Tony CHEMIT pushed to branch develop at ultreiaio / ird-t3 Commits: 3585d323 by Tony CHEMIT at 2018-03-23T13:30:48Z [N2][N3] Gestion des catégories de poids -10/+10kg dans la stratification N2 et N3 (See #263) - mise en place des filtres sur les strates - - - - - 29 changed files: - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratumLoader.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoader.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderAtlantic.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderIndian.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfiguration.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumResult.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2Action.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2OutputContext.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratumLoader.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratum.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoader.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderAtlantic.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderIndian.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfiguration.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumResult.java - t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3Action.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratum.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratumLoader.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratum.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratumLoader.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/Stratum.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java - t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumResult.java - t3-domain/src/main/java/fr/ird/t3/entities/cache/LengthWeightConversionCache.java - t3-domain/src/main/java/fr/ird/t3/entities/data/ActivityImpl.java - t3-domain/src/main/xmi/t3-persistence.zargo Changes: ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratum.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratum.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratum.java @@ -23,13 +23,9 @@ package fr.ird.t3.actions.data.level2; import com.google.common.collect.HashMultimap; import com.google.common.collect.Multimap; import com.google.common.collect.SetMultimap; -import fr.ird.t3.T3IOUtil; import fr.ird.t3.actions.stratum.CatchStratum; -import fr.ird.t3.actions.stratum.CatchStratumLoader; -import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.data.Activity; import fr.ird.t3.entities.data.CorrectedElementaryCatch; -import fr.ird.t3.entities.data.WeightCategoryTreatmentAware; import fr.ird.t3.entities.reference.Species; import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.models.WeightCompositionAggregateModel; @@ -42,12 +38,10 @@ import org.apache.commons.logging.LogFactory; import java.io.IOException; import java.util.Collection; -import java.util.HashMap; import java.util.List; import java.util.Locale; import java.util.Map; import java.util.Set; -import java.util.function.Function; import static org.nuiton.i18n.I18n.l; @@ -57,7 +51,7 @@ import static org.nuiton.i18n.I18n.l; * @author Tony Chemit - dev@tchemit.fr * @since 1.3 */ -public class L2CatchStratum extends CatchStratum<Level2Configuration, Level2Action> { +public class L2CatchStratum extends CatchStratum<Level2Configuration, Level2Action, L2StratumConfiguration> { private static final Log log = LogFactory.getLog(L2CatchStratum.class); /** @@ -101,14 +95,14 @@ public class L2CatchStratum extends CatchStratum<Level2Configuration, Level2Acti */ private WeightCompositionAggregateModel inputModelForSpeciesToFix; - private L2CatchStratum(StratumConfiguration<Level2Configuration> stratumConfiguration, Collection<Species> speciesToFix) { + private L2CatchStratum(L2StratumConfiguration stratumConfiguration, Collection<Species> speciesToFix) { super(stratumConfiguration, speciesToFix); weightCategoriesForSpecies = HashMultimap.create(); inputModelForAllSpecies = new WeightCompositionAggregateModel(); outputModelForAllSpecies = new WeightCompositionAggregateModel(); } - static L2CatchStratum newCatchStratum(StratumConfiguration<Level2Configuration> stratumConfiguration, + static L2CatchStratum newCatchStratum(L2StratumConfiguration stratumConfiguration, List<WeightCategoryTreatment> weightCategories, Collection<Species> species, Level2Action action) throws Exception { @@ -133,29 +127,6 @@ public class L2CatchStratum extends CatchStratum<Level2Configuration, Level2Acti return catchStratum; } - private static <X extends WeightCategoryTreatmentAware> void fillWeights( - WeightCategoryTreatment weightCategory, - Collection<X> data, - Map<Species, Float> weights, - Function<X, Float> function, - WeightCompositionAggregateModel model, - int divideFactor) { - if (weights == null) { - weights = new HashMap<>(); - } - for (X setSpeciesCatWeight : data) { - Species species = setSpeciesCatWeight.getSpecies(); - Float weight = weights.get(species); - if (weight == null) { - weight = 0f; - } - weight += function.apply(setSpeciesCatWeight) / divideFactor; - weights.put(species, weight); - } - if (model != null) { - model.addModel(weightCategory, weights); - } - } @Override public void close() throws IOException { @@ -242,11 +213,7 @@ public class L2CatchStratum extends CatchStratum<Level2Configuration, Level2Acti } @Override - public L2StratumConfiguration getConfiguration() { - return (L2StratumConfiguration) super.getConfiguration(); - } - @Override - protected CatchStratumLoader<Level2Configuration> newLoader() { + protected L2CatchStratumLoader newLoader() { return new L2CatchStratumLoader(); } @@ -258,23 +225,8 @@ public class L2CatchStratum extends CatchStratum<Level2Configuration, Level2Acti WeightCompositionAggregateModel sampleWeightModelForAllSpecies(Activity activity) { WeightCompositionAggregateModel sampleWeightModelFroAllSpecies = new WeightCompositionAggregateModel(); - L2SampleStratum.fillWeightsFromSetSpeciesCatWeight(activity, null, sampleWeightModelFroAllSpecies); + fillWeightsFromSamplesWeight(activity, null, sampleWeightModelFroAllSpecies); return sampleWeightModelFroAllSpecies; } - private void fillWeightsFromCatchesWeight(Activity activity, WeightCompositionAggregateModel model, int dividerFactor) { - Map<WeightCategoryTreatment, Map<Species, Float>> weights = new HashMap<>(); - Multimap<WeightCategoryTreatment, CorrectedElementaryCatch> data = getCorrectedElementaryCatchByCategory(activity); - T3IOUtil.fillMapWithDefaultValue(weights, data.keySet(), HashMap::new); - for (WeightCategoryTreatment weightCategory : data.keySet()) { - Map<Species, Float> speciesFloatMap = weights.get(weightCategory); - Collection<CorrectedElementaryCatch> correctedElementaryCatches = data.get(weightCategory); - fillWeights(weightCategory, - correctedElementaryCatches, - speciesFloatMap, - CorrectedElementaryCatch::getCatchWeight, - model, - dividerFactor); - } - } } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratumLoader.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratumLoader.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2CatchStratumLoader.java @@ -20,19 +20,12 @@ */ package fr.ird.t3.actions.data.level2; -import com.google.common.base.Preconditions; import fr.ird.t3.actions.stratum.CatchStratumLoader; -import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.data.Activity; import fr.ird.t3.entities.data.ActivityTopiaDao; -import fr.ird.t3.entities.data.Trip; -import fr.ird.t3.entities.reference.Vessel; -import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.services.ioc.InjectDAO; -import java.util.HashMap; import java.util.Map; -import java.util.Set; /** * To load a {@link L2CatchStratum} for a given stratum configuration. @@ -40,13 +33,13 @@ import java.util.Set; * @author Tony Chemit - dev@tchemit.fr * @since 1.3 */ -public class L2CatchStratumLoader extends CatchStratumLoader<Level2Configuration> { +public class L2CatchStratumLoader extends CatchStratumLoader<Level2Configuration, Level2Action, L2StratumConfiguration> { @InjectDAO(entityType = Activity.class) private ActivityTopiaDao activityDAO; @Override - public Map<Activity, Integer> loadData(StratumConfiguration<Level2Configuration> configuration) { + public Map<Activity, Integer> loadData(L2StratumConfiguration configuration) { // on commence par récupérer les activités : // - dans la zone // - avec le bon type de banc @@ -67,36 +60,4 @@ public class L2CatchStratumLoader extends CatchStratumLoader<Level2Configuration // - maree.bateau dans la bonne flotte OK return filterActivities(configuration, activityIds); } - - private Map<Activity, Integer> filterActivities(StratumConfiguration<Level2Configuration> configuration, Map<String, Integer> activityIds) { - Map<Activity, Integer> result = new HashMap<>(); - if (activityIds != null && activityIds.size() > 0) { - Set<Vessel> possibleVessels = configuration.getPossibleCatchVessels(); - WeightCategoryTreatment weightCategoryTreatment = configuration.getWeightCategoryTreatment(); - 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.isCorrectedElementaryCatchNotEmpty(), - String.format("Can not accept an activity (%s) with no catch", activity.getTopiaId())); - if (weightCategoryTreatment != null) { - // weight category is in stratum, check there is catch using this category - boolean foundWeightCategory = activity.withCorrectedElementaryCatch(weightCategoryTreatment); - if (!foundWeightCategory) { - // reject - the stratum weight category not found for this activity - continue; - } - } - result.put(activity, e.getValue()); - } - } - return result; - } -} +} \ No newline at end of file ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratum.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratum.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratum.java @@ -20,26 +20,17 @@ */ package fr.ird.t3.actions.data.level2; -import com.google.common.collect.ArrayListMultimap; -import com.google.common.collect.Multimap; -import com.google.common.collect.Multimaps; -import fr.ird.t3.T3IOUtil; import fr.ird.t3.actions.stratum.SampleStratum; -import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.data.Activity; -import fr.ird.t3.entities.data.SetSpeciesCatWeight; import fr.ird.t3.entities.data.SetSpeciesFrequency; -import fr.ird.t3.entities.data.WeightCategoryTreatmentAware; import fr.ird.t3.entities.reference.Species; import fr.ird.t3.entities.reference.WeightCategory; import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.models.WeightCompositionAggregateModel; import fr.ird.t3.models.WeightCompositionModelHelper; import fr.ird.t3.services.T3ServiceContext; -import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.nuiton.topia.persistence.TopiaException; import java.io.IOException; import java.util.Collection; @@ -48,7 +39,6 @@ import java.util.List; import java.util.Locale; import java.util.Map; import java.util.Set; -import java.util.function.Function; import static org.nuiton.i18n.I18n.l; @@ -58,20 +48,17 @@ import static org.nuiton.i18n.I18n.l; * @author Tony Chemit - dev@tchemit.fr * @since 1.2 */ -public class L2SampleStratum extends SampleStratum<Level2Configuration, Level2Action, L2SampleStratum> { +public class L2SampleStratum extends SampleStratum<Level2Configuration, Level2Action, L2StratumConfiguration, L2SampleStratum> { private static final Log log = LogFactory.getLog(L2SampleStratum.class); - /** * Total weight of the catch stratum. * <p/> * This is needed to test sample stratum quality when loading data. */ private final float catchStratumTotalWeight; - /** Weight composition for all species found in catches. */ private final WeightCompositionAggregateModel modelsForAllSpecies; - /** Weight composition model for only species to fix. */ private WeightCompositionAggregateModel modelsForSpeciesToFix; @@ -89,70 +76,22 @@ public class L2SampleStratum extends SampleStratum<Level2Configuration, Level2Ac */ private float sampleStratumTotalWeight; - private L2SampleStratum(StratumConfiguration<Level2Configuration> configuration, Collection<Species> speciesToFix, float catchStratumTotalWeight) { + private L2SampleStratum(L2StratumConfiguration configuration, L2CatchStratum catchStratum, Collection<Species> speciesToFix) { super(configuration, speciesToFix); - this.catchStratumTotalWeight = catchStratumTotalWeight; + this.catchStratumTotalWeight = catchStratum.getTotalCatchWeightForSpeciesToFix(); this.modelsForAllSpecies = new WeightCompositionAggregateModel(); } - static L2SampleStratum newSampleStratum(StratumConfiguration<Level2Configuration> stratumConfiguration, + static L2SampleStratum newSampleStratum(L2StratumConfiguration stratumConfiguration, + L2CatchStratum catchStratum, List<WeightCategoryTreatment> weightCategories, - float totalCatchWeight, Collection<Species> species, Level2Action action) throws Exception { - L2SampleStratum sampleStratum = new L2SampleStratum(stratumConfiguration, species, totalCatchWeight); + L2SampleStratum sampleStratum = new L2SampleStratum(stratumConfiguration, catchStratum, species); sampleStratum.init(action.getServiceContext(), weightCategories, action); return sampleStratum; } - public static void fillWeightsFromSetSpeciesCatWeight(Activity activity, - Map<WeightCategoryTreatment, Map<Species, Float>> weights, - WeightCompositionAggregateModel model) { - if (weights == null) { - weights = new HashMap<>(); - } - Multimap<WeightCategoryTreatment, SetSpeciesCatWeight> data = groupByWeightCategoryTreatment(activity.getSetSpeciesCatWeight()); - T3IOUtil.fillMapWithDefaultValue(weights, data.keySet(), HashMap::new); - for (WeightCategoryTreatment weightCategory : data.keySet()) { - Map<Species, Float> speciesFloatMap = weights.get(weightCategory); - Collection<SetSpeciesCatWeight> setSpeciesCatWeights = data.get(weightCategory); - fillWeights(weightCategory, setSpeciesCatWeights, speciesFloatMap, SetSpeciesCatWeight::getWeight, model); - } - } - - private static <X extends WeightCategoryTreatmentAware> Multimap<WeightCategoryTreatment, X> groupByWeightCategoryTreatment(Collection<X> activity) { - Multimap<WeightCategoryTreatment, X> index; - if (CollectionUtils.isEmpty(activity)) { - index = ArrayListMultimap.create(); - } else { - index = Multimaps.index(activity, WeightCategoryTreatmentAware::getWeightCategoryTreatment); - } - return index; - } - - private static <X extends WeightCategoryTreatmentAware> void fillWeights( - WeightCategoryTreatment weightCategory, - Collection<X> data, - Map<Species, Float> weights, - Function<X, Float> function, - WeightCompositionAggregateModel model) { - if (weights == null) { - weights = new HashMap<>(); - } - for (X setSpeciesCatWeight : data) { - Species species = setSpeciesCatWeight.getSpecies(); - Float weight = weights.get(species); - if (weight == null) { - weight = 0f; - } - weight += function.apply(setSpeciesCatWeight); - weights.put(species, weight); - } - if (model != null) { - model.addModel(weightCategory, weights); - } - } - @Override public void close() throws IOException { super.close(); @@ -189,23 +128,20 @@ public class L2SampleStratum extends SampleStratum<Level2Configuration, Level2Ac return sampleStratumTotalWeight; } - //FIXME-263 si la categorie de poids que faire ? @Override - protected void mergeNewActivities(T3ServiceContext serviceContext, Set<Activity> activities) throws TopiaException { + protected void mergeNewActivities(T3ServiceContext serviceContext, Set<Activity> activities) { Set<Species> species = getSpeciesToFix(); // all weights (for each species) for all weight categories found Map<WeightCategoryTreatment, Map<Species, Float>> weights = new HashMap<>(); for (Activity activity : activities) { // split cat weight by weight category - fillWeightsFromSetSpeciesCatWeight(activity, weights, null); + fillWeightsFromSamplesWeight(activity, weights, null); // obtain the set species frequencies for the current activity - Collection<SetSpeciesFrequency> setSpeciesFrequencies = activity.getSetSpeciesFrequency(); - if (activity.isSetSpeciesFrequencyNotEmpty()) { - // compute sample count for this activity - int newCount = computeSampleCount(setSpeciesFrequencies, species); - // merge it with final total count - sampleStratumTotalCount += newCount; - } + Collection<SetSpeciesFrequency> setSpeciesFrequencies = getSetSpeciesFrequency(activity); + // compute sample count for this activity + int newCount = computeSampleCount(setSpeciesFrequencies, species); + // merge it with final total count + sampleStratumTotalCount += newCount; } // add all weights to model for (Map.Entry<WeightCategoryTreatment, Map<Species, Float>> e : weights.entrySet()) { @@ -221,18 +157,6 @@ public class L2SampleStratum extends SampleStratum<Level2Configuration, Level2Ac log.info(String.format("sampleStratumTotalCount = %d / sampleStratumTotalWeight = %f", getSampleStratumTotalCount(), getSampleStratumTotalWeight())); } - //FIXME-263 si la categorie de poids que faire ? - private int computeSampleCount(Collection<SetSpeciesFrequency> setSpeciesFrequencies, Collection<Species> speciesToFix) { - int newCount = 0; - for (SetSpeciesFrequency setSpeciesFrequency : setSpeciesFrequencies) { - Species species = setSpeciesFrequency.getSpecies(); - if (speciesToFix.contains(species)) { - newCount += setSpeciesFrequency.getNumber(); - } - } - return newCount; - } - @Override public String logSampleStratumLevel(int substitutionLevel, Level2Action messager) { Locale l = messager.getLocale(); @@ -251,8 +175,14 @@ public class L2SampleStratum extends SampleStratum<Level2Configuration, Level2Ac modelsForSpeciesToFix); } - @Override - public L2StratumConfiguration getConfiguration() { - return (L2StratumConfiguration) super.getConfiguration(); + private int computeSampleCount(Collection<SetSpeciesFrequency> setSpeciesFrequencies, Collection<Species> speciesToFix) { + int newCount = 0; + for (SetSpeciesFrequency setSpeciesFrequency : setSpeciesFrequencies) { + Species species = setSpeciesFrequency.getSpecies(); + if (speciesToFix.contains(species)) { + newCount += setSpeciesFrequency.getNumber(); + } + } + return newCount; } } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoader.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoader.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoader.java @@ -28,6 +28,7 @@ import fr.ird.t3.entities.data.ActivityTopiaDao; import fr.ird.t3.entities.data.Trip; import fr.ird.t3.entities.reference.SchoolType; import fr.ird.t3.entities.reference.Vessel; +import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.entities.type.T3Date; import fr.ird.t3.services.ioc.InjectDAO; import org.apache.commons.logging.Log; @@ -43,7 +44,7 @@ import java.util.Set; * @author Tony Chemit - dev@tchemit.fr * @since 1.3 */ -public abstract class L2SampleStratumLoader extends SampleStratumLoader<Level2Configuration, Level2Action, L2SampleStratum> { +public abstract class L2SampleStratumLoader extends SampleStratumLoader<Level2Configuration, Level2Action, L2StratumConfiguration, L2SampleStratum> { private static final Log log = LogFactory.getLog(L2SampleStratumLoader.class); /** @@ -91,7 +92,7 @@ public abstract class L2SampleStratumLoader extends SampleStratumLoader<Level2Co @Override protected Set<String> findActivityIds(String schoolTypeId, T3Date beginDate, T3Date endDate, String... zoneIds) { - StratumConfiguration<Level2Configuration> configuration = getSampleStratum().getConfiguration(); + StratumConfiguration<Level2Configuration, Level2Action> configuration = getSampleStratum().getConfiguration(); Set<String> result = new HashSet<>(); for (String zoneId : zoneIds) { // on commence par récupérer les activités : @@ -110,28 +111,6 @@ public abstract class L2SampleStratumLoader extends SampleStratumLoader<Level2Co } @Override - protected Set<Activity> filterActivities(Set<String> activityIds) { - Set<Activity> result = new HashSet<>(); - StratumConfiguration<Level2Configuration> configuration = getSampleStratum().getConfiguration(); - Set<Vessel> possibleVessels = configuration.getPossibleSampleVessels(); - for (String activityId : activityIds) { - Activity activity = configuration.getActivity(activityId); - // recheck activity have some samples. - Preconditions.checkState( - !activity.isSetSpeciesCatWeightEmpty(), - String.format("Can not accept an activity (%s) with no sample", activity.getTopiaId())); - // get his trip - Trip trip = activity.getTrip(); - if (!possibleVessels.contains(trip.getVessel())) { - // not a matching boat - continue; - } - result.add(activity); - } - return result; - } - - @Override public boolean isStratumOk() { // test if we have enough sample weight L2SampleStratum sampleStratum = getSampleStratum(); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderAtlantic.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderAtlantic.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderAtlantic.java @@ -39,8 +39,7 @@ public class L2SampleStratumLoaderAtlantic extends L2SampleStratumLoader { @Override protected Set<String> findActivityIds(int level) { - - StratumConfiguration<Level2Configuration> configuration = getSampleStratum().getConfiguration(); + StratumConfiguration<Level2Configuration, Level2Action> configuration = getSampleStratum().getConfiguration(); String schoolTypeId = configuration.getSchoolType().getTopiaId(); String zoneId = configuration.getZone().getTopiaId(); T3Date beginDate = configuration.getBeginDate(); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderIndian.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderIndian.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2SampleStratumLoaderIndian.java @@ -40,7 +40,7 @@ public class L2SampleStratumLoaderIndian extends L2SampleStratumLoader { @Override protected Set<String> findActivityIds(int level) { - StratumConfiguration<Level2Configuration> configuration = getSampleStratum().getConfiguration(); + StratumConfiguration<Level2Configuration, Level2Action> configuration = getSampleStratum().getConfiguration(); String schoolTypeId = configuration.getSchoolType().getTopiaId(); String zoneId = configuration.getZone().getTopiaId(); T3Date beginDate = configuration.getBeginDate(); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfiguration.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfiguration.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumConfiguration.java @@ -35,9 +35,7 @@ import java.util.List; * * @author Tony Chemit - dev@tchemit.fr */ -public class L2StratumConfiguration extends StratumConfiguration<Level2Configuration> { - - private final List<WeightCategoryTreatment> weightCategoryTreatments; +class L2StratumConfiguration extends StratumConfiguration<Level2Configuration, Level2Action> { L2StratumConfiguration(Level2InputContext inputContext, SchoolType schoolType, @@ -48,23 +46,15 @@ public class L2StratumConfiguration extends StratumConfiguration<Level2Configura Collection<ZoneStratumAware> zones, List<WeightCategoryTreatment> weightCategoryTreatments) { super( - inputContext.getConfiguration(), - inputContext.getZoneMeta(), + inputContext, zone, schoolType, weightCategoryTreatment, beginDate, beginDate.incrementsMonths(inputContext.getConfiguration().getTimeStep() - 1), zones, - inputContext.getPossibleCatchVessels(), - inputContext.getPossibleSampleVessels(), null, - inputContext.getActivityCache(), + weightCategoryTreatments, stratumIndex); - this.weightCategoryTreatments = weightCategoryTreatments; - } - - public List<WeightCategoryTreatment> getWeightCategoryTreatments() { - return weightCategoryTreatments; } } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumResult.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumResult.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/L2StratumResult.java @@ -8,12 +8,12 @@ * 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% @@ -23,8 +23,6 @@ package fr.ird.t3.actions.data.level2; import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.actions.stratum.StratumResult; -import java.io.IOException; - /** * Result of a level 2 Stratum. * @@ -33,7 +31,7 @@ import java.io.IOException; */ public class L2StratumResult extends StratumResult<Level2Configuration> { - public L2StratumResult(StratumConfiguration<Level2Configuration> configuration, String label) { + public L2StratumResult(StratumConfiguration<Level2Configuration, Level2Action> configuration, String label) { super(configuration, label); } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2Action.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2Action.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2Action.java @@ -174,7 +174,7 @@ public class Level2Action extends T3Action<Level2Configuration> { incrementsProgression(); } else { // compute sample stratum - try (L2SampleStratum sampleStratum = L2SampleStratum.newSampleStratum(stratumConfiguration, weightCategories, catchStratum.getTotalCatchWeightForSpeciesToFix(), species, this)) { + try (L2SampleStratum sampleStratum = L2SampleStratum.newSampleStratum(stratumConfiguration, catchStratum, weightCategories, species, this)) { incrementsProgression(); // get the substitution level for the sample stratum Integer level = sampleStratum.getSubstitutionLevel(); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2OutputContext.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2OutputContext.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level2/Level2OutputContext.java @@ -40,16 +40,16 @@ import static org.nuiton.i18n.I18n.l; */ public class Level2OutputContext extends LevelOutputContext<Level2Configuration, Level2Action, Level2InputContext, L2StratumResult> { - private long totalCatchWeightForSpeciesFoFix; - private long totalCatchWeight; /** * Input Weight composition (based on {@link CorrectedElementaryCatch#getCatchWeight()}) for all species found in catches. */ - private WeightCompositionAggregateModel inputCatchModelForAllSpecies; + private final WeightCompositionAggregateModel inputCatchModelForAllSpecies; /** * Output Weight composition (based on {@link CorrectedElementaryCatch#getCorrectedCatchWeight()}) for all species found in catches. */ - private WeightCompositionAggregateModel outputCatchModelForAllSpecies; + private final WeightCompositionAggregateModel outputCatchModelForAllSpecies; + private long totalCatchWeightForSpeciesFoFix; + private long totalCatchWeight; public Level2OutputContext(Level2Action action, Level2InputContext inputContext) { super(action, inputContext); @@ -57,10 +57,12 @@ public class Level2OutputContext extends LevelOutputContext<Level2Configuration, this.outputCatchModelForAllSpecies = new WeightCompositionAggregateModel(); } + @SuppressWarnings("unused") public long getTotalCatchWeightForSpeciesFoFix() { return totalCatchWeightForSpeciesFoFix; } + @SuppressWarnings("unused") public long getTotalCatchWeight() { return totalCatchWeight; } @@ -72,22 +74,17 @@ public class Level2OutputContext extends LevelOutputContext<Level2Configuration, mergeResult(stratumResult); } + @SuppressWarnings("unused") public WeightCompositionAggregateModel getInputCatchModelForAllSpecies() { return inputCatchModelForAllSpecies; } - public void setInputCatchModelForAllSpecies(WeightCompositionAggregateModel inputCatchModelForAllSpecies) { - this.inputCatchModelForAllSpecies = inputCatchModelForAllSpecies; - } - + @SuppressWarnings("unused") public WeightCompositionAggregateModel getOutputCatchModelForAllSpecies() { return outputCatchModelForAllSpecies; } - public void setOutputCatchModelForAllSpecies(WeightCompositionAggregateModel outputCatchModelForAllSpecies) { - this.outputCatchModelForAllSpecies = outputCatchModelForAllSpecies; - } - + @SuppressWarnings("unused") public String getInputCatchStratumLog() { Collection<Species> species = getSpecies(); WeightCompositionAggregateModel inputCatchModelForSpeciesToFix = inputCatchModelForAllSpecies.extractForSpecies(species); @@ -99,6 +96,7 @@ public class Level2OutputContext extends LevelOutputContext<Level2Configuration, inputCatchModelForSpeciesToFix); } + @SuppressWarnings("unused") public String getOutputCatchStratumLog() { Collection<Species> species = getSpecies(); WeightCompositionAggregateModel outputCatchModelForSpeciesToFix = outputCatchModelForAllSpecies.extractForSpecies(species); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratum.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratum.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratum.java @@ -21,13 +21,10 @@ package fr.ird.t3.actions.data.level3; import fr.ird.t3.actions.stratum.CatchStratum; -import fr.ird.t3.actions.stratum.CatchStratumLoader; -import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.T3EntityHelper; import fr.ird.t3.entities.T3Suppliers; import fr.ird.t3.entities.data.Activity; import fr.ird.t3.entities.data.CorrectedElementaryCatch; -import fr.ird.t3.entities.data.SpeciesAware; import fr.ird.t3.entities.reference.Species; import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.services.T3ServiceContext; @@ -35,7 +32,6 @@ import fr.ird.t3.services.T3ServiceContext; import java.util.Collection; import java.util.List; import java.util.Map; -import java.util.function.Predicate; /** * Define a catch stratum for a given stratum of a level 2 treatment. @@ -43,16 +39,9 @@ import java.util.function.Predicate; * @author Tony Chemit - dev@tchemit.fr * @since 1.3 */ -public class L3CatchStratum extends CatchStratum<Level3Configuration, Level3Action> { +public class L3CatchStratum extends CatchStratum<Level3Configuration, Level3Action, L3StratumConfiguration> { /** - * Predicate to filter only species selected in configuration. - * - * @see #getSpeciesToFix() - * @since 1.4 - */ - private final Predicate<? super SpeciesAware> speciesToFixFilter; - /** * Keep the total weight of all the catches in the stratum. * <p/> * Used by sampleStratum for quality tests. @@ -61,17 +50,12 @@ public class L3CatchStratum extends CatchStratum<Level3Configuration, Level3Acti */ private float totalCatchWeight; - L3CatchStratum(StratumConfiguration<Level3Configuration> stratumConfiguration, Collection<Species> speciesToFix, Predicate<? super SpeciesAware> speciesToFixFilter) { + L3CatchStratum(L3StratumConfiguration stratumConfiguration, Collection<Species> speciesToFix) { super(stratumConfiguration, speciesToFix); - this.speciesToFixFilter = speciesToFixFilter; - } - @Override - public L3StratumConfiguration getConfiguration() { - return (L3StratumConfiguration) super.getConfiguration(); } @Override - protected CatchStratumLoader<Level3Configuration> newLoader() { + protected L3CatchStratumLoader newLoader() { return new L3CatchStratumLoader(); } @@ -87,7 +71,7 @@ public class L3CatchStratum extends CatchStratum<Level3Configuration, Level3Acti T3EntityHelper.getTotal( getCorrectedElementaryCatch(activity), CorrectedElementaryCatch::getCorrectedCatchWeight, - speciesToFixFilter, + getConfiguration().getSpeciesToFixFilter(), T3Suppliers.newActivityDecorateSupplier( serviceContext, activity, ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratumLoader.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratumLoader.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3CatchStratumLoader.java @@ -20,18 +20,12 @@ */ package fr.ird.t3.actions.data.level3; -import com.google.common.base.Preconditions; import fr.ird.t3.actions.stratum.CatchStratumLoader; -import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.data.Activity; import fr.ird.t3.entities.data.ActivityTopiaDao; -import fr.ird.t3.entities.data.Trip; -import fr.ird.t3.entities.reference.Vessel; import fr.ird.t3.services.ioc.InjectDAO; -import java.util.HashMap; import java.util.Map; -import java.util.Set; /** * To load a {@link L3CatchStratum} for a given stratum configuration. @@ -39,13 +33,13 @@ import java.util.Set; * @author Tony Chemit - dev@tchemit.fr * @since 1.3 */ -public class L3CatchStratumLoader extends CatchStratumLoader<Level3Configuration> { +public class L3CatchStratumLoader extends CatchStratumLoader<Level3Configuration, Level3Action, L3StratumConfiguration> { @InjectDAO(entityType = Activity.class) private ActivityTopiaDao activityDAO; @Override - public Map<Activity, Integer> loadData(StratumConfiguration<Level3Configuration> configuration) { + public Map<Activity, Integer> loadData(L3StratumConfiguration configuration) { // on commence par récupérer les activités : // - dans la zone // - avec le bon type de banc @@ -66,29 +60,4 @@ public class L3CatchStratumLoader extends CatchStratumLoader<Level3Configuration // - maree.bateau dans la bonne flotte OK return filterActivities(configuration, activityIds); } - - private Map<Activity, Integer> filterActivities(StratumConfiguration<Level3Configuration> configuration, Map<String, Integer> activityIds) { - - Set<Vessel> possibleVessels = configuration.getPossibleCatchVessels(); - - 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())); - result.put(activity, e.getValue()); - } - } - return result; - } } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratum.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratum.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratum.java @@ -25,7 +25,6 @@ import com.google.common.collect.Multimap; import com.google.common.collect.Multimaps; import fr.ird.t3.T3IOUtil; import fr.ird.t3.actions.stratum.SampleStratum; -import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.T3EntityHelper; import fr.ird.t3.entities.T3Suppliers; import fr.ird.t3.entities.cache.LengthWeightConversionWithContextCache; @@ -34,7 +33,6 @@ import fr.ird.t3.entities.data.Activity; import fr.ird.t3.entities.data.SetSpeciesCatWeight; import fr.ird.t3.entities.data.SetSpeciesFrequency; import fr.ird.t3.entities.data.SetSpeciesFrequencyTopiaDao; -import fr.ird.t3.entities.data.SpeciesAware; import fr.ird.t3.entities.reference.LengthWeightConversion; import fr.ird.t3.entities.reference.Species; import fr.ird.t3.entities.reference.WeightCategoryTreatment; @@ -54,7 +52,6 @@ import java.util.List; import java.util.Locale; import java.util.Map; import java.util.Set; -import java.util.function.Predicate; import static org.nuiton.i18n.I18n.l; @@ -64,7 +61,7 @@ import static org.nuiton.i18n.I18n.l; * @author Tony Chemit - dev@tchemit.fr * @since 1.2 */ -public class L3SampleStratum extends SampleStratum<Level3Configuration, Level3Action, L3SampleStratum> { +public class L3SampleStratum extends SampleStratum<Level3Configuration, Level3Action, L3StratumConfiguration, L3SampleStratum> { private static final Log log = LogFactory.getLog(L3SampleStratum.class); @@ -101,31 +98,22 @@ public class L3SampleStratum extends SampleStratum<Level3Configuration, Level3Ac */ private final LengthWeightConversionWithContextCache conversionHelper; /** - * Predicate to filter only species selected in configuration. - * - * @see #getSpeciesToFix() - * @since 1.4 - */ - private final Predicate<? super SpeciesAware> speciesToFixFilter; - /** * Total weight of the sample stratum. * <p/> * This is needed to test sample stratum quality when loading data. */ private float sampleStratumTotalWeight; - L3SampleStratum(StratumConfiguration<Level3Configuration> configuration, + L3SampleStratum(L3StratumConfiguration configuration, Collection<Species> speciesToFix, float catchStratumTotalWeight, - LengthWeightConversionWithContextCache conversionHelper, - Predicate<? super SpeciesAware> speciesToFixFilter) { + LengthWeightConversionWithContextCache conversionHelper) { super(configuration, speciesToFix); this.catchStratumTotalWeight = catchStratumTotalWeight; this.conversionHelper = conversionHelper; this.speciesCount = new HashMap<>(); this.compositionModel = new HashMap<>(); this.allSetSpeciesFrequenciesBySpecies = ArrayListMultimap.create(); - this.speciesToFixFilter = speciesToFixFilter; } @Override @@ -155,18 +143,13 @@ public class L3SampleStratum extends SampleStratum<Level3Configuration, Level3Ac } @Override - public L3StratumConfiguration getConfiguration() { - return (L3StratumConfiguration) super.getConfiguration(); - } - - @Override public void mergeNewActivities(T3ServiceContext serviceContext, Set<Activity> activities) { for (Activity activity : activities) { // add total weight of samples of the activity (only for selected species) float totalWeight = T3EntityHelper.getTotal( activity.getSetSpeciesCatWeight(), SetSpeciesCatWeight::getWeight, - speciesToFixFilter, + getConfiguration().getSpeciesToFixFilter(), T3Suppliers.newActivityDecorateSupplier( serviceContext, activity, ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoader.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoader.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoader.java @@ -20,14 +20,11 @@ */ package fr.ird.t3.actions.data.level3; -import com.google.common.base.Preconditions; import fr.ird.t3.actions.stratum.SampleStratumLoader; import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.entities.data.Activity; import fr.ird.t3.entities.data.ActivityTopiaDao; -import fr.ird.t3.entities.data.Trip; import fr.ird.t3.entities.reference.Species; -import fr.ird.t3.entities.reference.Vessel; import fr.ird.t3.entities.type.T3Date; import fr.ird.t3.services.ioc.InjectDAO; import org.apache.commons.logging.Log; @@ -45,7 +42,7 @@ import java.util.Set; * @author Tony Chemit - dev@tchemit.fr * @since 1.3 */ -public abstract class L3SampleStratumLoader extends SampleStratumLoader<Level3Configuration, Level3Action, L3SampleStratum> { +public abstract class L3SampleStratumLoader extends SampleStratumLoader<Level3Configuration, Level3Action, L3StratumConfiguration, L3SampleStratum> { private static final Log log = LogFactory.getLog(L3SampleStratumLoader.class); @@ -83,7 +80,7 @@ public abstract class L3SampleStratumLoader extends SampleStratumLoader<Level3Co @Override protected Set<String> findActivityIds(String schoolTypeId, T3Date beginDate, T3Date endDate, String... zoneIds) { Set<String> result = new HashSet<>(); - StratumConfiguration<Level3Configuration> configuration = getSampleStratum().getConfiguration(); + StratumConfiguration<Level3Configuration, Level3Action> configuration = getSampleStratum().getConfiguration(); for (String zoneId : zoneIds) { // on commence par récupérer les activités : // - dans la zone ET @@ -101,28 +98,6 @@ public abstract class L3SampleStratumLoader extends SampleStratumLoader<Level3Co } @Override - protected Set<Activity> filterActivities(Set<String> activityIds) { - Set<Activity> result = new HashSet<>(); - StratumConfiguration<Level3Configuration> configuration = getSampleStratum().getConfiguration(); - Set<Vessel> possibleVessels = configuration.getPossibleSampleVessels(); - for (String activityId : activityIds) { - 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 samples. - Preconditions.checkState( - !activity.isSetSpeciesCatWeightEmpty(), - String.format("Can not accept an activity (%s) with no sample", activity.getTopiaId())); - result.add(activity); - } - return result; - } - - @Override public boolean isStratumOk() { L3SampleStratum stratum = getSampleStratum(); // test if we have enough sample weight ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderAtlantic.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderAtlantic.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderAtlantic.java @@ -39,7 +39,7 @@ public class L3SampleStratumLoaderAtlantic extends L3SampleStratumLoader { @Override protected Set<String> findActivityIds(int level) { - StratumConfiguration<Level3Configuration> configuration = getSampleStratum().getConfiguration(); + StratumConfiguration<Level3Configuration, Level3Action> configuration = getSampleStratum().getConfiguration(); String schoolTypeId = configuration.getSchoolType().getTopiaId(); String zoneId = configuration.getZone().getTopiaId(); T3Date beginDate = configuration.getBeginDate(); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderIndian.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderIndian.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3SampleStratumLoaderIndian.java @@ -40,7 +40,7 @@ public class L3SampleStratumLoaderIndian extends L3SampleStratumLoader { @Override protected Set<String> findActivityIds(int level) { - StratumConfiguration<Level3Configuration> configuration = getSampleStratum().getConfiguration(); + StratumConfiguration<Level3Configuration, Level3Action> configuration = getSampleStratum().getConfiguration(); String schoolTypeId = configuration.getSchoolType().getTopiaId(); String zoneId = configuration.getZone().getTopiaId(); T3Date beginDate = configuration.getBeginDate(); ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfiguration.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfiguration.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumConfiguration.java @@ -22,7 +22,6 @@ package fr.ird.t3.actions.data.level3; */ import fr.ird.t3.actions.stratum.StratumConfiguration; -import fr.ird.t3.entities.cache.LengthWeightConversionWithContextCache; import fr.ird.t3.entities.reference.SchoolType; import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.entities.reference.zone.ZoneStratumAware; @@ -37,11 +36,9 @@ import java.util.Map; * * @author Tony Chemit - dev@tchemit.fr */ -public class L3StratumConfiguration extends StratumConfiguration<Level3Configuration> { +class L3StratumConfiguration extends StratumConfiguration<Level3Configuration, Level3Action> { - private final List<WeightCategoryTreatment> weightCategoryTreatments; private final Map<String, Integer> stratumMinimumSampleCount; - private final LengthWeightConversionWithContextCache conversionHelper; L3StratumConfiguration(Level3InputContext inputContext, SchoolType schoolType, @@ -53,33 +50,20 @@ public class L3StratumConfiguration extends StratumConfiguration<Level3Configura List<WeightCategoryTreatment> weightCategoryTreatments, Map<String, Integer> stratumMinimumSampleCount) { super( - inputContext.getConfiguration(), - inputContext.getZoneMeta(), + inputContext, zone, schoolType, weightCategoryTreatment, beginDate, beginDate.incrementsMonths(inputContext.getConfiguration().getTimeStep() - 1), zones, - inputContext.getPossibleCatchVessels(), - inputContext.getPossibleSampleVessels(), stratumMinimumSampleCount, - inputContext.getActivityCache(), + weightCategoryTreatments, stratumIndex); - this.weightCategoryTreatments = weightCategoryTreatments; this.stratumMinimumSampleCount = stratumMinimumSampleCount; - this.conversionHelper = inputContext.newLengthWeightConversionWithContextCache(zone.getOcean(), beginDate.toBeginDate()); - } - - public List<WeightCategoryTreatment> getWeightCategoryTreatments() { - return weightCategoryTreatments; } public Map<String, Integer> getStratumMinimumSampleCount() { return stratumMinimumSampleCount; } - - public LengthWeightConversionWithContextCache getConversionHelper() { - return conversionHelper; - } } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumResult.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumResult.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/L3StratumResult.java @@ -8,12 +8,12 @@ * 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% @@ -24,8 +24,6 @@ import fr.ird.t3.actions.stratum.StratumConfiguration; import fr.ird.t3.actions.stratum.StratumResult; import fr.ird.t3.models.SpeciesCountAggregateModel; -import java.io.IOException; - /** * Result of a level 3 Stratum. * @@ -42,7 +40,7 @@ public class L3StratumResult extends StratumResult<Level3Configuration> { */ private final SpeciesCountAggregateModel totalFishesCount; - public L3StratumResult(StratumConfiguration<Level3Configuration> configuration, String label) { + public L3StratumResult(StratumConfiguration<Level3Configuration, Level3Action> configuration, String label) { super(configuration, label); totalFishesCount = new SpeciesCountAggregateModel(); } @@ -52,7 +50,7 @@ public class L3StratumResult extends StratumResult<Level3Configuration> { } @Override - public void close() throws IOException { + public void close() { totalFishesCount.close(); } ===================================== t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3Action.java ===================================== --- a/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3Action.java +++ b/t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3Action.java @@ -405,7 +405,7 @@ public class Level3Action extends T3Action<Level3Configuration> { } private L3CatchStratum newCatchStratum(L3StratumConfiguration stratumConfiguration) throws Exception { - L3CatchStratum catchStratum = new L3CatchStratum(stratumConfiguration, inputContext.getSpecies(), inputContext.getSpeciesToFixFilter()); + L3CatchStratum catchStratum = new L3CatchStratum(stratumConfiguration, inputContext.getSpecies()); catchStratum.init(serviceContext, stratumConfiguration.getWeightCategoryTreatments(), this); // get the total weight of the catch stratum float catchStratumWeight = catchStratum.getTotalCatchWeight(); @@ -430,8 +430,8 @@ public class Level3Action extends T3Action<Level3Configuration> { new L3SampleStratum(stratumConfiguration, inputContext.getSpecies(), totalCatchWeight, - stratumConfiguration.getConversionHelper(), - inputContext.getSpeciesToFixFilter()); + stratumConfiguration.getConversionHelper() + ); sampleStratum.init(serviceContext, stratumConfiguration.getWeightCategoryTreatments(), this); return sampleStratum; } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratum.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratum.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratum.java @@ -20,12 +20,8 @@ */ package fr.ird.t3.actions.stratum; -import com.google.common.collect.Multimap; -import com.google.common.collect.Multimaps; import fr.ird.t3.actions.T3Action; import fr.ird.t3.entities.data.Activity; -import fr.ird.t3.entities.data.CorrectedElementaryCatch; -import fr.ird.t3.entities.data.WeightCategoryTreatmentAware; import fr.ird.t3.entities.reference.Species; import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.services.IOCService; @@ -33,9 +29,10 @@ import fr.ird.t3.services.T3ServiceContext; import fr.ird.t3.services.ioc.InjectDAO; import java.util.Collection; +import java.util.LinkedHashSet; import java.util.List; import java.util.Map; -import java.util.stream.Collectors; +import java.util.Set; /** * Base catch stratum. @@ -43,12 +40,13 @@ import java.util.stream.Collectors; * @author Tony Chemit - dev@tchemit.fr * @since 1.3 */ -public abstract class CatchStratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>> extends Stratum<C, A> { +public abstract class CatchStratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>, S extends StratumConfiguration<C, A>> extends Stratum<C, A, S> { - private int nbActivitiesWithSample; + private final Set<String> activityWithSampleIds; - protected CatchStratum(StratumConfiguration<C> configuration, Collection<Species> speciesToFix) { + protected CatchStratum(S configuration, Collection<Species> speciesToFix) { super(configuration, speciesToFix); + activityWithSampleIds = new LinkedHashSet<>(); } /** @@ -56,11 +54,11 @@ public abstract class CatchStratum<C extends LevelConfigurationWithStratum, A ex * * @return new instance of a catch stratum loader */ - protected abstract CatchStratumLoader<C> newLoader(); + protected abstract CatchStratumLoader<C, A, S> newLoader(); @Override public void init(T3ServiceContext serviceContext, List<WeightCategoryTreatment> weightCategories, A messager) throws Exception { - CatchStratumLoader<C> stratumLoader = newLoader(); + CatchStratumLoader<C, A, S> stratumLoader = newLoader(); // inject transaction in loader stratumLoader.setTransaction(serviceContext.getT3TopiaPersistenceContext()); // inject dao in loader @@ -68,7 +66,13 @@ public abstract class CatchStratum<C extends LevelConfigurationWithStratum, A ex // get all catches usable in this stratum grouped by their owing activity Map<Activity, Integer> activities = stratumLoader.loadData(getConfiguration()); setActivities(activities); - nbActivitiesWithSample = (int) activities.keySet().stream().filter(Activity::isSetSpeciesCatWeightNotEmpty).count(); + //FIXME- Ca doit etre dans SampleStratum ? + for (Activity activity : activities.keySet()) { + boolean withSample = !getSetSpeciesCatWeight(activity).isEmpty(); + if (withSample) { + activityWithSampleIds.add(activity.getTopiaId()); + } + } } /** @@ -81,18 +85,7 @@ public abstract class CatchStratum<C extends LevelConfigurationWithStratum, A ex } public int getNbActivitiesWithSample() { - return nbActivitiesWithSample; + return activityWithSampleIds.size(); } - public Collection<CorrectedElementaryCatch> getCorrectedElementaryCatch(Activity activity) { - WeightCategoryTreatment stratumWeightCategoryTreatment = getConfiguration().getWeightCategoryTreatment(); - if (stratumWeightCategoryTreatment == null) { - return activity.getCorrectedElementaryCatch(); - } - return activity.getCorrectedElementaryCatch().stream().filter(c -> stratumWeightCategoryTreatment.equals(c.getWeightCategoryTreatment())).collect(Collectors.toList()); - } - - public Multimap<WeightCategoryTreatment, CorrectedElementaryCatch> getCorrectedElementaryCatchByCategory(Activity activity) { - return Multimaps.index(getCorrectedElementaryCatch(activity), WeightCategoryTreatmentAware::getWeightCategoryTreatment); - } } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratumLoader.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratumLoader.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/CatchStratumLoader.java @@ -8,24 +8,32 @@ * it under the terms of the GNU Affero General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. - * + * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. - * + * * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. * #L% */ package fr.ird.t3.actions.stratum; +import com.google.common.base.Preconditions; +import fr.ird.t3.actions.T3Action; import fr.ird.t3.entities.T3TopiaPersistenceContext; import fr.ird.t3.entities.data.Activity; +import fr.ird.t3.entities.data.Trip; +import fr.ird.t3.entities.reference.Vessel; +import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.services.T3TopiaPersistenceContextAware; +import org.nuiton.topia.persistence.TopiaException; + +import java.util.HashMap; import java.util.Map; +import java.util.Set; import java.util.function.Supplier; -import org.nuiton.topia.persistence.TopiaException; /** * To loader a catch stratum. @@ -34,7 +42,7 @@ import org.nuiton.topia.persistence.TopiaException; * @see CatchStratum * @since 1.3 */ -public abstract class CatchStratumLoader<C extends LevelConfigurationWithStratum> implements T3TopiaPersistenceContextAware { +public abstract class CatchStratumLoader<C extends LevelConfigurationWithStratum, A extends T3Action<C>, S extends StratumConfiguration<C, A>> implements T3TopiaPersistenceContextAware { protected Supplier<T3TopiaPersistenceContext> transaction; @@ -42,10 +50,10 @@ public abstract class CatchStratumLoader<C extends LevelConfigurationWithStratum * To obtain all activities of the catch stratum. * * @param configuration stratum configuration - * @return the activites to use for the catch stratum + * @return activities to use for the catch stratum * @throws TopiaException if any pb while quering db */ - public abstract Map<Activity, Integer> loadData(StratumConfiguration<C> configuration) throws TopiaException; + public abstract Map<Activity, Integer> loadData(S configuration); @Override public Supplier<T3TopiaPersistenceContext> getT3TopiaPersistenceContext() { @@ -55,4 +63,33 @@ public abstract class CatchStratumLoader<C extends LevelConfigurationWithStratum public void setTransaction(Supplier<T3TopiaPersistenceContext> transaction) { this.transaction = transaction; } + + protected Map<Activity, Integer> filterActivities(S configuration, Map<String, Integer> activityIds) { + Map<Activity, Integer> result = new HashMap<>(); + if (activityIds != null && activityIds.size() > 0) { + Set<Vessel> possibleVessels = configuration.getPossibleCatchVessels(); + WeightCategoryTreatment weightCategoryTreatment = configuration.getWeightCategoryTreatment(); + 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())); + // weight category is in stratum, check there is catch using this category + if (weightCategoryTreatment != null && !activity.withCorrectedElementaryCatch(weightCategoryTreatment)) { + // reject - the stratum weight category not found for this activity + continue; + } + result.put(activity, e.getValue()); + } + } + return result; + } } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratum.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratum.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratum.java @@ -39,7 +39,7 @@ import java.util.Set; * @author Tony Chemit - dev@tchemit.fr * @since 1.3 */ -public abstract class SampleStratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>, S extends SampleStratum<C, A, S>> extends Stratum<C, A> { +public abstract class SampleStratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>, T extends StratumConfiguration<C, A>, S extends SampleStratum<C, A, T, S>> extends Stratum<C, A, T> { /** * Number of merged activites (counted when passing through method @@ -59,11 +59,11 @@ public abstract class SampleStratum<C extends LevelConfigurationWithStratum, A e */ private Integer substitutionLevel; - protected SampleStratum(StratumConfiguration<C> configuration, Collection<Species> speciesToFix) { + protected SampleStratum(T configuration, Collection<Species> speciesToFix) { super(configuration, speciesToFix); } - protected abstract SampleStratumLoader<C, A, S> newLoader(); + protected abstract SampleStratumLoader<C, A, T, S> newLoader(); protected abstract String logSampleStratumLevel(int substitutionLevel, A messager); @@ -93,7 +93,7 @@ public abstract class SampleStratum<C extends LevelConfigurationWithStratum, A e @Override public void init(T3ServiceContext serviceContext, List<WeightCategoryTreatment> weightCategories, A messager) throws Exception { - SampleStratumLoader<C, A, S> stratumLoader = newLoader(); + SampleStratumLoader<C, A, T, S> stratumLoader = newLoader(); // inject transaction in loader stratumLoader.setTransaction(serviceContext.getT3TopiaPersistenceContext()); @@ -115,4 +115,5 @@ public abstract class SampleStratum<C extends LevelConfigurationWithStratum, A e public final int getNbMergedActivities() { return nbMergedActivities; } + } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratumLoader.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratumLoader.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/SampleStratumLoader.java @@ -20,9 +20,13 @@ */ package fr.ird.t3.actions.stratum; +import com.google.common.base.Preconditions; import fr.ird.t3.actions.T3Action; import fr.ird.t3.entities.T3TopiaPersistenceContext; import fr.ird.t3.entities.data.Activity; +import fr.ird.t3.entities.data.Trip; +import fr.ird.t3.entities.reference.Vessel; +import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.entities.type.T3Date; import fr.ird.t3.services.T3ServiceContext; import fr.ird.t3.services.T3TopiaPersistenceContextAware; @@ -38,13 +42,13 @@ import java.util.Set; import java.util.function.Supplier; /** - * To loader a catch stratum. + * To loader a sample stratum. * * @author Tony Chemit - dev@tchemit.fr - * @see CatchStratum + * @see SampleStratum * @since 1.3 */ -public abstract class SampleStratumLoader<C extends LevelConfigurationWithStratum, A extends T3Action<C>, S extends SampleStratum<C, A, S>> implements T3TopiaPersistenceContextAware { +public abstract class SampleStratumLoader<C extends LevelConfigurationWithStratum, A extends T3Action<C>, T extends StratumConfiguration<C, A>, S extends SampleStratum<C, A, T, S>> implements T3TopiaPersistenceContextAware { private static final Log log = LogFactory.getLog(SampleStratumLoader.class); private final C levelConfiguration; @@ -60,7 +64,7 @@ public abstract class SampleStratumLoader<C extends LevelConfigurationWithStratu protected SampleStratumLoader(S sampleStratum) { this.sampleStratum = sampleStratum; - levelConfiguration = sampleStratum.getConfiguration().getConfiguration(); + this.levelConfiguration = sampleStratum.getConfiguration().getConfiguration(); } /** @@ -77,17 +81,6 @@ public abstract class SampleStratumLoader<C extends LevelConfigurationWithStratu protected abstract Set<String> findActivityIds(String schoolTypeId, T3Date beginDate, T3Date endDate, String... zoneIds); - /** - * From a set of activity ids, filter the one that can be use in this - * stratum. This mainly means to filter some of them using the stratum - * configuration. - * - * @param activityIds ids of activities to filter - * @return the set of usable activities after having - * @throws TopiaException if any database problem while loading data - */ - protected abstract Set<Activity> filterActivities(Set<String> activityIds); - protected abstract boolean isStratumOk(); @Override @@ -157,4 +150,41 @@ public abstract class SampleStratumLoader<C extends LevelConfigurationWithStratu return levelConfiguration.getTimeStep(); } + /** + * From a set of activity ids, filter the one that can be use in this + * stratum. This mainly means to filter some of them using the stratum + * configuration. + * + * @param activityIds ids of activities to filter + * @return the set of usable activities after having + * @throws TopiaException if any database problem while loading data + */ + private Set<Activity> filterActivities(Set<String> activityIds) { + Set<Activity> result = new HashSet<>(); + T configuration = getSampleStratum().getConfiguration(); + Set<Vessel> possibleVessels = configuration.getPossibleSampleVessels(); + WeightCategoryTreatment weightCategoryTreatment = configuration.getWeightCategoryTreatment(); + for (String activityId : activityIds) { + 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 samples. + Preconditions.checkState(activity.isSetSpeciesCatWeightNotEmpty(), + String.format("Can not accept an activity (%s) with no sample", activity.getTopiaId())); + if (weightCategoryTreatment != null) { + // weight category is in stratum, check there is catch using this category + boolean foundWeightCategory = activity.withSetSpeciesCatWeight(weightCategoryTreatment); + if (!foundWeightCategory) { + // reject - the stratum weight category not found for this activity + continue; + } + } + result.add(activity); + } + return result; + } } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/Stratum.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/Stratum.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/Stratum.java @@ -20,21 +20,40 @@ */ package fr.ird.t3.actions.stratum; +import com.google.common.collect.ArrayListMultimap; import com.google.common.collect.ImmutableSet; +import com.google.common.collect.Multimap; +import com.google.common.collect.Multimaps; +import fr.ird.t3.T3IOUtil; import fr.ird.t3.actions.T3Action; +import fr.ird.t3.entities.cache.LengthWeightConversionWithContextCache; import fr.ird.t3.entities.data.Activity; +import fr.ird.t3.entities.data.CorrectedElementaryCatch; +import fr.ird.t3.entities.data.SetSpeciesCatWeight; +import fr.ird.t3.entities.data.SetSpeciesFrequency; +import fr.ird.t3.entities.data.SetSpeciesFrequencyTopiaDao; +import fr.ird.t3.entities.data.WeightCategoryTreatmentAware; +import fr.ird.t3.entities.reference.LengthWeightConversion; import fr.ird.t3.entities.reference.Species; +import fr.ird.t3.entities.reference.SpeciesTopiaDao; import fr.ird.t3.entities.reference.WeightCategoryTreatment; +import fr.ird.t3.models.WeightCompositionAggregateModel; import fr.ird.t3.services.T3ServiceContext; import org.nuiton.topia.persistence.TopiaException; import java.io.Closeable; import java.io.IOException; +import java.util.ArrayList; import java.util.Collection; +import java.util.Collections; +import java.util.HashMap; import java.util.Iterator; +import java.util.LinkedList; import java.util.List; import java.util.Map; import java.util.Set; +import java.util.function.Function; +import java.util.stream.Collectors; /** * base class for any stratum. @@ -43,14 +62,14 @@ import java.util.Set; * @see CatchStratum * @since 1.0 */ -public abstract class Stratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>> implements Closeable, Iterable<Map.Entry<Activity, Integer>> { +public abstract class Stratum<C extends LevelConfigurationWithStratum, A extends T3Action<C>, S extends StratumConfiguration<C, A>> implements Closeable, Iterable<Map.Entry<Activity, Integer>> { /** * Stratum configuration of this stratum. * * @see StratumConfiguration */ - private final StratumConfiguration<C> configuration; + private final S configuration; /** * Selected set of species to fix. * @@ -67,7 +86,7 @@ public abstract class Stratum<C extends LevelConfigurationWithStratum, A extends */ private Map<Activity, Integer> activities; - protected Stratum(StratumConfiguration<C> configuration, Collection<Species> speciesToFix) { + protected Stratum(S configuration, Collection<Species> speciesToFix) { this.configuration = configuration; this.speciesToFix = ImmutableSet.copyOf(speciesToFix); } @@ -88,7 +107,7 @@ public abstract class Stratum<C extends LevelConfigurationWithStratum, A extends return activities.entrySet().iterator(); } - public StratumConfiguration<C> getConfiguration() { + public S getConfiguration() { return configuration; } @@ -128,4 +147,107 @@ public abstract class Stratum<C extends LevelConfigurationWithStratum, A extends throw new IllegalStateException("You must invoke the #init(tx) method before accessing stratum data."); } } + + public Collection<CorrectedElementaryCatch> getCorrectedElementaryCatch(Activity activity) { + WeightCategoryTreatment stratumWeightCategoryTreatment = getConfiguration().getWeightCategoryTreatment(); + if (stratumWeightCategoryTreatment == null) { + return activity.getCorrectedElementaryCatch(); + } + return activity.getCorrectedElementaryCatch().stream().filter(c -> stratumWeightCategoryTreatment.equals(c.getWeightCategoryTreatment())).collect(Collectors.toList()); + } + + public Multimap<WeightCategoryTreatment, CorrectedElementaryCatch> getCorrectedElementaryCatchByCategory(Activity activity) { + return Multimaps.index(getCorrectedElementaryCatch(activity), WeightCategoryTreatmentAware::getWeightCategoryTreatment); + } + + private Multimap<WeightCategoryTreatment, SetSpeciesCatWeight> getSetSpeciesCatWeightByCategory(Activity activity) { + return Multimaps.index(getSetSpeciesCatWeight(activity), WeightCategoryTreatmentAware::getWeightCategoryTreatment); + } + + Collection<SetSpeciesCatWeight> getSetSpeciesCatWeight(Activity activity) { + WeightCategoryTreatment stratumWeightCategoryTreatment = getConfiguration().getWeightCategoryTreatment(); + if (stratumWeightCategoryTreatment == null) { + return activity.getSetSpeciesCatWeight(); + } + return activity.getSetSpeciesCatWeight().stream().filter(c -> stratumWeightCategoryTreatment.equals(c.getWeightCategoryTreatment())).collect(Collectors.toList()); + } + + public Collection<SetSpeciesFrequency> getSetSpeciesFrequency(Activity activity) { + WeightCategoryTreatment stratumWeightCategoryTreatment = getConfiguration().getWeightCategoryTreatment(); + if (stratumWeightCategoryTreatment == null) { + return activity.getSetSpeciesFrequency(); + } + LengthWeightConversionWithContextCache conversionHelper = getConfiguration().getConversionHelper(); + + Multimap<Species, SetSpeciesFrequency> setSpeciesFrequencyBySpecies = SpeciesTopiaDao.groupBySpecies(activity.getSetSpeciesFrequency()); + Multimap<Species, Integer> lengthClassesBySpecies = ArrayListMultimap.create(); + // collect all length classes by species + SetSpeciesFrequencyTopiaDao.collectLengthClasses(setSpeciesFrequencyBySpecies, lengthClassesBySpecies); + List<SetSpeciesFrequency> result = new LinkedList<>(); + for (Map.Entry<Species, Collection<SetSpeciesFrequency>> entry : setSpeciesFrequencyBySpecies.asMap().entrySet()) { + Species species = entry.getKey(); + LengthWeightConversion conversion = conversionHelper.getConversions(species); + Collection<SetSpeciesFrequency> setSizes = entry.getValue(); + List<Integer> lengthClasses = new ArrayList<>(lengthClassesBySpecies.get(species)); + Collections.sort(lengthClasses); + List<Integer> lengthClassesAccepted = conversionHelper.getLengthClasses(conversion, stratumWeightCategoryTreatment, lengthClasses); + result.addAll(setSizes.stream().filter(f -> lengthClassesAccepted.contains(f.getLfLengthClass())).collect(Collectors.toList())); + } + return result; + } + + protected void fillWeightsFromCatchesWeight(Activity activity, WeightCompositionAggregateModel model, int dividerFactor) { + Map<WeightCategoryTreatment, Map<Species, Float>> weights = new HashMap<>(); + Multimap<WeightCategoryTreatment, CorrectedElementaryCatch> data = getCorrectedElementaryCatchByCategory(activity); + T3IOUtil.fillMapWithDefaultValue(weights, data.keySet(), HashMap::new); + for (WeightCategoryTreatment weightCategory : data.keySet()) { + Map<Species, Float> speciesFloatMap = weights.get(weightCategory); + Collection<CorrectedElementaryCatch> correctedElementaryCatches = data.get(weightCategory); + fillWeights(weightCategory, + correctedElementaryCatches, + speciesFloatMap, + CorrectedElementaryCatch::getCatchWeight, + model, + dividerFactor); + } + } + + protected void fillWeightsFromSamplesWeight(Activity activity, + Map<WeightCategoryTreatment, Map<Species, Float>> weights, + WeightCompositionAggregateModel model) { + if (weights == null) { + weights = new HashMap<>(); + } + Multimap<WeightCategoryTreatment, SetSpeciesCatWeight> data = getSetSpeciesCatWeightByCategory(activity); + T3IOUtil.fillMapWithDefaultValue(weights, data.keySet(), HashMap::new); + for (WeightCategoryTreatment weightCategory : data.keySet()) { + Map<Species, Float> speciesFloatMap = weights.get(weightCategory); + Collection<SetSpeciesCatWeight> setSpeciesCatWeights = data.get(weightCategory); + fillWeights(weightCategory, setSpeciesCatWeights, speciesFloatMap, SetSpeciesCatWeight::getWeight, model, 1); + } + } + + protected <X extends WeightCategoryTreatmentAware> void fillWeights(WeightCategoryTreatment weightCategory, + Collection<X> data, + Map<Species, Float> weights, + Function<X, Float> function, + WeightCompositionAggregateModel model, + int divideFactor) { + if (weights == null) { + weights = new HashMap<>(); + } + for (X datum : data) { + Species species = datum.getSpecies(); + Float weight = weights.get(species); + if (weight == null) { + weight = 0f; + } + weight += function.apply(datum) / divideFactor; + weights.put(species, weight); + } + if (model != null) { + model.addModel(weightCategory, weights); + } + } + } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumConfiguration.java @@ -20,11 +20,13 @@ */ package fr.ird.t3.actions.stratum; -import com.google.common.cache.LoadingCache; import com.google.common.collect.ImmutableSet; +import fr.ird.t3.actions.T3Action; +import fr.ird.t3.entities.cache.LengthWeightConversionWithContextCache; import fr.ird.t3.entities.data.Activity; -import fr.ird.t3.entities.reference.AbstractSchoolTypeTopiaDao; +import fr.ird.t3.entities.data.SpeciesAware; import fr.ird.t3.entities.reference.SchoolType; +import fr.ird.t3.entities.reference.SchoolTypeTopiaDao; import fr.ird.t3.entities.reference.Vessel; import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.entities.reference.zone.ZoneStratumAware; @@ -33,12 +35,14 @@ import fr.ird.t3.entities.type.T3Date; import java.util.Collection; import java.util.Iterator; +import java.util.List; import java.util.Map; import java.util.Objects; import java.util.Set; import java.util.concurrent.ExecutionException; import java.util.function.BiConsumer; import java.util.function.Function; +import java.util.function.Predicate; /** * Configuration of a stratum. @@ -46,57 +50,54 @@ import java.util.function.Function; * @author Tony Chemit - dev@tchemit.fr * @since 1.0 */ -public class StratumConfiguration<C extends LevelConfigurationWithStratum> { +public class StratumConfiguration<C extends LevelConfigurationWithStratum, A extends T3Action<C>> { - private final C configuration; + private final LevelInputContext<C, A> inputContext; private final Collection<ZoneStratumAware> zones; - private final ZoneStratumAwareMeta zoneMeta; private final ZoneStratumAware zone; private final SchoolType schoolType; private final WeightCategoryTreatment weightCategoryTreatment; private final T3Date beginDate; private final T3Date endDate; - private final Set<Vessel> possibleCatchVessels; - private final Set<Vessel> possibleSampleVessels; private final Map<String, Integer> stratumMinimumCountBySpecie; - private final LoadingCache<String, Activity> activityCache; + private final List<WeightCategoryTreatment> weightCategoryTreatments; private final int stratumIndex; + private final LengthWeightConversionWithContextCache conversionHelper; private String[] zoneIds; - protected StratumConfiguration(C configuration, - ZoneStratumAwareMeta zoneMeta, + protected StratumConfiguration(LevelInputContext<C, A> inputContext, ZoneStratumAware zone, SchoolType schoolType, WeightCategoryTreatment weightCategoryTreatment, T3Date beginDate, T3Date endDate, Collection<ZoneStratumAware> zones, - Set<Vessel> possibleCatchVessels, - Set<Vessel> possibleSampleVessels, Map<String, Integer> stratumMinimumCountBySpecie, - LoadingCache<String, Activity> activityCache, + List<WeightCategoryTreatment> weightCategoryTreatments, int stratumIndex) { - this.configuration = configuration; - this.zoneMeta = zoneMeta; + this.inputContext = inputContext; this.zone = zone; this.schoolType = schoolType; + this.weightCategoryTreatments = weightCategoryTreatments; this.weightCategoryTreatment = weightCategoryTreatment; this.beginDate = beginDate; this.endDate = endDate; this.zones = zones; - this.possibleCatchVessels = possibleCatchVessels; - this.possibleSampleVessels = possibleSampleVessels; this.stratumMinimumCountBySpecie = stratumMinimumCountBySpecie; - this.activityCache = activityCache; this.stratumIndex = stratumIndex; + this.conversionHelper = inputContext.newLengthWeightConversionWithContextCache(zone.getOcean(), beginDate.toBeginDate()); + } + + public LengthWeightConversionWithContextCache getConversionHelper() { + return conversionHelper; } public C getConfiguration() { - return configuration; + return inputContext.getConfiguration(); } private ZoneStratumAwareMeta getZoneMeta() { - return zoneMeta; + return inputContext.getZoneMeta(); } public String getZoneTableName() { @@ -113,15 +114,15 @@ public class StratumConfiguration<C extends LevelConfigurationWithStratum> { public Set<String> getSchoolTypeIds() { ImmutableSet.Builder<String> builder = ImmutableSet.<String>builder().add(getSchoolType().getTopiaId()); - switch (configuration.getSchoolTypeIndeterminate()) { + switch (getConfiguration().getSchoolTypeIndeterminate()) { case ALL_IN_BO: - if (AbstractSchoolTypeTopiaDao.SCHOOL_TYPE_BO_ID.equals(getSchoolType().getTopiaId())) { - builder.add(AbstractSchoolTypeTopiaDao.SCHOOL_TYPE_INDETERMINATE_ID); + if (SchoolTypeTopiaDao.SCHOOL_TYPE_BO_ID.equals(getSchoolType().getTopiaId())) { + builder.add(SchoolTypeTopiaDao.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); + if (SchoolTypeTopiaDao.SCHOOL_TYPE_BL_ID.equals(getSchoolType().getTopiaId())) { + builder.add(SchoolTypeTopiaDao.SCHOOL_TYPE_INDETERMINATE_ID); } break; case IGNORE: @@ -143,11 +144,11 @@ public class StratumConfiguration<C extends LevelConfigurationWithStratum> { } public Set<Vessel> getPossibleCatchVessels() { - return possibleCatchVessels; + return inputContext.getPossibleCatchVessels(); } public Set<Vessel> getPossibleSampleVessels() { - return possibleSampleVessels; + return inputContext.getPossibleSampleVessels(); } public Map<String, Integer> getStratumMinimumCountBySpecie() { @@ -162,6 +163,14 @@ public class StratumConfiguration<C extends LevelConfigurationWithStratum> { return stratumIndex; } + public List<WeightCategoryTreatment> getWeightCategoryTreatments() { + return weightCategoryTreatments; + } + + public Predicate<? super SpeciesAware> getSpeciesToFixFilter() { + return inputContext.getSpeciesToFixFilter(); + } + public String[] getZoneIds() { if (zoneIds == null) { Collection<ZoneStratumAware> allZones = getZones(); @@ -177,7 +186,7 @@ public class StratumConfiguration<C extends LevelConfigurationWithStratum> { public Activity getActivity(String activityId) { try { - return activityCache.get(activityId); + return inputContext.getActivityCache().get(activityId); } catch (ExecutionException e) { throw new RuntimeException(String.format("Could not obtain activity %s", activityId), e); } @@ -194,7 +203,7 @@ public class StratumConfiguration<C extends LevelConfigurationWithStratum> { if (currentLevel == null) { result = ""; } - result += String.format("(%s;%s;%d)", zone.getLabel1(), configuration.isUseWeightCategoriesInStratum() ? weightCategoryTreatment.getLabel1() : "NA", level); + result += String.format("(%s;%s;%d)", zone.getLabel1(), getConfiguration().isUseWeightCategoriesInStratum() ? weightCategoryTreatment.getLabel1() : "NA", level); Objects.requireNonNull(consumer).accept(activity, result); } } ===================================== t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumResult.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumResult.java +++ b/t3-domain/src/main/java/fr/ird/t3/actions/stratum/StratumResult.java @@ -8,12 +8,12 @@ * 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% @@ -32,7 +32,7 @@ import java.io.Closeable; */ public abstract class StratumResult<C extends LevelConfigurationWithStratum> implements Closeable { - private final StratumConfiguration<C> configuration; + private final StratumConfiguration<C, ?> configuration; private final String label; @@ -42,12 +42,12 @@ public abstract class StratumResult<C extends LevelConfigurationWithStratum> imp private int nbActivitiesWithSample; - protected StratumResult(StratumConfiguration<C> configuration, String label) { + protected StratumResult(StratumConfiguration<C, ?> configuration, String label) { this.configuration = configuration; this.label = label; } - public StratumConfiguration<C> getConfiguration() { + public StratumConfiguration<C, ?> getConfiguration() { return configuration; } @@ -59,30 +59,30 @@ public abstract class StratumResult<C extends LevelConfigurationWithStratum> imp return substitutionLevel; } - public int getNbActivities() { - return nbActivities; - } - - public int getNbActivitiesWithSample() { - return nbActivitiesWithSample; - } - - public int getNbActivitiesWithoutSample() { - return nbActivities - nbActivitiesWithSample; - } - public void setSubstitutionLevel(int substitutionLevel) { this.substitutionLevel = substitutionLevel; } + public int getNbActivities() { + return nbActivities; + } + public void setNbActivities(int nbActivities) { this.nbActivities = nbActivities; } + public int getNbActivitiesWithSample() { + return nbActivitiesWithSample; + } + public void setNbActivitiesWithSample(int nbActivitiesWithSample) { this.nbActivitiesWithSample = nbActivitiesWithSample; } + public int getNbActivitiesWithoutSample() { + return nbActivities - nbActivitiesWithSample; + } + public void addNbActivities(int nbActivities) { this.nbActivities += nbActivities; } ===================================== t3-domain/src/main/java/fr/ird/t3/entities/cache/LengthWeightConversionCache.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/entities/cache/LengthWeightConversionCache.java +++ b/t3-domain/src/main/java/fr/ird/t3/entities/cache/LengthWeightConversionCache.java @@ -25,12 +25,14 @@ import fr.ird.t3.entities.reference.LengthWeightConversionTopiaDao; import fr.ird.t3.entities.reference.Ocean; import fr.ird.t3.entities.reference.Species; import fr.ird.t3.entities.reference.WeightCategory; +import fr.ird.t3.entities.reference.WeightCategoryTreatment; import fr.ird.t3.entities.type.T3Date; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import java.util.Date; import java.util.Iterator; +import java.util.LinkedList; import java.util.List; import java.util.Map; import java.util.TreeMap; @@ -133,4 +135,24 @@ public class LengthWeightConversionCache { return result; } + public List<Integer> getLengthClasses(LengthWeightConversion conversion, WeightCategoryTreatment weightCategoryTreatment, List<Integer> lengthClasses) { + Integer min = weightCategoryTreatment.getMin(); + Integer minLengthClass = null; + if (min != null) { + minLengthClass = getSpecieHighestLengthClass(conversion, min); + } + Integer max = weightCategoryTreatment.getMax(); + Integer maxLengthClass = null; + if (max != null) { + maxLengthClass = getSpecieHighestLengthClass(conversion, max); + } + List<Integer> result = new LinkedList<>(); + for (Integer lengthClass : lengthClasses) { + if (minLengthClass != null && lengthClass < minLengthClass || maxLengthClass != null && lengthClass > maxLengthClass) { + continue; + } + result.add(lengthClass); + } + return result; + } } ===================================== t3-domain/src/main/java/fr/ird/t3/entities/data/ActivityImpl.java ===================================== --- a/t3-domain/src/main/java/fr/ird/t3/entities/data/ActivityImpl.java +++ b/t3-domain/src/main/java/fr/ird/t3/entities/data/ActivityImpl.java @@ -222,4 +222,9 @@ public class ActivityImpl extends ActivityAbstract { public boolean withCorrectedElementaryCatch(WeightCategoryTreatment weightCategoryTreatment) { return isCorrectedElementaryCatchNotEmpty() && getCorrectedElementaryCatch().stream().map(CorrectedElementaryCatch::getWeightCategoryTreatment).anyMatch(c -> c.equals(weightCategoryTreatment)); } + + @Override + public boolean withSetSpeciesCatWeight(WeightCategoryTreatment weightCategoryTreatment) { + return isSetSpeciesCatWeightNotEmpty() && getSetSpeciesCatWeight().stream().map(SetSpeciesCatWeight::getWeightCategoryTreatment).anyMatch(c -> c.equals(weightCategoryTreatment)); + } } ===================================== t3-domain/src/main/xmi/t3-persistence.zargo ===================================== Binary files a/t3-domain/src/main/xmi/t3-persistence.zargo and b/t3-domain/src/main/xmi/t3-persistence.zargo differ View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/3585d323448b384f491d7eb078d58a9dd... --- View it on GitLab: https://gitlab.com/ultreiaio/ird-t3/commit/3585d323448b384f491d7eb078d58a9dd... 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