GitLab

at 2018-03-07T19:42:54Z

fix typo

[N2][N3] Les calées de type banc indéterminé ne sont pas traitées au N2 et N3 (See #261)

  * 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%

     protected List<Harbour> landingHarbours;

     @InjectFromDAO(entityType = Species.class)

     protected List<Species> species;

-    protected int nbStratums;

+    protected int nbStratum;

     protected int nbTripsWithRF2;

     @InjectDAO(entityType = RaisingFactor2.class)

     private RaisingFactor2TopiaDao raisingFactor2DAO;

         super(Level0Step.COMPUTE_RF2);

     }

-    public int getNbStratums() {

-        return nbStratums;

+    public int getNbStratum() {

+        return nbStratum;

     }

     @SuppressWarnings("unused")

                         log.debug(String.format("found %d months.", tripsByMonth.size()));

                         for (T3Date month : tripsByMonth.keySet()) {

                             Collection<CompleteTrip> stratumTrips = tripsByMonth.get(month);

-                            nbStratums++;

+                            nbStratum++;

                             String message = l(locale, "t3.level0.computeRF2.nbTrips.for.stratum",

                                     stratumTrips.size(),

-                                    nbStratums,

+                                    nbStratum,

                                     harbourStr,

                                     countryStr,

                                     vesselSimpleTypeStr,

         Map<String, Integer> activityIds = activityDAO.findAllActivityIdsForCatchStratum(

                 configuration.getZoneTableName(),

                 configuration.getZone().getTopiaId(),

-                configuration.getSchoolType().getTopiaId(),

+                configuration.getSchoolTypeIds(),

                 configuration.getBeginDate(),

                 configuration.getEndDate());

         // ensuite pour chaque activité on récupère sa marée et on conserve

      * @since 1.4

      */

     private final float minimumSampleTotalWeight;

-

     /**

      * The minimum sample count required to obtain the correct

      * substitution level.

         float catchStratumTotalWeight = sampleStratum.getCatchStratumTotalWeight();

         float maximumWeightRatio = configuration.getStratumWeightRatio();

         minimumSampleTotalWeight = catchStratumTotalWeight / maximumWeightRatio;

-        SchoolType schoolType = sampleStratum.getConfiguration().getSampleSchoolType();

+        SchoolType schoolType = sampleStratum.getConfiguration().getSchoolType();

         int code = schoolType.getCode();

         switch (code) {

             case 1:

             List<String> activityIds = activityDAO.findAllActivityIdsForSampleStratum(

                     configuration.getZoneTableName(),

                     zoneId,

-                    schoolTypeId,

+                    configuration.getSchoolTypeIds(),

                     beginDate,

                     endDate);

             result.addAll(activityIds);

     protected Set<String> findActivityIds(int level) {

         StratumConfiguration<Level2Configuration> configuration = getSampleStratum().getConfiguration();

-        String schoolTypeId = configuration.getSampleSchoolType().getTopiaId();

+        String schoolTypeId = configuration.getSchoolType().getTopiaId();

         String zoneId = configuration.getZone().getTopiaId();

         T3Date beginDate = configuration.getBeginDate();

         T3Date endDate = configuration.getEndDate();

     protected Set<String> findActivityIds(int level) {

         StratumConfiguration<Level2Configuration> configuration = getSampleStratum().getConfiguration();

-        String schoolTypeId = configuration.getSampleSchoolType().getTopiaId();

+        String schoolTypeId = configuration.getSchoolType().getTopiaId();

         String zoneId = configuration.getZone().getTopiaId();

         T3Date beginDate = configuration.getBeginDate();

         T3Date endDate = configuration.getEndDate();

 import com.google.common.collect.Multimap;

 import fr.ird.t3.actions.T3Action;

 import fr.ird.t3.actions.stratum.OceanContext;

-import fr.ird.t3.actions.stratum.SampleStratum;

+import fr.ird.t3.actions.stratum.SchoolTypeIndeterminate;

 import fr.ird.t3.actions.stratum.StratumConfiguration;

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

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

     private CorrectedElementaryCatchTopiaDao correctedElementaryCatchDAO;

     @InjectDAO(entityType = Vessel.class)

     private VesselTopiaDao vesselDAO;

-    @InjectDAO(entityType = SchoolType.class)

-    private SchoolTypeTopiaDao schoolTypeDAO;

     private ZoneStratumAwareMeta zoneMeta;

     @InjectFromDAO(entityType = SchoolType.class, method = "findAllForStratum")

     private Set<SchoolType> schoolTypes;

     private Set<T3Date> startDates;

     private Set<Vessel> possibleCatchVessels;

     private Set<Vessel> possibleSampleVessels;

-    private int nbStratums;

+    private int nbStratum;

     private long totalCatchWeightForSpeciesFoFix;

     private long totalCatchWeight;

     private long totalCatchActivities;

     private long totalCatchActivitiesWithSample;

-    private SchoolType boSchoolType;

-    private SchoolType blSchoolType;

     public Level2Action() {

         activityCache = CacheBuilder.newBuilder().build(

     @Override

     protected void prepareAction() throws Exception {

         super.prepareAction();

-        this.boSchoolType = schoolTypeDAO.forCodeEquals(1).findUnique();

-        this.blSchoolType = schoolTypeDAO.forCodeEquals(2).findUnique();

         this.oceanContext.clear();

         Level2Configuration configuration = getConfiguration();

         configuration.setLocale(getLocale());

     }

     private void executeActionWithCategories(Level2Configuration configuration, Set<String> usedActivityIds) throws Exception {

-        nbStratums = 0;

+        nbStratum = 0;

         for (SchoolType schoolType : schoolTypes) {

             List<WeightCategoryTreatment> weightCategories = getWeightCategoryTreatments(schoolType);

             Collection<ZoneStratumAware> zones = getZones(schoolType);

-            nbStratums += startDates.size() * zones.size() * weightCategories.size();

+            nbStratum += startDates.size() * zones.size() * weightCategories.size();

         }

-        setNbSteps(3 * nbStratums);

+        setNbSteps(3 * nbStratum);

         int timeStep = configuration.getTimeStep();

         MutableInt stratumIndex = new MutableInt(1);

         for (SchoolType schoolType : schoolTypes) {

     }

     private void executeActionWithoutCategories(Level2Configuration configuration, Set<String> usedActivityIds) throws Exception {

-        nbStratums = 0;

+        nbStratum = 0;

         for (SchoolType schoolType : schoolTypes) {

             Collection<ZoneStratumAware> zones = getZones(schoolType);

-            nbStratums += startDates.size() * zones.size();

+            nbStratum += startDates.size() * zones.size();

         }

-        setNbSteps(3 * nbStratums);

+        setNbSteps(3 * nbStratum);

         int timeStep = configuration.getTimeStep();

         MutableInt stratumIndex = new MutableInt(1);

         for (SchoolType schoolType : schoolTypes) {

         }

     }

-    private List<WeightCategoryTreatment> getWeightCategoryTreatments(SchoolType schoolType) {

-        List<WeightCategoryTreatment> weightCategoryTreatments = oceanContext.values().stream().flatMap(o -> o.getWeightCategories(schoolType).stream()).distinct().collect(Collectors.toList());

-        WeightCategories.sort(weightCategoryTreatments);

-        return weightCategoryTreatments;

-    }

-

-    private Collection<ZoneStratumAware> getZones(SchoolType schoolType) {

-        return oceanContext.values().stream().flatMap(o -> o.getZones(schoolType).stream()).distinct().collect(Collectors.toList());

-    }

-

-    private void doIterateOnDates(int timeStep, Level2Configuration configuration, SchoolType schoolType, Collection<ZoneStratumAware> zones, ZoneStratumAware zone, List<WeightCategoryTreatment> weightCategories, WeightCategoryTreatment weightCategoryTreatment, Set<String> usedActivityIds, MutableInt stratumIndex) throws Exception {

-        SchoolType sampleSchoolType = SampleStratum.getSampleSchoolType(schoolType, configuration.getSchoolTypeIndeterminate(), boSchoolType, blSchoolType);

+    private void doIterateOnDates(int timeStep,

+                                  Level2Configuration configuration,

+                                  SchoolType schoolType,

+                                  Collection<ZoneStratumAware> zones,

+                                  ZoneStratumAware zone,

+                                  List<WeightCategoryTreatment> weightCategories,

+                                  WeightCategoryTreatment weightCategoryTreatment,

+                                  Set<String> usedActivityIds,

+                                  MutableInt stratumIndex) throws Exception {

         for (T3Date startDate : startDates) {

             // get end date (only increments on timeStep - 1 to have

             // exactly timeStep month from beginDate.toStartDate() to endDate.toEndDate()

                             zoneMeta,

                             zone,

                             schoolType,

-                            sampleSchoolType,

                             weightCategoryTreatment,

                             startDate,

                             endDate,

         }

     }

-    private L2StratumResult doExecuteStratum(

-            StratumConfiguration<Level2Configuration> stratumConfiguration,

-            List<WeightCategoryTreatment> weightCategories,

-            MutableInt stratumIndex,

-            Set<String> usedActivityIds) throws Exception {

+    private L2StratumResult doExecuteStratum(StratumConfiguration<Level2Configuration> stratumConfiguration,

+                                             List<WeightCategoryTreatment> weightCategories,

+                                             MutableInt stratumIndex,

+                                             Set<String> usedActivityIds) throws Exception {

         incrementsProgression();

         String stratumPrefix =

                 l(locale, "t3.level2.stratumLabel",

-                        stratumIndex, nbStratums,

+                        stratumIndex, nbStratum,

                         decorate(stratumConfiguration.getSchoolType()),

-                        decorate(stratumConfiguration.getSampleSchoolType()),

                         decorate(stratumConfiguration.getZone()),

                         stratumConfiguration.getBeginDate(),

                         stratumConfiguration.getEndDate());

         L2StratumResult result = new L2StratumResult(stratumConfiguration, stratumPrefix);

         String message = l(locale, "t3.level2.message.start.stratum", stratumPrefix);

-        if (log.isInfoEnabled()) {

-            log.info(message);

+        log.info(message);

+        if (SchoolTypeIndeterminate.IGNORE == getConfiguration().getSchoolTypeIndeterminate()) {

+            // Just report for all activities on School type indeterminate catch weight

+            Set<String> activityIds = activityDAO.findAllActivityIdsForCatchStratum(

+                    stratumConfiguration.getZoneTableName(),

+                    stratumConfiguration.getZone().getTopiaId(),

+                    Collections.singleton(SchoolTypeTopiaDao.SCHOOL_TYPE_INDETERMINATE_ID),

+                    stratumConfiguration.getBeginDate(),

+                    stratumConfiguration.getEndDate()).keySet();

+            for (String activityId : activityIds) {

+                for (CorrectedElementaryCatch correctedElementaryCatch : activityCache.get(activityId).getCorrectedElementaryCatch()) {

+                    correctedElementaryCatch.setCorrectedCatchWeight(correctedElementaryCatch.getCatchWeight());

+                }

+            }

         }

         addInfoMessage("==============================================================================================");

         addInfoMessage(message);

         return result;

     }

+    private List<WeightCategoryTreatment> getWeightCategoryTreatments(SchoolType schoolType) {

+        List<WeightCategoryTreatment> weightCategoryTreatments = oceanContext.values().stream().flatMap(o -> o.getWeightCategories(schoolType).stream()).distinct().collect(Collectors.toList());

+        WeightCategories.sort(weightCategoryTreatments);

+        return weightCategoryTreatments;

+    }

+

+    private Collection<ZoneStratumAware> getZones(SchoolType schoolType) {

+        return oceanContext.values().stream().flatMap(o -> o.getZones(schoolType).stream()).distinct().collect(Collectors.toList());

+    }

+

     private L2CatchStratum newCatchStratum(StratumConfiguration<Level2Configuration> stratumConfiguration,

                                            List<WeightCategoryTreatment> weightCategories) throws Exception {

         L2CatchStratum catchStratum = new L2CatchStratum(stratumConfiguration, species);

         catchStratum.addActivityOutputModel(correctedCatchWeightModel);

     }

-//    private void setZoneMeta(ZoneStratumAwareMeta zoneMeta) {

-//        this.zoneMeta = zoneMeta;

-//    }

-

-//    private void setSchoolTypes(Set<SchoolType> schoolTypes) {

-//        this.schoolTypes = schoolTypes;

-//    }

-

-//    private void setSpecies(Set<Species> species) {

-//        this.species = species;

-//    }

-

-//    private void setStartDates(Set<T3Date> startDates) {

-//        this.startDates = startDates;

-//    }

-

-//    private void setPossibleCatchVessels(Set<Vessel> possibleCatchVessels) {

-//        this.possibleCatchVessels = possibleCatchVessels;

-//    }

-

-//    private void setPossibleSampleVessels(Set<Vessel> possibleSampleVessels) {

-//        this.possibleSampleVessels = possibleSampleVessels;

-//    }

-

-//    private void setZoneVersion(ZoneVersion zoneVersion) {

-//        this.zoneVersion = zoneVersion;

-//    }

-

     // -------------------------------------------------------------------------

     // --- Results -------------------------------------------------------------

     // -------------------------------------------------------------------------

     }

     @SuppressWarnings("unused")

-    public int getNbStratums() {

-        return nbStratums;

+    public int getNbStratum() {

+        return nbStratum;

     }

     @SuppressWarnings("unused")

     @SuppressWarnings("unused")

     public String getInputCatchStratumLog() {

         WeightCompositionAggregateModel inputCatchModelForSpeciesToFix = inputCatchModelForAllSpecies.extractForSpecies(species);

-        String title = l(locale, "t3.level2.message.strateInputGlobalComposition.resume");

+        String title = l(locale, "t3.level2.message.stratumInputGlobalComposition.resume");

         return WeightCompositionModelHelper.decorateModel(

                 getDecoratorService(),

                 title,

     @SuppressWarnings("unused")

     public String getOutputCatchStratumLog() {

         WeightCompositionAggregateModel outputCatchModelForSpeciesToFix = outputCatchModelForAllSpecies.extractForSpecies(species);

-        String title = l(locale, "t3.level2.message.strateOutputGlobalComposition.resume");

+        String title = l(locale, "t3.level2.message.stratumOutputGlobalComposition.resume");

         return WeightCompositionModelHelper.decorateModel(

                 getDecoratorService(),

                 title,

  * 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%

         // - avec des captures

         // - dont la marée n'est pas samplesOnly

         // - dont la marée est complète

-

         Map<String, Integer> activityIds = activityDAO.findAllActivityIdsForCatchStratum(

                 configuration.getZoneTableName(),

                 configuration.getZone().getTopiaId(),

-                configuration.getSchoolType().getTopiaId(),

+                configuration.getSchoolTypeIds(),

                 configuration.getBeginDate(),

-                configuration.getEndDate()

-        );

-

+                configuration.getEndDate());

         // ensuite pour chaque activité on récupère sa marée et on conserve

         // l'activité uniquement ssi :

         // - maree.bateau de type senneur OK

         // - maree.bateau dans la bonne flotte OK

-

         return filterActivities(configuration, activityIds);

     }

         Map<Activity, Integer> result = new HashMap<>();

         if (activityIds != null && activityIds.size() > 0) {

             for (Map.Entry<String, Integer> e : activityIds.entrySet()) {

-

                 String activityId = e.getKey();

-

                 // get activity

                 Activity activity = configuration.getActivity(activityId);

-

                 // get his trip

                 Trip trip = activity.getTrip();

                 if (!possibleVessels.contains(trip.getVessel())) {

-

                     // not a matching boat

                     continue;

                 }

-

                 // recheck activity have some catches.

                 Preconditions.checkState(!activity.isCorrectedElementaryCatchEmpty(),

                         String.format("Can not accept an activity (%s) with no catch", activity.getTopiaId()));

             List<String> activityIds = activityDAO.findAllActivityIdsForSampleStratum(

                     configuration.getZoneTableName(),

                     zoneId,

-                    schoolTypeId,

+                    schoolTypeId == null ? null : configuration.getSchoolTypeIds(),

                     beginDate,

                     endDate);

             result.addAll(activityIds);

     @Override

     protected Set<String> findActivityIds(int level) {

         StratumConfiguration<Level3Configuration> configuration = getSampleStratum().getConfiguration();

-        String schoolTypeId = configuration.getSampleSchoolType().getTopiaId();

+        String schoolTypeId = configuration.getSchoolType().getTopiaId();

         String zoneId = configuration.getZone().getTopiaId();

         T3Date beginDate = configuration.getBeginDate();

         T3Date endDate = configuration.getEndDate();

     protected Set<String> findActivityIds(int level) {

         StratumConfiguration<Level3Configuration> configuration = getSampleStratum().getConfiguration();

-        String schoolTypeId = configuration.getSampleSchoolType().getTopiaId();

+        String schoolTypeId = configuration.getSchoolType().getTopiaId();

         String zoneId = configuration.getZone().getTopiaId();

         T3Date beginDate = configuration.getBeginDate();

         T3Date endDate = configuration.getEndDate();

 import com.google.common.collect.Sets;

 import fr.ird.t3.actions.T3Action;

 import fr.ird.t3.actions.stratum.OceanContext;

-import fr.ird.t3.actions.stratum.SampleStratum;

 import fr.ird.t3.actions.stratum.StratumConfiguration;

 import fr.ird.t3.actions.stratum.StratumMinimumSampleCount;

 import fr.ird.t3.entities.T3Predicates;

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

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

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

-import fr.ird.t3.entities.reference.SchoolTypeTopiaDao;

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

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

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

     private LengthWeightConversionTopiaDao lengthWeightConversionDAO;

     @InjectDAO(entityType = WeightCategoryTreatment.class)

     private WeightCategoryTreatmentTopiaDao weightCategoryTreatmentDAO;

-    //    @InjectDAO(entityType = SetSpeciesFrequency.class)

-//    private SetSpeciesFrequencyTopiaDao setSpeciesFrequencyDAO;

-//    @InjectDAO(entityType = SetSpeciesCatWeight.class)

-//    private SetSpeciesCatWeightTopiaDao setSpeciesCatWeightDAO;

-//    @InjectDAO(entityType = ExtrapolatedAllSetSpeciesFrequency.class)

-//    private ExtrapolatedAllSetSpeciesFrequencyTopiaDao extrapolatedAllSetSpeciesFrequencyDAO;

     @InjectDAO(entityType = Vessel.class)

     private VesselTopiaDao vesselDAO;

-    @InjectDAO(entityType = SchoolType.class)

-    private SchoolTypeTopiaDao schoolTypeDAO;

     private ZoneStratumAwareMeta zoneMeta;

     @InjectFromDAO(entityType = SchoolType.class, method = "findAllForStratum")

     private Set<SchoolType> schoolTypes;

-    //    @InjectEntityById(entityType = Ocean.class)

-//    private Ocean ocean;

     @InjectEntitiesById(entityType = Country.class)

     private Set<Country> catchFleets;

     @InjectEntitiesById(entityType = Species.class, path = "configuration.speciesIds")

     private Set<Vessel> possibleCatchVessels;

     private Set<Vessel> possibleSampleVessels;

     private Map<SchoolType, Map<String, Integer>> stratumMinimumSampleCountBySchoolType;

-    private int nbStratums;

+    private int nbStratum;

     private long nbCatchActivities;

     private long nbCatchActivitiesWithSample;

     /**

     private String topiaCreateDate;

     private int nbQuery;

     private StringBuilder queryBuffer = new StringBuilder();

-    private SchoolType boSchoolType;

-    private SchoolType blSchoolType;

     public Level3Action() {

         activityCache = CacheBuilder.newBuilder().build(

     @Override

     protected void prepareAction() throws Exception {

         super.prepareAction();

-        this.boSchoolType = schoolTypeDAO.forCodeEquals(1).findUnique();

-        this.blSchoolType = schoolTypeDAO.forCodeEquals(2).findUnique();

         this.totalFishesCount = new SpeciesCountAggregateModel();

         Level3Configuration configuration = getConfiguration();

         configuration.setLocale(getLocale());

                     }

                     break;

                 default:

-                    throw new IllegalStateException("Can not use the school fish " + code);

+                    throw new IllegalStateException(String.format("Can not use the school type %d", code));

             }

         }

         this.stratumMinimumSampleCountBySchoolType = minimumSampleCountBySchoolType;

     }

     private void executeActionWithCategories(Level3Configuration configuration, Set<String> usedActivityIds) throws Exception {

-        nbStratums = 0;

+        nbStratum = 0;

         for (SchoolType schoolType : schoolTypes) {

             List<WeightCategoryTreatment> weightCategories = getWeightCategoryTreatments(schoolType);

             Collection<ZoneStratumAware> zones = getZones(schoolType);

-            nbStratums += startDates.size() * zones.size() * weightCategories.size();

+            nbStratum += startDates.size() * zones.size() * weightCategories.size();

         }

-        setNbSteps(3 * nbStratums);

+        setNbSteps(3 * nbStratum);

         int timeStep = configuration.getTimeStep();

         MutableInt stratumIndex = new MutableInt(1);

         for (SchoolType schoolType : schoolTypes) {

     }

     private void executeActionWithoutCategories(Level3Configuration configuration, Set<String> usedActivityIds) throws Exception {

-        nbStratums = 0;

+        nbStratum = 0;

         for (SchoolType schoolType : schoolTypes) {

             Collection<ZoneStratumAware> zones = getZones(schoolType);

-            nbStratums += startDates.size() * zones.size();

+            nbStratum += startDates.size() * zones.size();

         }

-        setNbSteps(3 * nbStratums);

+        setNbSteps(3 * nbStratum);

         int timeStep = configuration.getTimeStep();

         MutableInt stratumIndex = new MutableInt(1);

         for (SchoolType schoolType : schoolTypes) {

     }

     private void doIterateOnDates(int timeStep, Level3Configuration configuration, SchoolType schoolType, Collection<ZoneStratumAware> zones, ZoneStratumAware zone, List<WeightCategoryTreatment> weightCategories, WeightCategoryTreatment weightCategoryTreatment, Set<String> usedActivityIds, MutableInt stratumIndex, Map<String, Integer> stratumMinimumCountBySpecie) throws Exception {

-        SchoolType sampleSchoolType = SampleStratum.getSampleSchoolType(schoolType, configuration.getSchoolTypeIndeterminate(), boSchoolType, blSchoolType);

         for (T3Date startDate : startDates) {

             // clear query buffer

             queryBuffer = new StringBuilder();

                             zoneMeta,

                             zone,

                             schoolType,

-                            sampleSchoolType,

                             weightCategoryTreatment,

                             startDate,

                             endDate,

         incrementsProgression();

         String stratumPrefix =

                 l(locale, "t3.level3.stratumLabel",

-                        stratumIndex, nbStratums,

+                        stratumIndex, nbStratum,

                         decorate(stratumConfiguration.getSchoolType()),

-                        decorate(stratumConfiguration.getSampleSchoolType()),

                         decorate(stratumConfiguration.getZone()),

                         stratumConfiguration.getBeginDate(),

                         stratumConfiguration.getEndDate());

         addInfoMessage("==============================================================================================");

         addInfoMessage(message);

         addInfoMessage("==============================================================================================");

+        //FIXME-261 Is there anything to do ?

+//        if (SchoolTypeIndeterminate.IGNORE == getConfiguration().getSchoolTypeIndeterminate()) {

+//            // Just report for all activities on School type indeterminate catch weight

+//            Set<String> activityIds = activityDAO.findAllActivityIdsForCatchStratum(

+//                    stratumConfiguration.getZoneTableName(),

+//                    stratumConfiguration.getZone().getTopiaId(),

+//                    Collections.singleton(SchoolTypeTopiaDao.SCHOOL_TYPE_INDETERMINATE_ID),

+//                    stratumConfiguration.getBeginDate(),

+//                    stratumConfiguration.getEndDate()).keySet();

+//            for (String activityId : activityIds) {

+//                for (CorrectedElementaryCatch correctedElementaryCatch : activityCache.get(activityId).getCorrectedElementaryCatch()) {

+//                    correctedElementaryCatch.setCorrectedCatchWeight(correctedElementaryCatch.getCatchWeight());

+//                }

+//            }

+//        }

         // get the catch stratum

         try (L3CatchStratum catchStratum = newCatchStratum(stratumConfiguration, weightCategories)) {

             incrementsProgression();

         return nbCatchActivitiesWithSample;

     }

-    public int getNbStratums() {

-        return nbStratums;

+    public int getNbStratum() {

+        return nbStratum;

     }

     @SuppressWarnings("unused")

 Indicateurs

 -----------

-- Nombre de strates                   : ${action.nbStratums}

+- Nombre de strates                   : ${action.nbStratum}

 - Nombre de marées                    : ${action.nbTrips}

 - Nombre de marées avec calcul du rf2 : ${action.nbTripsWithRF2}

 Indicators

 ----------

-- Number of stratums:                ${action.nbStratums}

+- Number of stratums:                ${action.nbStratum}

 - Number of trips:                   ${action.nbTrips}

 - Number of trips with computed rf2: ${action.nbTripsWithRF2}

 Indicateurs

 -----------

-- Nombre de strates                             : ${action.nbStratums}

+- Nombre de strates                             : ${action.nbStratum}

 - Nombre de strates corrigés                    : ${action.nbStrataFixed}

 - Nombre d'activités traités                    : ${action.totalCatchActivities}

 - Nombre d'activités traités (avec échantillon) : ${action.totalCatchActivitiesWithSample}

 Indicators

 ----------

-- Number of stratums:                    ${action.nbStratums}

+- Number of stratums:                    ${action.nbStratum}

 - Number of treated stratums:            ${action.nbStrataFixed}

 - Number of treated sets:                ${action.totalCatchActivities}

 - Number of treated sets (with samples): ${action.totalCatchActivitiesWithSample}

 Indicateurs

 -----------

-- Nombre de strates                             : ${action.nbStratums}

+- Nombre de strates                             : ${action.nbStratum}

 - Nombre de strates corrigés                    : ${action.nbStrataFixed}

 - Nombre d'activités traités                    : ${action.nbCatchActivities}

 - Nombre d'activités traités (avec échantillon) : ${action.nbCatchActivitiesWithSample}

 Indicators

 ----------

-- Number of stratums:                    ${action.nbStratums}

+- Number of stratums:                    ${action.nbStratum}

 - Number of treated stratums:            ${action.nbStrataFixed}

 - Number of treated sets:                ${action.nbCatchActivities}

 - Number of treated sets (with samples): ${action.nbCatchActivitiesWithSample}

 t3.level2.message.noCatch.in.stratum=No catches found in this stratum

 t3.level2.message.start.activity=Correct activity [%s/%s] \: %s (number of zones\: %s)

 t3.level2.message.start.stratum=Treat %s

-t3.level2.message.strateInputGlobalComposition.resume=Global specific composition (before correction)\:

-t3.level2.message.strateOutputGlobalComposition.resume=Global specific composition (after correction)\:

+t3.level2.message.stratumInputGlobalComposition.resume=Global specific composition (before correction)\:

+t3.level2.message.stratumOutputGlobalComposition.resume=Global specific composition (after correction)\:

 t3.level2.sampleStratum.resume.for.level=Sample stratum (lvevel %s)\n - Activity count %s\n - Fishes count (for species to fix) %s\n - Total weight (for species to fix) %s

-t3.level2.stratumLabel=Stratum [%s/%s] (%s (sample %s) - zone %s - [start %s - end %s])

+t3.level2.stratumLabel=Stratum [%s/%s] (%s - zone %s - [start %s - end %s])

 t3.level2.warning.missing.data.for.stratum=Impossible to compute sample stratum for %s, last substitution level reached.

 t3.level3.action=Level 3 Treatment

 t3.level3.catchStratum.nbFishesResume.title=Total count of fishes in catch stratum

 t3.level3.nbFishesResume.title=Total count of fishes

 t3.level3.sampleStratum.resume.for.level=Sample Stratum (level %s)\n - activity count %s\n - Total weight (for species to fix) %s\n - Count of fishes \:

 t3.level3.sampleStratum.resume.for.level.and.species=\n   Species %s \: %s

-t3.level3.stratumLabel=Stratum [%s/%s] (%s (sample %s) - zone %s - [begin %s - end %s])

+t3.level3.stratumLabel=Stratum [%s/%s] (%s - zone %s - [begin %s - end %s])

 t3.level3.warning.missing.data.for.stratum=Impossible de compute sample stratum for stratum %s, last substitution level reached.

 t3.level3.warning.missing.sample.species=Stratum %s, it miss a species %s in samples, can not extrapolate.

 t3.message.create.new.vessel=Create a new vessel %s and store in db.

 t3.level2.message.noCatch.in.stratum=Aucune capture trouvée dans cette strate

 t3.level2.message.start.activity=Correction de l'activité [%s/%s] \: %s (nombre de zones \: %s)

 t3.level2.message.start.stratum=Traitement %s

-t3.level2.message.strateInputGlobalComposition.resume=Composition globale des captures avant correction \:

-t3.level2.message.strateOutputGlobalComposition.resume=Composition globale des captures après correction \:

+t3.level2.message.stratumInputGlobalComposition.resume=Composition globale des captures avant correction \:

+t3.level2.message.stratumOutputGlobalComposition.resume=Composition globale des captures après correction \:

 t3.level2.sampleStratum.resume.for.level=Strate échantillon (niveau %s)\n - Nombre activités %s\n - Nombre de poissons (pour les espèces à corriger) %s\n - Poids total (pour les espèces à corriger) %s

-t3.level2.stratumLabel=Strate [%s/%s] (%s (échantillon %s) - zone %s - [debut %s - fin %s])

+t3.level2.stratumLabel=Strate [%s/%s] (%s - zone %s - [debut %s - fin %s])

 t3.level2.warning.missing.data.for.stratum=Impossible de calculer la strate échantillon pour la strate %s, dernier niveau de substitution atteint.

 t3.level3.action=Traitement de niveau 3

 t3.level3.catchStratum.nbFishesResume.title=Nombre total de poissons dans la strate capture

 t3.level3.nbFishesResume.title=Nombre total de poissons

 t3.level3.sampleStratum.resume.for.level=Strate échantillon (niveau %s)\n - Nombre activités %s\n - Poids total (pour les espèces à corriger) %s\n - Nombre de poissons \:

 t3.level3.sampleStratum.resume.for.level.and.species=\n   Espèce %s \: %s

-t3.level3.stratumLabel=Strate [%s/%s] (%s (échantillon %s) - zone %s - [debut %s - fin %s])

+t3.level3.stratumLabel=Strate [%s/%s] (%s - zone %s - [debut %s - fin %s])

 t3.level3.warning.missing.data.for.stratum=Impossible de calculer la strate échantillon pour la strate %s, dernier niveau de substitution atteint.

 t3.level3.warning.missing.sample.species=Strate %s, il manque une espèce %s dans les échantillons, extrapolation non possible.

 t3.message.create.new.vessel=Création d'un nouveau navire %s et sauvegarde en base

     protected void prepareAction(ComputeRF2Action action, Locale locale) {

         super.prepareAction(action, locale);

-        action.nbStratums = 100;

+        action.nbStratum = 100;

         action.nbTrips = 10;

         action.nbTripsWithRF2 = 5;

     }

     protected void prepareAction(ComputeRF2Action action, Locale locale) {

         super.prepareAction(action, locale);

-        action.nbStratums = 100;

+        action.nbStratum = 100;

         action.nbTrips = 10;

         action.nbTripsWithRF2 = 5;

     }

  * 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%

  */

 public abstract class CatchStratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>> extends Stratum<C, A> {

+    protected CatchStratum(StratumConfiguration<C> configuration, Collection<Species> speciesToFix) {

+        super(configuration, speciesToFix);

+    }

+

     /**

      * Gets a new loader of catch stratum.

      *

      */

     protected abstract CatchStratumLoader<C> newLoader();

-    protected CatchStratum(StratumConfiguration<C> configuration, Collection<Species> speciesToFix) {

-        super(configuration, speciesToFix);

-    }

-

     @Override

     public void init(T3ServiceContext serviceContext, List<WeightCategoryTreatment> weightCategories, A messager) throws Exception {

-

         CatchStratumLoader<C> stratumLoader = newLoader();

-

         // inject transaction in loader

         stratumLoader.setTransaction(serviceContext.getT3TopiaPersistenceContext());

-

-        // inject daos in loader

+        // inject dao in loader

         serviceContext.newService(IOCService.class).injectOnly(stratumLoader, InjectDAO.class);

-

         // get all catches usable in this stratum grouped by their owing activity

         Map<Activity, Integer> activities = stratumLoader.loadData(getConfiguration());

         setActivities(activities);

 import fr.ird.t3.actions.T3Action;

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

-import fr.ird.t3.entities.reference.SchoolType;

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

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

 import fr.ird.t3.services.IOCService;

 import fr.ird.t3.services.T3ServiceContext;

 import fr.ird.t3.services.ioc.InjectDAO;

+import org.nuiton.topia.persistence.TopiaException;

+

 import java.util.Collection;

 import java.util.List;

 import java.util.Map;

-import java.util.Objects;

 import java.util.Set;

-import org.nuiton.topia.persistence.TopiaException;

 /**

  * Base samle stratum.

      */

     private Integer substitutionLevel;

-    public static SchoolType getSampleSchoolType(SchoolType schoolType,SchoolTypeIndeterminate schoolTypeIndeterminate , SchoolType boSchoolType, SchoolType blSchoolType) {

-        if (Objects.requireNonNull(schoolType).getCode() == 3) {

-            switch (Objects.requireNonNull(schoolTypeIndeterminate)) {

-                case ALL_IN_BO:

-                    return boSchoolType;

-                case ALL_IN_BL:

-                    return blSchoolType;

-            }

-            throw new IllegalStateException("Can't deal with " + schoolTypeIndeterminate);

-        }

-        return schoolType;

-    }

-

     protected abstract SampleStratumLoader<C, A, S> newLoader();

     protected abstract String logSampleStratumLevel(int substitutionLevel,

  */

 public enum SchoolTypeIndeterminate {

     ALL_IN_BO, // consider as BO

-    ALL_IN_BL; // consider as BL

+    ALL_IN_BL, // consider as BL

+    IGNORE; // just report incoming data

     public String getLabel() {

         return I18nEnumHelper.getLabel(this);

  * 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%

 public abstract class Stratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>> implements Closeable, Iterable<Map.Entry<Activity, Integer>> {

     /**

-     * All activities selected for this stratum, with for catch stratum the number of zones where the activity should be used.

-     * <p/>

-     * see http://forge.codelutin.com/issues/1935

-     * <p/>

-     * <strong>Note:</strong> This data are available after invocation of method

-     * {@link Stratum#init(T3ServiceContext, List, T3Action)}.

-     */

-    private Map<Activity, Integer> activities;

-

-    /**

      * Stratum configuration of this stratum.

      *

      * @see StratumConfiguration

      */

     private final StratumConfiguration<C> configuration;

-

     /**

      * Selected set of species to fix.

      *

      * @since 1.3.1

      */

     private final Set<Species> speciesToFix;

+    /**

+     * All activities selected for this stratum, with for catch stratum the number of zones where the activity should be used.

+     * <p/>

+     * see http://forge.codelutin.com/issues/1935

+     * <p/>

+     * <strong>Note:</strong> This data are available after invocation of method

+     * {@link Stratum#init(T3ServiceContext, List, T3Action)}.

+     */

+    private Map<Activity, Integer> activities;

+

+    protected Stratum(StratumConfiguration<C> configuration, Collection<Species> speciesToFix) {

+        this.configuration = configuration;

+        this.speciesToFix = ImmutableSet.copyOf(speciesToFix);

+    }

     /**

      * Initialize the data of the stratum.

      */

     public abstract void init(T3ServiceContext serviceContext, List<WeightCategoryTreatment> weightCategories, A messager) throws Exception;

+    @SuppressWarnings("NullableProblems")

     @Override

     public Iterator<Map.Entry<Activity, Integer>> iterator() {

         return activities.entrySet().iterator();

     }

-    protected Stratum(StratumConfiguration<C> configuration, Collection<Species> speciesToFix) {

-        this.configuration = configuration;

-        this.speciesToFix = ImmutableSet.copyOf(speciesToFix);

-    }

-

     public final StratumConfiguration<C> getConfiguration() {

         return configuration;

     }

     }

     /**

-     * Obtain the activities selected for this stratum with the number of zones

-     * they are involved in.

+     * Obtain the activities selected for this stratum with the number of zones they are involved in.

      * <p/>

      * The number of zones (see http://forge.codelutin.com/issues/1935) is only

      * used for catch stratum, for sample stratum always used a single zone.

      * <p/>

-     * <strong>Note: </strong> to invoke this method, you need first to invoke

-     * the {@link Stratum#init(T3ServiceContext, List, T3Action}

+     * <strong>Note: </strong> to invoke this method, you need first to invoke the {@link #init(T3ServiceContext, List, T3Action)}

      *

      * @return the set of activities found for this stratum.

      */

 package fr.ird.t3.actions.stratum;

 import com.google.common.cache.LoadingCache;

+import com.google.common.collect.ImmutableSet;

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

+import fr.ird.t3.entities.reference.AbstractSchoolTypeTopiaDao;

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

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

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

     private final ZoneStratumAwareMeta zoneMeta;

     private final ZoneStratumAware zone;

     private final SchoolType schoolType;

-    private final SchoolType sampleSchoolType;

     private final WeightCategoryTreatment weightCategoryTreatment;

     private final T3Date beginDate;

     private final T3Date endDate;

                                    ZoneStratumAwareMeta zoneMeta,

                                    ZoneStratumAware zone,

                                    SchoolType schoolType,

-                                   SchoolType sampleSchoolType,

-                                   WeightCategoryTreatment weightCategoryTreatment, T3Date beginDate,

+                                   WeightCategoryTreatment weightCategoryTreatment,

+                                   T3Date beginDate,

                                    T3Date endDate,

                                    Collection<ZoneStratumAware> zones,

                                    Set<Vessel> possibleCatchVessels,

         this.zoneMeta = zoneMeta;

         this.zone = zone;

         this.schoolType = schoolType;

-        this.sampleSchoolType = sampleSchoolType;

         this.weightCategoryTreatment = weightCategoryTreatment;

         this.beginDate = beginDate;

         this.endDate = endDate;

      * Obtain a new stratum configuration given all his parameters.

      *

      * @param <C>                         type of configuration

-     * @param conf                        the level action configuration

+     * @param configuration               the level action configuration

      * @param zoneMeta                    type of zone to use

      * @param zone                        the zone of the stratum

      * @param schoolType                  the school type of the stratum

-     * @param sampleSchoolType            the school type of the sample stratum

      * @param weightCategoryTreatment     the weight category of the stratum (not nul only if {@link LevelConfigurationWithStratum#isUseWeightCategoriesInStratum()} is {@code true}.

      * @param startDate                   the start date of the stratum

      * @param endDate                     the end date of the stratum

-     * @param zones                       all the zones useable by the level action which used this stratum (can be used for sample stratum substitution)

+     * @param zones                       all the zones usable by the level action which used this stratum (can be used for sample stratum substitution)

      * @param possibleCatchVessels        set of possible vessels to use when selecting data in the catch stratum

      * @param possibleSampleVessels       set of possible vessels to use when selecting data in the sample stratum

      * @param stratumMinimumCountBySpecie minimum sample count needed by species for sample stratum substitution

      * @return the new instantiated stratum configuration

      */

     public static <C extends LevelConfigurationWithStratum> StratumConfiguration<C> newStratumConfiguration(

-            C conf,

+            C configuration,

             ZoneStratumAwareMeta zoneMeta,

             ZoneStratumAware zone,

             SchoolType schoolType,

-            SchoolType sampleSchoolType,

-            WeightCategoryTreatment weightCategoryTreatment, T3Date startDate,

+            WeightCategoryTreatment weightCategoryTreatment,

+            T3Date startDate,

             T3Date endDate,

             Collection<ZoneStratumAware> zones,

             Set<Vessel> possibleCatchVessels,

             LoadingCache<String, Activity> activityCache) {

         return new StratumConfiguration<>(

-                conf,

+                configuration,

                 zoneMeta,

                 zone,

                 schoolType,

-                sampleSchoolType,

                 weightCategoryTreatment,

                 startDate,

                 endDate,

         return configuration;

     }

-    public ZoneStratumAwareMeta getZoneMeta() {

+    private ZoneStratumAwareMeta getZoneMeta() {

         return zoneMeta;

     }

         return schoolType;

     }

-    public SchoolType getSampleSchoolType() {

-        return sampleSchoolType;

+    public Set<String> getSchoolTypeIds() {

+        ImmutableSet.Builder<String> builder = ImmutableSet.<String>builder().add(getSchoolType().getTopiaId());

+        switch (configuration.getSchoolTypeIndeterminate()) {

+            case ALL_IN_BO:

+                if (AbstractSchoolTypeTopiaDao.SCHOOL_TYPE_BO_ID.equals(getSchoolType().getTopiaId())) {

+                    builder.add(AbstractSchoolTypeTopiaDao.SCHOOL_TYPE_INDETERMINATE_ID);

+                }

+                break;

+            case ALL_IN_BL:

+                if (AbstractSchoolTypeTopiaDao.SCHOOL_TYPE_BL_ID.equals(getSchoolType().getTopiaId())) {

+                    builder.add(AbstractSchoolTypeTopiaDao.SCHOOL_TYPE_INDETERMINATE_ID);

+                }

+                break;

+            case IGNORE:

+                break;

+        }

+        return builder.build();

     }

     public T3Date getBeginDate() {

     @Override

     public String toString() {

-        return String.format("%s [schoolType: %s, sampleSchoolType: %s, zone: %s, startDate:%s, endDate:%s, weightCategory: %s]", super.toString(), schoolType.getLabel1(), sampleSchoolType.getLabel1(), zone.getTopiaId(), beginDate, endDate, weightCategoryTreatment);

+        return String.format("%s [schoolType: %s, zone: %s, startDate:%s, endDate:%s, weightCategory: %s]", super.toString(), schoolType.getLabel1(), zone.getTopiaId(), beginDate, endDate, weightCategoryTreatment);

     }

     public void addToActivity(Activity activity, Function<Activity, String> function, BiConsumer<Activity, String> consumer, int level) {

 import fr.ird.t3.entities.type.T3Date;

 import fr.ird.t3.models.WeightCompositionAggregateModel;

 import org.apache.commons.collections.CollectionUtils;

-import org.nuiton.topia.persistence.TopiaException;

 import org.nuiton.topia.persistence.support.TopiaSqlQuery;

 import org.nuiton.topia.persistence.support.TopiaSqlSupport;

         return correctedElementaryCatch.stream().map(SpeciesAware::getSpecies).collect(Collectors.toSet());

     }

-//    public boolean isActivityWithSample(Activity activity) throws TopiaException {

-//        SampleSetTopiaDao sampleSetDAO = topiaDaoSupplier.getDao(SampleSet.class, SampleSetTopiaDao.class);

-//        List<SampleSet> allByActivity = sampleSetDAO.forActivityEquals(activity).findAll();

-//        return CollectionUtils.isNotEmpty(allByActivity);

-//    }

-

     public Map<String, Integer> findAllActivityIdsForCatchStratum(String zoneTableName,

                                                                   String zoneId,

-                                                                  String schoolTypeId,

+                                                                  Set<String> schoolTypeIds,

                                                                   T3Date beginDate,

-                                                                  T3Date endDate) throws TopiaException {

-

+                                                                  T3Date endDate) {

         // ---

         // Get activities strictly inside the zone

         // ---

-        TopiaSqlQuery<String> query = new GetActivityIdsInZoneForCatchStratumQuery(zoneTableName, zoneId, schoolTypeId, beginDate, endDate);

+        TopiaSqlQuery<String> query = new GetActivityIdsInZoneForCatchStratumQuery(zoneTableName, zoneId, schoolTypeIds, beginDate, endDate);

         List<String> activityIds = topiaSqlSupport.findMultipleResult(query);

         Map<String, Integer> result = new HashMap<>();

         for (String activityId : activityIds) {

             // activity strictly inside a zone are exactly in one zone

             result.put(activityId, 1);

         }

-

         // ---

         // Get activities on the border of the zone

         // ---

-        query = new GetActivityIdsInBorderForCatchStratumQuery(zoneTableName, zoneId, schoolTypeId, beginDate, endDate);

+        query = new GetActivityIdsInBorderForCatchStratumQuery(zoneTableName, zoneId, schoolTypeIds, beginDate, endDate);

         activityIds = topiaSqlSupport.findMultipleResult(query);

-

         // ---

         // Get nb zones of such activities

         // ---

         return result;

     }

-//    public static void fillWeightsFromCorrectedCatchesWeight(Activity activity,

-//                                                             Map<WeightCategoryTreatment, Map<Species, Float>> weights,

-//                                                             WeightCompositionAggregateModel model) {

-//

-//        if (weights == null) {

-//            weights = new HashMap<>();

-//        }

-//        Multimap<WeightCategoryTreatment, CorrectedElementaryCatch> data =

-//                ActivityTopiaDao.groupByWeightCategoryTreatment(activity.getCorrectedElementaryCatch());

-//

-//        T3IOUtil.fillMapWithDefaultValue(

-//                weights, data.keySet(), T3Suppliers.MAP_SPECIES_FLOAT_SUPPLIER);

-//

-//        for (WeightCategoryTreatment weightCategory : data.keySet()) {

-//

-//            Map<Species, Float> speciesFloatMap = weights.get(weightCategory);

-//

-//            Collection<CorrectedElementaryCatch> correctedElementaryCatches = data.get(weightCategory);

-//

-//            fillWeights(weightCategory,

-//                        correctedElementaryCatches,

-//                        speciesFloatMap,

-//                        T3Functions.CORRECTED_ELEMENTARY_CATCH_TO_CORRECTED_CATCH_WEIGHT,

-//                        model

-//            );

-//        }

-//    }

-

     public List<String> findAllActivityIdsForSampleStratum(String zoneTableName,

                                                            String zoneId,

-                                                           String schoolTypeId,

+                                                           Set<String> schoolTypeIds,

                                                            T3Date beginDate,

-                                                           T3Date endDate) throws TopiaException {

+                                                           T3Date endDate) {

         TopiaSqlQuery<String> query;

-        if (schoolTypeId == null) {

+        if (schoolTypeIds == null) {

             // for any school type

             query = new GetActivityIdsForSampleStratumWithAnySchoolTypeQuery(zoneTableName, zoneId, beginDate, endDate);

         } else {

             // for a specific school type

-            query = new GetActivityIdsForSampleStratumQuery(zoneTableName, zoneId, schoolTypeId, beginDate, endDate);

+            query = new GetActivityIdsForSampleStratumQuery(zoneTableName, zoneId, schoolTypeIds, beginDate, endDate);

         }

         return topiaSqlSupport.findMultipleResult(query);

     }

-//    public Set<Species> getAllSpeciesFromCorrectedCatches(Activity activity) {

-//        Set<Species> result = new HashSet<>();

-//        for (CorrectedElementaryCatch aCatch : activity.getCorrectedElementaryCatch()) {

-//            result.add(aCatch.getSpecies());

-//        }

-//        return result;

-//    }

-

-//    public Set<Species> getAllSpeciesFromSetSpeciesFrequencies(Activity activity) {

-//        Set<Species> result = new HashSet<>();

-//        for (SetSpeciesFrequency frequency : activity.getSetSpeciesFrequency()) {

-//            result.add(frequency.getSpecies());

-//        }

-//        return result;

-//    }

-

     /**

      * Query to obtain from the given configuration, all the activity ids of a catch stratum.

      *

      * @since 1.0

      */

+    @SuppressWarnings("SqlResolve")

     public static class GetActivityIdsInZoneForCatchStratumQuery extends TopiaSqlQuery<String> {

         private final String zoneTableName;

-

         private final String zoneId;

-

-        private final String schoolTypeId;

-

+        private final Set<String> schoolTypeIds;

         private final T3Date beginDate;

-

         private final T3Date endDate;

         GetActivityIdsInZoneForCatchStratumQuery(String zoneTableName,

                                                  String zoneId,

-                                                 String schoolTypeId,

+                                                 Set<String> schoolTypeIds,

                                                  T3Date beginDate,

                                                  T3Date endDate) {

             this.zoneTableName = zoneTableName;

             this.zoneId = zoneId;

-            this.schoolTypeId = schoolTypeId;

+            this.schoolTypeIds = schoolTypeIds;

             this.beginDate = beginDate;

             this.endDate = endDate;

         }

         @Override

         public PreparedStatement prepareQuery(Connection connection) throws SQLException {

+            StringBuilder schoolTypeParameters = new StringBuilder();

+            for (String ignored : schoolTypeIds) {

+                schoolTypeParameters.append(", ?");

+            }

             PreparedStatement ps = connection.prepareStatement(

-                    "SELECT a.topiaid FROM trip t, activity a, " +

-                            zoneTableName + " z WHERE " +

-                            "a.trip = t.topiaId " +

+                    "SELECT a.topiaid FROM trip t, activity a, " + zoneTableName + " z " +

+                            "WHERE a.trip = t.topiaId " +

                             "AND t." + Trip.PROPERTY_TRIP_TYPE + " IN (0, 2)" +

                             "AND t." + Trip.PROPERTY_COMPLETION_STATUS + " IS NOT NULL " +

                             "AND t." + Trip.PROPERTY_COMPLETION_STATUS + " > 0 " +

                             "AND ST_WITHIN(a.the_geom, z.the_geom) " +

                             "AND z.topiaid = ? " +

                             "AND a.expertflag != 0 " +

-                            "AND a.schooltype = ? " +

+                            "AND a.schooltype IN (" + schoolTypeParameters.substring(2) + ")" +

                             "AND a.date::date >= ? " +

                             "AND a.date::date <= ? " +

                             "AND (SELECT COUNT(*) FROM CorrectedElementaryCatch c WHERE c.activity = a.topiaid) > 0"

             );

-            ps.setString(1, zoneId);

-            ps.setString(2, schoolTypeId);

-            ps.setDate(3, beginDate.toBeginSqlDate());

-            ps.setDate(4, endDate.toEndSqlDate());

+            int index = 0;

+            ps.setString(++index, zoneId);

+            for (String schoolTypeId : schoolTypeIds) {

+                ps.setString(++index, schoolTypeId);

+            }

+            ps.setDate(++index, beginDate.toBeginSqlDate());

+            ps.setDate(++index, endDate.toEndSqlDate());

             return ps;

         }

     }

     /**

-     * Query to obtain from the given configuration, all the activity ids of a

-     * catch stratum.

+     * Query to obtain from the given configuration, all the activity ids of a catch stratum.

      *

      * @since 1.0

      */

+    @SuppressWarnings("SqlResolve")

     public static class GetActivityIdsInBorderForCatchStratumQuery extends TopiaSqlQuery<String> {

         private final String zoneTableName;

-

         private final String zoneId;

-

-        private final String schoolTypeId;

-

+        private final Set<String> schoolTypeIds;

         private final T3Date beginDate;

-

         private final T3Date endDate;

         GetActivityIdsInBorderForCatchStratumQuery(String zoneTableName,

                                                    String zoneId,

-                                                   String schoolTypeId,

+                                                   Set<String> schoolTypeIds,

                                                    T3Date beginDate,

                                                    T3Date endDate) {

             this.zoneTableName = zoneTableName;

             this.zoneId = zoneId;

-            this.schoolTypeId = schoolTypeId;

+            this.schoolTypeIds = schoolTypeIds;

             this.beginDate = beginDate;

             this.endDate = endDate;

         }

         @Override

         public PreparedStatement prepareQuery(Connection connection) throws SQLException {

+            StringBuilder schoolTypeParameters = new StringBuilder();

+            for (String ignored : schoolTypeIds) {

+                schoolTypeParameters.append(", ?");

+            }

             PreparedStatement ps = connection.prepareStatement(

                     "SELECT a.topiaid FROM trip t, activity a, " +

                             zoneTableName + " z WHERE " +

                             "AND NOT ST_WITHIN(a.the_geom, z.the_geom) " +

                             "AND z.topiaid = ? " +

                             "AND a.expertflag != 0 " +

-                            "AND a.schooltype = ? " +

+                            "AND a.schooltype = IN (" + schoolTypeParameters.substring(2) + ") " +

                             "AND a.date::date >= ? " +

                             "AND a.date::date <= ? " +

-                            "AND (SELECT COUNT(*) FROM CorrectedElementaryCatch c WHERE c.activity = a.topiaid) > 0"

-            );

+                            "AND (SELECT COUNT(*) FROM CorrectedElementaryCatch c WHERE c.activity = a.topiaid) > 0");

-            ps.setString(1, zoneId);

-            ps.setString(2, schoolTypeId);

-            ps.setDate(3, beginDate.toBeginSqlDate());

-            ps.setDate(4, endDate.toEndSqlDate());

+            int index = 0;

+            ps.setString(++index, zoneId);

+            for (String schoolTypeId : schoolTypeIds) {

+                ps.setString(++index, schoolTypeId);

+            }

+            ps.setDate(++index, beginDate.toBeginSqlDate());

+            ps.setDate(++index, endDate.toEndSqlDate());

             return ps;

         }

     }

     /**

-     * Query to obtain from the given configuration, all the activity ids of a

-     * sample stratum.

+     * Query to obtain from the given configuration, all the activity ids of a sample stratum.

      *

      * @since 1.0

      */

+    @SuppressWarnings("SqlResolve")

     public static class GetActivityIdsForSampleStratumQuery extends TopiaSqlQuery<String> {

         private final String zoneTableName;

-

         private final String zoneId;

-

-        private final String schoolTypeId;

-

+        private final Set<String> schoolTypeIds;

         private final T3Date beginDate;

-

         private final T3Date endDate;

         GetActivityIdsForSampleStratumQuery(String zoneTableName,

                                             String zoneId,

-                                            String schoolTypeId,

+                                            Set<String> schoolTypeIds,

                                             T3Date beginDate,

                                             T3Date endDate) {

             this.zoneTableName = zoneTableName;

             this.zoneId = zoneId;

-            this.schoolTypeId = schoolTypeId;

+            this.schoolTypeIds = schoolTypeIds;

             this.beginDate = beginDate;

             this.endDate = endDate;

         }

         @Override

         public PreparedStatement prepareQuery(Connection connection) throws SQLException {

+            StringBuilder schoolTypeParameters = new StringBuilder();

+            for (String ignored : schoolTypeIds) {

+                schoolTypeParameters.append(", ?");

+            }

             PreparedStatement ps = connection.prepareStatement(

                     "SELECT a.topiaid FROM trip t, activity a, " +

                             zoneTableName + " z WHERE " +

                             "AND t." + Trip.PROPERTY_COMPLETION_STATUS + " > 0 ))" +

                             "AND ST_WITHIN(a.the_geom, z.the_geom) " +

                             "AND z.topiaid = ? " +

-                            "AND a.schooltype = ?" +

+                            "AND a.schooltype = IN (" + schoolTypeParameters.substring(2) + ")" +

                             "AND a.date::date >= ? " +

                             "AND a.date::date <= ? " +

-                            "AND (SELECT COUNT(*) FROM SetSpeciesCatWeight c WHERE c.activity = a.topiaid) > 0"

-            );

-            ps.setString(1, zoneId);

-            ps.setString(2, schoolTypeId);

-            ps.setDate(3, beginDate.toBeginSqlDate());

-            ps.setDate(4, endDate.toEndSqlDate());

+                            "AND (SELECT COUNT(*) FROM SetSpeciesCatWeight c WHERE c.activity = a.topiaid) > 0");

+            int index = 0;

+            ps.setString(++index, zoneId);

+            for (String schoolTypeId : schoolTypeIds) {

+                ps.setString(++index, schoolTypeId);

+            }

+            ps.setDate(++index, beginDate.toBeginSqlDate());

+            ps.setDate(++index, endDate.toEndSqlDate());

             return ps;

         }

     /**

      * Query to obtain from the given configuration, all the activity ids of a

-     * sample stratum for any school type (used by level 3 last substitution

-     * level).

+     * sample stratum for any school type (used by level 3 last substitution level).

      *

      * @since 1.4

      */

+    @SuppressWarnings("SqlResolve")

     public static class GetActivityIdsForSampleStratumWithAnySchoolTypeQuery extends TopiaSqlQuery<String> {

         private final String zoneTableName;

-

         private final String zoneId;

-

         private final T3Date beginDate;

-

         private final T3Date endDate;

-        GetActivityIdsForSampleStratumWithAnySchoolTypeQuery(String zoneTableName,

-                                                             String zoneId,

-                                                             T3Date beginDate,

-                                                             T3Date endDate) {

+        GetActivityIdsForSampleStratumWithAnySchoolTypeQuery(String zoneTableName, String zoneId, T3Date beginDate, T3Date endDate) {

             this.zoneTableName = zoneTableName;

             this.zoneId = zoneId;

             this.beginDate = beginDate;

     }

     /**

-     * Query to obtain from the given configuration, all the activity ids of a

-     * sample stratum.

+     * Query to obtain from the given configuration, all the activity ids of a sample stratum.

      *

      * @since 1.4

      */

+    @SuppressWarnings("SqlResolve")

     public static class GetActivityIdsAndNbZonesQuery extends TopiaSqlQuery<Integer> {

         private final String zoneTableName;

         @Override

         public PreparedStatement prepareQuery(Connection connection) throws SQLException {

             PreparedStatement ps = connection.prepareStatement(

-                    "SELECT count(*) " +

-                            "FROM activity a, " + zoneTableName + " z " +

+                    "SELECT count(*) FROM activity a, " + zoneTableName + " z " +

                             "WHERE a.topiaId  = ? " +

                             "AND ST_INTERSECTS(a.the_geom, z.the_geom) " +

-                            "AND z.schoolType = a.schoolType"

-            );

+                            "AND z.schoolType = a.schoolType");

             ps.setString(1, activityId);

             return ps;

         }

             return set.getInt(1);

         }

-        public int getNbZones(TopiaSqlSupport context, String activityId) throws TopiaException {

+        int getNbZones(TopiaSqlSupport context, String activityId) {

             this.activityId = activityId;

             return context.findSingleResult(this);

         }

     }

+

+//    public boolean isActivityWithSample(Activity activity) {

+//        SampleSetTopiaDao sampleSetDAO = topiaDaoSupplier.getDao(SampleSet.class, SampleSetTopiaDao.class);

+//        List<SampleSet> allByActivity = sampleSetDAO.forActivityEquals(activity).findAll();

+//        return CollectionUtils.isNotEmpty(allByActivity);

+//    }

+

+//    public static void fillWeightsFromCorrectedCatchesWeight(Activity activity,

+//                                                             Map<WeightCategoryTreatment, Map<Species, Float>> weights,

+//                                                             WeightCompositionAggregateModel model) {

+//

+//        if (weights == null) {

+//            weights = new HashMap<>();

+//        }

+//        Multimap<WeightCategoryTreatment, CorrectedElementaryCatch> data =

+//                ActivityTopiaDao.groupByWeightCategoryTreatment(activity.getCorrectedElementaryCatch());

+//

+//        T3IOUtil.fillMapWithDefaultValue(

+//                weights, data.keySet(), T3Suppliers.MAP_SPECIES_FLOAT_SUPPLIER);

+//

+//        for (WeightCategoryTreatment weightCategory : data.keySet()) {

+//

+//            Map<Species, Float> speciesFloatMap = weights.get(weightCategory);

+//

+//            Collection<CorrectedElementaryCatch> correctedElementaryCatches = data.get(weightCategory);

+//

+//            fillWeights(weightCategory,

+//                        correctedElementaryCatches,

+//                        speciesFloatMap,

+//                        T3Functions.CORRECTED_ELEMENTARY_CATCH_TO_CORRECTED_CATCH_WEIGHT,

+//                        model

+//            );

+//        }

+//    }

+

+//    public Set<Species> getAllSpeciesFromCorrectedCatches(Activity activity) {

+//        Set<Species> result = new HashSet<>();

+//        for (CorrectedElementaryCatch aCatch : activity.getCorrectedElementaryCatch()) {

+//            result.add(aCatch.getSpecies());

+//        }

+//        return result;

+//    }

+

+//    public Set<Species> getAllSpeciesFromSetSpeciesFrequencies(Activity activity) {

+//        Set<Species> result = new HashSet<>();

+//        for (SetSpeciesFrequency frequency : activity.getSetSpeciesFrequency()) {

+//            result.add(frequency.getSpecies());

+//        }

+//        return result;

+//    }

+

 }

 public class AbstractSchoolTypeTopiaDao<E extends SchoolType> extends GeneratedSchoolTypeTopiaDao<E> {

+    public static final String SCHOOL_TYPE_INDETERMINATE_ID = "fr.ird.t3.entities.reference.SchoolType#1297580528908#0.9747685881931636";

+    public static final String SCHOOL_TYPE_BL_ID = "fr.ird.t3.entities.reference.SchoolType#1297580528908#0.633774803291473";

+    public static final String SCHOOL_TYPE_BO_ID = "fr.ird.t3.entities.reference.SchoolType#1297580528908#0.8923578380543445";

+

     /**

-     * Obtain the two school types usabel while doing level 2 and 3 : says the

-     * free school type (code = 1) and the object school type.

+     * Obtain the two school types usable while doing level 2 and 3 : says the

+     * free school type and the object school type.

      *

      * @return the two school types

      * @throws TopiaException if any problem while loading data form database

     @SuppressWarnings("unused")

     public Set<E> findAllForStratum() {

         Set<E> result = new HashSet<>();

-        result.add(forCodeEquals(1).findUnique());

-        result.add(forCodeEquals(2).findUnique());

-        result.add(forCodeEquals(3).findUnique());

+        result.add(forTopiaIdEquals(SCHOOL_TYPE_BL_ID).findUnique());

+        result.add(forTopiaIdEquals(SCHOOL_TYPE_BO_ID).findUnique());

         return result;

     }

 }
 t3.config.users.file.description=Application users file

 t3.enum.fr.ird.t3.actions.stratum.SchoolTypeIndeterminate.ALL_IN_BL=Use Free school type

 t3.enum.fr.ird.t3.actions.stratum.SchoolTypeIndeterminate.ALL_IN_BO=Use Object school type

+t3.enum.fr.ird.t3.actions.stratum.SchoolTypeIndeterminate.IGNORE=Do not process

 t3.enum.fr.ird.t3.entities.data.TripType.LOGBOOKMISSING=Without Logbook

 t3.enum.fr.ird.t3.entities.data.TripType.SAMPLEONLY=Samples only

 t3.enum.fr.ird.t3.entities.data.TripType.STANDARD=Standard

 t3.config.users.file.description=Fichier contenant les utilisateurs de l'application

 t3.enum.fr.ird.t3.actions.stratum.SchoolTypeIndeterminate.ALL_IN_BL=Traiter comme des Bancs objets

 t3.enum.fr.ird.t3.actions.stratum.SchoolTypeIndeterminate.ALL_IN_BO=Traiter comme des Bancs libres

+t3.enum.fr.ird.t3.actions.stratum.SchoolTypeIndeterminate.IGNORE=Ne pas traiter

 t3.enum.fr.ird.t3.entities.data.TripType.LOGBOOKMISSING=Sans logbook

 t3.enum.fr.ird.t3.entities.data.TripType.SAMPLEONLY=Echantillons uniquement

 t3.enum.fr.ird.t3.entities.data.TripType.STANDARD=Standard

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

Commits:

30 changed files:

Changes: