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

Commits:

14 changed files:

Changes:

  • t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3Action.java
    ... ... @@ -334,7 +334,6 @@ public class Level3Action extends T3Action<Level3Configuration> {
    334 334
                     String key = aCatch.getWeightCategoryTreatment().getTopiaId() + aCatch.getSpecies().getTopiaId();
    
    335 335
                     linearCorrectedCatches.put(key, aCatch);
    
    336 336
                 }
    
    337
    -            boolean useWeightCategories = getConfiguration().isUseWeightCategories();
    
    338 337
                 // Generate for each species to fix
    
    339 338
                 for (Species aSpecies : catchSpecies) {
    
    340 339
                     // get all compositions for this species
    
    ... ... @@ -350,34 +349,19 @@ public class Level3Action extends T3Action<Level3Configuration> {
    350 349
                         continue;
    
    351 350
                     }
    
    352 351
                     LengthWeightConversion conversions = catchStratum.getConfiguration().getConversionHelper().getConversions(aSpecies);
    
    353
    -                if (useWeightCategories) {
    
    354
    -                    for (WeightCategoryTreatment weightCategory : weightCategories) {
    
    355
    -                        // get total catch weight for this species and weight category
    
    356
    -                        String key = weightCategory.getTopiaId() + aSpecies.getTopiaId();
    
    357
    -                        CorrectedElementaryCatch aCatch = linearCorrectedCatches.get(key);
    
    358
    -                        if (aCatch != null) {
    
    359
    -                            // get weight to use in this stratum (in kg)
    
    360
    -                            float totalWeight = 1000 * aCatch.getCorrectedCatchWeight() / nbZones;
    
    361
    -                            // get composition for this weight category
    
    362
    -                            LengthCompositionModel model = compositionModel.getModel(weightCategory);
    
    363
    -                            generateFrequencies(activity, aSpecies, previousValues, model, totalWeight, speciesCountModel, conversions);
    
    364
    -                        }
    
    365
    -                    }
    
    366
    -                } else {
    
    367
    -                    float totalWeight = 0f;
    
    368
    -                    for (WeightCategoryTreatment weightCategory : weightCategories) {
    
    369
    -                        // get total catch weight for this species and weight category
    
    370
    -                        String key = weightCategory.getTopiaId() + aSpecies.getTopiaId();
    
    371
    -                        CorrectedElementaryCatch aCatch = linearCorrectedCatches.get(key);
    
    372
    -                        if (aCatch != null) {
    
    373
    -                            totalWeight += aCatch.getCorrectedCatchWeight();
    
    374
    -                        }
    
    352
    +                float totalWeight = 0f;
    
    353
    +                for (WeightCategoryTreatment weightCategory : weightCategories) {
    
    354
    +                    // get total catch weight for this species and weight category
    
    355
    +                    String key = weightCategory.getTopiaId() + aSpecies.getTopiaId();
    
    356
    +                    CorrectedElementaryCatch aCatch = linearCorrectedCatches.get(key);
    
    357
    +                    if (aCatch != null) {
    
    358
    +                        totalWeight += aCatch.getCorrectedCatchWeight();
    
    375 359
                         }
    
    376
    -                    totalWeight = 1000 * totalWeight / nbZones;
    
    377
    -                    // get composition for all weight categories
    
    378
    -                    LengthCompositionModel model = compositionModel.getTotalModel();
    
    379
    -                    generateFrequencies(activity, aSpecies, previousValues, model, totalWeight, speciesCountModel, conversions);
    
    380 360
                     }
    
    361
    +                totalWeight = 1000 * totalWeight / nbZones;
    
    362
    +                // get composition for all weight categories
    
    363
    +                LengthCompositionModel model = compositionModel.getTotalModel();
    
    364
    +                generateFrequencies(activity, aSpecies, previousValues, model, totalWeight, speciesCountModel, conversions);
    
    381 365
                 }
    
    382 366
             }
    
    383 367
         }
    

  • t3-actions/src/main/java/fr/ird/t3/actions/data/level3/Level3Configuration.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%
    
    ... ... @@ -48,13 +48,6 @@ public class Level3Configuration extends LevelConfigurationWithStratum {
    48 48
          */
    
    49 49
         private boolean useAllSamplesOfStratum;
    
    50 50
     
    
    51
    -    /**
    
    52
    -     * Use weight categories when generating frequencies, or not.
    
    53
    -     *
    
    54
    -     * @since 2.0
    
    55
    -     */
    
    56
    -    private boolean useWeightCategories;
    
    57
    -
    
    58 51
         public Map<String, StratumMinimumSampleCount> getStratumMinimumSampleCount() {
    
    59 52
             return stratumMinimumSampleCount;
    
    60 53
         }
    
    ... ... @@ -71,14 +64,6 @@ public class Level3Configuration extends LevelConfigurationWithStratum {
    71 64
             this.useAllSamplesOfStratum = useAllSamplesOfStratum;
    
    72 65
         }
    
    73 66
     
    
    74
    -    public boolean isUseWeightCategories() {
    
    75
    -        return useWeightCategories;
    
    76
    -    }
    
    77
    -
    
    78
    -    public void setUseWeightCategories(boolean useWeightCategories) {
    
    79
    -        this.useWeightCategories = useWeightCategories;
    
    80
    -    }
    
    81
    -
    
    82 67
         @Override
    
    83 68
         public String getName(Locale locale) {
    
    84 69
             return l(locale, "t3.level3.action");
    

  • t3-actions/src/main/resources/ftl/fr/ird/t3/actions/data/level3/Level3Action.ftl
    ... ... @@ -42,12 +42,6 @@ Utilisation des catégories de poids +10/-10 dans la stratification.
    42 42
     Catégories de poids +10/-10 non utilisés dans la stratification.
    
    43 43
     </#if>
    
    44 44
     
    
    45
    -<#if configuration.useWeightCategories>
    
    46
    -Générer les structures de tailles par catégories de poids
    
    47
    -<#else>
    
    48
    -Générer les structures de tailles toutes catégories de poids confondues
    
    49
    -</#if>
    
    50
    -
    
    51 45
     <#list oceans?values as ocean>
    
    52 46
     Océan sélectionné : ${ocean}
    
    53 47
     </#list>
    

  • t3-actions/src/main/resources/ftl/fr/ird/t3/actions/data/level3/Level3Action_en.ftl
    ... ... @@ -42,12 +42,6 @@ Use weight categories +10/-10 in stratification.
    42 42
     Do not use weight categories +10/-10 in stratification.
    
    43 43
     </#if>
    
    44 44
     
    
    45
    -<#if configuration.useWeightCategories>
    
    46
    -Generate length structures by weight category
    
    47
    -<#else>
    
    48
    -Generate length structures for all weight categories
    
    49
    -</#if>
    
    50
    -
    
    51 45
     <#list oceans?values as ocean>
    
    52 46
     Selected ocean: ${ocean}
    
    53 47
     </#list>
    

  • t3-web/src/main/java/fr/ird/t3/web/actions/T3ActionSupport.java
    ... ... @@ -316,12 +316,6 @@ public class T3ActionSupport extends ActionSupport implements T3TopiaPersistence
    316 316
                     "true", t("t3.label.data.level3.configuration.useAllSamples"));
    
    317 317
         }
    
    318 318
     
    
    319
    -    protected ImmutableMap<String, String> createLevel3UseWeightCategoriesOrNotMap() {
    
    320
    -        return ImmutableMap.of(
    
    321
    -                "true", t("t3.label.data.level3.configuration.useWeightCategories"),
    
    322
    -                "false", t("t3.label.data.level3.configuration.ignoreWeightCategories"));
    
    323
    -    }
    
    324
    -
    
    325 319
         protected ImmutableMap<String, String> createUseRfMinus10AndRfPlus10OrNot() {
    
    326 320
             return ImmutableMap.of(
    
    327 321
                     "true", t("t3.label.data.level1.configuration.useRfMinus10AndRfPlus10"),
    

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level3/ConfigureLevel3Step1Action.java
    ... ... @@ -109,7 +109,6 @@ public class ConfigureLevel3Step1Action extends AbstractConfigureAction<Level3Co
    109 109
                 conf.setOceans(sortToList(oceanDAO.findAllUsedInActivity()));
    
    110 110
                 conf.setSpecies(sortToList(specieDAO.findAllSpeciesUsedInCatch()));
    
    111 111
                 conf.setZoneTypes(sortToList(getZoneStratumService().getZoneStratumAwareMetas()));
    
    112
    -            conf.setUseWeightCategories(true);
    
    113 112
             }
    
    114 113
             if (StringUtils.isNotEmpty(conf.getZoneTypeId())) {
    
    115 114
                 // let's fill the zone versions for the selected zone type
    

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level3/ConfigureLevel3Step2Action.java
    ... ... @@ -25,7 +25,6 @@ import fr.ird.t3.actions.stratum.SchoolTypeIndeterminate;
    25 25
     import fr.ird.t3.actions.stratum.StratumMinimumSampleCount;
    
    26 26
     import fr.ird.t3.entities.reference.Country;
    
    27 27
     import fr.ird.t3.entities.reference.CountryTopiaDao;
    
    28
    -import fr.ird.t3.entities.reference.SchoolTypeTopiaDao;
    
    29 28
     import fr.ird.t3.entities.reference.Species;
    
    30 29
     import fr.ird.t3.services.ioc.InjectDAO;
    
    31 30
     import fr.ird.t3.services.ioc.InjectDecoratedBeans;
    
    ... ... @@ -66,7 +65,6 @@ public class ConfigureLevel3Step2Action extends AbstractConfigureAction<Level3Co
    66 65
         private Map<String, String> species;
    
    67 66
         private Map<String, String> schoolTypeIndeterminate;
    
    68 67
         private Map<String, String> useSamplesOrNot;
    
    69
    -    private Map<String, String> useWeightCategoriesOrNot;
    
    70 68
         private Map<String, String> useWeightCategoriesInStratumOrNot;
    
    71 69
         /**
    
    72 70
          * Flag to know if some data are missing.
    
    ... ... @@ -82,7 +80,6 @@ public class ConfigureLevel3Step2Action extends AbstractConfigureAction<Level3Co
    82 80
         @Override
    
    83 81
         public void prepare() throws Exception {
    
    84 82
             useSamplesOrNot = createLevel3UseSamplesOrNotMap();
    
    85
    -        useWeightCategoriesOrNot = createLevel3UseWeightCategoriesOrNotMap();
    
    86 83
             useWeightCategoriesInStratumOrNot = createUseWeightCategoriesInStratumOrNot();
    
    87 84
             schoolTypeIndeterminate = sortAndDecorateIdAbles(Arrays.asList(SchoolTypeIndeterminate.values()));
    
    88 85
             // on level 3, can't treat Indeterminate school type
    
    ... ... @@ -279,11 +276,6 @@ public class ConfigureLevel3Step2Action extends AbstractConfigureAction<Level3Co
    279 276
         }
    
    280 277
     
    
    281 278
         @SuppressWarnings("unused")
    
    282
    -    public Map<String, String> getUseWeightCategoriesOrNot() {
    
    283
    -        return useWeightCategoriesOrNot;
    
    284
    -    }
    
    285
    -
    
    286
    -    @SuppressWarnings("unused")
    
    287 279
         public Map<String, String> getUseWeightCategoriesInStratumOrNot() {
    
    288 280
             return useWeightCategoriesInStratumOrNot;
    
    289 281
         }
    

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level3/Level3ConfigureAction.java
    ... ... @@ -74,7 +74,6 @@ public class Level3ConfigureAction extends AbstractConfigureAction<Level3Configu
    74 74
         private Map<String, String> sampleFlags;
    
    75 75
         private Map<String, String> schoolTypeIndeterminate;
    
    76 76
         private Map<String, String> useSamplesOrNot;
    
    77
    -    private Map<String, String> useWeightCategoriesOrNot;
    
    78 77
         private Map<String, String> useWeightCategoriesInStratumOrNot;
    
    79 78
     
    
    80 79
         public Level3ConfigureAction() {
    
    ... ... @@ -85,7 +84,6 @@ public class Level3ConfigureAction extends AbstractConfigureAction<Level3Configu
    85 84
         public void prepare() throws Exception {
    
    86 85
             log.info(String.format("Prepare with configuration %s", getConfiguration()));
    
    87 86
             useSamplesOrNot = createLevel3UseSamplesOrNotMap();
    
    88
    -        useWeightCategoriesOrNot = createLevel3UseWeightCategoriesOrNotMap();
    
    89 87
             useWeightCategoriesInStratumOrNot = createUseWeightCategoriesInStratumOrNot();
    
    90 88
             schoolTypeIndeterminate = sortAndDecorateIdAbles(Arrays.asList(SchoolTypeIndeterminate.values()));
    
    91 89
             // on level 3, can't treat Indeterminate school type
    
    ... ... @@ -165,11 +163,6 @@ public class Level3ConfigureAction extends AbstractConfigureAction<Level3Configu
    165 163
         }
    
    166 164
     
    
    167 165
         @SuppressWarnings("unused")
    
    168
    -    public Map<String, String> getUseWeightCategoriesOrNot() {
    
    169
    -        return useWeightCategoriesOrNot;
    
    170
    -    }
    
    171
    -
    
    172
    -    @SuppressWarnings("unused")
    
    173 166
         public Map<String, String> getUseWeightCategoriesInStratumOrNot() {
    
    174 167
             return useWeightCategoriesInStratumOrNot;
    
    175 168
         }
    

  • t3-web/src/main/java/fr/ird/t3/web/actions/data/level3/Level3RunAction.java
    ... ... @@ -72,7 +72,6 @@ public class Level3RunAction extends AbstractRunAction<Level3Configuration, Leve
    72 72
         private Map<String, String> sampleFlags;
    
    73 73
         private Map<String, String> schoolTypeIndeterminate;
    
    74 74
         private Map<String, String> useSamplesOrNot;
    
    75
    -    private Map<String, String> useWeightCategoriesOrNot;
    
    76 75
         private Map<String, String> useWeightCategoriesInStratumOrNot;
    
    77 76
     
    
    78 77
         public Level3RunAction() {
    
    ... ... @@ -145,11 +144,6 @@ public class Level3RunAction extends AbstractRunAction<Level3Configuration, Leve
    145 144
         }
    
    146 145
     
    
    147 146
         @SuppressWarnings("unused")
    
    148
    -    public Map<String, String> getUseWeightCategoriesOrNot() {
    
    149
    -        return useWeightCategoriesOrNot;
    
    150
    -    }
    
    151
    -
    
    152
    -    @SuppressWarnings("unused")
    
    153 147
         public Map<String, String> getUseWeightCategoriesInStratumOrNot() {
    
    154 148
             return useWeightCategoriesInStratumOrNot;
    
    155 149
         }
    
    ... ... @@ -157,7 +151,6 @@ public class Level3RunAction extends AbstractRunAction<Level3Configuration, Leve
    157 151
         @Override
    
    158 152
         public void prepare() throws Exception {
    
    159 153
             useSamplesOrNot = createLevel3UseSamplesOrNotMap();
    
    160
    -        useWeightCategoriesOrNot = createLevel3UseWeightCategoriesOrNotMap();
    
    161 154
             useWeightCategoriesInStratumOrNot = createUseWeightCategoriesInStratumOrNot();
    
    162 155
             schoolTypeIndeterminate = sortAndDecorateIdAbles(Arrays.asList(SchoolTypeIndeterminate.values()));
    
    163 156
             super.prepare();
    

  • t3-web/src/main/resources/i18n/t3-web_en_GB.properties
    ... ... @@ -263,15 +263,12 @@ t3.label.data.level2.configuration.step1=Level 2 configuration step 1
    263 263
     t3.label.data.level2.configuration.step2=Level 2 configuration step 2
    
    264 264
     t3.label.data.level2.configuration.useAllSamples=Use their own sample
    
    265 265
     t3.label.data.level2.configuration.useCatchSamples=Use their stratum sample
    
    266
    -t3.label.data.level3.configuration.ignoreWeightCategories=Do not use weight categories
    
    267 266
     t3.label.data.level3.configuration.resume=Level 3 configuration resume
    
    268 267
     t3.label.data.level3.configuration.samplesToUse=Treatment to apply to catches with samples
    
    269 268
     t3.label.data.level3.configuration.step1=Level 3 configuration step 1
    
    270 269
     t3.label.data.level3.configuration.step2=Level 3 configuration step 2
    
    271 270
     t3.label.data.level3.configuration.useAllSamples=Keep their own sample (do nothing)
    
    272 271
     t3.label.data.level3.configuration.useCatchSamples=Apply length structures from the sample stratum
    
    273
    -t3.label.data.level3.configuration.useWeightCategories=Use weight categories
    
    274
    -t3.label.data.level3.configuration.useWeightCategoriesOrNot=Extrapolation method
    
    275 272
     t3.label.data.treatment.level0=Level 0 treatment
    
    276 273
     t3.label.data.treatment.level1=Level 0 treatment
    
    277 274
     t3.label.data.treatment.level2=Level 2 treatment\: Species composition correction
    

  • t3-web/src/main/resources/i18n/t3-web_fr_FR.properties
    ... ... @@ -263,15 +263,12 @@ t3.label.data.level2.configuration.step1=Configuration du niveau 2 (étape 1)
    263 263
     t3.label.data.level2.configuration.step2=Configuration du niveau 2 (étape 2)
    
    264 264
     t3.label.data.level2.configuration.useAllSamples=Les échantillons de leur strate échantillon
    
    265 265
     t3.label.data.level2.configuration.useCatchSamples=Leur propre échantillon
    
    266
    -t3.label.data.level3.configuration.ignoreWeightCategories=Extrapoler les échantillons uniformément
    
    267 266
     t3.label.data.level3.configuration.resume=Résumé de la configuration
    
    268 267
     t3.label.data.level3.configuration.samplesToUse=Traitement à appliquer aux calées avec échantillon
    
    269 268
     t3.label.data.level3.configuration.step1=Configuration du niveau 3 (étape 1)
    
    270 269
     t3.label.data.level3.configuration.step2=Configuration du niveau 3 (étape 2)
    
    271 270
     t3.label.data.level3.configuration.useAllSamples=Appliquer les structures de tailles de la strate échantillons
    
    272 271
     t3.label.data.level3.configuration.useCatchSamples=Conserver leurs échantillons en l'état
    
    273
    -t3.label.data.level3.configuration.useWeightCategories=Extrapoler les échantillons proportionnellement aux captures des catégories de poids
    
    274
    -t3.label.data.level3.configuration.useWeightCategoriesOrNot=Méthode d'extrapolation
    
    275 272
     t3.label.data.treatment.level0=Traitement du niveau 0
    
    276 273
     t3.label.data.treatment.level1=Traitement du niveau 1
    
    277 274
     t3.label.data.treatment.level2=Traitement du niveau 2 \: Correction de la composition spécifique
    

  • t3-web/src/main/webapp/WEB-INF/jsp/data/level3/level3ConfigurationResume.jsp
    ... ... @@ -68,10 +68,6 @@
    68 68
       <s:radio key="configuration.useAllSamplesOfStratum" disabled="true" list="useSamplesOrNot"
    
    69 69
                label='%{getText("t3.label.data.level3.configuration.samplesToUse")}'/>
    
    70 70
     
    
    71
    -  <%-- use weight categories --%>
    
    72
    -  <s:radio key="configuration.useWeightCategories" disabled="true" list="useWeightCategoriesOrNot"
    
    73
    -           label='%{getText("t3.label.data.level3.configuration.useWeightCategoriesOrNot")}'/>
    
    74
    -
    
    75 71
       <%--use weight categories in stratum--%>
    
    76 72
       <s:radio key="configuration.useWeightCategoriesInStratum" disabled="true"
    
    77 73
                list="useWeightCategoriesInStratumOrNot" label='%{getText("t3.label.data.useWeightCategoriesInStratum")}'/>
    

  • t3-web/src/main/webapp/WEB-INF/jsp/data/level3/level3ConfigurationStep1.jsp
    ... ... @@ -99,10 +99,6 @@
    99 99
                        label='%{getText("t3.common.endDate")}' appendText=" (mm-yyyy)"/>
    
    100 100
     
    
    101 101
           <%-- selected species --%>
    
    102
    -      <%--<s:iterator value="configuration.speciesIds" var="id">--%>
    
    103
    -      <%--<s:hidden name="configuration.speciesIds" value='%{#id}'/>--%>
    
    104
    -      <%--</s:iterator>--%>
    
    105
    -
    
    106 102
         <s:checkboxlist key="configuration.speciesIds" requiredLabel="true" list="species"
    
    107 103
                         label='%{getText("t3.common.species")}' template="mycheckboxlist"/>
    
    108 104
     
    

  • t3-web/src/main/webapp/WEB-INF/jsp/data/level3/level3ConfigurationStep2.jsp
    ... ... @@ -57,10 +57,6 @@
    57 57
         <s:radio key="configuration.useAllSamplesOfStratum" requiredLabel="true" list="useSamplesOrNot"
    
    58 58
                  label='%{getText("t3.label.data.level3.configuration.samplesToUse")}'/>
    
    59 59
     
    
    60
    -      <%-- use weight categories --%>
    
    61
    -    <s:radio key="configuration.useWeightCategories" requiredLabel="true" list="useWeightCategoriesOrNot"
    
    62
    -             label='%{getText("t3.label.data.level3.configuration.useWeightCategoriesOrNot")}'/>
    
    63
    -
    
    64 60
           <%--use weight categories in stratum--%>
    
    65 61
         <s:radio key="configuration.useWeightCategoriesInStratum" requiredLabel="true"
    
    66 62
                  list="useWeightCategoriesInStratumOrNot" label='%{getText("t3.label.data.useWeightCategoriesInStratum")}'/>