[fix] Change EIS nexus url

[enh] Begin a new extraction service ExtractionPerformServiceNewImpl (need xmlquery 1.1+) NOT FINISHED (Mantis #49970)
Signed-off-by: lp1ee9d <ludovic.pecquot@e-is.pro>

pom.xml

@@ -172,6 +172,7 @@
 
     <!-- Quadrige3 Core version -->
     <quadrige3-core.version>3.6.5</quadrige3-core.version>
+<!--    <quadrige3-core.version>3.6.6-SNAPSHOT</quadrige3-core.version>-->
 
     <!-- Last ReefDb launcher version -->
     <launcherVersion>3.0.3</launcherVersion>
@@ -261,7 +262,7 @@
   <repositories>
     <repository>
       <id>reefdb-public-group</id>
-      <url>http://nexus.e-is.pro/nexus/content/groups/reefdb</url>
+      <url>http://server.e-is.pro/nexus/content/groups/reefdb</url>
       <snapshots>
         <enabled>true</enabled>
         <checksumPolicy>fail</checksumPolicy>
@@ -276,7 +277,7 @@
   <pluginRepositories>
     <pluginRepository>
       <id>reefdb-public-group</id>
-      <url>http://nexus.e-is.pro/nexus/content/groups/reefdb</url>
+      <url>http://server.e-is.pro/nexus/content/groups/reefdb</url>
       <snapshots>
         <enabled>true</enabled>
         <checksumPolicy>fail</checksumPolicy>
@@ -342,6 +343,18 @@
         <version>${junit.version}</version>
         <scope>test</scope>
       </dependency>
+      <dependency>
+        <groupId>junit-addons</groupId>
+        <artifactId>junit-addons</artifactId>
+        <version>1.4</version>
+        <scope>test</scope>
+        <exclusions>
+          <exclusion>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+          </exclusion>
+        </exclusions>
+      </dependency>
       <dependency>
         <groupId>fr.ifremer.quadrige3</groupId>
         <artifactId>quadrige3-test-shared</artifactId>
@@ -1119,10 +1132,10 @@
         <distribution.site.repository>scpexe://${distribution.site.host}${distribution.site.path}</distribution.site.repository>
 
         <distribution.repository.id>eis-nexus-deploy</distribution.repository.id>
-        <distribution.repository.url>http://nexus.e-is.pro/nexus/content/repositories/reefdb-releases</distribution.repository.url>
+        <distribution.repository.url>http://server.e-is.pro/nexus/content/repositories/reefdb-releases</distribution.repository.url>
 
         <distribution.snapshotRepository.id>eis-nexus-deploy</distribution.snapshotRepository.id>
-        <distribution.snapshotRepository.url>http://nexus.e-is.pro/nexus/content/repositories/reefdb-snapshots</distribution.snapshotRepository.url>
+        <distribution.snapshotRepository.url>http://server.e-is.pro/nexus/content/repositories/reefdb-snapshots</distribution.snapshotRepository.url>
 
         <distribution.internet.url>${distribution.repository.url}</distribution.internet.url>
       </properties>

reefdb-converter/pom.xml

@@ -76,7 +76,7 @@
 	<repositories>
 		<repository>
 			<id>reefdb-public-group</id>
-			<url>http://nexus.e-is.pro/nexus/content/groups/reefdb</url>
+			<url>http://server.e-is.pro/nexus/content/groups/reefdb</url>
 			<snapshots>
 				<enabled>true</enabled>
 				<checksumPolicy>fail</checksumPolicy>
@@ -91,7 +91,7 @@
 	<pluginRepositories>
 		<pluginRepository>
 			<id>reefdb-public-group</id>
-			<url>http://nexus.e-is.pro/nexus/content/groups/reefdb</url>
+			<url>http://server.e-is.pro/nexus/content/groups/reefdb</url>
 			<snapshots>
 				<enabled>true</enabled>
 				<checksumPolicy>fail</checksumPolicy>
@@ -242,12 +242,12 @@
 			<properties>
 
 				<distribution.repository.id>eis-nexus-deploy</distribution.repository.id>
-				<distribution.repository.url>http://nexus.e-is.pro/nexus/content/repositories/reefdb-releases</distribution.repository.url>
+				<distribution.repository.url>http://server.e-is.pro/nexus/content/repositories/reefdb-releases</distribution.repository.url>
 
 				<distribution.snapshotRepository.id>eis-nexus-deploy</distribution.snapshotRepository.id>
-				<distribution.snapshotRepository.url>http://nexus.e-is.pro/nexus/content/repositories/reefdb-snapshots</distribution.snapshotRepository.url>
+				<distribution.snapshotRepository.url>http://server.e-is.pro/nexus/content/repositories/reefdb-snapshots</distribution.snapshotRepository.url>
 
-				<distribution.internet.url>http://nexus.e-is.pro/nexus/content/groups/public</distribution.internet.url>
+				<distribution.internet.url>http://server.e-is.pro/nexus/content/groups/public</distribution.internet.url>
 
 			</properties>
 		</profile>

reefdb-core/pom.xml

@@ -60,6 +60,16 @@
       <artifactId>quadrige3-test-shared</artifactId>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>junit-addons</groupId>
+      <artifactId>junit-addons</artifactId>
+      <scope>test</scope>
+    </dependency>
 
   </dependencies>
 

reefdb-core/src/main/java/fr/ifremer/reefdb/dao/administration/strategy/ReefDbStrategyDao.java

@@ -102,6 +102,16 @@ public interface ReefDbStrategyDao {
     @Cacheable(value = PMFM_STRATEGIES_BY_PROG_LOC_DATE_CACHE)
     Set<PmfmStrategyDTO> getPmfmStrategiesByProgramCodeAndLocation(String programCode, Integer monitoringLocationId, LocalDate date);
 
+    /**
+     * Retrieve all PMFM strategies that are applied on given programs and date range
+     *
+     * @param programCodes program codes
+     * @param startDate
+     * @param endDate
+     * @return set of pmfm strategies
+     */
+    Set<PmfmStrategyDTO> getPmfmStrategiesByProgramCodesAndDates(Collection<String> programCodes, LocalDate startDate, LocalDate endDate);
+
     /**
      * Retrieve all strategies that are applied on the given program and monitoring location
      *

reefdb-core/src/main/java/fr/ifremer/reefdb/dao/administration/strategy/ReefDbStrategyDaoImpl.java

@@ -241,6 +241,39 @@ public class ReefDbStrategyDaoImpl extends StrategyDaoImpl implements ReefDbStra
         return ImmutableSet.copyOf(pmfmStrategies);
     }
 
+    @Override
+    public Set<PmfmStrategyDTO> getPmfmStrategiesByProgramCodesAndDates(Collection<String> programCodes, LocalDate startDate, LocalDate endDate) {
+        Set<PmfmStrategyDTO> pmfmStrategies = new HashSet<>();
+
+        List<ProgStratDTO> appliedStrategies = getAppliedStrategiesByProgramCodes(programCodes);
+        for (ProgStratDTO appliedStrategy: appliedStrategies) {
+            // filter on date range
+            if (appliedStrategy.getStartDate() != null && appliedStrategy.getEndDate() != null
+                && !appliedStrategy.getStartDate().isAfter(endDate) && !appliedStrategy.getEndDate().isBefore(startDate)) {
+                // add all pmfm strategies in date range
+                pmfmStrategies.addAll(getPmfmsAppliedStrategy(appliedStrategy.getId()));
+            }
+        }
+
+        return ImmutableSet.copyOf(pmfmStrategies);
+
+    }
+
+    @SuppressWarnings("unchecked")
+    private List<ProgStratDTO> getAppliedStrategiesByProgramCodes(Collection<String> programCodes) {
+        Query query = createQuery("appliedStrategiesByProgramCodes").setParameterList("programCodes", programCodes);
+        Iterator<Object[]> rows = query.iterate();
+
+        List<ProgStratDTO> result = Lists.newArrayList();
+        TimeZone dbTimezone = config.getDbTimezone();
+        while (rows.hasNext()) {
+            result.add(toProgStratDTO(Arrays.asList(rows.next()).iterator(), dbTimezone));
+        }
+
+        return result;
+    }
+
+
     /** {@inheritDoc} */
     @Override
     public List<ProgStratDTO> getStrategiesByProgramCodeAndMonitoringLocationId(String programCode, int monitoringLocationId) {
@@ -915,7 +948,7 @@ public class ReefDbStrategyDaoImpl extends StrategyDaoImpl implements ReefDbStra
             // code, name
             program.setCode((String) source.next());
             program.setName((String) source.next());
-            //TODO (report Q3): program.setStatus(Daos.getStatus((String) source.next()));
+            program.setStatus(Daos.getStatus((String) source.next()));
         }
 
         // strategy: id, name

reefdb-core/src/main/java/fr/ifremer/reefdb/dao/system/extraction/ReefDbExtractionResultDao.java

@@ -36,6 +36,14 @@ import java.util.Map;
  */
 public interface ReefDbExtractionResultDao extends CSVDao {
 
+    /**
+     * <p>queryCount.</p>
+     *
+     * @param query a {@link String} object.
+     * @return a {@link java.lang.Long} object.
+     */
+    long queryCount(String query);
+
     /**
      * <p>queryCount.</p>
      *
@@ -67,6 +75,14 @@ public interface ReefDbExtractionResultDao extends CSVDao {
 
     List<String> queryStringList(String query, Map<String, Object> queryBindings);
 
+    /**
+     * <p>queryUpdate</p>
+     *
+     * @param query a {@link java.lang.String} object.
+     * @return a int.
+     */
+    int queryUpdate(String query);
+
     /**
      * <p>queryUpdate.</p>
      *

reefdb-core/src/main/java/fr/ifremer/reefdb/dao/system/extraction/ReefDbExtractionResultDaoImpl.java

@@ -28,11 +28,11 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Lazy;
+import org.springframework.dao.DataRetrievalFailureException;
 import org.springframework.jdbc.core.RowMapper;
 import org.springframework.stereotype.Repository;
 
 import javax.sql.DataSource;
-import java.math.BigInteger;
 import java.util.List;
 import java.util.Map;
 import java.util.Properties;
@@ -78,24 +78,19 @@ public class ReefDbExtractionResultDaoImpl extends CSVDaoImpl implements ReefDbE
         this.connectionProperties = connectionProperties;
     }
 
+    @Override
+    public long queryCount(String query) {
+        return queryCount(query, null);
+    }
+
     /**
      * {@inheritDoc}
      */
     @Override
     public Long queryCount(String query, Map<String, Object> queryBindings) {
-
-        return query(connectionProperties, query, queryBindings, resultSet -> {
-            Object result = resultSet.getObject(1);
-            if (log.isDebugEnabled()) {
-                log.debug(String.format("queryCount result: %s", result));
-            }
-            if (result instanceof Integer) {
-                return ((Integer) result).longValue();
-            } else if (result instanceof BigInteger) {
-                return ((BigInteger) result).longValue();
-            }
-            return (Long) result;
-        });
+        Long count = queryCount(connectionProperties, query, queryBindings);
+        if (count == null) throw new DataRetrievalFailureException(String.format("query count result is null: %s ; bindings=%s", query, queryBindings));
+        return count;
     }
 
     /**
@@ -106,6 +101,11 @@ public class ReefDbExtractionResultDaoImpl extends CSVDaoImpl implements ReefDbE
         return query(connectionProperties, sql, queryBindings, rowMapper);
     }
 
+    @Override
+    public int queryUpdate(String query) {
+        return queryUpdate(query, null);
+    }
+
     /**
      * {@inheritDoc}
      */
@@ -126,4 +126,5 @@ public class ReefDbExtractionResultDaoImpl extends CSVDaoImpl implements ReefDbE
     public List<String> queryStringList(String query, Map<String, Object> queryBindings) {
         return query(connectionProperties, query, queryBindings, (resultSet, i) -> resultSet.getString(1));
     }
+
 }

reefdb-core/src/main/java/fr/ifremer/reefdb/dto/ReefDbBeans.java

@@ -896,6 +896,16 @@ public class ReefDbBeans extends QuadrigeBeans {
         return null;
     }
 
+    public static void setFilterElements(ExtractionDTO extraction, ExtractionFilterValues extractionFilter, List<? extends QuadrigeBean> elements) {
+        FilterDTO filter = getFilterOfType(extraction, extractionFilter);
+        if (filter == null) {
+            filter = ReefDbBeanFactory.newFilterDTO();
+            filter.setFilterTypeId(extractionFilter.getFilterTypeId());
+            extraction.addFilters(filter);
+        }
+        filter.setElements(elements);
+    }
+
     public static List<String> getIdsAsString(Collection<? extends QuadrigeBean> beans) {
         if (beans == null)
             return null;
@@ -903,4 +913,11 @@ public class ReefDbBeans extends QuadrigeBeans {
         return beans.stream().map(bean -> bean instanceof CodeOnly ? ((CodeOnly) bean).getCode() : bean.getId().toString()).collect(Collectors.toList());
     }
 
+    public static List<ExtractionPeriodDTO> getExtractionPeriods(ExtractionDTO extraction) {
+
+        FilterDTO periodFilter = getFilterOfType(extraction, ExtractionFilterValues.PERIOD);
+        if (periodFilter == null || periodFilter.getElements() == null) return new ArrayList<>();
+        return periodFilter.getElements().stream().map((Function<QuadrigeBean, ExtractionPeriodDTO>) ExtractionPeriodDTO.class::cast).collect(Collectors.toList());
+    }
+
 }

reefdb-core/src/main/java/fr/ifremer/reefdb/dto/enums/ExtractionFilterValues.java

@@ -36,7 +36,7 @@ public enum ExtractionFilterValues {
     PERIOD(null, n("reefdb.core.enums.extractionFilter.period"), false),
     PROGRAM(FilterTypeId.PROGRAM, n("reefdb.core.enums.extractionFilter.program"), false),
     LOCATION(FilterTypeId.MONITORING_LOCATION, n("reefdb.core.enums.extractionFilter.location"), false),
-//    CAMPAIGN(FilterTypeId.CAMPAIGN, n("reefdb.core.enums.extractionFilter.campaign"), false),
+    CAMPAIGN(FilterTypeId.CAMPAIGN, n("reefdb.core.enums.extractionFilter.campaign"), false),
     TAXON(FilterTypeId.TAXON_NAME, n("reefdb.core.enums.extractionFilter.taxon"), false),
     TAXON_GROUP(FilterTypeId.TAXON_GROUP, n("reefdb.core.enums.extractionFilter.taxonGroup"), false),
     DEPARTMENT(FilterTypeId.DEPARTMENT, n("reefdb.core.enums.extractionFilter.department"), false),

reefdb-core/src/main/java/fr/ifremer/reefdb/service/extraction/ExtractionPerformServiceImpl.java

@@ -148,7 +148,7 @@ public class ExtractionPerformServiceImpl implements ExtractionPerformService {
                 context.setUniqueId(System.currentTimeMillis());
                 context.setRawTableName(String.format(RAW_TABLE_NAME_PATTERN, context.getUniqueId()));
                 context.setCommonTableName(String.format(COMMON_TABLE_NAME_PATTERN, context.getUniqueId()));
-                context.setSplitTableName(String.format(SPLIT_TABLE_NAME_PATTERN, context.getUniqueId()));
+                context.setResultTableName(String.format(SPLIT_TABLE_NAME_PATTERN, context.getUniqueId()));
 
                 // create the first temp table
                 createRawTable(context, outputType);
@@ -220,7 +220,7 @@ public class ExtractionPerformServiceImpl implements ExtractionPerformService {
                 nbRowsInserted = insertSplitData(context, outputType);
                 progressionModel.increments(1);
                 if (LOG.isDebugEnabled()) {
-                    LOG.debug(String.format("%s rows of split data inserted into %s", nbRowsInserted, context.getSplitTableName()));
+                    LOG.debug(String.format("%s rows of split data inserted into %s", nbRowsInserted, context.getResultTableName()));
                 }
 
                 // final query and write to csv file
@@ -507,7 +507,7 @@ public class ExtractionPerformServiceImpl implements ExtractionPerformService {
     private void createSplitTable(ExtractionContextDTO context, ExtractionOutputType outputType) {
 
         StringBuilder queryBuilder = new StringBuilder();
-        queryBuilder.append("DECLARE LOCAL TEMPORARY TABLE ").append(context.getSplitTableName()).append(" (");
+        queryBuilder.append("DECLARE LOCAL TEMPORARY TABLE ").append(context.getResultTableName()).append(" (");
         queryBuilder.append("SURVEY_ID INTEGER, ");
         queryBuilder.append("SURVEY_PROG_CD VARCHAR(40), ");
         queryBuilder.append("MON_LOC_NM VARCHAR(100), ");
@@ -889,7 +889,7 @@ public class ExtractionPerformServiceImpl implements ExtractionPerformService {
 
         // common part
         StringBuilder insertPart = new StringBuilder();
-        insertPart.append("INSERT INTO ").append(context.getSplitTableName()).append(LS);
+        insertPart.append("INSERT INTO ").append(context.getResultTableName()).append(LS);
         insertPart.append("SELECT COMMON.SURVEY_ID, COMMON.SURVEY_PROG_CD, COMMON.MON_LOC_NM, COMMON.SURVEY_DT, COMMON.SAMPLING_OPER_ID, COMMON.SAMPLING_OPER_LB, COMMON.MON_LOC_ID, ");
         insertPart.append("COMMON.MON_LOC_LB, COMMON.ORDER_ITEM_NM, COMMON.SURVEY_POSITION_LONG, COMMON.SURVEY_POSITION_LAT, COMMON.SAMPLING_EQUIPMENT_NM, COMMON.SAMPLING_OPER_DEP_NM, ");
         if (outputType != ExtractionOutputType.PAMPA) {
@@ -989,7 +989,7 @@ public class ExtractionPerformServiceImpl implements ExtractionPerformService {
         query.append(join);
         // filter out already present individual measurements
         query.append("WHERE COMMON.MEAS_INDIV_ID IS NULL AND NOT EXISTS (SELECT * FROM ");
-        query.append(context.getSplitTableName());
+        query.append(context.getResultTableName());
         query.append(" SPLIT WHERE SPLIT.SURVEY_ID = COMMON.SURVEY_ID AND SPLIT.SAMPLING_OPER_ID = COMMON.SAMPLING_OPER_ID AND SPLIT.MEAS_INDIV_ID IS NOT NULL )");
 
         nbInsert += extractionResultDao.queryUpdate(query.toString(), null);
@@ -1198,7 +1198,7 @@ public class ExtractionPerformServiceImpl implements ExtractionPerformService {
 
         // add ordering clause
         query.append("FROM ");
-        query.append(context.getSplitTableName());
+        query.append(context.getResultTableName());
         query.append(" ORDER BY SURVEY_PROG_CD, MON_LOC_NM, SURVEY_DT, SAMPLING_OPER_LB, MEAS_INDIV_ID");
 
         // some field formats

reefdb-core/src/main/resources/i18n/reefdb-core_fr_FR.properties

@@ -291,10 +291,10 @@ reefdb.service.common.progression=%s \: traitement de %s/%s
 reefdb.service.control=Contrôle
 reefdb.service.controlRule.invalid.message=La règle de contrôle '%s' n'est pas respectée
 reefdb.service.extraction.error=Une erreur s'est produite lors de l'extration.
-reefdb.service.extraction.fieldName.INPUT_TAXON_NAME_ID=${reefdb.service.extraction.fieldNamePrefix.MEAS}_Identifiant_interne_TAXON_NAME_ID
-reefdb.service.extraction.fieldName.INPUT_TAXON_NAME_NM=Taxon_saisi
+reefdb.service.extraction.fieldName.TAXON_NAME_ID=${reefdb.service.extraction.fieldNamePrefix.MEAS}_Identifiant_interne_TAXON_NAME_ID
+reefdb.service.extraction.fieldName.TAXON_NAME_NM=Taxon_saisi
 reefdb.service.extraction.fieldName.MEAS_CM=${reefdb.service.extraction.fieldNamePrefix.MEAS}_Commentaires
-reefdb.service.extraction.fieldName.MEAS_DEP_NM=${reefdb.service.extraction.fieldNamePrefix.MEAS}_Organisme_analyste
+reefdb.service.extraction.fieldName.MEAS_ANALYST_NM=${reefdb.service.extraction.fieldNamePrefix.MEAS}_Organisme_analyste
 reefdb.service.extraction.fieldName.MEAS_IDS=${reefdb.service.extraction.fieldNamePrefix.MEAS}_Identifiants_interne_MEAS_ID
 reefdb.service.extraction.fieldName.MEAS_INDIV_ID=${reefdb.service.extraction.fieldNamePrefix.MEAS}_Numero_individu
 reefdb.service.extraction.fieldName.MON_LOC_ID=${reefdb.service.extraction.fieldNamePrefix.MON_LOC}_Identifiant
@@ -325,7 +325,7 @@ reefdb.service.extraction.fieldName.SAMPLING_OPER_POSITION_LONG_MAX=${reefdb.ser
 reefdb.service.extraction.fieldName.SAMPLING_OPER_POSITION_LONG_MIN=${reefdb.service.extraction.fieldNamePrefix.SAMPLING_OPER}_Coordonnees_MINX
 reefdb.service.extraction.fieldName.SAMPLING_OPER_QUALIF_CM=${reefdb.service.extraction.fieldNamePrefix.SAMPLING_OPER}_Commentaire_qualification
 reefdb.service.extraction.fieldName.SAMPLING_OPER_QUALIF_DT=${reefdb.service.extraction.fieldNamePrefix.SAMPLING_OPER}_Date_qualification
-reefdb.service.extraction.fieldName.SAMPLING_OPER_QUAL_FLAG=${reefdb.service.extraction.fieldNamePrefix.SAMPLING_OPER}_Niveau_qualite
+reefdb.service.extraction.fieldName.SAMPLING_OPER_QUAL_FLAG_NM=${reefdb.service.extraction.fieldNamePrefix.SAMPLING_OPER}_Niveau_qualite
 reefdb.service.extraction.fieldName.SAMPLING_OPER_SIZE=${reefdb.service.extraction.fieldNamePrefix.SAMPLING_OPER}_Taille
 reefdb.service.extraction.fieldName.SAMPLING_OPER_SIZE_UNIT_SYMBOL=${reefdb.service.extraction.fieldNamePrefix.SAMPLING_OPER}_Unite
 reefdb.service.extraction.fieldName.SAMPLING_OPER_TIME=${reefdb.service.extraction.fieldNamePrefix.SAMPLING_OPER}_Heure
@@ -343,13 +343,13 @@ reefdb.service.extraction.fieldName.SURVEY_POSITION_LONG_MIN=${reefdb.service.ex
 reefdb.service.extraction.fieldName.SURVEY_PROG_CD=Programme
 reefdb.service.extraction.fieldName.SURVEY_QUALIF_CM=${reefdb.service.extraction.fieldNamePrefix.SURVEY}_Commentaire_qualification
 reefdb.service.extraction.fieldName.SURVEY_QUALIF_DT=${reefdb.service.extraction.fieldNamePrefix.SURVEY}_Date_qualification
-reefdb.service.extraction.fieldName.SURVEY_QUAL_FLAG=${reefdb.service.extraction.fieldNamePrefix.SURVEY}_Niveau_qualite
+reefdb.service.extraction.fieldName.SURVEY_QUAL_FLAG_NM=${reefdb.service.extraction.fieldNamePrefix.SURVEY}_Niveau_qualite
 reefdb.service.extraction.fieldName.SURVEY_QUSERS=${reefdb.service.extraction.fieldNamePrefix.SURVEY}_Observateurs
 reefdb.service.extraction.fieldName.SURVEY_TIME=${reefdb.service.extraction.fieldNamePrefix.SURVEY}_Heure
 reefdb.service.extraction.fieldName.SURVEY_VALID_DT=${reefdb.service.extraction.fieldNamePrefix.SURVEY}_Date_validation
 reefdb.service.extraction.fieldName.TAXON_GROUP_NM=Groupe_taxons
 reefdb.service.extraction.fieldName.TAXON_MEAS_IDS=${reefdb.service.extraction.fieldNamePrefix.MEAS}_Identifiants_interne_TAXON_MEAS_ID
-reefdb.service.extraction.fieldName.TAXON_NAME_NM=Taxon
+reefdb.service.extraction.fieldName.REF_TAXON_NM=Taxon
 reefdb.service.extraction.fieldName.TAXON_PAMPA=Taxon_pampa
 reefdb.service.extraction.fieldNamePrefix.MEAS=MESURE
 reefdb.service.extraction.fieldNamePrefix.MON_LOC=STATION

reefdb-core/src/main/resources/reefdb-queries.hbm.xml

@@ -1754,6 +1754,32 @@
     <query-param name="programCode" type="java.lang.String"/>
   </query>
 
+  <query name="appliedStrategiesByProgramCodes">
+    <![CDATA[
+    SELECT DISTINCT
+      a.appliedStratId,
+      p.progCd,
+      p.progNm,
+      p.status.statusCd,
+      s.id,
+      s.stratNm,
+      ap.id.appliedPeriodStartDt as startDt,
+      ap.appliedPeriodEndDt as endDt,
+      dep.depId
+    FROM
+      AppliedStrategyImpl a
+      INNER JOIN a.strategy s
+      INNER JOIN s.program p
+      LEFT OUTER JOIN a.appliedPeriods ap
+      LEFT OUTER JOIN a.department dep
+    WHERE
+      p.progCd IN (:programCodes)
+    ORDER BY
+      a.strategy.stratNm, ap.id.appliedPeriodStartDt
+    ]]>
+    <query-param name="programCodes" type="java.lang.String"/>
+  </query>
+
   <query name="analysisDepartmentByAppliedStrategyId">
     <![CDATA[
       SELECT DISTINCT
@@ -1830,6 +1856,7 @@
       a.appliedStratId,
       p.progCd,
       p.progNm,
+      p.status.statusCd,
       s.id,
       s.stratNm,
       ap.id.appliedPeriodStartDt as startDt,

reefdb-core/src/main/resources/xmlQuery/extraction/cleanHermeticData.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  #%L
+  Dali :: Core
+  %%
+  Copyright (C) 2017 Ifremer
+  %%
+  This program is free software: you can redistribute it and/or modify
+  it under the terms of the GNU Affero General Public License as published by
+  the Free Software Foundation, either version 3 of the License, or
+  (at your option) any later version.
+  
+  This program is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+  
+  You should have received a copy of the GNU Affero General Public License
+  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+  #L%
+  -->
+
+<queries name="extractionCleanHermeticData">
+
+	<query type="delete" table="&amp;tableName">
+		<where><![CDATA[SURVEY_PROG_CD = '&programCode']]></where>
+		<where operator="AND"><![CDATA[REC_DEP_ID != &recDepId]]></where>
+	</query>
+
+</queries>
\ No newline at end of file

reefdb-core/src/main/resources/xmlQuery/extraction/cleanTaxon.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  #%L
+  Dali :: Core
+  %%
+  Copyright (C) 2017 Ifremer
+  %%
+  This program is free software: you can redistribute it and/or modify
+  it under the terms of the GNU Affero General Public License as published by
+  the Free Software Foundation, either version 3 of the License, or
+  (at your option) any later version.
+  
+  This program is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+  
+  You should have received a copy of the GNU Affero General Public License
+  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+  #L%
+  -->
+
+<queries name="extractionCleanRawData">
+
+	<query type="delete" table="&amp;tableName">
+		<where>1=2</where>
+		<where operator="OR" group="taxonGroup">
+			<where>TAXON_GROUP_ID IS NULL</where>
+			<where operator="OR">
+				<notin field="TAXON_GROUP_ID"><![CDATA[&taxonGroupIds]]></notin>
+			</where>
+		</where>
+		<where operator="OR" group="taxonName">
+			<where>REF_TAXON_ID IS NULL</where>
+			<where operator="OR">
+				<where>
+					<notin field="REF_TAXON_ID"><![CDATA[&taxonNameIds]]></notin>
+				</where>
+				<where operator="AND" group="simple,complete,sinp">
+					<notin field="TAXON_NAME_ID"><![CDATA[&taxonNameIds]]></notin>
+				</where>
+			</where>
+		</where>
+	</query>
+
+</queries>
\ No newline at end of file

reefdb-core/src/main/resources/xmlQuery/extraction/countFrom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  #%L
+  Dali :: Core
+  %%
+  Copyright (C) 2017 Ifremer
+  %%
+  This program is free software: you can redistribute it and/or modify
+  it under the terms of the GNU Affero General Public License as published by
+  the Free Software Foundation, either version 3 of the License, or
+  (at your option) any later version.
+  
+  This program is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+  
+  You should have received a copy of the GNU Affero General Public License
+  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+  #L%
+  -->
+
+<queries name="extractionCountFrom">
+
+  <query type="select">
+    <select alias="COUNT_ALL" type="number">COUNT(*)</select>
+    <from><![CDATA[&tableName]]></from>
+  </query>
+
+</queries>
\ No newline at end of file

reefdb-core/src/main/resources/xmlQuery/extraction/createCommonTable.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  #%L
+  Dali :: Core
+  %%
+  Copyright (C) 2017 Ifremer
+  %%
+  This program is free software: you can redistribute it and/or modify
+  it under the terms of the GNU Affero General Public License as published by
+  the Free Software Foundation, either version 3 of the License, or
+  (at your option) any later version.
+  
+  This program is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+  
+  You should have received a copy of the GNU Affero General Public License
+  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+  #L%
+  -->
+
+<queries name="extractionCreateCommonTable">
+
+	<query type="create" temp="false" table="&amp;commonTableName" option="DISTINCT">
+
+		<select alias="SURVEY_ID" type="number">RAW.SURVEY_ID</select>
+		<select alias="SAMPLING_OPER_ID" type="number">RAW.SAMPLING_OPER_ID</select>
+		<select alias="MEAS_INDIV_ID" type="number">RAW.MEAS_INDIV_ID</select>
+		<select alias="REF_TAXON_NM" type="text">RAW.REF_TAXON_NM</select>
+		<select alias="TAXON_NAME_ID" type="number">RAW.TAXON_NAME_ID</select>
+		<select alias="TAXON_NAME_NM" type="text">RAW.TAXON_NAME_NM</select>
+		<select alias="TAXON_GROUP_NM" type="text">RAW.TAXON_GROUP_NM</select>
+		<from alias="RAW"><![CDATA[&rawTableName]]></from>
+		<where><![CDATA[RAW.MEAS_INDIV_ID IS NOT NULL]]></where>
+
+		<union>
+			<subquery option="DISTINCT">
+				<subselect alias="SURVEY_ID" type="number">RAW.SURVEY_ID</subselect>
+				<subselect alias="SAMPLING_OPER_ID" type="number">RAW.SAMPLING_OPER_ID</subselect>
+				<subselect alias="MEAS_INDIV_ID" type="number">RAW.MEAS_INDIV_ID</subselect>
+				<subselect alias="REF_TAXON_NM" type="text">RAW.REF_TAXON_NM</subselect>
+				<subselect alias="TAXON_NAME_ID" type="number">RAW.TAXON_NAME_ID</subselect>
+				<subselect alias="TAXON_NAME_NM" type="text">RAW.TAXON_NAME_NM</subselect>
+				<subselect alias="TAXON_GROUP_NM" type="text">RAW.TAXON_GROUP_NM</subselect>
+				<from alias="RAW"><![CDATA[&rawTableName]]></from>
+				<where><![CDATA[RAW.MEAS_INDIV_ID IS NULL]]></where>
+				<where operator="AND"><![CDATA[NOT EXISTS (SELECT RAW2.SURVEY_ID FROM &rawTableName RAW2
+				  WHERE RAW.SURVEY_ID = RAW2.SURVEY_ID
+				  AND ((RAW.SAMPLING_OPER_ID IS NULL AND RAW2.SAMPLING_OPER_ID IS NULL) OR RAW.SAMPLING_OPER_ID = RAW2.SAMPLING_OPER_ID)
+				  AND RAW2.MEAS_INDIV_ID IS NOT NULL)]]></where>
+			</subquery>
+		</union>
+	</query>
+
+</queries>
\ No newline at end of file

reefdb-core/src/main/resources/xmlQuery/extraction/createPmfmTable.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  #%L
+  Dali :: Core
+  %%
+  Copyright (C) 2017 Ifremer
+  %%
+  This program is free software: you can redistribute it and/or modify
+  it under the terms of the GNU Affero General Public License as published by
+  the Free Software Foundation, either version 3 of the License, or
+  (at your option) any later version.
+  
+  This program is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+  
+  You should have received a copy of the GNU Affero General Public License
+  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+  #L%
+  -->
+
+<queries name="extractionCreatePmfmTable">
+
+  <query type="create" temp="false" table="&amp;pmfmTableName" option="DISTINCT">
+
+    <select alias="PARENT_ID" type="number"><![CDATA[&parentId]]></select>
+    <select alias="IS_SURVEY_MEAS" type="number">IS_SURVEY_MEAS</select>
+    <select alias="MEAS_INDIV_ID" type="number">MEAS_INDIV_ID</select>
+    <select alias="PMFM_ID" type="number">PMFM_ID</select>