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[Git][ultreiaio/ird-t3][develop] [jgitflow-maven-plugin]updating poms for 2.6-SNAPSHOT development[skip ci]
by Tony CHEMIT 23 Mar '18

23 Mar '18

Tony CHEMIT pushed to branch develop at ultreiaio / ird-t3 Commits: cdf9ffad by Tony CHEMIT at 2018-03-23T17:54:11Z [jgitflow-maven-plugin]updating poms for 2.6-SNAPSHOT development[skip ci] - - - - - 11 changed files: - pom.xml - t3-actions/pom.xml - t3-domain/pom.xml - t3-input-avdthv33/pom.xml - t3-input-avdthv35/pom.xml - t3-input-avdthv36/pom.xml - t3-installer/pom.xml - t3-msaccess-importer/pom.xml - t3-output-balbayav32/pom.xml - t3-web/pom.xml - t3/pom.xml Changes: ===================================== pom.xml ===================================== --- a/pom.xml +++ b/pom.xml @@ -28,7 +28,7 @@ <groupId>fr.ird.t3</groupId> <artifactId>ird-t3</artifactId> - <version>2.5-SNAPSHOT</version> + <version>2.6-SNAPSHOT</version> <packaging>pom</packaging> <name>T3 :: Pom</name> ===================================== t3-actions/pom.xml ===================================== --- a/t3-actions/pom.xml +++ b/t3-actions/pom.xml @@ -24,7 +24,7 @@ <parent> <groupId>fr.ird.t3</groupId> <artifactId>ird-t3</artifactId> - <version>2.5-SNAPSHOT</version> + <version>2.6-SNAPSHOT</version> </parent> <artifactId>t3-actions</artifactId> ===================================== t3-domain/pom.xml ===================================== --- a/t3-domain/pom.xml +++ b/t3-domain/pom.xml @@ -24,7 +24,7 @@ <parent> <groupId>fr.ird.t3</groupId> <artifactId>ird-t3</artifactId> - <version>2.5-SNAPSHOT</version> + <version>2.6-SNAPSHOT</version> </parent> <artifactId>t3-domain</artifactId> ===================================== t3-input-avdthv33/pom.xml ===================================== --- a/t3-input-avdthv33/pom.xml +++ b/t3-input-avdthv33/pom.xml @@ -24,7 +24,7 @@ <parent> <groupId>fr.ird.t3</groupId> <artifactId>ird-t3</artifactId> - <version>2.5-SNAPSHOT</version> + <version>2.6-SNAPSHOT</version> </parent> <artifactId>t3-input-avdthv33</artifactId> ===================================== t3-input-avdthv35/pom.xml ===================================== --- a/t3-input-avdthv35/pom.xml +++ b/t3-input-avdthv35/pom.xml @@ -24,7 +24,7 @@ <parent> <groupId>fr.ird.t3</groupId> <artifactId>ird-t3</artifactId> - <version>2.5-SNAPSHOT</version> + <version>2.6-SNAPSHOT</version> </parent> <artifactId>t3-input-avdthv35</artifactId> ===================================== t3-input-avdthv36/pom.xml ===================================== --- a/t3-input-avdthv36/pom.xml +++ b/t3-input-avdthv36/pom.xml @@ -24,7 +24,7 @@ <parent> <groupId>fr.ird.t3</groupId> <artifactId>ird-t3</artifactId> - <version>2.5-SNAPSHOT</version> + <version>2.6-SNAPSHOT</version> </parent> <artifactId>t3-input-avdthv36</artifactId> ===================================== t3-installer/pom.xml ===================================== --- a/t3-installer/pom.xml +++ b/t3-installer/pom.xml @@ -24,7 +24,7 @@ <parent> <groupId>fr.ird.t3</groupId> <artifactId>ird-t3</artifactId> - <version>2.5-SNAPSHOT</version> + <version>2.6-SNAPSHOT</version> </parent> <artifactId>t3-installer</artifactId> ===================================== t3-msaccess-importer/pom.xml ===================================== --- a/t3-msaccess-importer/pom.xml +++ b/t3-msaccess-importer/pom.xml @@ -24,7 +24,7 @@ <parent> <groupId>fr.ird.t3</groupId> <artifactId>ird-t3</artifactId> - <version>2.5-SNAPSHOT</version> + <version>2.6-SNAPSHOT</version> </parent> <artifactId>t3-msaccess-importer</artifactId> ===================================== t3-output-balbayav32/pom.xml ===================================== --- a/t3-output-balbayav32/pom.xml +++ b/t3-output-balbayav32/pom.xml @@ -24,7 +24,7 @@ <parent> <groupId>fr.ird.t3</groupId> <artifactId>ird-t3</artifactId> - <version>2.5-SNAPSHOT</version> + <version>2.6-SNAPSHOT</version> </parent> <artifactId>t3-output-balbayav32</artifactId> ===================================== t3-web/pom.xml ===================================== --- a/t3-web/pom.xml +++ b/t3-web/pom.xml @@ -24,7 +24,7 @@ <parent> <groupId>fr.ird.t3</groupId> <artifactId>ird-t3</artifactId> - <version>2.5-SNAPSHOT</version> + <version>2.6-SNAPSHOT</version> </parent> <artifactId>t3-web</artifactId> ===================================== t3/pom.xml ===================================== --- a/t3/pom.xml +++ b/t3/pom.xml @@ -26,7 +26,7 @@ <parent> <groupId>fr.ird.t3</groupId> <artifactId>ird-t3</artifactId> - <version>2.5-SNAPSHOT</version> + <version>2.6-SNAPSHOT</version> </parent> <artifactId>t3</artifactId> View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/cdf9ffad7f04258a53c81954f5495c0d… --- View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/cdf9ffad7f04258a53c81954f5495c0d… You're receiving this email because of your account on gitlab.com.

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[Git][ultreiaio/ird-t3] Pushed new branch release/2.5
by Tony CHEMIT 23 Mar '18

23 Mar '18

Tony CHEMIT pushed new branch release/2.5 at ultreiaio / ird-t3 --- View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/tree/release/2.5 You're receiving this email because of your account on gitlab.com.

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[Git][ultreiaio/ird-t3][develop] Simplification des bases en entrée (Closes #302)
by Tony CHEMIT 23 Mar '18

23 Mar '18

Tony CHEMIT pushed to branch develop at ultreiaio / ird-t3 Commits: d5e63496 by Tony CHEMIT at 2018-03-23T17:41:36Z Simplification des bases en entrée (Closes #302) - - - - - 7 changed files: - t3-domain/src/main/java/fr/ird/t3/entities/user/UserDatabase.java - t3-domain/src/main/java/fr/ird/t3/services/UserService.java - t3-web/src/main/java/fr/ird/t3/web/actions/admin/AbstractUserDatabaseAction.java - t3-web/src/main/resources/i18n/t3-web_en_GB.properties - t3-web/src/main/resources/i18n/t3-web_fr_FR.properties - t3-web/src/main/webapp/WEB-INF/jsp/admin/databaseConfigurationForm.jsp - t3-web/src/main/webapp/WEB-INF/jsp/user/selectUserInputDatabase.jsp Changes: ===================================== t3-domain/src/main/java/fr/ird/t3/entities/user/UserDatabase.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/entities/user/UserDatabase.java +++ b/t3-domain/src/main/java/fr/ird/t3/entities/user/UserDatabase.java @@ -10,12 +10,12 @@ package fr.ird.t3.entities.user; * 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% @@ -34,6 +34,8 @@ public class UserDatabase extends AbstractJavaBean implements Idable { protected String login; + protected String password; + protected String id; public String getUrl() { @@ -67,4 +69,12 @@ public class UserDatabase extends AbstractJavaBean implements Idable { public void setId(String id) { this.id = id; } + + public String getPassword() { + return password; + } + + public void setPassword(String password) { + this.password = password; + } } ===================================== t3-domain/src/main/java/fr/ird/t3/services/UserService.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/services/UserService.java +++ b/t3-domain/src/main/java/fr/ird/t3/services/UserService.java @@ -8,12 +8,12 @@ * 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% @@ -40,6 +40,10 @@ import java.util.UUID; */ public class UserService extends T3ServiceSupport implements T3ServiceInjectable { + private static String encodePassword(String password) { + return StringUtil.encodeMD5(password); + } + public Optional<T3User> getUserByLogin(String login) { return getT3Users().usersStream().whereLogin().isEquals(login).filter().findFirst(); } @@ -79,7 +83,6 @@ public class UserService extends T3ServiceSupport implements T3ServiceInjectable commit(); } - public void deleteUser(String userId) { T3User user = getUserById(userId); getT3Users().getUsers().remove(user); @@ -93,6 +96,7 @@ public class UserService extends T3ServiceSupport implements T3ServiceInjectable .description(dbConfiguration.getDescription()) .login(dbConfiguration.getLogin()) .url(dbConfiguration.getUrl()) + .password(dbConfiguration.getPassword()) .build(); user.getInputs().add(dbConfigurationToSave); dbConfiguration.setId(dbConfigurationToSave.getId()); @@ -101,7 +105,7 @@ public class UserService extends T3ServiceSupport implements T3ServiceInjectable public void updateUserInputDatabase(UserDatabase dbConfiguration) { UserDatabase dbConfigurationToSave = getUserInputDatabase(dbConfiguration.getId()); - updateDatabaseConfiguration(dbConfiguration, dbConfigurationToSave); + dbConfiguration.copy(dbConfigurationToSave); commit(); } @@ -119,6 +123,7 @@ public class UserService extends T3ServiceSupport implements T3ServiceInjectable .description(dbConfiguration.getDescription()) .login(dbConfiguration.getLogin()) .url(dbConfiguration.getUrl()) + .password(dbConfiguration.getPassword()) .build(); user.getOutputs().add(dbConfigurationToSave); dbConfiguration.setId(dbConfigurationToSave.getId()); @@ -127,7 +132,7 @@ public class UserService extends T3ServiceSupport implements T3ServiceInjectable public void updateUserOutputDatabase(UserDatabase dbConfiguration) { UserDatabase dbConfigurationToSave = getUserOutputDatabase(dbConfiguration.getId()); - updateDatabaseConfiguration(dbConfiguration, dbConfigurationToSave); + dbConfiguration.copy(dbConfigurationToSave); commit(); } @@ -151,16 +156,6 @@ public class UserService extends T3ServiceSupport implements T3ServiceInjectable return s.equals(user.getPassword()); } - private static String encodePassword(String password) { - return StringUtil.encodeMD5(password); - } - - private void updateDatabaseConfiguration(UserDatabase dbConfiguration, UserDatabase dbConfigurationToSave) { - dbConfigurationToSave.setDescription(dbConfiguration.getDescription()); - dbConfigurationToSave.setUrl(dbConfiguration.getUrl()); - dbConfigurationToSave.setLogin(dbConfiguration.getLogin()); - } - private void commit() { getT3Users().save(); } ===================================== t3-web/src/main/java/fr/ird/t3/web/actions/admin/AbstractUserDatabaseAction.java ===================================== --- a/t3-web/src/main/java/fr/ird/t3/web/actions/admin/AbstractUserDatabaseAction.java +++ b/t3-web/src/main/java/fr/ird/t3/web/actions/admin/AbstractUserDatabaseAction.java @@ -108,6 +108,7 @@ public abstract class AbstractUserDatabaseAction extends T3ActionSupport impleme String userId = getUser().getId(); String description = configuration.getDescription(); String login = configuration.getLogin(); + String password = configuration.getPassword(); String url = configuration.getUrl(); String id = configuration.getId(); boolean noError = true; @@ -129,7 +130,11 @@ public abstract class AbstractUserDatabaseAction extends T3ActionSupport impleme addFieldError("databaseConfiguration.login", t("t3.error.required.login")); noError = false; } - + if (StringUtils.isEmpty(password)) { + // empty user password + addFieldError("databaseConfiguration.password", t("t3.error.required.password")); + noError = false; + } if (noError) { // check now the configuration does not already exist with same description for this user T3User t3User = getUserService().getUserById(userId); @@ -169,6 +174,11 @@ public abstract class AbstractUserDatabaseAction extends T3ActionSupport impleme addFieldError("databaseConfiguration.login", t("t3.error.required.login")); noError = false; } + if (StringUtils.isEmpty(password)) { + // empty user password + addFieldError("databaseConfiguration.password", t("t3.error.required.password")); + noError = false; + } if (noError) { // check now the configuration does not already exist with same description for this user T3User t3User = getUserService().getUserById(userId); ===================================== t3-web/src/main/resources/i18n/t3-web_en_GB.properties ===================================== --- a/t3-web/src/main/resources/i18n/t3-web_en_GB.properties +++ b/t3-web/src/main/resources/i18n/t3-web_en_GB.properties @@ -1,3 +1,4 @@ +t3.common.password=Password t3.action.applyFilter=Apply t3.action.back.to.configuration.step1=Back to step 1 of configuration t3.action.back.to.configuration.step2=Back to step 2 of configuration ===================================== t3-web/src/main/resources/i18n/t3-web_fr_FR.properties ===================================== --- a/t3-web/src/main/resources/i18n/t3-web_fr_FR.properties +++ b/t3-web/src/main/resources/i18n/t3-web_fr_FR.properties @@ -9,6 +9,7 @@ t3.action.connectToDatabase=Se connecter à la base t3.action.create=Créer t3.action.create.parametersProfile=Créer un profile de paramètre t3.action.create.user=Créer un utilisateur +t3.common.password=Mot de passe t3.action.delete=Supprimer t3.action.deleteComputedData=Suppression des données calculées t3.action.deleteTrips=Suppression des marées ===================================== t3-web/src/main/webapp/WEB-INF/jsp/admin/databaseConfigurationForm.jsp ===================================== --- a/t3-web/src/main/webapp/WEB-INF/jsp/admin/databaseConfigurationForm.jsp +++ b/t3-web/src/main/webapp/WEB-INF/jsp/admin/databaseConfigurationForm.jsp @@ -37,16 +37,13 @@ </s:elseif> <s:if test="databaseEditAction == 'create'"> - <s:set name="title"><s:text - name="t3.label.admin.databaseconfiguration.create"/></s:set> + <s:set name="title"><s:text name="t3.label.admin.databaseconfiguration.create"/></s:set> </s:if> <s:elseif test="databaseEditAction =='edit'"> - <s:set name="title"><s:text - name="t3.label.admin.databaseconfiguration.edit"/></s:set> + <s:set name="title"><s:text name="t3.label.admin.databaseconfiguration.edit"/></s:set> </s:elseif> <s:elseif test="databaseEditAction == 'delete'"> - <s:set name="title"><s:text - name="t3.label.admin.databaseconfiguration.delete"/></s:set> + <s:set name="title"><s:text name="t3.label.admin.databaseconfiguration.delete"/></s:set> </s:elseif> <title><s:property value="#title"/></title> @@ -65,8 +62,12 @@ <s:hidden name="userEditAction" value="edit"/> <s:hidden key="user.id" label=""/> <s:textfield key="databaseConfiguration.url" label="%{getText('t3.common.url')}" size="40" requiredLabel="true"/> - <s:textfield key="databaseConfiguration.description" label="%{getText('t3.common.description')}" size="40" requiredLabel="true"/> - <s:textfield key="databaseConfiguration.login" label="%{getText('t3.common.login')}" size="40" requiredLabel="true"/> + <s:textfield key="databaseConfiguration.description" label="%{getText('t3.common.description')}" size="40" + requiredLabel="true"/> + <s:textfield key="databaseConfiguration.login" label="%{getText('t3.common.login')}" size="40" + requiredLabel="true"/> + <s:textfield key="databaseConfiguration.password" label="%{getText('t3.common.password')}" size="40" + requiredLabel="true"/> </fieldset> <s:submit action="%{databaseAction}!doCreate" key="t3.action.create" align="right"/> @@ -86,8 +87,12 @@ <s:hidden key="user.id" label=""/> <s:hidden name="databaseConfiguration.id" label=""/> <s:textfield key="databaseConfiguration.url" label="%{getText('t3.common.url')}" size="40" requiredLabel="true"/> - <s:textfield key="databaseConfiguration.description" label="%{getText('t3.common.description')}" size="40" requiredLabel="true"/> - <s:textfield key="databaseConfiguration.login" label="%{getText('t3.common.login')}" size="40" requiredLabel="true"/> + <s:textfield key="databaseConfiguration.description" label="%{getText('t3.common.description')}" size="40" + requiredLabel="true"/> + <s:textfield key="databaseConfiguration.login" label="%{getText('t3.common.login')}" size="40" + requiredLabel="true"/> + <s:textfield key="databaseConfiguration.password" label="%{getText('t3.common.password')}" size="40" + requiredLabel="true"/> </fieldset> <s:submit action="%{databaseAction}!doUpdate" key="t3.action.save" align="right"/> @@ -105,26 +110,18 @@ <s:hidden key="userEditAction" label="" value="edit"/> <s:hidden key="user.id" label=""/> <s:hidden name="databaseConfiguration.id" label=""/> - <s:textfield key="databaseConfiguration.url" - label="%{getText('t3.common.url')}" - size="40" disabled="true"/> - <s:textfield key="databaseConfiguration.description" - label="%{getText('t3.common.description')}" size="40" - disabled="true"/> - <s:textfield key="databaseConfiguration.login" - label="%{getText('t3.common.login')}" - size="40" disabled="true"/> + <s:textfield key="databaseConfiguration.url" label="%{getText('t3.common.url')}" size="40" disabled="true"/> + <s:textfield key="databaseConfiguration.description" label="%{getText('t3.common.description')}" size="40" disabled="true"/> + <s:textfield key="databaseConfiguration.login" label="%{getText('t3.common.login')}" size="40" disabled="true"/> </fieldset> - <s:submit action="%{databaseAction}!doDelete" key="t3.action.delete" - align="right"/> + <s:submit action="%{databaseAction}!doDelete" key="t3.action.delete" align="right"/> </s:form> </s:elseif> <s:form method="post" namespace="/user"> <s:hidden name="userEditAction" value="edit"/> <s:hidden key="user.id" label=""/> - <s:submit action="userForm!input" key="t3.label.admin.backToUser" - align="right"/> + <s:submit action="userForm!input" key="t3.label.admin.backToUser" align="right"/> </s:form> ===================================== t3-web/src/main/webapp/WEB-INF/jsp/user/selectUserInputDatabase.jsp ===================================== --- a/t3-web/src/main/webapp/WEB-INF/jsp/user/selectUserInputDatabase.jsp +++ b/t3-web/src/main/webapp/WEB-INF/jsp/user/selectUserInputDatabase.jsp @@ -35,7 +35,7 @@ var database = data.database; $('[name="database.url"]').attr('value', database.url ? database.url : ''); $('[name="database.login"]').attr('value', database.login ? database.login : ''); - $('[name="database.password"]').attr('value', ""); + $('[name="database.password"]').attr('value', database.password ? database.password : ''); } ); }); View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/d5e63496d000fbda8b8e3e911656ee86… --- View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/d5e63496d000fbda8b8e3e911656ee86… You're receiving this email because of your account on gitlab.com.

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[Git][ultreiaio/ird-t3][develop] use t3 data 1.6 + introduce Activity cache
by Tony CHEMIT 23 Mar '18

23 Mar '18

Tony CHEMIT pushed to branch develop at ultreiaio / ird-t3 Commits: 772a1f75 by Tony CHEMIT at 2018-03-23T17:00:07Z use t3 data 1.6 + introduce Activity cache - - - - - 7 changed files: - pom.xml - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2InputContext.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelInputContext.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelStratumConfigurationIterator.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java - t3-domain/src/main/java/fr/ird/t3/entities/T3TopiaPersistenceContext.java - + t3-domain/src/main/java/fr/ird/t3/entities/cache/ActivityCache.java Changes: ===================================== pom.xml ===================================== --- a/pom.xml +++ b/pom.xml @@ -99,7 +99,7 @@ <projectId>ird-t3</projectId> <stageId>frirdt3</stageId> <applicationName>t3</applicationName> - <t3-data.version>1.6-SNAPSHOT</t3-data.version> + <t3-data.version>1.6</t3-data.version> <lib.version.java4all.i18n>4.0-alpha-11</lib.version.java4all.i18n> <env>dev</env> ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2InputContext.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2InputContext.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2InputContext.java @@ -25,7 +25,6 @@ import fr.ird.t3.actions.stratum.LevelInputContext; import fr.ird.t3.entities.data.CorrectedElementaryCatch; import java.util.Collection; -import java.util.concurrent.ExecutionException; /** * A context to get all input data for the execution of action. @@ -40,8 +39,8 @@ public class Level2InputContext extends LevelInputContext<Level2Configuration, L super(action); } - public Collection<CorrectedElementaryCatch> getCorrectedElementaryCatch(String activityId) throws ExecutionException { - return getActivityCache().get(activityId).getCorrectedElementaryCatch(); + public Collection<CorrectedElementaryCatch> getCorrectedElementaryCatch(String activityId) { + return getActivityCache().forId(activityId).getCorrectedElementaryCatch(); } } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelInputContext.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelInputContext.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelInputContext.java @@ -21,12 +21,10 @@ package fr.ird.t3.actions.stratum; * #L% */ -import com.google.common.cache.CacheBuilder; -import com.google.common.cache.CacheLoader; -import com.google.common.cache.LoadingCache; import fr.ird.t3.actions.T3Action; import fr.ird.t3.entities.T3Predicates; import fr.ird.t3.entities.T3TopiaPersistenceContext; +import fr.ird.t3.entities.cache.ActivityCache; import fr.ird.t3.entities.cache.LengthWeightConversionWithContextCache; import fr.ird.t3.entities.cache.WeightCategoryTreatmentCache; import fr.ird.t3.entities.cache.ZoneStratumCache; @@ -53,7 +51,6 @@ import fr.ird.t3.services.ioc.InjectFromDAO; import java.util.Collection; import java.util.Date; import java.util.List; -import java.util.Objects; import java.util.Set; import java.util.function.Predicate; import java.util.function.Supplier; @@ -70,7 +67,7 @@ public abstract class LevelInputContext<C extends LevelConfigurationWithStratum, /** * Cache of activity (to avoid to reload them for catch and sample stratum). */ - private final LoadingCache<String, Activity> activityCache; + private final ActivityCache activityCache; /** * Cache of {@link WeightCategoryTreatment}. */ @@ -155,14 +152,8 @@ public abstract class LevelInputContext<C extends LevelConfigurationWithStratum, } catch (Exception e) { throw new IllegalStateException("can't inject to " + this, e); } - this.activityCache = CacheBuilder.newBuilder().build( - new CacheLoader<String, Activity>() { - @Override - public Activity load(@SuppressWarnings("NullableProblems") String key) { - return activityDAO.forTopiaIdEquals(Objects.requireNonNull(key)).findUnique(); - } - }); T3TopiaPersistenceContext persistenceContext = action.getT3TopiaPersistenceContext().get(); + this.activityCache = persistenceContext.newActivityCache(); this.weightCategoryCache = persistenceContext.newWeightCategoryTreatmentCache(); C configuration = action.getConfiguration(); configuration.setLocale(action.getLocale()); @@ -216,7 +207,7 @@ public abstract class LevelInputContext<C extends LevelConfigurationWithStratum, return nbStratum; } - public LoadingCache<String, Activity> getActivityCache() { + public ActivityCache getActivityCache() { return activityCache; } @@ -281,6 +272,6 @@ public abstract class LevelInputContext<C extends LevelConfigurationWithStratum, } public void clear() { - activityCache.invalidateAll(); + activityCache.clear(); } } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelStratumConfigurationIterator.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelStratumConfigurationIterator.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelStratumConfigurationIterator.java @@ -119,6 +119,8 @@ public abstract class LevelStratumConfigurationIterator<C extends LevelConfigura } protected void nextSchoolType() { + // each time we change school type, we are sure to not cross again a previous loaded activity, so can clear cache + inputContext.getActivityCache().clear(); currentSchoolType = schoolTypeIterator.next(); currentZones = inputContext.getZones(currentSchoolType); currentWeightCategoryTreatments = inputContext.getWeightCategoryTreatments(currentSchoolType); ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java @@ -39,7 +39,6 @@ import java.util.List; import java.util.Map; import java.util.Objects; import java.util.Set; -import java.util.concurrent.ExecutionException; import java.util.function.BiConsumer; import java.util.function.Function; import java.util.function.Predicate; @@ -185,11 +184,7 @@ public class StratumConfiguration<C extends LevelConfigurationWithStratum, A ext } public Activity getActivity(String activityId) { - try { - return inputContext.getActivityCache().get(activityId); - } catch (ExecutionException e) { - throw new RuntimeException(String.format("Could not obtain activity %s", activityId), e); - } + return inputContext.getActivityCache().forId(activityId); } @Override ===================================== t3-domain/src/main/java/fr/ird/t3/entities/T3TopiaPersistenceContext.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/entities/T3TopiaPersistenceContext.java +++ b/t3-domain/src/main/java/fr/ird/t3/entities/T3TopiaPersistenceContext.java @@ -21,6 +21,7 @@ package fr.ird.t3.entities; * #L% */ +import fr.ird.t3.entities.cache.ActivityCache; import fr.ird.t3.entities.cache.LengthWeightConversionCache; import fr.ird.t3.entities.cache.LengthWeightConversionWithContextCache; import fr.ird.t3.entities.cache.WeightCategoryTreatmentCache; @@ -37,6 +38,10 @@ public class T3TopiaPersistenceContext extends AbstractT3TopiaPersistenceContext super(parameter); } + public ActivityCache newActivityCache() { + return new ActivityCache(getActivityDao()); + } + public WeightCategoryTreatmentCache newWeightCategoryTreatmentCache() { return new WeightCategoryTreatmentCache(getWeightCategoryTreatmentDao()); } ===================================== t3-domain/src/main/java/fr/ird/t3/entities/cache/ActivityCache.java ===================================== --- /dev/null +++ b/t3-domain/src/main/java/fr/ird/t3/entities/cache/ActivityCache.java @@ -0,0 +1,59 @@ +/* + * #%L + * T3 :: Domain + * %% + * Copyright (C) 2010 - 2018 IRD, Code Lutin, Ultreia.io + * %% + * 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.ird.t3.entities.cache; + +import fr.ird.t3.entities.data.Activity; +import fr.ird.t3.entities.data.ActivityTopiaDao; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +import java.util.Map; +import java.util.TreeMap; + +/** + * Created by tchemit on 23/03/2018. + * + * @author Tony Chemit - dev(a)tchemit.fr + */ +public class ActivityCache { + + private static final Log log = LogFactory.getLog(ActivityCache.class); + private final Map<String, Activity> cache; + private final ActivityTopiaDao activityDAO; + + public ActivityCache(ActivityTopiaDao activityDAO) { + this.activityDAO = activityDAO; + this.cache = new TreeMap<>(); + } + + public Activity forId(String activityId) { + Activity result = cache.get(activityId); + if (result == null) { + log.info(String.format("Cache Activity [%d] for %s", cache.size(), activityId)); + cache.put(activityId, result = activityDAO.forTopiaIdEquals(activityId).findUnique()); + } + return result; + } + + public void clear() { + cache.clear(); + } +} View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/772a1f75b68d30b42bad1caad164acc5… --- View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/772a1f75b68d30b42bad1caad164acc5… You're receiving this email because of your account on gitlab.com.

1 0

[Git][ultreiaio/ird-t3][develop] use t3 data 1.6 + introduce Activity cache
by Tony CHEMIT 23 Mar '18

23 Mar '18

Tony CHEMIT pushed to branch develop at ultreiaio / ird-t3 Commits: 620e32dd by Tony CHEMIT at 2018-03-23T16:54:04Z use t3 data 1.6 + introduce Activity cache - - - - - 6 changed files: - pom.xml - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2InputContext.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelInputContext.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java - t3-domain/src/main/java/fr/ird/t3/entities/T3TopiaPersistenceContext.java - + t3-domain/src/main/java/fr/ird/t3/entities/cache/ActivityCache.java Changes: ===================================== pom.xml ===================================== --- a/pom.xml +++ b/pom.xml @@ -99,7 +99,7 @@ <projectId>ird-t3</projectId> <stageId>frirdt3</stageId> <applicationName>t3</applicationName> - <t3-data.version>1.6-SNAPSHOT</t3-data.version> + <t3-data.version>1.6</t3-data.version> <lib.version.java4all.i18n>4.0-alpha-11</lib.version.java4all.i18n> <env>dev</env> ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2InputContext.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2InputContext.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2InputContext.java @@ -25,7 +25,6 @@ import fr.ird.t3.actions.stratum.LevelInputContext; import fr.ird.t3.entities.data.CorrectedElementaryCatch; import java.util.Collection; -import java.util.concurrent.ExecutionException; /** * A context to get all input data for the execution of action. @@ -40,8 +39,8 @@ public class Level2InputContext extends LevelInputContext<Level2Configuration, L super(action); } - public Collection<CorrectedElementaryCatch> getCorrectedElementaryCatch(String activityId) throws ExecutionException { - return getActivityCache().get(activityId).getCorrectedElementaryCatch(); + public Collection<CorrectedElementaryCatch> getCorrectedElementaryCatch(String activityId) { + return getActivityCache().forId(activityId).getCorrectedElementaryCatch(); } } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelInputContext.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelInputContext.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelInputContext.java @@ -21,12 +21,10 @@ package fr.ird.t3.actions.stratum; * #L% */ -import com.google.common.cache.CacheBuilder; -import com.google.common.cache.CacheLoader; -import com.google.common.cache.LoadingCache; import fr.ird.t3.actions.T3Action; import fr.ird.t3.entities.T3Predicates; import fr.ird.t3.entities.T3TopiaPersistenceContext; +import fr.ird.t3.entities.cache.ActivityCache; import fr.ird.t3.entities.cache.LengthWeightConversionWithContextCache; import fr.ird.t3.entities.cache.WeightCategoryTreatmentCache; import fr.ird.t3.entities.cache.ZoneStratumCache; @@ -53,7 +51,6 @@ import fr.ird.t3.services.ioc.InjectFromDAO; import java.util.Collection; import java.util.Date; import java.util.List; -import java.util.Objects; import java.util.Set; import java.util.function.Predicate; import java.util.function.Supplier; @@ -70,7 +67,7 @@ public abstract class LevelInputContext<C extends LevelConfigurationWithStratum, /** * Cache of activity (to avoid to reload them for catch and sample stratum). */ - private final LoadingCache<String, Activity> activityCache; + private final ActivityCache activityCache; /** * Cache of {@link WeightCategoryTreatment}. */ @@ -155,14 +152,8 @@ public abstract class LevelInputContext<C extends LevelConfigurationWithStratum, } catch (Exception e) { throw new IllegalStateException("can't inject to " + this, e); } - this.activityCache = CacheBuilder.newBuilder().build( - new CacheLoader<String, Activity>() { - @Override - public Activity load(@SuppressWarnings("NullableProblems") String key) { - return activityDAO.forTopiaIdEquals(Objects.requireNonNull(key)).findUnique(); - } - }); T3TopiaPersistenceContext persistenceContext = action.getT3TopiaPersistenceContext().get(); + this.activityCache = persistenceContext.newActivityCache(); this.weightCategoryCache = persistenceContext.newWeightCategoryTreatmentCache(); C configuration = action.getConfiguration(); configuration.setLocale(action.getLocale()); @@ -216,7 +207,7 @@ public abstract class LevelInputContext<C extends LevelConfigurationWithStratum, return nbStratum; } - public LoadingCache<String, Activity> getActivityCache() { + public ActivityCache getActivityCache() { return activityCache; } @@ -281,6 +272,6 @@ public abstract class LevelInputContext<C extends LevelConfigurationWithStratum, } public void clear() { - activityCache.invalidateAll(); + activityCache.clear(); } } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java @@ -39,7 +39,6 @@ import java.util.List; import java.util.Map; import java.util.Objects; import java.util.Set; -import java.util.concurrent.ExecutionException; import java.util.function.BiConsumer; import java.util.function.Function; import java.util.function.Predicate; @@ -185,11 +184,7 @@ public class StratumConfiguration<C extends LevelConfigurationWithStratum, A ext } public Activity getActivity(String activityId) { - try { - return inputContext.getActivityCache().get(activityId); - } catch (ExecutionException e) { - throw new RuntimeException(String.format("Could not obtain activity %s", activityId), e); - } + return inputContext.getActivityCache().forId(activityId); } @Override ===================================== t3-domain/src/main/java/fr/ird/t3/entities/T3TopiaPersistenceContext.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/entities/T3TopiaPersistenceContext.java +++ b/t3-domain/src/main/java/fr/ird/t3/entities/T3TopiaPersistenceContext.java @@ -21,6 +21,7 @@ package fr.ird.t3.entities; * #L% */ +import fr.ird.t3.entities.cache.ActivityCache; import fr.ird.t3.entities.cache.LengthWeightConversionCache; import fr.ird.t3.entities.cache.LengthWeightConversionWithContextCache; import fr.ird.t3.entities.cache.WeightCategoryTreatmentCache; @@ -37,6 +38,10 @@ public class T3TopiaPersistenceContext extends AbstractT3TopiaPersistenceContext super(parameter); } + public ActivityCache newActivityCache() { + return new ActivityCache(getActivityDao()); + } + public WeightCategoryTreatmentCache newWeightCategoryTreatmentCache() { return new WeightCategoryTreatmentCache(getWeightCategoryTreatmentDao()); } ===================================== t3-domain/src/main/java/fr/ird/t3/entities/cache/ActivityCache.java ===================================== --- /dev/null +++ b/t3-domain/src/main/java/fr/ird/t3/entities/cache/ActivityCache.java @@ -0,0 +1,59 @@ +/* + * #%L + * T3 :: Domain + * %% + * Copyright (C) 2010 - 2018 IRD, Code Lutin, Ultreia.io + * %% + * 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.ird.t3.entities.cache; + +import fr.ird.t3.entities.data.Activity; +import fr.ird.t3.entities.data.ActivityTopiaDao; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +import java.util.Map; +import java.util.TreeMap; + +/** + * Created by tchemit on 23/03/2018. + * + * @author Tony Chemit - dev(a)tchemit.fr + */ +public class ActivityCache { + + private static final Log log = LogFactory.getLog(ActivityCache.class); + private final Map<String, Activity> cache; + private final ActivityTopiaDao activityDAO; + + public ActivityCache(ActivityTopiaDao activityDAO) { + this.activityDAO = activityDAO; + this.cache = new TreeMap<>(); + } + + public Activity forId(String activityId) { + Activity result = cache.get(activityId); + if (result == null) { + log.info(String.format("Cache Activity [%d] for %s", cache.size(), activityId)); + cache.put(activityId, result = activityDAO.forTopiaIdEquals(activityId).findUnique()); + } + return result; + } + + public void clear() { + cache.clear(); + } +} View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/620e32dde6c9a0d4b7c2aaec09f837c6… --- View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/620e32dde6c9a0d4b7c2aaec09f837c6… You're receiving this email because of your account on gitlab.com.

1 0

[Git][ultreiaio/ird-t3][develop] add more tests for cache + fix some harbour oceans and fix his request)
by Tony CHEMIT 23 Mar '18

23 Mar '18

Tony CHEMIT pushed to branch develop at ultreiaio / ird-t3 Commits: 179ad7bb by Tony CHEMIT at 2018-03-23T15:01:26Z add more tests for cache + fix some harbour oceans and fix his request) - - - - - 10 changed files: - t3-actions/src/main/java/fr/ird/t3/FakeT3ServiceContext.java - t3-domain/pom.xml - t3-domain/src/main/java/fr/ird/t3/entities/cache/WeightCategoryTreatmentCache.java - t3-domain/src/main/java/fr/ird/t3/entities/cache/ZoneStratumCache.java - t3-domain/src/main/java/fr/ird/t3/entities/reference/AbstractOceanTopiaDao.java - t3-domain/src/main/java/fr/ird/t3/test/T3H2Database.java - t3-domain/src/main/resources/db/migration/V2_1_09_fill-Harbour-ocean.sql - + t3-domain/src/test/java/fr/ird/t3/entities/cache/WeightCategoryTreatmentCacheTest.java - + t3-domain/src/test/java/fr/ird/t3/entities/cache/ZoneStratumCacheTest.java - t3-domain/src/test/java/fr/ird/t3/entities/reference/OceanTopiaDaoPgTest.java Changes: ===================================== t3-actions/src/main/java/fr/ird/t3/FakeT3ServiceContext.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/FakeT3ServiceContext.java +++ b/t3-actions/src/main/java/fr/ird/t3/FakeT3ServiceContext.java @@ -21,28 +21,16 @@ package fr.ird.t3; import fr.ird.t3.entities.T3TopiaApplicationContext; -import fr.ird.t3.entities.T3TopiaApplicationContextBuilder; import fr.ird.t3.entities.T3TopiaPersistenceContext; import fr.ird.t3.entities.user.T3Users; import fr.ird.t3.services.T3Service; import fr.ird.t3.services.T3ServiceContext; import fr.ird.t3.services.T3ServiceFactory; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.junit.Assume; -import org.junit.rules.TestRule; -import org.junit.runner.Description; -import org.junit.runners.model.Statement; -import org.mockito.Mockito; +import fr.ird.t3.test.T3H2Database; import org.nuiton.topia.persistence.TopiaException; -import org.nuiton.util.FileUtil; -import org.nuiton.version.Version; -import java.io.Closeable; -import java.io.File; import java.util.Date; import java.util.Locale; -import java.util.Properties; import java.util.function.Supplier; /** @@ -51,25 +39,19 @@ import java.util.function.Supplier; * @author Tony Chemit - dev(a)tchemit.fr * @since 1.1.1 */ -public class FakeT3ServiceContext implements TestRule, T3ServiceContext, Closeable { - - private static final Log log = LogFactory.getLog(FakeT3ServiceContext.class); +public class FakeT3ServiceContext extends T3H2Database implements T3ServiceContext { private final T3ServiceFactory serviceFactory = new T3ServiceFactory(); - private final boolean injectReferential; protected T3TopiaPersistenceContext transaction; - private T3TopiaApplicationContext rootContext; - private File testDir; - private T3Config applicationConfiguration; private Locale locale; - private boolean initOk; + public FakeT3ServiceContext() { this(false); } public FakeT3ServiceContext(boolean injectReferential) { - this.injectReferential = injectReferential; + super(injectReferential); setLocale(Locale.FRANCE); } @@ -78,10 +60,6 @@ public class FakeT3ServiceContext implements TestRule, T3ServiceContext, Closeab return null; } - public boolean isInitOk() { - return initOk; - } - /** May be used in test to get a fresh transaction. */ @Override public Supplier<T3TopiaPersistenceContext> getT3TopiaPersistenceContext() { @@ -90,11 +68,11 @@ public class FakeT3ServiceContext implements TestRule, T3ServiceContext, Closeab @Override public T3TopiaApplicationContext getApplicationContext() { - return rootContext; + return topiaApplicationContext; } - public T3TopiaPersistenceContext newTransaction() throws TopiaException { - return rootContext.newPersistenceContext(); + private T3TopiaPersistenceContext newTransaction() throws TopiaException { + return topiaApplicationContext.newPersistenceContext(); } @Override @@ -108,11 +86,6 @@ public class FakeT3ServiceContext implements TestRule, T3ServiceContext, Closeab } @Override - public T3Config getApplicationConfiguration() { - return applicationConfiguration; - } - - @Override public T3ServiceFactory getServiceFactory() { return serviceFactory; } @@ -132,58 +105,4 @@ public class FakeT3ServiceContext implements TestRule, T3ServiceContext, Closeab return new Date(); } - public File getTestDir() { - return testDir; - } - - private void starting(Description description) { - testDir = T3IOUtil.getTestSpecificDirectory(description.getTestClass(), description.getMethodName()); - log.info(String.format("Test dir = %s", testDir)); - Properties defaultProps = new Properties(); - defaultProps.put(T3ConfigOption.DATA_DIRECTORY.getKey(), testDir); - File treatmentDirectory = new File(testDir, "treatment"); - FileUtil.createDirectoryIfNecessary(treatmentDirectory); - T3Config realConfiguration = new T3Config(defaultProps) { - @Override - public void init() { - parse(); - } - }; - realConfiguration.init(); - Version t3DataVersion = realConfiguration.getT3DataVersion(); - applicationConfiguration = Mockito.mock(T3Config.class); - Mockito.when(applicationConfiguration.getDataDirectory()).thenReturn(testDir); - Mockito.when(applicationConfiguration.getTreatmentWorkingDirectory()).thenReturn(treatmentDirectory); - Mockito.when(applicationConfiguration.getT3DataVersion()).thenReturn(t3DataVersion); - Mockito.when(applicationConfiguration.getTreatmentWorkingDirectory(Mockito.anyString(), Mockito.anyBoolean())).thenCallRealMethod(); - Mockito.when(applicationConfiguration.getApplicationVersion()).thenReturn(realConfiguration.getApplicationVersion()); - rootContext = T3TopiaApplicationContextBuilder.forH2Referential(testDir.toPath(), injectReferential ? t3DataVersion : null).build(); - } - - @Override - public void close() { - if (transaction != null) { - transaction.close(); - } - } - - @Override - public Statement apply(Statement base, Description description) { - return new Statement() { - @Override - public void evaluate() throws Throwable { - try { - starting(description); - initOk=true; - } catch (Exception e) { - Assume.assumeNoException("Can't start test: " + e.getMessage(), e); - } - try { - base.evaluate(); - } finally { - close(); - } - } - }; - } } ===================================== t3-domain/pom.xml ===================================== --- a/t3-domain/pom.xml +++ b/t3-domain/pom.xml @@ -178,6 +178,12 @@  <scope>provided</scope> </dependency> + <dependency> + <groupId>org.mockito</groupId> + <artifactId>mockito-core</artifactId> +  + <scope>provided</scope> + </dependency> <dependency> <groupId>com.h2database</groupId> ===================================== t3-domain/src/main/java/fr/ird/t3/entities/cache/WeightCategoryTreatmentCache.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/entities/cache/WeightCategoryTreatmentCache.java +++ b/t3-domain/src/main/java/fr/ird/t3/entities/cache/WeightCategoryTreatmentCache.java @@ -56,24 +56,29 @@ public class WeightCategoryTreatmentCache { return forOceanAndSchoolType(activity.getOcean(), activity.getSchoolType()); } - private List<WeightCategoryTreatment> forOceanAndSchoolType(Ocean ocean, SchoolType schoolType) { + List<WeightCategoryTreatment> forOceanAndSchoolType(Ocean ocean, SchoolType schoolType) { String key = ocean.getLabel1() + "#" + schoolType.getLabel1(); - List<WeightCategoryTreatment> weightCategoryTreatments = cache.get(key); - if (weightCategoryTreatments == null) { - weightCategoryTreatments = dao.forOceanEquals(ocean).addEquals(WeightCategoryTreatment.PROPERTY_SCHOOL_TYPE, schoolType).findAll(); - WeightCategories.sort(weightCategoryTreatments); - cache.putAll(key, weightCategoryTreatments); + List<WeightCategoryTreatment> result; + if (cache.containsKey(key)) { + result = cache.get(key); + } else { + result = dao.forOceanEquals(ocean).addEquals(WeightCategoryTreatment.PROPERTY_SCHOOL_TYPE, schoolType).findAll(); + WeightCategories.sort(result); + cache.putAll(key, result); + log.info(String.format("Cache WeightCategoryTreatment [%d] for %s (%d categories)", cache.keySet().size(), key, result.size())); } - return weightCategoryTreatments; + return result; } public List<WeightCategoryTreatment> forOceansAndSchoolType(Collection<Ocean> oceans, SchoolType schoolType) { String key = Joiner.on("#").join(oceans.stream().map(Ocean::getLabel1).collect(Collectors.toList())) + "#" + schoolType.getLabel1(); - List<WeightCategoryTreatment> result = cache.get(key); - if (result == null) { + List<WeightCategoryTreatment> result; + if (cache.containsKey(key)) { + result = cache.get(key); + } else { result = dao.forOceanIn(oceans).addEquals(WeightCategoryTreatment.PROPERTY_SCHOOL_TYPE, schoolType).findAll(); WeightCategories.sort(result); - log.info(String.format("Cache WeightCategoryTreatment [%d] for %s (%d categories)", cache.size(), key, result.size())); + log.info(String.format("Cache WeightCategoryTreatment [%d] for %s (%d categories)", cache.keySet().size(), key, result.size())); cache.putAll(key, result); } return result; ===================================== t3-domain/src/main/java/fr/ird/t3/entities/cache/ZoneStratumCache.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/entities/cache/ZoneStratumCache.java +++ b/t3-domain/src/main/java/fr/ird/t3/entities/cache/ZoneStratumCache.java @@ -1,5 +1,26 @@ package fr.ird.t3.entities.cache; +/*- + * #%L + * T3 :: Domain + * %% + * Copyright (C) 2010 - 2018 IRD, Code Lutin, Ultreia.io + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + * #L% + */ + import com.google.common.base.Joiner; import com.google.common.collect.ArrayListMultimap; import fr.ird.t3.entities.T3TopiaPersistenceContext; @@ -39,10 +60,12 @@ public class ZoneStratumCache { public List<ZoneStratumAware> forOceansAndSchoolType(Collection<Ocean> oceans, SchoolType schoolType) { String key = Joiner.on("#").join(oceans.stream().map(Ocean::getLabel1).collect(Collectors.toList())) + "#" + schoolType.getLabel1(); - List<ZoneStratumAware> result = cache.get(key); - if (result == null) { + List<ZoneStratumAware> result; + if (cache.containsKey(key)) { + result = cache.get(key); + } else { result = zoneMeta.getZones(oceans, schoolType, zoneVersion, persistenceContext); - log.info(String.format("Cache Zone [%d] for %s (%d zones)", cache.size(), key, result.size())); + log.info(String.format("Cache Zone [%d] for %s (%d zones)", cache.keySet().size(), key, result.size())); cache.putAll(key, result); } return result; ===================================== t3-domain/src/main/java/fr/ird/t3/entities/reference/AbstractOceanTopiaDao.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/entities/reference/AbstractOceanTopiaDao.java +++ b/t3-domain/src/main/java/fr/ird/t3/entities/reference/AbstractOceanTopiaDao.java @@ -84,7 +84,7 @@ public class AbstractOceanTopiaDao<E extends Ocean> extends GeneratedOceanTopiaD public PreparedStatement prepareQuery(Connection connection) throws SQLException { @SuppressWarnings("SqlResolve") PreparedStatement ps = connection.prepareStatement( - String.format("SELECT o.topiaid FROM %s a, Ocean o WHERE a.topiaId = ? AND ST_Contains(o.the_geom, a.%s)", tableName, geoColumnName)); + String.format("SELECT o.topiaid FROM %s a, Ocean o WHERE a.topiaId = ? AND ST_DWithin(a.the_geom, o.%s, 1)", tableName, geoColumnName)); ps.setString(1, id); return ps; } ===================================== t3-domain/src/main/java/fr/ird/t3/test/T3H2Database.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/test/T3H2Database.java +++ b/t3-domain/src/main/java/fr/ird/t3/test/T3H2Database.java @@ -21,18 +21,27 @@ package fr.ird.t3.test; * #L% */ +import fr.ird.t3.T3Config; +import fr.ird.t3.T3ConfigOption; import fr.ird.t3.T3IOUtil; import fr.ird.t3.entities.T3EntityHelper; import fr.ird.t3.entities.T3TopiaApplicationContext; import fr.ird.t3.entities.T3TopiaApplicationContextBuilder; import fr.ird.t3.entities.T3TopiaPersistenceContext; -import org.junit.rules.TestWatcher; +import org.junit.Assume; +import org.junit.rules.TestRule; import org.junit.runner.Description; +import org.junit.runners.model.Statement; +import org.mockito.Mockito; import org.nuiton.topia.persistence.TopiaException; +import org.nuiton.util.FileUtil; +import org.nuiton.version.Version; +import java.io.Closeable; import java.io.File; import java.io.IOException; import java.io.InputStream; +import java.util.Properties; /** * A new database created for each test. @@ -40,21 +49,48 @@ import java.io.InputStream; * @author Tony Chemit - dev(a)tchemit.fr * @since 1.0 */ -public class T3H2Database extends TestWatcher { +public class T3H2Database implements TestRule, Closeable { + private final boolean injectReferential; private File testBasedir; + protected T3TopiaApplicationContext topiaApplicationContext; + private T3Config applicationConfiguration; + private boolean initOk; + public T3H2Database() { + this(false); + } - private T3TopiaApplicationContext topiaApplicationContext; + public T3H2Database(boolean injectReferential) { + this.injectReferential = injectReferential; + } - @Override - protected void starting(Description description) { + private void starting(Description description) { testBasedir = T3IOUtil.getTestSpecificDirectory(description.getTestClass(), description.getMethodName()); - topiaApplicationContext = T3TopiaApplicationContextBuilder.forH2(testBasedir.toPath()).build(); - } - @Override - public void finished(Description description) { - T3EntityHelper.releaseRootContext(topiaApplicationContext); + Properties defaultProps = new Properties(); + defaultProps.put(T3ConfigOption.DATA_DIRECTORY.getKey(), testBasedir); + File treatmentDirectory = new File(testBasedir, "treatment"); + FileUtil.createDirectoryIfNecessary(treatmentDirectory); + T3Config realConfiguration = new T3Config(defaultProps) { + @Override + public void init() { + parse(); + } + }; + realConfiguration.init(); + Version t3DataVersion = realConfiguration.getT3DataVersion(); + applicationConfiguration = Mockito.mock(T3Config.class); + Mockito.when(applicationConfiguration.getDataDirectory()).thenReturn(testBasedir); + Mockito.when(applicationConfiguration.getTreatmentWorkingDirectory()).thenReturn(treatmentDirectory); + Mockito.when(applicationConfiguration.getT3DataVersion()).thenReturn(t3DataVersion); + Mockito.when(applicationConfiguration.getTreatmentWorkingDirectory(Mockito.anyString(), Mockito.anyBoolean())).thenCallRealMethod(); + Mockito.when(applicationConfiguration.getApplicationVersion()).thenReturn(realConfiguration.getApplicationVersion()); + + if (injectReferential) { + topiaApplicationContext = T3TopiaApplicationContextBuilder.forH2Referential(testBasedir.toPath(), t3DataVersion).build(); + } else { + topiaApplicationContext = T3TopiaApplicationContextBuilder.forH2(testBasedir.toPath()).build(); + } } public T3TopiaPersistenceContext beginTransaction() throws TopiaException { @@ -69,7 +105,43 @@ public class T3H2Database extends TestWatcher { } } + @SuppressWarnings("unused") public File getTestBasedir() { return testBasedir; } + + public T3Config getApplicationConfiguration() { + return applicationConfiguration; + } + + @Override + public void close() { + if (topiaApplicationContext != null) { + T3EntityHelper.releaseRootContext(topiaApplicationContext); + } + } + + @Override + public Statement apply(Statement base, Description description) { + return new Statement() { + @Override + public void evaluate() throws Throwable { + try { + starting(description); + initOk=true; + } catch (Exception e) { + Assume.assumeNoException("Can't start test: " + e.getMessage(), e); + } + try { + base.evaluate(); + } finally { + close(); + } + } + }; + } + + public boolean isInitOk() { + return initOk; + } } ===================================== t3-domain/src/main/resources/db/migration/V2_1_09_fill-Harbour-ocean.sql ===================================== --- a/t3-domain/src/main/resources/db/migration/V2_1_09_fill-Harbour-ocean.sql +++ b/t3-domain/src/main/resources/db/migration/V2_1_09_fill-Harbour-ocean.sql @@ -53,3 +53,27 @@ UPDATE Harbour SET ocean='fr.ird.t3.entities.reference.Ocean#1297580528924#0.024 UPDATE Harbour SET ocean='fr.ird.t3.entities.reference.Ocean#1297580528924#0.02462443299831396' WHERE topiaId = 'fr.ird.t3.entities.reference.Harbour#1297580528933#0.4894751387384305'; UPDATE Harbour SET ocean='fr.ird.t3.entities.reference.Ocean#1297580528924#0.02462443299831396' WHERE topiaId = 'fr.ird.t3.entities.reference.Harbour#1297580528934#0.17822915599428157'; UPDATE Harbour SET ocean='fr.ird.t3.entities.reference.Ocean#1297580528924#0.02462443299831396' WHERE topiaId = 'fr.ird.t3.entities.reference.Harbour#1297580528932#0.21164070994041773'; + +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528930#0.09848580496276282'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528930#0.4358849181824964'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528930#0.5213952546445324'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528932#0.05217800949850426'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528932#0.09458236901561745'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1464000000000#0.00115115'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1464000000000#0.00116116'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1464000000000#0.00117117'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528935#0.5032524703497515'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528930#0.3128607487452171'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528930#0.7077375683910743'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528930#0.37146946328714225'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528930#0.1776110119020825'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528930#0.10672736119748483'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528929#0.29263430155373604'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528932#0.23227601066196246'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528934#0.5223852489420004'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528929#0.037238377699795766'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528934#0.9698949751160373'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528933#0.2600646486222412'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528934#0.35235641408050444'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1297580528934#0.45885264373047663'; +UPDATE Harbour SET ocean ='fr.ird.t3.entities.reference.Ocean#1297580528924#0.4917298410119624' WHERE topiaId ='fr.ird.t3.entities.reference.Harbour#1460000000000#0.19'; ===================================== t3-domain/src/test/java/fr/ird/t3/entities/cache/WeightCategoryTreatmentCacheTest.java ===================================== --- /dev/null +++ b/t3-domain/src/test/java/fr/ird/t3/entities/cache/WeightCategoryTreatmentCacheTest.java @@ -0,0 +1,83 @@ +package fr.ird.t3.entities.cache; + +/*- + * #%L + * T3 :: Domain + * %% + * Copyright (C) 2010 - 2018 IRD, Code Lutin, Ultreia.io + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + * #L% + */ + +import com.google.common.collect.ImmutableSet; +import fr.ird.t3.entities.T3TopiaPersistenceContext; +import fr.ird.t3.entities.reference.Ocean; +import fr.ird.t3.entities.reference.SchoolType; +import fr.ird.t3.entities.reference.WeightCategoryTreatment; +import fr.ird.t3.test.T3H2Database; +import org.junit.Assert; +import org.junit.Before; +import org.junit.ClassRule; +import org.junit.Test; + +import java.util.List; +import java.util.Set; + +/** + * Created by tchemit on 23/03/2018. + * + * @author Tony Chemit - dev(a)tchemit.fr + */ +public class WeightCategoryTreatmentCacheTest { + + @ClassRule + public static final T3H2Database db = new T3H2Database(true); + + private WeightCategoryTreatmentCache cache; + private T3TopiaPersistenceContext persistenceContext; + + @Before + public void setUp() { + persistenceContext = db.beginTransaction(); + cache = persistenceContext.newWeightCategoryTreatmentCache(); + } + + @Test + public void forOceanAndSchoolType() { + List<Ocean> oceans = persistenceContext.getOceanDao().findAll(); + List<SchoolType> schoolTypes = persistenceContext.getSchoolTypeDao().findAll(); + Set<Integer> oceanCodesWithCategories = ImmutableSet.of(1, 2); + for (Ocean ocean : oceans) { + for (SchoolType schoolType : schoolTypes) { + List<WeightCategoryTreatment> weightCategoryTreatments = cache.forOceanAndSchoolType(ocean, schoolType); + Assert.assertNotNull(weightCategoryTreatments); + if (oceanCodesWithCategories.contains(ocean.getCode())) { + Assert.assertFalse(weightCategoryTreatments.isEmpty()); + } + } + } + } + + @Test + public void forOceansAndSchoolType() { + List<Ocean> oceans = persistenceContext.getOceanDao().findAll(); + List<SchoolType> schoolTypes = persistenceContext.getSchoolTypeDao().findAll(); + for (SchoolType schoolType : schoolTypes) { + List<WeightCategoryTreatment> weightCategoryTreatments = cache.forOceansAndSchoolType(oceans, schoolType); + Assert.assertNotNull(weightCategoryTreatments); + Assert.assertFalse(weightCategoryTreatments.isEmpty()); + } + } +} ===================================== t3-domain/src/test/java/fr/ird/t3/entities/cache/ZoneStratumCacheTest.java ===================================== --- /dev/null +++ b/t3-domain/src/test/java/fr/ird/t3/entities/cache/ZoneStratumCacheTest.java @@ -0,0 +1,66 @@ +package fr.ird.t3.entities.cache; + +/*- + * #%L + * T3 :: Domain + * %% + * Copyright (C) 2010 - 2018 IRD, Code Lutin, Ultreia.io + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + * #L% + */ + +import fr.ird.t3.entities.T3TopiaPersistenceContext; +import fr.ird.t3.entities.reference.Ocean; +import fr.ird.t3.entities.reference.SchoolType; +import fr.ird.t3.entities.reference.zone.ZoneETMeta; +import fr.ird.t3.entities.reference.zone.ZoneStratumAware; +import fr.ird.t3.test.T3PostgresqlDatabase; +import org.junit.Assert; +import org.junit.Before; +import org.junit.ClassRule; +import org.junit.Test; + +import java.util.List; + +/** + * Created by tchemit on 23/03/2018. + * + * @author Tony Chemit - dev(a)tchemit.fr + */ +public class ZoneStratumCacheTest { + + @ClassRule + public static final T3PostgresqlDatabase db = new T3PostgresqlDatabase(); + + private ZoneStratumCache cache; + private T3TopiaPersistenceContext persistenceContext; + + @Before + public void setUp() { + persistenceContext = db.beginTransaction(); + cache = persistenceContext.newZoneStratumCache(new ZoneETMeta(), "v2011"); + } + + @Test + public void forOceansAndSchoolType() { + List<Ocean> oceans = persistenceContext.getOceanDao().findAll(); + List<SchoolType> schoolTypes = persistenceContext.getSchoolTypeDao().findAll(); + for (SchoolType schoolType : schoolTypes) { + List<ZoneStratumAware> zones = cache.forOceansAndSchoolType(oceans, schoolType); + Assert.assertNotNull(zones); + Assert.assertFalse(zones.isEmpty()); + } + } +} ===================================== t3-domain/src/test/java/fr/ird/t3/entities/reference/OceanTopiaDaoPgTest.java ===================================== --- a/t3-domain/src/test/java/fr/ird/t3/entities/reference/OceanTopiaDaoPgTest.java +++ b/t3-domain/src/test/java/fr/ird/t3/entities/reference/OceanTopiaDaoPgTest.java @@ -43,6 +43,8 @@ public class OceanTopiaDaoPgTest { @Test public void findOceanByHarbour() { + int wrongOcean = 0; + int fixOcean = 0; StringBuilder queryBuilder = new StringBuilder(); try (T3TopiaPersistenceContext persistenceContext = db.beginTransaction()) { OceanTopiaDao oceanDao = persistenceContext.getOceanDao(); @@ -55,11 +57,13 @@ public class OceanTopiaDaoPgTest { if (harbour.getOcean() == null) { log.warn(String.format("Harbour %s [%s] with no ocean, can use now %s [%s]", harbour.getLabel1(), harbour.getTopiaId(), oceanByHarbour.getLabel1(), oceanByHarbour.getTopiaId())); queryBuilder.append(String.format("UPDATE Harbour SET ocean ='%s' WHERE topiaId ='%s';\n", oceanByHarbour.getTopiaId(), harbour.getTopiaId())); + fixOcean++; } else { try { Assert.assertEquals(String.format("Wrong ocean for %s", harbour.getLabel1()), harbour.getOcean().getLabel1(), oceanByHarbour.getLabel1()); } catch (Throwable e) { log.error(e.getMessage()); + wrongOcean++; } } } @@ -68,5 +72,7 @@ public class OceanTopiaDaoPgTest { if (queryBuilder.length() > 0) { log.warn("You can update your database with thoses queries to fill missing harbour ocean:\n" + queryBuilder.toString()); } + log.info("Number of wrong oceans: " + wrongOcean); + log.info("Number of fixed oceans: " + fixOcean); } } View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/179ad7bbf9a63bad33d568c32c232cee… --- View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/179ad7bbf9a63bad33d568c32c232cee… You're receiving this email because of your account on gitlab.com.

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[Git][ultreiaio/ird-t3][develop] [N2][N3] Gestion des catégories de poids -10/+10kg dans la stratification N2 et…
by Tony CHEMIT 23 Mar '18

23 Mar '18

Tony CHEMIT pushed to branch develop at ultreiaio / ird-t3 Commits: 3585d323 by Tony CHEMIT at 2018-03-23T13:30:48Z [N2][N3] Gestion des catégories de poids -10/+10kg dans la stratification N2 et N3 (See #263) - mise en place des filtres sur les strates - - - - - 29 changed files: - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratumLoader.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoader.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderAtlantic.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderIndian.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfiguration.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumResult.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2Action.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2OutputContext.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratumLoader.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoader.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderAtlantic.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderIndian.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfiguration.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumResult.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3Action.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratum.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratumLoader.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratum.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratumLoader.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/Stratum.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumResult.java - t3-domain/src/main/java/fr/ird/t3/entities/cache/LengthWeightConversionCache.java - t3-domain/src/main/java/fr/ird/t3/entities/data/ActivityImpl.java - t3-domain/src/main/xmi/t3-persistence.zargo Changes: ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratum.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratum.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratum.java @@ -23,13 +23,9 @@ package fr.ird.t3.actions.data.level2; import com.google.common.collect.HashMultimap; import com.google.common.collect.Multimap; import com.google.common.collect.SetMultimap; -import fr.ird.t3.T3IOUtil; import fr.ird.t3.actions.stratum.CatchStratum; -import fr.ird.t3.actions.stratum.CatchStratumLoader; -import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.data.Activity; import fr.ird.t3.entities.data.CorrectedElementaryCatch; -import fr.ird.t3.entities.data.WeightCategoryTreatmentAware; import fr.ird.t3.entities.reference.Species; import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.models.WeightCompositionAggregateModel; @@ -42,12 +38,10 @@ import org.apache.commons.logging.LogFactory; import java.io.IOException; import java.util.Collection; -import java.util.HashMap; import java.util.List; import java.util.Locale; import java.util.Map; import java.util.Set; -import java.util.function.Function; import static org.nuiton.i18n.I18n.l; @@ -57,7 +51,7 @@ import static org.nuiton.i18n.I18n.l; * @author Tony Chemit - dev(a)tchemit.fr * @since 1.3 */ -public class L2CatchStratum extends CatchStratum<Level2Configuration, Level2Action> { +public class L2CatchStratum extends CatchStratum<Level2Configuration, Level2Action, L2StratumConfiguration> { private static final Log log = LogFactory.getLog(L2CatchStratum.class); /** @@ -101,14 +95,14 @@ public class L2CatchStratum extends CatchStratum<Level2Configuration, Level2Acti */ private WeightCompositionAggregateModel inputModelForSpeciesToFix; - private L2CatchStratum(StratumConfiguration<Level2Configuration> stratumConfiguration, Collection<Species> speciesToFix) { + private L2CatchStratum(L2StratumConfiguration stratumConfiguration, Collection<Species> speciesToFix) { super(stratumConfiguration, speciesToFix); weightCategoriesForSpecies = HashMultimap.create(); inputModelForAllSpecies = new WeightCompositionAggregateModel(); outputModelForAllSpecies = new WeightCompositionAggregateModel(); } - static L2CatchStratum newCatchStratum(StratumConfiguration<Level2Configuration> stratumConfiguration, + static L2CatchStratum newCatchStratum(L2StratumConfiguration stratumConfiguration, List<WeightCategoryTreatment> weightCategories, Collection<Species> species, Level2Action action) throws Exception { @@ -133,29 +127,6 @@ public class L2CatchStratum extends CatchStratum<Level2Configuration, Level2Acti return catchStratum; } - private static <X extends WeightCategoryTreatmentAware> void fillWeights( - WeightCategoryTreatment weightCategory, - Collection<X> data, - Map<Species, Float> weights, - Function<X, Float> function, - WeightCompositionAggregateModel model, - int divideFactor) { - if (weights == null) { - weights = new HashMap<>(); - } - for (X setSpeciesCatWeight : data) { - Species species = setSpeciesCatWeight.getSpecies(); - Float weight = weights.get(species); - if (weight == null) { - weight = 0f; - } - weight += function.apply(setSpeciesCatWeight) / divideFactor; - weights.put(species, weight); - } - if (model != null) { - model.addModel(weightCategory, weights); - } - } @Override public void close() throws IOException { @@ -242,11 +213,7 @@ public class L2CatchStratum extends CatchStratum<Level2Configuration, Level2Acti } @Override - public L2StratumConfiguration getConfiguration() { - return (L2StratumConfiguration) super.getConfiguration(); - } - @Override - protected CatchStratumLoader<Level2Configuration> newLoader() { + protected L2CatchStratumLoader newLoader() { return new L2CatchStratumLoader(); } @@ -258,23 +225,8 @@ public class L2CatchStratum extends CatchStratum<Level2Configuration, Level2Acti WeightCompositionAggregateModel sampleWeightModelForAllSpecies(Activity activity) { WeightCompositionAggregateModel sampleWeightModelFroAllSpecies = new WeightCompositionAggregateModel(); - L2SampleStratum.fillWeightsFromSetSpeciesCatWeight(activity, null, sampleWeightModelFroAllSpecies); + fillWeightsFromSamplesWeight(activity, null, sampleWeightModelFroAllSpecies); return sampleWeightModelFroAllSpecies; } - private void fillWeightsFromCatchesWeight(Activity activity, WeightCompositionAggregateModel model, int dividerFactor) { - Map<WeightCategoryTreatment, Map<Species, Float>> weights = new HashMap<>(); - Multimap<WeightCategoryTreatment, CorrectedElementaryCatch> data = getCorrectedElementaryCatchByCategory(activity); - T3IOUtil.fillMapWithDefaultValue(weights, data.keySet(), HashMap::new); - for (WeightCategoryTreatment weightCategory : data.keySet()) { - Map<Species, Float> speciesFloatMap = weights.get(weightCategory); - Collection<CorrectedElementaryCatch> correctedElementaryCatches = data.get(weightCategory); - fillWeights(weightCategory, - correctedElementaryCatches, - speciesFloatMap, - CorrectedElementaryCatch::getCatchWeight, - model, - dividerFactor); - } - } } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratumLoader.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratumLoader.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratumLoader.java @@ -20,19 +20,12 @@ */ package fr.ird.t3.actions.data.level2; -import com.google.common.base.Preconditions; import fr.ird.t3.actions.stratum.CatchStratumLoader; -import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.data.Activity; import fr.ird.t3.entities.data.ActivityTopiaDao; -import fr.ird.t3.entities.data.Trip; -import fr.ird.t3.entities.reference.Vessel; -import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.services.ioc.InjectDAO; -import java.util.HashMap; import java.util.Map; -import java.util.Set; /** * To load a {@link L2CatchStratum} for a given stratum configuration. @@ -40,13 +33,13 @@ import java.util.Set; * @author Tony Chemit - dev(a)tchemit.fr * @since 1.3 */ -public class L2CatchStratumLoader extends CatchStratumLoader<Level2Configuration> { +public class L2CatchStratumLoader extends CatchStratumLoader<Level2Configuration, Level2Action, L2StratumConfiguration> { @InjectDAO(entityType = Activity.class) private ActivityTopiaDao activityDAO; @Override - public Map<Activity, Integer> loadData(StratumConfiguration<Level2Configuration> configuration) { + public Map<Activity, Integer> loadData(L2StratumConfiguration configuration) { // on commence par récupérer les activités : // - dans la zone // - avec le bon type de banc @@ -67,36 +60,4 @@ public class L2CatchStratumLoader extends CatchStratumLoader<Level2Configuration // - maree.bateau dans la bonne flotte OK return filterActivities(configuration, activityIds); } - - private Map<Activity, Integer> filterActivities(StratumConfiguration<Level2Configuration> configuration, Map<String, Integer> activityIds) { - Map<Activity, Integer> result = new HashMap<>(); - if (activityIds != null && activityIds.size() > 0) { - Set<Vessel> possibleVessels = configuration.getPossibleCatchVessels(); - WeightCategoryTreatment weightCategoryTreatment = configuration.getWeightCategoryTreatment(); - for (Map.Entry<String, Integer> e : activityIds.entrySet()) { - String activityId = e.getKey(); - // get activity - Activity activity = configuration.getActivity(activityId); - // get his trip - Trip trip = activity.getTrip(); - if (!possibleVessels.contains(trip.getVessel())) { - // not a matching boat - continue; - } - // recheck activity have some catches. - Preconditions.checkState(activity.isCorrectedElementaryCatchNotEmpty(), - String.format("Can not accept an activity (%s) with no catch", activity.getTopiaId())); - if (weightCategoryTreatment != null) { - // weight category is in stratum, check there is catch using this category - boolean foundWeightCategory = activity.withCorrectedElementaryCatch(weightCategoryTreatment); - if (!foundWeightCategory) { - // reject - the stratum weight category not found for this activity - continue; - } - } - result.put(activity, e.getValue()); - } - } - return result; - } -} +} \ No newline at end of file ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratum.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratum.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratum.java @@ -20,26 +20,17 @@ */ package fr.ird.t3.actions.data.level2; -import com.google.common.collect.ArrayListMultimap; -import com.google.common.collect.Multimap; -import com.google.common.collect.Multimaps; -import fr.ird.t3.T3IOUtil; import fr.ird.t3.actions.stratum.SampleStratum; -import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.data.Activity; -import fr.ird.t3.entities.data.SetSpeciesCatWeight; import fr.ird.t3.entities.data.SetSpeciesFrequency; -import fr.ird.t3.entities.data.WeightCategoryTreatmentAware; import fr.ird.t3.entities.reference.Species; import fr.ird.t3.entities.reference.WeightCategory; import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.models.WeightCompositionAggregateModel; import fr.ird.t3.models.WeightCompositionModelHelper; import fr.ird.t3.services.T3ServiceContext; -import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.nuiton.topia.persistence.TopiaException; import java.io.IOException; import java.util.Collection; @@ -48,7 +39,6 @@ import java.util.List; import java.util.Locale; import java.util.Map; import java.util.Set; -import java.util.function.Function; import static org.nuiton.i18n.I18n.l; @@ -58,20 +48,17 @@ import static org.nuiton.i18n.I18n.l; * @author Tony Chemit - dev(a)tchemit.fr * @since 1.2 */ -public class L2SampleStratum extends SampleStratum<Level2Configuration, Level2Action, L2SampleStratum> { +public class L2SampleStratum extends SampleStratum<Level2Configuration, Level2Action, L2StratumConfiguration, L2SampleStratum> { private static final Log log = LogFactory.getLog(L2SampleStratum.class); - /** * Total weight of the catch stratum. * * This is needed to test sample stratum quality when loading data. */ private final float catchStratumTotalWeight; - /** Weight composition for all species found in catches. */ private final WeightCompositionAggregateModel modelsForAllSpecies; - /** Weight composition model for only species to fix. */ private WeightCompositionAggregateModel modelsForSpeciesToFix; @@ -89,70 +76,22 @@ public class L2SampleStratum extends SampleStratum<Level2Configuration, Level2Ac */ private float sampleStratumTotalWeight; - private L2SampleStratum(StratumConfiguration<Level2Configuration> configuration, Collection<Species> speciesToFix, float catchStratumTotalWeight) { + private L2SampleStratum(L2StratumConfiguration configuration, L2CatchStratum catchStratum, Collection<Species> speciesToFix) { super(configuration, speciesToFix); - this.catchStratumTotalWeight = catchStratumTotalWeight; + this.catchStratumTotalWeight = catchStratum.getTotalCatchWeightForSpeciesToFix(); this.modelsForAllSpecies = new WeightCompositionAggregateModel(); } - static L2SampleStratum newSampleStratum(StratumConfiguration<Level2Configuration> stratumConfiguration, + static L2SampleStratum newSampleStratum(L2StratumConfiguration stratumConfiguration, + L2CatchStratum catchStratum, List<WeightCategoryTreatment> weightCategories, - float totalCatchWeight, Collection<Species> species, Level2Action action) throws Exception { - L2SampleStratum sampleStratum = new L2SampleStratum(stratumConfiguration, species, totalCatchWeight); + L2SampleStratum sampleStratum = new L2SampleStratum(stratumConfiguration, catchStratum, species); sampleStratum.init(action.getServiceContext(), weightCategories, action); return sampleStratum; } - public static void fillWeightsFromSetSpeciesCatWeight(Activity activity, - Map<WeightCategoryTreatment, Map<Species, Float>> weights, - WeightCompositionAggregateModel model) { - if (weights == null) { - weights = new HashMap<>(); - } - Multimap<WeightCategoryTreatment, SetSpeciesCatWeight> data = groupByWeightCategoryTreatment(activity.getSetSpeciesCatWeight()); - T3IOUtil.fillMapWithDefaultValue(weights, data.keySet(), HashMap::new); - for (WeightCategoryTreatment weightCategory : data.keySet()) { - Map<Species, Float> speciesFloatMap = weights.get(weightCategory); - Collection<SetSpeciesCatWeight> setSpeciesCatWeights = data.get(weightCategory); - fillWeights(weightCategory, setSpeciesCatWeights, speciesFloatMap, SetSpeciesCatWeight::getWeight, model); - } - } - - private static <X extends WeightCategoryTreatmentAware> Multimap<WeightCategoryTreatment, X> groupByWeightCategoryTreatment(Collection<X> activity) { - Multimap<WeightCategoryTreatment, X> index; - if (CollectionUtils.isEmpty(activity)) { - index = ArrayListMultimap.create(); - } else { - index = Multimaps.index(activity, WeightCategoryTreatmentAware::getWeightCategoryTreatment); - } - return index; - } - - private static <X extends WeightCategoryTreatmentAware> void fillWeights( - WeightCategoryTreatment weightCategory, - Collection<X> data, - Map<Species, Float> weights, - Function<X, Float> function, - WeightCompositionAggregateModel model) { - if (weights == null) { - weights = new HashMap<>(); - } - for (X setSpeciesCatWeight : data) { - Species species = setSpeciesCatWeight.getSpecies(); - Float weight = weights.get(species); - if (weight == null) { - weight = 0f; - } - weight += function.apply(setSpeciesCatWeight); - weights.put(species, weight); - } - if (model != null) { - model.addModel(weightCategory, weights); - } - } - @Override public void close() throws IOException { super.close(); @@ -189,23 +128,20 @@ public class L2SampleStratum extends SampleStratum<Level2Configuration, Level2Ac return sampleStratumTotalWeight; } - //FIXME-263 si la categorie de poids que faire ? @Override - protected void mergeNewActivities(T3ServiceContext serviceContext, Set<Activity> activities) throws TopiaException { + protected void mergeNewActivities(T3ServiceContext serviceContext, Set<Activity> activities) { Set<Species> species = getSpeciesToFix(); // all weights (for each species) for all weight categories found Map<WeightCategoryTreatment, Map<Species, Float>> weights = new HashMap<>(); for (Activity activity : activities) { // split cat weight by weight category - fillWeightsFromSetSpeciesCatWeight(activity, weights, null); + fillWeightsFromSamplesWeight(activity, weights, null); // obtain the set species frequencies for the current activity - Collection<SetSpeciesFrequency> setSpeciesFrequencies = activity.getSetSpeciesFrequency(); - if (activity.isSetSpeciesFrequencyNotEmpty()) { - // compute sample count for this activity - int newCount = computeSampleCount(setSpeciesFrequencies, species); - // merge it with final total count - sampleStratumTotalCount += newCount; - } + Collection<SetSpeciesFrequency> setSpeciesFrequencies = getSetSpeciesFrequency(activity); + // compute sample count for this activity + int newCount = computeSampleCount(setSpeciesFrequencies, species); + // merge it with final total count + sampleStratumTotalCount += newCount; } // add all weights to model for (Map.Entry<WeightCategoryTreatment, Map<Species, Float>> e : weights.entrySet()) { @@ -221,18 +157,6 @@ public class L2SampleStratum extends SampleStratum<Level2Configuration, Level2Ac log.info(String.format("sampleStratumTotalCount = %d / sampleStratumTotalWeight = %f", getSampleStratumTotalCount(), getSampleStratumTotalWeight())); } - //FIXME-263 si la categorie de poids que faire ? - private int computeSampleCount(Collection<SetSpeciesFrequency> setSpeciesFrequencies, Collection<Species> speciesToFix) { - int newCount = 0; - for (SetSpeciesFrequency setSpeciesFrequency : setSpeciesFrequencies) { - Species species = setSpeciesFrequency.getSpecies(); - if (speciesToFix.contains(species)) { - newCount += setSpeciesFrequency.getNumber(); - } - } - return newCount; - } - @Override public String logSampleStratumLevel(int substitutionLevel, Level2Action messager) { Locale l = messager.getLocale(); @@ -251,8 +175,14 @@ public class L2SampleStratum extends SampleStratum<Level2Configuration, Level2Ac modelsForSpeciesToFix); } - @Override - public L2StratumConfiguration getConfiguration() { - return (L2StratumConfiguration) super.getConfiguration(); + private int computeSampleCount(Collection<SetSpeciesFrequency> setSpeciesFrequencies, Collection<Species> speciesToFix) { + int newCount = 0; + for (SetSpeciesFrequency setSpeciesFrequency : setSpeciesFrequencies) { + Species species = setSpeciesFrequency.getSpecies(); + if (speciesToFix.contains(species)) { + newCount += setSpeciesFrequency.getNumber(); + } + } + return newCount; } } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoader.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoader.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoader.java @@ -28,6 +28,7 @@ import fr.ird.t3.entities.data.ActivityTopiaDao; import fr.ird.t3.entities.data.Trip; import fr.ird.t3.entities.reference.SchoolType; import fr.ird.t3.entities.reference.Vessel; +import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.entities.type.T3Date; import fr.ird.t3.services.ioc.InjectDAO; import org.apache.commons.logging.Log; @@ -43,7 +44,7 @@ import java.util.Set; * @author Tony Chemit - dev(a)tchemit.fr * @since 1.3 */ -public abstract class L2SampleStratumLoader extends SampleStratumLoader<Level2Configuration, Level2Action, L2SampleStratum> { +public abstract class L2SampleStratumLoader extends SampleStratumLoader<Level2Configuration, Level2Action, L2StratumConfiguration, L2SampleStratum> { private static final Log log = LogFactory.getLog(L2SampleStratumLoader.class); /** @@ -91,7 +92,7 @@ public abstract class L2SampleStratumLoader extends SampleStratumLoader<Level2Co @Override protected Set<String> findActivityIds(String schoolTypeId, T3Date beginDate, T3Date endDate, String... zoneIds) { - StratumConfiguration<Level2Configuration> configuration = getSampleStratum().getConfiguration(); + StratumConfiguration<Level2Configuration, Level2Action> configuration = getSampleStratum().getConfiguration(); Set<String> result = new HashSet<>(); for (String zoneId : zoneIds) { // on commence par récupérer les activités : @@ -110,28 +111,6 @@ public abstract class L2SampleStratumLoader extends SampleStratumLoader<Level2Co } @Override - protected Set<Activity> filterActivities(Set<String> activityIds) { - Set<Activity> result = new HashSet<>(); - StratumConfiguration<Level2Configuration> configuration = getSampleStratum().getConfiguration(); - Set<Vessel> possibleVessels = configuration.getPossibleSampleVessels(); - for (String activityId : activityIds) { - Activity activity = configuration.getActivity(activityId); - // recheck activity have some samples. - Preconditions.checkState( - !activity.isSetSpeciesCatWeightEmpty(), - String.format("Can not accept an activity (%s) with no sample", activity.getTopiaId())); - // get his trip - Trip trip = activity.getTrip(); - if (!possibleVessels.contains(trip.getVessel())) { - // not a matching boat - continue; - } - result.add(activity); - } - return result; - } - - @Override public boolean isStratumOk() { // test if we have enough sample weight L2SampleStratum sampleStratum = getSampleStratum(); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderAtlantic.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderAtlantic.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderAtlantic.java @@ -39,8 +39,7 @@ public class L2SampleStratumLoaderAtlantic extends L2SampleStratumLoader { @Override protected Set<String> findActivityIds(int level) { - - StratumConfiguration<Level2Configuration> configuration = getSampleStratum().getConfiguration(); + StratumConfiguration<Level2Configuration, Level2Action> configuration = getSampleStratum().getConfiguration(); String schoolTypeId = configuration.getSchoolType().getTopiaId(); String zoneId = configuration.getZone().getTopiaId(); T3Date beginDate = configuration.getBeginDate(); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderIndian.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderIndian.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderIndian.java @@ -40,7 +40,7 @@ public class L2SampleStratumLoaderIndian extends L2SampleStratumLoader { @Override protected Set<String> findActivityIds(int level) { - StratumConfiguration<Level2Configuration> configuration = getSampleStratum().getConfiguration(); + StratumConfiguration<Level2Configuration, Level2Action> configuration = getSampleStratum().getConfiguration(); String schoolTypeId = configuration.getSchoolType().getTopiaId(); String zoneId = configuration.getZone().getTopiaId(); T3Date beginDate = configuration.getBeginDate(); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfiguration.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfiguration.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfiguration.java @@ -35,9 +35,7 @@ import java.util.List; * * @author Tony Chemit - dev(a)tchemit.fr */ -public class L2StratumConfiguration extends StratumConfiguration<Level2Configuration> { - - private final List<WeightCategoryTreatment> weightCategoryTreatments; +class L2StratumConfiguration extends StratumConfiguration<Level2Configuration, Level2Action> { L2StratumConfiguration(Level2InputContext inputContext, SchoolType schoolType, @@ -48,23 +46,15 @@ public class L2StratumConfiguration extends StratumConfiguration<Level2Configura Collection<ZoneStratumAware> zones, List<WeightCategoryTreatment> weightCategoryTreatments) { super( - inputContext.getConfiguration(), - inputContext.getZoneMeta(), + inputContext, zone, schoolType, weightCategoryTreatment, beginDate, beginDate.incrementsMonths(inputContext.getConfiguration().getTimeStep() - 1), zones, - inputContext.getPossibleCatchVessels(), - inputContext.getPossibleSampleVessels(), null, - inputContext.getActivityCache(), + weightCategoryTreatments, stratumIndex); - this.weightCategoryTreatments = weightCategoryTreatments; - } - - public List<WeightCategoryTreatment> getWeightCategoryTreatments() { - return weightCategoryTreatments; } } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumResult.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumResult.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumResult.java @@ -8,12 +8,12 @@ * 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% @@ -23,8 +23,6 @@ package fr.ird.t3.actions.data.level2; import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.actions.stratum.StratumResult; -import java.io.IOException; - /** * Result of a level 2 Stratum. * @@ -33,7 +31,7 @@ import java.io.IOException; */ public class L2StratumResult extends StratumResult<Level2Configuration> { - public L2StratumResult(StratumConfiguration<Level2Configuration> configuration, String label) { + public L2StratumResult(StratumConfiguration<Level2Configuration, Level2Action> configuration, String label) { super(configuration, label); } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2Action.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2Action.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2Action.java @@ -174,7 +174,7 @@ public class Level2Action extends T3Action<Level2Configuration> { incrementsProgression(); } else { // compute sample stratum - try (L2SampleStratum sampleStratum = L2SampleStratum.newSampleStratum(stratumConfiguration, weightCategories, catchStratum.getTotalCatchWeightForSpeciesToFix(), species, this)) { + try (L2SampleStratum sampleStratum = L2SampleStratum.newSampleStratum(stratumConfiguration, catchStratum, weightCategories, species, this)) { incrementsProgression(); // get the substitution level for the sample stratum Integer level = sampleStratum.getSubstitutionLevel(); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2OutputContext.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2OutputContext.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2OutputContext.java @@ -40,16 +40,16 @@ import static org.nuiton.i18n.I18n.l; */ public class Level2OutputContext extends LevelOutputContext<Level2Configuration, Level2Action, Level2InputContext, L2StratumResult> { - private long totalCatchWeightForSpeciesFoFix; - private long totalCatchWeight; /** * Input Weight composition (based on {@link CorrectedElementaryCatch#getCatchWeight()}) for all species found in catches. */ - private WeightCompositionAggregateModel inputCatchModelForAllSpecies; + private final WeightCompositionAggregateModel inputCatchModelForAllSpecies; /** * Output Weight composition (based on {@link CorrectedElementaryCatch#getCorrectedCatchWeight()}) for all species found in catches. */ - private WeightCompositionAggregateModel outputCatchModelForAllSpecies; + private final WeightCompositionAggregateModel outputCatchModelForAllSpecies; + private long totalCatchWeightForSpeciesFoFix; + private long totalCatchWeight; public Level2OutputContext(Level2Action action, Level2InputContext inputContext) { super(action, inputContext); @@ -57,10 +57,12 @@ public class Level2OutputContext extends LevelOutputContext<Level2Configuration, this.outputCatchModelForAllSpecies = new WeightCompositionAggregateModel(); } + @SuppressWarnings("unused") public long getTotalCatchWeightForSpeciesFoFix() { return totalCatchWeightForSpeciesFoFix; } + @SuppressWarnings("unused") public long getTotalCatchWeight() { return totalCatchWeight; } @@ -72,22 +74,17 @@ public class Level2OutputContext extends LevelOutputContext<Level2Configuration, mergeResult(stratumResult); } + @SuppressWarnings("unused") public WeightCompositionAggregateModel getInputCatchModelForAllSpecies() { return inputCatchModelForAllSpecies; } - public void setInputCatchModelForAllSpecies(WeightCompositionAggregateModel inputCatchModelForAllSpecies) { - this.inputCatchModelForAllSpecies = inputCatchModelForAllSpecies; - } - + @SuppressWarnings("unused") public WeightCompositionAggregateModel getOutputCatchModelForAllSpecies() { return outputCatchModelForAllSpecies; } - public void setOutputCatchModelForAllSpecies(WeightCompositionAggregateModel outputCatchModelForAllSpecies) { - this.outputCatchModelForAllSpecies = outputCatchModelForAllSpecies; - } - + @SuppressWarnings("unused") public String getInputCatchStratumLog() { Collection<Species> species = getSpecies(); WeightCompositionAggregateModel inputCatchModelForSpeciesToFix = inputCatchModelForAllSpecies.extractForSpecies(species); @@ -99,6 +96,7 @@ public class Level2OutputContext extends LevelOutputContext<Level2Configuration, inputCatchModelForSpeciesToFix); } + @SuppressWarnings("unused") public String getOutputCatchStratumLog() { Collection<Species> species = getSpecies(); WeightCompositionAggregateModel outputCatchModelForSpeciesToFix = outputCatchModelForAllSpecies.extractForSpecies(species); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratum.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratum.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratum.java @@ -21,13 +21,10 @@ package fr.ird.t3.actions.data.level3; import fr.ird.t3.actions.stratum.CatchStratum; -import fr.ird.t3.actions.stratum.CatchStratumLoader; -import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.T3EntityHelper; import fr.ird.t3.entities.T3Suppliers; import fr.ird.t3.entities.data.Activity; import fr.ird.t3.entities.data.CorrectedElementaryCatch; -import fr.ird.t3.entities.data.SpeciesAware; import fr.ird.t3.entities.reference.Species; import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.services.T3ServiceContext; @@ -35,7 +32,6 @@ import fr.ird.t3.services.T3ServiceContext; import java.util.Collection; import java.util.List; import java.util.Map; -import java.util.function.Predicate; /** * Define a catch stratum for a given stratum of a level 2 treatment. @@ -43,16 +39,9 @@ import java.util.function.Predicate; * @author Tony Chemit - dev(a)tchemit.fr * @since 1.3 */ -public class L3CatchStratum extends CatchStratum<Level3Configuration, Level3Action> { +public class L3CatchStratum extends CatchStratum<Level3Configuration, Level3Action, L3StratumConfiguration> { /** - * Predicate to filter only species selected in configuration. - * - * @see #getSpeciesToFix() - * @since 1.4 - */ - private final Predicate<? super SpeciesAware> speciesToFixFilter; - /** * Keep the total weight of all the catches in the stratum. * * Used by sampleStratum for quality tests. @@ -61,17 +50,12 @@ public class L3CatchStratum extends CatchStratum<Level3Configuration, Level3Acti */ private float totalCatchWeight; - L3CatchStratum(StratumConfiguration<Level3Configuration> stratumConfiguration, Collection<Species> speciesToFix, Predicate<? super SpeciesAware> speciesToFixFilter) { + L3CatchStratum(L3StratumConfiguration stratumConfiguration, Collection<Species> speciesToFix) { super(stratumConfiguration, speciesToFix); - this.speciesToFixFilter = speciesToFixFilter; - } - @Override - public L3StratumConfiguration getConfiguration() { - return (L3StratumConfiguration) super.getConfiguration(); } @Override - protected CatchStratumLoader<Level3Configuration> newLoader() { + protected L3CatchStratumLoader newLoader() { return new L3CatchStratumLoader(); } @@ -87,7 +71,7 @@ public class L3CatchStratum extends CatchStratum<Level3Configuration, Level3Acti T3EntityHelper.getTotal( getCorrectedElementaryCatch(activity), CorrectedElementaryCatch::getCorrectedCatchWeight, - speciesToFixFilter, + getConfiguration().getSpeciesToFixFilter(), T3Suppliers.newActivityDecorateSupplier( serviceContext, activity, ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratumLoader.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratumLoader.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratumLoader.java @@ -20,18 +20,12 @@ */ package fr.ird.t3.actions.data.level3; -import com.google.common.base.Preconditions; import fr.ird.t3.actions.stratum.CatchStratumLoader; -import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.data.Activity; import fr.ird.t3.entities.data.ActivityTopiaDao; -import fr.ird.t3.entities.data.Trip; -import fr.ird.t3.entities.reference.Vessel; import fr.ird.t3.services.ioc.InjectDAO; -import java.util.HashMap; import java.util.Map; -import java.util.Set; /** * To load a {@link L3CatchStratum} for a given stratum configuration. @@ -39,13 +33,13 @@ import java.util.Set; * @author Tony Chemit - dev(a)tchemit.fr * @since 1.3 */ -public class L3CatchStratumLoader extends CatchStratumLoader<Level3Configuration> { +public class L3CatchStratumLoader extends CatchStratumLoader<Level3Configuration, Level3Action, L3StratumConfiguration> { @InjectDAO(entityType = Activity.class) private ActivityTopiaDao activityDAO; @Override - public Map<Activity, Integer> loadData(StratumConfiguration<Level3Configuration> configuration) { + public Map<Activity, Integer> loadData(L3StratumConfiguration configuration) { // on commence par récupérer les activités : // - dans la zone // - avec le bon type de banc @@ -66,29 +60,4 @@ public class L3CatchStratumLoader extends CatchStratumLoader<Level3Configuration // - maree.bateau dans la bonne flotte OK return filterActivities(configuration, activityIds); } - - private Map<Activity, Integer> filterActivities(StratumConfiguration<Level3Configuration> configuration, Map<String, Integer> activityIds) { - - Set<Vessel> possibleVessels = configuration.getPossibleCatchVessels(); - - Map<Activity, Integer> result = new HashMap<>(); - if (activityIds != null && activityIds.size() > 0) { - for (Map.Entry<String, Integer> e : activityIds.entrySet()) { - String activityId = e.getKey(); - // get activity - Activity activity = configuration.getActivity(activityId); - // get his trip - Trip trip = activity.getTrip(); - if (!possibleVessels.contains(trip.getVessel())) { - // not a matching boat - continue; - } - // recheck activity have some catches. - Preconditions.checkState(!activity.isCorrectedElementaryCatchEmpty(), - String.format("Can not accept an activity (%s) with no catch", activity.getTopiaId())); - result.put(activity, e.getValue()); - } - } - return result; - } } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratum.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratum.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratum.java @@ -25,7 +25,6 @@ import com.google.common.collect.Multimap; import com.google.common.collect.Multimaps; import fr.ird.t3.T3IOUtil; import fr.ird.t3.actions.stratum.SampleStratum; -import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.T3EntityHelper; import fr.ird.t3.entities.T3Suppliers; import fr.ird.t3.entities.cache.LengthWeightConversionWithContextCache; @@ -34,7 +33,6 @@ import fr.ird.t3.entities.data.Activity; import fr.ird.t3.entities.data.SetSpeciesCatWeight; import fr.ird.t3.entities.data.SetSpeciesFrequency; import fr.ird.t3.entities.data.SetSpeciesFrequencyTopiaDao; -import fr.ird.t3.entities.data.SpeciesAware; import fr.ird.t3.entities.reference.LengthWeightConversion; import fr.ird.t3.entities.reference.Species; import fr.ird.t3.entities.reference.WeightCategoryTreatment; @@ -54,7 +52,6 @@ import java.util.List; import java.util.Locale; import java.util.Map; import java.util.Set; -import java.util.function.Predicate; import static org.nuiton.i18n.I18n.l; @@ -64,7 +61,7 @@ import static org.nuiton.i18n.I18n.l; * @author Tony Chemit - dev(a)tchemit.fr * @since 1.2 */ -public class L3SampleStratum extends SampleStratum<Level3Configuration, Level3Action, L3SampleStratum> { +public class L3SampleStratum extends SampleStratum<Level3Configuration, Level3Action, L3StratumConfiguration, L3SampleStratum> { private static final Log log = LogFactory.getLog(L3SampleStratum.class); @@ -101,31 +98,22 @@ public class L3SampleStratum extends SampleStratum<Level3Configuration, Level3Ac */ private final LengthWeightConversionWithContextCache conversionHelper; /** - * Predicate to filter only species selected in configuration. - * - * @see #getSpeciesToFix() - * @since 1.4 - */ - private final Predicate<? super SpeciesAware> speciesToFixFilter; - /** * Total weight of the sample stratum. * * This is needed to test sample stratum quality when loading data. */ private float sampleStratumTotalWeight; - L3SampleStratum(StratumConfiguration<Level3Configuration> configuration, + L3SampleStratum(L3StratumConfiguration configuration, Collection<Species> speciesToFix, float catchStratumTotalWeight, - LengthWeightConversionWithContextCache conversionHelper, - Predicate<? super SpeciesAware> speciesToFixFilter) { + LengthWeightConversionWithContextCache conversionHelper) { super(configuration, speciesToFix); this.catchStratumTotalWeight = catchStratumTotalWeight; this.conversionHelper = conversionHelper; this.speciesCount = new HashMap<>(); this.compositionModel = new HashMap<>(); this.allSetSpeciesFrequenciesBySpecies = ArrayListMultimap.create(); - this.speciesToFixFilter = speciesToFixFilter; } @Override @@ -155,18 +143,13 @@ public class L3SampleStratum extends SampleStratum<Level3Configuration, Level3Ac } @Override - public L3StratumConfiguration getConfiguration() { - return (L3StratumConfiguration) super.getConfiguration(); - } - - @Override public void mergeNewActivities(T3ServiceContext serviceContext, Set<Activity> activities) { for (Activity activity : activities) { // add total weight of samples of the activity (only for selected species) float totalWeight = T3EntityHelper.getTotal( activity.getSetSpeciesCatWeight(), SetSpeciesCatWeight::getWeight, - speciesToFixFilter, + getConfiguration().getSpeciesToFixFilter(), T3Suppliers.newActivityDecorateSupplier( serviceContext, activity, ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoader.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoader.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoader.java @@ -20,14 +20,11 @@ */ package fr.ird.t3.actions.data.level3; -import com.google.common.base.Preconditions; import fr.ird.t3.actions.stratum.SampleStratumLoader; import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.data.Activity; import fr.ird.t3.entities.data.ActivityTopiaDao; -import fr.ird.t3.entities.data.Trip; import fr.ird.t3.entities.reference.Species; -import fr.ird.t3.entities.reference.Vessel; import fr.ird.t3.entities.type.T3Date; import fr.ird.t3.services.ioc.InjectDAO; import org.apache.commons.logging.Log; @@ -45,7 +42,7 @@ import java.util.Set; * @author Tony Chemit - dev(a)tchemit.fr * @since 1.3 */ -public abstract class L3SampleStratumLoader extends SampleStratumLoader<Level3Configuration, Level3Action, L3SampleStratum> { +public abstract class L3SampleStratumLoader extends SampleStratumLoader<Level3Configuration, Level3Action, L3StratumConfiguration, L3SampleStratum> { private static final Log log = LogFactory.getLog(L3SampleStratumLoader.class); @@ -83,7 +80,7 @@ public abstract class L3SampleStratumLoader extends SampleStratumLoader<Level3Co @Override protected Set<String> findActivityIds(String schoolTypeId, T3Date beginDate, T3Date endDate, String... zoneIds) { Set<String> result = new HashSet<>(); - StratumConfiguration<Level3Configuration> configuration = getSampleStratum().getConfiguration(); + StratumConfiguration<Level3Configuration, Level3Action> configuration = getSampleStratum().getConfiguration(); for (String zoneId : zoneIds) { // on commence par récupérer les activités : // - dans la zone ET @@ -101,28 +98,6 @@ public abstract class L3SampleStratumLoader extends SampleStratumLoader<Level3Co } @Override - protected Set<Activity> filterActivities(Set<String> activityIds) { - Set<Activity> result = new HashSet<>(); - StratumConfiguration<Level3Configuration> configuration = getSampleStratum().getConfiguration(); - Set<Vessel> possibleVessels = configuration.getPossibleSampleVessels(); - for (String activityId : activityIds) { - Activity activity = configuration.getActivity(activityId); - // get his trip - Trip trip = activity.getTrip(); - if (!possibleVessels.contains(trip.getVessel())) { - // not a matching boat - continue; - } - // recheck activity have some samples. - Preconditions.checkState( - !activity.isSetSpeciesCatWeightEmpty(), - String.format("Can not accept an activity (%s) with no sample", activity.getTopiaId())); - result.add(activity); - } - return result; - } - - @Override public boolean isStratumOk() { L3SampleStratum stratum = getSampleStratum(); // test if we have enough sample weight ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderAtlantic.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderAtlantic.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderAtlantic.java @@ -39,7 +39,7 @@ public class L3SampleStratumLoaderAtlantic extends L3SampleStratumLoader { @Override protected Set<String> findActivityIds(int level) { - StratumConfiguration<Level3Configuration> configuration = getSampleStratum().getConfiguration(); + StratumConfiguration<Level3Configuration, Level3Action> configuration = getSampleStratum().getConfiguration(); String schoolTypeId = configuration.getSchoolType().getTopiaId(); String zoneId = configuration.getZone().getTopiaId(); T3Date beginDate = configuration.getBeginDate(); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderIndian.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderIndian.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderIndian.java @@ -40,7 +40,7 @@ public class L3SampleStratumLoaderIndian extends L3SampleStratumLoader { @Override protected Set<String> findActivityIds(int level) { - StratumConfiguration<Level3Configuration> configuration = getSampleStratum().getConfiguration(); + StratumConfiguration<Level3Configuration, Level3Action> configuration = getSampleStratum().getConfiguration(); String schoolTypeId = configuration.getSchoolType().getTopiaId(); String zoneId = configuration.getZone().getTopiaId(); T3Date beginDate = configuration.getBeginDate(); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfiguration.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfiguration.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfiguration.java @@ -22,7 +22,6 @@ package fr.ird.t3.actions.data.level3; */ import fr.ird.t3.actions.stratum.StratumConfiguration; -import fr.ird.t3.entities.cache.LengthWeightConversionWithContextCache; import fr.ird.t3.entities.reference.SchoolType; import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.entities.reference.zone.ZoneStratumAware; @@ -37,11 +36,9 @@ import java.util.Map; * * @author Tony Chemit - dev(a)tchemit.fr */ -public class L3StratumConfiguration extends StratumConfiguration<Level3Configuration> { +class L3StratumConfiguration extends StratumConfiguration<Level3Configuration, Level3Action> { - private final List<WeightCategoryTreatment> weightCategoryTreatments; private final Map<String, Integer> stratumMinimumSampleCount; - private final LengthWeightConversionWithContextCache conversionHelper; L3StratumConfiguration(Level3InputContext inputContext, SchoolType schoolType, @@ -53,33 +50,20 @@ public class L3StratumConfiguration extends StratumConfiguration<Level3Configura List<WeightCategoryTreatment> weightCategoryTreatments, Map<String, Integer> stratumMinimumSampleCount) { super( - inputContext.getConfiguration(), - inputContext.getZoneMeta(), + inputContext, zone, schoolType, weightCategoryTreatment, beginDate, beginDate.incrementsMonths(inputContext.getConfiguration().getTimeStep() - 1), zones, - inputContext.getPossibleCatchVessels(), - inputContext.getPossibleSampleVessels(), stratumMinimumSampleCount, - inputContext.getActivityCache(), + weightCategoryTreatments, stratumIndex); - this.weightCategoryTreatments = weightCategoryTreatments; this.stratumMinimumSampleCount = stratumMinimumSampleCount; - this.conversionHelper = inputContext.newLengthWeightConversionWithContextCache(zone.getOcean(), beginDate.toBeginDate()); - } - - public List<WeightCategoryTreatment> getWeightCategoryTreatments() { - return weightCategoryTreatments; } public Map<String, Integer> getStratumMinimumSampleCount() { return stratumMinimumSampleCount; } - - public LengthWeightConversionWithContextCache getConversionHelper() { - return conversionHelper; - } } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumResult.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumResult.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumResult.java @@ -8,12 +8,12 @@ * 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% @@ -24,8 +24,6 @@ import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.actions.stratum.StratumResult; import fr.ird.t3.models.SpeciesCountAggregateModel; -import java.io.IOException; - /** * Result of a level 3 Stratum. * @@ -42,7 +40,7 @@ public class L3StratumResult extends StratumResult<Level3Configuration> { */ private final SpeciesCountAggregateModel totalFishesCount; - public L3StratumResult(StratumConfiguration<Level3Configuration> configuration, String label) { + public L3StratumResult(StratumConfiguration<Level3Configuration, Level3Action> configuration, String label) { super(configuration, label); totalFishesCount = new SpeciesCountAggregateModel(); } @@ -52,7 +50,7 @@ public class L3StratumResult extends StratumResult<Level3Configuration> { } @Override - public void close() throws IOException { + public void close() { totalFishesCount.close(); } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3Action.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3Action.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3Action.java @@ -405,7 +405,7 @@ public class Level3Action extends T3Action<Level3Configuration> { } private L3CatchStratum newCatchStratum(L3StratumConfiguration stratumConfiguration) throws Exception { - L3CatchStratum catchStratum = new L3CatchStratum(stratumConfiguration, inputContext.getSpecies(), inputContext.getSpeciesToFixFilter()); + L3CatchStratum catchStratum = new L3CatchStratum(stratumConfiguration, inputContext.getSpecies()); catchStratum.init(serviceContext, stratumConfiguration.getWeightCategoryTreatments(), this); // get the total weight of the catch stratum float catchStratumWeight = catchStratum.getTotalCatchWeight(); @@ -430,8 +430,8 @@ public class Level3Action extends T3Action<Level3Configuration> { new L3SampleStratum(stratumConfiguration, inputContext.getSpecies(), totalCatchWeight, - stratumConfiguration.getConversionHelper(), - inputContext.getSpeciesToFixFilter()); + stratumConfiguration.getConversionHelper() + ); sampleStratum.init(serviceContext, stratumConfiguration.getWeightCategoryTreatments(), this); return sampleStratum; } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratum.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratum.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratum.java @@ -20,12 +20,8 @@ */ package fr.ird.t3.actions.stratum; -import com.google.common.collect.Multimap; -import com.google.common.collect.Multimaps; import fr.ird.t3.actions.T3Action; import fr.ird.t3.entities.data.Activity; -import fr.ird.t3.entities.data.CorrectedElementaryCatch; -import fr.ird.t3.entities.data.WeightCategoryTreatmentAware; import fr.ird.t3.entities.reference.Species; import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.services.IOCService; @@ -33,9 +29,10 @@ import fr.ird.t3.services.T3ServiceContext; import fr.ird.t3.services.ioc.InjectDAO; import java.util.Collection; +import java.util.LinkedHashSet; import java.util.List; import java.util.Map; -import java.util.stream.Collectors; +import java.util.Set; /** * Base catch stratum. @@ -43,12 +40,13 @@ import java.util.stream.Collectors; * @author Tony Chemit - dev(a)tchemit.fr * @since 1.3 */ -public abstract class CatchStratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>> extends Stratum<C, A> { +public abstract class CatchStratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>, S extends StratumConfiguration<C, A>> extends Stratum<C, A, S> { - private int nbActivitiesWithSample; + private final Set<String> activityWithSampleIds; - protected CatchStratum(StratumConfiguration<C> configuration, Collection<Species> speciesToFix) { + protected CatchStratum(S configuration, Collection<Species> speciesToFix) { super(configuration, speciesToFix); + activityWithSampleIds = new LinkedHashSet<>(); } /** @@ -56,11 +54,11 @@ public abstract class CatchStratum<C extends LevelConfigurationWithStratum, A ex * * @return new instance of a catch stratum loader */ - protected abstract CatchStratumLoader<C> newLoader(); + protected abstract CatchStratumLoader<C, A, S> newLoader(); @Override public void init(T3ServiceContext serviceContext, List<WeightCategoryTreatment> weightCategories, A messager) throws Exception { - CatchStratumLoader<C> stratumLoader = newLoader(); + CatchStratumLoader<C, A, S> stratumLoader = newLoader(); // inject transaction in loader stratumLoader.setTransaction(serviceContext.getT3TopiaPersistenceContext()); // inject dao in loader @@ -68,7 +66,13 @@ public abstract class CatchStratum<C extends LevelConfigurationWithStratum, A ex // get all catches usable in this stratum grouped by their owing activity Map<Activity, Integer> activities = stratumLoader.loadData(getConfiguration()); setActivities(activities); - nbActivitiesWithSample = (int) activities.keySet().stream().filter(Activity::isSetSpeciesCatWeightNotEmpty).count(); + //FIXME- Ca doit etre dans SampleStratum ? + for (Activity activity : activities.keySet()) { + boolean withSample = !getSetSpeciesCatWeight(activity).isEmpty(); + if (withSample) { + activityWithSampleIds.add(activity.getTopiaId()); + } + } } /** @@ -81,18 +85,7 @@ public abstract class CatchStratum<C extends LevelConfigurationWithStratum, A ex } public int getNbActivitiesWithSample() { - return nbActivitiesWithSample; + return activityWithSampleIds.size(); } - public Collection<CorrectedElementaryCatch> getCorrectedElementaryCatch(Activity activity) { - WeightCategoryTreatment stratumWeightCategoryTreatment = getConfiguration().getWeightCategoryTreatment(); - if (stratumWeightCategoryTreatment == null) { - return activity.getCorrectedElementaryCatch(); - } - return activity.getCorrectedElementaryCatch().stream().filter(c -> stratumWeightCategoryTreatment.equals(c.getWeightCategoryTreatment())).collect(Collectors.toList()); - } - - public Multimap<WeightCategoryTreatment, CorrectedElementaryCatch> getCorrectedElementaryCatchByCategory(Activity activity) { - return Multimaps.index(getCorrectedElementaryCatch(activity), WeightCategoryTreatmentAware::getWeightCategoryTreatment); - } } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratumLoader.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratumLoader.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratumLoader.java @@ -8,24 +8,32 @@ * 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.ird.t3.actions.stratum; +import com.google.common.base.Preconditions; +import fr.ird.t3.actions.T3Action; import fr.ird.t3.entities.T3TopiaPersistenceContext; import fr.ird.t3.entities.data.Activity; +import fr.ird.t3.entities.data.Trip; +import fr.ird.t3.entities.reference.Vessel; +import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.services.T3TopiaPersistenceContextAware; +import org.nuiton.topia.persistence.TopiaException; + +import java.util.HashMap; import java.util.Map; +import java.util.Set; import java.util.function.Supplier; -import org.nuiton.topia.persistence.TopiaException; /** * To loader a catch stratum. @@ -34,7 +42,7 @@ import org.nuiton.topia.persistence.TopiaException; * @see CatchStratum * @since 1.3 */ -public abstract class CatchStratumLoader<C extends LevelConfigurationWithStratum> implements T3TopiaPersistenceContextAware { +public abstract class CatchStratumLoader<C extends LevelConfigurationWithStratum, A extends T3Action<C>, S extends StratumConfiguration<C, A>> implements T3TopiaPersistenceContextAware { protected Supplier<T3TopiaPersistenceContext> transaction; @@ -42,10 +50,10 @@ public abstract class CatchStratumLoader<C extends LevelConfigurationWithStratum * To obtain all activities of the catch stratum. * * @param configuration stratum configuration - * @return the activites to use for the catch stratum + * @return activities to use for the catch stratum * @throws TopiaException if any pb while quering db */ - public abstract Map<Activity, Integer> loadData(StratumConfiguration<C> configuration) throws TopiaException; + public abstract Map<Activity, Integer> loadData(S configuration); @Override public Supplier<T3TopiaPersistenceContext> getT3TopiaPersistenceContext() { @@ -55,4 +63,33 @@ public abstract class CatchStratumLoader<C extends LevelConfigurationWithStratum public void setTransaction(Supplier<T3TopiaPersistenceContext> transaction) { this.transaction = transaction; } + + protected Map<Activity, Integer> filterActivities(S configuration, Map<String, Integer> activityIds) { + Map<Activity, Integer> result = new HashMap<>(); + if (activityIds != null && activityIds.size() > 0) { + Set<Vessel> possibleVessels = configuration.getPossibleCatchVessels(); + WeightCategoryTreatment weightCategoryTreatment = configuration.getWeightCategoryTreatment(); + for (Map.Entry<String, Integer> e : activityIds.entrySet()) { + String activityId = e.getKey(); + // get activity + Activity activity = configuration.getActivity(activityId); + // get his trip + Trip trip = activity.getTrip(); + if (!possibleVessels.contains(trip.getVessel())) { + // not a matching boat + continue; + } + // recheck activity have some catches. + Preconditions.checkState(!activity.isCorrectedElementaryCatchEmpty(), + String.format("Can not accept an activity (%s) with no catch", activity.getTopiaId())); + // weight category is in stratum, check there is catch using this category + if (weightCategoryTreatment != null && !activity.withCorrectedElementaryCatch(weightCategoryTreatment)) { + // reject - the stratum weight category not found for this activity + continue; + } + result.put(activity, e.getValue()); + } + } + return result; + } } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratum.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratum.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratum.java @@ -39,7 +39,7 @@ import java.util.Set; * @author Tony Chemit - dev(a)tchemit.fr * @since 1.3 */ -public abstract class SampleStratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>, S extends SampleStratum<C, A, S>> extends Stratum<C, A> { +public abstract class SampleStratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>, T extends StratumConfiguration<C, A>, S extends SampleStratum<C, A, T, S>> extends Stratum<C, A, T> { /** * Number of merged activites (counted when passing through method @@ -59,11 +59,11 @@ public abstract class SampleStratum<C extends LevelConfigurationWithStratum, A e */ private Integer substitutionLevel; - protected SampleStratum(StratumConfiguration<C> configuration, Collection<Species> speciesToFix) { + protected SampleStratum(T configuration, Collection<Species> speciesToFix) { super(configuration, speciesToFix); } - protected abstract SampleStratumLoader<C, A, S> newLoader(); + protected abstract SampleStratumLoader<C, A, T, S> newLoader(); protected abstract String logSampleStratumLevel(int substitutionLevel, A messager); @@ -93,7 +93,7 @@ public abstract class SampleStratum<C extends LevelConfigurationWithStratum, A e @Override public void init(T3ServiceContext serviceContext, List<WeightCategoryTreatment> weightCategories, A messager) throws Exception { - SampleStratumLoader<C, A, S> stratumLoader = newLoader(); + SampleStratumLoader<C, A, T, S> stratumLoader = newLoader(); // inject transaction in loader stratumLoader.setTransaction(serviceContext.getT3TopiaPersistenceContext()); @@ -115,4 +115,5 @@ public abstract class SampleStratum<C extends LevelConfigurationWithStratum, A e public final int getNbMergedActivities() { return nbMergedActivities; } + } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratumLoader.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratumLoader.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratumLoader.java @@ -20,9 +20,13 @@ */ package fr.ird.t3.actions.stratum; +import com.google.common.base.Preconditions; import fr.ird.t3.actions.T3Action; import fr.ird.t3.entities.T3TopiaPersistenceContext; import fr.ird.t3.entities.data.Activity; +import fr.ird.t3.entities.data.Trip; +import fr.ird.t3.entities.reference.Vessel; +import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.entities.type.T3Date; import fr.ird.t3.services.T3ServiceContext; import fr.ird.t3.services.T3TopiaPersistenceContextAware; @@ -38,13 +42,13 @@ import java.util.Set; import java.util.function.Supplier; /** - * To loader a catch stratum. + * To loader a sample stratum. * * @author Tony Chemit - dev(a)tchemit.fr - * @see CatchStratum + * @see SampleStratum * @since 1.3 */ -public abstract class SampleStratumLoader<C extends LevelConfigurationWithStratum, A extends T3Action<C>, S extends SampleStratum<C, A, S>> implements T3TopiaPersistenceContextAware { +public abstract class SampleStratumLoader<C extends LevelConfigurationWithStratum, A extends T3Action<C>, T extends StratumConfiguration<C, A>, S extends SampleStratum<C, A, T, S>> implements T3TopiaPersistenceContextAware { private static final Log log = LogFactory.getLog(SampleStratumLoader.class); private final C levelConfiguration; @@ -60,7 +64,7 @@ public abstract class SampleStratumLoader<C extends LevelConfigurationWithStratu protected SampleStratumLoader(S sampleStratum) { this.sampleStratum = sampleStratum; - levelConfiguration = sampleStratum.getConfiguration().getConfiguration(); + this.levelConfiguration = sampleStratum.getConfiguration().getConfiguration(); } /** @@ -77,17 +81,6 @@ public abstract class SampleStratumLoader<C extends LevelConfigurationWithStratu protected abstract Set<String> findActivityIds(String schoolTypeId, T3Date beginDate, T3Date endDate, String... zoneIds); - /** - * From a set of activity ids, filter the one that can be use in this - * stratum. This mainly means to filter some of them using the stratum - * configuration. - * - * @param activityIds ids of activities to filter - * @return the set of usable activities after having - * @throws TopiaException if any database problem while loading data - */ - protected abstract Set<Activity> filterActivities(Set<String> activityIds); - protected abstract boolean isStratumOk(); @Override @@ -157,4 +150,41 @@ public abstract class SampleStratumLoader<C extends LevelConfigurationWithStratu return levelConfiguration.getTimeStep(); } + /** + * From a set of activity ids, filter the one that can be use in this + * stratum. This mainly means to filter some of them using the stratum + * configuration. + * + * @param activityIds ids of activities to filter + * @return the set of usable activities after having + * @throws TopiaException if any database problem while loading data + */ + private Set<Activity> filterActivities(Set<String> activityIds) { + Set<Activity> result = new HashSet<>(); + T configuration = getSampleStratum().getConfiguration(); + Set<Vessel> possibleVessels = configuration.getPossibleSampleVessels(); + WeightCategoryTreatment weightCategoryTreatment = configuration.getWeightCategoryTreatment(); + for (String activityId : activityIds) { + Activity activity = configuration.getActivity(activityId); + // get his trip + Trip trip = activity.getTrip(); + if (!possibleVessels.contains(trip.getVessel())) { + // not a matching boat + continue; + } + // recheck activity have some samples. + Preconditions.checkState(activity.isSetSpeciesCatWeightNotEmpty(), + String.format("Can not accept an activity (%s) with no sample", activity.getTopiaId())); + if (weightCategoryTreatment != null) { + // weight category is in stratum, check there is catch using this category + boolean foundWeightCategory = activity.withSetSpeciesCatWeight(weightCategoryTreatment); + if (!foundWeightCategory) { + // reject - the stratum weight category not found for this activity + continue; + } + } + result.add(activity); + } + return result; + } } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/Stratum.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/Stratum.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/Stratum.java @@ -20,21 +20,40 @@ */ package fr.ird.t3.actions.stratum; +import com.google.common.collect.ArrayListMultimap; import com.google.common.collect.ImmutableSet; +import com.google.common.collect.Multimap; +import com.google.common.collect.Multimaps; +import fr.ird.t3.T3IOUtil; import fr.ird.t3.actions.T3Action; +import fr.ird.t3.entities.cache.LengthWeightConversionWithContextCache; import fr.ird.t3.entities.data.Activity; +import fr.ird.t3.entities.data.CorrectedElementaryCatch; +import fr.ird.t3.entities.data.SetSpeciesCatWeight; +import fr.ird.t3.entities.data.SetSpeciesFrequency; +import fr.ird.t3.entities.data.SetSpeciesFrequencyTopiaDao; +import fr.ird.t3.entities.data.WeightCategoryTreatmentAware; +import fr.ird.t3.entities.reference.LengthWeightConversion; import fr.ird.t3.entities.reference.Species; +import fr.ird.t3.entities.reference.SpeciesTopiaDao; import fr.ird.t3.entities.reference.WeightCategoryTreatment; +import fr.ird.t3.models.WeightCompositionAggregateModel; import fr.ird.t3.services.T3ServiceContext; import org.nuiton.topia.persistence.TopiaException; import java.io.Closeable; import java.io.IOException; +import java.util.ArrayList; import java.util.Collection; +import java.util.Collections; +import java.util.HashMap; import java.util.Iterator; +import java.util.LinkedList; import java.util.List; import java.util.Map; import java.util.Set; +import java.util.function.Function; +import java.util.stream.Collectors; /** * base class for any stratum. @@ -43,14 +62,14 @@ import java.util.Set; * @see CatchStratum * @since 1.0 */ -public abstract class Stratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>> implements Closeable, Iterable<Map.Entry<Activity, Integer>> { +public abstract class Stratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>, S extends StratumConfiguration<C, A>> implements Closeable, Iterable<Map.Entry<Activity, Integer>> { /** * Stratum configuration of this stratum. * * @see StratumConfiguration */ - private final StratumConfiguration<C> configuration; + private final S configuration; /** * Selected set of species to fix. * @@ -67,7 +86,7 @@ public abstract class Stratum<C extends LevelConfigurationWithStratum, A extends */ private Map<Activity, Integer> activities; - protected Stratum(StratumConfiguration<C> configuration, Collection<Species> speciesToFix) { + protected Stratum(S configuration, Collection<Species> speciesToFix) { this.configuration = configuration; this.speciesToFix = ImmutableSet.copyOf(speciesToFix); } @@ -88,7 +107,7 @@ public abstract class Stratum<C extends LevelConfigurationWithStratum, A extends return activities.entrySet().iterator(); } - public StratumConfiguration<C> getConfiguration() { + public S getConfiguration() { return configuration; } @@ -128,4 +147,107 @@ public abstract class Stratum<C extends LevelConfigurationWithStratum, A extends throw new IllegalStateException("You must invoke the #init(tx) method before accessing stratum data."); } } + + public Collection<CorrectedElementaryCatch> getCorrectedElementaryCatch(Activity activity) { + WeightCategoryTreatment stratumWeightCategoryTreatment = getConfiguration().getWeightCategoryTreatment(); + if (stratumWeightCategoryTreatment == null) { + return activity.getCorrectedElementaryCatch(); + } + return activity.getCorrectedElementaryCatch().stream().filter(c -> stratumWeightCategoryTreatment.equals(c.getWeightCategoryTreatment())).collect(Collectors.toList()); + } + + public Multimap<WeightCategoryTreatment, CorrectedElementaryCatch> getCorrectedElementaryCatchByCategory(Activity activity) { + return Multimaps.index(getCorrectedElementaryCatch(activity), WeightCategoryTreatmentAware::getWeightCategoryTreatment); + } + + private Multimap<WeightCategoryTreatment, SetSpeciesCatWeight> getSetSpeciesCatWeightByCategory(Activity activity) { + return Multimaps.index(getSetSpeciesCatWeight(activity), WeightCategoryTreatmentAware::getWeightCategoryTreatment); + } + + Collection<SetSpeciesCatWeight> getSetSpeciesCatWeight(Activity activity) { + WeightCategoryTreatment stratumWeightCategoryTreatment = getConfiguration().getWeightCategoryTreatment(); + if (stratumWeightCategoryTreatment == null) { + return activity.getSetSpeciesCatWeight(); + } + return activity.getSetSpeciesCatWeight().stream().filter(c -> stratumWeightCategoryTreatment.equals(c.getWeightCategoryTreatment())).collect(Collectors.toList()); + } + + public Collection<SetSpeciesFrequency> getSetSpeciesFrequency(Activity activity) { + WeightCategoryTreatment stratumWeightCategoryTreatment = getConfiguration().getWeightCategoryTreatment(); + if (stratumWeightCategoryTreatment == null) { + return activity.getSetSpeciesFrequency(); + } + LengthWeightConversionWithContextCache conversionHelper = getConfiguration().getConversionHelper(); + + Multimap<Species, SetSpeciesFrequency> setSpeciesFrequencyBySpecies = SpeciesTopiaDao.groupBySpecies(activity.getSetSpeciesFrequency()); + Multimap<Species, Integer> lengthClassesBySpecies = ArrayListMultimap.create(); + // collect all length classes by species + SetSpeciesFrequencyTopiaDao.collectLengthClasses(setSpeciesFrequencyBySpecies, lengthClassesBySpecies); + List<SetSpeciesFrequency> result = new LinkedList<>(); + for (Map.Entry<Species, Collection<SetSpeciesFrequency>> entry : setSpeciesFrequencyBySpecies.asMap().entrySet()) { + Species species = entry.getKey(); + LengthWeightConversion conversion = conversionHelper.getConversions(species); + Collection<SetSpeciesFrequency> setSizes = entry.getValue(); + List<Integer> lengthClasses = new ArrayList<>(lengthClassesBySpecies.get(species)); + Collections.sort(lengthClasses); + List<Integer> lengthClassesAccepted = conversionHelper.getLengthClasses(conversion, stratumWeightCategoryTreatment, lengthClasses); + result.addAll(setSizes.stream().filter(f -> lengthClassesAccepted.contains(f.getLfLengthClass())).collect(Collectors.toList())); + } + return result; + } + + protected void fillWeightsFromCatchesWeight(Activity activity, WeightCompositionAggregateModel model, int dividerFactor) { + Map<WeightCategoryTreatment, Map<Species, Float>> weights = new HashMap<>(); + Multimap<WeightCategoryTreatment, CorrectedElementaryCatch> data = getCorrectedElementaryCatchByCategory(activity); + T3IOUtil.fillMapWithDefaultValue(weights, data.keySet(), HashMap::new); + for (WeightCategoryTreatment weightCategory : data.keySet()) { + Map<Species, Float> speciesFloatMap = weights.get(weightCategory); + Collection<CorrectedElementaryCatch> correctedElementaryCatches = data.get(weightCategory); + fillWeights(weightCategory, + correctedElementaryCatches, + speciesFloatMap, + CorrectedElementaryCatch::getCatchWeight, + model, + dividerFactor); + } + } + + protected void fillWeightsFromSamplesWeight(Activity activity, + Map<WeightCategoryTreatment, Map<Species, Float>> weights, + WeightCompositionAggregateModel model) { + if (weights == null) { + weights = new HashMap<>(); + } + Multimap<WeightCategoryTreatment, SetSpeciesCatWeight> data = getSetSpeciesCatWeightByCategory(activity); + T3IOUtil.fillMapWithDefaultValue(weights, data.keySet(), HashMap::new); + for (WeightCategoryTreatment weightCategory : data.keySet()) { + Map<Species, Float> speciesFloatMap = weights.get(weightCategory); + Collection<SetSpeciesCatWeight> setSpeciesCatWeights = data.get(weightCategory); + fillWeights(weightCategory, setSpeciesCatWeights, speciesFloatMap, SetSpeciesCatWeight::getWeight, model, 1); + } + } + + protected <X extends WeightCategoryTreatmentAware> void fillWeights(WeightCategoryTreatment weightCategory, + Collection<X> data, + Map<Species, Float> weights, + Function<X, Float> function, + WeightCompositionAggregateModel model, + int divideFactor) { + if (weights == null) { + weights = new HashMap<>(); + } + for (X datum : data) { + Species species = datum.getSpecies(); + Float weight = weights.get(species); + if (weight == null) { + weight = 0f; + } + weight += function.apply(datum) / divideFactor; + weights.put(species, weight); + } + if (model != null) { + model.addModel(weightCategory, weights); + } + } + } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java @@ -20,11 +20,13 @@ */ package fr.ird.t3.actions.stratum; -import com.google.common.cache.LoadingCache; import com.google.common.collect.ImmutableSet; +import fr.ird.t3.actions.T3Action; +import fr.ird.t3.entities.cache.LengthWeightConversionWithContextCache; import fr.ird.t3.entities.data.Activity; -import fr.ird.t3.entities.reference.AbstractSchoolTypeTopiaDao; +import fr.ird.t3.entities.data.SpeciesAware; import fr.ird.t3.entities.reference.SchoolType; +import fr.ird.t3.entities.reference.SchoolTypeTopiaDao; import fr.ird.t3.entities.reference.Vessel; import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.entities.reference.zone.ZoneStratumAware; @@ -33,12 +35,14 @@ import fr.ird.t3.entities.type.T3Date; import java.util.Collection; import java.util.Iterator; +import java.util.List; import java.util.Map; import java.util.Objects; import java.util.Set; import java.util.concurrent.ExecutionException; import java.util.function.BiConsumer; import java.util.function.Function; +import java.util.function.Predicate; /** * Configuration of a stratum. @@ -46,57 +50,54 @@ import java.util.function.Function; * @author Tony Chemit - dev(a)tchemit.fr * @since 1.0 */ -public class StratumConfiguration<C extends LevelConfigurationWithStratum> { +public class StratumConfiguration<C extends LevelConfigurationWithStratum, A extends T3Action<C>> { - private final C configuration; + private final LevelInputContext<C, A> inputContext; private final Collection<ZoneStratumAware> zones; - private final ZoneStratumAwareMeta zoneMeta; private final ZoneStratumAware zone; private final SchoolType schoolType; private final WeightCategoryTreatment weightCategoryTreatment; private final T3Date beginDate; private final T3Date endDate; - private final Set<Vessel> possibleCatchVessels; - private final Set<Vessel> possibleSampleVessels; private final Map<String, Integer> stratumMinimumCountBySpecie; - private final LoadingCache<String, Activity> activityCache; + private final List<WeightCategoryTreatment> weightCategoryTreatments; private final int stratumIndex; + private final LengthWeightConversionWithContextCache conversionHelper; private String[] zoneIds; - protected StratumConfiguration(C configuration, - ZoneStratumAwareMeta zoneMeta, + protected StratumConfiguration(LevelInputContext<C, A> inputContext, ZoneStratumAware zone, SchoolType schoolType, WeightCategoryTreatment weightCategoryTreatment, T3Date beginDate, T3Date endDate, Collection<ZoneStratumAware> zones, - Set<Vessel> possibleCatchVessels, - Set<Vessel> possibleSampleVessels, Map<String, Integer> stratumMinimumCountBySpecie, - LoadingCache<String, Activity> activityCache, + List<WeightCategoryTreatment> weightCategoryTreatments, int stratumIndex) { - this.configuration = configuration; - this.zoneMeta = zoneMeta; + this.inputContext = inputContext; this.zone = zone; this.schoolType = schoolType; + this.weightCategoryTreatments = weightCategoryTreatments; this.weightCategoryTreatment = weightCategoryTreatment; this.beginDate = beginDate; this.endDate = endDate; this.zones = zones; - this.possibleCatchVessels = possibleCatchVessels; - this.possibleSampleVessels = possibleSampleVessels; this.stratumMinimumCountBySpecie = stratumMinimumCountBySpecie; - this.activityCache = activityCache; this.stratumIndex = stratumIndex; + this.conversionHelper = inputContext.newLengthWeightConversionWithContextCache(zone.getOcean(), beginDate.toBeginDate()); + } + + public LengthWeightConversionWithContextCache getConversionHelper() { + return conversionHelper; } public C getConfiguration() { - return configuration; + return inputContext.getConfiguration(); } private ZoneStratumAwareMeta getZoneMeta() { - return zoneMeta; + return inputContext.getZoneMeta(); } public String getZoneTableName() { @@ -113,15 +114,15 @@ public class StratumConfiguration<C extends LevelConfigurationWithStratum> { public Set<String> getSchoolTypeIds() { ImmutableSet.Builder<String> builder = ImmutableSet.<String>builder().add(getSchoolType().getTopiaId()); - switch (configuration.getSchoolTypeIndeterminate()) { + switch (getConfiguration().getSchoolTypeIndeterminate()) { case ALL_IN_BO: - if (AbstractSchoolTypeTopiaDao.SCHOOL_TYPE_BO_ID.equals(getSchoolType().getTopiaId())) { - builder.add(AbstractSchoolTypeTopiaDao.SCHOOL_TYPE_INDETERMINATE_ID); + if (SchoolTypeTopiaDao.SCHOOL_TYPE_BO_ID.equals(getSchoolType().getTopiaId())) { + builder.add(SchoolTypeTopiaDao.SCHOOL_TYPE_INDETERMINATE_ID); } break; case ALL_IN_BL: - if (AbstractSchoolTypeTopiaDao.SCHOOL_TYPE_BL_ID.equals(getSchoolType().getTopiaId())) { - builder.add(AbstractSchoolTypeTopiaDao.SCHOOL_TYPE_INDETERMINATE_ID); + if (SchoolTypeTopiaDao.SCHOOL_TYPE_BL_ID.equals(getSchoolType().getTopiaId())) { + builder.add(SchoolTypeTopiaDao.SCHOOL_TYPE_INDETERMINATE_ID); } break; case IGNORE: @@ -143,11 +144,11 @@ public class StratumConfiguration<C extends LevelConfigurationWithStratum> { } public Set<Vessel> getPossibleCatchVessels() { - return possibleCatchVessels; + return inputContext.getPossibleCatchVessels(); } public Set<Vessel> getPossibleSampleVessels() { - return possibleSampleVessels; + return inputContext.getPossibleSampleVessels(); } public Map<String, Integer> getStratumMinimumCountBySpecie() { @@ -162,6 +163,14 @@ public class StratumConfiguration<C extends LevelConfigurationWithStratum> { return stratumIndex; } + public List<WeightCategoryTreatment> getWeightCategoryTreatments() { + return weightCategoryTreatments; + } + + public Predicate<? super SpeciesAware> getSpeciesToFixFilter() { + return inputContext.getSpeciesToFixFilter(); + } + public String[] getZoneIds() { if (zoneIds == null) { Collection<ZoneStratumAware> allZones = getZones(); @@ -177,7 +186,7 @@ public class StratumConfiguration<C extends LevelConfigurationWithStratum> { public Activity getActivity(String activityId) { try { - return activityCache.get(activityId); + return inputContext.getActivityCache().get(activityId); } catch (ExecutionException e) { throw new RuntimeException(String.format("Could not obtain activity %s", activityId), e); } @@ -194,7 +203,7 @@ public class StratumConfiguration<C extends LevelConfigurationWithStratum> { if (currentLevel == null) { result = ""; } - result += String.format("(%s;%s;%d)", zone.getLabel1(), configuration.isUseWeightCategoriesInStratum() ? weightCategoryTreatment.getLabel1() : "NA", level); + result += String.format("(%s;%s;%d)", zone.getLabel1(), getConfiguration().isUseWeightCategoriesInStratum() ? weightCategoryTreatment.getLabel1() : "NA", level); Objects.requireNonNull(consumer).accept(activity, result); } } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumResult.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumResult.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumResult.java @@ -8,12 +8,12 @@ * 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% @@ -32,7 +32,7 @@ import java.io.Closeable; */ public abstract class StratumResult<C extends LevelConfigurationWithStratum> implements Closeable { - private final StratumConfiguration<C> configuration; + private final StratumConfiguration<C, ?> configuration; private final String label; @@ -42,12 +42,12 @@ public abstract class StratumResult<C extends LevelConfigurationWithStratum> imp private int nbActivitiesWithSample; - protected StratumResult(StratumConfiguration<C> configuration, String label) { + protected StratumResult(StratumConfiguration<C, ?> configuration, String label) { this.configuration = configuration; this.label = label; } - public StratumConfiguration<C> getConfiguration() { + public StratumConfiguration<C, ?> getConfiguration() { return configuration; } @@ -59,30 +59,30 @@ public abstract class StratumResult<C extends LevelConfigurationWithStratum> imp return substitutionLevel; } - public int getNbActivities() { - return nbActivities; - } - - public int getNbActivitiesWithSample() { - return nbActivitiesWithSample; - } - - public int getNbActivitiesWithoutSample() { - return nbActivities - nbActivitiesWithSample; - } - public void setSubstitutionLevel(int substitutionLevel) { this.substitutionLevel = substitutionLevel; } + public int getNbActivities() { + return nbActivities; + } + public void setNbActivities(int nbActivities) { this.nbActivities = nbActivities; } + public int getNbActivitiesWithSample() { + return nbActivitiesWithSample; + } + public void setNbActivitiesWithSample(int nbActivitiesWithSample) { this.nbActivitiesWithSample = nbActivitiesWithSample; } + public int getNbActivitiesWithoutSample() { + return nbActivities - nbActivitiesWithSample; + } + public void addNbActivities(int nbActivities) { this.nbActivities += nbActivities; } ===================================== t3-domain/src/main/java/fr/ird/t3/entities/cache/LengthWeightConversionCache.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/entities/cache/LengthWeightConversionCache.java +++ b/t3-domain/src/main/java/fr/ird/t3/entities/cache/LengthWeightConversionCache.java @@ -25,12 +25,14 @@ import fr.ird.t3.entities.reference.LengthWeightConversionTopiaDao; import fr.ird.t3.entities.reference.Ocean; import fr.ird.t3.entities.reference.Species; import fr.ird.t3.entities.reference.WeightCategory; +import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.entities.type.T3Date; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import java.util.Date; import java.util.Iterator; +import java.util.LinkedList; import java.util.List; import java.util.Map; import java.util.TreeMap; @@ -133,4 +135,24 @@ public class LengthWeightConversionCache { return result; } + public List<Integer> getLengthClasses(LengthWeightConversion conversion, WeightCategoryTreatment weightCategoryTreatment, List<Integer> lengthClasses) { + Integer min = weightCategoryTreatment.getMin(); + Integer minLengthClass = null; + if (min != null) { + minLengthClass = getSpecieHighestLengthClass(conversion, min); + } + Integer max = weightCategoryTreatment.getMax(); + Integer maxLengthClass = null; + if (max != null) { + maxLengthClass = getSpecieHighestLengthClass(conversion, max); + } + List<Integer> result = new LinkedList<>(); + for (Integer lengthClass : lengthClasses) { + if (minLengthClass != null && lengthClass < minLengthClass || maxLengthClass != null && lengthClass > maxLengthClass) { + continue; + } + result.add(lengthClass); + } + return result; + } } ===================================== t3-domain/src/main/java/fr/ird/t3/entities/data/ActivityImpl.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/entities/data/ActivityImpl.java +++ b/t3-domain/src/main/java/fr/ird/t3/entities/data/ActivityImpl.java @@ -222,4 +222,9 @@ public class ActivityImpl extends ActivityAbstract { public boolean withCorrectedElementaryCatch(WeightCategoryTreatment weightCategoryTreatment) { return isCorrectedElementaryCatchNotEmpty() && getCorrectedElementaryCatch().stream().map(CorrectedElementaryCatch::getWeightCategoryTreatment).anyMatch(c -> c.equals(weightCategoryTreatment)); } + + @Override + public boolean withSetSpeciesCatWeight(WeightCategoryTreatment weightCategoryTreatment) { + return isSetSpeciesCatWeightNotEmpty() && getSetSpeciesCatWeight().stream().map(SetSpeciesCatWeight::getWeightCategoryTreatment).anyMatch(c -> c.equals(weightCategoryTreatment)); + } } ===================================== t3-domain/src/main/xmi/t3-persistence.zargo ===================================== Binary files a/t3-domain/src/main/xmi/t3-persistence.zargo and b/t3-domain/src/main/xmi/t3-persistence.zargo differ View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/3585d323448b384f491d7eb078d58a9d… --- View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/3585d323448b384f491d7eb078d58a9d… You're receiving this email because of your account on gitlab.com.

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[Git][ultreiaio/ird-t3][develop] Go to version 2.5 + [N1.5] Remplacer SetSpeciesCatWeight.WeightCategorySample…
by Tony CHEMIT 23 Mar '18

23 Mar '18

Tony CHEMIT pushed to branch develop at ultreiaio / ird-t3 Commits: 2f995491 by Tony CHEMIT at 2018-03-23T10:11:08Z Go to version 2.5 + [N1.5] Remplacer SetSpeciesCatWeight.WeightCategorySample par WeightCategoryTreatment (Closes #301) + Review cache API - - - - - 30 changed files: - pom.xml - t3-actions/pom.xml - t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ConvertSampleSetSpeciesFrequencyToWeightAction.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ConvertSetSpeciesFrequencyToWeightAction.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ExtrapolateSampleWeightToSetAction.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2Action.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2InputContext.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfiguration.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3Action.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3InputContext.java - t3-actions/src/test/java/fr/ird/t3/actions/ActionResumeTest.java - t3-domain/pom.xml - t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelInputContext.java - − t3-domain/src/main/java/fr/ird/t3/actions/stratum/WeightCategoryTreatmentToSample.java - t3-domain/src/main/java/fr/ird/t3/entities/T3TopiaPersistenceContext.java - t3-domain/src/main/java/fr/ird/t3/entities/conversion/LengthWeightConversionSimpleCache.java → t3-domain/src/main/java/fr/ird/t3/entities/cache/LengthWeightConversionCache.java - t3-domain/src/main/java/fr/ird/t3/entities/conversion/LengthWeightConversionWithContextCache.java → t3-domain/src/main/java/fr/ird/t3/entities/cache/LengthWeightConversionWithContextCache.java - + t3-domain/src/main/java/fr/ird/t3/entities/cache/WeightCategoryTreatmentCache.java - + t3-domain/src/main/java/fr/ird/t3/entities/cache/ZoneStratumCache.java - t3-domain/src/main/java/fr/ird/t3/entities/reference/zone/AbstractZoneStratumAwareMeta.java - t3-domain/src/main/java/fr/ird/t3/entities/reference/zone/AbstractZoneStratumAwareTopiaDao.java - t3-domain/src/main/java/fr/ird/t3/entities/reference/zone/ZoneStratumAwareMeta.java - t3-domain/src/main/java/fr/ird/t3/models/LengthCompositionAggregateModel.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/OceanContext.java → t3-domain/src/main/java/fr/ird/t3/services/migration/T3MigrationCallbackV2_5.java - + t3-domain/src/main/resources/db/migration/V2_5_01_change-weight-category.sql - t3-domain/src/main/xmi/t3-persistence.properties - t3-domain/src/main/xmi/t3-persistence.zargo - t3-domain/src/test/java/fr/ird/t3/entities/reference/LengthWeightConversionWithContextCacheTest.java The diff was not included because it is too large. View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/2f9954910642fbd06a0f019b3628dcda… --- View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/2f9954910642fbd06a0f019b3628dcda… You're receiving this email because of your account on gitlab.com.

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[Git][ultreiaio/ird-t3][develop] improve Level 2 and 3 API + conversion API (See #263)
by Tony CHEMIT 22 Mar '18

22 Mar '18

Tony CHEMIT pushed to branch develop at ultreiaio / ird-t3 Commits: 514feb71 by Tony CHEMIT at 2018-03-22T15:27:30Z improve Level 2 and 3 API + conversion API (See #263) - - - - - 30 changed files: - t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ConvertSampleSetSpeciesFrequencyToWeightAction.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ConvertSetSpeciesFrequencyToWeightAction.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ExtrapolateSampleWeightToSetAction.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoader.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfiguration.java - − t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfigurationIterator.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfigurationIteratorWithCategories.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfigurationIteratorWithoutCategories.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2Action.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2InputContext.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2OutputContext.java - − t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3ActionInputContext.java - − t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3ActionOutputContext.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfiguration.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfigurationIteratorWithCategories.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfigurationIteratorWithoutCategories.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3Action.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3InputContext.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3OutputContext.java - t3-actions/src/main/resources/ftl/fr/ird/t3/actions/data/level2/Level2Action.ftl - t3-actions/src/main/resources/ftl/fr/ird/t3/actions/data/level2/Level2Action_en.ftl - t3-actions/src/main/resources/ftl/fr/ird/t3/actions/data/level3/Level3Action.ftl - t3-actions/src/main/resources/ftl/fr/ird/t3/actions/data/level3/Level3Action_en.ftl - t3-actions/src/test/java/fr/ird/t3/actions/ActionResumeTest.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2ActionInputContext.java → t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelInputContext.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2ActionOutputContext.java → t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelOutputContext.java The diff was not included because it is too large. View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/514feb71ea2db506460bf5f04dccbfec… --- View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/514feb71ea2db506460bf5f04dccbfec… You're receiving this email because of your account on gitlab.com.

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[Git][ultreiaio/ird-t3][develop] improve Level 2 and 3 API + conversion API (See #263)
by Tony CHEMIT 22 Mar '18

22 Mar '18

Tony CHEMIT pushed to branch develop at ultreiaio / ird-t3 Commits: 98cdbd43 by Tony CHEMIT at 2018-03-22T15:23:02Z improve Level 2 and 3 API + conversion API (See #263) - - - - - 30 changed files: - t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ConvertSampleSetSpeciesFrequencyToWeightAction.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ConvertSetSpeciesFrequencyToWeightAction.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ExtrapolateSampleWeightToSetAction.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoader.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfiguration.java - − t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfigurationIterator.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfigurationIteratorWithCategories.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfigurationIteratorWithoutCategories.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2Action.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2InputContext.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2OutputContext.java - − t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3ActionInputContext.java - − t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3ActionOutputContext.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfiguration.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfigurationIteratorWithCategories.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfigurationIteratorWithoutCategories.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3Action.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3InputContext.java - + t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3OutputContext.java - t3-actions/src/main/resources/ftl/fr/ird/t3/actions/data/level2/Level2Action.ftl - t3-actions/src/main/resources/ftl/fr/ird/t3/actions/data/level2/Level2Action_en.ftl - t3-actions/src/main/resources/ftl/fr/ird/t3/actions/data/level3/Level3Action.ftl - t3-actions/src/main/resources/ftl/fr/ird/t3/actions/data/level3/Level3Action_en.ftl - t3-actions/src/test/java/fr/ird/t3/actions/ActionResumeTest.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2ActionInputContext.java → t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelInputContext.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2ActionOutputContext.java → t3-domain/src/main/java/fr/ird/t3/actions/stratum/LevelOutputContext.java The diff was not included because it is too large. View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/98cdbd43fae224d280da05070d828a76… --- View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/98cdbd43fae224d280da05070d828a76… You're receiving this email because of your account on gitlab.com.

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