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

Commits:

8 changed files:

Changes:

  • t3-actions/src/main/java/fr/ird/t3/actions/io/input/ImportInputSourceAction.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%
    ... ... @@ -24,9 +24,14 @@ import fr.ird.t3.actions.T3Action;
    24 24 
     import fr.ird.t3.entities.T3EntityEnum;
    25 25 
     import fr.ird.t3.entities.T3TopiaApplicationContext;
    26 26 
     import fr.ird.t3.entities.T3TopiaPersistenceContext;
    27 
    +import fr.ird.t3.entities.data.Activity;
    28 
    +import fr.ird.t3.entities.data.ActivityTopiaDao;
    27 29 
     import fr.ird.t3.entities.data.T3DataEntity;
    28 30 
     import fr.ird.t3.entities.data.Trip;
    29 31 
     import fr.ird.t3.entities.data.TripTopiaDao;
    32 
    +import fr.ird.t3.entities.data.TripType;
    33 
    +import fr.ird.t3.entities.reference.Ocean;
    34 
    +import fr.ird.t3.entities.reference.OceanTopiaDao;
    30 35 
     import fr.ird.t3.entities.reference.Vessel;
    31 36 
     import fr.ird.t3.entities.reference.VesselTopiaDao;
    32 37 
     import fr.ird.t3.services.ioc.InjectDAO;
    ... ... @@ -58,12 +63,16 @@ public class ImportInputSourceAction extends T3Action<ImportInputSourceConfigura
    58 63 
         //    public static final String PARAM_TRIPS_TO_IMPORT = "tripsToImport";
    59 64 
     //    public static final String PARAM_TRIPS_TO_DELETE = "tripsToDelete";
    60 65 
         private static final Log log = LogFactory.getLog(ImportInputSourceAction.class);
    61 
    -    protected Set<Trip> trips;
    62 66 
         @InjectDAO(entityType = Trip.class)
    63 
    -    protected TripTopiaDao tripDAO;
    64 
    -    private Set<Trip> tripToDelete;
    67 
    +    private TripTopiaDao tripDAO;
    65 68 
         @InjectDAO(entityType = Vessel.class)
    66 69 
         private VesselTopiaDao vesselDAO;
    70 
    +    @InjectDAO(entityType = Activity.class)
    71 
    +    private ActivityTopiaDao activityDAO;
    72 
    +    @InjectDAO(entityType = Ocean.class)
    73 
    +    private OceanTopiaDao oceanDAO;
    74 
    +    private Set<Trip> tripToDelete;
    75 
    +    private Set<Trip> trips;
    67 76
    68 77 
         @Override
    69 78 
         protected void prepareAction() throws Exception {
    ... ... @@ -109,7 +118,7 @@ public class ImportInputSourceAction extends T3Action<ImportInputSourceConfigura
    109 118 
                     addInfoMessage(message);
    110 119 
                 }
    111 120 
             }
    112 
    -
    121 
    +        boolean logbookMissing = TripType.LOGBOOKMISSING == getConfiguration().getTripType();
    113 122 
             boolean createVirtualVessel = getConfiguration().isCreateVirtualVessel();
    114 123 
             BuildVisitor builder = new BuildVisitor(getActionContext().getApplicationContext(), getT3TopiaPersistenceContext().get());
    115 124 
             for (Trip trip : trips) {
    ... ... @@ -130,6 +139,9 @@ public class ImportInputSourceAction extends T3Action<ImportInputSourceConfigura
    130 139 
                 String message = l(locale, "t3.message.trip.was.imported", tripLabel);
    131 140 
                 addInfoMessage(message);
    132 141
    142 
    +            if (logbookMissing) {
    143 
    +                fillActivityOcean(builder.activitiesWithNoOcean);
    144 
    +            }
    133 145 
                 // clean the builder after each entity (since each entity is
    134 146 
                 // standalone and does not share data with other trips)
    135 147 
                 builder.clear();
    ... ... @@ -138,13 +150,26 @@ public class ImportInputSourceAction extends T3Action<ImportInputSourceConfigura
    138 150 
             return true;
    139 151 
         }
    140 152
    153 
    +    private void fillActivityOcean(Set<Activity> ids) {
    154 
    +
    155 
    +        // Need to flush as we are going to query new data
    156 
    +        getT3TopiaPersistenceContext().get().getHibernateSupport().getHibernateSession().flush();
    157 
    +
    158 
    +        String prefix = Activity.class.getName() + "#";
    159 
    +        for (Activity activity : ids) {
    160 
    +            Ocean ocean = oceanDAO.findOceanByActivity(activity);
    161 
    +            activity.setOcean(ocean);
    162 
    +        }
    163 
    +    }
    164 
    +
    141 165 
         protected static class BuildVisitor implements TopiaEntityVisitor {
    142 166
    167 
    +        protected final Set<String> ids = new HashSet<>();
    168 
    +        final Set<Activity> activitiesWithNoOcean = new HashSet<>();
    143 169 
             final T3TopiaPersistenceContext tx;
    144 170 
             final T3TopiaApplicationContext rootTx;
    145 
    -        protected final Set<String> ids = new HashSet<>();
    146 
    -        protected TopiaEntity current;
    147 171 
             final Stack<TopiaEntity> stack = new Stack<>();
    172 
    +        protected TopiaEntity current;
    148 173
    149 174 
             BuildVisitor(T3TopiaApplicationContext rootTx, T3TopiaPersistenceContext tx) {
    150 175 
                 this.tx = tx;
    ... ... @@ -189,6 +214,12 @@ public class ImportInputSourceAction extends T3Action<ImportInputSourceConfigura
    189 214 
                     @SuppressWarnings("unchecked")
    190 215 
                     TopiaDao<TopiaEntity> dao = tx.getDao(T3EntityEnum.getContractClass((Class) entity.getClass()));
    191 216 
                     dao.update(entity);
    217 
    +                if (entity instanceof Activity) {
    218 
    +                    Activity activity = (Activity) entity;
    219 
    +                    if (activity.getOcean() == null) {
    220 
    +                        activitiesWithNoOcean.add(activity);
    221 
    +                    }
    222 
    +                }
    192 223 
                 } catch (TopiaException e) {
    193 224 
                     throw new IllegalStateException("Could not get dao for entity " + entity, e);
    194 225 
                 }
    ... ... @@ -224,6 +255,7 @@ public class ImportInputSourceAction extends T3Action<ImportInputSourceConfigura
    224 255 
             @Override
    225 256 
             public void clear() {
    226 257 
                 ids.clear();
    258 
    +            activitiesWithNoOcean.clear();
    227 259 
             }
    228 260 
         }
    229 261

  • t3-domain/src/main/java/fr/ird/t3/entities/reference/AbstractOceanTopiaDao.java
    ... ... @@ -20,8 +20,14 @@
    20 20 
      */
    21 21 
     package fr.ird.t3.entities.reference;
    22 22
    23 
    +import fr.ird.t3.entities.data.Activity;
    23 24 
     import fr.ird.t3.entities.data.Trip;
    25 
    +import org.nuiton.topia.persistence.support.TopiaSqlQuery;
    24 26
    27 
    +import java.sql.Connection;
    28 
    +import java.sql.PreparedStatement;
    29 
    +import java.sql.ResultSet;
    30 
    +import java.sql.SQLException;
    25 31 
     import java.util.Collection;
    26 32 
     import java.util.HashSet;
    27 33 
     import java.util.Set;
    ... ... @@ -51,4 +57,33 @@ public class AbstractOceanTopiaDao<E extends Ocean> extends GeneratedOceanTopiaD
    51 57 
             String hql = "SELECT DISTINCT(o) FROM OceanImpl o, ActivityImpl a WHERE a.ocean = o.id";
    52 58 
             return new HashSet<>(findAll(hql));
    53 59 
         }
    60 
    +
    61 
    +    public E findOceanByActivity(Activity activity) {
    62 
    +        GetOceanIdByActivityCoordinateQuery query = new GetOceanIdByActivityCoordinateQuery(activity.getTopiaId());
    63 
    +        String oceanId = topiaSqlSupport.findSingleResult(query);
    64 
    +        return forTopiaIdEquals(oceanId).findUnique();
    65 
    +    }
    66 
    +
    67 
    +    private static class GetOceanIdByActivityCoordinateQuery extends TopiaSqlQuery<String> {
    68 
    +
    69 
    +        private final String activity;
    70 
    +
    71 
    +        GetOceanIdByActivityCoordinateQuery(String activity) {
    72 
    +            this.activity = activity;
    73 
    +        }
    74 
    +
    75 
    +        @Override
    76 
    +        public PreparedStatement prepareQuery(Connection connection) throws SQLException {
    77 
    +            @SuppressWarnings("SqlResolve")
    78 
    +            PreparedStatement ps = connection.prepareStatement(
    79 
    +                    "SELECT o.topiaid FROM activity a, ocean o  WHERE a.topiaId = ? AND ST_Contains(o.the_geom, a.the_geom)");
    80 
    +            ps.setString(1, activity);
    81 
    +            return ps;
    82 
    +        }
    83 
    +
    84 
    +        @Override
    85 
    +        public String prepareResult(ResultSet set) throws SQLException {
    86 
    +            return set.getString(1);
    87 
    +        }
    88 
    +    }
    54 89 
     }

  • t3-domain/src/main/java/fr/ird/t3/io/input/access/T3AccessDataSource.java
    ... ... @@ -144,14 +144,6 @@ public class T3AccessDataSource extends AbstractAccessDataSource<T3EntityEnum, T
    144 144 
                     // on ne veut charger que les données observateurs, pas le referentiel
    145 145 
                     continue;
    146 146 
                 }
    147 
    -            if (TripType.LOGBOOKMISSING == tripType && meta.getType() == T3EntityEnum.Activity) {
    148 
    -                //FIXME-116 Just to test remove this ASAP
    149 
    -                cache.put(meta, new Map[]{});
    150 
    -            }
    151 
    -            if (TripType.LOGBOOKMISSING == tripType && meta.getType() == T3EntityEnum.WellPlan) {
    152 
    -                //FIXME-116 Just to test remove this ASAP
    153 
    -                cache.put(meta, new Map[]{});
    154 
    -            }
    155 147 
                 Map<String, Object>[] data = getTableData(meta);
    156 148 
                 if (hits != null) {
    157 149 
                     long hit = hits.getHit(meta.getType());

  • t3-domain/src/main/java/fr/ird/t3/io/input/access/T3AvdthDataEntityVisitor.java
    ... ... @@ -76,10 +76,6 @@ public abstract class T3AvdthDataEntityVisitor extends T3DataEntityVisitor {
    76 76 
                         activity.setLatitude(Objects.requireNonNull(sampleSet.getActivityLatitude()));
    77 77 
                         activity.setLongitude(Objects.requireNonNull(sampleSet.getActivityLongitude()));
    78 78 
                         activity.setSchoolType(Objects.requireNonNull(sampleSet.getActivitySchoolType()));
    79 
    -
    80 
    -                    //FIXME-116 Get ocean from coordinates
    81 
    -                    activity.setOcean(parent.getDepartureHarbour().getOcean());
    82 
    -
    83 79 
                         sampleSet.setActivity(endActivity(activity));
    84 80 
                         parent.addActivity(activity);
    85 81 
                     }

  • t3-domain/src/main/java/fr/ird/t3/services/migration/T3MigrationCallbackV2_3.java
    ... ... @@ -48,6 +48,7 @@ public class T3MigrationCallbackV2_3 extends T3MigrationCallbackSupport {
    48 48 
         @Override
    49 49 
         protected void prepareMigrationScript(TopiaSqlSupport sqlSupport, List<String> queries, boolean showSql, boolean showProgression) throws TopiaException {
    50 50 
             addScript("01", "add-Trip-tripType", queries);
    51 
    +        addScript("03", "spatialize-ocean", queries);
    51 52 
         }
    52 53
    53 54 
     }

  • t3-domain/src/main/resources/db/migration/V_2_3_03-spatialize-ocean.sql The diff for this file was not included because it is too large.
  • t3-input-avdthv35/src/test/java/fr/ird/t3/actions/io/input/AnalyzeInputSourceActionTest.java
    ... ... @@ -10,12 +10,12 @@ package fr.ird.t3.actions.io.input;
    10 10 
      * it under the terms of the GNU Affero General Public License as published by
    11 11 
      * the Free Software Foundation, either version 3 of the License, or
    12 12 
      * (at your option) any later version.
    13 
    - *
    13 
    + *
    14 14 
      * This program is distributed in the hope that it will be useful,
    15 15 
      * but WITHOUT ANY WARRANTY; without even the implied warranty of
    16 16 
      * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    17 17 
      * GNU General Public License for more details.
    18 
    - *
    18 
    + *
    19 19 
      * You should have received a copy of the GNU Affero General Public License
    20 20 
      * along with this program.  If not, see <http://www.gnu.org/licenses/>.
    21 21 
      * #L%
    ... ... @@ -40,7 +40,6 @@ public class AnalyzeInputSourceActionTest extends AnalyzeInputSourceActionTestSu
    40 40 
             return new MSAccessTestConfiguration("testExecute_([^_]*)_(\\d+)(_.+)*", "%s_%s_V35.mdb", T3InputProviderAvdth35.ID);
    41 41 
         }
    42 42
    43 
    -    @Ignore
    44 43 
         @Test
    45 44 
         public void testExecute_OA_2000() throws Exception {
    46 45 
             testExecute(AtlanticOceanFixtures.OA_2000);
    ... ... @@ -51,16 +50,4 @@ public class AnalyzeInputSourceActionTest extends AnalyzeInputSourceActionTestSu
    51 50 
             testExecute(IndianOceanFixtures.OI_2000);
    52 51 
         }
    53 52
    54 
    -    @Ignore
    55 
    -    @Test
    56 
    -    public void testExecute_OA_2000_withoutLogbook() throws Exception {
    57 
    -        testExecute(AtlanticOceanFixtures.OA_2000, TripType.LOGBOOKMISSING);
    58 
    -    }
    59 
    -
    60 
    -    @Ignore
    61 
    -    @Test
    62 
    -    public void testExecute_OI_2002_withoutLogbook() throws Exception {
    63 
    -        testExecute(IndianOceanFixtures.OI_2002,TripType.LOGBOOKMISSING);
    64 
    -    }
    65 
    -
    66 53 
     }

  • t3-input-avdthv35/src/test/java/fr/ird/t3/actions/io/input/ImportInputSourceActionTest.java
    ... ... @@ -23,9 +23,7 @@ package fr.ird.t3.actions.io.input;
    23 23
    24 24 
     import fr.ird.t3.actions.io.input.test.ImportInputSourceActionTestSupport;
    25 25 
     import fr.ird.t3.actions.io.input.test.MSAccessTestConfiguration;
    26 
    -import fr.ird.t3.entities.data.TripType;
    27 26 
     import fr.ird.t3.io.input.avdth.v35.T3InputProviderAvdth35;
    28 
    -import org.junit.Ignore;
    29 27 
     import org.junit.Test;
    30 28
    31 29 
     /**
    ... ... @@ -50,16 +48,4 @@ public class ImportInputSourceActionTest extends ImportInputSourceActionTestSupp
    50 48 
             testExecute(IndianOceanFixtures.OI_2000);
    51 49 
         }
    52 50
    53 
    -    @Ignore
    54 
    -    @Test
    55 
    -    public void testExecute_OA_2000_withoutLogbook() throws Exception {
    56 
    -        testExecute(AtlanticOceanFixtures.OA_2000, TripType.LOGBOOKMISSING);
    57 
    -    }
    58 
    -
    59 
    -    @Ignore
    60 
    -    @Test
    61 
    -    public void testExecute_OI_2002_withoutLogbook() throws Exception {
    62 
    -        testExecute(IndianOceanFixtures.OI_2002, TripType.LOGBOOKMISSING);
    63 
    -    }
    64 
    -
    65 51 
     }

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