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

Commits:

29 changed files:

Changes:

  • t3-actions/src/main/java/fr/ird/t3/actions/data/level0/ComputeSetDurationAndPositiveSetCountAction.java
    ... ... @@ -59,9 +59,9 @@ public class ComputeSetDurationAndPositiveSetCountAction extends AbstractLevel0A
    59 59 
         @InjectDAO(entityType = SetDuration.class)
    60 60 
         private SetDurationTopiaDao setDurationDAO;
    61 61 
         /** Count of treated activities. */
    62 
    -    private int nbActivities;
    62 
    +    int nbActivities;
    63 63 
         /** Count of positive activities found. */
    64 
    -    private int nbPositiveActivities;
    64 
    +    int nbPositiveActivities;
    65 65 
         /** Count of set (sum(a.setCount) on each activity trip). */
    66 66 
         private int nbSet;
    67 67 
         /**

  • t3-actions/src/main/java/fr/ird/t3/actions/data/level1/AbstractLevel1Action.java
    ... ... @@ -28,20 +28,17 @@ import fr.ird.t3.entities.data.N1ResultState;
    28 28 
     import fr.ird.t3.entities.data.Sample;
    29 29 
     import fr.ird.t3.entities.data.Trip;
    30 30 
     import fr.ird.t3.entities.data.TripTopiaDao;
    31 
    -import fr.ird.t3.entities.reference.Ocean;
    32 31 
     import fr.ird.t3.services.DecoratorService;
    33 32 
     import fr.ird.t3.services.ioc.InjectDAO;
    34 
    -import fr.ird.t3.services.ioc.InjectEntityById;
    33 
    +import org.apache.commons.collections.CollectionUtils;
    34 
    +import org.nuiton.topia.persistence.TopiaException;
    35 
    +
    35 36 
     import java.util.Collection;
    36 37 
     import java.util.Comparator;
    37 38 
     import java.util.List;
    38 39 
     import java.util.Set;
    39 40 
     import java.util.stream.Collectors;
    40 41
    41 
    -import org.apache.commons.collections.CollectionUtils;
    42 
    -import org.nuiton.topia.persistence.TopiaException;
    43 
    -
    44 
    -
    45 42 
     import static org.nuiton.i18n.I18n.l;
    46 43
    47 44 
     /**
    ... ... @@ -56,15 +53,12 @@ public abstract class AbstractLevel1Action extends T3Action<Level1Configuration>
    56 53 
                 .<Trip, Integer>comparing(t -> t.getVessel().getCode())
    57 54 
                 .thenComparing(Comparator.comparing(Trip::getLandingDate));
    58 55
    59 
    -    protected final Level1Step step;
    60 
    -
    61 
    -    protected final Set<Level1Step> higherSteps;
    62 
    -
    63 56 
         @InjectDAO(entityType = Trip.class)
    64 57 
         protected TripTopiaDao tripDAO;
    65 58
    66 
    -    @InjectEntityById(entityType = Ocean.class)
    67 
    -    protected Ocean ocean;
    59 
    +    protected final Level1Step step;
    60 
    +
    61 
    +    protected final Set<Level1Step> higherSteps;
    68 62
    69 63 
         /** For a trip, selected samples to treat. */
    70 64 
         protected Multimap<Trip, Sample> samplesByTrip;
    ... ... @@ -77,10 +71,6 @@ public abstract class AbstractLevel1Action extends T3Action<Level1Configuration>
    77 71 
             higherSteps = Level1Step.allAfter(step);
    78 72 
         }
    79 73
    80 
    -    public Ocean getOcean() {
    81 
    -        return ocean;
    82 
    -    }
    83 
    -
    84 74 
         public Multimap<Trip, Sample> getSamplesByTrip() {
    85 75 
             return samplesByTrip;
    86 76 
         }

  • t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ComputeWeightOfCategoriesForSetAction.java
    ... ... @@ -27,9 +27,9 @@ import fr.ird.t3.entities.data.Trip;
    27 27 
     import fr.ird.t3.entities.data.WellSetAllSpecies;
    28 28 
     import fr.ird.t3.entities.data.WellSetAllSpeciesTopiaDao;
    29 29 
     import fr.ird.t3.services.ioc.InjectDAO;
    30 
    -import java.util.Collection;
    31 30 
     import org.nuiton.topia.persistence.TopiaException;
    32 31
    32 
    +import java.util.Collection;
    33 33
    34 34 
     import static org.nuiton.i18n.I18n.l;
    35 35
    ... ... @@ -127,9 +127,7 @@ public class ComputeWeightOfCategoriesForSetAction extends AbstractLevel1Action
    127 127
    128 128 
                 // can not  compute propMinus10Weight and propPlus10Weight
    129 129
    130 
    -            String message =
    131 
    -                    l(locale, "t3.level1.computeWeightOfCategoriesForSet.sample.noComputePropWeight"
    132 
    -                    );
    130 
    +            String message = l(locale, "t3.level1.computeWeightOfCategoriesForSet.sample.noComputePropWeight");
    133 131 
                 addInfoMessage(message);
    134 132
    135 133 
             } else {

  • t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ConvertSampleSetSpeciesFrequencyToWeightAction.java
    ... ... @@ -21,12 +21,10 @@ package fr.ird.t3.actions.data.level1;
    21 21 
      * #L%
    22 22 
      */
    23 23
    24 
    -import com.google.common.base.Preconditions;
    25 24 
     import com.google.common.collect.ArrayListMultimap;
    26 25 
     import com.google.common.collect.Lists;
    27 26 
     import com.google.common.collect.Maps;
    28 27 
     import com.google.common.collect.Multimap;
    29 
    -import com.google.common.collect.Sets;
    30 28 
     import fr.ird.t3.T3IOUtil;
    31 29 
     import fr.ird.t3.entities.CountAndWeight;
    32 30 
     import fr.ird.t3.entities.T3Suppliers;
    ... ... @@ -51,16 +49,17 @@ import fr.ird.t3.entities.reference.WeightCategorySample;
    51 49 
     import fr.ird.t3.entities.reference.WeightCategorySampleTopiaDao;
    52 50 
     import fr.ird.t3.services.DecoratorService;
    53 51 
     import fr.ird.t3.services.ioc.InjectDAO;
    52 
    +import org.nuiton.topia.persistence.TopiaException;
    53 
    +import org.nuiton.util.TimeLog;
    54 
    +
    54 55 
     import java.util.Collection;
    55 56 
     import java.util.Collections;
    56 57 
     import java.util.Date;
    57 58 
     import java.util.HashMap;
    58 59 
     import java.util.List;
    59 60 
     import java.util.Map;
    61 
    +import java.util.Objects;
    60 62 
     import java.util.Set;
    61 
    -import org.nuiton.topia.persistence.TopiaException;
    62 
    -import org.nuiton.util.TimeLog;
    63 
    -
    64 63
    65 64 
     import static org.nuiton.i18n.I18n.l;
    66 65
    ... ... @@ -72,38 +71,27 @@ import static org.nuiton.i18n.I18n.l;
    72 71 
      */
    73 72 
     public class ConvertSampleSetSpeciesFrequencyToWeightAction extends AbstractLevel1Action {
    74 73
    74 
    +    private final Map<String, List<WeightCategorySample>> weightCategoryCache;
    75 75 
         @InjectDAO(entityType = LengthWeightConversion.class)
    76 
    -    protected LengthWeightConversionTopiaDao lengthWeightConversionDAO;
    77 
    -
    76 
    +    private LengthWeightConversionTopiaDao lengthWeightConversionDAO;
    78 77 
         @InjectDAO(entityType = SampleSetSpeciesCatWeight.class)
    79 
    -    protected SampleSetSpeciesCatWeightTopiaDao sampleSetSpeciesCatWeightDAO;
    80 
    -
    78 
    +    private SampleSetSpeciesCatWeightTopiaDao sampleSetSpeciesCatWeightDAO;
    81 79 
         @InjectDAO(entityType = WeightCategorySample.class)
    82 
    -    protected WeightCategorySampleTopiaDao weightCategorySampleDAO;
    83 
    -
    84 
    -    protected LengthWeightConversionHelper conversionHelper;
    85 
    -
    86 
    -    protected final Map<String, List<WeightCategorySample>> weightCategoryCache;
    80 
    +    private WeightCategorySampleTopiaDao weightCategorySampleDAO;
    81 
    +    private LengthWeightConversionHelper conversionHelper;
    87 82
    88 83 
         protected List<WeightCategorySample> getWeightCategories(SampleSet sampleSet) throws TopiaException {
    89 
    -
    90 84 
             Activity activity = sampleSet.getActivity();
    91 
    -        Ocean ocean1 = activity.getOcean();
    85 
    +        Ocean ocean = activity.getOcean();
    92 86 
             SchoolType schoolType = activity.getSchoolType();
    93 
    -        String key = ocean1.getTopiaId() + "-" + schoolType.getTopiaId();
    87 
    +        String key = ocean.getTopiaId() + "-" + schoolType.getTopiaId();
    94 88 
             List<WeightCategorySample> result = weightCategoryCache.get(key);
    95 
    -
    96 89 
             if (result == null) {
    97 
    -
    98 
    -            result = weightCategorySampleDAO.forOceanEquals(ocean1).findAll();
    90 
    +            result = weightCategorySampleDAO.forOceanEquals(ocean).findAll();
    99 91 
                 WeightCategories.sort(result);
    100 92 
                 weightCategoryCache.put(key, result);
    101 93 
             }
    102 
    -
    103 
    -        Preconditions.checkNotNull(
    104 
    -                result,
    105 
    -                "Could not find any weight categories for ocean " + ocean.getLabel1() );
    106 
    -        return result;
    94 
    +        return Objects.requireNonNull(result, "Could not find any weight categories for ocean " + ocean.getLabel1());
    107 95 
         }
    108 96
    109 97 
         public ConvertSampleSetSpeciesFrequencyToWeightAction() {
    ... ... @@ -141,21 +129,18 @@ public class ConvertSampleSetSpeciesFrequencyToWeightAction extends AbstractLeve
    141 129
    142 130 
                 String tripStr = decorate(trip, DecoratorService.WITH_ID);
    143 131
    144 
    -            getTimeLog().log(s0, "treat trip " + tripStr);
    132 
    +            getTimeLog().log(s0, String.format("treat trip %s", tripStr));
    145 133
    146 134 
                 // flush transaction otherwise too much data in memory
    147 
    -            flushTransaction("Flush transaction for " + tripStr);
    135 
    +            flushTransaction(String.format("Flush transaction for %s", tripStr));
    148 136 
             }
    149 137 
             return true;
    150 138 
         }
    151 139
    152 
    -    protected void doExecuteTrip(Trip trip,
    153 
    -                                 Collection<Sample> samples) throws TopiaException {
    140 
    +    protected void doExecuteTrip(Trip trip, Collection<Sample> samples) throws TopiaException {
    154 141
    155 142 
             incrementsProgression();
    156 143
    157 
    -        Set<Activity> tripActivities = Sets.newHashSet();
    158 
    -
    159 144 
             // extrapolate for each sample set number to set
    160 145 
             for (Sample sample : samples) {
    161 146
    ... ... @@ -173,16 +158,14 @@ public class ConvertSampleSetSpeciesFrequencyToWeightAction extends AbstractLeve
    173 158 
                     // found a new activity to convert
    174 159 
                     convertFrequenciesToCatWeight(sampleSet);
    175 160
    176 
    -                getTimeLog().log(s1,
    177 
    -                                 "convertSampleSetSpeciesFrequencyToWeight for " +
    178 
    -                                 tripActivities.size() + " sets.");
    161 
    +                getTimeLog().log(s1, String.format("convertSampleSetSpeciesFrequencyToWeight for %d sets.", sample.sizeSampleSet()));
    179 162
    180 163 
                 }
    181 164
    182 165 
                 // mark sample as treated for this step of level 1 treatment
    183 166 
                 markAsTreated(sample);
    184 167
    185 
    -            getTimeLog().log(s0, "treat sample " + sampleStr);
    168 
    +            getTimeLog().log(s0, String.format("treat sample %s", sampleStr));
    186 169 
             }
    187 170
    188 171 
             // mar trip as treated for this level 1 step
    ... ... @@ -191,8 +174,7 @@ public class ConvertSampleSetSpeciesFrequencyToWeightAction extends AbstractLeve
    191 174
    192 175 
         protected void convertFrequenciesToCatWeight(SampleSet sampleSet) throws TopiaException {
    193 176
    194 
    -        Collection<SampleSetSpeciesFrequency> frequencies =
    195 
    -                sampleSet.getSampleSetSpeciesFrequency();
    177 
    +        Collection<SampleSetSpeciesFrequency> frequencies = sampleSet.getSampleSetSpeciesFrequency();
    196 178
    197 179 
             Activity activity = sampleSet.getActivity();
    198 180
    ... ... @@ -200,15 +182,12 @@ public class ConvertSampleSetSpeciesFrequencyToWeightAction extends AbstractLeve
    200 182 
             Ocean activityOcean = activity.getOcean();
    201 183
    202 184 
             // group frequencies by species
    203 
    -        Multimap<Species, SampleSetSpeciesFrequency> frequenciesBySpecies =
    204 
    -                SpeciesTopiaDao.groupBySpecies(frequencies);
    185 
    +        Multimap<Species, SampleSetSpeciesFrequency> frequenciesBySpecies = SpeciesTopiaDao.groupBySpecies(frequencies);
    205 186
    206 
    -        Multimap<Species, Integer> lengthClassesBySpecies =
    207 
    -                ArrayListMultimap.create();
    187 
    +        Multimap<Species, Integer> lengthClassesBySpecies = ArrayListMultimap.create();
    208 188
    209 189 
             // collect all length classes by species
    210 
    -        SampleSetSpeciesFrequencyTopiaDao.collectLengthClasses(
    211 
    -                frequenciesBySpecies, lengthClassesBySpecies);
    190 
    +        SampleSetSpeciesFrequencyTopiaDao.collectLengthClasses(frequenciesBySpecies, lengthClassesBySpecies);
    212 191
    213 192 
             // get all available weight categories
    214 193 
             List<WeightCategorySample> weightCategories = getWeightCategories(sampleSet);
    ... ... @@ -216,19 +195,11 @@ public class ConvertSampleSetSpeciesFrequencyToWeightAction extends AbstractLeve
    216 195 
             for (Species species : frequenciesBySpecies.keySet()) {
    217 196
    218 197 
                 // get conversion for species
    219 
    -            LengthWeightConversion conversion =
    220 
    -                    conversionHelper.getConversions(
    221 
    -                            species,
    222 
    -                            activityOcean,
    223 
    -                            0,
    224 
    -                            date
    225 
    -                    );
    226 
    -
    227 
    -            Collection<SampleSetSpeciesFrequency> frequenciesForSpecies =
    228 
    -                    frequenciesBySpecies.get(species);
    229 
    -
    230 
    -            List<Integer> lengthClasses =
    231 
    -                    Lists.newArrayList(lengthClassesBySpecies.get(species));
    198 
    +            LengthWeightConversion conversion = conversionHelper.getConversions(species, activityOcean, 0, date);
    199 
    +
    200 
    +            Collection<SampleSetSpeciesFrequency> frequenciesForSpecies = frequenciesBySpecies.get(species);
    201 
    +
    202 
    +            List<Integer> lengthClasses = Lists.newArrayList(lengthClassesBySpecies.get(species));
    232 203 
                 Collections.sort(lengthClasses);
    233 204
    234 205 
                 Map<WeightCategorySample, CountAndWeight> countAndWeightsByCategories =
    ... ... @@ -238,9 +209,7 @@ public class ConvertSampleSetSpeciesFrequencyToWeightAction extends AbstractLeve
    238 209 
                                 frequenciesForSpecies,
    239 210 
                                 lengthClasses);
    240 211
    241 
    -            // now we can build for the given activity and species the entries
    242 
    -            // in SetWeight
    243 
    -
    212 
    +            // now we can build for the given activity and species the entries in SetWeight
    244 213 
                 fill(sampleSet, species, countAndWeightsByCategories);
    245 214 
             }
    246 215 
         }
    ... ... @@ -250,17 +219,12 @@ public class ConvertSampleSetSpeciesFrequencyToWeightAction extends AbstractLeve
    250 219 
                                                                                   Collection<SampleSetSpeciesFrequency> frequencies,
    251 220 
                                                                                   List<Integer> lengthClasses) throws TopiaException {
    252 221
    253 
    -        Map<Integer, WeightCategorySample> weightCategorie =
    254 
    -                conversionHelper.getWeightCategoriesDistribution(
    255 
    -                        conversion,
    256 
    -                        weightCategories,
    257 
    -                        lengthClasses);
    222 
    +        Map<Integer, WeightCategorySample> weightCategoryMap =
    223 
    +                conversionHelper.getWeightCategoriesDistribution(conversion, weightCategories, lengthClasses);
    258 224
    259 225 
             Map<WeightCategorySample, CountAndWeight> result = new HashMap<>();
    260 226
    261 
    -        T3IOUtil.fillMapWithDefaultValue(result,
    262 
    -                                         weightCategorie.values(),
    263 
    -                                         T3Suppliers.COUNT_AND_WEIGHT_DEFAULT_VALUE);
    227 
    +        T3IOUtil.fillMapWithDefaultValue(result, weightCategoryMap.values(), T3Suppliers.COUNT_AND_WEIGHT_DEFAULT_VALUE);
    264 228
    265 229 
             for (SampleSetSpeciesFrequency setSize : frequencies) {
    266 230
    ... ... @@ -268,7 +232,7 @@ public class ConvertSampleSetSpeciesFrequencyToWeightAction extends AbstractLeve
    268 232 
                 int lfLengthClass = setSize.getLfLengthClass();
    269 233
    270 234 
                 // find the correct category for this length class
    271 
    -            WeightCategorySample weightCategory = weightCategorie.get(lfLengthClass);
    235 
    +            WeightCategorySample weightCategory = weightCategoryMap.get(lfLengthClass);
    272 236
    273 237 
                 CountAndWeight countAndWeight = result.get(weightCategory);
    274 238
    ... ... @@ -276,8 +240,7 @@ public class ConvertSampleSetSpeciesFrequencyToWeightAction extends AbstractLeve
    276 240
    277 241 
                 countAndWeight.addCount(number);
    278 242 
                 // convert to weight from lf length class
    279 
    -            countAndWeight.addWeight(number *
    280 
    -                      conversion.computeWeightFromLFLengthClass(lfLengthClass));
    243 
    +            countAndWeight.addWeight(number * conversion.computeWeightFromLFLengthClass(lfLengthClass));
    281 244
    282 245 
             }
    283 246
    ... ... @@ -295,7 +258,7 @@ public class ConvertSampleSetSpeciesFrequencyToWeightAction extends AbstractLeve
    295 258 
                 CountAndWeight countAndWeight  = e2.getValue();
    296 259 
                 float count = countAndWeight.getCount();
    297 260
    298 
    -            // weight must be stored in tons but are in kilogramms
    261 
    +            // weight must be stored in tons but are in kilograms
    299 262 
                 Float weight = countAndWeight.getWeight() / 1000;
    300 263
    301 264 
                 SampleSetSpeciesCatWeight setSpeciesCatWeight = sampleSetSpeciesCatWeightDAO.create(

  • t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ConvertSetSpeciesFrequencyToWeightAction.java
    ... ... @@ -8,19 +8,18 @@
    8 8 
      * it under the terms of the GNU Affero General Public License as published by
    9 9 
      * the Free Software Foundation, either version 3 of the License, or
    10 10 
      * (at your option) any later version.
    11 
    - *
    11 
    + *
    12 12 
      * This program is distributed in the hope that it will be useful,
    13 13 
      * but WITHOUT ANY WARRANTY; without even the implied warranty of
    14 14 
      * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    15 15 
      * GNU General Public License for more details.
    16 
    - *
    16 
    + *
    17 17 
      * You should have received a copy of the GNU Affero General Public License
    18 18 
      * along with this program.  If not, see <http://www.gnu.org/licenses/>.
    19 19 
      * #L%
    20 20 
      */
    21 21 
     package fr.ird.t3.actions.data.level1;
    22 22
    23 
    -import com.google.common.base.Preconditions;
    24 23 
     import com.google.common.collect.ArrayListMultimap;
    25 24 
     import com.google.common.collect.Lists;
    26 25 
     import com.google.common.collect.Maps;
    ... ... @@ -49,16 +48,17 @@ import fr.ird.t3.entities.reference.WeightCategorySample;
    49 48 
     import fr.ird.t3.entities.reference.WeightCategorySampleTopiaDao;
    50 49 
     import fr.ird.t3.services.DecoratorService;
    51 50 
     import fr.ird.t3.services.ioc.InjectDAO;
    51 
    +import org.nuiton.topia.persistence.TopiaException;
    52 
    +import org.nuiton.util.TimeLog;
    53 
    +
    52 54 
     import java.util.Collection;
    53 55 
     import java.util.Collections;
    54 56 
     import java.util.Date;
    55 57 
     import java.util.HashMap;
    56 58 
     import java.util.List;
    57 59 
     import java.util.Map;
    60 
    +import java.util.Objects;
    58 61 
     import java.util.Set;
    59 
    -import org.nuiton.topia.persistence.TopiaException;
    60 
    -import org.nuiton.util.TimeLog;
    61 
    -
    62 62
    63 63 
     import static org.nuiton.i18n.I18n.l;
    64 64
    ... ... @@ -70,48 +70,34 @@ import static org.nuiton.i18n.I18n.l;
    70 70 
      */
    71 71 
     public class ConvertSetSpeciesFrequencyToWeightAction extends AbstractLevel1Action {
    72 72
    73 
    +    protected final Map<String, List<WeightCategorySample>> weightCategoryCache;
    73 74 
         @InjectDAO(entityType = LengthWeightConversion.class)
    74 75 
         protected LengthWeightConversionTopiaDao lengthWeightConversionDAO;
    75 
    -
    76 76 
         @InjectDAO(entityType = SetSpeciesCatWeight.class)
    77 77 
         protected SetSpeciesCatWeightTopiaDao setSpeciesCatWeightDAO;
    78 
    -
    79 78 
         @InjectDAO(entityType = WeightCategorySample.class)
    80 79 
         protected WeightCategorySampleTopiaDao weightCategorySampleDAO;
    81 
    -
    82 80 
         protected int nbTreatedSets;
    83 
    -
    84 81 
         protected float nbTreatedFishesInSamples;
    85 
    -
    86 82 
         protected float nbCreatedFishesInSetSpeciesFrequency;
    87 
    -
    88 83 
         protected LengthWeightConversionHelper conversionHelper;
    89 84
    90 
    -    protected final Map<String, List<WeightCategorySample>> weightCategoryCache;
    85 
    +    public ConvertSetSpeciesFrequencyToWeightAction() {
    86 
    +        super(Level1Step.CONVERT_SET_SPECIES_FREQUENCY_TO_WEIGHT);
    87 
    +        weightCategoryCache = Maps.newTreeMap();
    88 
    +    }
    91 89
    92 90 
         protected List<WeightCategorySample> getWeightCategories(Activity activity) throws TopiaException {
    93 
    -
    94 
    -        Ocean ocean1 = activity.getOcean();
    91 
    +        Ocean ocean = activity.getOcean();
    95 92 
             SchoolType schoolType = activity.getSchoolType();
    96 
    -        String key = ocean1.getTopiaId() + "-" + schoolType.getTopiaId();
    93 
    +        String key = ocean.getTopiaId() + "-" + schoolType.getTopiaId();
    97 94 
             List<WeightCategorySample> result = weightCategoryCache.get(key);
    98 
    -
    99 95 
             if (result == null) {
    100 
    -
    101 
    -            result = weightCategorySampleDAO.findAllByOcean(ocean1);
    96 
    +            result = weightCategorySampleDAO.forOceanEquals(ocean).findAll();
    102 97 
                 WeightCategories.sort(result);
    103 98 
                 weightCategoryCache.put(key, result);
    104 99 
             }
    105 
    -
    106 
    -        Preconditions.checkNotNull(
    107 
    -                result,
    108 
    -                "Could not find any weight categories for ocean " + ocean.getLabel1());
    109 
    -        return result;
    110 
    -    }
    111 
    -
    112 
    -    public ConvertSetSpeciesFrequencyToWeightAction() {
    113 
    -        super(Level1Step.CONVERT_SET_SPECIES_FREQUENCY_TO_WEIGHT);
    114 
    -        weightCategoryCache = Maps.newTreeMap();
    100 
    +        return Objects.requireNonNull(result, "Could not find any weight categories for ocean " + ocean.getLabel1());
    115 101 
         }
    116 102
    117 103 
         public int getNbTreatedSets() {
    ... ... @@ -140,7 +126,7 @@ public class ConvertSetSpeciesFrequencyToWeightAction extends AbstractLevel1Acti
    140 126 
         }
    141 127
    142 128 
         @Override
    143 
    -    protected boolean executeAction() throws Exception {
    129 
    +    protected boolean executeAction() {
    144 130
    145 131 
             Set<Trip> trips = samplesByTrip.keySet();
    146 132 
             setNbSteps(samplesByTrip.size() + trips.size());
    ... ... @@ -164,8 +150,7 @@ public class ConvertSetSpeciesFrequencyToWeightAction extends AbstractLevel1Acti
    164 150 
             return true;
    165 151 
         }
    166 152
    167 
    -    protected void doExecuteTrip(Trip trip,
    168 
    -                                 Collection<Sample> samples) throws TopiaException {
    153 
    +    protected void doExecuteTrip(Trip trip, Collection<Sample> samples) throws TopiaException {
    169 154
    170 155 
             incrementsProgression();
    171 156
    ... ... @@ -184,8 +169,7 @@ public class ConvertSetSpeciesFrequencyToWeightAction extends AbstractLevel1Acti
    184 169 
                 float nb = sample.getTotalStandardiseSampleSpeciesFrequencyNumber();
    185 170
    186 171 
                 addInfoMessage(
    187 
    -                    l(locale, "t3.level1.convertSetSpeciesFrequencyToWeight.sample.nbFishes",
    188 
    -                            sampleStr, nb));
    172 
    +                    l(locale, "t3.level1.convertSetSpeciesFrequencyToWeight.sample.nbFishes", sampleStr, nb));
    189 173 
                 nbTreatedFishesInSamples += nb;
    190 174
    191 175 
                 for (SampleSet sampleSet : sample.getSampleSet()) {
    ... ... @@ -200,17 +184,14 @@ public class ConvertSetSpeciesFrequencyToWeightAction extends AbstractLevel1Acti
    200 184 
                         // found a new activity to convert
    201 185 
                         convertFrequenciesToCatWeight(activity);
    202 186
    203 
    -                    getTimeLog().log(
    204 
    -                            s1,
    205 
    -                            "convertSetSpeciesFrequencyToWeight for " +
    206 
    -                                    tripActivities.size() + " sets.");
    187 
    +                    getTimeLog().log(s1, String.format("convertSetSpeciesFrequencyToWeight for %d sets.", tripActivities.size()));
    207 188 
                     }
    208 189 
                 }
    209 190
    210 191 
                 // mark sample as treated for this step of level 1 treatment
    211 192 
                 markAsTreated(sample);
    212 193
    213 
    -            getTimeLog().log(s0, "treat sample " + sampleStr);
    194 
    +            getTimeLog().log(s0, String.format("treat sample %s", sampleStr));
    214 195 
             }
    215 196
    216 197 
             nbTreatedSets += tripActivities.size();
    ... ... @@ -226,50 +207,32 @@ public class ConvertSetSpeciesFrequencyToWeightAction extends AbstractLevel1Acti
    226 207 
             Date date = activity.getDate();
    227 208 
             Ocean activityOcean = activity.getOcean();
    228 209
    229 
    -
    230 210 
             // group frequencies by species
    231 211 
             Multimap<Species, SetSpeciesFrequency> setSpeciesFrequencyBySpecies =
    232 212 
                     SpeciesTopiaDao.groupBySpecies(frequencies);
    233 213
    234 
    -        Multimap<Species, Integer> lengthClassesBySpecies =
    235 
    -                ArrayListMultimap.create();
    214 
    +        Multimap<Species, Integer> lengthClassesBySpecies = ArrayListMultimap.create();
    236 215
    237 216 
             // collect all length classes by species
    238 
    -        SetSpeciesFrequencyTopiaDao.collectLengthClasses(
    239 
    -                setSpeciesFrequencyBySpecies, lengthClassesBySpecies);
    217 
    +        SetSpeciesFrequencyTopiaDao.collectLengthClasses(setSpeciesFrequencyBySpecies, lengthClassesBySpecies);
    240 218
    241 219 
             // get all available weight categories
    242 
    -        List<WeightCategorySample> weightCategories =
    243 
    -                getWeightCategories(activity);
    220 
    +        List<WeightCategorySample> weightCategories = getWeightCategories(activity);
    244 221
    245 222 
             for (Species species : setSpeciesFrequencyBySpecies.keySet()) {
    246 223
    247 224 
                 // get conversion for species
    248 
    -            LengthWeightConversion conversion =
    249 
    -                    conversionHelper.getConversions(
    250 
    -                            species,
    251 
    -                            activityOcean,
    252 
    -                            0,
    253 
    -                            date
    254 
    -                    );
    255 
    -
    256 
    -            Collection<SetSpeciesFrequency> setSizes =
    257 
    -                    setSpeciesFrequencyBySpecies.get(species);
    258 
    -
    259 
    -            List<Integer> lengthClasses =
    260 
    -                    Lists.newArrayList(lengthClassesBySpecies.get(species));
    225 
    +            LengthWeightConversion conversion = conversionHelper.getConversions(species, activityOcean, 0, date);
    226 
    +
    227 
    +            Collection<SetSpeciesFrequency> setSizes = setSpeciesFrequencyBySpecies.get(species);
    228 
    +
    229 
    +            List<Integer> lengthClasses = Lists.newArrayList(lengthClassesBySpecies.get(species));
    261 230 
                 Collections.sort(lengthClasses);
    262 231
    263 232 
                 Map<WeightCategorySample, CountAndWeight> countAndWeightsByCategories =
    264 
    -                    convertForSpecies(
    265 
    -                            weightCategories,
    266 
    -                            conversion,
    267 
    -                            setSizes,
    268 
    -                            lengthClasses);
    269 
    -
    270 
    -            // now we can build for the given activity and species the entries
    271 
    -            // in SetWeight
    233 
    +                    convertForSpecies(weightCategories, conversion, setSizes, lengthClasses);
    272 234
    235 
    +            // now we can build for the given activity and species the entries in SetWeight
    273 236 
                 fill(activity, species, countAndWeightsByCategories);
    274 237 
             }
    275 238 
         }
    ... ... @@ -279,7 +242,7 @@ public class ConvertSetSpeciesFrequencyToWeightAction extends AbstractLevel1Acti
    279 242 
                                                                             Collection<SetSpeciesFrequency> setSizes,
    280 243 
                                                                             List<Integer> lengthClasses) throws TopiaException {
    281 244
    282 
    -        Map<Integer, WeightCategorySample> weightCategorie = conversionHelper.getWeightCategoriesDistribution(
    245 
    +        Map<Integer, WeightCategorySample> weightCategoryMap = conversionHelper.getWeightCategoriesDistribution(
    283 246 
                     conversion,
    284 247 
                     weightCategories,
    285 248 
                     lengthClasses
    ... ... @@ -287,9 +250,7 @@ public class ConvertSetSpeciesFrequencyToWeightAction extends AbstractLevel1Acti
    287 250
    288 251 
             Map<WeightCategorySample, CountAndWeight> result = new HashMap<>();
    289 252
    290 
    -        T3IOUtil.fillMapWithDefaultValue(result,
    291 
    -                weightCategorie.values(),
    292 
    -                T3Suppliers.COUNT_AND_WEIGHT_DEFAULT_VALUE);
    253 
    +        T3IOUtil.fillMapWithDefaultValue(result, weightCategoryMap.values(), T3Suppliers.COUNT_AND_WEIGHT_DEFAULT_VALUE);
    293 254
    294 255 
             for (SetSpeciesFrequency setSize : setSizes) {
    295 256
    ... ... @@ -297,8 +258,7 @@ public class ConvertSetSpeciesFrequencyToWeightAction extends AbstractLevel1Acti
    297 258 
                 int lfLengthClass = setSize.getLfLengthClass();
    298 259
    299 260 
                 // find the correct category for this length class
    300 
    -            WeightCategorySample weightCategory =
    301 
    -                    weightCategorie.get(lfLengthClass);
    261 
    +            WeightCategorySample weightCategory = weightCategoryMap.get(lfLengthClass);
    302 262
    303 263 
                 CountAndWeight countAndWeight = result.get(weightCategory);
    304 264
    ... ... @@ -313,12 +273,9 @@ public class ConvertSetSpeciesFrequencyToWeightAction extends AbstractLevel1Acti
    313 273 
             return result;
    314 274 
         }
    315 275
    316 
    -    private void fill(Activity activity,
    317 
    -                      Species species,
    318 
    -                      Map<WeightCategorySample, CountAndWeight> countAndWeightsByCategories) throws TopiaException {
    276 
    +    private void fill(Activity activity, Species species, Map<WeightCategorySample, CountAndWeight> countAndWeightsByCategories) throws TopiaException {
    319 277
    320 
    -        for (Map.Entry<WeightCategorySample, CountAndWeight> e2 :
    321 
    -                countAndWeightsByCategories.entrySet()) {
    278 
    +        for (Map.Entry<WeightCategorySample, CountAndWeight> e2 : countAndWeightsByCategories.entrySet()) {
    322 279 
                 WeightCategorySample categorySample = e2.getKey();
    323 280
    324 281 
                 CountAndWeight countAndWeight = e2.getValue();

  • t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ExtrapolateSampleCountedAndMeasuredAction.java
    ... ... @@ -28,11 +28,11 @@ import fr.ird.t3.entities.data.SampleSpecies;
    28 28 
     import fr.ird.t3.entities.data.Trip;
    29 29 
     import fr.ird.t3.entities.reference.Species;
    30 30 
     import fr.ird.t3.entities.reference.SpeciesTopiaDao;
    31 
    +
    31 32 
     import java.util.Collection;
    32 33 
     import java.util.List;
    33 34 
     import java.util.Map;
    34 35
    35 
    -
    36 36 
     import static org.nuiton.i18n.I18n.l;
    37 37
    38 38 
     /**
    ... ... @@ -50,9 +50,7 @@ public class ExtrapolateSampleCountedAndMeasuredAction extends AbstractLevel1Act
    50 50 
         }
    51 51
    52 52 
         public List<SpeciesCountAndMeasuredModel> getResultSpeciesModel() {
    53 
    -        List<SpeciesCountAndMeasuredModel> result =
    54 
    -                getResultAsList(RESULT_SPECIES_MODEL, SpeciesCountAndMeasuredModel.class);
    55 
    -        return result;
    53 
    +        return getResultAsList(RESULT_SPECIES_MODEL, SpeciesCountAndMeasuredModel.class);
    56 54 
         }
    57 55
    58 56 
         public SpeciesCountAndMeasuredModel getTotalSpeciesModel() {
    ... ... @@ -81,7 +79,7 @@ public class ExtrapolateSampleCountedAndMeasuredAction extends AbstractLevel1Act
    81 79 
         }
    82 80
    83 81 
         @Override
    84 
    -    protected boolean executeAction() throws Exception {
    82 
    +    protected boolean executeAction() {
    85 83
    86 84 
             Map<Species, SpeciesCountAndMeasuredModel> model = Maps.newHashMap();
    87 85
    ... ... @@ -110,8 +108,7 @@ public class ExtrapolateSampleCountedAndMeasuredAction extends AbstractLevel1Act
    110 108 
             return true;
    111 109 
         }
    112 110
    113 
    -    protected void doExecuteSample(Sample sample,
    114 
    -                                   Map<Species, SpeciesCountAndMeasuredModel> model) {
    111 
    +    protected void doExecuteSample(Sample sample, Map<Species, SpeciesCountAndMeasuredModel> model) {
    115 112
    116 113 
             incrementsProgression();
    117 114
    ... ... @@ -120,7 +117,6 @@ public class ExtrapolateSampleCountedAndMeasuredAction extends AbstractLevel1Act
    120 117 
                        sample.getSampleNumber()));
    121 118
    122 119 
             if (sample.isSampleSpeciesEmpty()) {
    123 
    -
    124 120 
                 // no sample species, nothing to do...
    125 121 
                 return;
    126 122 
             }
    ... ... @@ -145,9 +141,7 @@ public class ExtrapolateSampleCountedAndMeasuredAction extends AbstractLevel1Act
    145 141 
                 float measuredCount = 0;
    146 142 
                 for (SampleSpecies aSampleSpecies : sampleSpecies) {
    147 143 
                     totalCount += aSampleSpecies.getTotalCount();
    148 
    -
    149 
    -                measuredCount +=
    150 
    -                        aSampleSpecies.getTotalSampleSpeciesFrequencyNumber();
    144 
    +                measuredCount += aSampleSpecies.getTotalSampleSpeciesFrequencyNumber();
    151 145 
                 }
    152 146 
                 float rf0 = totalCount / measuredCount;
    153 147
    ... ... @@ -161,7 +155,6 @@ public class ExtrapolateSampleCountedAndMeasuredAction extends AbstractLevel1Act
    161 155
    162 156 
                 // apply rf0 on each sample
    163 157 
                 for (SampleSpecies sampleSpecie : sampleSpecies) {
    164 
    -
    165 158 
                     sampleSpecie.applyRf0(rf0);
    166 159 
                 }
    167 160 
             }

  • t3-actions/src/main/java/fr/ird/t3/actions/data/level1/ExtrapolateSampleWeightToSetAction.java
    ... ... @@ -20,9 +20,7 @@
    20 20 
      */
    21 21 
     package fr.ird.t3.actions.data.level1;
    22 22
    23 
    -import com.google.common.collect.Maps;
    24 23 
     import com.google.common.collect.Multimap;
    25 
    -import com.google.common.collect.Sets;
    26 24 
     import fr.ird.t3.entities.data.Activity;
    27 25 
     import fr.ird.t3.entities.data.RfUsageStatus;
    28 26 
     import fr.ird.t3.entities.data.Sample;
    ... ... @@ -45,14 +43,16 @@ import fr.ird.t3.entities.reference.WeightCategoryWellPlan;
    45 43 
     import fr.ird.t3.entities.reference.WeightCategoryWellPlanTopiaDao;
    46 44 
     import fr.ird.t3.services.DecoratorService;
    47 45 
     import fr.ird.t3.services.ioc.InjectDAO;
    48 
    -import java.util.Collection;
    49 
    -import java.util.Map;
    50 
    -import java.util.Set;
    51 46 
     import org.apache.commons.logging.Log;
    52 47 
     import org.apache.commons.logging.LogFactory;
    53 48 
     import org.nuiton.topia.persistence.TopiaException;
    54 49 
     import org.nuiton.util.TimeLog;
    55 50
    51 
    +import java.util.Collection;
    52 
    +import java.util.HashMap;
    53 
    +import java.util.HashSet;
    54 
    +import java.util.Map;
    55 
    +import java.util.Set;
    56 56
    57 57 
     import static org.nuiton.i18n.I18n.l;
    58 58
    ... ... @@ -125,7 +125,7 @@ public class ExtrapolateSampleWeightToSetAction extends AbstractLevel1Action {
    125 125 
         }
    126 126
    127 127 
         @Override
    128 
    -    protected boolean executeAction() throws Exception {
    128 
    +    protected boolean executeAction() {
    129 129
    130 130 
             Set<Trip> trips = samplesByTrip.keySet();
    131 131 
             setNbSteps(samplesByTrip.size() + trips.size());
    ... ... @@ -153,11 +153,11 @@ public class ExtrapolateSampleWeightToSetAction extends AbstractLevel1Action {
    153 153
    154 154 
             incrementsProgression();
    155 155
    156 
    +        //FIXME I replace ocean by trip.departureHarbour.ocean, check this is ok (See #260)
    156 157 
             // get the length class +10kg limit
    157 
    -        Map<Species, Integer> limitLengthClassBySpecie =
    158 
    -                getThredHoldPlus10ForSpecies(trip, samples, ocean);
    158 
    +        Map<Species, Integer> limitLengthClassBySpecie = getThredHoldPlus10ForSpecies(trip, samples, trip.getDepartureHarbour().getOcean());
    159 159
    160 
    -        Set<Activity> tripActivities = Sets.newHashSet();
    160 
    +        Set<Activity> tripActivities = new HashSet<>();
    161 161
    162 162 
             // extrapolate for each sample set number to set
    163 163 
             for (Sample sample : samples) {
    ... ... @@ -187,11 +187,7 @@ public class ExtrapolateSampleWeightToSetAction extends AbstractLevel1Action {
    187 187 
                         activity.clearSetSpeciesCatWeight();
    188 188 
                     }
    189 189
    190 
    -                doExecuteSampleWell(
    191 
    -                        activity,
    192 
    -                        sampleSet,
    193 
    -                        sampleStr,
    194 
    -                        limitLengthClassBySpecie);
    190 
    +                doExecuteSampleWell(activity, sampleSet, sampleStr, limitLengthClassBySpecie);
    195 191
    196 192 
                 }
    197 193
    ... ... @@ -244,11 +240,7 @@ public class ExtrapolateSampleWeightToSetAction extends AbstractLevel1Action {
    244 240 
             sampleSet.setRfTot(rfContext.getRfTot());
    245 241
    246 242 
             // fill the SetSpecieFrequency table
    247 
    -        fillSetSpeciesFrequency(
    248 
    -                activity,
    249 
    -                limitLengthClassBySpecie,
    250 
    -                sampleSet,
    251 
    -                rfContext);
    243 
    +        fillSetSpeciesFrequency(activity, limitLengthClassBySpecie, sampleSet, rfContext);
    252 244
    253 245 
         }
    254 246
    ... ... @@ -330,9 +322,7 @@ public class ExtrapolateSampleWeightToSetAction extends AbstractLevel1Action {
    330 322 
          * @throws TopiaException if any pb while finding convertors
    331 323 
          * @see SampleWellSampleWeight
    332 324 
          */
    333 
    -    protected SampleWellSetWeight computeSampleWellSetWeight(
    334 
    -            String sampleWellStr,
    335 
    -            SampleSet sampleSet) throws TopiaException {
    325 
    +    protected SampleWellSetWeight computeSampleWellSetWeight(String sampleWellStr, SampleSet sampleSet) throws TopiaException {
    336 326
    337 327 
             float pondt = sampleSet.getWeightedWeight();
    338 328 
             Float pondm = sampleSet.getWeightedWeightMinus10();
    ... ... @@ -489,11 +479,7 @@ public class ExtrapolateSampleWeightToSetAction extends AbstractLevel1Action {
    489 479 
             return rfContext;
    490 480 
         }
    491 481
    492 
    -    public void fillSetSpeciesFrequency(
    493 
    -            Activity activity,
    494 
    -            Map<Species, Integer> limitLengthClassBySpecies,
    495 
    -            SampleSet sampleSet,
    496 
    -            RFContext rfContext) throws TopiaException {
    482 
    +    public void fillSetSpeciesFrequency(Activity activity, Map<Species, Integer> limitLengthClassBySpecies, SampleSet sampleSet, RFContext rfContext) throws TopiaException {
    497 483
    498 484 
             // group sample set frequencies by species
    499 485 
             Multimap<Species, SampleSetSpeciesFrequency> sampleSetSpeciesFrequencyBySpecies =
    ... ... @@ -542,18 +528,15 @@ public class ExtrapolateSampleWeightToSetAction extends AbstractLevel1Action {
    542 528 
          * @param trip    the trip where samples are done
    543 529 
          * @param samples the sample to scan
    544 530 
          * @param ocean   ocean where trip happens
    545 
    -     * @return the universe of legnth class limits computed indexed by species
    531 
    +     * @return the universe of length class limits computed indexed by species
    546 532 
          * @throws TopiaException if any db problems while requesting
    547 533 
          */
    548 
    -    public Map<Species, Integer> getThredHoldPlus10ForSpecies(Trip trip,
    549 
    -                                                              Collection<Sample> samples,
    550 
    -                                                              Ocean ocean) throws TopiaException {
    534 
    +    public Map<Species, Integer> getThredHoldPlus10ForSpecies(Trip trip, Collection<Sample> samples, Ocean ocean) throws TopiaException {
    551 535
    552 536 
             Set<Species> species = SpeciesTopiaDao.getAllSpeciesFromSampleSpecies(samples);
    553 537
    554 
    -        // for each of those species, found the length class wich matches a
    555 
    -        // weight > 10Kg
    556 
    -        Map<Species, Integer> result = Maps.newHashMap();
    538 
    +        // for each of those species, found the length class which matches a weight > 10Kg
    539 
    +        Map<Species, Integer> result = new HashMap<>();
    557 540 
             for (Species specie : species) {
    558 541
    559 542 
                 LengthWeightConversion conversion = conversionHelper.getConversions(
    ... ... @@ -577,8 +560,7 @@ public class ExtrapolateSampleWeightToSetAction extends AbstractLevel1Action {
    577 560
    578 561 
             if (log.isDebugEnabled()) {
    579 562 
                 for (Map.Entry<Species, Integer> entry : result.entrySet()) {
    580 
    -                log.debug("Species " + entry.getKey().getCode() +
    581 
    -                        " - limit 10Kg length class : " + entry.getValue());
    563 
    +                log.debug(String.format("Species %d - limit 10Kg length class : %d", entry.getKey().getCode(), entry.getValue()));
    582 564
    583 565 
                 }
    584 566 
             }

  • t3-actions/src/main/java/fr/ird/t3/actions/data/level1/Level1Configuration.java
    ... ... @@ -20,9 +20,7 @@
    20 20 
      */
    21 21 
     package fr.ird.t3.actions.data.level1;
    22 22
    23 
    -import com.google.common.base.Preconditions;
    24 23 
     import com.google.common.base.Predicate;
    25 
    -import com.google.common.collect.Iterables;
    26 24 
     import com.google.common.collect.Lists;
    27 25 
     import com.google.common.collect.Maps;
    28 26 
     import com.google.common.collect.Multimap;
    ... ... @@ -44,13 +42,13 @@ import org.apache.commons.logging.Log;
    44 42 
     import org.apache.commons.logging.LogFactory;
    45 43 
     import org.nuiton.decorator.Decorator;
    46 44
    47 
    -import java.util.Arrays;
    48 45 
     import java.util.Collection;
    49 46 
     import java.util.EnumSet;
    50 47 
     import java.util.List;
    51 48 
     import java.util.Locale;
    52 49 
     import java.util.Map;
    53 50 
     import java.util.Set;
    51 
    +import java.util.stream.Collectors;
    54 52
    55 53 
     import static org.nuiton.i18n.I18n.l;
    56 54
    ... ... @@ -84,11 +82,12 @@ public class Level1Configuration implements T3ActionConfiguration {
    84 82 
         /** Ids of fleet countries to use. */
    85 83 
         protected List<String> fleetIds;
    86 84
    85 
    +    /** Ids of ocean to use. */
    86 
    +    protected List<String> oceanIds;
    87 
    +
    87 88 
         /** Ids of trips to use. */
    88 89 
         protected Multimap<String, String> sampleIdsByTripId;
    89 90
    90 
    -    /** Id of selected ocean. */
    91 
    -    protected String oceanId;
    92 91
    93 92 
         /** begin date to use. */
    94 93 
         protected T3Date beginDate;
    ... ... @@ -150,12 +149,12 @@ public class Level1Configuration implements T3ActionConfiguration {
    150 149 
             getExecutedSteps().add(step);
    151 150 
         }
    152 151
    153 
    -    public String getOceanId() {
    154 
    -        return oceanId;
    152 
    +    public List<String> getOceanIds() {
    153 
    +        return oceanIds;
    155 154 
         }
    156 155
    157 
    -    public void setOceanId(String oceanId) {
    158 
    -        this.oceanId = oceanId;
    156 
    +    public void setOceanIds(List<String> oceanIds) {
    157 
    +        this.oceanIds = oceanIds;
    159 158 
         }
    160 159
    161 160 
         public Multimap<String, String> getSampleIdsByTripId() {
    ... ... @@ -306,32 +305,23 @@ public class Level1Configuration implements T3ActionConfiguration {
    306 305
    307 306 
             Multimap<String, String> result = TreeMultimap.create();
    308 307
    309 
    -        if (oceanId == null) {
    308 
    +        if (oceanIds == null) {
    310 309
    311 310 
                 // no matching trips (so no matching trip
    312 311 
                 return result;
    313 312 
             }
    314 
    -        Preconditions.checkNotNull(oceanId);
    315 
    -
    316 
    -        Ocean ocean =
    317 
    -                Iterables.find(oceans, T3Predicates.equalsTopiaEntity(oceanId));
    318 313
    319 
    -        Preconditions.checkNotNull(ocean);
    314 
    +        Set<Ocean> usableOceans = oceans.stream().filter(o -> oceanIds.contains(o.getTopiaId())).collect(Collectors.toSet());
    320 315
    321 
    -        Predicate<Trip> tripPredicate =
    322 
    -                T3Predicates.tripUsingOcean(Arrays.asList(ocean));
    316 
    +        Predicate<Trip> tripPredicate = T3Predicates.tripUsingOcean(usableOceans);
    323 317
    324 
    -        Decorator<Trip> tripDecorator =
    325 
    -                decoratorService.getDecorator(locale, Trip.class, DecoratorService.WITH_ID);
    318 
    +        Decorator<Trip> tripDecorator = decoratorService.getDecorator(locale, Trip.class, DecoratorService.WITH_ID);
    326 319
    327 
    -        Decorator<Sample> sampleDecorator =
    328 
    -                decoratorService.getDecorator(locale, Sample.class, DecoratorService.WITH_ID);
    320 
    +        Decorator<Sample> sampleDecorator = decoratorService.getDecorator(locale, Sample.class, DecoratorService.WITH_ID);
    329 321
    330 
    -        String sampleWellEmptyReason =
    331 
    -                l(locale, "t3.level1.notSelectedSample.sampleWellEmpty");
    322 
    +        String sampleWellEmptyReason = l(locale, "t3.level1.notSelectedSample.sampleWellEmpty");
    332 323
    333 
    -        String sampleNoMatchingActivityReason =
    334 
    -                l(locale, "t3.level1.notSelectedSample.sampleNoMatchingActivity");
    324 
    +        String sampleNoMatchingActivityReason = l(locale, "t3.level1.notSelectedSample.sampleNoMatchingActivity");
    335 325
    336 326 
             Decorator<SampleQuality> sampleQualityDecorator = decoratorService.getDecorator(locale, SampleQuality.class, null);
    337 327 
             Decorator<SampleType> sampleTypeDecorator = decoratorService.getDecorator(locale, SampleType.class, null);

  • t3-actions/src/main/java/fr/ird/t3/actions/data/level1/RedistributeSampleNumberToSetAction.java
    ... ... @@ -31,11 +31,11 @@ import fr.ird.t3.entities.data.Trip;
    31 31 
     import fr.ird.t3.entities.reference.Species;
    32 32 
     import fr.ird.t3.entities.reference.SpeciesTopiaDao;
    33 33 
     import fr.ird.t3.services.ioc.InjectDAO;
    34 
    +import org.nuiton.topia.persistence.TopiaException;
    35 
    +
    34 36 
     import java.util.Collection;
    35 37 
     import java.util.Map;
    36 38 
     import java.util.Set;
    37 
    -import org.nuiton.topia.persistence.TopiaException;
    38 
    -
    39 39
    40 40 
     import static org.nuiton.i18n.I18n.l;
    41 41
    ... ... @@ -55,9 +55,7 @@ public class RedistributeSampleNumberToSetAction extends AbstractLevel1Action {
    55 55 
         }
    56 56
    57 57 
         public Set<Species> getSpeciesOfSample(Sample sample) {
    58 
    -        Set<Species> result = SpeciesTopiaDao.getAllSpecies(
    59 
    -                sample.getStandardiseSampleSpecies());
    60 
    -        return result;
    58 
    +        return SpeciesTopiaDao.getAllSpecies(sample.getStandardiseSampleSpecies());
    61 59 
         }
    62 60
    63 61 
         public SpeciesModel getResultSpeciesModel(Sample sample, Species species) {
    ... ... @@ -88,7 +86,7 @@ public class RedistributeSampleNumberToSetAction extends AbstractLevel1Action {
    88 86 
         }
    89 87
    90 88 
         @Override
    91 
    -    protected boolean executeAction() throws Exception {
    89 
    +    protected boolean executeAction() {
    92 90
    93 91 
             setNbSteps(2 * samplesByTrip.size());
    94 92
    ... ... @@ -125,8 +123,8 @@ public class RedistributeSampleNumberToSetAction extends AbstractLevel1Action {
    125 123 
             }
    126 124 
             incrementsProgression();
    127 125
    128 
    -        long sampleTotalNumber = 0l;
    129 
    -        long sampleWellTotalNumber = 0l;
    126 
    +        long sampleTotalNumber = 0L;
    127 
    +        long sampleWellTotalNumber = 0L;
    130 128
    131 129 
             for (StandardiseSampleSpecies sampleSpecies :
    132 130 
                     sample.getStandardiseSampleSpecies()) {

  • t3-actions/src/main/java/fr/ird/t3/actions/data/level1/StandardizeSampleMeasuresAction.java
    ... ... @@ -8,12 +8,12 @@
    8 8 
      * it under the terms of the GNU Affero General Public License as published by
    9 9 
      * the Free Software Foundation, either version 3 of the License, or
    10 10 
      * (at your option) any later version.
    11 
    - *
    11 
    + *
    12 12 
      * This program is distributed in the hope that it will be useful,
    13 13 
      * but WITHOUT ANY WARRANTY; without even the implied warranty of
    14 14 
      * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    15 15 
      * GNU General Public License for more details.
    16 
    - *
    16 
    + *
    17 17 
      * You should have received a copy of the GNU Affero General Public License
    18 18 
      * along with this program.  If not, see <http://www.gnu.org/licenses/>.
    19 19 
      * #L%
    ... ... @@ -36,14 +36,15 @@ import fr.ird.t3.entities.reference.SpeciesLengthStep;
    36 36 
     import fr.ird.t3.entities.reference.SpeciesLengthStepTopiaDao;
    37 37 
     import fr.ird.t3.entities.reference.SpeciesTopiaDao;
    38 38 
     import fr.ird.t3.services.ioc.InjectDAO;
    39 
    -import java.util.Collection;
    40 
    -import java.util.List;
    41 
    -import java.util.Map;
    42 39 
     import org.apache.commons.collections.CollectionUtils;
    43 40 
     import org.apache.commons.logging.Log;
    44 41 
     import org.apache.commons.logging.LogFactory;
    45 42 
     import org.nuiton.topia.persistence.TopiaException;
    46 43
    44 
    +import java.util.Collection;
    45 
    +import java.util.List;
    46 
    +import java.util.Map;
    47 
    +import java.util.TreeMap;
    47 48
    48 49 
     import static org.nuiton.i18n.I18n.l;
    49 50
    ... ... @@ -61,29 +62,22 @@ import static org.nuiton.i18n.I18n.l;
    61 62 
      */
    62 63 
     public class StandardizeSampleMeasuresAction extends AbstractLevel1Action {
    63 64
    65 
    +    public static final String RESULT_SPECIES_MODEL = "speciesModel";
    64 66 
         /** Logger. */
    65 
    -    private static final Log log =
    66 
    -            LogFactory.getLog(StandardizeSampleMeasuresAction.class);
    67 
    -
    67 
    +    private static final Log log = LogFactory.getLog(StandardizeSampleMeasuresAction.class);
    68 68 
         @InjectDAO(entityType = StandardiseSampleSpecies.class)
    69 
    -    protected StandardiseSampleSpeciesTopiaDao standardiseSampleSpeciesDAO;
    70 
    -
    69 
    +    private StandardiseSampleSpeciesTopiaDao standardiseSampleSpeciesDAO;
    71 70 
         @InjectDAO(entityType = StandardiseSampleSpeciesFrequency.class)
    72 
    -    protected StandardiseSampleSpeciesFrequencyTopiaDao standardiseSampleSpeciesFrequencyDAO;
    73 
    -
    71 
    +    private StandardiseSampleSpeciesFrequencyTopiaDao standardiseSampleSpeciesFrequencyDAO;
    74 72 
         @InjectDAO(entityType = SpeciesLengthStep.class)
    75 
    -    protected SpeciesLengthStepTopiaDao speciesLengthStepDAO;
    76 
    -
    77 
    -    public static final String RESULT_SPECIES_MODEL = "speciesModel";
    73 
    +    private SpeciesLengthStepTopiaDao speciesLengthStepDAO;
    78 74
    79 75 
         public StandardizeSampleMeasuresAction() {
    80 76 
             super(Level1Step.STANDARDIZE_SAMPLE_MEASURE);
    81 77 
         }
    82 78
    83 79 
         public List<StandardizeSpeciesCountModel> getResultSpeciesModel() {
    84 
    -        List<StandardizeSpeciesCountModel> result =
    85 
    -                getResultAsList(RESULT_SPECIES_MODEL, StandardizeSpeciesCountModel.class);
    86 
    -        return result;
    80 
    +        return getResultAsList(RESULT_SPECIES_MODEL, StandardizeSpeciesCountModel.class);
    87 81 
         }
    88 82
    89 83 
         public StandardizeSpeciesCountModel getTotalSpeciesModel() {
    ... ... @@ -101,7 +95,7 @@ public class StandardizeSampleMeasuresAction extends AbstractLevel1Action {
    101 95 
         }
    102 96
    103 97 
         @Override
    104 
    -    protected boolean executeAction() throws Exception {
    98 
    +    protected boolean executeAction() {
    105 99
    106 100 
             Map<Species, StandardizeSpeciesCountModel> model = Maps.newHashMap();
    107 101
    ... ... @@ -114,11 +108,7 @@ public class StandardizeSampleMeasuresAction extends AbstractLevel1Action {
    114 108
    115 109 
                 for (Sample sample : samples) {
    116 110
    117 
    -                doExecuteSample(
    118 
    -                        trip,
    119 
    -                        sample,
    120 
    -                        model
    121 
    -                );
    111 
    +                doExecuteSample(trip, sample, model);
    122 112
    123 113 
                     // mark sample as treated for this step of level 1 treatment
    124 114 
                     markAsTreated(sample);
    ... ... @@ -135,23 +125,20 @@ public class StandardizeSampleMeasuresAction extends AbstractLevel1Action {
    135 125 
             return true;
    136 126 
         }
    137 127
    138 
    -    protected void doExecuteSample(Trip trip,
    139 
    -                                   Sample sample,
    140 
    -                                   Map<Species, StandardizeSpeciesCountModel> model) throws TopiaException {
    128 
    +    private void doExecuteSample(Trip trip, Sample sample, Map<Species, StandardizeSpeciesCountModel> model) throws TopiaException {
    141 129
    142 130 
             incrementsProgression();
    143 131
    144 132 
             String tripStr = decorate(trip);
    145 133
    146 
    -        addInfoMessage(l(locale, "t3.level1.standardizeSampleMeasures.treat.sample",
    147 
    -                          tripStr, sample.getSampleNumber()));
    134 
    +        addInfoMessage(l(locale, "t3.level1.standardizeSampleMeasures.treat.sample", tripStr, sample.getSampleNumber()));
    148 135
    149 136 
             if (!sample.isStandardiseSampleSpeciesEmpty()) {
    150 137
    151 138 
                 // was already computed, remove previous data
    152 139 
                 addInfoMessage(
    153 140 
                         l(locale, "t3.level1.standardizeSampleMeasures.treat.remove.previously.treated.data",
    154 
    -                       sample.sizeStandardiseSampleSpecies()));
    141 
    +                            sample.sizeStandardiseSampleSpecies()));
    155 142 
                 sample.clearStandardiseSampleSpecies();
    156 143 
             }
    157 144
    ... ... @@ -162,8 +149,7 @@ public class StandardizeSampleMeasuresAction extends AbstractLevel1Action {
    162 149 
             }
    163 150
    164 151 
             // split sample species by species
    165 
    -        Multimap<Species, SampleSpecies> sampleSpeciesBySpecies =
    166 
    -                SpeciesTopiaDao.groupBySpecies(sample.getSampleSpecies());
    152 
    +        Multimap<Species, SampleSpecies> sampleSpeciesBySpecies = SpeciesTopiaDao.groupBySpecies(sample.getSampleSpecies());
    167 153
    168 154 
             for (Species species : sampleSpeciesBySpecies.keySet()) {
    169 155
    ... ... @@ -175,22 +161,14 @@ public class StandardizeSampleMeasuresAction extends AbstractLevel1Action {
    175 161 
                 }
    176 162
    177 163 
                 // get sample species for this species
    178 
    -            Collection<SampleSpecies> sampleSpecies =
    179 
    -                    sampleSpeciesBySpecies.get(species);
    164 
    +            Collection<SampleSpecies> sampleSpecies = sampleSpeciesBySpecies.get(species);
    180 165
    181 
    -            // obtain once for all the length classes for this species on
    182 
    -            // this ocean
    166 
    +            //FIXME I replace ocean by trip.departureHarbour.ocean, check this is ok (See #260)
    167 
    +            // obtain once for all the length classes for this species on this ocean
    183 168 
                 Multimap<Integer, SpeciesLengthStep> proportionsForSpecies =
    184 
    -                    speciesLengthStepDAO.findAllByOceanAndSpeciesGroupByLd1Class(
    185 
    -                            ocean,
    186 
    -                            species);
    187 
    -
    188 
    -            doExecuteSampleSpecies(species,
    189 
    -                                   sampleSpecies,
    190 
    -                                   sample,
    191 
    -                                   speciesCountModel,
    192 
    -                                   proportionsForSpecies
    193 
    -            );
    169 
    +                    speciesLengthStepDAO.findAllByOceanAndSpeciesGroupByLd1Class(trip.getDepartureHarbour().getOcean(), species);
    170 
    +
    171 
    +            doExecuteSampleSpecies(species, sampleSpecies, sample, speciesCountModel, proportionsForSpecies);
    194 172 
             }
    195 173 
         }
    196 174
    ... ... @@ -204,23 +182,16 @@ public class StandardizeSampleMeasuresAction extends AbstractLevel1Action {
    204 182
    205 183 
             // each species will give exactly one entry in StandardiseSampleSpecies table
    206 184 
             StandardiseSampleSpecies standardiseSampleSpecies =
    207 
    -                standardiseSampleSpeciesDAO.create(
    208 
    -                        StandardiseSampleSpecies.PROPERTY_SPECIES, species
    209 
    -                );
    185 
    +                standardiseSampleSpeciesDAO.create(StandardiseSampleSpecies.PROPERTY_SPECIES, species);
    210 186
    211 
    -        // contains for each lflengthclass, the number of fishes
    187 
    +        // contains for each lfLengthClass, the number of fishes
    212 188 
             Map<Integer, Float> frequencies = Maps.newTreeMap();
    213 189 
             float measuredCount = 0;
    214 190 
             float totalCount = 0;
    215 191 
             for (SampleSpecies sampleSpecie : sampleSpecies) {
    216 192 
                 measuredCount += sampleSpecie.getMeasuredCount();
    217 193 
                 totalCount += sampleSpecie.getTotalCount();
    218 
    -
    219 
    -            collectSampleSpeciesFrequencies(
    220 
    -                    proportionsForSpecies,
    221 
    -                    sampleSpecie,
    222 
    -                    frequencies
    223 
    -            );
    194 
    +            collectSampleSpeciesFrequencies(proportionsForSpecies, sampleSpecie, frequencies);
    224 195 
             }
    225 196
    226 197 
             // set the total measured count computed
    ... ... @@ -238,13 +209,12 @@ public class StandardizeSampleMeasuresAction extends AbstractLevel1Action {
    238 209
    239 210 
                 // must recode length classes
    240 211
    241 
    -            finalFrequencies = Maps.newTreeMap();
    212 
    +            finalFrequencies = new TreeMap<>();
    242 213
    243 214 
                 for (Map.Entry<Integer, Float> ee : frequencies.entrySet()) {
    244 215 
                     Integer lfLengthClass = ee.getKey();
    245 216 
                     Float numberExtrapolated = ee.getValue();
    246 
    -                int finalLengthClass = lfLengthClass -
    247 
    -                                       lfLengthClass % lfLengthClassStep;
    217 
    +                int finalLengthClass = lfLengthClass - lfLengthClass % lfLengthClassStep;
    248 218
    249 219 
                     Float finalNumber = finalFrequencies.get(finalLengthClass);
    250 220 
                     if (finalNumber == null) {
    ... ... @@ -277,10 +247,7 @@ public class StandardizeSampleMeasuresAction extends AbstractLevel1Action {
    277 247 
             // attach to sample new data
    278 248 
             sample.addStandardiseSampleSpecies(standardiseSampleSpecies);
    279 249 
             addInfoMessage(l(locale, "t3.level1.standardizeSampleMeasures.treat.resume.for.species",
    280 
    -                          decorate(species),
    281 
    -                          oldCOunt,
    282 
    -                          newCount
    283 
    -        ));
    250 
    +                decorate(species), oldCOunt, newCount));
    284 251 
         }
    285 252
    286 253 
         protected void collectSampleSpeciesFrequencies(Multimap<Integer, SpeciesLengthStep> proportionsForSpecies,
    ... ... @@ -304,16 +271,15 @@ public class StandardizeSampleMeasuresAction extends AbstractLevel1Action {
    304 271
    305 272 
                     // ld1 length class is in cm in sample, but in milimeter in SpeciesLengthStep table
    306 273 
                     int ld1LengthClass = sampleSpeciesFrequency.getLengthClass() * 10;
    307 
    -                Collection<SpeciesLengthStep> proportions =
    308 
    -                        proportionsForSpecies.get(ld1LengthClass);
    274 
    +                Collection<SpeciesLengthStep> proportions = proportionsForSpecies.get(ld1LengthClass);
    309 275
    310 276 
                     if (CollectionUtils.isEmpty(proportions)) {
    311 277
    312 278 
                         //TODO This should be an error ?
    313 279 
                         String message = l(locale, "t3.level1.standardizeSampleMeasures.warning.lfConversion.not.found",
    314 
    -                                        decorate(ocean),
    315 
    -                                        decorate(species),
    316 
    -                                        ld1LengthClass);
    280 
    +                            decorate(getConfiguration().getOceans()),
    281 
    +                            decorate(species),
    282 
    +                            ld1LengthClass);
    317 283 
                         if (log.isWarnEnabled()) {
    318 284 
                             log.warn(message);
    319 285 
                         }
    ... ... @@ -336,14 +302,8 @@ public class StandardizeSampleMeasuresAction extends AbstractLevel1Action {
    336 302
    337 303 
                 // just add lf frequencies
    338 304
    339 
    -            for (SampleSpeciesFrequency sampleSpecyFrequency :
    340 
    -                    sampleSpecies.getSampleSpeciesFrequency()) {
    341 
    -
    342 
    -                addLFFrequency(
    343 
    -                        sampleSpecyFrequency.getLengthClass(),
    344 
    -                        sampleSpecyFrequency.getNumberExtrapolated(),
    345 
    -                        frequencies
    346 
    -                );
    305 
    +            for (SampleSpeciesFrequency sampleSpecyFrequency : sampleSpecies.getSampleSpeciesFrequency()) {
    306 
    +                addLFFrequency(sampleSpecyFrequency.getLengthClass(), sampleSpecyFrequency.getNumberExtrapolated(), frequencies);
    347 307 
                 }
    348 308 
             }
    349 309 
         }
    ... ... @@ -352,12 +312,7 @@ public class StandardizeSampleMeasuresAction extends AbstractLevel1Action {
    352 312 
                                    float number,
    353 313 
                                    Map<Integer, Float> frequencies) throws TopiaException {
    354 314
    355 
    -        Float standardiseSampleSpecieFrequency = frequencies.get(lengthClass);
    356 
    -        if (standardiseSampleSpecieFrequency == null) {
    357 
    -
    358 
    -            standardiseSampleSpecieFrequency = 0.f;
    359 
    -            frequencies.put(lengthClass, standardiseSampleSpecieFrequency);
    360 
    -        }
    315 
    +        Float standardiseSampleSpecieFrequency = frequencies.computeIfAbsent(lengthClass, k -> 0.f);
    361 316
    362 317 
             standardiseSampleSpecieFrequency += number;
    363 318

  • t3-actions/src/test/java/fr/ird/t3/actions/data/level0/ComputeSetDurationAndPositiveSetCountActionResumeTest.java
    ... ... @@ -60,13 +60,11 @@ public class ComputeSetDurationAndPositiveSetCountActionResumeTest extends Abstr
    60 60
    61 61 
             Map<String, Object> parameters = super.createTemplateParameters();
    62 62
    63 
    -        Map<String, String> vesselSimpleTypes = new TreeMap<String, String>();
    64 
    -        putInMap(vesselSimpleTypes,
    65 
    -                 fixtures.vesselSimpleTypeCanneur(),
    66 
    -                 fixtures.vesselSimpleTypeSenneur());
    63 
    +        Map<String, String> vesselSimpleTypes = new TreeMap<>();
    64 
    +        putInMap(vesselSimpleTypes, fixtures.vesselSimpleTypeCanneur(), fixtures.vesselSimpleTypeSenneur());
    67 65 
             parameters.put("vesselSimpleTypes", vesselSimpleTypes);
    68 66
    69 
    -        Map<String, String> fleets = new TreeMap<String, String>();
    67 
    +        Map<String, String> fleets = new TreeMap<>();
    70 68 
             putInMap(fleets, fixtures.frenchCountry());
    71 69 
             parameters.put("fleets", fleets);
    72 70

  • t3-actions/src/test/java/fr/ird/t3/actions/data/level1/ComputeWeightOfCategoriesForSetActionResumeTest.java
    ... ... @@ -23,7 +23,6 @@ package fr.ird.t3.actions.data.level1;
    23 23 
     import org.junit.Test;
    24 24
    25 25 
     import java.util.Locale;
    26 
    -import java.util.Map;
    27 26
    28 27 
     /**
    29 28 
      * To test the resume generation of action
    ... ... @@ -44,13 +43,13 @@ public class ComputeWeightOfCategoriesForSetActionResumeTest extends AbstractLev
    44 43 
             action.nbSampleWithoutWell = 1;
    45 44 
         }
    46 45
    47 
    -    @Override
    48 
    -    protected Map<String, Object> createTemplateParameters() {
    49 
    -
    50 
    -        Map<String, Object> parameters = super.createTemplateParameters();
    51 
    -
    52 
    -        return parameters;
    53 
    -    }
    46 
    +//    @Override
    47 
    +//    protected Map<String, Object> createTemplateParameters() {
    48 
    +//
    49 
    +//        Map<String, Object> parameters = super.createTemplateParameters();
    50 
    +//
    51 
    +//        return parameters;
    52 
    +//    }
    54 53
    55 54 
         @Test
    56 55 
         public void testRender() throws Exception {

  • t3-actions/src/test/java/fr/ird/t3/actions/data/level1/ConvertSampleSetSpeciesFrequencyToWeightActionResumeTest.java
    ... ... @@ -24,7 +24,6 @@ package fr.ird.t3.actions.data.level1;
    24 24 
     import org.junit.Test;
    25 25
    26 26 
     import java.util.Locale;
    27 
    -import java.util.Map;
    28 27
    29 28 
     /**
    30 29 
      * Tests the {@link ConvertSampleSetSpeciesFrequencyToWeightAction}.
    ... ... @@ -43,13 +42,13 @@ public class ConvertSampleSetSpeciesFrequencyToWeightActionResumeTest extends Ab
    43 42 
             super.prepareAction(action, locale);
    44 43 
         }
    45 44
    46 
    -    @Override
    47 
    -    protected Map<String, Object> createTemplateParameters() {
    48 
    -
    49 
    -        Map<String, Object> parameters = super.createTemplateParameters();
    50 
    -
    51 
    -        return parameters;
    52 
    -    }
    45 
    +//    @Override
    46 
    +//    protected Map<String, Object> createTemplateParameters() {
    47 
    +//
    48 
    +//        Map<String, Object> parameters = super.createTemplateParameters();
    49 
    +//
    50 
    +//        return parameters;
    51 
    +//    }
    53 52
    54 53 
         @Test
    55 54 
         public void testRender() throws Exception {

  • t3-actions/src/test/java/fr/ird/t3/actions/data/level1/ConvertSetSpeciesFrequencyToWeightActionResumeTest.java
    ... ... @@ -23,7 +23,6 @@ package fr.ird.t3.actions.data.level1;
    23 23 
     import org.junit.Test;
    24 24
    25 25 
     import java.util.Locale;
    26 
    -import java.util.Map;
    27 26
    28 27 
     /**
    29 28 
      * Tests the {@link ConvertSetSpeciesFrequencyToWeightAction}.
    ... ... @@ -45,13 +44,13 @@ public class ConvertSetSpeciesFrequencyToWeightActionResumeTest extends Abstract
    45 44 
             action.nbCreatedFishesInSetSpeciesFrequency = 102;
    46 45 
         }
    47 46
    48 
    -    @Override
    49 
    -    protected Map<String, Object> createTemplateParameters() {
    50 
    -
    51 
    -        Map<String, Object> parameters = super.createTemplateParameters();
    52 
    -
    53 
    -        return parameters;
    54 
    -    }
    47 
    +//    @Override
    48 
    +//    protected Map<String, Object> createTemplateParameters() {
    49 
    +//
    50 
    +//        Map<String, Object> parameters = super.createTemplateParameters();
    51 
    +//
    52 
    +//        return parameters;
    53 
    +//    }
    55 54
    56 55 
         @Test
    57 56 
         public void testRender() throws Exception {

  • t3-actions/src/test/java/fr/ird/t3/actions/data/level1/ExtrapolateSampleWeightToSetActionResumeTest.java
    ... ... @@ -23,7 +23,6 @@ package fr.ird.t3.actions.data.level1;
    23 23 
     import org.junit.Test;
    24 24
    25 25 
     import java.util.Locale;
    26 
    -import java.util.Map;
    27 26
    28 27 
     /**
    29 28 
      * To test the resume generation of action
    ... ... @@ -46,13 +45,13 @@ public class ExtrapolateSampleWeightToSetActionResumeTest extends AbstractLevel1
    46 45 
             action.nbCreatedFishesInSetSpeciesFrequency = 102;
    47 46 
         }
    48 47
    49 
    -    @Override
    50 
    -    protected Map<String, Object> createTemplateParameters() {
    51 
    -
    52 
    -        Map<String, Object> parameters = super.createTemplateParameters();
    53 
    -
    54 
    -        return parameters;
    55 
    -    }
    48 
    +//    @Override
    49 
    +//    protected Map<String, Object> createTemplateParameters() {
    50 
    +//
    51 
    +//        Map<String, Object> parameters = super.createTemplateParameters();
    52 
    +//
    53 
    +//        return parameters;
    54 
    +//    }
    56 55
    57 56 
         @Test
    58 57 
         public void testRender() throws Exception {

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level1/AbstractLevel1ConfigureAction.java
    ... ... @@ -33,15 +33,16 @@ import fr.ird.t3.entities.reference.SampleType;
    33 33 
     import fr.ird.t3.services.ioc.InjectDAO;
    34 34 
     import fr.ird.t3.services.ioc.InjectDecoratedBeans;
    35 35 
     import fr.ird.t3.web.actions.AbstractConfigureAction;
    36 
    +import org.apache.commons.collections.MapUtils;
    37 
    +import org.apache.commons.logging.Log;
    38 
    +import org.apache.commons.logging.LogFactory;
    39 
    +
    36 40 
     import java.util.Arrays;
    37 41 
     import java.util.Collection;
    38 42 
     import java.util.EnumSet;
    39 43 
     import java.util.Iterator;
    40 44 
     import java.util.Map;
    41 45 
     import java.util.Set;
    42 
    -import org.apache.commons.collections.MapUtils;
    43 
    -import org.apache.commons.logging.Log;
    44 
    -import org.apache.commons.logging.LogFactory;
    45 46
    46 47 
     /**
    47 48 
      * Abstract run action for all level1 actions.
    ... ... @@ -57,26 +58,26 @@ public class AbstractLevel1ConfigureAction extends AbstractConfigureAction<Level
    57 58
    58 59 
         private static final long serialVersionUID = 1L;
    59 60
    60 
    -    protected final Level1Step[] requiredSteps;
    61 
    +    private final Level1Step[] requiredSteps;
    61 62
    62 
    -    protected final Level1Step currentStep;
    63 
    +    private final Level1Step currentStep;
    63 64
    64 65 
         @InjectDAO(entityType = Sample.class)
    65 
    -    protected transient SampleTopiaDao sampleDAO;
    66 
    +    private transient SampleTopiaDao sampleDAO;
    66 67
    67 68 
         @InjectDecoratedBeans(beanType = SampleQuality.class, filterById = true, pathIds = "sampleQualityIds")
    68 
    -    protected Map<String, String> sampleQualities;
    69 
    +    private Map<String, String> sampleQualities;
    69 70
    70 71 
         @InjectDecoratedBeans(beanType = SampleType.class, filterById = true)
    71 
    -    protected Map<String, String> sampleTypes;
    72 
    +    private Map<String, String> sampleTypes;
    72 73
    73 74 
         @InjectDecoratedBeans(beanType = Country.class)
    74 
    -    protected Map<String, String> fleets;
    75 
    +    private Map<String, String> fleets;
    75 76
    76 
    -    @InjectDecoratedBeans(beanType = Ocean.class)
    77 
    -    protected Map<String, String> oceans;
    77 
    +    @InjectDecoratedBeans(beanType = Ocean.class, filterById = true)
    78 
    +    private Map<String, String> oceans;
    78 79
    79 
    -    protected Map<String, String> useRfMinus10AndRfPlus10OrNot;
    80 
    +    private Map<String, String> useRfMinus10AndRfPlus10OrNot;
    80 81
    81 82 
         public AbstractLevel1ConfigureAction(Level1Step currentStep) {
    82 83 
             super(Level1Configuration.class);
    ... ... @@ -110,7 +111,7 @@ public class AbstractLevel1ConfigureAction extends AbstractConfigureAction<Level
    110 111 
                 log.info("Selected fleet countries  : " + configuration.getFleetIds());
    111 112 
                 log.info("Selected sample qualities : " + configuration.getSampleQualityIds());
    112 113 
                 log.info("Selected sample types     : " + configuration.getSampleTypeIds());
    113 
    -            log.info("Selected ocean            : " + configuration.getOceanId());
    114 
    +            log.info("Selected oceans           : " + configuration.getOceanIds());
    114 115 
                 log.info("Selected begin date       : " + configuration.getBeginDate());
    115 116 
                 log.info("Selected end   date       : " + configuration.getEndDate());
    116 117 
                 log.info("Executed steps            : " + configuration.getExecutedSteps());
    ... ... @@ -118,12 +119,12 @@ public class AbstractLevel1ConfigureAction extends AbstractConfigureAction<Level
    118 119 
         }
    119 120
    120 121 
         @Override
    121 
    -    public String input() throws Exception {
    122 
    +    public String input() {
    122 123 
             return INPUT;
    123 124 
         }
    124 125
    125 126 
         @Override
    126 
    -    public String execute() throws Exception {
    127 
    +    public String execute() {
    127 128
    128 129 
             prepareActionContext();
    129 130 
             return SUCCESS;
    ... ... @@ -136,14 +137,12 @@ public class AbstractLevel1ConfigureAction extends AbstractConfigureAction<Level
    136 137
    137 138 
                 // all required step already executed with this configuration
    138 139 
                 if (log.isInfoEnabled()) {
    139 
    -                log.info("Current configuration already treats all required step " +
    140 
    -                                 Arrays.toString(requiredSteps));
    140 
    +                log.info(String.format("Current configuration already treats all required step %s", Arrays.toString(requiredSteps)));
    141 141 
                 }
    142 142
    143 143 
             } else {
    144 144
    145 
    -            // check on each selected sample of the configuration which steps
    146 
    -            // are missing
    145 
    +            // check on each selected sample of the configuration which steps are missing
    147 146
    148 147 
                 Multimap<Level1Step, Sample> missingSteps =
    149 148 
                         getMissingRequiredStepsExecutedOnSample();
    ... ... @@ -152,10 +151,7 @@ public class AbstractLevel1ConfigureAction extends AbstractConfigureAction<Level
    152 151
    153 152 
                     // ok every steps were previously executed on selected sample
    154 153 
                     if (log.isInfoEnabled()) {
    155 
    -                    log.info("All required steps " +
    156 
    -                                     Arrays.toString(requiredSteps) +
    157 
    -                                     "were already executed on selected samples " +
    158 
    -                                     "of current configuration.");
    154 
    +                    log.info(String.format("All required steps %s were already executed on selected samples of current configuration.", Arrays.toString(requiredSteps)));
    159 155 
                     }
    160 156 
                 } else {
    161 157
    ... ... @@ -209,8 +205,7 @@ public class AbstractLevel1ConfigureAction extends AbstractConfigureAction<Level
    209 205 
         }
    210 206
    211 207 
         public Multimap<String, String> getTripIds() {
    212 
    -        Multimap<String, String> ids = getConfiguration().getSampleIdsByTripId();
    213 
    -        return ids;
    208 
    +        return getConfiguration().getSampleIdsByTripId();
    214 209 
         }
    215 210
    216 211 
         /**
    ... ... @@ -228,7 +223,7 @@ public class AbstractLevel1ConfigureAction extends AbstractConfigureAction<Level
    228 223 
                 if (!executedSteps.contains(requiredStep)) {
    229 224
    230 225 
                     if (log.isWarnEnabled()) {
    231 
    -                    log.warn("A required step [" + requiredStep + "] was still not executed with this configuration ");
    226 
    +                    log.warn(String.format("A required step [%s] was still not executed with this configuration ", requiredStep));
    232 227 
                     }
    233 228 
                     return false;
    234 229 
                 }
    ... ... @@ -249,19 +244,17 @@ public class AbstractLevel1ConfigureAction extends AbstractConfigureAction<Level
    249 244
    250 245 
             Collection<String> sampleIds = getTripIds().values();
    251 246
    252 
    -        Multimap<Level1Step, Sample> missingStates =
    253 
    -                HashMultimap.create();
    247 
    +        Multimap<Level1Step, Sample> missingStates = HashMultimap.create();
    254 248 
             for (String sampleId : sampleIds) {
    255 249
    256 
    -            Sample sample = sampleDAO.findByTopiaId(sampleId);
    250 
    +            Sample sample = sampleDAO.forTopiaIdEquals(sampleId).findUnique();
    257 251
    258 252 
                 for (Level1Step requiredStep : requiredSteps) {
    259 253
    260 254 
                     boolean sampleState = requiredStep.getState(sample);
    261 255 
                     if (!sampleState) {
    262 256 
                         if (log.isWarnEnabled()) {
    263 
    -                        log.warn("Required step " + requiredStep +
    264 
    -                                         " is missing for sample " + sampleId);
    257 
    +                        log.warn(String.format("Required step %s is missing for sample %s", requiredStep, sampleId));
    265 258 
                         }
    266 259 
                         missingStates.put(requiredStep, sample);
    267 260 
                     }

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level1/AbstractLevel1RunAction.java
    ... ... @@ -34,7 +34,6 @@ import org.apache.commons.collections.MapUtils;
    34 34
    35 35 
     import java.util.Collection;
    36 36 
     import java.util.Date;
    37 
    -import java.util.Iterator;
    38 37 
     import java.util.Map;
    39 38 
     import java.util.Set;
    40 39
    ... ... @@ -48,24 +47,18 @@ public abstract class AbstractLevel1RunAction<A extends AbstractLevel1Action> ex
    48 47
    49 48 
         private static final long serialVersionUID = 1L;
    50 49
    51 
    -    protected final Level1Step currentStep;
    52 
    -
    50 
    +    private final Level1Step currentStep;
    53 51 
         @InjectDecoratedBeans(beanType = SampleQuality.class, filterById = true, pathIds = "sampleQualityIds")
    54 
    -    protected Map<String, String> sampleQualities;
    55 
    -
    52 
    +    private Map<String, String> sampleQualities;
    56 53 
         @InjectDecoratedBeans(beanType = SampleType.class, filterById = true)
    57 
    -    protected Map<String, String> sampleTypes;
    58 
    -
    54 
    +    private Map<String, String> sampleTypes;
    59 55 
         @InjectDecoratedBeans(beanType = Country.class, filterById = true)
    60 
    -    protected Map<String, String> fleets;
    56 
    +    private Map<String, String> fleets;
    57 
    +    @InjectDecoratedBeans(beanType = Ocean.class, filterById = true)
    58 
    +    private Map<String, String> oceans;
    59 
    +    private Map<String, String> useRfMinus10AndRfPlus10OrNot;
    61 60
    62 
    -    @InjectDecoratedBeans(beanType = Ocean.class, filterById = true, filterBySingleId = true)
    63 
    -    protected Map<String, String> oceans;
    64 
    -
    65 
    -    protected Map<String, String> useRfMinus10AndRfPlus10OrNot;
    66 
    -
    67 
    -    protected AbstractLevel1RunAction(Class<A> actionType,
    68 
    -                                      Level1Step currentStep) {
    61 
    +    AbstractLevel1RunAction(Class<A> actionType, Level1Step currentStep) {
    69 62 
             super(actionType);
    70 63 
             this.currentStep = currentStep;
    71 64 
         }
    ... ... @@ -73,21 +66,13 @@ public abstract class AbstractLevel1RunAction<A extends AbstractLevel1Action> ex
    73 66 
         @Override
    74 67 
         protected void executeAction(A action) throws Exception {
    75 68
    76 
    -        // when beginning a step, remove from executed one all the step with
    77 
    -        // higher ranks...
    69 
    +        // when beginning a step, remove from executed one all the step with higher ranks...
    78 70
    79 71 
             Level1Configuration configuration = getConfiguration();
    80 
    -        Set<Level1Step> executedSteps =
    81 
    -                configuration.getExecutedSteps();
    72 
    +        Set<Level1Step> executedSteps = configuration.getExecutedSteps();
    82 73 
             int ordinal = currentStep.ordinal();
    83 74
    84 
    -        Iterator<Level1Step> itr = executedSteps.iterator();
    85 
    -        while (itr.hasNext()) {
    86 
    -            Level1Step step = itr.next();
    87 
    -            if (step.ordinal() >= ordinal) {
    88 
    -                itr.remove();
    89 
    -            }
    90 
    -        }
    75 
    +        executedSteps.removeIf(step -> step.ordinal() >= ordinal);
    91 76
    92 77 
             super.executeAction(action);
    93 78
    ... ... @@ -134,8 +119,7 @@ public abstract class AbstractLevel1RunAction<A extends AbstractLevel1Action> ex
    134 119 
         }
    135 120
    136 121 
         public Multimap<String, String> getTripIds() {
    137 
    -        Multimap<String, String> ids = getConfiguration().getSampleIdsByTripId();
    138 
    -        return ids;
    122 
    +        return getConfiguration().getSampleIdsByTripId();
    139 123 
         }
    140 124
    141 125 
         public Map<String, String> getUseRfMinus10AndRfPlus10OrNot() {
    ... ... @@ -143,14 +127,8 @@ public abstract class AbstractLevel1RunAction<A extends AbstractLevel1Action> ex
    143 127 
         }
    144 128
    145 129 
         @Override
    146 
    -    protected Map<String, Object> prepareResumeParameters(A action,
    147 
    -                                                          Exception error,
    148 
    -                                                          Date startDate,
    149 
    -                                                          Date endDate) {
    150 
    -        Map<String, Object> map = super.prepareResumeParameters(action,
    151 
    -                                                                error,
    152 
    -                                                                startDate,
    153 
    -                                                                endDate);
    130 
    +    protected Map<String, Object> prepareResumeParameters(A action, Exception error, Date startDate, Date endDate) {
    131 
    +        Map<String, Object> map = super.prepareResumeParameters(action, error, startDate, endDate);
    154 132 
             map.put("oceans", oceans);
    155 133 
             map.put("sampleQualities", sampleQualities);
    156 134 
             map.put("sampleTypes", sampleTypes);

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level1/ComputeWeightOfCategoriesForSetRunAction.java
    ... ... @@ -34,7 +34,6 @@ public class ComputeWeightOfCategoriesForSetRunAction extends AbstractLevel1RunA
    34 34 
         private static final long serialVersionUID = 1L;
    35 35
    36 36 
         public ComputeWeightOfCategoriesForSetRunAction() {
    37 
    -        super(ComputeWeightOfCategoriesForSetAction.class,
    38 
    -              Level1Step.COMPUTE_WEIGHT_OF_CATEGORIES_FOR_SET);
    37 
    +        super(ComputeWeightOfCategoriesForSetAction.class, Level1Step.COMPUTE_WEIGHT_OF_CATEGORIES_FOR_SET);
    39 38 
         }
    40 39 
     }

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level1/ConvertSampleSetSpeciesFrequencyToWeightRunAction.java
    ... ... @@ -35,7 +35,6 @@ public class ConvertSampleSetSpeciesFrequencyToWeightRunAction extends AbstractL
    35 35 
         private static final long serialVersionUID = 1L;
    36 36
    37 37 
         public ConvertSampleSetSpeciesFrequencyToWeightRunAction() {
    38 
    -        super(ConvertSampleSetSpeciesFrequencyToWeightAction.class,
    39 
    -              Level1Step.CONVERT_SAMPLE_SET_SPECIES_FREQUENCY_TO_WEIGHT);
    38 
    +        super(ConvertSampleSetSpeciesFrequencyToWeightAction.class, Level1Step.CONVERT_SAMPLE_SET_SPECIES_FREQUENCY_TO_WEIGHT);
    40 39 
         }
    41 40 
     }

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level1/ConvertSetSpeciesFrequencyToWeightRunAction.java
    ... ... @@ -34,7 +34,6 @@ public class ConvertSetSpeciesFrequencyToWeightRunAction extends AbstractLevel1R
    34 34 
         private static final long serialVersionUID = 1L;
    35 35
    36 36 
         public ConvertSetSpeciesFrequencyToWeightRunAction() {
    37 
    -        super(ConvertSetSpeciesFrequencyToWeightAction.class,
    38 
    -              Level1Step.CONVERT_SET_SPECIES_FREQUENCY_TO_WEIGHT);
    37 
    +        super(ConvertSetSpeciesFrequencyToWeightAction.class, Level1Step.CONVERT_SET_SPECIES_FREQUENCY_TO_WEIGHT);
    39 38 
         }
    40 39 
     }

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level1/ExtrapolateSampleCountedAndMeasuredRunAction.java
    ... ... @@ -38,24 +38,13 @@ public class ExtrapolateSampleCountedAndMeasuredRunAction extends AbstractLevel1
    38 38 
         private static final long serialVersionUID = 1L;
    39 39
    40 40 
         public ExtrapolateSampleCountedAndMeasuredRunAction() {
    41 
    -        super(ExtrapolateSampleCountedAndMeasuredAction.class,
    42 
    -              Level1Step.EXTRAPOLATE_SAMPLE_COUNTED_AND_MEASURED);
    41 
    +        super(ExtrapolateSampleCountedAndMeasuredAction.class, Level1Step.EXTRAPOLATE_SAMPLE_COUNTED_AND_MEASURED);
    43 42 
         }
    44 43
    45 44 
         @Override
    46 
    -    protected Map<String, Object> prepareResumeParameters(
    47 
    -            ExtrapolateSampleCountedAndMeasuredAction action,
    48 
    -            Exception error,
    49 
    -            Date startDate,
    50 
    -            Date endDate) {
    51 
    -        Map<String, Object> parameters =
    52 
    -                super.prepareResumeParameters(action,
    53 
    -                                              error,
    54 
    -                                              startDate,
    55 
    -                                              endDate
    56 
    -                );
    45 
    +    protected Map<String, Object> prepareResumeParameters(ExtrapolateSampleCountedAndMeasuredAction action, Exception error, Date startDate, Date endDate) {
    46 
    +        Map<String, Object> parameters = super.prepareResumeParameters(action, error, startDate, endDate);
    57 47 
             parameters.put("speciesDecorator", getDecorator(Species.class));
    58 
    -
    59 48 
             return parameters;
    60 49 
         }
    61 50

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level1/ExtrapolateSampleWeightToSetRunAction.java
    ... ... @@ -34,7 +34,6 @@ public class ExtrapolateSampleWeightToSetRunAction extends AbstractLevel1RunActi
    34 34 
         private static final long serialVersionUID = 1L;
    35 35
    36 36 
         public ExtrapolateSampleWeightToSetRunAction() {
    37 
    -        super(ExtrapolateSampleWeightToSetAction.class,
    38 
    -              Level1Step.EXTRAPOLATE_SAMPLE_WEIGHT_TO_SET);
    37 
    +        super(ExtrapolateSampleWeightToSetAction.class, Level1Step.EXTRAPOLATE_SAMPLE_WEIGHT_TO_SET);
    39 38 
         }
    40 39 
     }

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level1/ManageLevel1ConfigurationAction.java
    ... ... @@ -35,22 +35,21 @@ import fr.ird.t3.entities.reference.SampleType;
    35 35 
     import fr.ird.t3.entities.reference.SampleTypeTopiaDao;
    36 36 
     import fr.ird.t3.entities.type.T3Date;
    37 37 
     import fr.ird.t3.services.DecoratorService;
    38 
    -import fr.ird.t3.services.ioc.InjectDAO;
    39 38 
     import fr.ird.t3.services.ioc.InjectDecoratedBeans;
    40 39 
     import fr.ird.t3.services.ioc.InjectFromDAO;
    41 40 
     import fr.ird.t3.web.actions.AbstractConfigureAction;
    42 
    -import java.util.Collection;
    43 
    -import java.util.Date;
    44 
    -import java.util.List;
    45 
    -import java.util.Map;
    46 41 
     import org.apache.commons.collections.CollectionUtils;
    47 42 
     import org.apache.commons.collections.MapUtils;
    48 
    -import org.apache.commons.lang3.StringUtils;
    49 43 
     import org.apache.commons.lang3.tuple.MutablePair;
    50 44 
     import org.apache.struts2.interceptor.validation.SkipValidation;
    51 45 
     import org.nuiton.decorator.Decorator;
    52 46 
     import org.nuiton.topia.persistence.util.TopiaEntityHelper;
    53 47
    48 
    +import java.util.Collection;
    49 
    +import java.util.Date;
    50 
    +import java.util.List;
    51 
    +import java.util.Map;
    52 
    +
    54 53 
     /**
    55 54 
      * Action to manage the configuration of level 1.
    56 55 
      *
    ... ... @@ -62,26 +61,23 @@ public class ManageLevel1ConfigurationAction extends AbstractConfigureAction<Lev
    62 61 
         private static final long serialVersionUID = 1L;
    63 62
    64 63 
         @InjectDecoratedBeans(beanType = SampleQuality.class)
    65 
    -    protected Map<String, String> sampleQualities;
    64 
    +    private Map<String, String> sampleQualities;
    66 65
    67 66 
         @InjectDecoratedBeans(beanType = SampleType.class)
    68 
    -    protected Map<String, String> sampleTypes;
    67 
    +    private Map<String, String> sampleTypes;
    69 68
    70 69 
         @InjectDecoratedBeans(beanType = Country.class)
    71 
    -    protected Map<String, String> fleets;
    70 
    +    private Map<String, String> fleets;
    72 71
    73 72 
         @InjectDecoratedBeans(beanType = Ocean.class)
    74 
    -    protected Map<String, String> oceans;
    73 
    +    private Map<String, String> oceans;
    75 74
    76 75 
         @InjectFromDAO(entityType = Trip.class, method = "findAllForLevel1")
    77 
    -    protected Collection<Trip> trips;
    76 
    +    private Collection<Trip> trips;
    78 77
    79 
    -    @InjectDAO(entityType = Ocean.class)
    80 
    -    protected transient OceanTopiaDao oceanDAO;
    78 
    +    private Map<String, Trip> tripByTopiaIds;
    81 79
    82 
    -    protected Map<String, Trip> tripByTopiaIds;
    83 
    -
    84 
    -    protected Map<String, String> useRfMinus10AndRfPlus10OrNot;
    80 
    +    private Map<String, String> useRfMinus10AndRfPlus10OrNot;
    85 81
    86 82 
         public ManageLevel1ConfigurationAction() {
    87 83 
             super(Level1Configuration.class);
    ... ... @@ -124,18 +120,17 @@ public class ManageLevel1ConfigurationAction extends AbstractConfigureAction<Lev
    124 120 
                 conf.setSampleTypes(sortToList(SampleTypeTopiaDao.getAllSampleTypes(trips)));
    125 121 
                 conf.setFleets(sortToList(CountryTopiaDao.getAllFleetCountries(trips)));
    126 122 
                 conf.setOceans(sortToList(OceanTopiaDao.getAllOcean(trips)));
    127 
    -            if (StringUtils.isEmpty(conf.getOceanId()) &&
    128 
    -                CollectionUtils.isNotEmpty(conf.getOceans())) {
    129 
    -                conf.setOceanId(conf.getOceans().get(0).getTopiaId());
    130 
    -            }
    123 
    +//            if (StringUtils.isEmpty(conf.getOceanId()) &&
    124 
    +//                CollectionUtils.isNotEmpty(conf.getOceans())) {
    125 
    +//                conf.setOceanId(conf.getOceans().get(0).getTopiaId());
    126 
    +//            }
    131 127
    132 128 
                 // set ids list to empty lists
    133 129 
                 List<String> ids;
    134 130
    135 131 
                 // use default sample qualities
    136 132 
                 ids = T3EntityHelper.selectIdsByCodes(conf.getSampleQualities(), 1, 2, 3, 9);
    137 
    -            conf.setSampleQualityIds(
    138 
    -                    ids);
    133 
    +            conf.setSampleQualityIds(ids);
    139 134
    140 135 
                 // use default sample types
    141 136 
                 ids = T3EntityHelper.selectIdsByCodes(conf.getSampleTypes(), 1, 2, 3, 9);
    ... ... @@ -165,8 +160,7 @@ public class ManageLevel1ConfigurationAction extends AbstractConfigureAction<Lev
    165 160 
             injectOnly(InjectDecoratedBeans.class);
    166 161
    167 162 
             DecoratorService decoratorService = newService(DecoratorService.class);
    168 
    -        Multimap<String, String> matchingTrips = conf.getMatchingTrips(
    169 
    -                trips, getLocale(), decoratorService);
    163 
    +        Multimap<String, String> matchingTrips = conf.getMatchingTrips(trips, getLocale(), decoratorService);
    170 164 
             conf.setSampleIdsByTripId(matchingTrips);
    171 165 
         }
    172 166
    ... ... @@ -179,7 +173,7 @@ public class ManageLevel1ConfigurationAction extends AbstractConfigureAction<Lev
    179 173 
             }
    180 174 
         }
    181 175
    182 
    -    public final String prepareConfiguration() throws Exception {
    176 
    +    public final String prepareConfiguration() {
    183 177
    184 178 
             if (!isConfigurationInSession() && !hasFieldErrors()) {
    185 179
    ... ... @@ -189,7 +183,7 @@ public class ManageLevel1ConfigurationAction extends AbstractConfigureAction<Lev
    189 183 
             return INPUT;
    190 184 
         }
    191 185
    192 
    -    public String saveConfiguration() throws Exception {
    186 
    +    public String saveConfiguration() {
    193 187 
             Level1Configuration config = getConfiguration();
    194 188
    195 189 
             // each time configuration is modified, reset executed steps for
    ... ... @@ -205,7 +199,7 @@ public class ManageLevel1ConfigurationAction extends AbstractConfigureAction<Lev
    205 199 
         }
    206 200
    207 201 
         @SkipValidation
    208 
    -    public String removeConfiguration() throws Exception {
    202 
    +    public String removeConfiguration() {
    209 203
    210 204 
             boolean saved = isConfigurationInSession();
    211 205 
             if (saved) {
    ... ... @@ -238,9 +232,7 @@ public class ManageLevel1ConfigurationAction extends AbstractConfigureAction<Lev
    238 232 
         }
    239 233
    240 234 
         public Map<String, Collection<String>> getTripIds() {
    241 
    -        Map<String, Collection<String>> ids =
    242 
    -                getConfiguration().getSampleIdsByTripId().asMap();
    243 
    -        return ids;
    235 
    +        return getConfiguration().getSampleIdsByTripId().asMap();
    244 236 
         }
    245 237
    246 238 
         public Map<String, String> getSampleQualities() {

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level1/RedistributeSampleNumberToSetRunAction.java
    ... ... @@ -41,23 +41,12 @@ public class RedistributeSampleNumberToSetRunAction extends AbstractLevel1RunAct
    41 41 
         private static final long serialVersionUID = 1L;
    42 42
    43 43 
         public RedistributeSampleNumberToSetRunAction() {
    44 
    -        super(RedistributeSampleNumberToSetAction.class,
    45 
    -              Level1Step.REDISTRIBUTE_SAMPLE_SET_TO_SET);
    44 
    +        super(RedistributeSampleNumberToSetAction.class, Level1Step.REDISTRIBUTE_SAMPLE_SET_TO_SET);
    46 45 
         }
    47 46
    48 47 
         @Override
    49 
    -    protected Map<String, Object> prepareResumeParameters(
    50 
    -            RedistributeSampleNumberToSetAction action,
    51 
    -            Exception error,
    52 
    -            Date startDate,
    53 
    -            Date endDate) {
    54 
    -        Map<String, Object> parameters = super.prepareResumeParameters(
    55 
    -                action,
    56 
    -                error,
    57 
    -                startDate,
    58 
    -                endDate
    59 
    -        );
    60 
    -
    48 
    +    protected Map<String, Object> prepareResumeParameters(RedistributeSampleNumberToSetAction action, Exception error, Date startDate, Date endDate) {
    49 
    +        Map<String, Object> parameters = super.prepareResumeParameters(action, error, startDate, endDate);
    61 50 
             parameters.put("speciesDecorator", getDecorator(Species.class));
    62 51 
             parameters.put("tripDecorator", getDecorator(Trip.class, DecoratorService.WITH_ID));
    63 52 
             parameters.put("activityDecorator", getDecorator(Activity.class));

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level1/StandardizeSampleMeasuresRunAction.java
    ... ... @@ -38,24 +38,13 @@ public class StandardizeSampleMeasuresRunAction extends AbstractLevel1RunAction<
    38 38 
         private static final long serialVersionUID = 1L;
    39 39
    40 40 
         public StandardizeSampleMeasuresRunAction() {
    41 
    -        super(StandardizeSampleMeasuresAction.class,
    42 
    -              Level1Step.STANDARDIZE_SAMPLE_MEASURE);
    41 
    +        super(StandardizeSampleMeasuresAction.class, Level1Step.STANDARDIZE_SAMPLE_MEASURE);
    43 42 
         }
    44 43
    45 44 
         @Override
    46 
    -    protected Map<String, Object> prepareResumeParameters(
    47 
    -            StandardizeSampleMeasuresAction action,
    48 
    -            Exception error,
    49 
    -            Date startDate,
    50 
    -            Date endDate) {
    51 
    -        Map<String, Object> parameters =
    52 
    -                super.prepareResumeParameters(action,
    53 
    -                                              error,
    54 
    -                                              startDate,
    55 
    -                                              endDate
    56 
    -                );
    45 
    +    protected Map<String, Object> prepareResumeParameters(StandardizeSampleMeasuresAction action, Exception error, Date startDate, Date endDate) {
    46 
    +        Map<String, Object> parameters = super.prepareResumeParameters(action, error, startDate, endDate);
    57 47 
             parameters.put("speciesDecorator", getDecorator(Species.class));
    58 
    -
    59 48 
             return parameters;
    60 49 
         }
    61 50 
     }

  • t3-web/src/main/resources/fr/ird/t3/web/actions/data/level1/ManageLevel1ConfigurationAction-validateLevel1Configuration-validation.xml
    ... ... @@ -48,9 +48,10 @@
    48 48
    49 49 
       </field>
    50 50
    51 
    -  <field name="configuration.oceanId">
    51 
    +  <field name="configuration.oceanIds">
    52 52
    53 
    -    <field-validator type="requiredstring">
    53 
    +    <field-validator type="fieldexpression">
    54 
    +      <param name="expression">!configuration.oceanIds.empty</param>
    54 55 
           <message key="t3.error.no.ocean.selected"/>
    55 56 
         </field-validator>
    56 57

  • t3-web/src/main/resources/fr/ird/t3/web/actions/data/level1/ManageLevel1ConfigurationAction-validation.xml
    ... ... @@ -48,7 +48,7 @@
    48 48
    49 49 
       </field>
    50 50
    51 
    -  <field name="configuration.oceanId">
    51 
    +  <field name="configuration.oceanIds">
    52 52
    53 53 
         <field-validator type="fieldexpression">
    54 54 
           <param name="expression">!configuration.oceans.empty</param>

  • t3-web/src/main/webapp/WEB-INF/jsp/data/level1/level1Configuration.jsp
    ... ... @@ -56,8 +56,9 @@
    56 56 
                         list="fleets" template="mycheckboxlist"/>
    57 57
    58 58 
           <%-- selected ocean --%>
    59 
    -    <s:select key="configuration.oceanId" list="oceans" requiredLabel="true"
    60 
    -              label='%{getText("t3.common.ocean")}'/>
    59 
    +    <s:checkboxlist key="configuration.oceanIds" requiredLabel="true"
    60 
    +                    label='%{getText("t3.common.ocean")}'
    61 
    +                    list="oceans" template="mycheckboxlist"/>
    61 62
    62 63 
           <%-- selected begin date --%>
    63 64 
         <sj:datepicker key="configuration.beginDate" requiredLabel="true"

  • t3-web/src/main/webapp/WEB-INF/jsp/data/level1/level1ConfigurationResume.jsp
    ... ... @@ -45,8 +45,9 @@
    45 45 
                         label='%{getText("t3.common.fleetCountry")}'/>
    46 46
    47 47 
           <%-- selected ocean --%>
    48 
    -    <s:select key="configuration.oceanId" disabled="true" list="oceans"
    49 
    -              label='%{getText("t3.common.ocean")}'/>
    48 
    +    <s:checkboxlist key="configuration.oceanIds" disabled="true"
    49 
    +                    list="fleets" template="mycheckboxlist"
    50 
    +                    label='%{getText("t3.common.ocean")}'/>
    50 51
    51 52 
           <%-- selected begin date --%>
    52 53 
         <s:textfield key="configuration.beginDate" disabled="true"

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