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

Commits:

1 changed file:

Changes:

  • persistence/src/main/java/fr/ird/observe/persistence/migration/DataSourceMigrationForVersion_6_0.java
    ... ... @@ -25,6 +25,7 @@ package fr.ird.observe.persistence.migration;
    25 25 
     import com.google.common.base.Joiner;
    26 26 
     import com.google.common.collect.ImmutableMap;
    27 27 
     import org.apache.commons.lang3.StringUtils;
    28 
    +import org.apache.commons.lang3.tuple.Pair;
    28 29 
     import org.apache.commons.logging.Log;
    29 30 
     import org.apache.commons.logging.LogFactory;
    30 31 
     import org.nuiton.topia.persistence.support.TopiaSqlQuery;
    ... ... @@ -35,10 +36,9 @@ import java.sql.PreparedStatement;
    35 36 
     import java.sql.ResultSet;
    36 37 
     import java.sql.SQLException;
    37 38 
     import java.util.HashSet;
    38 
    -import java.util.Iterator;
    39 
    -import java.util.LinkedHashSet;
    40 39 
     import java.util.List;
    41 40 
     import java.util.Set;
    41 
    +import java.util.stream.Collectors;
    42 42
    43 43 
     /**
    44 44 
      * Created on 27/10/16.
    ... ... @@ -90,32 +90,79 @@ public class DataSourceMigrationForVersion_6_0 extends AbstractObserveMigrationC
    90 90
    91 91 
         private void evol8391(TopiaSqlSupport topiaSqlSupport, List<String> queries) {
    92 92
    93 
    -        ImmutableMap<String, String> missingCodesMapping = ImmutableMap.<String, String>builder()
    94 
    -                .put("LT ?", "TL")
    95 
    -                .put("LF", "FL")
    96 
    -                .put("L1", "PDL")
    97 
    -                .put("LC", "DL")
    98 
    -                .put("LT", "TL")
    99 
    -                .put("", "TL")
    93 
    +        ImmutableMap<String, String> sqlMappingByCode =
    94 
    +                ImmutableMap.<String, String>builder()
    95 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499465700#0.0902433863375336", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499465700#0.0902433863375336', 2, '2015-06-05', '2016-10-18 11:51:54.099140','FL', 1, null, 'Fork Length', 'Fork Length', 'Fork Length', null, null, null, null, null, false);")
    96 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499465999#0.707568018231541", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499465999#0.707568018231541', 3, '2015-06-05', '2016-10-18 11:51:54.099140', 'CFL', 1, null, 'Curved Fork Length', 'Curved Fork Length', 'Curved Fork Length', null, null, null, null, null, false);")
    97 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466255#0.444246932631359", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466255#0.444246932631359', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'PAL', 1, null, 'Pectoral-Anal Length', 'Pectoral-Anal Length', 'Pectoral-Anal Length', null, null, null, null, null, false);")
    98 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466532#0.844473292818293", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466532#0.844473292818293', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'TL', 1, null, 'Total Length', 'Total Length', 'Total Length', null, null, null, null, null, false);")
    99 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466774#0.529249255312607", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466774#0.529249255312607', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'PD1', 1, null, 'Predorsal Length', 'Predorsal Length', 'Predorsal Length', null, null, null, null, null, false);")
    100 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467059#0.563144549960271", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467059#0.563144549960271', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'SL', 1, null, 'Standard Length', 'Standard Length', 'Standard Length', null, null, null, null, null, false);")
    101 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467326#0.537910396233201", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467326#0.537910396233201', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'LJFL', 1, null, 'Lower Jaw-Fork Length', 'Lower Jaw-Fork Length', 'Lower Jaw-Fork Length', null, null, null, null, null, false);")
    102 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467638#0.409153908025473", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467638#0.409153908025473', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'CLJFL', 1, null, 'Curved Lower Jaw-Fork Length', 'Curved Lower Jaw-Fork Length', 'Curved Lower Jaw-Fork Length', null, null, null, null, null, false);")
    103 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467945#0.249704661779106", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467945#0.249704661779106', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'IDL', 1, null, 'Interdorsal Length', 'Interdorsal Length', 'Interdorsal Length', null, null, null, null, null, false);")
    104 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499468283#0.152317869942635", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499468283#0.152317869942635', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'EFL', 1, null, 'Eye-Fork Length', 'Eye-Fork Length', 'Eye-Fork Length', null, null, null, null, null, false);")
    105 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499468646#0.710986209334806", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499468646#0.710986209334806', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'DW', 1, null, 'Disk Width', 'Disk Width', 'Disk Width', null, null, null, null, null, false);")
    106 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499469115#0.42996318358928", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499469115#0.42996318358928', 2, '2015-06-05', '2016-10-18 11:51:54.099140',  'DL', 1, null, 'Disk Length', 'Disk Length', 'Disk Length', null, null, null, null, null, false);")
    107 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499469572#0.969587777974084", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499469572#0.969587777974084', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'TW', 1, null, 'Total Weight', 'Total Weight', 'Total Weight', null, null, null, null, null, false);")
    108 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499470528#0.813851526239887", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499470528#0.813851526239887', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'CTL', 1, null, 'Curved Total Length', 'Curved Total Length', 'Curved Total Length', null, null, null, null, null, false);")
    109 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499470887#0.950930784922093", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499470887#0.950930784922093', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'DML', 1, null, 'Dorsal Mantle Length', 'Dorsal Mantle Length', 'Dorsal Mantle Length', null, null, null, null, null, false);")
    110 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499471278#0.425988764036447", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499471278#0.425988764036447', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'CDML', 1, null, 'Curved Dorsal Mantle Length', 'Curved Dorsal Mantle Length', 'Curved Dorsal Mantle Length', null, null, null, null, null, false);")
    111 
    +                        .put("fr.ird.observe.entities.referentiel.SizeMeasureType#1433499472220#0.885759855154902", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499472220#0.885759855154902', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'PFL', 1, null, 'Pectoral-Fork Length', 'Pectoral-Fork Length', 'Pectoral-Fork Length', null, null, null, null, null, false);")
    112 
    +                        .build();
    113 
    +
    114 
    +        ImmutableMap<String, String> knownSizeMeasureTypeMapping = ImmutableMap.<String, String>builder()
    115 
    +                .put("LT ?", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466532#0.844473292818293")
    116 
    +                .put("LF", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499465700#0.0902433863375336")
    117 
    +                .put("L1", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466774#0.529249255312607")
    118 
    +                .put("LC", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499469115#0.42996318358928")
    119 
    +                .put("LT", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466532#0.844473292818293")
    120 
    +                .put("", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466532#0.844473292818293")
    121 
    +                .put("FL", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499465700#0.0902433863375336")
    122 
    +                .put("CFL", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499465999#0.707568018231541")
    123 
    +                .put("PAL", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466255#0.444246932631359")
    124 
    +                .put("TL", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466532#0.844473292818293")
    125 
    +                .put("PD1", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466774#0.529249255312607")
    126 
    +                .put("PDL", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466774#0.529249255312607")
    127 
    +                .put("SL", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467059#0.563144549960271")
    128 
    +                .put("LJFL", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467326#0.537910396233201")
    129 
    +                .put("CLJFL", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467638#0.409153908025473")
    130 
    +                .put("IDL", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467945#0.249704661779106")
    131 
    +                .put("EFL", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499468283#0.152317869942635")
    132 
    +                .put("DW", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499468646#0.710986209334806")
    133 
    +                .put("DL", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499469115#0.42996318358928")
    134 
    +                .put("TW", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499469572#0.969587777974084")
    135 
    +                .put("CTL", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499470528#0.813851526239887")
    136 
    +                .put("DML", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499470887#0.950930784922093")
    137 
    +                .put("CDML", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499471278#0.425988764036447")
    138 
    +                .put("PFL", "fr.ird.observe.entities.referentiel.SizeMeasureType#1433499472220#0.885759855154902")
    100 139 
                     .build();
    101 
    -        List<String> lengthMeasureTypes = topiaSqlSupport.findMultipleResult(new TopiaSqlQuery<String>() {
    140 
    +
    141 
    +        ImmutableMap.Builder<String, String> existingSizeMeasureMappingBuilder = ImmutableMap.builder();
    142 
    +
    143 
    +        topiaSqlSupport.findMultipleResult(new TopiaSqlQuery<Pair<String, String>>() {
    102 144
    103 145 
                 @Override
    104 146 
                 public PreparedStatement prepareQuery(Connection connection) throws SQLException {
    105 
    -                return connection.prepareStatement("SELECT DISTINCT(lengthmeasuretype) FROM observe_common.species WHERE lengthmeasuretype IS NOT NULL");
    147 
    +                // Attention à ce moment là ce référentiel est encore dans le schema longline
    148 
    +                return connection.prepareStatement("SELECT code, topiaid FROM observe_longline.sizemeasuretype ");
    106 149 
                 }
    107 150
    108 151 
                 @Override
    109 
    -            public String prepareResult(ResultSet set) throws SQLException {
    110 
    -                return set.getString(1);
    152 
    +            public Pair<String, String> prepareResult(ResultSet set) throws SQLException {
    153 
    +                String code = set.getString(1);
    154 
    +                String topiaId = set.getString(2);
    155 
    +                return Pair.of(code, StringUtils.replace(topiaId, ".longline", ""));
    111 156 
                 }
    112 
    -        });
    113 
    -        List<String> existingLengthMeasureTypes = topiaSqlSupport.findMultipleResult(new TopiaSqlQuery<String>() {
    157 
    +        }).forEach(p -> existingSizeMeasureMappingBuilder.put(p.getKey(), p.getValue()));
    158 
    +
    159 
    +        ImmutableMap<String, String> existingSizeMeasureMapping = existingSizeMeasureMappingBuilder.build();
    160 
    +
    161 
    +        List<String> lengthMeasureTypes = topiaSqlSupport.findMultipleResult(new TopiaSqlQuery<String>() {
    114 162
    115 163 
                 @Override
    116 164 
                 public PreparedStatement prepareQuery(Connection connection) throws SQLException {
    117 
    -                // Attention à ce moment là ce référentiel est encore dans le schema longline
    118 
    -                return connection.prepareStatement("SELECT DISTINCT(code) FROM observe_longline.sizemeasuretype ");
    165 
    +                return connection.prepareStatement("SELECT DISTINCT(lengthmeasuretype) FROM observe_common.species WHERE lengthmeasuretype IS NOT NULL");
    119 166 
                 }
    120 167
    121 168 
                 @Override
    ... ... @@ -124,115 +171,35 @@ public class DataSourceMigrationForVersion_6_0 extends AbstractObserveMigrationC
    124 171 
                 }
    125 172 
             });
    126 173
    127 
    -        Set<String> missingLengthMeasureTypeCodes = new HashSet<>();
    128 
    -        for (String lengthMeasureType : lengthMeasureTypes) {
    129 
    -            lengthMeasureType = lengthMeasureType.trim();
    130 
    -            String realCode = missingCodesMapping.get(lengthMeasureType);
    131 
    -            if (realCode == null) {
    132 
    -                realCode = lengthMeasureType;
    133 
    -            }
    134 
    -            missingLengthMeasureTypeCodes.add(realCode);
    135 
    -        }
    136 
    -        missingLengthMeasureTypeCodes.removeAll(existingLengthMeasureTypes);
    137 
    -
    138 
    -        ImmutableMap.Builder<String, String> extraTopiaIdsByCodeBuilder = ImmutableMap.builder();
    139 
    -
    140 
    -        if (!missingLengthMeasureTypeCodes.isEmpty()) {
    141 
    -
    142 
    -            // il manque des référentiels on va les ajouter
    143 
    -            ImmutableMap<String, String> sqlMappingByCode =
    144 
    -                    ImmutableMap.<String, String>builder()
    145 
    -                            .put("FL", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499465700#0.0902433863375336', 2, '2015-06-05', '2016-10-18 11:51:54.099140','FL', 1, null, 'Fork Length', 'Fork Length', 'Fork Length', null, null, null, null, null, false);")
    146 
    -                            .put("CFL", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499465999#0.707568018231541', 3, '2015-06-05', '2016-10-18 11:51:54.099140', 'CFL', 1, null, 'Curved Fork Length', 'Curved Fork Length', 'Curved Fork Length', null, null, null, null, null, false);")
    147 
    -                            .put("PAL", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466255#0.444246932631359', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'PAL', 1, null, 'Pectoral-Anal Length', 'Pectoral-Anal Length', 'Pectoral-Anal Length', null, null, null, null, null, false);")
    148 
    -                            .put("TL", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466532#0.844473292818293', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'TL', 1, null, 'Total Length', 'Total Length', 'Total Length', null, null, null, null, null, false);")
    149 
    -                            .put("PDL", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499466774#0.529249255312607', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'PDL', 1, null, 'Predorsal Length', 'Predorsal Length', 'Predorsal Length', null, null, null, null, null, false);")
    150 
    -                            .put("SL", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467059#0.563144549960271', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'SL', 1, null, 'Standard Length', 'Standard Length', 'Standard Length', null, null, null, null, null, false);")
    151 
    -                            .put("LJFL", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467326#0.537910396233201', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'LJFL', 1, null, 'Lower Jaw-Fork Length', 'Lower Jaw-Fork Length', 'Lower Jaw-Fork Length', null, null, null, null, null, false);")
    152 
    -                            .put("CLJFL", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467638#0.409153908025473', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'CLJFL', 1, null, 'Curved Lower Jaw-Fork Length', 'Curved Lower Jaw-Fork Length', 'Curved Lower Jaw-Fork Length', null, null, null, null, null, false);")
    153 
    -                            .put("IDL", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499467945#0.249704661779106', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'IDL', 1, null, 'Interdorsal Length', 'Interdorsal Length', 'Interdorsal Length', null, null, null, null, null, false);")
    154 
    -                            .put("EFL", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499468283#0.152317869942635', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'EFL', 1, null, 'Eye-Fork Length', 'Eye-Fork Length', 'Eye-Fork Length', null, null, null, null, null, false);")
    155 
    -                            .put("DW", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499468646#0.710986209334806', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'DW', 1, null, 'Disk Width', 'Disk Width', 'Disk Width', null, null, null, null, null, false);")
    156 
    -                            .put("DL", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499469115#0.42996318358928', 2, '2015-06-05', '2016-10-18 11:51:54.099140',  'DL', 1, null, 'Disk Length', 'Disk Length', 'Disk Length', null, null, null, null, null, false);")
    157 
    -                            .put("TW", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499469572#0.969587777974084', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'TW', 1, null, 'Total Weight', 'Total Weight', 'Total Weight', null, null, null, null, null, false);")
    158 
    -                            .put("CTL", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499470528#0.813851526239887', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'CTL', 1, null, 'Curved Total Length', 'Curved Total Length', 'Curved Total Length', null, null, null, null, null, false);")
    159 
    -                            .put("DML", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499470887#0.950930784922093', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'DML', 1, null, 'Dorsal Mantle Length', 'Dorsal Mantle Length', 'Dorsal Mantle Length', null, null, null, null, null, false);")
    160 
    -                            .put("CDML", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499471278#0.425988764036447', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'CDML', 1, null, 'Curved Dorsal Mantle Length', 'Curved Dorsal Mantle Length', 'Curved Dorsal Mantle Length', null, null, null, null, null, false);")
    161 
    -                            .put("PFL", "INSERT INTO observe_common.sizemeasuretype (topiaid, topiaversion, topiacreatedate, lastupdatedate, code, status, uri, label1, label2, label3, label4, label5, label6, label7, label8, needcomment) VALUES ('fr.ird.observe.entities.referentiel.SizeMeasureType#1433499472220#0.885759855154902', 2, '2015-06-05', '2016-10-18 11:51:54.099140', 'PFL', 1, null, 'Pectoral-Fork Length', 'Pectoral-Fork Length', 'Pectoral-Fork Length', null, null, null, null, null, false);")
    162 
    -                            .build();
    163 
    -
    164 
    -            Iterator<String> iterator = missingLengthMeasureTypeCodes.iterator();
    165 
    -            while (iterator.hasNext()) {
    166 
    -                String code = iterator.next();
    167 
    -                String sql = sqlMappingByCode.get(code);
    168 
    -                if (sql != null) {
    169 
    -                    queries.add(sql);
    170 
    -                    iterator.remove();
    171 
    -                    int i = sql.indexOf("'");
    172 
    -                    String topiaId = sql.substring(i + 1);
    173 
    -                    int j = topiaId.indexOf("'");
    174 
    -                    topiaId = topiaId.substring(0, j);
    175 
    -                    if (log.isInfoEnabled()) {
    176 
    -                        log.info("Add " + code + "::" + topiaId);
    177 
    -                    }
    178 
    -                    extraTopiaIdsByCodeBuilder.put(code, topiaId);
    179 
    -                }
    180 
    -            }
    174 
    +        Set<String> unkownCodes = new HashSet<>(lengthMeasureTypes);
    175 
    +        unkownCodes.removeAll(knownSizeMeasureTypeMapping.keySet());
    176 
    +        unkownCodes.removeAll(existingSizeMeasureMapping.keySet());
    181 177
    182 
    -            if (!missingLengthMeasureTypeCodes.isEmpty()) {
    178 
    +        if (!unkownCodes.isEmpty()) {
    183 179
    184 
    -                // migration impossible, il manque encore des référentiels
    185 
    -                // ce cas ne devrait jamais arrivé
    186 
    -                throw new IllegalStateException("Les types de mesure de taille pour les codes suivants :\n\t" + Joiner.on("\n\t").join(missingLengthMeasureTypeCodes) + " sont requis pour la migration mais n'ont pas été trouvés en base.");
    187 
    -            }
    180 
    +            // migration impossible, il manque encore des référentiels
    181 
    +            // ce cas ne devrait jamais arrivé
    182 
    +            throw new IllegalStateException("Les types de mesure de taille pour les codes suivants :\n\t" + Joiner.on("\n\t").join(unkownCodes) + " sont requis pour la migration mais n'ont pas été trouvés en base.");
    188 183
    189 184 
             }
    190 185
    191 
    -        ImmutableMap<String, String> extraTopiaIdsByCode = extraTopiaIdsByCodeBuilder.build();
    186 
    +        Set<String> missingSizeMeasureTypeIds = knownSizeMeasureTypeMapping.values().stream().filter(id -> !existingSizeMeasureMapping.values().contains(id)).collect(Collectors.toSet());
    192 187
    193 
    -        Set<String> invalidCodes = new LinkedHashSet<>();
    194 
    -        for (String lengthMeasureType : lengthMeasureTypes) {
    195 
    -
    196 
    -            lengthMeasureType = lengthMeasureType.trim();
    197 
    -            if (lengthMeasureType.isEmpty()) {
    198 
    -                continue;
    199 
    -            }
    200 
    -            if (missingCodesMapping.containsKey(lengthMeasureType)) {
    201 
    -                lengthMeasureType = missingCodesMapping.get(lengthMeasureType);
    202 
    -            }
    188 
    +        for (String missingSizeMeasureTypeId : missingSizeMeasureTypeIds) {
    189 
    +            queries.add(sqlMappingByCode.get(missingSizeMeasureTypeId));
    190 
    +        }
    203 191
    204 
    -            String finalLengthMeasureType = lengthMeasureType;
    205 
    -            String sizeMeasureTypeId = extraTopiaIdsByCode.get(lengthMeasureType);
    206 
    -            if (sizeMeasureTypeId == null) {
    207 
    -                sizeMeasureTypeId = topiaSqlSupport.findSingleResult(new TopiaSqlQuery<String>() {
    208 
    -
    209 
    -                    @Override
    210 
    -                    public PreparedStatement prepareQuery(Connection connection) throws SQLException {
    211 
    -                        return connection.prepareStatement("SELECT topiaId FROM observe_longline.sizeMeasureType WHERE code = '" + finalLengthMeasureType + "'");
    212 
    -                    }
    213 
    -
    214 
    -                    @Override
    215 
    -                    public String prepareResult(ResultSet set) throws SQLException {
    216 
    -                        return set.getString(1);
    217 
    -                    }
    218 
    -                });
    219 
    -            }
    192 
    +        ImmutableMap.Builder<String, String> allSizeMeasureTypeMappingBuilder = ImmutableMap.<String, String>builder().putAll(existingSizeMeasureMapping);
    193 
    +        knownSizeMeasureTypeMapping.entrySet().stream().filter(e -> !existingSizeMeasureMapping.containsKey(e.getKey())).forEach(e -> allSizeMeasureTypeMappingBuilder.put(e.getKey(), e.getValue()));
    194 
    +        ImmutableMap<String, String> allSizeMeasureTypeMapping = allSizeMeasureTypeMappingBuilder.build();
    220 195
    221 
    -            if (sizeMeasureTypeId == null) {
    196 
    +        for (String lengthMeasureType : lengthMeasureTypes) {
    222 197
    223 
    -                if (log.isWarnEnabled()) {
    224 
    -                    log.warn("Impossible de trouver la type de mesure de taille pour le code: " + lengthMeasureType);
    225 
    -                }
    226 
    -                invalidCodes.add(lengthMeasureType);
    227 
    -            } else {
    228 
    -                sizeMeasureTypeId = StringUtils.replace(sizeMeasureTypeId, ".longline", "");
    229 
    -                queries.add(String.format("UPDATE observe_common.species SET sizeMeasureType = '%s' WHERE lengthMeasureType = '%s'", sizeMeasureTypeId, lengthMeasureType));
    230 
    -            }
    231 
    -        }
    198 
    +            lengthMeasureType = lengthMeasureType.trim();
    232 199
    233 
    -        if (!invalidCodes.isEmpty()) {
    200 
    +            String sizeMeasureTypeId = allSizeMeasureTypeMapping.get(lengthMeasureType);
    201 
    +            queries.add(String.format("UPDATE observe_common.species SET sizeMeasureType = '%s' WHERE lengthMeasureType = '%s'", sizeMeasureTypeId, lengthMeasureType));
    234 202
    235 
    -            throw new IllegalStateException("Impossible de trouver la type de mesure de taille pour les codes suivants :\n\t" + Joiner.on("\n\t").join(invalidCodes));
    236 203 
             }
    237 204
    238 205 
         }

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