[Echobase-commits] r199 - in trunk: echobase-entities/src/main/java/fr/ifremer/echobase echobase-entities/src/main/resources/i18n echobase-entities/src/main/xmi echobase-tools echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders src/doc/reunions

16 Dec 2011

Author: tchemit
Date: 2011-12-16 18:54:16 +0100 (Fri, 16 Dec 2011)
New Revision: 199

Url: http://forge.codelutin.com/repositories/revision/echobase/199

Log:
- fix test resources
- continue Catches legacy datas import


Modified:
   trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseFunctions.java
   trunk/echobase-entities/src/main/resources/i18n/echobase-entities_fr_FR.properties
   trunk/echobase-entities/src/main/xmi/echobase.zargo
   trunk/echobase-tools/pom.xml
   trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoader.java
   trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/OperationLoader.java
   trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SampleLoader.java
   trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SampleLoaderIT.java
   trunk/src/doc/reunions/reunion-2011-12-14.txt

Modified: trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseFunctions.java
===================================================================

--- trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseFunctions.java	2011-12-16 01:46:20 UTC (rev 198)
+++ trunk/echobase-entities/src/main/java/fr/ifremer/echobase/EchoBaseFunctions.java	2011-12-16 17:54:16 UTC (rev 199)
@@ -45,7 +45,6 @@
 import org.apache.commons.lang3.StringUtils;
 import org.nuiton.topia.persistence.TopiaEntity;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.Map;
 
@@ -165,7 +164,7 @@
             return input.getName();
         }
     };
-    public static final Function<SampleDataType, String> SAMPLE_DATA_TYPE_RAPRI_CODE = new Function<SampleDataType, String>() {
+    public static final Function<SampleDataType, String> SAMPLE_DATA_TYPE_RAPTRI_CODE = new Function<SampleDataType, String>() {
         @Override
         public String apply(SampleDataType input) {
             return String.valueOf(input.getRaptriBiometryDataType());
@@ -186,6 +185,7 @@
             return StringUtils.isEmpty(casinoGearName) ? input.getName() : casinoGearName;
         }
     };
+
     public static final Function<Operation, String> OPERATION_ID = new Function<Operation, String>() {
         @Override
         public String apply(Operation input) {

Modified: trunk/echobase-entities/src/main/resources/i18n/echobase-entities_fr_FR.properties
===================================================================
--- trunk/echobase-entities/src/main/resources/i18n/echobase-entities_fr_FR.properties	2011-12-16 01:46:20 UTC (rev 198)
+++ trunk/echobase-entities/src/main/resources/i18n/echobase-entities_fr_FR.properties	2011-12-16 17:54:16 UTC (rev 199)
@@ -138,6 +138,8 @@
 echobase.common.metadata=metadata
 echobase.common.metadataGroup=
 echobase.common.metadataType=
+echobase.common.midHauleLatitude=
+echobase.common.midHauleLongitude=
 echobase.common.minLatitude=
 echobase.common.minLongitude=
 echobase.common.mission=mission

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

Modified: trunk/echobase-tools/pom.xml
===================================================================
--- trunk/echobase-tools/pom.xml	2011-12-16 01:46:20 UTC (rev 198)
+++ trunk/echobase-tools/pom.xml	2011-12-16 17:54:16 UTC (rev 199)
@@ -205,6 +205,12 @@
               <include>**/*.csv</include>
             </includes>
           </testResource>
+          <testResource>
+            <directory>src/test/resources</directory>
+            <includes>
+              <include>**/*.properties</include>
+            </includes>
+          </testResource>
         </testResources>
       </build>
     </profile>

Modified: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoader.java
===================================================================
--- trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoader.java	2011-12-16 01:46:20 UTC (rev 198)
+++ trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/BiometryScaleLoader.java	2011-12-16 17:54:16 UTC (rev 199)
@@ -58,7 +58,7 @@
         /*
         raptriBiometryDataType;ScaleCode;ScaleMeaningEng;ScaleMeaningFr
          */
-        model.addForeignKeyForImport("raptriBiometryDataType", BiometryScale.PROPERTY_SAMPLE_DATA_TYPE, SampleDataType.class, sampleDataTypes, EchoBaseFunctions.SAMPLE_DATA_TYPE_RAPRI_CODE);
+        model.addForeignKeyForImport("raptriBiometryDataType", BiometryScale.PROPERTY_SAMPLE_DATA_TYPE, SampleDataType.class, sampleDataTypes, EchoBaseFunctions.SAMPLE_DATA_TYPE_RAPTRI_CODE);
         model.addDefaultColumn("ScaleCode",BiometryScale.PROPERTY_CODE, int.class);
         model.newMandatoryColumn("ScaleMeaningEng",BiometryScale.PROPERTY_MEANING_EN);
         model.newMandatoryColumn("ScaleMeaningFr",BiometryScale.PROPERTY_MEANING_FR);

Modified: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/OperationLoader.java
===================================================================
--- trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/OperationLoader.java	2011-12-16 01:46:20 UTC (rev 198)
+++ trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/OperationLoader.java	2011-12-16 17:54:16 UTC (rev 199)
@@ -119,40 +119,63 @@
 
         copyAndLoadEntities(outputDir, meta.getAssociations(Operation.PROPERTY_OPERATION_METADATA_VALUE), false, FileType.ASSOCIATION);
         copyAndLoadEntities(outputDir, meta.getAssociations(Operation.PROPERTY_GEAR_METADATA_VALUE), false, FileType.ASSOCIATION);
-
     }
 
+    //SONDE
+    OperationMetadata MeanWaterDepthOperationMeta;
+    //JOUR_NUIT
+    OperationMetadata DielPeriodOperationMeta;
+    //SONDEDEB
+    OperationMetadata StartWaterDepthOperationMeta;
+    //SONDEFIN
+    OperationMetadata EndWaterDepthOperationMeta;
+
+    //LFUNES
+    GearMetadata CableLengthGearMeta;
+    //VMIN
+    GearMetadata MinSpeedGearMeta;
+    //VMAX
+    GearMetadata MaxSpeedGearMeta;
+
+    TopiaDAO<Operation> dao;
+    TopiaDAO<OperationMetadataValue> operationMetadataValueDAO;
+    TopiaDAO<GearMetadataValue> gearMetadataValueDAO;
+
+    Map<String, DepthStratum> depthStratumByName;
+    Map<String, Gear> gearByCasinoGearName;
+
     @Override
-    protected void importBaracoudaEntities(Database db) throws IOException, TopiaException {
+    protected void importBaracoudaEntities(Database db) throws
+            IOException, TopiaException {
 
         Map<String, Voyage> voyagesByName = getUniverse(
                 Voyage.class, EchoBaseFunctions.VOYAGE_NAME);
 
-        Map<String, DepthStratum> depthStratumByName = getUniverse(
+        depthStratumByName = getUniverse(
                 DepthStratum.class, EchoBaseFunctions.DEPTH_STRATUM_ID);
 
-        Map<String, Gear> gearByCasinoGearName = getUniverse(
+        gearByCasinoGearName = getUniverse(
                 Gear.class, EchoBaseFunctions.GEAR_CASINO_GEAR_NAME);
 
         OperationMetadataDAO operationMetadataDAO =
                 (OperationMetadataDAO) getDAO(OperationMetadata.class);
 
         //SONDE
-        OperationMetadata MeanWaterDepthOperationMeta =
+        MeanWaterDepthOperationMeta =
                 operationMetadataDAO.findByName("MeanWaterDepth");
         Preconditions.checkNotNull(MeanWaterDepthOperationMeta);
         //JOUR_NUIT
-        OperationMetadata DielPeriodOperationMeta =
+        DielPeriodOperationMeta =
                 operationMetadataDAO.findByName("DielPeriod");
         Preconditions.checkNotNull(DielPeriodOperationMeta);
         //SONDEDEB
-        OperationMetadata StartWaterDepthOperationMeta = operationMetadataDAO.findByProperties(
+        StartWaterDepthOperationMeta = operationMetadataDAO.findByProperties(
                 OperationMetadata.PROPERTY_NAME, "WaterDepth",
                 OperationMetadata.PROPERTY_OPERATION_EVENT + "." + OperationEvent.PROPERTY_NAME, "ShootingStart"
         );
         Preconditions.checkNotNull(StartWaterDepthOperationMeta);
         //SONDEFIN
-        OperationMetadata EndWaterDepthOperationMeta = operationMetadataDAO.findByProperties(
+        EndWaterDepthOperationMeta = operationMetadataDAO.findByProperties(
                 OperationMetadata.PROPERTY_NAME, "WaterDepth",
                 OperationMetadata.PROPERTY_OPERATION_EVENT + "." + OperationEvent.PROPERTY_NAME, "HaulingEnd"
         );
@@ -162,24 +185,19 @@
                 (GearMetadataDAO) getDAO(GearMetadata.class);
 
         //LFUNES
-        GearMetadata CableLengthGearMeta = gearMetadataDAO.findByType("CableLength");
+        CableLengthGearMeta = gearMetadataDAO.findByType("CableLength");
         Preconditions.checkNotNull(CableLengthGearMeta);
-
         //VMIN
-        GearMetadata MinSpeedGearMeta = gearMetadataDAO.findByType("MinSpeed");
+        MinSpeedGearMeta = gearMetadataDAO.findByType("MinSpeed");
         Preconditions.checkNotNull(MinSpeedGearMeta);
-
         //VMAX
-        GearMetadata MaxSpeedGearMeta = gearMetadataDAO.findByType("MaxSpeed");
+        MaxSpeedGearMeta = gearMetadataDAO.findByType("MaxSpeed");
         Preconditions.checkNotNull(MaxSpeedGearMeta);
 
-        TopiaDAO<Operation> dao = getDAO();
-        TopiaDAO<OperationMetadataValue> operationMetadataValueDAO =
-                getDAO(OperationMetadataValue.class);
+        dao = getDAO();
+        operationMetadataValueDAO = getDAO(OperationMetadataValue.class);
+        gearMetadataValueDAO = getDAO(GearMetadataValue.class);
 
-        TopiaDAO<GearMetadataValue> gearMetadataValueDAO =
-                getDAO(GearMetadataValue.class);
-
         Multimap<String, Map<String, Object>> stationByCampagneName = Multimaps.index(
                 db.getTable("STATIONS"), EchoBaseFunctions.newRowFunction("CAMPAGNE"));
 
@@ -196,142 +214,169 @@
             Preconditions.checkNotNull(transect);
             Collection<Map<String, Object>> rows =
                     stationByCampagneName.get(voyageName);
+
             for (Map<String, Object> row : rows) {
 
-                String status = (String) row.get("ETAT");
-                if ("FICTIF".equalsIgnoreCase(status)) {
+                Operation operation = addOperation(row, messages);
+                if (operation != null) {
+                    operations.add(operation);
+                    transect.addOperation(operation);
 
-                    // skip fictif operation
-                    continue;
-                }
-                String operationId = (String) row.get("NOSTA");
+                    if (!messages.isEmpty()) {
 
-                DepthStratum depthStratum = null;
-                String depthStratumId = (String) row.get("STA_IMAGES");
-                if (StringUtils.isBlank(depthStratumId) ||
-                        "nul".equals(depthStratumId)) {
-                    messages.add("No depthStraum defined");
-                } else {
-                    depthStratum = getFK(depthStratumByName, depthStratumId.trim());
+                        if (log.isWarnEnabled()) {
+                            log.warn("For operation " + operation.getId() + " : " + messages);
+                        }
+                        messages.clear();
+                    }
                 }
+            }
+        }
 
-                String gearId = (String) row.get("ENGIN");
-                if (gearId == null) {
-                    messages.add("No gear id");
-                } else {
-                    Gear gear = getFK(gearByCasinoGearName, gearId);
+        if (log.isInfoEnabled()) {
+            log.info("Found " + operations.size() + " operation(s).");
+        }
+    }
 
-                    Float shootingStartLatitude = (Float) row.get("LATDEB");
-                    if (shootingStartLatitude == null) {
-                        messages.add("No shootingStartLatitude");
-                        shootingStartLatitude = 0f;
-                    }
-                    Float shootingEndLatitude = (Float) row.get("LATDD");
-                    if (shootingEndLatitude == null) {
-                        messages.add("No shootingEndLatitude");
-                        shootingEndLatitude = 0f;
-                    }
-                    Float shootingStartLongitude = (Float) row.get("LGDEB");
-                    if (shootingStartLongitude == null) {
-                        messages.add("No shootingStartLongitude");
-                        shootingStartLongitude = 0f;
-                    }
-                    Float shootingEndLongitude = (Float) row.get("LGDD");
-                    if (shootingEndLongitude == null) {
-                        messages.add("No shootingEndLongitude");
-                        shootingEndLongitude = 0f;
-                    }
+    protected Operation addOperation(Map<String, Object> row,
+                                     List<String> messages) throws TopiaException {
+        String status = (String) row.get("ETAT");
 
-                    Date shootingStartTime = (Date) row.get("DHTUDEB");
-                    Date shootingEndTime = (Date) row.get("DHTUFIN");
+        if ("FICTIF".equalsIgnoreCase(status)) {
 
-                    String comment = (String) row.get("COMMENTAIRE");
+            // skip fictif operation
+            return null;
+        }
 
-                    // create a operation
-                    Operation operation = dao.create(
-                            Operation.PROPERTY_ID, operationId,
-                            Operation.PROPERTY_DEPTH_STRATUM, depthStratum,
-                            Operation.PROPERTY_GEAR, gear,
-                            Operation.PROPERTY_GEAR_SHOOTING_START_LATITUDE, shootingStartLatitude,
-                            Operation.PROPERTY_GEAR_SHOOTING_END_LATITUDE, shootingEndLatitude,
-                            Operation.PROPERTY_GEAR_SHOOTING_START_LONGITUDE, shootingStartLongitude,
-                            Operation.PROPERTY_GEAR_SHOOTING_END_LONGITUDE, shootingEndLongitude,
-                            Operation.PROPERTY_GEAR_SHOOTING_START_TIME, shootingStartTime,
-                            Operation.PROPERTY_GEAR_SHOOTING_END_TIME, shootingEndTime,
-                            Operation.PROPERTY_COMMENT, comment
-                    );
+        String operationId = (String) row.get("NOSTA");
 
-                    addOperationMetadataValue(operationMetadataValueDAO,
-                                              operation,
-                                              MeanWaterDepthOperationMeta,
-                                              row.get("SONDE"));
+        String gearId = (String) row.get("ENGIN");
+        if (gearId == null) {
+            if (log.isWarnEnabled()) {
+                log.warn("No gear id for Operation " + operationId);
+            }
+            return null;
+        }
 
-                    addOperationMetadataValue(operationMetadataValueDAO,
-                                              operation,
-                                              DielPeriodOperationMeta,
-                                              row.get("JOUR_NUIT"));
+        DepthStratum depthStratum = null;
+        String depthStratumId = (String) row.get("STA_IMAGES");
+        if (StringUtils.isBlank(depthStratumId) ||
+                "nul".equals(depthStratumId)) {
+            messages.add("No depthStraum defined");
+        } else {
+            depthStratum = getFK(depthStratumByName, depthStratumId.trim());
+        }
 
-                    addOperationMetadataValue(operationMetadataValueDAO,
-                                              operation,
-                                              StartWaterDepthOperationMeta,
-                                              row.get("SONDEDEB"));
+        Gear gear = getFK(gearByCasinoGearName, gearId);
 
-                    addOperationMetadataValue(operationMetadataValueDAO,
-                                              operation,
-                                              EndWaterDepthOperationMeta,
-                                              row.get("SONDEFIN"));
+        Float shootingStartLatitude = (Float) row.get("LATDEB");
+        if (shootingStartLatitude == null) {
+            messages.add("No shootingStartLatitude");
+        }
 
-                    addGearMetadataValue(gearMetadataValueDAO,
-                                         operation,
-                                         CableLengthGearMeta,
-                                         row.get("LFUNES"));
+        Double doubleValue = (Double) row.get("LATFIN");
+        Float shootingEndLatitude;
+        if (doubleValue == null) {
+            messages.add("No shootingEndLatitude");
+            shootingEndLatitude = null;
+        } else {
+            shootingEndLatitude = doubleValue.floatValue();
+        }
 
-                    addGearMetadataValue(gearMetadataValueDAO,
-                                         operation,
-                                         MinSpeedGearMeta,
-                                         row.get("VMIN"));
+        Float shootingStartLongitude = (Float) row.get("LGDEB");
+        if (shootingStartLongitude == null) {
+            messages.add("No shootingStartLongitude");
+        }
 
-                    addGearMetadataValue(gearMetadataValueDAO,
-                                         operation,
-                                         MaxSpeedGearMeta,
-                                         row.get("VMAX"));
+        doubleValue = (Double) row.get("LGFIN");
+        Float shootingEndLongitude;
+        if (doubleValue == null) {
+            messages.add("No shootingEndLongitude");
+            shootingEndLongitude = null;
+        } else {
+            shootingEndLongitude = doubleValue.floatValue();
+        }
 
-                    operations.add(operation);
-                    transect.addOperation(operation);
+        Float midHauleLatitude = (Float) row.get("LATDD");
+        Preconditions.checkNotNull(midHauleLatitude);
+//                    if (midHauleLatitude == null) {
+//                        messages.add("No midHauleLatitude");
+//                        midHauleLatitude = 0f;
+//                    }
 
-                }
-                if (!messages.isEmpty()) {
+        Float midHauleLongitude = (Float) row.get("LGDD");
+        Preconditions.checkNotNull(midHauleLongitude);
+//                    if (midHauleLongitude== null) {
+//                        messages.add("No midHauleLongitude");
+//                        midHauleLongitude = 0f;
+//                    }
 
-                    if (log.isWarnEnabled()) {
-                        log.warn("For operation " + operationId + ", status " + status + " : " + messages);
-                    }
-                    messages.clear();
-                }
-            }
-        }
+        Date shootingStartTime = (Date) row.get("DHTUDEB");
+        Date shootingEndTime = (Date) row.get("DHTUFIN");
+        String comment = (String) row.get("COMMENTAIRE");
 
-        if (log.isInfoEnabled()) {
-            log.info("Found " + operations.size() + " operation(s).");
-        }
+        // create a operation
+        Operation operation = dao.create(
+                Operation.PROPERTY_ID, operationId,
+                Operation.PROPERTY_DEPTH_STRATUM, depthStratum,
+                Operation.PROPERTY_GEAR, gear,
+                Operation.PROPERTY_GEAR_SHOOTING_START_LATITUDE, shootingStartLatitude,
+                Operation.PROPERTY_GEAR_SHOOTING_END_LATITUDE, shootingEndLatitude,
+                Operation.PROPERTY_GEAR_SHOOTING_START_LONGITUDE, shootingStartLongitude,
+                Operation.PROPERTY_GEAR_SHOOTING_END_LONGITUDE, shootingEndLongitude,
+                Operation.PROPERTY_GEAR_SHOOTING_START_TIME, shootingStartTime,
+                Operation.PROPERTY_GEAR_SHOOTING_END_TIME, shootingEndTime,
+                Operation.PROPERTY_MID_HAULE_LATITUDE, midHauleLatitude,
+                Operation.PROPERTY_MID_HAULE_LONGITUDE, midHauleLongitude,
+                Operation.PROPERTY_COMMENT, comment
+        );
+
+        addOperationMetadataValue(operation,
+                                  MeanWaterDepthOperationMeta,
+                                  row.get("SONDE"));
+
+        addOperationMetadataValue(operation,
+                                  DielPeriodOperationMeta,
+                                  row.get("JOUR_NUIT"));
+
+        addOperationMetadataValue(operation,
+                                  StartWaterDepthOperationMeta,
+                                  row.get("SONDEDEB"));
+
+        addOperationMetadataValue(operation,
+                                  EndWaterDepthOperationMeta,
+                                  row.get("SONDEFIN"));
+
+        addGearMetadataValue(operation,
+                             CableLengthGearMeta,
+                             row.get("LFUNES"));
+
+        addGearMetadataValue(operation,
+                             MinSpeedGearMeta,
+                             row.get("VMIN"));
+
+        addGearMetadataValue(operation,
+                             MaxSpeedGearMeta,
+                             row.get("VMAX"));
+
+        return operation;
     }
 
-    protected void addOperationMetadataValue(TopiaDAO<OperationMetadataValue> dao,
-                                             Operation operation,
+    protected void addOperationMetadataValue(Operation operation,
                                              OperationMetadata meta,
                                              Object value
     ) throws TopiaException {
         if (value == null) {
             return;
         }
-        OperationMetadataValue operationMetadataValue = dao.create(
+        OperationMetadataValue operationMetadataValue = operationMetadataValueDAO.create(
                 OperationMetadataValue.PROPERTY_OPERATION_METADATA, meta,
                 OperationMetadataValue.PROPERTY_DATA_VALUE, value.toString()
         );
         operation.addOperationMetadataValue(operationMetadataValue);
     }
 
-    protected void addGearMetadataValue(TopiaDAO<GearMetadataValue> dao,
-                                        Operation operation,
+    protected void addGearMetadataValue(Operation operation,
                                         GearMetadata meta,
                                         Object value
     ) throws TopiaException {
@@ -339,7 +384,7 @@
         if (value == null) {
             return;
         }
-        GearMetadataValue gearMetadataValue = dao.create(
+        GearMetadataValue gearMetadataValue = gearMetadataValueDAO.create(
                 GearMetadataValue.PROPERTY_GEAR_METADATA, meta,
                 GearMetadataValue.PROPERTY_DATA_VALUE, value.toString(),
                 GearMetadataValue.PROPERTY_GEAR, operation.getGear()

Modified: trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SampleLoader.java
===================================================================
--- trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SampleLoader.java	2011-12-16 01:46:20 UTC (rev 198)
+++ trunk/echobase-tools/src/main/java/fr/ifremer/echobase/tools/loaders/SampleLoader.java	2011-12-16 17:54:16 UTC (rev 199)
@@ -26,6 +26,7 @@
 import com.google.common.base.Preconditions;
 import com.google.common.collect.Multimap;
 import com.google.common.collect.Multimaps;
+import com.google.common.collect.Sets;
 import com.healthmarketscience.jackcess.Database;
 import fr.ifremer.echobase.EchoBaseFunctions;
 import fr.ifremer.echobase.entities.EchoBaseEntityEnum;
@@ -35,7 +36,6 @@
 import fr.ifremer.echobase.entities.data.SampleDataDAO;
 import fr.ifremer.echobase.entities.meta.TableMeta;
 import fr.ifremer.echobase.entities.references.SampleDataType;
-import fr.ifremer.echobase.entities.references.SampleDataTypeDAO;
 import fr.ifremer.echobase.entities.references.SampleType;
 import fr.ifremer.echobase.entities.references.SampleTypeDAO;
 import fr.ifremer.echobase.entities.references.Species;
@@ -49,6 +49,7 @@
 import java.io.IOException;
 import java.util.Collection;
 import java.util.Map;
+import java.util.Set;
 
 /**
  * To load {@link Sample} entities.
@@ -100,9 +101,9 @@
         TableMeta meta = getMeta();
 
         copyAndLoadEntities(outputDir, meta.getAssociations(Sample.PROPERTY_SAMPLE_DATA), false, FileType.ASSOCIATION);
-
     }
 
+
     @Override
     protected void importBaracoudaEntities(Database db) throws IOException, TopiaException {
 
@@ -112,6 +113,9 @@
         Map<String, Species> speciesByName = getUniverse(
                 Species.class, EchoBaseFunctions.SPECIES_BARACOUDA_CODE);
 
+        Map<String, SampleDataType> sampleDataTypeByRaptriCode = getUniverse(
+                SampleDataType.class, EchoBaseFunctions.SAMPLE_DATA_TYPE_RAPTRI_CODE);
+
         Multimap<String, Map<String, Object>> mensurationByNosta = Multimaps.index(
                 db.getTable("MENSURATIONS", true),
                 EchoBaseFunctions.newRowFunction("NOSTA")
@@ -121,6 +125,16 @@
                 db.getTable("CAPTURES", true),
                 EchoBaseFunctions.newRowFunction("NOSTA")
         );
+
+        Multimap<Integer, Map<String, Object>> biometryScalesByRaptri = Multimaps.index(
+                db.getTable("BIOMETRIE_ECHELLE", true),
+                EchoBaseFunctions.newRowIntegerFunction("Code_Param_Biometrie_Echelle")
+        );
+
+        Multimap<String, Map<String, Object>> biometryValuesByNosta = Multimaps.index(
+                db.getTable("BIOMETRIE_VALEUR", true),
+                EchoBaseFunctions.newRowFunction("NOSTA_VALEUR_BIOMETRIE")
+        );
         SampleTypeDAO sampleTypeDAO =
                 (SampleTypeDAO) getDAO(SampleType.class);
 
@@ -130,28 +144,32 @@
         Preconditions.checkNotNull(sampleTypeUnsorted);
         SampleType sampleTypeSubsample = sampleTypeDAO.findByName("Subsample");
         Preconditions.checkNotNull(sampleTypeSubsample);
+        SampleType sampleTypeIndividual = sampleTypeDAO.findByName("Individual");
+        Preconditions.checkNotNull(sampleTypeIndividual);
 
-        SampleDataTypeDAO sampleDataTypeDAO =
-                (SampleDataTypeDAO) getDAO(SampleDataType.class);
+//        SampleDataTypeDAO sampleDataTypeDAO =
+//                (SampleDataTypeDAO) getDAO(SampleDataType.class);
 
         SampleDataDAO sampleDataDAO = (SampleDataDAO) getDAO(SampleData.class);
 
-        SampleDataType sampleDataTypeMeanLength = sampleDataTypeDAO.findByName("MeanLengthcm");
-        Preconditions.checkNotNull(sampleDataTypeMeanLength);
-        SampleDataType sampleDataTypeMeanWeight = sampleDataTypeDAO.findByName("MeanWeightg");
-        Preconditions.checkNotNull(sampleDataTypeMeanWeight);
-        SampleDataType sampleDataTypeNoPerKg = sampleDataTypeDAO.findByName("NoPerKg");
-        Preconditions.checkNotNull(sampleDataTypeNoPerKg);
-        SampleDataType sampleDataTypeNumberAtLength = sampleDataTypeDAO.findByName("NumberAtLength");
-        Preconditions.checkNotNull(sampleDataTypeNumberAtLength);
-        SampleDataType sampleDataTypeWeightAtLength = sampleDataTypeDAO.findByName("WeightAtLengthkg");
-        Preconditions.checkNotNull(sampleDataTypeWeightAtLength);
+//        SampleDataType sampleDataTypeMeanLength = sampleDataTypeDAO.findByName("MeanLengthcm");
+        SampleDataType sampleDataTypeMeanLength = getFK(sampleDataTypeByRaptriCode, "114");
+//        SampleDataType sampleDataTypeMeanWeight = sampleDataTypeDAO.findByName("MeanWeightg");
+        SampleDataType sampleDataTypeMeanWeight = getFK(sampleDataTypeByRaptriCode, "115");
 
+//        SampleDataType sampleDataTypeNoPerKg = sampleDataTypeDAO.findByName("NoPerKg");
+        SampleDataType sampleDataTypeNoPerKg = getFK(sampleDataTypeByRaptriCode, "116");
+//        SampleDataType sampleDataTypeNumberAtLength = sampleDataTypeDAO.findByName("NumberAtLength");
+        SampleDataType sampleDataTypeNumberAtLength = getFK(sampleDataTypeByRaptriCode, "112");
+//        SampleDataType sampleDataTypeWeightAtLength = sampleDataTypeDAO.findByName("WeightAtLengthkg");
+        SampleDataType sampleDataTypeWeightAtLength = getFK(sampleDataTypeByRaptriCode, "113");
+
         TopiaDAO<Sample> dao = getDAO();
 
         int nbSampleUnsorted = 0;
         int nbSampleTotal = 0;
         int nbSubSample = 0;
+        int nbIndividualSample = 0;
 
         for (String operationId : capturesByNosta.keySet()) {
             Preconditions.checkNotNull(operationId);
@@ -162,6 +180,13 @@
                 }
                 continue;
             }
+            Collection<Map<String, Object>> biometryValues =
+                    biometryValuesByNosta.get(operationId);
+
+            Multimap<String, Map<String, Object>> biometryValuesBySpecies = Multimaps.index(
+                    biometryValues,
+                    EchoBaseFunctions.newRowFunction("GENRE_ESP_VALEUR_BIOMETRIE")
+            );
             for (Map<String, Object> row : capturesByNosta.get(operationId)) {
                 String type = (String) row.get("CATEG");
 
@@ -214,7 +239,7 @@
                               "NA",
                               row.get("MOULE_MENS"));
 
-                Collection<Map<String, Object>> mesnurationRows =
+                Collection<Map<String, Object>> mensurationRows =
                         mensurationByNosta.get(operationId);
 
                 Float sampleWeight = (Float) row.get("PESP_MENS");
@@ -224,6 +249,7 @@
                     }
                     sampleWeight = 0f;
                 }
+
                 addSubSamples(dao,
                               sampleDataDAO,
                               sampleTypeSubsample,
@@ -233,22 +259,105 @@
                               type,
                               species,
                               sampleWeight,
-                              mesnurationRows);
+                              mensurationRows);
 
                 int nbSamples = operation.sizeSample();
                 nbSubSample += nbSamples - 1;
+
+                Collection<Map<String, Object>> biometryValuesRows =
+                        biometryValuesBySpecies.get(speciesId);
+
+                int nbSampleIndiv = addSampleIndividuals(dao,
+                                                         sampleDataDAO,
+                                                         operation,
+                                                         species,
+                                                         sampleTypeIndividual,
+                                                         sampleDataTypeByRaptriCode,
+                                                         biometryScalesByRaptri,
+                                                         biometryValuesRows);
+                nbIndividualSample += nbSampleIndiv;
+
             }
         }
 
-
         if (log.isInfoEnabled()) {
             log.info("Found " + nbSampleTotal + " 'total' sample(s).");
             log.info("Found " + nbSampleUnsorted + " 'unsorted' sample(s).");
             log.info("Found " + nbSubSample + " 'sub' sample(s).");
-            log.info("Total " + (nbSampleTotal + nbSampleUnsorted + nbSubSample) + " sample(s).");
+            log.info("Found " + nbIndividualSample + " 'Individual' sample(s).");
+            log.info("Total " + (nbSampleTotal + nbSampleUnsorted + nbIndividualSample + nbSubSample) + " sample(s).");
         }
     }
 
+    private int addSampleIndividuals(TopiaDAO<Sample> dao,
+                                     SampleDataDAO sampleDataDAO,
+                                     Operation operation,
+                                     Species species,
+                                     SampleType sampleTypeIndividual,
+                                     Map<String, SampleDataType> sampleDataTypeByRaptriCode,
+                                     Multimap<Integer, Map<String, Object>> biometryScalesByRaptri,
+                                     Collection<Map<String, Object>> biometryValuesRows) throws TopiaException {
+        int result = 0;
+        Sample sample = null;
+        Set<Integer> individus = Sets.newHashSet();
+        for (Map<String, Object> biometryValuesRow : biometryValuesRows) {
+            Integer ind = Integer.valueOf(biometryValuesRow.get("NUMIND_VALEUR_BIOMETRIE").toString());
+            Integer codeParameter = (Integer) biometryValuesRow.get("CODE_PARAM_VALEUR_BIOMETRIE");
+            String label = null;
+            Float value = (Float) biometryValuesRow.get("VALEUR_BIOMETRIE");
+            if (value==null) {
+                if (log.isWarnEnabled()) {
+                    log.warn("Null value of VALEUR_BIOMETRIE for operationId/Species/Individu/Code param " + operation.getId() + "/" + species.getBaracoudaCode() + "/" + ind+"/"+codeParameter);
+                }
+                continue;
+            }
+            Preconditions.checkNotNull(value, "Null value of VALEUR_BIOMETRIE for operationId/Species/Individu/Code param " + operation.getId() + "/" + species.getBaracoudaCode() + "/" + ind+"/"+codeParameter);
+            SampleDataType sampleDataType = getFK(sampleDataTypeByRaptriCode, String.valueOf(codeParameter));
+
+            boolean add = individus.add(ind);
+            if (add) {
+
+                // new sample
+                sample = dao.create(
+                        Sample.PROPERTY_SPECIES, species,
+                        Sample.PROPERTY_SAMPLE_TYPE, sampleTypeIndividual
+                );
+
+                operation.addSample(sample);
+                result++;
+            }
+
+            Collection<Map<String, Object>> scalesRows =
+                    biometryScalesByRaptri.get(codeParameter);
+
+            if (scalesRows == null) {
+
+                label = "NA";
+            } else {
+
+                // find the correct line
+                int valueAsInteger = value.intValue();
+
+                for (Map<String, Object> scalesRow : scalesRows) {
+                    Float scaleCode = (Float) scalesRow.get("Code_echelle");
+                    if (valueAsInteger == scaleCode.intValue()) {
+
+                        // ok find the correct scale
+                        label = (String) scalesRow.get("Descriptif");
+                        break;
+                    }
+                }
+            }
+            addSampleData(sampleDataDAO,
+                          sample,
+                          sampleDataType,
+                          label,
+                          value
+            );
+        }
+        return result;
+    }
+
     private void addSubSamples(TopiaDAO<Sample> dao,
                                SampleDataDAO sampleDataDAO,
                                SampleType sampleTypeSubsample,

Modified: trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SampleLoaderIT.java
===================================================================
--- trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SampleLoaderIT.java	2011-12-16 01:46:20 UTC (rev 198)
+++ trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/loaders/SampleLoaderIT.java	2011-12-16 17:54:16 UTC (rev 199)
@@ -35,7 +35,7 @@
 public class SampleLoaderIT extends AbstractLoaderIT<Sample, SampleLoader> {
 
     public SampleLoaderIT() {
-        super(SampleLoader.class, 0, 208199);
+        super(SampleLoader.class, 0, 324809);
     }
 
     @Test

Modified: trunk/src/doc/reunions/reunion-2011-12-14.txt
===================================================================
--- trunk/src/doc/reunions/reunion-2011-12-14.txt	2011-12-16 01:46:20 UTC (rev 198)
+++ trunk/src/doc/reunions/reunion-2011-12-14.txt	2011-12-16 17:54:16 UTC (rev 199)
@@ -50,6 +50,7 @@
 - Remplissage du référentiel Gear
 
 - Import des opérations (depuis table STATIONS)
+- Import des samples (depuis table CAPTURES/MENSURATIONS/BIOMETRIE_VALEURS)
 
 Action
 ------

    

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