r1503 - in trunk: tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/entities/protocol tutti-persistence/src/main/resources/i18n tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/content/protocol tutti-ui-swing/src/main/resources/i18n - Tutti-commits

18 Jan 2014

Author: tchemit
Date: 2014-01-18 16:13:52 +0100 (Sat, 18 Jan 2014)
New Revision: 1503

Url: http://forge.codelutin.com/projects/tutti/repository/revisions/1503

Log:
fixes #4145: [PROTOCOLE] erreur apr?\195?\168s import protocole (d'avant 3.0), changement nom, et enregistrement. Urgent car bloque cr?\195?\169ation protocole

Modified:
   trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/entities/protocol/TuttiProtocols.java
   trunk/tutti-persistence/src/main/resources/i18n/tutti-persistence_en_GB.properties
   trunk/tutti-persistence/src/main/resources/i18n/tutti-persistence_fr_FR.properties
   trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action/ImportProtocolAction.java
   trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/content/protocol/EditProtocolUIHandler.java
   trunk/tutti-ui-swing/src/main/resources/i18n/tutti-ui-swing_en_GB.properties
   trunk/tutti-ui-swing/src/main/resources/i18n/tutti-ui-swing_fr_FR.properties

Modified: trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/entities/protocol/TuttiProtocols.java
===================================================================

--- trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/entities/protocol/TuttiProtocols.java	2014-01-18 00:01:01 UTC (rev 1502)
+++ trunk/tutti-persistence/src/main/java/fr/ifremer/tutti/persistence/entities/protocol/TuttiProtocols.java	2014-01-18 15:13:52 UTC (rev 1503)
@@ -52,7 +52,9 @@
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.Reader;
+import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import static org.nuiton.i18n.I18n._;
@@ -195,6 +197,16 @@
         }
     }
 
+    public static void removeBadSpecies(Set<Integer> speciesIds, List<SpeciesProtocol> protocol) {
+        Iterator<SpeciesProtocol> iterator = protocol.iterator();
+        while (iterator.hasNext()) {
+            SpeciesProtocol next = iterator.next();
+            if (speciesIds.contains(next.getSpeciesReferenceTaxonId())) {
+                iterator.remove();
+            }
+        }
+    }
+
     public static String getBadCategoriesMessage(Set<Integer> badCategories,
                                                  Decorator<Caracteristic> decorator,
                                                  TuttiPersistence persistenceService) {
@@ -217,6 +229,26 @@
         return message;
     }
 
+    public static String getBadSpeciesMessage(Map<Integer, String> badSpecies) {
+        List<String> badCategoriesStr = Lists.newArrayList();
+
+        for (Map.Entry<Integer, String> id : badSpecies.entrySet()) {
+            badCategoriesStr.add("<li>" + id.getKey() + " : " + (id.getValue() == null ? "" : id.getValue()) + "</li>");
+        }
+        String message = _("tutti.persistence.error.protocol.species.not.found", Joiner.on("").join(badCategoriesStr));
+        return message;
+    }
+
+    public static String getBadBenthosMessage(Map<Integer, String> badSpecies) {
+        List<String> badCategoriesStr = Lists.newArrayList();
+
+        for (Map.Entry<Integer, String> id : badSpecies.entrySet()) {
+            badCategoriesStr.add("<li>" + id.getKey() + " : " + (id.getValue() == null ? "" : id.getValue()) + "</li>");
+        }
+        String message = _("tutti.persistence.error.protocol.benthos.not.found", Joiner.on("").join(badCategoriesStr));
+        return message;
+    }
+
     protected static TuttiProtocol fromTuttiProtocol1(TuttiEnumerationFile enumeration, TuttiProtocol1 tuttiProtocol1) {
         TuttiProtocol result = newTuttiProtocol();
         Binder<TuttiProtocol1, TuttiProtocol> binder = BinderFactory.newBinder(TuttiProtocol1.class, TuttiProtocol.class);

Modified: trunk/tutti-persistence/src/main/resources/i18n/tutti-persistence_en_GB.properties
===================================================================
--- trunk/tutti-persistence/src/main/resources/i18n/tutti-persistence_en_GB.properties	2014-01-18 00:01:01 UTC (rev 1502)
+++ trunk/tutti-persistence/src/main/resources/i18n/tutti-persistence_en_GB.properties	2014-01-18 15:13:52 UTC (rev 1503)
@@ -95,7 +95,9 @@
 tutti.persistence.dbMetadata.instanciation.error=
 tutti.persistence.error.caracteristic.notFound=
 tutti.persistence.error.no.convertor=
+tutti.persistence.error.protocol.benthos.not.found=
 tutti.persistence.error.protocol.categories.not.compatible=
+tutti.persistence.error.protocol.species.not.found=
 tutti.persistence.loader.error=
 tutti.persistence.protocol.delete.error=
 tutti.persistence.protocol.fromFile.error=

Modified: trunk/tutti-persistence/src/main/resources/i18n/tutti-persistence_fr_FR.properties
===================================================================
--- trunk/tutti-persistence/src/main/resources/i18n/tutti-persistence_fr_FR.properties	2014-01-18 00:01:01 UTC (rev 1502)
+++ trunk/tutti-persistence/src/main/resources/i18n/tutti-persistence_fr_FR.properties	2014-01-18 15:13:52 UTC (rev 1503)
@@ -95,7 +95,9 @@
 tutti.persistence.dbMetadata.instanciation.error=Erreur lors de l'initialisation des metadata de la base de données par la connexion %s
 tutti.persistence.error.caracteristic.notFound=Caractéristique inconnue
 tutti.persistence.error.no.convertor=Impossible de convertir en modèle de catégorie le type %s avec la valeur %s
+tutti.persistence.error.protocol.benthos.not.found=Le protocole utilise des benthos non connus dans le référentiel \: <ul>%s</ul>
 tutti.persistence.error.protocol.categories.not.compatible=Le protocole utilise des catégories non connues par la configuration des catégorisations \: <ul>%s</ul>
+tutti.persistence.error.protocol.species.not.found=Le protocole utilise des espèces non connues dans le référentiel \: <ul>%s</ul>
 tutti.persistence.loader.error=Erreur de conversion du dossier %s en URL
 tutti.persistence.protocol.delete.error=Erreur lors de la suppression du protocole %1s (fichier %2s)
 tutti.persistence.protocol.fromFile.error=Erreur lors de l'import du protocole du fichier %s

Modified: trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action/ImportProtocolAction.java
===================================================================
--- trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action/ImportProtocolAction.java	2014-01-18 00:01:01 UTC (rev 1502)
+++ trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/action/ImportProtocolAction.java	2014-01-18 15:13:52 UTC (rev 1503)
@@ -25,15 +25,20 @@
  */
 
 import com.google.common.base.Preconditions;
+import com.google.common.collect.Maps;
 import com.google.common.collect.Sets;
+import fr.ifremer.tutti.persistence.entities.TuttiEntities;
 import fr.ifremer.tutti.persistence.entities.data.SampleCategoryModel;
+import fr.ifremer.tutti.persistence.entities.protocol.SpeciesProtocol;
 import fr.ifremer.tutti.persistence.entities.protocol.TuttiProtocol;
 import fr.ifremer.tutti.persistence.entities.protocol.TuttiProtocols;
 import fr.ifremer.tutti.persistence.entities.referential.Caracteristic;
+import fr.ifremer.tutti.persistence.entities.referential.Species;
 import fr.ifremer.tutti.service.protocol.ProtocolImportExportService;
 import fr.ifremer.tutti.ui.swing.TuttiScreen;
 import fr.ifremer.tutti.ui.swing.content.MainUIHandler;
 import fr.ifremer.tutti.ui.swing.util.AbstractTuttiUIHandler;
+import jaxx.runtime.JAXXUtil;
 import jaxx.runtime.context.JAXXContextEntryDef;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -41,6 +46,7 @@
 import javax.swing.JOptionPane;
 import javax.swing.UIManager;
 import java.io.File;
+import java.util.Map;
 import java.util.Set;
 
 import static org.nuiton.i18n.I18n._;
@@ -57,7 +63,8 @@
     private static final Log log =
             LogFactory.getLog(ImportProtocolAction.class);
 
-    public static final JAXXContextEntryDef<TuttiProtocol> IMPORT_PROTOCOL_ENTRY = new JAXXContextEntryDef<TuttiProtocol>("importProtocol", TuttiProtocol.class);
+    public static final JAXXContextEntryDef<TuttiProtocol> IMPORT_PROTOCOL_ENTRY =
+            JAXXUtil.newContextEntryDef("importProtocol", TuttiProtocol.class);
 
     protected TuttiProtocol protocol;
 
@@ -101,66 +108,30 @@
             protocol.setId((String) null);
 
             sendMessage(_("tutti.importProtocol.action.success", protocol.getName()));
+        }
 
+        if (doAction) {
+
             // check that protocol is compatible with sample category model
-            SampleCategoryModel sampleCategoryModel =
-                    getDataContext().getSampleCategoryModel();
+            doAction = cleanCategories(protocol);
 
-            Set<Integer> badCategories = Sets.newHashSet();
+        }
 
-            TuttiProtocols.checkSampleCategories(sampleCategoryModel,
-                                                 protocol,
-                                                 badCategories);
+        if (doAction) {
 
-            if (!badCategories.isEmpty()) {
+            Map<String, Species> allReferentSpeciesByTaxonId = TuttiEntities.splitByTaxonId(
+                    getDataContext().getReferentSpecies());
 
-                // detect some bad categories
-                if (log.isWarnEnabled()) {
-                    log.warn("There is some bad categories: " + badCategories);
-                }
+            // clean species
+            doAction = cleanSpecies(allReferentSpeciesByTaxonId, protocol);
 
-                String message = TuttiProtocols.getBadCategoriesMessage(
-                        badCategories,
-                        getDecorator(Caracteristic.class, null),
-                        getContext().getPersistenceService());
+            if (doAction) {
 
-                String htmlMessage = String.format(
-                        AbstractTuttiUIHandler.CONFIRMATION_FORMAT,
-                        message,
-                        _("tutti.common.askBeforeImportProtocol.help"));
-                int response = JOptionPane.showOptionDialog(
-                        getContext().getActionUI(),
-                        htmlMessage,
-                        _("tutti.common.askBeforeEditProtocol.title"),
-                        JOptionPane.YES_NO_OPTION,
-                        JOptionPane.WARNING_MESSAGE,
-                        UIManager.getIcon("warning"),
-                        new Object[]{_("tutti.option.cleanAndImport"), _("tutti.option.import"), _("tutti.option.cancel")},
-                        _("tutti.option.cancel")
-                );
-
-                switch (response) {
-                    case 0:
-                        // clean and import
-                        if (log.isInfoEnabled()) {
-                            log.info("Clean and Import");
-                        }
-                        TuttiProtocols.removeBadCategories(sampleCategoryModel,
-                                                           protocol);
-                        break;
-                    case 1:
-                        // import with no clean
-                        if (log.isInfoEnabled()) {
-                            log.info("Import with no cleaning");
-                        }
-                        break;
-                    default:
-
-                        // cancel
-                        doAction = false;
-                }
+                // clean benthos
+                doAction = cleanBenthos(allReferentSpeciesByTaxonId, protocol);
             }
         }
+
         return doAction;
     }
 
@@ -177,4 +148,176 @@
         getContext().setProtocolId(null);
         super.doAction();
     }
+
+    protected boolean cleanCategories(TuttiProtocol protocol) {
+
+        boolean doAction = true;
+        SampleCategoryModel sampleCategoryModel =
+                getDataContext().getSampleCategoryModel();
+
+        Set<Integer> badCategories = Sets.newHashSet();
+
+        TuttiProtocols.checkSampleCategories(sampleCategoryModel,
+                                             protocol,
+                                             badCategories);
+
+        if (!badCategories.isEmpty()) {
+
+            if (log.isWarnEnabled()) {
+                log.warn("There is some bad categories: " + badCategories);
+            }
+
+            String message = TuttiProtocols.getBadCategoriesMessage(
+                    badCategories,
+                    getDecorator(Caracteristic.class, null),
+                    getContext().getPersistenceService());
+
+            String htmlMessage = String.format(
+                    AbstractTuttiUIHandler.CONFIRMATION_FORMAT,
+                    message,
+                    _("tutti.common.askBeforeImportProtocol.help"));
+            int response = JOptionPane.showOptionDialog(
+                    getContext().getActionUI(),
+                    htmlMessage,
+                    _("tutti.common.askBeforeEditProtocol.title"),
+                    JOptionPane.YES_NO_OPTION,
+                    JOptionPane.WARNING_MESSAGE,
+                    UIManager.getIcon("warning"),
+                    new Object[]{_("tutti.option.cleanAndImport"), _("tutti.option.import"), _("tutti.option.cancel")},
+                    _("tutti.option.cancel")
+            );
+
+            switch (response) {
+                case 0:
+                    if (log.isInfoEnabled()) {
+                        log.info("Clean and Import");
+                    }
+                    TuttiProtocols.removeBadCategories(sampleCategoryModel,
+                                                       protocol);
+                    break;
+                case 1:
+                    if (log.isInfoEnabled()) {
+                        log.info("Import with no cleaning");
+                    }
+                    break;
+                default:
+
+                    // cancel
+                    doAction = false;
+            }
+        }
+        return doAction;
+    }
+
+
+    protected boolean cleanSpecies(Map<String, Species> allReferentSpeciesByTaxonId, TuttiProtocol protocol) {
+
+        boolean doAction = true;
+
+        Map<Integer, String> badSpecies = Maps.newLinkedHashMap();
+
+        for (SpeciesProtocol speciesProtocol : protocol.getSpecies()) {
+            Integer taxonId = speciesProtocol.getSpeciesReferenceTaxonId();
+            if (!allReferentSpeciesByTaxonId.containsKey(String.valueOf(taxonId))) {
+
+                badSpecies.put(taxonId, speciesProtocol.getSpeciesSurveyCode());
+            }
+        }
+
+        if (!badSpecies.isEmpty()) {
+
+            if (log.isWarnEnabled()) {
+                log.warn("There is some bad species: " + badSpecies);
+            }
+
+            String message = TuttiProtocols.getBadSpeciesMessage(badSpecies);
+
+            String htmlMessage = String.format(
+                    AbstractTuttiUIHandler.CONFIRMATION_FORMAT,
+                    message,
+                    _("tutti.common.askBeforeImportProtocolSpecies.help"));
+
+            int response = JOptionPane.showOptionDialog(
+                    getContext().getActionUI(),
+                    htmlMessage,
+                    _("tutti.common.askBeforeEditProtocolSpecies.title"),
+                    JOptionPane.YES_NO_OPTION,
+                    JOptionPane.WARNING_MESSAGE,
+                    UIManager.getIcon("warning"),
+                    new Object[]{_("tutti.option.cleanAndImport"), _("tutti.option.cancel")},
+                    _("tutti.option.cancel")
+            );
+
+            switch (response) {
+                case 0:
+
+                    if (log.isInfoEnabled()) {
+                        log.info("Clean species and Import");
+                    }
+                    TuttiProtocols.removeBadSpecies(badSpecies.keySet(),
+                                                    protocol.getSpecies());
+                    break;
+                default:
+
+                    // cancel
+                    doAction = false;
+            }
+        }
+        return doAction;
+    }
+
+    protected boolean cleanBenthos(Map<String, Species> allReferentSpeciesByTaxonId, TuttiProtocol protocol) {
+
+        boolean doAction = true;
+
+        Map<Integer, String> badBenthos = Maps.newLinkedHashMap();
+
+        for (SpeciesProtocol speciesProtocol : protocol.getBenthos()) {
+            Integer taxonId = speciesProtocol.getSpeciesReferenceTaxonId();
+            if (!allReferentSpeciesByTaxonId.containsKey(String.valueOf(taxonId))) {
+
+                badBenthos.put(taxonId, speciesProtocol.getSpeciesSurveyCode());
+            }
+        }
+
+        if (!badBenthos.isEmpty()) {
+
+            if (log.isWarnEnabled()) {
+                log.warn("There is some bad benthos: " + badBenthos);
+            }
+
+            String message = TuttiProtocols.getBadBenthosMessage(badBenthos);
+
+            String htmlMessage = String.format(
+                    AbstractTuttiUIHandler.CONFIRMATION_FORMAT,
+                    message,
+                    _("tutti.common.askBeforeImportProtocolBenthos.help"));
+
+            int response = JOptionPane.showOptionDialog(
+                    getContext().getActionUI(),
+                    htmlMessage,
+                    _("tutti.common.askBeforeEditProtocolBenthos.title"),
+                    JOptionPane.YES_NO_OPTION,
+                    JOptionPane.WARNING_MESSAGE,
+                    UIManager.getIcon("warning"),
+                    new Object[]{_("tutti.option.cleanAndImport"), _("tutti.option.cancel")},
+                    _("tutti.option.cancel")
+            );
+
+            switch (response) {
+                case 0:
+
+                    if (log.isInfoEnabled()) {
+                        log.info("Clean benthos and Import");
+                    }
+                    TuttiProtocols.removeBadSpecies(badBenthos.keySet(), protocol.getSpecies());
+                    break;
+                default:
+
+                    // cancel
+                    doAction = false;
+            }
+        }
+        return doAction;
+    }
 }

Modified: trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/content/protocol/EditProtocolUIHandler.java
===================================================================
--- trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/content/protocol/EditProtocolUIHandler.java	2014-01-18 00:01:01 UTC (rev 1502)
+++ trunk/tutti-ui-swing/src/main/java/fr/ifremer/tutti/ui/swing/content/protocol/EditProtocolUIHandler.java	2014-01-18 15:13:52 UTC (rev 1503)
@@ -502,6 +502,8 @@
                 // get species referent taxon
                 Species species = allReferentSpeciesByTaxonId.get(taxonIdStr);
 
+                // make sure it exists
+                Preconditions.checkNotNull(species, "Espèce inconnue : "+taxonIdStr);
                 speciesSet.add(species);
 
                 EditProtocolSpeciesRowModel row = EditProtocolSpeciesTableModel.newRow(sampleCategoryModel);

Modified: trunk/tutti-ui-swing/src/main/resources/i18n/tutti-ui-swing_en_GB.properties
===================================================================
--- trunk/tutti-ui-swing/src/main/resources/i18n/tutti-ui-swing_en_GB.properties	2014-01-18 00:01:01 UTC (rev 1502)
+++ trunk/tutti-ui-swing/src/main/resources/i18n/tutti-ui-swing_en_GB.properties	2014-01-18 15:13:52 UTC (rev 1503)
@@ -68,7 +68,11 @@
 tutti.common.askBeforeCloneProtocol.help=
 tutti.common.askBeforeEditProtocol.help=
 tutti.common.askBeforeEditProtocol.title=
+tutti.common.askBeforeEditProtocolBenthos.title=
+tutti.common.askBeforeEditProtocolSpecies.title=
 tutti.common.askBeforeImportProtocol.help=
+tutti.common.askBeforeImportProtocolBenthos.help=
+tutti.common.askBeforeImportProtocolSpecies.help=
 tutti.common.askBeforeUpdate.help=
 tutti.common.cancel=
 tutti.common.cancel.mnemonic=

Modified: trunk/tutti-ui-swing/src/main/resources/i18n/tutti-ui-swing_fr_FR.properties
===================================================================
--- trunk/tutti-ui-swing/src/main/resources/i18n/tutti-ui-swing_fr_FR.properties	2014-01-18 00:01:01 UTC (rev 1502)
+++ trunk/tutti-ui-swing/src/main/resources/i18n/tutti-ui-swing_fr_FR.properties	2014-01-18 15:13:52 UTC (rev 1503)
@@ -61,7 +61,11 @@
 tutti.common.askBeforeCloneProtocol.help=Que voulez-vous faire?<ul><li><strong>Annuler</strong> pour ne pas cloner le protocole</li><li><strong>Cloner</strong> pour cloner le protocole en conservant les catégories non connues (elle ne seront pas affichées)</li><li><strong>Nettoyer et Cloner</strong> pour supprimer les catégories non compatibles dans le protocole cloné</li></ul>
 tutti.common.askBeforeEditProtocol.help=Que voulez-vous faire?<ul><li><strong>Annuler</strong> pour ne pas éditer le protocole</li><li><strong>Éditer</strong> pour éditer le protocole en conservant les catégories non connues (elle ne seront pas affichées)</li><li><strong>Nettoyer et Éditer</strong> pour supprimer les catégories non compatibles et éditer le protocole</li></ul>
 tutti.common.askBeforeEditProtocol.title=Catégories non compatibles détectées dans le protocole
+tutti.common.askBeforeEditProtocolBenthos.title=Des espèces (benthos) non reconnues dans le protocole
+tutti.common.askBeforeEditProtocolSpecies.title=Des espèces non reconnues dans le protocole
 tutti.common.askBeforeImportProtocol.help=Que voulez-vous faire?<ul><li><strong>Annuler</strong> pour ne pas importer le protocole</li><li><strong>Importer</strong> pour importer le protocole en conservant les catégories non connues (elle ne seront pas affichées)</li><li><strong>Nettoyer et Importer</strong> pour supprimer les catégories non compatibles dans le protocole importé</li></ul>
+tutti.common.askBeforeImportProtocolBenthos.help=Que voulez-vous faire?<ul><li><strong>Annuler</strong> pour ne pas importer le protocole</li><li><strong>Nettoyer et Importer</strong> pour supprimer les catégories non compatibles dans le protocole importé</li></ul>
+tutti.common.askBeforeImportProtocolSpecies.help=Que voulez-vous faire?<ul><li><strong>Annuler</strong> pour ne pas importer le protocole</li><li><strong>Nettoyer et Importer</strong> pour supprimer les catégories non compatibles dans le protocole importé</li></ul>
 tutti.common.askBeforeUpdate.help=Que voulez-vous faire ?<ul><li><strong>Annuler</strong> pour ne pas effectuer la mise à jour</li><li><strong>OK</strong> pour lancer la mise à jour</li></ul>
 tutti.common.cancel=Annuler
 tutti.common.cancel.mnemonic=A

    

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