GitLab

at 2018-03-08T12:55:59Z

Marées sans logbooks : gestion de leurs échantillons - ajout de check de cohérence sur Trip.logbookAvaibility (See #116) + fix typo

 Treatment to apply to catches with samples:

 <#if configuration.useAllSamplesOfStratum>

-Apply length structures from the sample statrum

+Apply length structures from the sample stratum

 <#else>

 Keep their own samples (do nothing)

 </#if>

 import java.sql.ResultSet;

 import java.sql.SQLException;

 import java.util.ArrayList;

+import java.util.Arrays;

 import java.util.Collection;

 import java.util.Collections;

 import java.util.Comparator;

 public class AbstractTripTopiaDao<E extends Trip> extends GeneratedTripTopiaDao<E> {

     public static final Ocean EMPTY_OCEAN = new OceanImpl();

+    private static final int TRIP_WITHOUT_LOGBOOK = 0;

+    private static final int TRIP_WITH_LOGBOOK = 1;

     private static final Log log = LogFactory.getLog(AbstractTripTopiaDao.class);

     static {

         EMPTY_OCEAN.setTopiaId("fr.ird.t3.entities.reference.Ocean#EMPTY#EMPTY");

     }

+    /**

+     * Check that a standard trip ({@link TripType#STANDARD}) is consistent around {@link Trip#getLogBookAvailability()}.

+     *

+     * @param trip trip to check

+     * @param pKey primary key of this trip

+     */

+    public static void checkStandardTrip(Trip trip, Object[] pKey) {

+        int logBookAvailability = trip.getLogBookAvailability();

+        if (AbstractTripTopiaDao.TRIP_WITHOUT_LOGBOOK == logBookAvailability && trip.isActivityNotEmpty()) {

+            throw new IllegalStateException(String.format("Trip [%s] has some logBook but logBookAvailability says the opposite, please fix this trip..", Arrays.toString(pKey)));

+        }

+        if (AbstractTripTopiaDao.TRIP_WITH_LOGBOOK == logBookAvailability && trip.isActivityEmpty()) {

+            throw new IllegalStateException(String.format("Trip [%s] has some logBook but logBookAvailability says the opposite, please fix this trip..", Arrays.toString(pKey)));

+        }

+    }

+

+    /**

+     * Check that a standard trip ({@link TripType#LOGBOOKMISSING}) is consistent around {@link Trip#getLogBookAvailability()}.

+     *

+     * @param trip trip to check

+     * @param pKey primary key of this trip

+     */

+    public static void checkLogbookMissingTrip(Trip trip, Object[] pKey) {

+        int logBookAvailability = trip.getLogBookAvailability();

+        if (AbstractTripTopiaDao.TRIP_WITH_LOGBOOK == logBookAvailability) {

+            throw new IllegalStateException(String.format("Trip [%s] has no logBook but logBookAvailability says the opposite, please fix this trip.", Arrays.toString(pKey)));

+        }

+    }

+

     public static String getSamplesOnlyFilter(String prefix, Boolean samplesOnly) {

         if (samplesOnly == null) {

             return "";

 import fr.ird.t3.entities.T3EntityEnum;

 import fr.ird.t3.entities.T3EntityMap;

 import fr.ird.t3.entities.data.Trip;

+import fr.ird.t3.entities.data.TripTopiaDao;

 import fr.ird.t3.entities.data.TripType;

 import fr.ird.t3.entities.reference.Vessel;

 import fr.ird.t3.io.input.MissingForeignKey;

 import java.util.Arrays;

 import java.util.HashMap;

 import java.util.HashSet;

+import java.util.LinkedHashMap;

 import java.util.List;

 import java.util.Map;

 import java.util.Set;

         T3AccessHitModel hitModel = new T3AccessHitModel();

         hitModel.addPropertyChangeListener(new LoadDbPropertyChangeListener(t3DataTypes));

         // analyse data source

-        if (configuration.getTripType() == TripType.LOGBOOKMISSING) {

-            dataSource.analyzeDb(TripType.LOGBOOKMISSING, hitModel);

-        } else {

-            dataSource.analyzeDb(hitModel);

-        }

+        dataSource.analyzeDb(hitModel);

         if (dataSource.hasError()) {

             errors = dataSource.getErrors();

         }

         T3EntityEnum constant = T3EntityEnum.valueOf(Trip.class);

         T3AccessEntityMeta meta = dataSource.getMeta(constant);

         List<Trip> entities = dataSource.loadEntities(meta);

-        Map<Trip, T3EntityMap> result = Maps.newLinkedHashMap();

+        Map<Trip, T3EntityMap> result = new LinkedHashMap<>();

         missingFK = new HashMap<>();

         T3DataEntityVisitor dataVisitor = newDataVisitor(dataSource, safeReferences);

         try {

             // remove proxy on data

             Trip loadedTrip = visitor.doVisit(trip);

             // set tripType flag

-            loadedTrip.setTripType(tripType);

+            T3AccessEntity a = (T3AccessEntity) trip;

+            int logBookAvailability = loadedTrip.getLogBookAvailability();

+            Object[] pKey = a.getPKey();

+            switch (tripType) {

+                case STANDARD:

+                    TripTopiaDao.checkStandardTrip(loadedTrip, pKey);

+                    loadedTrip.setTripType(TripType.STANDARD);

+                    break;

+                case SAMPLEONLY:

+                    // no check

+                    loadedTrip.setTripType(TripType.SAMPLEONLY);

+                    break;

+                case LOGBOOKMISSING:

+                    if (TripType.LOGBOOKMISSING == loadedTrip.getTripType()) {

+                        // That trip was marked to be without logbook, check that

+                        TripTopiaDao.checkLogbookMissingTrip(loadedTrip, pKey);

+                    } else {

+                        // standard trip, just check logBookAvailability value is correct

+                        TripTopiaDao.checkStandardTrip(loadedTrip, pKey);

+                        loadedTrip.setTripType(TripType.STANDARD);

+                    }

+                    break;

+            }

             if (trip.getVessel() == null && canCreateVessel) {

                 // use new created vessel

                 Vessel vessel = getNewVessels().get(vesselCode);

 import fr.ird.msaccess.importer.AbstractAccessDataSource;

 import fr.ird.t3.entities.T3EntityEnum;

-import fr.ird.t3.entities.data.TripType;

 import fr.ird.t3.entities.reference.T3ReferenceEntity;

 import org.apache.commons.logging.Log;

 import org.apache.commons.logging.LogFactory;

     }

     public void analyzeDb(T3AccessHitModel hits) throws Exception {

-        analyzeDb(null, hits);

-    }

-

-    public void analyzeDb(TripType tripType, T3AccessHitModel hits) throws Exception {

         // always init the data source

         init();

         Set<String> tables = getTableNames();

                     activity.setSchoolType(Objects.requireNonNull(sampleSet.getActivitySchoolType()));

                     sampleSet.setActivity(endActivity(activity));

                     parent.addActivity(activity);

+                    parent.setTripType(TripType.LOGBOOKMISSING);

                 }

             };

         } else {

  */

 package fr.ird.t3.entities.reference;

-import com.google.common.collect.Maps;

 import fr.ird.t3.entities.AbstractDatabaseTest;

 import fr.ird.t3.entities.T3TopiaPersistenceContext;

 import org.junit.Assert;

 import java.util.ArrayList;

 import java.util.Comparator;

+import java.util.LinkedHashMap;

 import java.util.List;

 import java.util.Map;

         catUnbound.setMax(null);

         Map<WeightCategoryTreatment, Integer> weightCategories =

-                Maps.newLinkedHashMap();

+                new LinkedHashMap<>();

         weightCategories.put(catBound, 20);

         weightCategories.put(catUnbound, Integer.MAX_VALUE);

         catUnbound.setMax(null);

         Map<WeightCategoryTreatment, Integer> weightCategories =

-                Maps.newLinkedHashMap();

+                new LinkedHashMap<>();

         weightCategories.put(catBound, 20);

         weightCategories.put(catBound2, 40);

 package fr.ird.t3.web.actions;

 import com.google.common.collect.ImmutableMap;

-import com.google.common.collect.Maps;

 import com.google.common.collect.Multimap;

 import com.opensymphony.xwork2.ActionContext;

 import com.opensymphony.xwork2.ActionSupport;

 import java.util.Arrays;

 import java.util.Collection;

 import java.util.Date;

+import java.util.LinkedHashMap;

 import java.util.List;

 import java.util.Map;

 import java.util.function.Supplier;

     }

     protected Map<String, String> createTimeSteps() {

-        Map<String, String> timeSteps = Maps.newLinkedHashMap();

+        Map<String, String> timeSteps = new LinkedHashMap<>();

         for (int i = 1; i < 13; i++) {

             timeSteps.put("" + i, "" + i);

         }

  * 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.web.actions.io.output;

-import com.google.common.collect.Maps;

 import fr.ird.t3.actions.io.output.ExportConfiguration;

 import fr.ird.t3.entities.T3EntityHelper;

 import fr.ird.t3.entities.data.Trip;

 import java.util.Arrays;

 import java.util.Collection;

 import java.util.HashMap;

+import java.util.LinkedHashMap;

 import java.util.List;

 import java.util.Map;

         // make sur configuration is inited before all

         getConfiguration();

-        operations = Maps.newLinkedHashMap();

+        operations = new LinkedHashMap<>();

-        for (T3OutputOperation operation :

-                getT3OutputService().getOperations(configuration.getOutputProviderId())) {

+        for (T3OutputOperation operation : getT3OutputService().getOperations(configuration.getOutputProviderId())) {

             operations.put(operation.getId(), operation.getLibelle(getLocale()));

         }

-        // inject everything needed (daos, ...)

+        // inject everything needed (dao, ...)

         injectExcept(InjectDecoratedBeans.class);

         boolean configurationInSession = isConfigurationInSession();

  * 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.web.actions.json;

-import com.google.common.collect.Maps;

 import fr.ird.t3.io.output.T3OutputOperation;

 import fr.ird.t3.web.actions.T3ActionSupport;

 import org.apache.commons.logging.Log;

 import org.apache.commons.logging.LogFactory;

+import java.util.LinkedHashMap;

 import java.util.Map;

     private static final long serialVersionUID = 1L;

-    /** Logger. */

-    private static final Log log =

-            LogFactory.getLog(GetOutputProviderOperationsAction.class);

+    private static final Log log = LogFactory.getLog(GetOutputProviderOperationsAction.class);

-    protected String outputProviderId;

-

-    protected Map<String, String> operations;

+    private String outputProviderId;

+    private Map<String, String> operations;

     public void setOutputProviderId(String outputProviderId) {

         this.outputProviderId = outputProviderId;

     @Override

     public String execute() {

-

-        if (log.isInfoEnabled()) {

-            log.info("outputProviderId = " + outputProviderId);

-        }

-

-        operations = Maps.newLinkedHashMap();

-

-        for (T3OutputOperation operation :

-                getT3OutputService().getOperations(outputProviderId)) {

+        log.info(String.format("outputProviderId = %s", outputProviderId));

+        operations = new LinkedHashMap<>();

+        for (T3OutputOperation operation : getT3OutputService().getOperations(outputProviderId)) {

             operations.put(operation.getId(), operation.getLibelle(getLocale()));

         }

-

         return SUCCESS;

     }

 }
  * 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.web.actions.json;

-import com.google.common.collect.Maps;

 import fr.ird.t3.entities.reference.zone.ZoneStratumAwareMeta;

 import fr.ird.t3.entities.reference.zone.ZoneVersion;

 import fr.ird.t3.web.actions.T3ActionSupport;

 import org.apache.commons.logging.Log;

 import org.apache.commons.logging.LogFactory;

+import java.util.LinkedHashMap;

 import java.util.List;

 import java.util.Map;

     private static final long serialVersionUID = 1L;

-    /** Logger. */

-    private static final Log log =

-            LogFactory.getLog(GetZoneVersionsAction.class);

+    private static final Log log = LogFactory.getLog(GetZoneVersionsAction.class);

     /** Selected zoneTypeId. */

-    protected String zoneTypeId;

-

-    protected Map<String, String> zoneVersions;

+    private String zoneTypeId;

+    private Map<String, String> zoneVersions;

     public void setZoneTypeId(String zoneTypeId) {

         this.zoneTypeId = zoneTypeId;

     @Override

     public String execute() {

-

-        if (log.isInfoEnabled()) {

-            log.info("zoneTypeId = " + zoneTypeId);

-        }

-

-        zoneVersions = Maps.newLinkedHashMap();

-

+        log.info(String.format("zoneTypeId = %s", zoneTypeId));

+        zoneVersions = new LinkedHashMap<>();

         if (!StringUtils.isEmpty(zoneTypeId)) {

-

-            ZoneStratumAwareMeta zoneType =

-                    getZoneStratumService().getZoneMetaById(zoneTypeId);

-

-            List<ZoneVersion> allVersions =

-                    zoneType.getAllZoneVersions(getT3TopiaPersistenceContext().get());

-

+            ZoneStratumAwareMeta zoneType = getZoneStratumService().getZoneMetaById(zoneTypeId);

+            List<ZoneVersion> allVersions = zoneType.getAllZoneVersions(getT3TopiaPersistenceContext().get());

             zoneVersions = sortAndDecorateIdAbles(allVersions);

-

         }

         return SUCCESS;

     }

 t3.label.data.level3.configuration.step1=Level 3 configuration step 1

 t3.label.data.level3.configuration.step2=Level 3 configuration step 2

 t3.label.data.level3.configuration.useAllSamples=Keep their own sample (do nothing)

-t3.label.data.level3.configuration.useCatchSamples=Apply length structures from the sample statrum

+t3.label.data.level3.configuration.useCatchSamples=Apply length structures from the sample stratum

 t3.label.data.level3.configuration.useWeightCategories=Use weight categories

 t3.label.data.level3.configuration.useWeightCategoriesOrNot=Extrapolation method

 t3.label.data.treatment.level0=Level 0 treatment

Tony CHEMIT pushed to branch develop at ultreiaio / ird-t3

Commits:

11 changed files:

Changes: