ @@ -55,4 +71,4 @@ Prochaine réunion : - - Lundi 19 à 10h00 à l'Ifremer avec Mathieu \ No newline at end of file + - Mercredi 4 janvier 10h00 à l'Ifremer avec Mathieu \ No newline at end of file

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r203 - in trunk/echobase-tools: . src/main/java/fr/ifremer/echobase/tools/loaders src/test/java/fr/ifremer/echobase/tools/loaders src/test/resources/csv/new
by tchemit＠users.forge.codelutin.com 19 Dec '11

19 Dec '11

Author: tchemit Date: 2011-12-19 20:16:34 +0100 (Mon, 19 Dec 2011) New Revision: 203 Url: http://forge.codelutin.com/repositories/revision/echobase/203 Log: continue catches import Added: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/LengthAgeKeyLoader.java trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/LengthWeightKeyLoader.java trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/LengthAgeKeyLoaderIT.java trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/LengthWeightKeyLoaderIT.java Removed: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoader.java trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoaderIT.java trunk/echobase-tools/src/test/resources/csv/new/input-BiometryScale.csv Modified: trunk/echobase-tools/pom.xml trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/OperationLoader.java trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SampleLoader.java trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SpeciesCategoryLoader.java trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/AbstractLoaderIT.java trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/OperationLoaderIT.java trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SampleLoaderIT.java trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SpeciesCategoryLoaderIT.java trunk/echobase-tools/src/test/resources/csv/new/input-SexCategory.csv trunk/echobase-tools/src/test/resources/csv/new/input-SizeCategory.csv Modified: trunk/echobase-tools/pom.xml =================================================================== --- trunk/echobase-tools/pom.xml 2011-12-19 19:16:01 UTC (rev 202) +++ trunk/echobase-tools/pom.xml 2011-12-19 19:16:34 UTC (rev 203) @@ -65,7 +65,7 @@ <groupId>org.apache.commons</groupId> <artifactId>commons-lang3</artifactId> </dependency> - + <dependency> <groupId>commons-logging</groupId> <artifactId>commons-logging</artifactId> @@ -213,7 +213,7 @@ <testResource> <directory>src/test/resources</directory> <includes> - <include>**/*.properties</include> + <include>**/*.*</include> </includes> </testResource> </testResources> Deleted: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoader.java =================================================================== --- trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoader.java 2011-12-19 19:16:01 UTC (rev 202) +++ trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoader.java 2011-12-19 19:16:34 UTC (rev 203) @@ -1,67 +0,0 @@ -/* - * #%L - * EchoBase :: Tools - * - * $Id$ - * $HeadURL$ - * %% - * Copyright (C) 2011 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% - */ -package fr.ifremer.echobase.tools.loaders; - -import fr.ifremer.echobase.EchoBaseFunctions; -import fr.ifremer.echobase.entities.meta.TableMeta; -import fr.ifremer.echobase.entities.references.BiometryScale; -import fr.ifremer.echobase.entities.references.SampleDataType; -import fr.ifremer.echobase.services.models.EntityCsvModel; -import fr.ifremer.echobase.tools.FileType; - -import java.util.List; - -/** - * {@link BiometryScale} loader. - * - * @author tchemit <chemit(a)codelutin.com> - * @since 0.2 - */ -public class BiometryScaleLoader extends EntityLoader<BiometryScale> { - - public BiometryScaleLoader() { - super(BiometryScale.class, FileType.NEW); - } - - @Override - protected EntityCsvModel<BiometryScale> createCsvImportModel(TableMeta meta) { - - List<SampleDataType> sampleDataTypes = - getEntities(SampleDataType.class); - - EntityCsvModel<BiometryScale> model = EntityCsvModel.newModel( - getCsvSeparator(), - meta - ); - - /* - raptriBiometryDataType;ScaleCode;ScaleMeaningEng;ScaleMeaningFr - */ - model.addForeignKeyForImport("raptriBiometryDataType", BiometryScale.PROPERTY_SAMPLE_DATA_TYPE, SampleDataType.class, sampleDataTypes, EchoBaseFunctions.SAMPLE_DATA_TYPE_RAPTRI_CODE); - model.addDefaultColumn("ScaleCode",BiometryScale.PROPERTY_CODE, int.class); - model.newMandatoryColumn("ScaleMeaningEng",BiometryScale.PROPERTY_MEANING_EN); - model.newMandatoryColumn("ScaleMeaningFr",BiometryScale.PROPERTY_MEANING_FR); - return model; - } -} \ No newline at end of file Added: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/LengthAgeKeyLoader.java =================================================================== --- trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/LengthAgeKeyLoader.java (rev 0) +++ trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/LengthAgeKeyLoader.java 2011-12-19 19:16:34 UTC (rev 203) @@ -0,0 +1,102 @@ +/* + * #%L + * EchoBase :: Tools + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2011 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% + */ +package fr.ifremer.echobase.tools.loaders; + +import com.google.common.collect.Lists; +import com.healthmarketscience.jackcess.Database; +import fr.ifremer.echobase.EchoBaseFunctions; +import fr.ifremer.echobase.entities.EchoBaseEntityEnum; +import fr.ifremer.echobase.entities.data.Voyage; +import fr.ifremer.echobase.entities.references.LengthAgeKey; +import fr.ifremer.echobase.entities.references.Species; +import fr.ifremer.echobase.tools.FileType; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.topia.TopiaException; +import org.nuiton.topia.persistence.TopiaDAO; + +import java.io.IOException; +import java.util.List; +import java.util.Map; + +/** + * {@link LengthAgeKey} loader. + * + * @author tchemit <chemit(a)codelutin.com> + * @since 0.2 + */ +public class LengthAgeKeyLoader extends EntityLoader<LengthAgeKey> { + + /** Logger. */ + private static final Log log = + LogFactory.getLog(LengthAgeKeyLoader.class); + + public LengthAgeKeyLoader() { + super(LengthAgeKey.class, EchoBaseEntityEnum.Voyage, + Voyage.PROPERTY_LENGTH_AGE_KEY, + FileType.BARACOUDA); + } + + @Override + protected void importBaracoudaEntities(Database db) throws IOException, TopiaException { + + Map<String, Voyage> voyagesByName = getUniverse( + Voyage.class, EchoBaseFunctions.VOYAGE_NAME); + + Map<String, Species> speciesByName = getUniverse( + Species.class, EchoBaseFunctions.SPECIES_BARACOUDA_CODE); + + TopiaDAO<LengthAgeKey> dao = getDAO(); + + List<LengthAgeKey> lengthAgeKeys = Lists.newArrayList(); + + for (Map<String, Object> row : db.getTable("CLE_TAILLE_AGE")) { + + String voyageName = (String) row.get("CAMPAGNE"); + Voyage voyage = getFK(voyagesByName, voyageName); + + String speciesCode = (String) row.get("GENRE_ESP"); + Species species = getFK(speciesByName, speciesCode); + + Integer age = Integer.valueOf(row.get("AGE").toString()); + Float length = (Float) row.get("TAILLE"); + Float percentAtAge = (Float) row.get("POURCENTAGE"); + String metadata = (String) row.get("Origine_Data"); + + LengthAgeKey lengthAgeKey = dao.create( + LengthAgeKey.PROPERTY_SPECIES, species, + LengthAgeKey.PROPERTY_LENGTH, length, + LengthAgeKey.PROPERTY_AGE, age, + LengthAgeKey.PROPERTY_PERCENT_AT_AGE, percentAtAge, + LengthAgeKey.PROPERTY_METADATA, metadata + ); + lengthAgeKeys.add(lengthAgeKey); + voyage.addLengthAgeKey(lengthAgeKey); + } + if (log.isInfoEnabled()) { + log.info("Found " + lengthAgeKeys.size() + " lengthAgeKey(s)."); + } + } + +} \ No newline at end of file Property changes on: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/LengthAgeKeyLoader.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Added: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/LengthWeightKeyLoader.java =================================================================== --- trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/LengthWeightKeyLoader.java (rev 0) +++ trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/LengthWeightKeyLoader.java 2011-12-19 19:16:34 UTC (rev 203) @@ -0,0 +1,130 @@ +/* + * #%L + * EchoBase :: Tools + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2011 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% + */ +package fr.ifremer.echobase.tools.loaders; + +import com.google.common.collect.Lists; +import com.healthmarketscience.jackcess.Database; +import fr.ifremer.echobase.EchoBaseFunctions; +import fr.ifremer.echobase.entities.EchoBaseEntityEnum; +import fr.ifremer.echobase.entities.data.Voyage; +import fr.ifremer.echobase.entities.references.LengthWeightKey; +import fr.ifremer.echobase.entities.references.SizeCategory; +import fr.ifremer.echobase.entities.references.Species; +import fr.ifremer.echobase.entities.references.SpeciesCategory; +import fr.ifremer.echobase.tools.FileType; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.topia.TopiaException; +import org.nuiton.topia.persistence.TopiaDAO; + +import java.io.IOException; +import java.util.List; +import java.util.Map; + +/** + * {@link LengthWeightKey} loader. + * + * @author tchemit <chemit(a)codelutin.com> + * @since 0.2 + */ +public class LengthWeightKeyLoader extends EntityLoader<LengthWeightKey> { + + /** Logger. */ + private static final Log log = + LogFactory.getLog(LengthWeightKeyLoader.class); + + public LengthWeightKeyLoader() { + super(LengthWeightKey.class, EchoBaseEntityEnum.Voyage, + Voyage.PROPERTY_LENGTH_WEIGHT_KEY, + FileType.BARACOUDA); + } + + @Override + protected void importBaracoudaEntities(Database db) throws IOException, TopiaException { + + Map<String, Voyage> voyagesByName = getUniverse( + Voyage.class, EchoBaseFunctions.VOYAGE_NAME); + + Map<String, Species> speciesByName = getUniverse( + Species.class, EchoBaseFunctions.SPECIES_BARACOUDA_CODE); + + Map<String, SizeCategory> sizeCategoryByName = getUniverse( + SizeCategory.class, EchoBaseFunctions.SIZE_CATEGORY_NAME); + + Map<String, SpeciesCategory> speciesCategoryBySizeAndName = getUniverse( + SpeciesCategory.class, EchoBaseFunctions.SPECIES_CATEGORY_SPIECIES); + + TopiaDAO<LengthWeightKey> dao = getDAO(); + + List<LengthWeightKey> lengthWeightKeys = Lists.newArrayList(); + + for (Map<String, Object> row : db.getTable("TAILLE_POIDS")) { + + String voyageName = (String) row.get("Campagne"); + Voyage voyage = getFK(voyagesByName, voyageName); + + String speciesCode = (String) row.get("Genre_esp"); + Species species = getFK(speciesByName, speciesCode); + + String sizeCode = (String) row.get("Categorie"); + if ("NA".equals(sizeCode) || "H".equals(sizeCode)) { + sizeCode = "0"; + } + + SizeCategory sizeCategory = getFK(sizeCategoryByName, sizeCode); + SpeciesCategory speciesCategory = getSpeciesCategory( + species, + sizeCategory, + speciesCategoryBySizeAndName); + + Float aParameter = (Float) row.get("Coeff_A_RTP"); + Float bParameter = (Float) row.get("Exposant_N_RTP"); + String metadata = (String) row.get("Origine_DATA"); + + LengthWeightKey lengthWeightKey = dao.create( + LengthWeightKey.PROPERTY_SPECIES_CATEGORY, speciesCategory, + LengthWeightKey.PROPERTY_APARAMETER, aParameter, + LengthWeightKey.PROPERTY_BPARAMETER, bParameter, + LengthWeightKey.PROPERTY_METADATA, metadata + ); + voyage.addLengthWeightKey(lengthWeightKey); + lengthWeightKeys.add(lengthWeightKey); + } + if (log.isInfoEnabled()) { + log.info("Found " + lengthWeightKeys.size() + " lengthWeightKey(s)."); + } + } + + protected SpeciesCategory getSpeciesCategory(Species species, + SizeCategory sizeCategory, + Map<String, SpeciesCategory> speciesCategoryByName) throws TopiaException { + + String speciesCategoryKey = EchoBaseFunctions.getSpeciesCategoryKey(species, sizeCategory, null); + + // get species category to use + SpeciesCategory speciesCategory = getFK(speciesCategoryByName, speciesCategoryKey); + return speciesCategory; + } + +} \ No newline at end of file Property changes on: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/LengthWeightKeyLoader.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Modified: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/OperationLoader.java =================================================================== --- trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/OperationLoader.java 2011-12-19 19:16:01 UTC (rev 202) +++ trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/OperationLoader.java 2011-12-19 19:16:34 UTC (rev 203) @@ -299,17 +299,9 @@ Float midHauleLatitude = (Float) row.get("LATDD"); Preconditions.checkNotNull(midHauleLatitude); -// if (midHauleLatitude == null) { -// messages.add("No midHauleLatitude"); -// midHauleLatitude = 0f; -// } Float midHauleLongitude = (Float) row.get("LGDD"); Preconditions.checkNotNull(midHauleLongitude); -// if (midHauleLongitude== null) { -// messages.add("No midHauleLongitude"); -// midHauleLongitude = 0f; -// } Date shootingStartTime = (Date) row.get("DHTUDEB"); Date shootingEndTime = (Date) row.get("DHTUFIN"); Modified: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SampleLoader.java =================================================================== --- trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SampleLoader.java 2011-12-19 19:16:01 UTC (rev 202) +++ trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SampleLoader.java 2011-12-19 19:16:34 UTC (rev 203) @@ -24,6 +24,7 @@ package fr.ifremer.echobase.tools.loaders; import com.google.common.base.Preconditions; +import com.google.common.collect.Lists; import com.google.common.collect.Multimap; import com.google.common.collect.Multimaps; import com.google.common.collect.Sets; @@ -38,16 +39,22 @@ import fr.ifremer.echobase.entities.references.SampleDataType; import fr.ifremer.echobase.entities.references.SampleType; import fr.ifremer.echobase.entities.references.SampleTypeDAO; +import fr.ifremer.echobase.entities.references.SexCategory; +import fr.ifremer.echobase.entities.references.SizeCategory; import fr.ifremer.echobase.entities.references.Species; +import fr.ifremer.echobase.entities.references.SpeciesCategory; +import fr.ifremer.echobase.entities.references.SpeciesCategoryDAO; import fr.ifremer.echobase.tools.FileType; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.topia.TopiaException; import org.nuiton.topia.persistence.TopiaDAO; +import org.nuiton.util.StringUtil; import java.io.File; import java.io.IOException; import java.util.Collection; +import java.util.List; import java.util.Map; import java.util.Set; @@ -103,7 +110,15 @@ copyAndLoadEntities(outputDir, meta.getAssociations(Sample.PROPERTY_SAMPLE_DATA), false, FileType.ASSOCIATION); } + protected SampleDataDAO sampleDataDAO; + protected SpeciesCategoryDAO speciesCategoryDAO; + protected TopiaDAO<Sample> dao; + + protected Map<String, SizeCategory> sizeCategoryByName; + protected Map<String, SexCategory> sexCategoryByName; + protected Map<String, SpeciesCategory> speciesCategoryByName; + @Override protected void importBaracoudaEntities(Database db) throws IOException, TopiaException { @@ -116,6 +131,15 @@ Map<String, SampleDataType> sampleDataTypeByRaptriCode = getUniverse( SampleDataType.class, EchoBaseFunctions.SAMPLE_DATA_TYPE_RAPTRI_CODE); + sizeCategoryByName = getUniverse( + SizeCategory.class, EchoBaseFunctions.SIZE_CATEGORY_NAME); + + sexCategoryByName = getUniverse( + SexCategory.class, EchoBaseFunctions.SEX_CATEGORY_NAME); + + speciesCategoryByName = getUniverse( + SpeciesCategory.class, EchoBaseFunctions.SPECIES_CATEGORY_SPIECIES); + Multimap<String, Map<String, Object>> mensurationByNosta = Multimaps.index( db.getTable("MENSURATIONS", true), EchoBaseFunctions.newRowFunction("NOSTA") @@ -147,37 +171,36 @@ SampleType sampleTypeIndividual = sampleTypeDAO.findByName("Individual"); Preconditions.checkNotNull(sampleTypeIndividual); -// SampleDataTypeDAO sampleDataTypeDAO = -// (SampleDataTypeDAO) getDAO(SampleDataType.class); + sampleDataDAO = (SampleDataDAO) getDAO(SampleData.class); - SampleDataDAO sampleDataDAO = (SampleDataDAO) getDAO(SampleData.class); - -// SampleDataType sampleDataTypeMeanLength = sampleDataTypeDAO.findByName("MeanLengthcm"); + //MeanLengthcm SampleDataType sampleDataTypeMeanLength = getFK(sampleDataTypeByRaptriCode, "114"); -// SampleDataType sampleDataTypeMeanWeight = sampleDataTypeDAO.findByName("MeanWeightg"); + //MeanWeightg SampleDataType sampleDataTypeMeanWeight = getFK(sampleDataTypeByRaptriCode, "115"); - -// SampleDataType sampleDataTypeNoPerKg = sampleDataTypeDAO.findByName("NoPerKg"); + //NoPerKg SampleDataType sampleDataTypeNoPerKg = getFK(sampleDataTypeByRaptriCode, "116"); -// SampleDataType sampleDataTypeNumberAtLength = sampleDataTypeDAO.findByName("NumberAtLength"); + //NumberAtLength SampleDataType sampleDataTypeNumberAtLength = getFK(sampleDataTypeByRaptriCode, "112"); -// SampleDataType sampleDataTypeWeightAtLength = sampleDataTypeDAO.findByName("WeightAtLengthkg"); + //WeightAtLengthkg SampleDataType sampleDataTypeWeightAtLength = getFK(sampleDataTypeByRaptriCode, "113"); - TopiaDAO<Sample> dao = getDAO(); - + dao = getDAO(); + speciesCategoryDAO = (SpeciesCategoryDAO) getDAO(SpeciesCategory.class); int nbSampleUnsorted = 0; int nbSampleTotal = 0; int nbSubSample = 0; int nbIndividualSample = 0; + List<String> operationNotFound = Lists.newArrayList(); + List<String> ntotNull = Lists.newArrayList(); + List<String> pmensNull = Lists.newArrayList(); + List<String> valeurBiometryNull = Lists.newArrayList(); + for (String operationId : capturesByNosta.keySet()) { Preconditions.checkNotNull(operationId); Operation operation = operationById.get(operationId); if (operation == null) { - if (log.isWarnEnabled()) { - log.warn("Operation " + operationId + " not found..."); - } + operationNotFound.add(operationId); continue; } Collection<Map<String, Object>> biometryValues = @@ -187,33 +210,53 @@ biometryValues, EchoBaseFunctions.newRowFunction("GENRE_ESP_VALEUR_BIOMETRIE") ); + + SpeciesCategory speciesCategory; + SpeciesCategory speciesCategoryForSpecies; + for (Map<String, Object> row : capturesByNosta.get(operationId)) { String type = (String) row.get("CATEG"); SampleType sampleType; + String speciesId = (String) row.get("GENRE_ESP"); + Species species = getFK(speciesByName, speciesId); + if ("H".equals(type)) { + + speciesCategory = getSpeciesCategory(species, "0", null); + speciesCategoryForSpecies = getSpeciesCategory(species, null, null); sampleType = sampleTypeUnsorted; nbSampleUnsorted++; } else { sampleType = sampleTypeTotal; + + if ("F".equals(type) || "M".equals(type)) { + + speciesCategory = getSpeciesCategory( + species, + null, + type); + } else { + + speciesCategory = getSpeciesCategory( + species, + type, + null); + } + + speciesCategoryForSpecies = getSpeciesCategory(species, null, null); nbSampleTotal++; } - String speciesId = (String) row.get("GENRE_ESP"); - Species species = getFK(speciesByName, speciesId); - Integer number = (Integer) row.get("NTOT"); if (number == null) { - if (log.isWarnEnabled()) { - log.warn("NTOT is null for operation " + operationId + "/" + speciesId); - } - number = 0; + ntotNull.add(operationId + "/" + speciesId); } Float weight = (Float) row.get("PT_ESP"); Sample sample = dao.create( - Sample.PROPERTY_SPECIES, species, + Sample.PROPERTY_SPECIES_CATEGORY, speciesCategory, Sample.PROPERTY_SAMPLE_TYPE, sampleType, Sample.PROPERTY_NUMBER_SAMPLED, number, Sample.PROPERTY_SAMPLE_WEIGHT, weight @@ -221,20 +264,17 @@ operation.addSample(sample); - addSampleData(sampleDataDAO, - sample, + addSampleData(sample, sampleDataTypeMeanWeight, "NA", row.get("PMOY")); - addSampleData(sampleDataDAO, - sample, + addSampleData(sample, sampleDataTypeMeanLength, "NA", row.get("LMOY")); - addSampleData(sampleDataDAO, - sample, + addSampleData(sample, sampleDataTypeNoPerKg, "NA", row.get("MOULE_MENS")); @@ -244,20 +284,15 @@ Float sampleWeight = (Float) row.get("PESP_MENS"); if (sampleWeight == null) { - if (log.isWarnEnabled()) { - log.warn("PESP_MENS is null for operation " + operationId + "/" + speciesId); - } - sampleWeight = 0f; + pmensNull.add(operationId + "/" + speciesId); } - addSubSamples(dao, - sampleDataDAO, + addSubSamples(speciesCategory, sampleTypeSubsample, sampleDataTypeNumberAtLength, sampleDataTypeWeightAtLength, operation, type, - species, sampleWeight, mensurationRows); @@ -267,19 +302,39 @@ Collection<Map<String, Object>> biometryValuesRows = biometryValuesBySpecies.get(speciesId); - int nbSampleIndiv = addSampleIndividuals(dao, - sampleDataDAO, - operation, - species, + int nbSampleIndiv = addSampleIndividuals(operation, + speciesCategoryForSpecies, sampleTypeIndividual, sampleDataTypeByRaptriCode, biometryScalesByRaptri, - biometryValuesRows); + biometryValuesRows, + valeurBiometryNull); nbIndividualSample += nbSampleIndiv; } } + if (!operationNotFound.isEmpty()) { + if (log.isWarnEnabled()) { + log.warn("operation not found : \n" + StringUtil.join(operationNotFound, "\n", false)); + } + } + + if (!ntotNull.isEmpty()) { + if (log.isWarnEnabled()) { + log.warn("NTOT is null for operation :\n" + StringUtil.join(ntotNull, "\n", false)); + } + } + if (!pmensNull.isEmpty()) { + if (log.isWarnEnabled()) { + log.warn("PESP_MENS is null for operation\n" + StringUtil.join(pmensNull, "\n", false)); + } + } + if (!valeurBiometryNull.isEmpty()) { + if (log.isWarnEnabled()) { + log.warn("Null value of VALEUR_BIOMETRIE for operationId/Species/Individu/Code param\n" + StringUtil.join(valeurBiometryNull, "\n", false)); + } + } if (log.isInfoEnabled()) { log.info("Found " + nbSampleTotal + " 'total' sample(s)."); log.info("Found " + nbSampleUnsorted + " 'unsorted' sample(s)."); @@ -289,29 +344,78 @@ } } - private int addSampleIndividuals(TopiaDAO<Sample> dao, - SampleDataDAO sampleDataDAO, - Operation operation, - Species species, + private void addSubSamples(SpeciesCategory speciesCategory, + SampleType sampleTypeSubsample, + SampleDataType sampleDataTypeNumberAtLength, + SampleDataType sampleDataTypeWeightAtLength, + Operation operation, + String type, + Float sampleWeight, + Collection<Map<String, Object>> mesnurationRows) throws TopiaException { + + String speciesId = speciesCategory.getSpecies().getBaracoudaCode(); + + for (Map<String, Object> row : mesnurationRows) { + String categ = (String) row.get("CATEG"); + if (!type.equals(categ)) { + + // not good category + continue; + } + String rowSpeciesId = (String) row.get("GENRE_ESP"); + if (!speciesId.equals(rowSpeciesId)) { + + // not good species + continue; + } + + // ok found a good row + Sample subsample = dao.create( + Sample.PROPERTY_SPECIES_CATEGORY, speciesCategory, + Sample.PROPERTY_SAMPLE_TYPE, sampleTypeSubsample, + Sample.PROPERTY_SAMPLE_WEIGHT, sampleWeight + ); + + Object lengthClass = row.get("TAILLE"); + + addSampleData(subsample, + sampleDataTypeNumberAtLength, + lengthClass, + row.get("NBIND") + ); + + addSampleData(subsample, + sampleDataTypeWeightAtLength, + lengthClass, + row.get("POIDSTAILLE") + ); + + operation.addSample(subsample); + + } + } + + private int addSampleIndividuals(Operation operation, + SpeciesCategory speciesCategory, SampleType sampleTypeIndividual, Map<String, SampleDataType> sampleDataTypeByRaptriCode, Multimap<Integer, Map<String, Object>> biometryScalesByRaptri, - Collection<Map<String, Object>> biometryValuesRows) throws TopiaException { + Collection<Map<String, Object>> biometryValuesRows, + List<String> valeurBiometryNull) throws TopiaException { int result = 0; Sample sample = null; Set<Integer> individus = Sets.newHashSet(); + String speciesId = speciesCategory.getSpecies().getBaracoudaCode(); for (Map<String, Object> biometryValuesRow : biometryValuesRows) { Integer ind = Integer.valueOf(biometryValuesRow.get("NUMIND_VALEUR_BIOMETRIE").toString()); Integer codeParameter = (Integer) biometryValuesRow.get("CODE_PARAM_VALEUR_BIOMETRIE"); String label = null; Float value = (Float) biometryValuesRow.get("VALEUR_BIOMETRIE"); - if (value==null) { - if (log.isWarnEnabled()) { - log.warn("Null value of VALEUR_BIOMETRIE for operationId/Species/Individu/Code param " + operation.getId() + "/" + species.getBaracoudaCode() + "/" + ind+"/"+codeParameter); - } + if (value == null) { + valeurBiometryNull.add(operation.getId() + "/" + speciesId + "/" + ind + "/" + codeParameter); continue; } - Preconditions.checkNotNull(value, "Null value of VALEUR_BIOMETRIE for operationId/Species/Individu/Code param " + operation.getId() + "/" + species.getBaracoudaCode() + "/" + ind+"/"+codeParameter); + Preconditions.checkNotNull(value, "Null value of VALEUR_BIOMETRIE for operationId/Species/Individu/Code param " + operation.getId() + "/" + speciesId + "/" + ind + "/" + codeParameter); SampleDataType sampleDataType = getFK(sampleDataTypeByRaptriCode, String.valueOf(codeParameter)); boolean add = individus.add(ind); @@ -319,7 +423,7 @@ // new sample sample = dao.create( - Sample.PROPERTY_SPECIES, species, + Sample.PROPERTY_SPECIES_CATEGORY, speciesCategory, Sample.PROPERTY_SAMPLE_TYPE, sampleTypeIndividual ); @@ -348,8 +452,7 @@ } } } - addSampleData(sampleDataDAO, - sample, + addSampleData(sample, sampleDataType, label, value @@ -358,65 +461,7 @@ return result; } - private void addSubSamples(TopiaDAO<Sample> dao, - SampleDataDAO sampleDataDAO, - SampleType sampleTypeSubsample, - SampleDataType sampleDataTypeNumberAtLength, - SampleDataType sampleDataTypeWeightAtLength, - Operation operation, - String type, - Species species, - Float sampleWeight, - Collection<Map<String, Object>> mesnurationRows) throws TopiaException { - - String speciesId = species.getBaracoudaCode(); - - for (Map<String, Object> row : mesnurationRows) { - String categ = (String) row.get("CATEG"); - if (!type.equals(categ)) { - - // not good category - continue; - } - String rowSpeciesId = (String) row.get("GENRE_ESP"); - if (!speciesId.equals(rowSpeciesId)) { - - // not good species - continue; - } - - // ok found a good row - Sample subsample = dao.create( - Sample.PROPERTY_SPECIES, species, - Sample.PROPERTY_SAMPLE_TYPE, sampleTypeSubsample, - Sample.PROPERTY_SAMPLE_WEIGHT, sampleWeight - ); - - Object lengthClass = row.get("TAILLE"); - - addSampleData(sampleDataDAO, - subsample, - sampleDataTypeNumberAtLength, - lengthClass, - row.get("NBIND") - ); - - addSampleData(sampleDataDAO, - subsample, - sampleDataTypeWeightAtLength, - lengthClass, - row.get("POIDSTAILLE") - ); - - - operation.addSample(subsample); - - } - } - - - protected void addSampleData(TopiaDAO<SampleData> dao, - Sample operation, + protected void addSampleData(Sample operation, SampleDataType sampleDataType, Object label, Object value @@ -426,7 +471,7 @@ return; } - SampleData sampleData = dao.create( + SampleData sampleData = sampleDataDAO.create( SampleData.PROPERTY_SAMPLE_DATA_TYPE, sampleDataType, SampleData.PROPERTY_DATA_LABEL, label.toString(), SampleData.PROPERTY_DATA_VALUE, Float.valueOf(value.toString()) @@ -434,5 +479,23 @@ operation.addSampleData(sampleData); } + protected SpeciesCategory getSpeciesCategory(Species species, + String sizeName, + String sexName) throws TopiaException { + SexCategory sexCategory = null; + if (sexName != null) { + sexCategory = getFK(sexCategoryByName, sexName); + } + + SizeCategory sizeCategory = null; + if (sizeName != null) { + sizeCategory = getFK(sizeCategoryByName, sizeName); + } + String speciesCategoryKey = EchoBaseFunctions.getSpeciesCategoryKey(species, sizeCategory, sexCategory); + + // get species category to use + SpeciesCategory speciesCategory = getFK(speciesCategoryByName, speciesCategoryKey); + return speciesCategory; + } } \ No newline at end of file Modified: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SpeciesCategoryLoader.java =================================================================== --- trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SpeciesCategoryLoader.java 2011-12-19 19:16:01 UTC (rev 202) +++ trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SpeciesCategoryLoader.java 2011-12-19 19:16:34 UTC (rev 203) @@ -23,11 +23,24 @@ */ package fr.ifremer.echobase.tools.loaders; -import fr.ifremer.echobase.entities.meta.TableMeta; +import com.google.common.collect.Lists; +import com.healthmarketscience.jackcess.Database; +import fr.ifremer.echobase.EchoBaseFunctions; +import fr.ifremer.echobase.entities.references.LengthWeightKey; +import fr.ifremer.echobase.entities.references.SexCategory; +import fr.ifremer.echobase.entities.references.SizeCategory; +import fr.ifremer.echobase.entities.references.Species; import fr.ifremer.echobase.entities.references.SpeciesCategory; -import fr.ifremer.echobase.services.models.EntityCsvModel; +import fr.ifremer.echobase.entities.references.SpeciesCategoryDAO; import fr.ifremer.echobase.tools.FileType; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.topia.TopiaException; +import java.io.IOException; +import java.util.List; +import java.util.Map; + /** * To load {@link SpeciesCategory} entities. * @@ -36,23 +49,148 @@ */ public class SpeciesCategoryLoader extends EntityLoader<SpeciesCategory> { + /** Logger. */ + private static final Log log = + LogFactory.getLog(SpeciesCategoryLoader.class); + public SpeciesCategoryLoader() { - super(SpeciesCategory.class, FileType.NEW); + super(SpeciesCategory.class, FileType.BARACOUDA); } - @Override - protected EntityCsvModel<SpeciesCategory> createCsvImportModel(TableMeta meta) { + protected void importBaracoudaEntities(Database db) throws IOException, TopiaException { - EntityCsvModel<SpeciesCategory> model = EntityCsvModel.newModel( - getCsvSeparator(), - meta + Map<String, Species> speciesByName = getUniverse( + Species.class, EchoBaseFunctions.SPECIES_BARACOUDA_CODE); + + Map<String, SizeCategory> sizeCategoryByName = getUniverse( + SizeCategory.class, EchoBaseFunctions.SIZE_CATEGORY_NAME); + + Map<String, SexCategory> sexCategoryByName = getUniverse( + SexCategory.class, EchoBaseFunctions.SEX_CATEGORY_NAME); + + SpeciesCategoryDAO speciesCategoryDAO = + (SpeciesCategoryDAO) getDAO(SpeciesCategory.class); + + List<LengthWeightKey> lengthWeightKeys = Lists.newArrayList(); + + for (Map<String, Object> row : db.getTable("TAILLE_POIDS")) { + + String speciesCode = (String) row.get("Genre_esp"); + Species species = getFK(speciesByName, speciesCode); + + String sizeCode = (String) row.get("Categorie"); + if ("NA".equals(sizeCode) || "H".equals(sizeCode)) { + sizeCode = "0"; + } + + SizeCategory sizeCategory = getFK(sizeCategoryByName, sizeCode); + getSpeciesCategory(speciesCategoryDAO, species, sizeCategory); + } + + for (Map<String, Object> row : db.getTable("CAPTURES")) { + + String speciesCode = (String) row.get("GENRE_ESP"); + Species species = getFK(speciesByName, speciesCode); + + String sizeCode = (String) row.get("CATEG"); + if ("H".equals(sizeCode)) { + sizeCode = "0"; + } + + if ("F".equals(sizeCode) || "M".equals(sizeCode)) { + + SexCategory sexCategory = getFK(sexCategoryByName, sizeCode); + getSpeciesCategory(speciesCategoryDAO, species, sexCategory); + + } else { + + SizeCategory sizeCategory = getFK(sizeCategoryByName, sizeCode); + getSpeciesCategory(speciesCategoryDAO, species, sizeCategory); + } + + getSpeciesCategory(speciesCategoryDAO, species); + } + + if (log.isInfoEnabled()) { + log.info("Found " + lengthWeightKeys.size() + " speciesCategories."); + } + } + + protected SpeciesCategory getSpeciesCategory(SpeciesCategoryDAO speciesCategoryDAO, + Species species, + SizeCategory sizeCategory) throws TopiaException { + + // get species category to use + SpeciesCategory speciesCategory = speciesCategoryDAO.findByProperties( + SpeciesCategory.PROPERTY_SPECIES, species, + SpeciesCategory.PROPERTY_SIZE_CATEGORY, sizeCategory ); - model.newMandatoryColumn(SpeciesCategory.PROPERTY_SPECIES); - model.newMandatoryColumn(SpeciesCategory.PROPERTY_SIZE_CATEGORY); - model.newMandatoryColumn(SpeciesCategory.PROPERTY_AGE_CATEGORY); - model.newMandatoryColumn(SpeciesCategory.PROPERTY_SEX_CATEGORY); - return model; + if (speciesCategory == null) { + + // create it in db + speciesCategory = speciesCategoryDAO.create( + SpeciesCategory.PROPERTY_SPECIES, species, + SpeciesCategory.PROPERTY_SIZE_CATEGORY, sizeCategory + ); + + if (log.isInfoEnabled()) { + log.info("Create speciesCategory speciesBaracoudaCode/size : " + + species.getBaracoudaCode() + "/" + + (sizeCategory == null ? null : sizeCategory.getName())); + } + } + return speciesCategory; } + protected SpeciesCategory getSpeciesCategory(SpeciesCategoryDAO speciesCategoryDAO, + Species species, + SexCategory sexCategory) throws TopiaException { + + // get species category to use + SpeciesCategory speciesCategory = speciesCategoryDAO.findByProperties( + SpeciesCategory.PROPERTY_SPECIES, species, + SpeciesCategory.PROPERTY_SEX_CATEGORY, sexCategory + ); + if (speciesCategory == null) { + + // create it in db + speciesCategory = speciesCategoryDAO.create( + SpeciesCategory.PROPERTY_SPECIES, species, + SpeciesCategory.PROPERTY_SEX_CATEGORY, sexCategory + ); + + if (log.isInfoEnabled()) { + log.info("Create speciesCategory speciesBaracoudaCode/sex : " + + species.getBaracoudaCode() + "/" + + (sexCategory == null ? null : sexCategory.getName())); + } + } + return speciesCategory; + } + + protected SpeciesCategory getSpeciesCategory(SpeciesCategoryDAO speciesCategoryDAO, + Species species) throws TopiaException { + + // get species category to use + SpeciesCategory speciesCategory = speciesCategoryDAO.findByProperties( + SpeciesCategory.PROPERTY_SPECIES, species, + SpeciesCategory.PROPERTY_SEX_CATEGORY, null, + SpeciesCategory.PROPERTY_SIZE_CATEGORY, null + ); + + if (speciesCategory == null) { + + // create it in db + speciesCategory = speciesCategoryDAO.create( + SpeciesCategory.PROPERTY_SPECIES, species + ); + + if (log.isInfoEnabled()) { + log.info("Create speciesCategory speciesBaracoudaCode : " + + species.getBaracoudaCode()); + } + } + return speciesCategory; + } } \ No newline at end of file Modified: trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/AbstractLoaderIT.java =================================================================== --- trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/AbstractLoaderIT.java 2011-12-19 19:16:01 UTC (rev 202) +++ trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/AbstractLoaderIT.java 2011-12-19 19:16:34 UTC (rev 203) @@ -357,7 +357,8 @@ entityLoaders.add(newService(OperationEventLoader.class)); entityLoaders.add(newService(SampleDataTypeLoader.class)); entityLoaders.add(newService(SampleTypeLoader.class)); - entityLoaders.add(newService(BiometryScaleLoader.class)); + entityLoaders.add(newService(LengthAgeKeyLoader.class)); + entityLoaders.add(newService(LengthWeightKeyLoader.class)); entityLoaders.add(newService(SexCategoryLoader.class)); entityLoaders.add(newService(SizeCategoryLoader.class)); entityLoaders.add(newService(OperationMetadataLoader.class)); Deleted: trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoaderIT.java =================================================================== --- trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoaderIT.java 2011-12-19 19:16:01 UTC (rev 202) +++ trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoaderIT.java 2011-12-19 19:16:34 UTC (rev 203) @@ -1,45 +0,0 @@ -/* - * #%L - * EchoBase :: Tools - * - * $Id$ - * $HeadURL$ - * %% - * Copyright (C) 2011 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% - */ -package fr.ifremer.echobase.tools.loaders; - -import fr.ifremer.echobase.entities.references.BiometryScale; -import org.junit.Test; - -/** - * To test the {@link BiometryScaleLoader}. - * - * @author tchemit <chemit(a)codelutin.com> - * @since 0.2 - */ -public class BiometryScaleLoaderIT extends AbstractLoaderIT<BiometryScale, BiometryScaleLoader> { - - public BiometryScaleLoaderIT() { - super(BiometryScaleLoader.class, 44, 0); - } - - @Test - public void testGenerateNewEntities() throws Exception { - generateNewEntities(); - } -} Added: trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/LengthAgeKeyLoaderIT.java =================================================================== --- trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/LengthAgeKeyLoaderIT.java (rev 0) +++ trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/LengthAgeKeyLoaderIT.java 2011-12-19 19:16:34 UTC (rev 203) @@ -0,0 +1,46 @@ +/* + * #%L + * EchoBase :: Tools + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2011 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% + */ +package fr.ifremer.echobase.tools.loaders; + +import fr.ifremer.echobase.entities.references.LengthAgeKey; +import org.junit.Test; + +/** + * To test the {@link LengthAgeKeyLoader}. + * + * @author tchemit <chemit(a)codelutin.com> + * @since 0.2 + */ +public class LengthAgeKeyLoaderIT extends AbstractLoaderIT<LengthAgeKey, LengthAgeKeyLoader> { + + public LengthAgeKeyLoaderIT() { + super(LengthAgeKeyLoader.class, 0, 1637); + } + + @Test + public void testGenerateEntitiesFromBaracouda() throws Exception { + generateBaracoudaEntities(); + } + +} \ No newline at end of file Property changes on: trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/LengthAgeKeyLoaderIT.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Added: trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/LengthWeightKeyLoaderIT.java =================================================================== --- trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/LengthWeightKeyLoaderIT.java (rev 0) +++ trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/LengthWeightKeyLoaderIT.java 2011-12-19 19:16:34 UTC (rev 203) @@ -0,0 +1,46 @@ +/* + * #%L + * EchoBase :: Tools + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2011 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% + */ +package fr.ifremer.echobase.tools.loaders; + +import fr.ifremer.echobase.entities.references.LengthWeightKey; +import org.junit.Test; + +/** + * To test the {@link LengthWeightKeyLoader}. + * + * @author tchemit <chemit(a)codelutin.com> + * @since 0.2 + */ +public class LengthWeightKeyLoaderIT extends AbstractLoaderIT<LengthWeightKey, LengthWeightKeyLoader> { + + public LengthWeightKeyLoaderIT() { + super(LengthWeightKeyLoader.class, 0, 218); + } + + @Test + public void testGenerateEntitiesFromBaracouda() throws Exception { + generateBaracoudaEntities(); + } + +} \ No newline at end of file Property changes on: trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/LengthWeightKeyLoaderIT.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Modified: trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/OperationLoaderIT.java =================================================================== --- trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/OperationLoaderIT.java 2011-12-19 19:16:01 UTC (rev 202) +++ trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/OperationLoaderIT.java 2011-12-19 19:16:34 UTC (rev 203) @@ -35,7 +35,7 @@ public class OperationLoaderIT extends AbstractLoaderIT<Operation, OperationLoader> { public OperationLoaderIT() { - super(OperationLoader.class, 0, 1374); + super(OperationLoader.class, 0, 1489); } @Test Modified: trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SampleLoaderIT.java =================================================================== --- trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SampleLoaderIT.java 2011-12-19 19:16:01 UTC (rev 202) +++ trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SampleLoaderIT.java 2011-12-19 19:16:34 UTC (rev 203) @@ -35,7 +35,7 @@ public class SampleLoaderIT extends AbstractLoaderIT<Sample, SampleLoader> { public SampleLoaderIT() { - super(SampleLoader.class, 0, 324809); + super(SampleLoader.class, 0, 333783); } @Test Modified: trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SpeciesCategoryLoaderIT.java =================================================================== --- trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SpeciesCategoryLoaderIT.java 2011-12-19 19:16:01 UTC (rev 202) +++ trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SpeciesCategoryLoaderIT.java 2011-12-19 19:16:34 UTC (rev 203) @@ -35,12 +35,12 @@ public class SpeciesCategoryLoaderIT extends AbstractLoaderIT<SpeciesCategory, SpeciesCategoryLoader> { public SpeciesCategoryLoaderIT() { - super(SpeciesCategoryLoader.class, 0, 0); + super(SpeciesCategoryLoader.class, 0, 443); } @Test - public void testGenerateNewEntities() throws Exception { - generateNewEntities(); + public void testGenerateEntitiesFromBaracouda() throws Exception { + generateBaracoudaEntities(); } } \ No newline at end of file Deleted: trunk/echobase-tools/src/test/resources/csv/new/input-BiometryScale.csv =================================================================== --- trunk/echobase-tools/src/test/resources/csv/new/input-BiometryScale.csv 2011-12-19 19:16:01 UTC (rev 202) +++ trunk/echobase-tools/src/test/resources/csv/new/input-BiometryScale.csv 2011-12-19 19:16:34 UTC (rev 203) @@ -1,45 +0,0 @@ -raptriBiometryDataType;ScaleCode;ScaleMeaningEng;ScaleMeaningFr -3;0;Undetermined;indeterminé -3;1;Male;male -3;2;Female;femelle -3;3;NA (IEO- Pelacus1007);Non renseigné (IEO- Pelacus1007) -4;1;Immature/virgin;Immature/virgin -4;2;Developing;Developing -4;3;Prespawning;Prespawning -4;4;Spawning;Spawning -4;5;Spent;Spent -4;6;Resting;Resting -7;0;Easily readable;facile à lire -7;1;Hardly readable;difficile à lire -7;2;Unreadable;illisible -7;3;Estimated (ex. juvenile otoliths);Estimée (ex. Otolimetrie juvenile) -8;-1;To be checked by PG;à faire préciser par PG -8;1;"opaque (""H"")";"opaque (""H"")" -8;2;"hyalin (""O"")";"hyalin (""O"")" -8;3;opaque/hyalin;opaque/hyalin -23;1;No fat;No fat -23;2;Low fat;Low fat -23;3;Fat;Fat -23;4;High fat;High fat -24;0;no anisakis;zéro anisakis -24;1;1-10 anisakis;1 à 10 anisakis -24;2;10-20 anisakis;10 à 20 anisakis -24;3;>20 anisakis;> 20 anisakis -25;0;; -25;1;IFREMER - NANTES (PG);IFREMER - NANTES (PG) -25;2;IFREMER - LORIENT (ED);IFREMER - LORIENT (ED) -25;3;AZTI + (PP);AZTI + (PP) -25;4;AZTI (lecture AGE) + IFREMER Nantes (PG) (mesure rayon);AZTI (lecture AGE) + IFREMER Nantes (PG) (mesure rayon) -25;5;EPHE - PERPIGNAN (PL);EPHE - PERPIGNAN (PL) -25;6;IFREMER - IEO (double lecture à bord : Patrick-Carla);IFREMER - IEO (double lecture à bord : Patrick-Carla) -25;7;biometrie et otolithe IFREMER-NANTES (PG) - génétique : EPHE;biometrie et otolithe IFREMER-NANTES (PG) - génétique : EPHE -26;0;clé Taille/Age : NON Valide;clé Taille/Age : NON Valide -26;1;clé Taille/Age : VALIDE;clé Taille/Age : VALIDE -45;0;NA;NA -45;1;Blanc ?;Blanc ? -45;2;?;? -45;3;Complète;Complète -45;4;partielle;partielle -49;0;NA;NA -49;1;DROIT;DROIT -49;2;GAUCHE;GAUCHE \ No newline at end of file Modified: trunk/echobase-tools/src/test/resources/csv/new/input-SexCategory.csv =================================================================== --- trunk/echobase-tools/src/test/resources/csv/new/input-SexCategory.csv 2011-12-19 19:16:01 UTC (rev 202) +++ trunk/echobase-tools/src/test/resources/csv/new/input-SexCategory.csv 2011-12-19 19:16:34 UTC (rev 203) @@ -1,5 +1,5 @@ CategoryID;CategoryName -0;All -G;Large -P;Small -TP;Very small +N;Not determined +F;Female +M;Male +I;Immature \ No newline at end of file Modified: trunk/echobase-tools/src/test/resources/csv/new/input-SizeCategory.csv =================================================================== --- trunk/echobase-tools/src/test/resources/csv/new/input-SizeCategory.csv 2011-12-19 19:16:01 UTC (rev 202) +++ trunk/echobase-tools/src/test/resources/csv/new/input-SizeCategory.csv 2011-12-19 19:16:34 UTC (rev 203) @@ -1,5 +1,5 @@ CategoryID;CategoryName -N;Not determined -F;Female +0;All G;Large -I;Immature \ No newline at end of file +P;Small +TP;Very small \ No newline at end of file

1 0

r202 - in trunk/echobase-entities/src/main: java/fr/ifremer/echobase java/fr/ifremer/echobase/entities resources/i18n xmi
by tchemit＠users.forge.codelutin.com 19 Dec '11

19 Dec '11

Author: tchemit Date: 2011-12-19 20:16:01 +0100 (Mon, 19 Dec 2011) New Revision: 202 Url: http://forge.codelutin.com/repositories/revision/echobase/202 Log: fix entity name + properties Modified: trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseDecoratorProvider.java trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseFunctions.java trunk/echobase-entities/src/main/java/fr/ifremer/echobase/entities/EntitiesUtil.java trunk/echobase-entities/src/main/resources/i18n/echobase-entities_fr_FR.properties trunk/echobase-entities/src/main/xmi/echobase.zargo Modified: trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseDecoratorProvider.java =================================================================== --- trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseDecoratorProvider.java 2011-12-19 08:20:03 UTC (rev 201) +++ trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseDecoratorProvider.java 2011-12-19 19:16:01 UTC (rev 202) @@ -61,6 +61,7 @@ import fr.ifremer.echobase.entities.references.GearMetadata; import fr.ifremer.echobase.entities.references.Impacte; import fr.ifremer.echobase.entities.references.LengthAgeKey; +import fr.ifremer.echobase.entities.references.LengthWeightKey; import fr.ifremer.echobase.entities.references.MeasureType; import fr.ifremer.echobase.entities.references.MeasurementMetadata; import fr.ifremer.echobase.entities.references.Mission; @@ -80,7 +81,6 @@ import fr.ifremer.echobase.entities.references.TSParameters; import fr.ifremer.echobase.entities.references.Vessel; import fr.ifremer.echobase.entities.references.VesselType; -import fr.ifremer.echobase.entities.references.WeightLengthKey; import org.nuiton.util.decorator.DecoratorMulti18nProvider; import java.util.Locale; @@ -233,8 +233,8 @@ // VesselType decorator registerJXPathDecorator(locale, VesselType.class, "${name}$s"); - // WeightLengthKey decorator - registerJXPathDecorator(locale, WeightLengthKey.class, "Species ${species.genusSpecies}$s - a=${aParameter}$s, b=${bParameter}$s"); + // LengthWeightKey decorator + registerJXPathDecorator(locale, LengthWeightKey.class, "Species ${species.genusSpecies}$s - a=${aParameter}$s, b=${bParameter}$s"); // Cell decorator registerJXPathDecorator(locale, Cell.class, "${name}$s"); Modified: trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseFunctions.java =================================================================== --- trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseFunctions.java 2011-12-19 08:20:03 UTC (rev 201) +++ trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseFunctions.java 2011-12-19 19:16:01 UTC (rev 202) @@ -40,7 +40,10 @@ import fr.ifremer.echobase.entities.references.ReferenceDatum; import fr.ifremer.echobase.entities.references.ReferenceDatumType; import fr.ifremer.echobase.entities.references.SampleDataType; +import fr.ifremer.echobase.entities.references.SexCategory; +import fr.ifremer.echobase.entities.references.SizeCategory; import fr.ifremer.echobase.entities.references.Species; +import fr.ifremer.echobase.entities.references.SpeciesCategory; import fr.ifremer.echobase.entities.references.Vessel; import org.apache.commons.lang3.StringUtils; import org.nuiton.topia.persistence.TopiaEntity; @@ -192,7 +195,38 @@ return input.getId(); } }; + public static final Function<SizeCategory, String> SIZE_CATEGORY_NAME = new Function<SizeCategory, String>() { + @Override + public String apply(SizeCategory input) { + return input.getName(); + } + }; + public static final Function<SpeciesCategory, String> SPECIES_CATEGORY_SPIECIES = new Function<SpeciesCategory, String>() { + @Override + public String apply(SpeciesCategory input) { + return getSpeciesCategoryKey(input.getSpecies(), input.getSizeCategory(), input.getSexCategory()); + } + }; + + public static final Function<SexCategory, String> SEX_CATEGORY_NAME = new Function<SexCategory, String>() { + @Override + public String apply(SexCategory input) { + return input.getName(); + } + }; + + public static String getSpeciesCategoryKey(Species species, SizeCategory sizeCategory,SexCategory sexCategory) { + String key = species.getBaracoudaCode(); + if (sizeCategory != null) { + key += "_" + sizeCategory.getName(); + } + if (sexCategory != null) { + key += "_" + sexCategory.getName(); + } + return key; + } + public static Function<Map<String, Object>, String> newRowFunction(final String key) { return new Function<Map<String, Object>, String>() { Modified: trunk/echobase-entities/src/main/java/fr/ifremer/echobase/entities/EntitiesUtil.java =================================================================== --- trunk/echobase-entities/src/main/java/fr/ifremer/echobase/entities/EntitiesUtil.java 2011-12-19 08:20:03 UTC (rev 201) +++ trunk/echobase-entities/src/main/java/fr/ifremer/echobase/entities/EntitiesUtil.java 2011-12-19 19:16:01 UTC (rev 202) @@ -118,13 +118,12 @@ result.add(EchoBaseEntityEnum.OperationType); result.add(EchoBaseEntityEnum.MeasurementMetadata); result.add(EchoBaseEntityEnum.SampleDataType); - result.add(EchoBaseEntityEnum.BiometryScale); result.add(EchoBaseEntityEnum.SampleType); result.add(EchoBaseEntityEnum.Vessel); result.add(EchoBaseEntityEnum.Echotype); result.add(EchoBaseEntityEnum.DataMetadata); result.add(EchoBaseEntityEnum.LengthAgeKey); - result.add(EchoBaseEntityEnum.WeightLengthKey); + result.add(EchoBaseEntityEnum.LengthWeightKey); result.add(EchoBaseEntityEnum.CellType); result.add(EchoBaseEntityEnum.Impacte); result.add(EchoBaseEntityEnum.Mission); Modified: trunk/echobase-entities/src/main/resources/i18n/echobase-entities_fr_FR.properties =================================================================== --- trunk/echobase-entities/src/main/resources/i18n/echobase-entities_fr_FR.properties 2011-12-19 08:20:03 UTC (rev 201) +++ trunk/echobase-entities/src/main/resources/i18n/echobase-entities_fr_FR.properties 2011-12-19 19:16:01 UTC (rev 202) @@ -1,5 +1,6 @@ +echobase.common.AParameter= +echobase.common.BParameter= echobase.common.TSParameters= -echobase.common.aParameter= echobase.common.accuracyEstimate= echobase.common.acknowledgement= echobase.common.acousticDensityUnit= @@ -18,12 +19,10 @@ echobase.common.authorReference= echobase.common.axis= echobase.common.b= -echobase.common.bParameter= echobase.common.baracoudaCode= echobase.common.binSizePingAxis= echobase.common.binSizeRangeAxis= echobase.common.binUnitsPingAxis= -echobase.common.biometryScale= echobase.common.calendar= echobase.common.calibration=calibration echobase.common.callsign= @@ -95,7 +94,6 @@ echobase.common.gearShootingStartLatitude= echobase.common.gearShootingStartLongitude= echobase.common.gearShootingStartTime= -echobase.common.gearType= echobase.common.genusSpecies= echobase.common.geospatialLatMax= echobase.common.geospatialLatMin= @@ -104,7 +102,6 @@ echobase.common.geospatialVerticalMax= echobase.common.geospatialVerticalMin= echobase.common.geospatialVerticalPositive= -echobase.common.group= echobase.common.history= echobase.common.id=Identifiant echobase.common.imo= @@ -117,6 +114,7 @@ echobase.common.lastModifiedUser=Utilisateur de dernière modification echobase.common.length= echobase.common.lengthAgeKey= +echobase.common.lengthWeightKey= echobase.common.level= echobase.common.licence= echobase.common.linestring= @@ -137,7 +135,6 @@ echobase.common.measurementUnit= echobase.common.metadata=metadata echobase.common.metadataGroup= -echobase.common.metadataType= echobase.common.midHauleLatitude= echobase.common.midHauleLongitude= echobase.common.minLatitude= @@ -188,7 +185,6 @@ echobase.common.sampleDataType= echobase.common.sampleType= echobase.common.sampleWeight= -echobase.common.sampling= echobase.common.scaleFactor= echobase.common.seafloorSubstrate= echobase.common.sexCategory= @@ -257,5 +253,4 @@ echobase.common.vessel=Navire echobase.common.vesselType= echobase.common.voyage=Campagne -echobase.common.weightLengthKey= echobase.config.data.directory.description=Chemin de l'application Modified: trunk/echobase-entities/src/main/xmi/echobase.zargo =================================================================== (Binary files differ)

1 0

r201 - in trunk: . echobase-services echobase-tools
by tchemit＠users.forge.codelutin.com 19 Dec '11

19 Dec '11

Author: tchemit Date: 2011-12-19 09:20:03 +0100 (Mon, 19 Dec 2011) New Revision: 201 Url: http://forge.codelutin.com/repositories/revision/echobase/201 Log: optimize dependencies Modified: trunk/echobase-services/pom.xml trunk/echobase-tools/pom.xml trunk/pom.xml Modified: trunk/echobase-services/pom.xml =================================================================== --- trunk/echobase-services/pom.xml 2011-12-19 08:10:42 UTC (rev 200) +++ trunk/echobase-services/pom.xml 2011-12-19 08:20:03 UTC (rev 201) @@ -55,10 +55,10 @@ <artifactId>commons-lang3</artifactId> </dependency> -  + <dependency> + <groupId>net.sourceforge.javacsv</groupId> + <artifactId>javacsv</artifactId> + </dependency> <dependency> <groupId>commons-beanutils</groupId> Modified: trunk/echobase-tools/pom.xml =================================================================== --- trunk/echobase-tools/pom.xml 2011-12-19 08:10:42 UTC (rev 200) +++ trunk/echobase-tools/pom.xml 2011-12-19 08:20:03 UTC (rev 201) @@ -62,6 +62,11 @@  <dependency> + <groupId>org.apache.commons</groupId> + <artifactId>commons-lang3</artifactId> + </dependency> + + <dependency> <groupId>commons-logging</groupId> <artifactId>commons-logging</artifactId> </dependency> Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2011-12-19 08:10:42 UTC (rev 200) +++ trunk/pom.xml 2011-12-19 08:20:03 UTC (rev 201) @@ -309,6 +309,12 @@ <version>10.0.1</version> </dependency> + <dependency> + <groupId>net.sourceforge.javacsv</groupId> + <artifactId>javacsv</artifactId> + <version>2.0</version> + </dependency> +  <dependency>

1 0

r200 - in trunk: echobase-entities/src/main/java/fr/ifremer/echobase/entities echobase-entities/src/main/xmi echobase-services/src/main/java/fr/ifremer/echobase/services src/doc/reunions
by tchemit＠users.forge.codelutin.com 19 Dec '11

19 Dec '11

Author: tchemit Date: 2011-12-19 09:10:42 +0100 (Mon, 19 Dec 2011) New Revision: 200 Url: http://forge.codelutin.com/repositories/revision/echobase/200 Log: little stuff before small release Added: trunk/src/doc/reunions/reunion-2011-12-19.txt Modified: trunk/echobase-entities/src/main/java/fr/ifremer/echobase/entities/EntitiesUtil.java trunk/echobase-entities/src/main/xmi/echobase.zargo trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/DbImportService.java Modified: trunk/echobase-entities/src/main/java/fr/ifremer/echobase/entities/EntitiesUtil.java =================================================================== --- trunk/echobase-entities/src/main/java/fr/ifremer/echobase/entities/EntitiesUtil.java 2011-12-16 17:54:16 UTC (rev 199) +++ trunk/echobase-entities/src/main/java/fr/ifremer/echobase/entities/EntitiesUtil.java 2011-12-19 08:10:42 UTC (rev 200) @@ -169,6 +169,9 @@ result.add(EchoBaseEntityEnum.DataQuality); result.add(EchoBaseEntityEnum.CellMethod); result.add(EchoBaseEntityEnum.CellType); + result.add(EchoBaseEntityEnum.OperationEvent); + result.add(EchoBaseEntityEnum.SampleDataType); + result.add(EchoBaseEntityEnum.SampleType); result.add(EchoBaseEntityEnum.DataMetadata); result.add(EchoBaseEntityEnum.OperationMetadata); result.add(EchoBaseEntityEnum.GearMetadata); Modified: trunk/echobase-entities/src/main/xmi/echobase.zargo =================================================================== (Binary files differ) Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/DbImportService.java =================================================================== --- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/DbImportService.java 2011-12-16 17:54:16 UTC (rev 199) +++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/DbImportService.java 2011-12-19 08:10:42 UTC (rev 200) @@ -294,7 +294,6 @@ importer.close(); } - } } @@ -320,10 +319,6 @@ TableMeta tableMeta = getTableMeta(type); entities.add(tableMeta); - -// for (AssociationMeta associationMeta : tableMeta.getAssociations()) { -// associations.add(associationMeta); -// } associations.addAll(tableMeta.getAssociations()); } } Added: trunk/src/doc/reunions/reunion-2011-12-19.txt =================================================================== --- trunk/src/doc/reunions/reunion-2011-12-19.txt (rev 0) +++ trunk/src/doc/reunions/reunion-2011-12-19.txt 2011-12-19 08:10:42 UTC (rev 200) @@ -0,0 +1,58 @@ +projet echobase +--------------- + +Lundi 19-12-2011 (Ifremer) + +Présents : Mathieu et Tony + +Planning +-------- + +- Revoir quelques points sur le modèle + +Modèle pêche +------------ + +- SpeciesCategory ? +- Sample est lié à SpeciesCategory et Species ? +- LengthAgeKey ? +- WeightLengthKey ? +- BiometryScale ? + +Import nouvelles données +------------------------ + +- Planning ? + +Réalisation modèle pêche +------------------------ + +- Report des modifications du modèle +- Remplissage du référentiel OperationEvent +- Remplissage du référentiel SampleDataType +- Remplissage du référentiel SampleType +- Création entité BiometryScale +- Remplissage du référentiel BiometryScale +- Remplissage du référentiel SexCategory +- Remplissage du référentiel SizeCategory +- Remplissage du référentiel OperationMetadata +- Remplissage du référentiel GearMetadata +- Remplissage du référentiel Gear + +- Import des opérations (depuis table STATIONS) +- Import des samples (depuis table CAPTURES/MENSURATIONS/BIOMETRIE_VALEURS) + +Action +------ + +- Code + + - livraison 0.2 avec toutes les données anciennes + +- Ifremer + + - fournir les référentiels manquants + +Prochaine réunion : + + - Lundi 19 à 10h00 à l'Ifremer avec Mathieu \ No newline at end of file Property changes on: trunk/src/doc/reunions/reunion-2011-12-19.txt ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native

1 0

r199 - in trunk: echobase-entities/src/main/java/fr/ifremer/echobase echobase-entities/src/main/resources/i18n echobase-entities/src/main/xmi echobase-tools echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders src/doc/reunions
by tchemit＠users.forge.codelutin.com 16 Dec '11

16 Dec '11

Author: tchemit Date: 2011-12-16 18:54:16 +0100 (Fri, 16 Dec 2011) New Revision: 199 Url: http://forge.codelutin.com/repositories/revision/echobase/199 Log: - fix test resources - continue Catches legacy datas import Modified: trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseFunctions.java trunk/echobase-entities/src/main/resources/i18n/echobase-entities_fr_FR.properties trunk/echobase-entities/src/main/xmi/echobase.zargo trunk/echobase-tools/pom.xml trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoader.java trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/OperationLoader.java trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SampleLoader.java trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SampleLoaderIT.java trunk/src/doc/reunions/reunion-2011-12-14.txt Modified: trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseFunctions.java =================================================================== --- trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseFunctions.java 2011-12-16 01:46:20 UTC (rev 198) +++ trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseFunctions.java 2011-12-16 17:54:16 UTC (rev 199) @@ -45,7 +45,6 @@ import org.apache.commons.lang3.StringUtils; import org.nuiton.topia.persistence.TopiaEntity; -import javax.annotation.Nullable; import java.io.File; import java.util.Map; @@ -165,7 +164,7 @@ return input.getName(); } }; - public static final Function<SampleDataType, String> SAMPLE_DATA_TYPE_RAPRI_CODE = new Function<SampleDataType, String>() { + public static final Function<SampleDataType, String> SAMPLE_DATA_TYPE_RAPTRI_CODE = new Function<SampleDataType, String>() { @Override public String apply(SampleDataType input) { return String.valueOf(input.getRaptriBiometryDataType()); @@ -186,6 +185,7 @@ return StringUtils.isEmpty(casinoGearName) ? input.getName() : casinoGearName; } }; + public static final Function<Operation, String> OPERATION_ID = new Function<Operation, String>() { @Override public String apply(Operation input) { Modified: trunk/echobase-entities/src/main/resources/i18n/echobase-entities_fr_FR.properties =================================================================== --- trunk/echobase-entities/src/main/resources/i18n/echobase-entities_fr_FR.properties 2011-12-16 01:46:20 UTC (rev 198) +++ trunk/echobase-entities/src/main/resources/i18n/echobase-entities_fr_FR.properties 2011-12-16 17:54:16 UTC (rev 199) @@ -138,6 +138,8 @@ echobase.common.metadata=metadata echobase.common.metadataGroup= echobase.common.metadataType= +echobase.common.midHauleLatitude= +echobase.common.midHauleLongitude= echobase.common.minLatitude= echobase.common.minLongitude= echobase.common.mission=mission Modified: trunk/echobase-entities/src/main/xmi/echobase.zargo =================================================================== (Binary files differ) Modified: trunk/echobase-tools/pom.xml =================================================================== --- trunk/echobase-tools/pom.xml 2011-12-16 01:46:20 UTC (rev 198) +++ trunk/echobase-tools/pom.xml 2011-12-16 17:54:16 UTC (rev 199) @@ -205,6 +205,12 @@ <include>**/*.csv</include> </includes> </testResource> + <testResource> + <directory>src/test/resources</directory> + <includes> + <include>**/*.properties</include> + </includes> + </testResource> </testResources> </build> </profile> Modified: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoader.java =================================================================== --- trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoader.java 2011-12-16 01:46:20 UTC (rev 198) +++ trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoader.java 2011-12-16 17:54:16 UTC (rev 199) @@ -58,7 +58,7 @@ /* raptriBiometryDataType;ScaleCode;ScaleMeaningEng;ScaleMeaningFr */ - model.addForeignKeyForImport("raptriBiometryDataType", BiometryScale.PROPERTY_SAMPLE_DATA_TYPE, SampleDataType.class, sampleDataTypes, EchoBaseFunctions.SAMPLE_DATA_TYPE_RAPRI_CODE); + model.addForeignKeyForImport("raptriBiometryDataType", BiometryScale.PROPERTY_SAMPLE_DATA_TYPE, SampleDataType.class, sampleDataTypes, EchoBaseFunctions.SAMPLE_DATA_TYPE_RAPTRI_CODE); model.addDefaultColumn("ScaleCode",BiometryScale.PROPERTY_CODE, int.class); model.newMandatoryColumn("ScaleMeaningEng",BiometryScale.PROPERTY_MEANING_EN); model.newMandatoryColumn("ScaleMeaningFr",BiometryScale.PROPERTY_MEANING_FR); Modified: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/OperationLoader.java =================================================================== --- trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/OperationLoader.java 2011-12-16 01:46:20 UTC (rev 198) +++ trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/OperationLoader.java 2011-12-16 17:54:16 UTC (rev 199) @@ -119,40 +119,63 @@ copyAndLoadEntities(outputDir, meta.getAssociations(Operation.PROPERTY_OPERATION_METADATA_VALUE), false, FileType.ASSOCIATION); copyAndLoadEntities(outputDir, meta.getAssociations(Operation.PROPERTY_GEAR_METADATA_VALUE), false, FileType.ASSOCIATION); - } + //SONDE + OperationMetadata MeanWaterDepthOperationMeta; + //JOUR_NUIT + OperationMetadata DielPeriodOperationMeta; + //SONDEDEB + OperationMetadata StartWaterDepthOperationMeta; + //SONDEFIN + OperationMetadata EndWaterDepthOperationMeta; + + //LFUNES + GearMetadata CableLengthGearMeta; + //VMIN + GearMetadata MinSpeedGearMeta; + //VMAX + GearMetadata MaxSpeedGearMeta; + + TopiaDAO<Operation> dao; + TopiaDAO<OperationMetadataValue> operationMetadataValueDAO; + TopiaDAO<GearMetadataValue> gearMetadataValueDAO; + + Map<String, DepthStratum> depthStratumByName; + Map<String, Gear> gearByCasinoGearName; + @Override - protected void importBaracoudaEntities(Database db) throws IOException, TopiaException { + protected void importBaracoudaEntities(Database db) throws + IOException, TopiaException { Map<String, Voyage> voyagesByName = getUniverse( Voyage.class, EchoBaseFunctions.VOYAGE_NAME); - Map<String, DepthStratum> depthStratumByName = getUniverse( + depthStratumByName = getUniverse( DepthStratum.class, EchoBaseFunctions.DEPTH_STRATUM_ID); - Map<String, Gear> gearByCasinoGearName = getUniverse( + gearByCasinoGearName = getUniverse( Gear.class, EchoBaseFunctions.GEAR_CASINO_GEAR_NAME); OperationMetadataDAO operationMetadataDAO = (OperationMetadataDAO) getDAO(OperationMetadata.class); //SONDE - OperationMetadata MeanWaterDepthOperationMeta = + MeanWaterDepthOperationMeta = operationMetadataDAO.findByName("MeanWaterDepth"); Preconditions.checkNotNull(MeanWaterDepthOperationMeta); //JOUR_NUIT - OperationMetadata DielPeriodOperationMeta = + DielPeriodOperationMeta = operationMetadataDAO.findByName("DielPeriod"); Preconditions.checkNotNull(DielPeriodOperationMeta); //SONDEDEB - OperationMetadata StartWaterDepthOperationMeta = operationMetadataDAO.findByProperties( + StartWaterDepthOperationMeta = operationMetadataDAO.findByProperties( OperationMetadata.PROPERTY_NAME, "WaterDepth", OperationMetadata.PROPERTY_OPERATION_EVENT + "." + OperationEvent.PROPERTY_NAME, "ShootingStart" ); Preconditions.checkNotNull(StartWaterDepthOperationMeta); //SONDEFIN - OperationMetadata EndWaterDepthOperationMeta = operationMetadataDAO.findByProperties( + EndWaterDepthOperationMeta = operationMetadataDAO.findByProperties( OperationMetadata.PROPERTY_NAME, "WaterDepth", OperationMetadata.PROPERTY_OPERATION_EVENT + "." + OperationEvent.PROPERTY_NAME, "HaulingEnd" ); @@ -162,24 +185,19 @@ (GearMetadataDAO) getDAO(GearMetadata.class); //LFUNES - GearMetadata CableLengthGearMeta = gearMetadataDAO.findByType("CableLength"); + CableLengthGearMeta = gearMetadataDAO.findByType("CableLength"); Preconditions.checkNotNull(CableLengthGearMeta); - //VMIN - GearMetadata MinSpeedGearMeta = gearMetadataDAO.findByType("MinSpeed"); + MinSpeedGearMeta = gearMetadataDAO.findByType("MinSpeed"); Preconditions.checkNotNull(MinSpeedGearMeta); - //VMAX - GearMetadata MaxSpeedGearMeta = gearMetadataDAO.findByType("MaxSpeed"); + MaxSpeedGearMeta = gearMetadataDAO.findByType("MaxSpeed"); Preconditions.checkNotNull(MaxSpeedGearMeta); - TopiaDAO<Operation> dao = getDAO(); - TopiaDAO<OperationMetadataValue> operationMetadataValueDAO = - getDAO(OperationMetadataValue.class); + dao = getDAO(); + operationMetadataValueDAO = getDAO(OperationMetadataValue.class); + gearMetadataValueDAO = getDAO(GearMetadataValue.class); - TopiaDAO<GearMetadataValue> gearMetadataValueDAO = - getDAO(GearMetadataValue.class); - Multimap<String, Map<String, Object>> stationByCampagneName = Multimaps.index( db.getTable("STATIONS"), EchoBaseFunctions.newRowFunction("CAMPAGNE")); @@ -196,142 +214,169 @@ Preconditions.checkNotNull(transect); Collection<Map<String, Object>> rows = stationByCampagneName.get(voyageName); + for (Map<String, Object> row : rows) { - String status = (String) row.get("ETAT"); - if ("FICTIF".equalsIgnoreCase(status)) { + Operation operation = addOperation(row, messages); + if (operation != null) { + operations.add(operation); + transect.addOperation(operation); - // skip fictif operation - continue; - } - String operationId = (String) row.get("NOSTA"); + if (!messages.isEmpty()) { - DepthStratum depthStratum = null; - String depthStratumId = (String) row.get("STA_IMAGES"); - if (StringUtils.isBlank(depthStratumId) || - "nul".equals(depthStratumId)) { - messages.add("No depthStraum defined"); - } else { - depthStratum = getFK(depthStratumByName, depthStratumId.trim()); + if (log.isWarnEnabled()) { + log.warn("For operation " + operation.getId() + " : " + messages); + } + messages.clear(); + } } + } + } - String gearId = (String) row.get("ENGIN"); - if (gearId == null) { - messages.add("No gear id"); - } else { - Gear gear = getFK(gearByCasinoGearName, gearId); + if (log.isInfoEnabled()) { + log.info("Found " + operations.size() + " operation(s)."); + } + } - Float shootingStartLatitude = (Float) row.get("LATDEB"); - if (shootingStartLatitude == null) { - messages.add("No shootingStartLatitude"); - shootingStartLatitude = 0f; - } - Float shootingEndLatitude = (Float) row.get("LATDD"); - if (shootingEndLatitude == null) { - messages.add("No shootingEndLatitude"); - shootingEndLatitude = 0f; - } - Float shootingStartLongitude = (Float) row.get("LGDEB"); - if (shootingStartLongitude == null) { - messages.add("No shootingStartLongitude"); - shootingStartLongitude = 0f; - } - Float shootingEndLongitude = (Float) row.get("LGDD"); - if (shootingEndLongitude == null) { - messages.add("No shootingEndLongitude"); - shootingEndLongitude = 0f; - } + protected Operation addOperation(Map<String, Object> row, + List<String> messages) throws TopiaException { + String status = (String) row.get("ETAT"); - Date shootingStartTime = (Date) row.get("DHTUDEB"); - Date shootingEndTime = (Date) row.get("DHTUFIN"); + if ("FICTIF".equalsIgnoreCase(status)) { - String comment = (String) row.get("COMMENTAIRE"); + // skip fictif operation + return null; + } - // create a operation - Operation operation = dao.create( - Operation.PROPERTY_ID, operationId, - Operation.PROPERTY_DEPTH_STRATUM, depthStratum, - Operation.PROPERTY_GEAR, gear, - Operation.PROPERTY_GEAR_SHOOTING_START_LATITUDE, shootingStartLatitude, - Operation.PROPERTY_GEAR_SHOOTING_END_LATITUDE, shootingEndLatitude, - Operation.PROPERTY_GEAR_SHOOTING_START_LONGITUDE, shootingStartLongitude, - Operation.PROPERTY_GEAR_SHOOTING_END_LONGITUDE, shootingEndLongitude, - Operation.PROPERTY_GEAR_SHOOTING_START_TIME, shootingStartTime, - Operation.PROPERTY_GEAR_SHOOTING_END_TIME, shootingEndTime, - Operation.PROPERTY_COMMENT, comment - ); + String operationId = (String) row.get("NOSTA"); - addOperationMetadataValue(operationMetadataValueDAO, - operation, - MeanWaterDepthOperationMeta, - row.get("SONDE")); + String gearId = (String) row.get("ENGIN"); + if (gearId == null) { + if (log.isWarnEnabled()) { + log.warn("No gear id for Operation " + operationId); + } + return null; + } - addOperationMetadataValue(operationMetadataValueDAO, - operation, - DielPeriodOperationMeta, - row.get("JOUR_NUIT")); + DepthStratum depthStratum = null; + String depthStratumId = (String) row.get("STA_IMAGES"); + if (StringUtils.isBlank(depthStratumId) || + "nul".equals(depthStratumId)) { + messages.add("No depthStraum defined"); + } else { + depthStratum = getFK(depthStratumByName, depthStratumId.trim()); + } - addOperationMetadataValue(operationMetadataValueDAO, - operation, - StartWaterDepthOperationMeta, - row.get("SONDEDEB")); + Gear gear = getFK(gearByCasinoGearName, gearId); - addOperationMetadataValue(operationMetadataValueDAO, - operation, - EndWaterDepthOperationMeta, - row.get("SONDEFIN")); + Float shootingStartLatitude = (Float) row.get("LATDEB"); + if (shootingStartLatitude == null) { + messages.add("No shootingStartLatitude"); + } - addGearMetadataValue(gearMetadataValueDAO, - operation, - CableLengthGearMeta, - row.get("LFUNES")); + Double doubleValue = (Double) row.get("LATFIN"); + Float shootingEndLatitude; + if (doubleValue == null) { + messages.add("No shootingEndLatitude"); + shootingEndLatitude = null; + } else { + shootingEndLatitude = doubleValue.floatValue(); + } - addGearMetadataValue(gearMetadataValueDAO, - operation, - MinSpeedGearMeta, - row.get("VMIN")); + Float shootingStartLongitude = (Float) row.get("LGDEB"); + if (shootingStartLongitude == null) { + messages.add("No shootingStartLongitude"); + } - addGearMetadataValue(gearMetadataValueDAO, - operation, - MaxSpeedGearMeta, - row.get("VMAX")); + doubleValue = (Double) row.get("LGFIN"); + Float shootingEndLongitude; + if (doubleValue == null) { + messages.add("No shootingEndLongitude"); + shootingEndLongitude = null; + } else { + shootingEndLongitude = doubleValue.floatValue(); + } - operations.add(operation); - transect.addOperation(operation); + Float midHauleLatitude = (Float) row.get("LATDD"); + Preconditions.checkNotNull(midHauleLatitude); +// if (midHauleLatitude == null) { +// messages.add("No midHauleLatitude"); +// midHauleLatitude = 0f; +// } - } - if (!messages.isEmpty()) { + Float midHauleLongitude = (Float) row.get("LGDD"); + Preconditions.checkNotNull(midHauleLongitude); +// if (midHauleLongitude== null) { +// messages.add("No midHauleLongitude"); +// midHauleLongitude = 0f; +// } - if (log.isWarnEnabled()) { - log.warn("For operation " + operationId + ", status " + status + " : " + messages); - } - messages.clear(); - } - } - } + Date shootingStartTime = (Date) row.get("DHTUDEB"); + Date shootingEndTime = (Date) row.get("DHTUFIN"); + String comment = (String) row.get("COMMENTAIRE"); - if (log.isInfoEnabled()) { - log.info("Found " + operations.size() + " operation(s)."); - } + // create a operation + Operation operation = dao.create( + Operation.PROPERTY_ID, operationId, + Operation.PROPERTY_DEPTH_STRATUM, depthStratum, + Operation.PROPERTY_GEAR, gear, + Operation.PROPERTY_GEAR_SHOOTING_START_LATITUDE, shootingStartLatitude, + Operation.PROPERTY_GEAR_SHOOTING_END_LATITUDE, shootingEndLatitude, + Operation.PROPERTY_GEAR_SHOOTING_START_LONGITUDE, shootingStartLongitude, + Operation.PROPERTY_GEAR_SHOOTING_END_LONGITUDE, shootingEndLongitude, + Operation.PROPERTY_GEAR_SHOOTING_START_TIME, shootingStartTime, + Operation.PROPERTY_GEAR_SHOOTING_END_TIME, shootingEndTime, + Operation.PROPERTY_MID_HAULE_LATITUDE, midHauleLatitude, + Operation.PROPERTY_MID_HAULE_LONGITUDE, midHauleLongitude, + Operation.PROPERTY_COMMENT, comment + ); + + addOperationMetadataValue(operation, + MeanWaterDepthOperationMeta, + row.get("SONDE")); + + addOperationMetadataValue(operation, + DielPeriodOperationMeta, + row.get("JOUR_NUIT")); + + addOperationMetadataValue(operation, + StartWaterDepthOperationMeta, + row.get("SONDEDEB")); + + addOperationMetadataValue(operation, + EndWaterDepthOperationMeta, + row.get("SONDEFIN")); + + addGearMetadataValue(operation, + CableLengthGearMeta, + row.get("LFUNES")); + + addGearMetadataValue(operation, + MinSpeedGearMeta, + row.get("VMIN")); + + addGearMetadataValue(operation, + MaxSpeedGearMeta, + row.get("VMAX")); + + return operation; } - protected void addOperationMetadataValue(TopiaDAO<OperationMetadataValue> dao, - Operation operation, + protected void addOperationMetadataValue(Operation operation, OperationMetadata meta, Object value ) throws TopiaException { if (value == null) { return; } - OperationMetadataValue operationMetadataValue = dao.create( + OperationMetadataValue operationMetadataValue = operationMetadataValueDAO.create( OperationMetadataValue.PROPERTY_OPERATION_METADATA, meta, OperationMetadataValue.PROPERTY_DATA_VALUE, value.toString() ); operation.addOperationMetadataValue(operationMetadataValue); } - protected void addGearMetadataValue(TopiaDAO<GearMetadataValue> dao, - Operation operation, + protected void addGearMetadataValue(Operation operation, GearMetadata meta, Object value ) throws TopiaException { @@ -339,7 +384,7 @@ if (value == null) { return; } - GearMetadataValue gearMetadataValue = dao.create( + GearMetadataValue gearMetadataValue = gearMetadataValueDAO.create( GearMetadataValue.PROPERTY_GEAR_METADATA, meta, GearMetadataValue.PROPERTY_DATA_VALUE, value.toString(), GearMetadataValue.PROPERTY_GEAR, operation.getGear() Modified: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SampleLoader.java =================================================================== --- trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SampleLoader.java 2011-12-16 01:46:20 UTC (rev 198) +++ trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SampleLoader.java 2011-12-16 17:54:16 UTC (rev 199) @@ -26,6 +26,7 @@ import com.google.common.base.Preconditions; import com.google.common.collect.Multimap; import com.google.common.collect.Multimaps; +import com.google.common.collect.Sets; import com.healthmarketscience.jackcess.Database; import fr.ifremer.echobase.EchoBaseFunctions; import fr.ifremer.echobase.entities.EchoBaseEntityEnum; @@ -35,7 +36,6 @@ import fr.ifremer.echobase.entities.data.SampleDataDAO; import fr.ifremer.echobase.entities.meta.TableMeta; import fr.ifremer.echobase.entities.references.SampleDataType; -import fr.ifremer.echobase.entities.references.SampleDataTypeDAO; import fr.ifremer.echobase.entities.references.SampleType; import fr.ifremer.echobase.entities.references.SampleTypeDAO; import fr.ifremer.echobase.entities.references.Species; @@ -49,6 +49,7 @@ import java.io.IOException; import java.util.Collection; import java.util.Map; +import java.util.Set; /** * To load {@link Sample} entities. @@ -100,9 +101,9 @@ TableMeta meta = getMeta(); copyAndLoadEntities(outputDir, meta.getAssociations(Sample.PROPERTY_SAMPLE_DATA), false, FileType.ASSOCIATION); - } + @Override protected void importBaracoudaEntities(Database db) throws IOException, TopiaException { @@ -112,6 +113,9 @@ Map<String, Species> speciesByName = getUniverse( Species.class, EchoBaseFunctions.SPECIES_BARACOUDA_CODE); + Map<String, SampleDataType> sampleDataTypeByRaptriCode = getUniverse( + SampleDataType.class, EchoBaseFunctions.SAMPLE_DATA_TYPE_RAPTRI_CODE); + Multimap<String, Map<String, Object>> mensurationByNosta = Multimaps.index( db.getTable("MENSURATIONS", true), EchoBaseFunctions.newRowFunction("NOSTA") @@ -121,6 +125,16 @@ db.getTable("CAPTURES", true), EchoBaseFunctions.newRowFunction("NOSTA") ); + + Multimap<Integer, Map<String, Object>> biometryScalesByRaptri = Multimaps.index( + db.getTable("BIOMETRIE_ECHELLE", true), + EchoBaseFunctions.newRowIntegerFunction("Code_Param_Biometrie_Echelle") + ); + + Multimap<String, Map<String, Object>> biometryValuesByNosta = Multimaps.index( + db.getTable("BIOMETRIE_VALEUR", true), + EchoBaseFunctions.newRowFunction("NOSTA_VALEUR_BIOMETRIE") + ); SampleTypeDAO sampleTypeDAO = (SampleTypeDAO) getDAO(SampleType.class); @@ -130,28 +144,32 @@ Preconditions.checkNotNull(sampleTypeUnsorted); SampleType sampleTypeSubsample = sampleTypeDAO.findByName("Subsample"); Preconditions.checkNotNull(sampleTypeSubsample); + SampleType sampleTypeIndividual = sampleTypeDAO.findByName("Individual"); + Preconditions.checkNotNull(sampleTypeIndividual); - SampleDataTypeDAO sampleDataTypeDAO = - (SampleDataTypeDAO) getDAO(SampleDataType.class); +// SampleDataTypeDAO sampleDataTypeDAO = +// (SampleDataTypeDAO) getDAO(SampleDataType.class); SampleDataDAO sampleDataDAO = (SampleDataDAO) getDAO(SampleData.class); - SampleDataType sampleDataTypeMeanLength = sampleDataTypeDAO.findByName("MeanLengthcm"); - Preconditions.checkNotNull(sampleDataTypeMeanLength); - SampleDataType sampleDataTypeMeanWeight = sampleDataTypeDAO.findByName("MeanWeightg"); - Preconditions.checkNotNull(sampleDataTypeMeanWeight); - SampleDataType sampleDataTypeNoPerKg = sampleDataTypeDAO.findByName("NoPerKg"); - Preconditions.checkNotNull(sampleDataTypeNoPerKg); - SampleDataType sampleDataTypeNumberAtLength = sampleDataTypeDAO.findByName("NumberAtLength"); - Preconditions.checkNotNull(sampleDataTypeNumberAtLength); - SampleDataType sampleDataTypeWeightAtLength = sampleDataTypeDAO.findByName("WeightAtLengthkg"); - Preconditions.checkNotNull(sampleDataTypeWeightAtLength); +// SampleDataType sampleDataTypeMeanLength = sampleDataTypeDAO.findByName("MeanLengthcm"); + SampleDataType sampleDataTypeMeanLength = getFK(sampleDataTypeByRaptriCode, "114"); +// SampleDataType sampleDataTypeMeanWeight = sampleDataTypeDAO.findByName("MeanWeightg"); + SampleDataType sampleDataTypeMeanWeight = getFK(sampleDataTypeByRaptriCode, "115"); +// SampleDataType sampleDataTypeNoPerKg = sampleDataTypeDAO.findByName("NoPerKg"); + SampleDataType sampleDataTypeNoPerKg = getFK(sampleDataTypeByRaptriCode, "116"); +// SampleDataType sampleDataTypeNumberAtLength = sampleDataTypeDAO.findByName("NumberAtLength"); + SampleDataType sampleDataTypeNumberAtLength = getFK(sampleDataTypeByRaptriCode, "112"); +// SampleDataType sampleDataTypeWeightAtLength = sampleDataTypeDAO.findByName("WeightAtLengthkg"); + SampleDataType sampleDataTypeWeightAtLength = getFK(sampleDataTypeByRaptriCode, "113"); + TopiaDAO<Sample> dao = getDAO(); int nbSampleUnsorted = 0; int nbSampleTotal = 0; int nbSubSample = 0; + int nbIndividualSample = 0; for (String operationId : capturesByNosta.keySet()) { Preconditions.checkNotNull(operationId); @@ -162,6 +180,13 @@ } continue; } + Collection<Map<String, Object>> biometryValues = + biometryValuesByNosta.get(operationId); + + Multimap<String, Map<String, Object>> biometryValuesBySpecies = Multimaps.index( + biometryValues, + EchoBaseFunctions.newRowFunction("GENRE_ESP_VALEUR_BIOMETRIE") + ); for (Map<String, Object> row : capturesByNosta.get(operationId)) { String type = (String) row.get("CATEG"); @@ -214,7 +239,7 @@ "NA", row.get("MOULE_MENS")); - Collection<Map<String, Object>> mesnurationRows = + Collection<Map<String, Object>> mensurationRows = mensurationByNosta.get(operationId); Float sampleWeight = (Float) row.get("PESP_MENS"); @@ -224,6 +249,7 @@ } sampleWeight = 0f; } + addSubSamples(dao, sampleDataDAO, sampleTypeSubsample, @@ -233,22 +259,105 @@ type, species, sampleWeight, - mesnurationRows); + mensurationRows); int nbSamples = operation.sizeSample(); nbSubSample += nbSamples - 1; + + Collection<Map<String, Object>> biometryValuesRows = + biometryValuesBySpecies.get(speciesId); + + int nbSampleIndiv = addSampleIndividuals(dao, + sampleDataDAO, + operation, + species, + sampleTypeIndividual, + sampleDataTypeByRaptriCode, + biometryScalesByRaptri, + biometryValuesRows); + nbIndividualSample += nbSampleIndiv; + } } - if (log.isInfoEnabled()) { log.info("Found " + nbSampleTotal + " 'total' sample(s)."); log.info("Found " + nbSampleUnsorted + " 'unsorted' sample(s)."); log.info("Found " + nbSubSample + " 'sub' sample(s)."); - log.info("Total " + (nbSampleTotal + nbSampleUnsorted + nbSubSample) + " sample(s)."); + log.info("Found " + nbIndividualSample + " 'Individual' sample(s)."); + log.info("Total " + (nbSampleTotal + nbSampleUnsorted + nbIndividualSample + nbSubSample) + " sample(s)."); } } + private int addSampleIndividuals(TopiaDAO<Sample> dao, + SampleDataDAO sampleDataDAO, + Operation operation, + Species species, + SampleType sampleTypeIndividual, + Map<String, SampleDataType> sampleDataTypeByRaptriCode, + Multimap<Integer, Map<String, Object>> biometryScalesByRaptri, + Collection<Map<String, Object>> biometryValuesRows) throws TopiaException { + int result = 0; + Sample sample = null; + Set<Integer> individus = Sets.newHashSet(); + for (Map<String, Object> biometryValuesRow : biometryValuesRows) { + Integer ind = Integer.valueOf(biometryValuesRow.get("NUMIND_VALEUR_BIOMETRIE").toString()); + Integer codeParameter = (Integer) biometryValuesRow.get("CODE_PARAM_VALEUR_BIOMETRIE"); + String label = null; + Float value = (Float) biometryValuesRow.get("VALEUR_BIOMETRIE"); + if (value==null) { + if (log.isWarnEnabled()) { + log.warn("Null value of VALEUR_BIOMETRIE for operationId/Species/Individu/Code param " + operation.getId() + "/" + species.getBaracoudaCode() + "/" + ind+"/"+codeParameter); + } + continue; + } + Preconditions.checkNotNull(value, "Null value of VALEUR_BIOMETRIE for operationId/Species/Individu/Code param " + operation.getId() + "/" + species.getBaracoudaCode() + "/" + ind+"/"+codeParameter); + SampleDataType sampleDataType = getFK(sampleDataTypeByRaptriCode, String.valueOf(codeParameter)); + + boolean add = individus.add(ind); + if (add) { + + // new sample + sample = dao.create( + Sample.PROPERTY_SPECIES, species, + Sample.PROPERTY_SAMPLE_TYPE, sampleTypeIndividual + ); + + operation.addSample(sample); + result++; + } + + Collection<Map<String, Object>> scalesRows = + biometryScalesByRaptri.get(codeParameter); + + if (scalesRows == null) { + + label = "NA"; + } else { + + // find the correct line + int valueAsInteger = value.intValue(); + + for (Map<String, Object> scalesRow : scalesRows) { + Float scaleCode = (Float) scalesRow.get("Code_echelle"); + if (valueAsInteger == scaleCode.intValue()) { + + // ok find the correct scale + label = (String) scalesRow.get("Descriptif"); + break; + } + } + } + addSampleData(sampleDataDAO, + sample, + sampleDataType, + label, + value + ); + } + return result; + } + private void addSubSamples(TopiaDAO<Sample> dao, SampleDataDAO sampleDataDAO, SampleType sampleTypeSubsample, Modified: trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SampleLoaderIT.java =================================================================== --- trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SampleLoaderIT.java 2011-12-16 01:46:20 UTC (rev 198) +++ trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SampleLoaderIT.java 2011-12-16 17:54:16 UTC (rev 199) @@ -35,7 +35,7 @@ public class SampleLoaderIT extends AbstractLoaderIT<Sample, SampleLoader> { public SampleLoaderIT() { - super(SampleLoader.class, 0, 208199); + super(SampleLoader.class, 0, 324809); } @Test Modified: trunk/src/doc/reunions/reunion-2011-12-14.txt =================================================================== --- trunk/src/doc/reunions/reunion-2011-12-14.txt 2011-12-16 01:46:20 UTC (rev 198) +++ trunk/src/doc/reunions/reunion-2011-12-14.txt 2011-12-16 17:54:16 UTC (rev 199) @@ -50,6 +50,7 @@ - Remplissage du référentiel Gear - Import des opérations (depuis table STATIONS) +- Import des samples (depuis table CAPTURES/MENSURATIONS/BIOMETRIE_VALEURS) Action ------

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