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@@ -23,6 +23,7 @@ package fr.ird.observe.spi.migration.v9; |
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*/
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import com.google.auto.service.AutoService;
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+import fr.ird.observe.spi.context.DataDtoEntityContext;
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import fr.ird.observe.spi.migration.ByMajorMigrationVersionResource;
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import io.ultreia.java4all.util.Version;
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import io.ultreia.java4all.util.sql.SqlQuery;
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@@ -32,9 +33,13 @@ import org.apache.logging.log4j.Logger; |
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import org.nuiton.topia.service.migration.resources.MigrationVersionResource;
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import org.nuiton.topia.service.migration.resources.MigrationVersionResourceExecutor;
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+import java.sql.ResultSet;
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+import java.sql.SQLException;
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+import java.sql.Timestamp;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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+import java.util.TreeMap;
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/**
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* Created on 19/01/2021.
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@@ -124,6 +129,11 @@ public class DataSourceMigrationForVersion_9_0 extends ByMajorMigrationVersionRe |
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addNewTable(executor, withIds, "03", "table-ps_observation_catch", "table-ps_observation_sample");
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+ if (withIds) {
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+ // See https://gitlab.com/ultreiaio/ird-observe/-/issues/2436
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+ migrateSample(executor);
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+ }
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+
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executor.addScript("04_0", "adapt_table-ps_observation_activity");
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executor.addScript("04_1", "adapt_table-ps_observation_set");
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@@ -189,6 +199,310 @@ public class DataSourceMigrationForVersion_9_0 extends ByMajorMigrationVersionRe |
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}
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}
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+ static class Sample {
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+ String topiaId;
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+ long topiaVersion;
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+ Timestamp topiaCreateDate;
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+ Timestamp lastUpdateDate;
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+ String homeId;
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+ String comment;
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+ String set;
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+
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+ public Sample(ResultSet resultSet) throws SQLException {
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+ this.topiaId = resultSet.getString(1);
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+ this.topiaVersion = resultSet.getLong(2);
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+ this.topiaCreateDate = resultSet.getTimestamp(3);
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+ this.homeId = resultSet.getString(4);
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+ this.comment = resultSet.getString(5);
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+ this.set = resultSet.getString(6);
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+ this.lastUpdateDate = resultSet.getTimestamp(7);
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+ }
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+
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+ public void addHomeId(String homeId) {
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+ if (homeId == null) {
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+ return;
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+ }
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+ if (this.homeId == null) {
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+ this.homeId = homeId;
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+ return;
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+ }
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+ this.homeId += " - " + homeId;
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+ }
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+
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+ public void addComment(String comment) {
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+ if (comment == null) {
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+ return;
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+ }
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+ if (this.comment == null) {
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+ this.comment = comment;
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+ return;
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+ }
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+ this.comment += " - " + comment;
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+ }
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+
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+ }
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+
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+
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+ static class SampleMeasure {
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+ String topiaId;
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+ long topiaVersion;
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+ Timestamp topiaCreateDate;
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+ Timestamp lastUpdateDate;
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+ String homeId;
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+ Float length;
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+ Boolean isLengthComputed;
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+ String picturesReferences;
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+ Float weight;
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+ Boolean isWeightComputed;
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+ int count;
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+ int acquisitionMode;
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+ String species;
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+ String sample;
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+ String sex;
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+ String sizeMeasureType;
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+ String weightMeasureType;
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+ String tagNumber;
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+ String speciesFate;
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+ int sample_idx;
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+ String lengthMeasureMethod;
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+ String weightMeasureMethod;
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+
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+ public SampleMeasure(ResultSet resultSet) throws SQLException {
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+ this.topiaId = resultSet.getString(1);
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+ this.topiaVersion = resultSet.getLong(2);
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+ this.topiaCreateDate = resultSet.getTimestamp(3);
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+ this.homeId = resultSet.getString(4);
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+ this.length = resultSet.getFloat(5);
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+ this.isLengthComputed = resultSet.getBoolean(6);
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+ this.picturesReferences = resultSet.getString(7);
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+ this.weight = resultSet.getFloat(8);
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+ this.isWeightComputed = resultSet.getBoolean(9);
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+ this.count = resultSet.getInt(10);
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+ this.acquisitionMode = resultSet.getInt(11);
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+ this.species = resultSet.getString(12);
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+ this.sample = resultSet.getString(13);
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+ this.sex = resultSet.getString(14);
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+ this.lastUpdateDate = resultSet.getTimestamp(15);
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+ this.sizeMeasureType = resultSet.getString(16);
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+ this.weightMeasureType = resultSet.getString(17);
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+ this.tagNumber = resultSet.getString(18);
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+ this.speciesFate = resultSet.getString(19);
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+ this.sample_idx = resultSet.getInt(20);
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+ this.lengthMeasureMethod = resultSet.getString(21);
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+ this.weightMeasureMethod = resultSet.getString(22);
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+ }
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+
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+ }
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+
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+ private void migrateSample(MigrationVersionResourceExecutor executor) {
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+
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+ Map<String, Sample> setToSampleMap = new TreeMap<>();
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+ Map<String, String> sampleMapping = new TreeMap<>();
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+
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+ addSample(executor, setToSampleMap, sampleMapping, "SELECT REPLACE(topiaId, '.NonTargetSample', '.Sample'), topiaVersion, topiaCreateDate, homeId, substr(trim(comment), 0, 1024), set, lastUpdateDate FROM ps_observation.nontargetsample order by set, topiaId");
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+
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+ addSample(executor, setToSampleMap, sampleMapping, "SELECT REPLACE(topiaId, '.TargetSample', '.Sample'), topiaVersion, topiaCreateDate, homeId, substr(trim(comment), 0, 1024), set, lastUpdateDate FROM ps_observation.targetsample order by set, topiaId");
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+
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+ //fr.ird.data.ps.observation.Set#1307366814753#0.10928986819912401
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+ //fr.ird.data.ps.observation.Sample#1307366814761#0.8029664353471644
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+ for (Sample sample : setToSampleMap.values()) {
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+ executor.writeSql(String.format("INSERT INTO ps_observation.Sample(topiaId, topiaVersion, topiaCreateDate, homeId, comment, set, lastUpdateDate) VALUES('%s', %s, '%s'::timestamp, %s, %s, '%s', '%s'::timestamp);",
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+ sample.topiaId,
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+ sample.topiaVersion,
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+ sample.topiaCreateDate,
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+ DataDtoEntityContext.escapeString(sample.homeId),
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+ DataDtoEntityContext.escapeComment(sample.comment),
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+ sample.set,
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+ sample.lastUpdateDate
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+ ));
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+ }
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+
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+ migrateSampleMeasure(executor, sampleMapping);
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+ }
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+
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+ private void migrateSampleMeasure(MigrationVersionResourceExecutor executor, Map<String, String> sampleMapping) {
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+ // nonTargetSampleMeasure
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+ addSampleMeasure(executor, sampleMapping, "SELECT " +
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+ "REPLACE(topiaId, '.NonTargetLength', '.SampleMeasure'), " +
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+ "topiaVersion + 1, " +
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+ "topiaCreateDate, " +
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+ "homeId, " +
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+ "length, " +
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+ "isLengthComputed, " +
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+ "picturesReferences, " +
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+ "weight, " +
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+ "isWeightComputed, " +
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+ "count, " +
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+ "acquisitionMode, " +
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+ "species, " +
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+ "REPLACE(nonTargetSample, '.NonTargetSample', '.Sample'), " +
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+ "sex, " +
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+ "lastUpdateDate, " +
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+ "sizeMeasureType, " +
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+ "weightMeasureType, " +
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+ "tagNumber, " +
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+ "speciesFate, " +
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+ "nonTargetSample_idx, " +
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+ "lengthMeasureMethod, " +
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+ "weightMeasureMethod " +
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+ "FROM ps_observation.NonTargetLength");
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+
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+ // discardedTargetSampleMeasure
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+ addSampleMeasure(executor, sampleMapping, "SELECT " +
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+ "REPLACE(tl.topiaId, '.TargetLength', '.SampleMeasure'), " +
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+ "tl.topiaVersion + 1, " +
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+ "tl.topiaCreateDate, " +
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+ "tl.homeId, " +
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+ "tl.length, " +
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+ "tl.isLengthComputed, " +
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+ "NULL, " +
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+ "tl.weight, " +
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+ "tl.isWeightComputed, " +
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+ "tl.count, " +
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+ "tl.acquisitionMode, " +
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+ "tl.species, " +
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+ "REPLACE(tl.targetSample, '.TargetSample', '.Sample'), " +
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+ "'fr.ird.referential.common.Sex#1239832686121#0.0', " +
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+ "tl.lastUpdateDate, " +
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+ "tl.sizeMeasureType, " +
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+ "tl.weightMeasureType, " +
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+ "tl.tagNumber, " +
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+ "'fr.ird.referential.ps.common.SpeciesFate#1239832683619#0.6250731662108877', " +
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+ "-tl.targetsample_idx, " +
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+ "tl.lengthMeasureMethod, " +
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+ "tl.weightMeasureMethod " +
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+ "FROM ps_observation.TargetSample ts " +
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+ "INNER JOIN ps_observation.TargetLength tl ON (tl.targetSample=ts.topiaId) " +
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+ "WHERE ts.discarded");
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+
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+ // notDiscardedTargetSampleMeasure
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+ addSampleMeasure(executor, sampleMapping, "SELECT " +
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+ "REPLACE(tl.topiaId, '.TargetLength', '.SampleMeasure'), " +
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+ "tl.topiaVersion + 1, " +
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+ "tl.topiaCreateDate, " +
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+ "tl.homeId, " +
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+ "tl.length, " +
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+ "tl.isLengthComputed, " +
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+ "NULL, " +
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+ "tl.weight, " +
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+ "tl.isWeightComputed, " +
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+ "tl.count, " +
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+ "tl.acquisitionMode, " +
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+ "tl.species, " +
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+ "REPLACE(tl.targetSample, '.TargetSample', '.Sample'), " +
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+ "'fr.ird.referential.common.Sex#1239832686121#0.0', " +
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+ "tl.lastUpdateDate, " +
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+ "tl.sizeMeasureType, " +
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+ "tl.weightMeasureType, " +
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+ "tl.tagNumber, " +
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+ "'fr.ird.referential.ps.common.SpeciesFate#1239832683619#0.5722739932065866', " +
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+ "-tl.targetsample_idx, " +
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+ "tl.lengthMeasureMethod, " +
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+ "tl.weightMeasureMethod " +
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+ "FROM ps_observation.TargetSample ts " +
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+ "INNER JOIN ps_observation.TargetLength tl ON (tl.targetSample=ts.topiaId) " +
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+ "WHERE NOT ts.discarded");
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405
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+ }
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406
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+
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407
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+ private void addSample(MigrationVersionResourceExecutor executor, Map<String, Sample> setToSampleMap, Map<String, String> sampleMapping, String query) {
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408
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+ List<Sample> targetSample = executor.findMultipleResult(SqlQuery.wrap(query, Sample::new));
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409
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+ for (Sample sample : targetSample) {
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410
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+ Sample existingSample = setToSampleMap.get(sample.set);
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411
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+ if (existingSample == null) {
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412
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+ // new sample
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+ setToSampleMap.put(sample.set, sample);
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414
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+// sampleMapping.put(sample.topiaId, sample.topiaId);
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415
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+ } else {
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416
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+ // add to sample mapping
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417
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+ sampleMapping.put(sample.topiaId, existingSample.topiaId);
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418
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+ // update homeId
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419
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+ existingSample.addHomeId(sample.homeId);
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420
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+ // update comment
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421
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+ existingSample.addComment(sample.comment);
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422
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+ }
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423
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+ }
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424
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+ }
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+
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426
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+ private void addSampleMeasure(MigrationVersionResourceExecutor executor, Map<String, String> sampleMapping, String query) {
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427
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+ List<SampleMeasure> sampleMeasureList = executor.findMultipleResult(SqlQuery.wrap(query, SampleMeasure::new));
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428
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+ for (SampleMeasure sampleMeasure : sampleMeasureList) {
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429
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+ String sampleId = sampleMapping.get(sampleMeasure.sample);
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430
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+ if (sampleId == null) {
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431
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+ sampleId = sampleMeasure.sample;
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432
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+ }
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433
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+ executor.writeSql(String.format("INSERT INTO ps_observation.SampleMeasure(" +
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434
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+ " topiaId," +
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435
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+ " topiaVersion," +
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436
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+ " topiaCreateDate," +
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437
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+ " homeId," +
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438
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+ " length," +
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439
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+ " isLengthComputed," +
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440
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+ " picturesReferences," +
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441
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+ " weight," +
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442
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+ " isWeightComputed," +
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443
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+ " count," +
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444
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+ " acquisitionMode," +
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445
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+ " species," +
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446
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+ " sample," +
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447
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+ " sex," +
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448
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+ " lastUpdateDate," +
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449
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+ " sizeMeasureType," +
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450
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+ " weightMeasureType," +
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451
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+ " tagNumber," +
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452
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+ " speciesFate," +
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453
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+ " sample_idx," +
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454
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+ " lengthMeasureMethod," +
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455
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+ " weightMeasureMethod)" +
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456
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+ " VALUES(" +
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457
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+ "'%s', " +
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458
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+ "%s, " +
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459
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+ "'%s'::timestamp, " +
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460
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+ "%s, " +
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461
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+ "%s, " +
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462
|
+ "%s, " +
|
|
|
463
|
+ "%s, " +
|
|
|
464
|
+ "%s, " +
|
|
|
465
|
+ "%s, " +
|
|
|
466
|
+ "%s, " +
|
|
|
467
|
+ "%s, " +
|
|
|
468
|
+ "%s, " +
|
|
|
469
|
+ "'%s', " +
|
|
|
470
|
+ "%s, " +
|
|
|
471
|
+ "'%s'::timestamp, " +
|
|
|
472
|
+ "%s, " +
|
|
|
473
|
+ "%s, " +
|
|
|
474
|
+ "%s, " +
|
|
|
475
|
+ "%s, " +
|
|
|
476
|
+ "%s, " +
|
|
|
477
|
+ "%s, " +
|
|
|
478
|
+ "%s " +
|
|
|
479
|
+ ");",
|
|
|
480
|
+ sampleMeasure.topiaId,
|
|
|
481
|
+ sampleMeasure.topiaVersion,
|
|
|
482
|
+ sampleMeasure.topiaCreateDate,
|
|
|
483
|
+ DataDtoEntityContext.escapeString(sampleMeasure.homeId == null ? null : sampleMeasure.homeId.replaceAll("'", "")),
|
|
|
484
|
+ sampleMeasure.length,
|
|
|
485
|
+ sampleMeasure.isLengthComputed,
|
|
|
486
|
+ DataDtoEntityContext.escapeString(sampleMeasure.picturesReferences == null ? null : sampleMeasure.picturesReferences.replaceAll("'", "")),
|
|
|
487
|
+ sampleMeasure.weight,
|
|
|
488
|
+ sampleMeasure.isWeightComputed,
|
|
|
489
|
+ sampleMeasure.count,
|
|
|
490
|
+ sampleMeasure.acquisitionMode,
|
|
|
491
|
+ DataDtoEntityContext.escapeString(sampleMeasure.species),
|
|
|
492
|
+ sampleId,
|
|
|
493
|
+ DataDtoEntityContext.escapeString(sampleMeasure.sex),
|
|
|
494
|
+ sampleMeasure.lastUpdateDate,
|
|
|
495
|
+ DataDtoEntityContext.escapeString(sampleMeasure.sizeMeasureType),
|
|
|
496
|
+ DataDtoEntityContext.escapeString(sampleMeasure.weightMeasureType),
|
|
|
497
|
+ DataDtoEntityContext.escapeString(sampleMeasure.tagNumber),
|
|
|
498
|
+ DataDtoEntityContext.escapeString(sampleMeasure.speciesFate),
|
|
|
499
|
+ sampleMeasure.sample_idx,
|
|
|
500
|
+ DataDtoEntityContext.escapeString(sampleMeasure.lengthMeasureMethod),
|
|
|
501
|
+ DataDtoEntityContext.escapeString(sampleMeasure.weightMeasureMethod)
|
|
|
502
|
+ ));
|
|
|
503
|
+ }
|
|
|
504
|
+ }
|
|
|
505
|
+
|
|
192
|
506
|
@Override
|
|
193
|
507
|
public void generateFinalizeSqlScript(MigrationVersionResourceExecutor executor) {
|
|
194
|
508
|
migrateIdx(executor, "ps_observation", "catch", "set");
|