[Tutti-commits] r1818 - in trunk: . tutti-persistence/src/main/java/fr/ifremer/tutti/persistence tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/util tutti-persistence/src/main/resources tutti-persistence/src/main/xmi tutti-service/src/main/java/fr/ifremer/tutti/service tutti-ui-swing/src/license tutti-ui-swing/src/main/filtered-resources tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action

28 May 2014

Author: tchemit
Date: 2014-05-28 17:35:16 +0200 (Wed, 28 May 2014)
New Revision: 1818

Url: http://forge.codelutin.com/projects/tutti/repository/revisions/1818

Log:
refs #4959 implements it

Modified:
   trunk/pom.xml
   trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/TuttiPersistenceImpl.java
   trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/TuttiPersistenceNoDbImpl.java
   trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/BenthosBatchPersistenceServiceImpl.java
   trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/CatchBatchPersistenceService.java
   trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/CatchBatchPersistenceServiceImpl.java
   trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/MarineLitterBatchPersistenceServiceImpl.java
   trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/SpeciesBatchPersistenceServiceImpl.java
   trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/util/BatchPersistenceHelper.java
   trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/util/BatchTreeHelper.java
   trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/util/MeasurementPersistenceHelper.java
   trunk/tutti-persistence/src/main/resources/queries-failsafe.hbm.xml
   trunk/tutti-persistence/src/main/xmi/tutti-persistence.zargo
   trunk/tutti-service/src/main/java/fr/ifremer/tutti/service/PersistenceService.java
   trunk/tutti-ui-swing/src/license/THIRD-PARTY.properties
   trunk/tutti-ui-swing/src/main/filtered-resources/log4j.properties
   trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action/ComputeBatchWeightsAction.java
   trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action/SaveCruiseToReadyToSynchAction.java

Modified: trunk/pom.xml
===================================================================

--- trunk/pom.xml	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/pom.xml	2014-05-28 15:35:16 UTC (rev 1818)
@@ -146,7 +146,7 @@
     <jaxxVersion>2.8.5</jaxxVersion>
     <swingXVersion>1.6.4</swingXVersion>
     <slf4jVersion>1.7.5</slf4jVersion>
-    <adagioVersion>3.5.2</adagioVersion>
+    <adagioVersion>3.5.5-SNAPSHOT</adagioVersion>
     <bluecoveVersion>2.1.0</bluecoveVersion>
     <hibernateVersion>4.3.1.Final</hibernateVersion>
     <springVersion>4.0.1.RELEASE</springVersion>
@@ -425,7 +425,7 @@
       <dependency>
         <groupId>com.esotericsoftware.yamlbeans</groupId>
         <artifactId>yamlbeans</artifactId>
-        <version>1.06</version>
+        <version>1.08</version>
       </dependency>
 
       <!-- flying-saucer -->

Modified: trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/TuttiPersistenceImpl.java
===================================================================
--- trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/TuttiPersistenceImpl.java	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/TuttiPersistenceImpl.java	2014-05-28 15:35:16 UTC (rev 1818)
@@ -734,6 +734,11 @@
         catchBatchService.deleteCatchBatch(fishingOperationId);
     }
 
+    @Override
+    public void recomputeCatchBatchSampleRatios(String fishingOperationId) {
+        catchBatchService.recomputeCatchBatchSampleRatios(fishingOperationId);
+    }
+
     //------------------------------------------------------------------------//
     //-- Species Batch methods                                              --//
     //------------------------------------------------------------------------//

Modified: trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/TuttiPersistenceNoDbImpl.java
===================================================================
--- trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/TuttiPersistenceNoDbImpl.java	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/TuttiPersistenceNoDbImpl.java	2014-05-28 15:35:16 UTC (rev 1818)
@@ -493,6 +493,11 @@
     }
 
     @Override
+    public void recomputeCatchBatchSampleRatios(String fishingOperationId) {
+        throw notImplemented();
+    }
+
+    @Override
     public BatchContainer<SpeciesBatch> getRootSpeciesBatch(String fishingOperationId, boolean validateTree) throws InvalidBatchModelException {
         throw notImplemented();
     }

Modified: trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/BenthosBatchPersistenceServiceImpl.java
===================================================================
--- trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/BenthosBatchPersistenceServiceImpl.java	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/BenthosBatchPersistenceServiceImpl.java	2014-05-28 15:35:16 UTC (rev 1818)
@@ -3,10 +3,8 @@
 /*
  * #%L
  * Tutti :: Persistence
- * $Id$
- * $HeadURL$
  * %%
- * Copyright (C) 2012 - 2013 Ifremer
+ * Copyright (C) 2012 - 2014 Ifremer
  * %%
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as
@@ -28,18 +26,13 @@
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Multimap;
-import com.google.common.collect.Sets;
 import fr.ifremer.adagio.core.dao.data.batch.Batch;
 import fr.ifremer.adagio.core.dao.data.batch.CatchBatch;
 import fr.ifremer.adagio.core.dao.data.batch.SortingBatch;
-import fr.ifremer.adagio.core.dao.data.measure.QuantificationMeasurement;
 import fr.ifremer.adagio.core.dao.data.measure.SortingMeasurement;
 import fr.ifremer.adagio.core.dao.referential.QualityFlag;
 import fr.ifremer.adagio.core.dao.referential.QualityFlagCode;
-import fr.ifremer.adagio.core.dao.referential.QualityFlagImpl;
-import fr.ifremer.adagio.core.dao.referential.pmfm.PmfmId2;
 import fr.ifremer.adagio.core.dao.referential.taxon.ReferenceTaxon;
-import fr.ifremer.adagio.core.dao.referential.taxon.ReferenceTaxonImpl;
 import fr.ifremer.tutti.persistence.InvalidBatchModelException;
 import fr.ifremer.tutti.persistence.entities.data.BatchContainer;
 import fr.ifremer.tutti.persistence.entities.data.BenthosBatch;
@@ -59,10 +52,8 @@
 import org.springframework.stereotype.Service;
 
 import javax.annotation.Resource;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
-import java.util.Set;
 
 import static org.nuiton.i18n.I18n.t;
 
@@ -315,7 +306,7 @@
                 target = SortingBatch.Factory.newInstance();
 
                 // Fill the sorting batch from the source
-                beanToEntity(source, target, parentBatch, rankOrder);
+                batchHelper.beanToEntity(source, target, parentBatch, rankOrder);
 
                 // Create the targeted batch, then update the source id
                 batchHelper.createSortingBatch(source, catchBatch, target);
@@ -326,7 +317,7 @@
                 target = batchHelper.getSortingBatchById(catchBatch, source.getIdAsInt());
 
                 // Fill the sorting batch from the source
-                beanToEntity(source, target, parentBatch, rankOrder);
+                batchHelper.beanToEntity(source, target, parentBatch, rankOrder);
 
                 // Add the batch into a list (will be update later, using this list)
                 batchsToUpdate.add(target);
@@ -375,6 +366,14 @@
             target.setSampleCategoryWeight(source.getWeightBeforeSampling());
         }
 
+        if (CollectionUtils.isNotEmpty(source.getChildBatchs()) && target.getWeight() != null) {
+
+            // can't use this sample weight on a node
+            // the weight comes from sampleRatioText, but must NOT be used here
+            target.setWeight(null);
+
+        }
+
         // Comments
         target.setComment(source.getComments());
 
@@ -434,20 +433,6 @@
         Preconditions.checkNotNull(source.getFishingOperation());
         Preconditions.checkNotNull(source.getFishingOperation().getId());
 
-        Collection<QuantificationMeasurement> quantificationMeasurements = target.getQuantificationMeasurements();
-        Collection<SortingMeasurement> sortingMeasurements = target.getSortingMeasurements();
-
-        // Create lists to store all updates, then remove not updated items
-
-        Set<QuantificationMeasurement> notChangedQuantificationMeasurements = Sets.newHashSet();
-        if (quantificationMeasurements != null) {
-            notChangedQuantificationMeasurements.addAll(quantificationMeasurements);
-        }
-        Set<SortingMeasurement> notChangedSortingMeasurements = Sets.newHashSet();
-        if (sortingMeasurements != null) {
-            notChangedSortingMeasurements.addAll(sortingMeasurements);
-        }
-
         // If parent and root need to be set
         if (target.getId() == null
             || target.getRootBatch() == null
@@ -460,179 +445,75 @@
                     catchBatch);
         }
 
-        // RankOrder (initialize once, at creation)
-        if (target.getRankOrder() == null) {
-            // Start rank order at 1
-            short rankOrder = (short) 1;
-            if (source.getParentBatch() != null && source.getParentBatch().getChildBatchs() != null) {
-                int maxRankOrder = 0;
-                for (BenthosBatch batch : source.getParentBatch().getChildBatchs()) {
-                    Integer r = batch.getRankOrder();
-                    if (r != null && r > maxRankOrder) {
-                        maxRankOrder = r;
-                    }
-                }
-                rankOrder += (short) maxRankOrder;
-
-            } else if (target.getParentBatch() != null && target.getParentBatch().getChildBatchs() != null) {
-                short maxRankOrder = 0;
-                for (Batch batch : target.getParentBatch().getChildBatchs()) {
-                    Short r = batch.getRankOrder();
-                    if (r != null && r > maxRankOrder) {
-                        maxRankOrder = r;
-                    }
-                }
-                rankOrder += maxRankOrder;
-            }
-            target.setRankOrder(rankOrder);
-        }
-
-        // Force subgroup count to '1', as Allegro
-        target.setSubgroupCount(1f);
-
-        // Weight or SampleCategoryWeight
-        if (source.getWeight() == null && source.getSampleCategoryWeight() != null) {
-            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
-                    target,
-                    source.getSampleCategoryWeight());
-            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
-        } else if (source.getWeight() != null && source.getSampleCategoryWeight() == null) {
-            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
-                    target,
-                    source.getWeight());
-            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
-        }
-
-        // Sampling Ratio
-        if (source.getSampleCategoryWeight() == null || source.getWeight() == null) {
-            target.setSamplingRatio(null);
-            target.setSamplingRatioText(null);
-        } else {
-            String samplingRatioText = source.getWeight() + "/" + source.getSampleCategoryWeight();
-            samplingRatioText = samplingRatioText.replaceAll(",", ".");
-            target.setSamplingRatioText(samplingRatioText);
-            target.setSamplingRatio(source.getWeight() / source.getSampleCategoryWeight());
-            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
-                    target,
-                    source.getWeight());
-            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
-        }
-
-        // Sorting measurement
-        if (source.getSampleCategoryId() != null && source.getSampleCategoryValue() != null) {
-            Integer pmfmId = source.getSampleCategoryId();
-            // Do not store sorting measurement if pmfm = SORTED (already store in an ancestor batch)
-            if (!pmfmId.equals(PmfmId2.SORTED_UNSORTED.getValue())) {
-                SortingMeasurement sortingMeasurement = measurementPersistenceHelper.setSortingMeasurement(
-                        target,
-                        pmfmId,
-                        source.getSampleCategoryValue());
-                notChangedSortingMeasurements.remove(sortingMeasurement);
-            }
-        }
-
-        // Individual count
-        target.setIndividualCount(source.getNumber());
-
-        // Species
-        ReferenceTaxon referenceTaxon;
-        if (source.getSpecies() == null || parentBatchId != null) {
-            referenceTaxon = null;
-        } else {
-            referenceTaxon = load(ReferenceTaxonImpl.class, source.getSpecies().getReferenceTaxonId());
-        }
-        target.setReferenceTaxon(referenceTaxon);
-
-        // QualityFlag
-        String qualityFlag;
-        if (source.isSpeciesToConfirm()) {
-            qualityFlag = QualityFlagCode.DOUBTFUL.getValue();
-        } else {
-            qualityFlag = QualityFlagCode.NOTQUALIFIED.getValue();
-        }
-        target.setQualityFlag(load(QualityFlagImpl.class, qualityFlag));
-
-        // Comments
-        target.setComments(source.getComment());
-
-        // Exhaustive inventory (always true under a species batch)
-        target.setExhaustiveInventory(true);
-
-        // Removed not changed measurements (in sorting and quantification measurement lists)
-        if (quantificationMeasurements != null) {
-            quantificationMeasurements.removeAll(notChangedQuantificationMeasurements);
-        }
-        if (sortingMeasurements != null) {
-            sortingMeasurements.removeAll(notChangedSortingMeasurements);
-        }
+        batchHelper.beanToEntity(parentBatchId, source, target);
     }
 
-    protected void beanToEntity(BenthosBatchFrequency source,
-                                SortingBatch target,
-                                SortingBatch parentBatch,
-                                short rankOrder) {
-        Preconditions.checkNotNull(source.getBatch());
-        Preconditions.checkNotNull(source.getBatch().getId());
-
-        Collection<QuantificationMeasurement> quantificationMeasurements = target.getQuantificationMeasurements();
-        Collection<SortingMeasurement> sortingMeasurements = target.getSortingMeasurements();
-
-        // Create lists to store all updates, then remove not updated items
-        Set<QuantificationMeasurement> notChangedQuantificationMeasurements = Sets.newHashSet();
-        if (quantificationMeasurements != null) {
-            notChangedQuantificationMeasurements.addAll(quantificationMeasurements);
-        }
-        Set<SortingMeasurement> notChangedSortingMeasurements = Sets.newHashSet();
-        if (sortingMeasurements != null) {
-            notChangedSortingMeasurements.addAll(sortingMeasurements);
-        }
-
-        // If parent and root need to be set
-        if (target.getId() == null
-            || target.getRootBatch() == null
-            || (target.getParentBatch() != null && !target.getParentBatch().getId().equals(parentBatch.getId()))) {
-
-            target.setParentBatch(parentBatch);
-            target.setRootBatch(parentBatch.getRootBatch());
-        }
-
-        // RankOrder
-        target.setRankOrder(rankOrder);
-
-        // Weight or SampleCategoryWeight
-        if (source.getWeight() != null) {
-            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
-                    target,
-                    source.getWeight());
-            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
-        }
-
-        // Sorting measurement
-        if ((source.getLengthStepCaracteristic() != null && source.getLengthStep() != null)) {
-            Integer pmfmId = source.getLengthStepCaracteristic().getIdAsInt();
-            SortingMeasurement sortingMeasurement = measurementPersistenceHelper.setSortingMeasurement(target, pmfmId,
-                                                                                                       source.getLengthStep());
-            notChangedSortingMeasurements.remove(sortingMeasurement);
-        }
-
-        // Individual count
-        target.setIndividualCount(source.getNumber());
-
-        // Species
-        target.setReferenceTaxon(null);
-
-        // QualityFlag
-        target.setQualityFlag(parentBatch.getQualityFlag());
-
-        // Exhaustive inventory (always true under a species batch)
-        target.setExhaustiveInventory(true);
-
-        // Removed not changed measurements (in sorting and quantification measurement lists)
-        if (quantificationMeasurements != null) {
-            quantificationMeasurements.removeAll(notChangedQuantificationMeasurements);
-        }
-        if (sortingMeasurements != null) {
-            sortingMeasurements.removeAll(notChangedSortingMeasurements);
-        }
-    }
+//    protected void beanToEntity(BenthosBatchFrequency source,
+//                                SortingBatch target,
+//                                SortingBatch parentBatch,
+//                                short rankOrder) {
+//        Preconditions.checkNotNull(source.getBatch());
+//        Preconditions.checkNotNull(source.getBatch().getId());
+//
+//        Collection<QuantificationMeasurement> quantificationMeasurements = target.getQuantificationMeasurements();
+//        Collection<SortingMeasurement> sortingMeasurements = target.getSortingMeasurements();
+//
+//        // Create lists to store all updates, then remove not updated items
+//        Set<QuantificationMeasurement> notChangedQuantificationMeasurements = Sets.newHashSet();
+//        if (quantificationMeasurements != null) {
+//            notChangedQuantificationMeasurements.addAll(quantificationMeasurements);
+//        }
+//        Set<SortingMeasurement> notChangedSortingMeasurements = Sets.newHashSet();
+//        if (sortingMeasurements != null) {
+//            notChangedSortingMeasurements.addAll(sortingMeasurements);
+//        }
+//
+//        // If parent and root need to be set
+//        if (target.getId() == null
+//            || target.getRootBatch() == null
+//            || (target.getParentBatch() != null && !target.getParentBatch().getId().equals(parentBatch.getId()))) {
+//
+//            target.setParentBatch(parentBatch);
+//            target.setRootBatch(parentBatch.getRootBatch());
+//        }
+//
+//        // RankOrder
+//        target.setRankOrder(rankOrder);
+//
+//        // Weight or SampleCategoryWeight
+//        if (source.getWeight() != null) {
+//            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
+//                    target,
+//                    source.getWeight());
+//            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
+//        }
+//
+//        // Sorting measurement
+//        if ((source.getLengthStepCaracteristic() != null && source.getLengthStep() != null)) {
+//            Integer pmfmId = source.getLengthStepCaracteristic().getIdAsInt();
+//            SortingMeasurement sortingMeasurement = measurementPersistenceHelper.setSortingMeasurement(target, pmfmId,
+//                                                                                                       source.getLengthStep());
+//            notChangedSortingMeasurements.remove(sortingMeasurement);
+//        }
+//
+//        // Individual count
+//        target.setIndividualCount(source.getNumber());
+//
+//        // Species
+//        target.setReferenceTaxon(null);
+//
+//        // QualityFlag
+//        target.setQualityFlag(parentBatch.getQualityFlag());
+//
+//        // Exhaustive inventory (always true under a species batch)
+//        target.setExhaustiveInventory(true);
+//
+//        // Removed not changed measurements (in sorting and quantification measurement lists)
+//        if (quantificationMeasurements != null) {
+//            quantificationMeasurements.removeAll(notChangedQuantificationMeasurements);
+//        }
+//        if (sortingMeasurements != null) {
+//            sortingMeasurements.removeAll(notChangedSortingMeasurements);
+//        }
+//    }
 }

Modified: trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/CatchBatchPersistenceService.java
===================================================================
--- trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/CatchBatchPersistenceService.java	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/CatchBatchPersistenceService.java	2014-05-28 15:35:16 UTC (rev 1818)
@@ -77,4 +77,13 @@
     @Transactional(readOnly = false)
     void deleteCatchBatch(String fishingOperationId);
 
+    /**
+     * Recompute all the sampleRatio and sampleRatioText for the catch batch
+     * and all his children batches for the given fishing operation id.
+     *
+     * @param fishingOperationId id of the fihsing operation
+     * @since 3.5
+     */
+    @Transactional(readOnly = false)
+    void recomputeCatchBatchSampleRatios(String fishingOperationId);
 }

Modified: trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/CatchBatchPersistenceServiceImpl.java
===================================================================
--- trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/CatchBatchPersistenceServiceImpl.java	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/CatchBatchPersistenceServiceImpl.java	2014-05-28 15:35:16 UTC (rev 1818)
@@ -24,19 +24,22 @@
 
 
 import com.google.common.base.Preconditions;
-import com.google.common.collect.Sets;
+import fr.ifremer.adagio.core.dao.data.batch.Batch;
 import fr.ifremer.adagio.core.dao.data.batch.CatchBatchImpl;
 import fr.ifremer.adagio.core.dao.data.batch.SortingBatch;
 import fr.ifremer.adagio.core.dao.data.measure.QuantificationMeasurement;
 import fr.ifremer.adagio.core.dao.data.operation.FishingOperationImpl;
 import fr.ifremer.adagio.core.dao.referential.QualityFlagCode;
 import fr.ifremer.adagio.core.dao.referential.QualityFlagImpl;
+import fr.ifremer.tutti.persistence.entities.TuttiEntities;
 import fr.ifremer.tutti.persistence.entities.data.CatchBatch;
 import fr.ifremer.tutti.persistence.entities.data.CatchBatchBean;
 import fr.ifremer.tutti.persistence.service.util.BatchPersistenceHelper;
 import fr.ifremer.tutti.persistence.service.util.BatchTreeHelper;
 import fr.ifremer.tutti.persistence.service.util.MeasurementPersistenceHelper;
 import fr.ifremer.tutti.persistence.service.util.SynchronizationStatusHelper;
+import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.lang3.BooleanUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.hibernate.FlushMode;
@@ -46,8 +49,12 @@
 import org.springframework.stereotype.Service;
 
 import javax.annotation.Resource;
+import java.math.BigDecimal;
 import java.util.Collection;
+import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
+import java.util.TreeMap;
 
 @Service("batchPersistenceService")
 public class CatchBatchPersistenceServiceImpl
@@ -170,6 +177,75 @@
         batchHelper.deleteCatchBatch(fishingOperationId, catchBatchId);
     }
 
+    @Override
+    public void recomputeCatchBatchSampleRatios(String fishingOperationId) {
+
+        Preconditions.checkNotNull(fishingOperationId);
+        Integer catchBatchId = batchHelper.getCatchBatchIdByFishingOperationId(Integer.valueOf(fishingOperationId));
+
+        if (catchBatchId == null) {
+            throw new DataRetrievalFailureException("Could not retrieve catch batch for fishingOperation id=" + fishingOperationId);
+        }
+
+        fr.ifremer.adagio.core.dao.data.batch.CatchBatch catchBatch = batchTreeHelper.loadCatchBatch(catchBatchId);
+
+        // To store computed indirect weights by batch
+        // If a batch has a weight before sampling then nothing is computed
+        Map<Integer, SortingBatch> indirectWeightByBatch = new TreeMap<>();
+
+        // To store quantification measurement ids which need to update to pass
+        // is_reference_quantification to false
+        // such measurements are only on batch nodes (leaf always keep the value to true)
+        Set<Integer> quantificationMeasurementIds = new HashSet<>();
+
+        Set<Integer> indirectWeightByBatchSkip = new HashSet<>();
+
+        for (Batch rootBatch : catchBatch.getChildBatchs()) {
+
+            computeIndirectWeight(rootBatch,
+                                  indirectWeightByBatch,
+                                  indirectWeightByBatchSkip,
+                                  quantificationMeasurementIds);
+
+        }
+
+        if (!indirectWeightByBatch.isEmpty()) {
+
+            // update batchs sample ratio
+            for (SortingBatch batch : indirectWeightByBatch.values()) {
+
+                Float weight = batch.getWeight();
+                Float indirectWeight = batch.getIndirectWeight();
+                batch.setIndirectWeight(null);
+
+                if (indirectWeight == null) {
+
+                    // will reuse then the weight
+                    indirectWeight = weight;
+                }
+
+                if (log.isInfoEnabled()) {
+                    log.info(String.format("setWeightAndSampleRatio :: %d (%s // %s)", batch.getId(), weight, indirectWeight));
+                }
+
+                batchTreeHelper.setSortingSamplingRatio(batch, indirectWeight, weight);
+
+            }
+
+        }
+        if (!quantificationMeasurementIds.isEmpty()) {
+
+            // update measurements
+            if (log.isInfoEnabled()) {
+                log.info("updateQuantificationMeasurementsForBatchNodes :: " + quantificationMeasurementIds);
+            }
+            queryUpdate("updateQuantificationMeasurementsForBatchNodes",
+                        "ids", IntegerType.INSTANCE, quantificationMeasurementIds);
+
+        }
+
+    }
+
     //------------------------------------------------------------------------//
     //-- Internal methods                                                   --//
     //------------------------------------------------------------------------//
@@ -264,39 +340,27 @@
         Preconditions.checkNotNull(source.getFishingOperation());
         Preconditions.checkNotNull(source.getFishingOperation().getId());
 
-        // Retrieve recorder department
-
         // First initialization (when created)
         Integer fishingOperationId = source.getFishingOperation().getIdAsInt();
         target.setFishingOperation(load(FishingOperationImpl.class, fishingOperationId));
 
+        // Quality flag
         target.setQualityFlag(load(QualityFlagImpl.class, QualityFlagCode.NOTQUALIFIED.getValue()));
+
+        // Rank order
         target.setRankOrder((short) 1);
 
         // Synchronization status
         synchronizationStatusHelper.setDirty(target);
 
-        // Create lists to store all updates, then remove not updated items
-        Collection<QuantificationMeasurement> quantificationMeasurements = target.getQuantificationMeasurements();
-        Set<QuantificationMeasurement> notChangedQuantificationMeasurements = Sets.newHashSet();
-        if (quantificationMeasurements != null) {
-            notChangedQuantificationMeasurements.addAll(quantificationMeasurements);
-        }
-
         // Total Weight
         if (source.getCatchTotalWeight() != null) {
 
-            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
+            measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
                     target,
                     source.getCatchTotalWeight());
-            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
         }
 
-        // Removed not changed measurements (in sorting and quantification measurement lists)
-        if (quantificationMeasurements != null) {
-            quantificationMeasurements.removeAll(notChangedQuantificationMeasurements);
-        }
-
         SortingBatch vracBatch = batchTreeHelper.getVracBatch(target);
 
         SortingBatch horsVracBatch = batchTreeHelper.getHorsVracBatch(target);
@@ -486,4 +550,130 @@
         }
     }
 
+    protected void computeIndirectWeight(Batch batch,
+                                         Map<Integer, SortingBatch> indirectWeightByBatch,
+                                         Set<Integer> indirectWeightByBatchSkip,
+                                         Set<Integer> quantificationMeasurements) {
+
+        Integer batchId = batch.getId();
+
+        if (indirectWeightByBatch.containsKey(batchId) ||
+            indirectWeightByBatchSkip.contains(batchId)) {
+
+            // already computed
+            return;
+
+        }
+
+        Collection<Batch> childBatchs = batch.getChildBatchs();
+        boolean batchIsLeaf = CollectionUtils.isEmpty(childBatchs);
+
+        if (batchIsLeaf) {
+
+            // on a leaf, nothing else to do
+            if (log.isDebugEnabled()) {
+                log.debug("[BATCH :: " + batchId + "] - Do not compute on a leaf ");
+            }
+            return;
+
+        }
+
+        QuantificationMeasurement measurement = measurementPersistenceHelper.getWeightMeasurementQuantificationMeasurement(batch);
+        if (measurement != null &&
+            BooleanUtils.isTrue(measurement.getIsReferenceQuantification())) {
+
+            // need to pass this to false
+            quantificationMeasurements.add(measurement.getId());
+
+            if (log.isDebugEnabled()) {
+                log.debug("[BATCH :: " + batchId + "] - Need to update the quantification measurement (not a leaf) :: " + measurement.getId());
+            }
+
+        }
+
+        // compute indirect weights of childs before all
+
+        for (Batch childBatch : childBatchs) {
+
+            computeIndirectWeight(childBatch, indirectWeightByBatch, indirectWeightByBatchSkip, quantificationMeasurements);
+
+        }
+
+//        if (batch.getWeight() == null) {
+//
+//            // no need to compute indirect weight, mark batch
+//            indirectWeightByBatchSkip.add(batchId);
+//
+//            if (log.isDebugEnabled()) {
+//                log.debug("[BATCH :: " + batchId + "] - No need of indirect weight (no weight on it) ");
+//            }
+//            return;
+//
+//        }
+        if (batch.getWeightBeforeSampling() != null) {
+
+            // no need to compute indirect weight, mark batch
+            indirectWeightByBatchSkip.add(batchId);
+
+            if (log.isDebugEnabled()) {
+                log.debug("[BATCH :: " + batchId + "] - No need of indirect weight (there is a weight before sampling) ");
+            }
+            return;
+
+        }
+
+        // At last, compute the indirect weight
+        Float indirectWeight = computeIndirectWeight(batch);
+        batch.setIndirectWeight(indirectWeight);
+
+        if (batch.getWeight() != null) {
+
+            // Can only update the sample ratio if there is a weight on the batch
+            indirectWeightByBatch.put(batchId, (SortingBatch) batch);
+
+        }
+
+        if (log.isDebugEnabled()) {
+            log.debug("[BATCH :: " + batchId + "] - " + "Computed indirect weight " + indirectWeight);
+        }
+
+    }
+
+    protected Float computeIndirectWeight(Batch batch) {
+
+        if (log.isDebugEnabled()) {
+            log.debug("[BATCH :: " + batch.getId() + "] compute indirect weight");
+        }
+
+        BigDecimal result = new BigDecimal(0);
+
+        for (Batch childBatch : batch.getChildBatchs()) {
+
+            Float weight = TuttiEntities.getValueOrComputedValue(childBatch.getWeightBeforeSampling(),
+                                                                 childBatch.getWeight());
+
+            if (weight == null) {
+
+                //  at last use the indirectWeight
+                weight = childBatch.getIndirectWeight();
+
+            }
+
+            if (weight == null) {
+
+                if (log.isDebugEnabled()) {
+                    log.debug("[BATCH :: " + batch.getId() + "] Found a child batch " + childBatch.getId() + " has no weight, skip computing indirect weight for batch :: ...");
+                }
+
+                return null;
+
+            }
+            result = result.add(new BigDecimal(String.valueOf(weight)));
+
+        }
+
+        return TuttiEntities.roundKiloGram(result.floatValue());
+
+    }
+
 }

Modified: trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/MarineLitterBatchPersistenceServiceImpl.java
===================================================================
--- trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/MarineLitterBatchPersistenceServiceImpl.java	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/MarineLitterBatchPersistenceServiceImpl.java	2014-05-28 15:35:16 UTC (rev 1818)
@@ -27,7 +27,6 @@
 import fr.ifremer.adagio.core.dao.data.batch.Batch;
 import fr.ifremer.adagio.core.dao.data.batch.CatchBatch;
 import fr.ifremer.adagio.core.dao.data.batch.SortingBatch;
-import fr.ifremer.adagio.core.dao.data.measure.QuantificationMeasurement;
 import fr.ifremer.adagio.core.dao.data.measure.SortingMeasurement;
 import fr.ifremer.adagio.core.dao.referential.QualityFlagCode;
 import fr.ifremer.adagio.core.dao.referential.QualityFlagImpl;
@@ -206,20 +205,6 @@
         Preconditions.checkNotNull(source.getFishingOperation());
         Preconditions.checkNotNull(source.getFishingOperation().getId());
 
-        Collection<QuantificationMeasurement> quantificationMeasurements = target.getQuantificationMeasurements();
-        Collection<SortingMeasurement> sortingMeasurements = target.getSortingMeasurements();
-
-        // Create lists to store all updates, then remove not updated items
-
-        Set<QuantificationMeasurement> notChangedQuantificationMeasurements = Sets.newHashSet();
-        if (quantificationMeasurements != null) {
-            notChangedQuantificationMeasurements.addAll(quantificationMeasurements);
-        }
-        Set<SortingMeasurement> notChangedSortingMeasurements = Sets.newHashSet();
-        if (sortingMeasurements != null) {
-            notChangedSortingMeasurements.addAll(sortingMeasurements);
-        }
-
         // If parent and root need to be set
         if (target.getId() == null || target.getRootBatch() == null) {
             batchHelper.setMarineLitterBatchParents(target, catchBatch);
@@ -245,40 +230,44 @@
         // Force subgroup count to '1', as Allegro
         target.setSubgroupCount(1f);
 
-        // Weight
-        if (source.getWeight() != null) {
+        // Sorting Measurements
+        {
+            Collection<SortingMeasurement> sortingMeasurements = target.getSortingMeasurements();
 
-            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
-                    target,
-                    source.getWeight());
-            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
-        }
+            Set<SortingMeasurement> notChangedSortingMeasurements = Sets.newHashSet();
+            if (sortingMeasurements != null) {
+                notChangedSortingMeasurements.addAll(sortingMeasurements);
+            }
 
-        // MarineLitterCategory
-        if (source.getMarineLitterCategory() != null) {
+            // MarineLitterCategory
+            if (source.getMarineLitterCategory() != null) {
 
-            SortingMeasurement measurement = measurementPersistenceHelper.setSortingMeasurement(
-                    target,
-                    marineLitterCategory,
-                    source.getMarineLitterCategory().getIdAsInt()
-            );
-            notChangedSortingMeasurements.remove(measurement);
-        }
+                SortingMeasurement measurement = measurementPersistenceHelper.setSortingMeasurement(
+                        target,
+                        marineLitterCategory,
+                        source.getMarineLitterCategory().getIdAsInt()
+                );
+                notChangedSortingMeasurements.remove(measurement);
+            }
 
-        // MarineLitterSizeCategory
-        if (source.getMarineLitterSizeCategory() != null) {
+            // MarineLitterSizeCategory
+            if (source.getMarineLitterSizeCategory() != null) {
 
-            SortingMeasurement measurement = measurementPersistenceHelper.setSortingMeasurement(
-                    target,
-                    marineLitterSizeCategory,
-                    source.getMarineLitterSizeCategory().getIdAsInt()
-            );
-            notChangedSortingMeasurements.remove(measurement);
+                SortingMeasurement measurement = measurementPersistenceHelper.setSortingMeasurement(
+                        target,
+                        marineLitterSizeCategory,
+                        source.getMarineLitterSizeCategory().getIdAsInt()
+                );
+                notChangedSortingMeasurements.remove(measurement);
+            }
+
+            if (sortingMeasurements != null) {
+                sortingMeasurements.removeAll(notChangedSortingMeasurements);
+            }
         }
 
-        // Sampling Ratio
-        target.setSamplingRatio(1.0f);
-        target.setSamplingRatioText(null);
+        // Sampling Ratio + Weight
+        batchTreeHelper.setWeightAndSampleRatio(target, source.getWeight(), null);
 
         // Individual count
         target.setIndividualCount(source.getNumber());
@@ -293,12 +282,5 @@
         // Exhaustive inventory (always true under a marine litter batch)
         target.setExhaustiveInventory(true);
 
-        // Removed not changed measurements (in sorting and quantification measurement lists)
-        if (quantificationMeasurements != null) {
-            quantificationMeasurements.removeAll(notChangedQuantificationMeasurements);
-        }
-        if (sortingMeasurements != null) {
-            sortingMeasurements.removeAll(notChangedSortingMeasurements);
-        }
     }
 }

Modified: trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/SpeciesBatchPersistenceServiceImpl.java
===================================================================
--- trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/SpeciesBatchPersistenceServiceImpl.java	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/SpeciesBatchPersistenceServiceImpl.java	2014-05-28 15:35:16 UTC (rev 1818)
@@ -3,10 +3,8 @@
 /*
  * #%L
  * Tutti :: Persistence
- * $Id$
- * $HeadURL$
  * %%
- * Copyright (C) 2012 - 2013 Ifremer
+ * Copyright (C) 2012 - 2014 Ifremer
  * %%
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as
@@ -28,18 +26,13 @@
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Multimap;
-import com.google.common.collect.Sets;
 import fr.ifremer.adagio.core.dao.data.batch.Batch;
 import fr.ifremer.adagio.core.dao.data.batch.CatchBatch;
 import fr.ifremer.adagio.core.dao.data.batch.SortingBatch;
-import fr.ifremer.adagio.core.dao.data.measure.QuantificationMeasurement;
 import fr.ifremer.adagio.core.dao.data.measure.SortingMeasurement;
 import fr.ifremer.adagio.core.dao.referential.QualityFlag;
 import fr.ifremer.adagio.core.dao.referential.QualityFlagCode;
-import fr.ifremer.adagio.core.dao.referential.QualityFlagImpl;
-import fr.ifremer.adagio.core.dao.referential.pmfm.PmfmId2;
 import fr.ifremer.adagio.core.dao.referential.taxon.ReferenceTaxon;
-import fr.ifremer.adagio.core.dao.referential.taxon.ReferenceTaxonImpl;
 import fr.ifremer.tutti.persistence.InvalidBatchModelException;
 import fr.ifremer.tutti.persistence.entities.data.BatchContainer;
 import fr.ifremer.tutti.persistence.entities.data.SampleCategoryModel;
@@ -59,10 +52,8 @@
 import org.springframework.stereotype.Service;
 
 import javax.annotation.Resource;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
-import java.util.Set;
 
 import static org.nuiton.i18n.I18n.t;
 
@@ -333,7 +324,7 @@
                 target = SortingBatch.Factory.newInstance();
 
                 // Fill the sorting batch from the source
-                beanToEntity(source, target, parentBatch, rankOrder);
+                batchHelper.beanToEntity(source, target, parentBatch, rankOrder);
 
                 // Create the targeted batch, then update the source id
                 batchHelper.createSortingBatch(source, catchBatch, target);
@@ -350,7 +341,7 @@
                 target = batchHelper.loadSortingBatch(source.getIdAsInt(), catchBatch);
 
                 // Fill the sorting batch from the source
-                beanToEntity(source, target, parentBatch, rankOrder);
+                batchHelper.beanToEntity(source, target, parentBatch, rankOrder);
 
                 // Add the batch into a list (will be update later, using this list)
                 batchsToUpdate.add(target);
@@ -389,7 +380,8 @@
     //-- Internal methods                                                   --//
     //------------------------------------------------------------------------//
 
-    protected SpeciesBatch entityToBean(SampleCategoryModel sampleCategoryModel, SortingBatch source,
+    protected SpeciesBatch entityToBean(SampleCategoryModel sampleCategoryModel,
+                                        SortingBatch source,
                                         SpeciesBatch target) {
 
         Preconditions.checkNotNull(target.getSpecies());
@@ -410,6 +402,15 @@
             target.setSampleCategoryWeight(source.getWeightBeforeSampling());
         }
 
+        if (CollectionUtils.isNotEmpty(source.getChildBatchs()) && target.getWeight() != null) {
+
+            // can't use this sample weight on a node
+            // the weight comes from sampleRatioText, but must NOT be used here
+            target.setWeight(null);
+
+        }
+
+
         // Comments
         target.setComment(source.getComments());
 
@@ -470,20 +471,6 @@
         Preconditions.checkNotNull(source.getFishingOperation());
         Preconditions.checkNotNull(source.getFishingOperation().getId());
 
-        Collection<QuantificationMeasurement> quantificationMeasurements = target.getQuantificationMeasurements();
-        Collection<SortingMeasurement> sortingMeasurements = target.getSortingMeasurements();
-
-        // Create lists to store all updates, then remove not updated items
-
-        Set<QuantificationMeasurement> notChangedQuantificationMeasurements = Sets.newHashSet();
-        if (quantificationMeasurements != null) {
-            notChangedQuantificationMeasurements.addAll(quantificationMeasurements);
-        }
-        Set<SortingMeasurement> notChangedSortingMeasurements = Sets.newHashSet();
-        if (sortingMeasurements != null) {
-            notChangedSortingMeasurements.addAll(sortingMeasurements);
-        }
-
         // If parent and root need to be set
         if (target.getId() == null
             || target.getRootBatch() == null
@@ -498,181 +485,77 @@
             );
         }
 
-        // RankOrder (initialize once, at creation)
-        if (target.getRankOrder() == null) {
-            // Start rank order at 1
-            short rankOrder = (short) 1;
-            if (source.getParentBatch() != null && source.getParentBatch().getChildBatchs() != null) {
-                int maxRankOrder = 0;
-                for (SpeciesBatch batch : source.getParentBatch().getChildBatchs()) {
-                    Integer r = batch.getRankOrder();
-                    if (r != null && r > maxRankOrder) {
-                        maxRankOrder = r;
-                    }
-                }
-                rankOrder += (short) maxRankOrder;
+        batchHelper.beanToEntity(parentBatchId, source, target);
 
-            } else if (target.getParentBatch() != null && target.getParentBatch().getChildBatchs() != null) {
-                short maxRankOrder = 0;
-                for (Batch batch : target.getParentBatch().getChildBatchs()) {
-                    Short r = batch.getRankOrder();
-                    if (r != null && r > maxRankOrder) {
-                        maxRankOrder = r;
-                    }
-                }
-                rankOrder += maxRankOrder;
-            }
-
-            target.setRankOrder(rankOrder);
-        }
-
-        // Force subgroup count to '1', as Allegro
-        target.setSubgroupCount(1f);
-
-        // Weight or SampleCategoryWeight
-        if (source.getSampleCategoryWeight() != null && source.getWeight() == null) {
-            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
-                    target,
-                    source.getSampleCategoryWeight());
-            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
-        } else if (source.getWeight() != null && source.getSampleCategoryWeight() == null) {
-            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
-                    target,
-                    source.getWeight());
-            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
-        }
-
-        // Sampling Ratio
-        if (source.getSampleCategoryWeight() == null || source.getWeight() == null) {
-            target.setSamplingRatio(null);
-            target.setSamplingRatioText(null);
-        } else {
-            String samplingRatioText = source.getWeight() + "/" + source.getSampleCategoryWeight();
-            samplingRatioText = samplingRatioText.replaceAll(",", ".");
-            target.setSamplingRatioText(samplingRatioText);
-            target.setSamplingRatio(source.getWeight() / source.getSampleCategoryWeight());
-            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
-                    target,
-                    source.getWeight());
-            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
-        }
-
-        // Sorting measurement
-        if (source.getSampleCategoryId() != null && source.getSampleCategoryValue() != null) {
-            Integer pmfmId = source.getSampleCategoryId();
-            // Do not store sorting measurement if pmfm = SORTED (already store in an ancestor batch)
-            if (!pmfmId.equals(PmfmId2.SORTED_UNSORTED.getValue())) {
-                SortingMeasurement sortingMeasurement = measurementPersistenceHelper.setSortingMeasurement(
-                        target,
-                        pmfmId,
-                        source.getSampleCategoryValue());
-                notChangedSortingMeasurements.remove(sortingMeasurement);
-            }
-        }
-
-        // Individual count
-        target.setIndividualCount(source.getNumber());
-
-        // Species
-        ReferenceTaxon referenceTaxon;
-        if (source.getSpecies() == null || parentBatchId != null) {
-            referenceTaxon = null;
-        } else {
-            referenceTaxon = load(ReferenceTaxonImpl.class, source.getSpecies().getReferenceTaxonId());
-        }
-        target.setReferenceTaxon(referenceTaxon);
-
-        // QualityFlag
-        String qualityFlag;
-        if (source.isSpeciesToConfirm()) {
-            qualityFlag = QualityFlagCode.DOUBTFUL.getValue();
-        } else {
-            qualityFlag = QualityFlagCode.NOTQUALIFIED.getValue();
-        }
-        target.setQualityFlag(load(QualityFlagImpl.class, qualityFlag));
-
-        // Comments
-        target.setComments(source.getComment());
-
-        // Exhaustive inventory (always true under a species batch)
-        target.setExhaustiveInventory(true);
-
-        // Removed not changed measurements (in sorting and quantification measurement lists)
-        if (quantificationMeasurements != null) {
-            quantificationMeasurements.removeAll(notChangedQuantificationMeasurements);
-        }
-        if (sortingMeasurements != null) {
-            sortingMeasurements.removeAll(notChangedSortingMeasurements);
-        }
     }
 
-    protected void beanToEntity(SpeciesBatchFrequency source,
-                                SortingBatch target,
-                                SortingBatch parentBatch,
-                                short rankOrder) {
-        Preconditions.checkNotNull(source.getBatch());
-        Preconditions.checkNotNull(source.getBatch().getId());
+//    protected void beanToEntity(SpeciesBatchFrequency source,
+//                                SortingBatch target,
+//                                SortingBatch parentBatch,
+//                                short rankOrder) {
+//        Preconditions.checkNotNull(source.getBatch());
+//        Preconditions.checkNotNull(source.getBatch().getId());
+//
+//        Collection<QuantificationMeasurement> quantificationMeasurements = target.getQuantificationMeasurements();
+//        Collection<SortingMeasurement> sortingMeasurements = target.getSortingMeasurements();
+//
+//        // Create lists to store all updates, then remove not updated items
+//        Set<QuantificationMeasurement> notChangedQuantificationMeasurements = Sets.newHashSet();
+//        if (quantificationMeasurements != null) {
+//            notChangedQuantificationMeasurements.addAll(quantificationMeasurements);
+//        }
+//        Set<SortingMeasurement> notChangedSortingMeasurements = Sets.newHashSet();
+//        if (sortingMeasurements != null) {
+//            notChangedSortingMeasurements.addAll(sortingMeasurements);
+//        }
+//
+//        // If parent and root need to be set
+//        if (target.getId() == null
+//            || target.getRootBatch() == null
+//            || (target.getParentBatch() != null && !target.getParentBatch().getId().equals(parentBatch.getId()))) {
+//
+//            target.setParentBatch(parentBatch);
+//            target.setRootBatch(parentBatch.getRootBatch());
+//        }
+//
+//        // RankOrder
+//        target.setRankOrder(rankOrder);
+//
+//        // Weight or SampleCategoryWeight
+//        if (source.getWeight() != null) {
+//            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
+//                    target,
+//                    source.getWeight());
+//            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
+//        }
+//
+//        // Sorting measurement
+//        if ((source.getLengthStepCaracteristic() != null && source.getLengthStep() != null)) {
+//            Integer pmfmId = source.getLengthStepCaracteristic().getIdAsInt();
+//            SortingMeasurement sortingMeasurement = measurementPersistenceHelper.setSortingMeasurement(target, pmfmId,
+//                                                                                                       source.getLengthStep());
+//            notChangedSortingMeasurements.remove(sortingMeasurement);
+//        }
+//
+//        // Individual count
+//        target.setIndividualCount(source.getNumber());
+//
+//        // Species
+//        target.setReferenceTaxon(null);
+//
+//        // QualityFlag
+//        target.setQualityFlag(parentBatch.getQualityFlag());
+//
+//        // Exhaustive inventory (always true under a species batch)
+//        target.setExhaustiveInventory(true);
+//
+//        // Removed not changed measurements (in sorting and quantification measurement lists)
+//        if (quantificationMeasurements != null) {
+//            quantificationMeasurements.removeAll(notChangedQuantificationMeasurements);
+//        }
+//        if (sortingMeasurements != null) {
+//            sortingMeasurements.removeAll(notChangedSortingMeasurements);
+//        }
+//    }
 
-        Collection<QuantificationMeasurement> quantificationMeasurements = target.getQuantificationMeasurements();
-        Collection<SortingMeasurement> sortingMeasurements = target.getSortingMeasurements();
-
-        // Create lists to store all updates, then remove not updated items
-        Set<QuantificationMeasurement> notChangedQuantificationMeasurements = Sets.newHashSet();
-        if (quantificationMeasurements != null) {
-            notChangedQuantificationMeasurements.addAll(quantificationMeasurements);
-        }
-        Set<SortingMeasurement> notChangedSortingMeasurements = Sets.newHashSet();
-        if (sortingMeasurements != null) {
-            notChangedSortingMeasurements.addAll(sortingMeasurements);
-        }
-
-        // If parent and root need to be set
-        if (target.getId() == null
-            || target.getRootBatch() == null
-            || (target.getParentBatch() != null && !target.getParentBatch().getId().equals(parentBatch.getId()))) {
-
-            target.setParentBatch(parentBatch);
-            target.setRootBatch(parentBatch.getRootBatch());
-        }
-
-        // RankOrder
-        target.setRankOrder(rankOrder);
-
-        // Weight or SampleCategoryWeight
-        if (source.getWeight() != null) {
-            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
-                    target,
-                    source.getWeight());
-            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
-        }
-
-        // Sorting measurement
-        if ((source.getLengthStepCaracteristic() != null && source.getLengthStep() != null)) {
-            Integer pmfmId = source.getLengthStepCaracteristic().getIdAsInt();
-            SortingMeasurement sortingMeasurement = measurementPersistenceHelper.setSortingMeasurement(target, pmfmId,
-                                                                                                       source.getLengthStep());
-            notChangedSortingMeasurements.remove(sortingMeasurement);
-        }
-
-        // Individual count
-        target.setIndividualCount(source.getNumber());
-
-        // Species
-        target.setReferenceTaxon(null);
-
-        // QualityFlag
-        target.setQualityFlag(parentBatch.getQualityFlag());
-
-        // Exhaustive inventory (always true under a species batch)
-        target.setExhaustiveInventory(true);
-
-        // Removed not changed measurements (in sorting and quantification measurement lists)
-        if (quantificationMeasurements != null) {
-            quantificationMeasurements.removeAll(notChangedQuantificationMeasurements);
-        }
-        if (sortingMeasurements != null) {
-            sortingMeasurements.removeAll(notChangedSortingMeasurements);
-        }
-    }
-
 }

Modified: trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/util/BatchPersistenceHelper.java
===================================================================
--- trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/util/BatchPersistenceHelper.java	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/util/BatchPersistenceHelper.java	2014-05-28 15:35:16 UTC (rev 1818)
@@ -3,10 +3,8 @@
 /*
  * #%L
  * Tutti :: Persistence
- * $Id$
- * $HeadURL$
  * %%
- * Copyright (C) 2012 - 2013 Ifremer
+ * Copyright (C) 2012 - 2014 Ifremer
  * %%
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as
@@ -27,7 +25,7 @@
 import com.google.common.base.Joiner;
 import com.google.common.base.Preconditions;
 import com.google.common.collect.Lists;
-import fr.ifremer.adagio.core.dao.administration.user.DepartmentId;
+import com.google.common.collect.Sets;
 import fr.ifremer.adagio.core.dao.data.batch.Batch;
 import fr.ifremer.adagio.core.dao.data.batch.CatchBatch;
 import fr.ifremer.adagio.core.dao.data.batch.CatchBatchExtendDao;
@@ -38,10 +36,14 @@
 import fr.ifremer.adagio.core.dao.data.measure.SortingMeasurement;
 import fr.ifremer.adagio.core.dao.data.operation.FishingOperation;
 import fr.ifremer.adagio.core.dao.data.operation.FishingOperationDao;
+import fr.ifremer.adagio.core.dao.referential.QualityFlagCode;
+import fr.ifremer.adagio.core.dao.referential.QualityFlagImpl;
 import fr.ifremer.adagio.core.dao.referential.pmfm.ObjectTypeCode2;
 import fr.ifremer.adagio.core.dao.referential.pmfm.Pmfm;
 import fr.ifremer.adagio.core.dao.referential.pmfm.PmfmId2;
 import fr.ifremer.adagio.core.dao.referential.pmfm.QualitativeValueId;
+import fr.ifremer.adagio.core.dao.referential.taxon.ReferenceTaxon;
+import fr.ifremer.adagio.core.dao.referential.taxon.ReferenceTaxonImpl;
 import fr.ifremer.tutti.persistence.InvalidBatchModelException;
 import fr.ifremer.tutti.persistence.entities.TuttiEntity;
 import fr.ifremer.tutti.persistence.entities.data.BatchContainer;
@@ -71,6 +73,7 @@
 import java.text.MessageFormat;
 import java.util.Collection;
 import java.util.List;
+import java.util.Set;
 
 import static org.nuiton.i18n.I18n.t;
 
@@ -108,6 +111,9 @@
     @Resource(name = "scientificCruiseCatchBatchValidator")
     protected TuttiCatchBatchValidator catchBatchValidator;
 
+    @Resource(name = "measurementPersistenceHelper")
+    protected MeasurementPersistenceHelper measurementPersistenceHelper;
+
     @Resource(name = "batchTreeHelper")
     protected BatchTreeHelper batchTreeHelper;
 
@@ -276,13 +282,13 @@
         if (validate) {
 
             try {
-                result = catchBatchDao.loadFullTree(catchBatchId, true, false);
+                result = catchBatchDao.loadFullTree(catchBatchId, PmfmId2.WEIGHT_MEASURED.getValue(), true, false);
             } catch (CatchBatchValidationException e) {
                 throw new InvalidBatchModelException(
                         "L'arbre d'échantillonage n'est pas compatible avec celui de Tutti.", e);
             }
         } else {
-            result = catchBatchDao.loadFullTree(catchBatchId);
+            result = catchBatchDao.loadFullTree(catchBatchId, PmfmId2.WEIGHT_MEASURED.getValue());
         }
         Preconditions.checkNotNull(result);
         return result;
@@ -305,7 +311,7 @@
         // whenever want to repair anything from Tutti
         fr.ifremer.adagio.core.dao.data.batch.CatchBatch result;
 
-        result = catchBatchDao.loadFullTree(catchBatchId);
+        result = catchBatchDao.loadFullTree(catchBatchId, PmfmId2.WEIGHT_MEASURED.getValue());
 
         Preconditions.checkNotNull(result);
         return result;
@@ -488,6 +494,201 @@
         target.setRootBatch(catchBatch);
     }
 
+    public void beanToEntity(String parentBatchId,
+                             SpeciesAbleBatch source,
+                             SortingBatch target) {
+
+        // --- RankOrder (initialize once, at creation) --- //
+        {
+            if (target.getRankOrder() == null) {
+                // Start rank order at 1
+                short rankOrder = (short) 1;
+                if (source.getParentBatch() != null && source.getParentBatch().getChildBatchs() != null) {
+                    int maxRankOrder = 0;
+                    for (SpeciesAbleBatch batch : source.getParentBatch().getChildBatchs()) {
+                        Integer r = batch.getRankOrder();
+                        if (r != null && r > maxRankOrder) {
+                            maxRankOrder = r;
+                        }
+                    }
+                    rankOrder += (short) maxRankOrder;
+
+                } else if (target.getParentBatch() != null && target.getParentBatch().getChildBatchs() != null) {
+                    short maxRankOrder = 0;
+                    for (Batch batch : target.getParentBatch().getChildBatchs()) {
+                        Short r = batch.getRankOrder();
+                        if (r != null && r > maxRankOrder) {
+                            maxRankOrder = r;
+                        }
+                    }
+                    rankOrder += maxRankOrder;
+                }
+
+                target.setRankOrder(rankOrder);
+            }
+        }
+
+        // --- Force subgroup count to '1', as Allegro --- //
+        target.setSubgroupCount(1f);
+
+        // --- Individual count --- //
+        target.setIndividualCount(source.getNumber());
+
+        // --- Comments --- //
+        target.setComments(source.getComment());
+
+        // --- Exhaustive inventory (always true under a species batch) --- //
+        target.setExhaustiveInventory(true);
+
+        // --- Species --- //
+        {
+            ReferenceTaxon referenceTaxon;
+            if (source.getSpecies() == null || parentBatchId != null) {
+                referenceTaxon = null;
+            } else {
+                referenceTaxon = load(ReferenceTaxonImpl.class, source.getSpecies().getReferenceTaxonId());
+            }
+            target.setReferenceTaxon(referenceTaxon);
+        }
+
+        // --- QualityFlag --- //
+        {
+            String qualityFlag;
+            if (source.isSpeciesToConfirm()) {
+                qualityFlag = QualityFlagCode.DOUBTFUL.getValue();
+            } else {
+                qualityFlag = QualityFlagCode.NOTQUALIFIED.getValue();
+            }
+            target.setQualityFlag(load(QualityFlagImpl.class, qualityFlag));
+        }
+
+        Float weight = source.getWeight();
+        Float sampleCategoryWeight = source.getSampleCategoryWeight();
+
+        // --- Sampling Ratio + QuantificationMeasurement --- //
+        batchTreeHelper.setWeightAndSampleRatio(target, weight, sampleCategoryWeight);
+
+//        // --- QuantificationMeasurement --- //
+//        {
+//            Float weightMeasurement = sampleCategoryWeight;
+//
+//            if (weight != null) {
+//
+//                // on converse toujours les poids le plus fin
+//                weightMeasurement = weight;
+//            }
+//
+////            Float weightMeasurement = null;
+////            if (weight == null && sampleCategoryWeight != null) {
+////                weightMeasurement = sampleCategoryWeight;
+////
+////            } else if (weight != null && sampleCategoryWeight == null) {
+////                weightMeasurement = weight;
+////            }
+////
+////            if (sampleCategoryWeight != null && weight != null) {
+////                weightMeasurement = weight;
+////            }
+//
+//            Collection<QuantificationMeasurement> quantificationMeasurements = target.getQuantificationMeasurements();
+//            Set<QuantificationMeasurement> notChangedQuantificationMeasurements = Sets.newHashSet();
+//            if (quantificationMeasurements != null) {
+//                notChangedQuantificationMeasurements.addAll(quantificationMeasurements);
+//            }
+//
+//            if (weightMeasurement != null) {
+//                QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
+//                        target,
+//                        weightMeasurement);
+//                notChangedQuantificationMeasurements.remove(quantificationMeasurement);
+//            }
+//
+//            if (quantificationMeasurements != null) {
+//                quantificationMeasurements.removeAll(notChangedQuantificationMeasurements);
+//            }
+//        }
+
+        // --- Sorting measurement --- //
+        {
+            Collection<SortingMeasurement> sortingMeasurements = target.getSortingMeasurements();
+            Set<SortingMeasurement> notChangedSortingMeasurements = Sets.newHashSet();
+            if (sortingMeasurements != null) {
+                notChangedSortingMeasurements.addAll(sortingMeasurements);
+            }
+
+            if (source.getSampleCategoryId() != null && source.getSampleCategoryValue() != null) {
+                Integer pmfmId = source.getSampleCategoryId();
+                // Do not store sorting measurement if pmfm = SORTED (already store in an ancestor batch)
+                if (!pmfmId.equals(PmfmId2.SORTED_UNSORTED.getValue())) {
+                    SortingMeasurement sortingMeasurement = measurementPersistenceHelper.setSortingMeasurement(
+                            target,
+                            pmfmId,
+                            source.getSampleCategoryValue());
+                    notChangedSortingMeasurements.remove(sortingMeasurement);
+                }
+            }
+            if (sortingMeasurements != null) {
+                sortingMeasurements.removeAll(notChangedSortingMeasurements);
+            }
+        }
+
+    }
+
+
+    public void beanToEntity(SpeciesAbleBatchFrequency source,
+                             SortingBatch target,
+                             SortingBatch parentBatch,
+                             short rankOrder) {
+        Preconditions.checkNotNull(source.getBatch());
+        Preconditions.checkNotNull(source.getBatch().getId());
+
+        // If parent and root need to be set
+        if (target.getId() == null
+            || target.getRootBatch() == null
+            || (target.getParentBatch() != null && !target.getParentBatch().getId().equals(parentBatch.getId()))) {
+
+            target.setParentBatch(parentBatch);
+            target.setRootBatch(parentBatch.getRootBatch());
+        }
+
+        // --- RankOrder --- //
+        target.setRankOrder(rankOrder);
+
+        // --- Individual count --- //
+        target.setIndividualCount(source.getNumber());
+
+        // --- Species --- //
+        target.setReferenceTaxon(null);
+
+        // --- QualityFlag --- //
+        target.setQualityFlag(parentBatch.getQualityFlag());
+
+        // --- Exhaustive inventory (always true under a species batch) --- //
+        target.setExhaustiveInventory(true);
+
+        // --- Sampling Ratio + QuantificationMeasurement --- //
+        batchTreeHelper.setWeightAndSampleRatio(target, source.getWeight(), null);
+
+        // --- Sorting measurement --- //
+        {
+            Collection<SortingMeasurement> sortingMeasurements = target.getSortingMeasurements();
+            Set<SortingMeasurement> notChangedSortingMeasurements = Sets.newHashSet();
+            if (sortingMeasurements != null) {
+                notChangedSortingMeasurements.addAll(sortingMeasurements);
+            }
+            if ((source.getLengthStepCaracteristic() != null && source.getLengthStep() != null)) {
+                Integer pmfmId = source.getLengthStepCaracteristic().getIdAsInt();
+                SortingMeasurement sortingMeasurement = measurementPersistenceHelper.setSortingMeasurement(target, pmfmId,
+                                                                                                           source.getLengthStep());
+                notChangedSortingMeasurements.remove(sortingMeasurement);
+            }
+            if (sortingMeasurements != null) {
+                sortingMeasurements.removeAll(notChangedSortingMeasurements);
+            }
+        }
+
+    }
+
     public Integer convertSampleCategoryValueIntoQualitativeId(Serializable value) {
         if (value == null) {
             return null;
@@ -632,11 +833,6 @@
     //-- Internal methods                                                   --//
     //------------------------------------------------------------------------//
 
-    protected Integer getRecorderDepartmentId() {
-        // TODO BL : voir si on peut récupérer le departement (du 1er saisisseur ?)
-        return DepartmentId.UNKOWN_RECODER_DEPARTMENT.getValue();
-    }
-
     /**
      * Check if the given {@code sortingBatch} is a frequency one.
      * <p/>
@@ -665,124 +861,4 @@
         return result;
     }
 
-//    protected SortingBatch getOrCreate(fr.ifremer.adagio.core.dao.data.batch.CatchBatch target,
-//                                       Batch batch,
-//                                       Integer pmfmId,
-//                                       Integer pmfmValue,
-//                                       Float totalWeight,
-//                                       short rankOrder) {
-//        return getOrCreate(
-//                target,
-//                batch,
-//                pmfmId,
-//                pmfmValue,
-//                totalWeight,
-//                null,
-//                rankOrder
-//        );
-//    }
-
-//    protected SortingBatch getOrCreate(fr.ifremer.adagio.core.dao.data.batch.CatchBatch rootBatch,
-//                                       Batch parentBatch,
-//                                       Integer sortingPmfmId,
-//                                       Integer sortingQualitativeValueId,
-//                                       Float weight,
-//                                       Float weightBeforeSampling,
-//                                       short rankOrder) {
-//        SortingBatch result = batchTreeHelper.get(
-//                parentBatch,
-//                sortingPmfmId,
-//                sortingQualitativeValueId);
-//
-//        if (result == null) {
-//
-//            result = SortingBatch.Factory.newInstance();
-//            if (parentBatch.getChildBatchs() == null) {
-//                parentBatch.setChildBatchs(Sets.<Batch>newHashSet());
-//            }
-//            parentBatch.getChildBatchs().add(result);
-//
-//            Collection<SortingMeasurement> sortingMeasurements = result.getSortingMeasurements();
-//
-//            // Create lists to store all updates, then remove not updated items
-//            Set<SortingMeasurement> notChangedSortingMeasurements = Sets.newHashSet();
-//            if (sortingMeasurements != null) {
-//                notChangedSortingMeasurements.addAll(sortingMeasurements);
-//            }
-//
-//            // Some mandatory properties :
-//            QualityFlagImpl qualityFlag = load(QualityFlagImpl.class, enumeration.QUALITY_FLAG_CODE_NOT_QUALIFIED);
-//            result.setQualityFlag(qualityFlag);
-//            result.setRootBatch(rootBatch);
-//            result.setParentBatch(parentBatch);
-//            result.setExhaustiveInventory(true);
-//
-//            // No taxon or taxon group
-//            result.setReferenceTaxon(null);
-//            result.setTaxonGroup(null);
-//
-//            result.setRankOrder(rankOrder);
-//
-//            // Sorting measurement
-//            if (sortingPmfmId != null && sortingQualitativeValueId != null) {
-//                SortingMeasurement sm = setSortingMeasurement(
-//                        result,
-//                        sortingPmfmId,
-//                        sortingQualitativeValueId);
-//                notChangedSortingMeasurements.remove(sm);
-//            }
-//            // Removed not changed sorting measurements
-//            if (sortingMeasurements != null) {
-//                sortingMeasurements.removeAll(notChangedSortingMeasurements);
-//            }
-//
-//            catchBatchDao.createSortingBatch(result, rootBatch);
-//        }
-//
-//        Collection<QuantificationMeasurement> quantificationMeasurements = result.getQuantificationMeasurements();
-//        Set<QuantificationMeasurement> notChangedQuantificationMeasurements = Sets.newHashSet();
-//        if (quantificationMeasurements != null) {
-//            notChangedQuantificationMeasurements.addAll(quantificationMeasurements);
-//        }
-//
-//        // Sampling Ratio
-//        if (weightBeforeSampling == null || weight == null) {
-//            result.setSamplingRatio(null);
-//            result.setSamplingRatioText(null);
-//        } else {
-//            String samplingRatioText = weight + "/" + weightBeforeSampling;
-//            samplingRatioText = samplingRatioText.replaceAll(",", ".");
-//            result.setSamplingRatioText(samplingRatioText);
-//            result.setSamplingRatio(weight / weightBeforeSampling);
-//        }
-//
-//        // Weight
-//        if (weightBeforeSampling != null || weight != null) {
-//            Float batchReferenceWeight = weight;
-//            if (batchReferenceWeight == null) {
-//                batchReferenceWeight = weightBeforeSampling;
-//            }
-//            QuantificationMeasurement quantificationMeasurement = setWeightMeasurementQuantificationMeasurement(
-//                    result,
-//                    batchReferenceWeight);
-//            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
-//        }
-//        // Removed not changed quantification measurements
-//        if (quantificationMeasurements != null) {
-//            quantificationMeasurements.removeAll(notChangedQuantificationMeasurements);
-//        }
-//
-//        return result;
-//    }
-
-//    protected SortingBatch get(Batch parentBatch,
-//                               Integer sortingPmfmId,
-//                               Integer sortingQualitativeValueId) {
-//        SortingBatch result = getSortingBatch(
-//                parentBatch,
-//                null,
-//                sortingPmfmId,
-//                sortingQualitativeValueId);
-//        return result;
-//    }
 }

Modified: trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/util/BatchTreeHelper.java
===================================================================
--- trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/util/BatchTreeHelper.java	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/util/BatchTreeHelper.java	2014-05-28 15:35:16 UTC (rev 1818)
@@ -1,5 +1,27 @@
 package fr.ifremer.tutti.persistence.service.util;
 
+/*
+ * #%L
+ * Tutti :: Persistence
+ * %%
+ * Copyright (C) 2012 - 2014 Ifremer
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU 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 General Public
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-3.0.html>.
+ * #L%
+ */
+
 import com.google.common.base.Joiner;
 import com.google.common.collect.Sets;
 import fr.ifremer.adagio.core.dao.data.batch.Batch;
@@ -310,7 +332,6 @@
                 "Vrac > Benthos > Alive Itemized",
                 SORTING_TYPE2_ID,
                 QualitativeValueId.SORTING_TYPE2_ALIVE_ITEMIZED.getValue(),
-                null,
                 (short) 3
         );
     }
@@ -365,7 +386,6 @@
                 "Vrac > Benthos > Alive Itemized",
                 SORTING_TYPE2_ID,
                 QualitativeValueId.SORTING_TYPE2_ALIVE_ITEMIZED.getValue(),
-                null,
                 (short) 3
         );
     }
@@ -377,7 +397,6 @@
                 "Hors Vrac",
                 PmfmId2.SORTED_UNSORTED.getValue(),
                 QualitativeValueId.SORTED_HORS_VRAC.getValue(),
-                null,
                 (short) 2
         );
     }
@@ -390,7 +409,6 @@
                 "Hors Vrac > Species",
                 SORTING_TYPE_ID,
                 QualitativeValueId.SORTING_TYPE_SPECIES.getValue(),
-                null,
                 (short) 1
         );
     }
@@ -403,7 +421,6 @@
                 "Hors Vrac > Benthos",
                 SORTING_TYPE_ID,
                 QualitativeValueId.SORTING_TYPE_BENTHOS.getValue(),
-                null,
                 (short) 2
         );
     }
@@ -436,6 +453,24 @@
         );
     }
 
+    public void setWeightAndSampleRatio(SortingBatch target, Float weight, Float weightBeforeSampling) {
+
+        catchBatchDao.setSortingBatchWeights(target,
+                                             weight,
+                                             weightBeforeSampling,
+                                             PmfmId2.WEIGHT_MEASURED.getValue(),
+                                             measurementPersistenceHelper.getRecorderDepartmentId());
+
+    }
+
+    public void setSortingSamplingRatio(SortingBatch target, Float weight, Float weightBeforeSampling) {
+
+        catchBatchDao.setSortingSamplingRatio(target,
+                                             weight,
+                                             weightBeforeSampling);
+
+    }
+
     //------------------------------------------------------------------------//
     //-- Internal methods                                                   --//
     //------------------------------------------------------------------------//
@@ -484,6 +519,24 @@
                                        String debugMessage,
                                        Integer sortingPmfmId,
                                        Integer sortingQualitativeValueId,
+                                       short rankOrder) {
+        return getOrCreate(
+                rootBatch,
+                batch,
+                debugMessage,
+                sortingPmfmId,
+                sortingQualitativeValueId,
+                null,
+                null,
+                rankOrder
+        );
+    }
+
+    protected SortingBatch getOrCreate(fr.ifremer.adagio.core.dao.data.batch.CatchBatch rootBatch,
+                                       Batch batch,
+                                       String debugMessage,
+                                       Integer sortingPmfmId,
+                                       Integer sortingQualitativeValueId,
                                        Float totalWeight,
                                        short rankOrder) {
         return getOrCreate(
@@ -506,6 +559,7 @@
                                        Float weight,
                                        Float weightBeforeSampling,
                                        short rankOrder) {
+
         SortingBatch result = getSortingBatch(
                 batch,
                 debugMessage,
@@ -520,28 +574,27 @@
             }
             batch.getChildBatchs().add(result);
 
-            Collection<SortingMeasurement> sortingMeasurements = result.getSortingMeasurements();
+            // --- Some mandatory properties --- //
 
-            // Create lists to store all updates, then remove not updated items
-            Set<SortingMeasurement> notChangedSortingMeasurements = Sets.newHashSet();
-            if (sortingMeasurements != null) {
-                notChangedSortingMeasurements.addAll(sortingMeasurements);
-            }
-
-            // Some mandatory properties :
             QualityFlagImpl qualityFlag = load(QualityFlagImpl.class, QualityFlagCode.NOTQUALIFIED.getValue());
             result.setQualityFlag(qualityFlag);
             result.setRootBatch(rootBatch);
             result.setParentBatch(batch);
             result.setExhaustiveInventory(true);
+            result.setRankOrder(rankOrder);
 
             // No taxon or taxon group
             result.setReferenceTaxon(null);
             result.setTaxonGroup(null);
 
-            result.setRankOrder(rankOrder);
+            // --- Sorting measurement --- //
 
-            // Sorting measurement
+            Collection<SortingMeasurement> sortingMeasurements = result.getSortingMeasurements();
+            Set<SortingMeasurement> notChangedSortingMeasurements = Sets.newHashSet();
+            if (sortingMeasurements != null) {
+                notChangedSortingMeasurements.addAll(sortingMeasurements);
+            }
+
             if (sortingPmfmId != null && sortingQualitativeValueId != null) {
                 SortingMeasurement sm = measurementPersistenceHelper.setSortingMeasurement(
                         result,
@@ -549,7 +602,6 @@
                         sortingQualitativeValueId);
                 notChangedSortingMeasurements.remove(sm);
             }
-            // Removed not changed sorting measurements
             if (sortingMeasurements != null) {
                 sortingMeasurements.removeAll(notChangedSortingMeasurements);
             }
@@ -557,38 +609,43 @@
             catchBatchDao.createSortingBatch(result, rootBatch);
         }
 
-        Collection<QuantificationMeasurement> quantificationMeasurements = result.getQuantificationMeasurements();
-        Set<QuantificationMeasurement> notChangedQuantificationMeasurements = Sets.newHashSet();
-        if (quantificationMeasurements != null) {
-            notChangedQuantificationMeasurements.addAll(quantificationMeasurements);
-        }
+        // --- Sampling Ratio + QuantificationMeasurement --- //
 
-        // Sampling Ratio
-        if (weightBeforeSampling == null || weight == null) {
-            result.setSamplingRatio(null);
-            result.setSamplingRatioText(null);
-        } else {
-            String samplingRatioText = weight + "/" + weightBeforeSampling;
-            samplingRatioText = samplingRatioText.replaceAll(",", ".");
-            result.setSamplingRatioText(samplingRatioText);
-            result.setSamplingRatio(weight / weightBeforeSampling);
-        }
+        setWeightAndSampleRatio(result, weight, weightBeforeSampling);
 
-        // Weight
-        if (weightBeforeSampling != null || weight != null) {
-            Float batchReferenceWeight = weight;
-            if (batchReferenceWeight == null) {
-                batchReferenceWeight = weightBeforeSampling;
-            }
-            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
-                    result,
-                    batchReferenceWeight);
-            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
-        }
-        // Removed not changed quantification measurements
-        if (quantificationMeasurements != null) {
-            quantificationMeasurements.removeAll(notChangedQuantificationMeasurements);
-        }
+//        // --- QuantificationMeasurement --- //
+//
+//        Collection<QuantificationMeasurement> quantificationMeasurements = result.getQuantificationMeasurements();
+//        Set<QuantificationMeasurement> notChangedQuantificationMeasurements = Sets.newHashSet();
+//        if (quantificationMeasurements != null) {
+//            notChangedQuantificationMeasurements.addAll(quantificationMeasurements);
+//        }
+//
+//        Float batchReferenceWeight = weightBeforeSampling;
+//        if (weight != null) {
+//            batchReferenceWeight = weight;
+//        }
+//
+//        if (batchReferenceWeight != null) {
+//            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
+//                    result,
+//                    batchReferenceWeight);
+//            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
+//        }
+//
+////        if (weightBeforeSampling != null || weight != null) {
+////            Float batchReferenceWeight = weight;
+////            if (batchReferenceWeight == null) {
+////                batchReferenceWeight = weightBeforeSampling;
+////            }
+////            QuantificationMeasurement quantificationMeasurement = measurementPersistenceHelper.setWeightMeasurementQuantificationMeasurement(
+////                    result,
+////                    batchReferenceWeight);
+////            notChangedQuantificationMeasurements.remove(quantificationMeasurement);
+////        }
+//        if (quantificationMeasurements != null) {
+//            quantificationMeasurements.removeAll(notChangedQuantificationMeasurements);
+//        }
 
         return result;
     }
@@ -675,7 +732,11 @@
         }
     }
 
+    public CatchBatch loadCatchBatch(Integer catchBatchId) {
+        return catchBatchDao.loadFullTreeWithCache(catchBatchId, PmfmId2.WEIGHT_MEASURED.getValue(), true, true);
+    }
 
+
     static final class BatchTreeToStringStyle extends ToStringStyle {
 
         private static final long serialVersionUID = 1L;

Modified: trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/util/MeasurementPersistenceHelper.java
===================================================================
--- trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/util/MeasurementPersistenceHelper.java	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/service/util/MeasurementPersistenceHelper.java	2014-05-28 15:35:16 UTC (rev 1818)
@@ -53,6 +53,8 @@
 
 import javax.annotation.Resource;
 import java.io.Serializable;
+import java.util.Collection;
+import java.util.Set;
 
 /**
  * Helper around {@link Measurement}.
@@ -117,11 +119,25 @@
     }
 
     public QuantificationMeasurement setWeightMeasurementQuantificationMeasurement(Batch batch, Float weightValue) {
-        return catchBatchDao.setQuantificationMeasurement(batch, PmfmId2.WEIGHT_MEASURED.getValue(), getRecorderDepartmentId(), weightValue, true);
+
+        Collection<QuantificationMeasurement> quantificationMeasurements = batch.getQuantificationMeasurements();
+        Set<QuantificationMeasurement> notChangedQuantificationMeasurements = Sets.newHashSet();
+        if (quantificationMeasurements != null) {
+            notChangedQuantificationMeasurements.addAll(quantificationMeasurements);
+        }
+
+        QuantificationMeasurement quantificationMeasurement = catchBatchDao.setQuantificationMeasurement(batch, PmfmId2.WEIGHT_MEASURED.getValue(), getRecorderDepartmentId(), weightValue, true);
+
+        // Removed not changed measurements (in sorting and quantification measurement lists)
+        if (quantificationMeasurements != null) {
+            quantificationMeasurements.removeAll(notChangedQuantificationMeasurements);
+        }
+
+        return quantificationMeasurement;
     }
 
     public QuantificationMeasurement getWeightMeasurementQuantificationMeasurement(Batch batch) {
-        QuantificationMeasurement quantificationMeasurement = catchBatchDao.getQuantificationMeasurement(batch, PmfmId2.WEIGHT_MEASURED.getValue(), getRecorderDepartmentId(), false);
+        QuantificationMeasurement quantificationMeasurement = catchBatchDao.getQuantificationMeasurement(batch, PmfmId2.WEIGHT_MEASURED.getValue());
         return quantificationMeasurement;
     }
 
@@ -283,7 +299,7 @@
         } else if (measurement.getAlphanumericalValue() != null) {
             value = measurement.getAlphanumericalValue();
         }
-        return pmfm.getParameter().getName() + " (" + pmfm.getId() + ") / " + value;
+        return "[id:" + measurement.getId() + "] - " + pmfm.getParameter().getName() + " (" + pmfm.getId() + ") / " + value;
     }
 
     //------------------------------------------------------------------------//
@@ -368,7 +384,7 @@
         return result;
     }
 
-    protected Integer getRecorderDepartmentId() {
+    public Integer getRecorderDepartmentId() {
         // TODO BL : voir si on peut récupérer le departement (du 1er saisisseur ?)
         return DepartmentId.UNKOWN_RECODER_DEPARTMENT.getValue();
     }

Modified: trunk/tutti-persistence/src/main/resources/queries-failsafe.hbm.xml
===================================================================
--- trunk/tutti-persistence/src/main/resources/queries-failsafe.hbm.xml	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-persistence/src/main/resources/queries-failsafe.hbm.xml	2014-05-28 15:35:16 UTC (rev 1818)
@@ -432,6 +432,16 @@
     <query-param name="catchBatchId" type="java.lang.Integer"/>
   </query>
 
+  <query cacheable="true" name="updateQuantificationMeasurementsForBatchNodes">
+    <![CDATA[
+    UPDATE QuantificationMeasurementImpl qm
+    SET isReferenceQuantification = false
+	  WHERE qm.id IN (:ids)
+    ]]>
+    <query-param name="ids" type="java.lang.List"/>
+  </query>
+
+
   <query cacheable="true" name="allFishingOperationSamplesWithoutBatch">
     <![CDATA[
     SELECT
@@ -484,7 +494,7 @@
     <query-param name="sampleId" type="java.lang.Integer"/>
   </query>
 
-  <query cacheable="true" name="catchBatch">
+  <!--query cacheable="true" name="catchBatch">
     <![CDATA[
     SELECT 
       cb.id AS catchBatchId,
@@ -513,7 +523,7 @@
     <query-param name="fishingOperationId" type="java.lang.Integer"/>
     <query-param name="pmfmIdSorted" type="java.lang.Integer"/>
     <query-param name="pmfmIdSortingType" type="java.lang.Integer"/>
-  </query>
+  </query-->
 
   <query cacheable="true" name="allSpeciesBatchFrequency">
     <![CDATA[

Modified: trunk/tutti-persistence/src/main/xmi/tutti-persistence.zargo
===================================================================
(Binary files differ)

Modified: trunk/tutti-service/src/main/java/fr/ifremer/tutti/service/PersistenceService.java
===================================================================
--- trunk/tutti-service/src/main/java/fr/ifremer/tutti/service/PersistenceService.java	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-service/src/main/java/fr/ifremer/tutti/service/PersistenceService.java	2014-05-28 15:35:16 UTC (rev 1818)
@@ -1202,6 +1202,11 @@
         driver.deleteCatchBatch(fishingOperationId);
     }
 
+    @Override
+    public void recomputeCatchBatchSampleRatios(String fishingOperationId) {
+        driver.recomputeCatchBatchSampleRatios(fishingOperationId);
+    }
+
     //------------------------------------------------------------------------//
     //-- Species Batch methods                                              --//
     //------------------------------------------------------------------------//

Modified: trunk/tutti-ui-swing/src/license/THIRD-PARTY.properties
===================================================================
--- trunk/tutti-ui-swing/src/license/THIRD-PARTY.properties	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-ui-swing/src/license/THIRD-PARTY.properties	2014-05-28 15:35:16 UTC (rev 1818)
@@ -39,7 +39,7 @@
 # Please fill the missing licenses for dependencies :
 #
 #
-#Thu Apr 24 15:55:59 CEST 2014
+#Tue May 27 17:05:30 CEST 2014
 batik--batik-awt-util--1.6=The Apache Software License, Version 2.0
 batik--batik-bridge--1.6=The Apache Software License, Version 2.0
 batik--batik-css--1.6=The Apache Software License, Version 2.0
@@ -55,3 +55,4 @@
 batik--batik-xml--1.6=The Apache Software License, Version 2.0
 commons-primitives--commons-primitives--1.0=The Apache Software License, Version 2.0
 dom4j--dom4j--1.6.1=BSD License
+org.hibernate--hibernate-spatial--4.3-20140213=Lesser General Public License (LGPL)

Modified: trunk/tutti-ui-swing/src/main/filtered-resources/log4j.properties
===================================================================
--- trunk/tutti-ui-swing/src/main/filtered-resources/log4j.properties	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-ui-swing/src/main/filtered-resources/log4j.properties	2014-05-28 15:35:16 UTC (rev 1818)
@@ -36,6 +36,7 @@
 #See https://forum.hibernate.org/viewtopic.php?p=2404391
 log4j.logger.org.hibernate.engine.StatefulPersistenceContext.ProxyWarnLog=ERROR
 log4j.logger.fr.ifremer.adagio.core.service.technical.synchro=DEBUG
+log4j.logger.fr.ifremer.tutti.persistence.service.CatchBatchPersistenceServiceImpl=DEBUG
 
 log4j.appender.file=org.apache.log4j.RollingFileAppender
 log4j.appender.file.file=${tutti.log.file}

Modified: trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action/ComputeBatchWeightsAction.java
===================================================================
--- trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action/ComputeBatchWeightsAction.java	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action/ComputeBatchWeightsAction.java	2014-05-28 15:35:16 UTC (rev 1818)
@@ -243,6 +243,8 @@
             }
         }
 
+//        persistenceService.recomputeCatchBatchSampleRatios(operationId);
+
         boolean modified = model.isModify();
         CatchBatch catchBatch = model.toEntity();
         weightComputingService.computeCatchBatchWeights(catchBatch,

Modified: trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action/SaveCruiseToReadyToSynchAction.java
===================================================================
--- trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action/SaveCruiseToReadyToSynchAction.java	2014-05-23 07:57:44 UTC (rev 1817)
+++ trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action/SaveCruiseToReadyToSynchAction.java	2014-05-28 15:35:16 UTC (rev 1818)
@@ -23,6 +23,7 @@
  */
 
 import com.google.common.base.Preconditions;
+import fr.ifremer.tutti.persistence.ProgressionModel;
 import fr.ifremer.tutti.service.PersistenceService;
 import fr.ifremer.tutti.ui.swing.content.cruise.ValidateCruiseUI;
 import fr.ifremer.tutti.ui.swing.content.cruise.ValidateCruiseUIHandler;
@@ -31,6 +32,7 @@
 import org.apache.commons.logging.LogFactory;
 
 import javax.swing.JOptionPane;
+import java.util.List;
 
 import static org.nuiton.i18n.I18n.t;
 
@@ -60,6 +62,11 @@
                                                        JOptionPane.YES_NO_OPTION);
             doAction = answer == JOptionPane.YES_OPTION;
         }
+
+        PersistenceService persistenceService = getContext().getPersistenceService();
+        int fishingOperationCount = persistenceService.getFishingOperationCount(getModel().getCruise().getId());
+        createProgressionModelIfRequired(fishingOperationCount + 1);
+        
         return doAction;
     }
 
@@ -70,12 +77,31 @@
         Preconditions.checkState(getContext().isCruiseFilled());
 
         PersistenceService persistenceService = getContext().getPersistenceService();
+
+        ProgressionModel progressionModel = getProgressionModel();
+
+        List<String> allFishingOperation = persistenceService.getAllFishingOperationIds(getModel().getCruise().getId());
+
+        for (String fishingOperationId : allFishingOperation) {
+
+            if (log.isInfoEnabled()) {
+                log.info("Recompute sample ratios for operation " + fishingOperationId);
+            }
+            persistenceService.recomputeCatchBatchSampleRatios(fishingOperationId);
+
+            progressionModel.increments("Recalcul des poids référents pour l'opération " + fishingOperationId);
+        }
+
         Integer cruiseId = getModel().getCruise().getIdAsInt();
 
         if (log.isInfoEnabled()) {
             log.info("Pass synchronizationStatus to *ready to synch* for cruise: " + cruiseId);
         }
+
+        progressionModel.increments("Mise en place des données synchronisables");
+
         persistenceService.setCruiseReadyToSynch(cruiseId);
+
     }
 
     @Override
@@ -84,7 +110,7 @@
 
         // reload cruise in data context
         getDataContext().reloadCruise();
-        
+
         // reload it in our model
         getModel().setCruise(getDataContext().getCruise());
     }

    

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