Update models and repositories for Postgres

src/main/java/org/genesys2/server/model/dataset/DSRow.java

@@ -46,13 +46,13 @@ public class DSRow implements EntityId {
 	private List<DSValue<?>> values;
 
 	@Id
-	@GeneratedValue(strategy = GenerationType.TABLE)
+	@GeneratedValue(strategy = GenerationType.AUTO)
 	private Long id;
 
-	@Column(columnDefinition = "binary(16)", updatable = false)
+	@Column(updatable = false, length=16)
 	private byte[] md5;
 
-	@Column(columnDefinition = "binary(20)", updatable = false)
+	@Column(updatable = false, length=20)
 	private byte[] sha1;
 
 	@PrePersist

src/main/java/org/genesys2/server/model/dataset/DSRowQualifier.java

@@ -32,7 +32,7 @@ import javax.persistence.Table;
 @DiscriminatorColumn(discriminatorType = DiscriminatorType.INTEGER, name = "typ")
 public abstract class DSRowQualifier<T> {
 	@Id
-	@GeneratedValue(strategy = GenerationType.TABLE)
+	@GeneratedValue(strategy = GenerationType.AUTO)
 	private Long id;
 
 	@ManyToOne(fetch=FetchType.LAZY, optional = false)

src/main/java/org/genesys2/server/model/dataset/DSValue.java

@@ -20,7 +20,7 @@ import javax.persistence.Table;
 @DiscriminatorColumn(discriminatorType = DiscriminatorType.INTEGER, name = "typ")
 public abstract class DSValue<T> {
 	@Id
-	@GeneratedValue(strategy = GenerationType.TABLE)
+	@GeneratedValue(strategy = GenerationType.AUTO)
 	private Long id;
 
 	@ManyToOne(fetch=FetchType.LAZY, optional = false)

src/main/java/org/genesys2/server/model/kpi/DimensionKey.java

@@ -40,7 +40,7 @@ public class DimensionKey implements EntityId, Serializable {
 	private static final long serialVersionUID = 1232115638223004469L;
 
 	@Id
-	@GeneratedValue(strategy = GenerationType.TABLE)
+	@GeneratedValue(strategy = GenerationType.AUTO)
 	private Long id;
 
 	@Column(length = 100, nullable = false, updatable = false)

src/main/java/org/genesys2/server/model/kpi/Observation.java

@@ -52,7 +52,7 @@ public class Observation implements EntityId, Serializable {
 	private static final long serialVersionUID = -7621192124417368090L;
 
 	@Id
-	@GeneratedValue(strategy = GenerationType.TABLE)
+	@GeneratedValue(strategy = GenerationType.AUTO)
 	private Long id;
 
 	@Column(name = "`value`")

src/main/java/org/genesys2/server/persistence/Taxonomy2Repository.java

@@ -32,37 +32,37 @@ public interface Taxonomy2Repository extends JpaRepository<Taxonomy2, Long> {
 	@Query("select distinct t.genus from Taxonomy2 t where t.genus like ?1")
 	List<String> autocompleteGenus(String term, Pageable page);
 
-	@Query("select distinct t.genus from Taxonomy2 t join t.cropTaxonomies ct where t.genus like ?1 and ct.crop = ?2")
+	@Query("select distinct t.genus from Taxonomy2 t join t.cropTaxonomies ct where lower(t.genus) like lower(?1) and ct.crop = ?2")
 	List<String> autocompleteGenusByCrop(String term, Crop crop, Pageable page);
 
-	@Query("select distinct t.species from Taxonomy2 t where t.species like ?1)")
+	@Query("select distinct t.species from Taxonomy2 t where lower(t.species) like lower(?1)")
 	List<String> autocompleteSpecies(String term, Pageable page);
 
-	@Query("select distinct t.species from Taxonomy2 t join t.cropTaxonomies ct where t.species like ?1 and ct.crop = ?2")
+	@Query("select distinct t.species from Taxonomy2 t join t.cropTaxonomies ct where lower(t.species) like lower(?1) and ct.crop = ?2")
 	List<String> autocompleteSpeciesByCrop(String term, Crop crop, Pageable page);
 
-	@Query("select distinct t.species from Taxonomy2 t where t.species like ?1 and t.genus in (?2)")
+	@Query("select distinct t.species from Taxonomy2 t where lower(t.species) like lower(?1) and t.genus in (?2)")
 	List<String> autocompleteSpeciesByGenus(String term, List<String> genus, Pageable page);
 
-	@Query("select distinct t.taxonName from Taxonomy2 t where t.taxonName like ?1)")
+	@Query("select distinct t.taxonName from Taxonomy2 t where lower(t.taxonName) like lower(?1)")
 	List<String> autocompleteTaxonomy(String term, Pageable page);
 
-	@Query("select distinct t.subtaxa from Taxonomy2 t where t.subtaxa like ?1)")
+	@Query("select distinct t.subtaxa from Taxonomy2 t where lower(t.subtaxa) like lower(?1)")
 	List<String> autocompleteSubtaxa(String string, Pageable page);
 
-	@Query("select distinct t.subtaxa from Taxonomy2 t join t.cropTaxonomies ct where t.subtaxa like ?1 and ct.crop = ?2")
+	@Query("select distinct t.subtaxa from Taxonomy2 t join t.cropTaxonomies ct where lower(t.subtaxa) like lower(?1) and ct.crop = ?2")
 	List<String> autocompleteSubtaxaByCrop(String string, Crop crop, Pageable page);
 
-	@Query("select distinct t.subtaxa from Taxonomy2 t where t.subtaxa like ?1 and t.genus in (?2)")
+	@Query("select distinct t.subtaxa from Taxonomy2 t where lower(t.subtaxa) like lower(?1) and t.genus in (?2)")
 	List<String> autocompleteSubtaxaByGenus(String string, List<String> genus, Pageable page);
 
-	@Query("select distinct t.subtaxa from Taxonomy2 t where t.subtaxa like ?1 and t.species in (?2)")
+	@Query("select distinct t.subtaxa from Taxonomy2 t where lower(t.subtaxa) like lower(?1) and t.species in (?2)")
 	List<String> autocompleteSubtaxaBySpecies(String string, List<String> species, Pageable page);
 
-	@Query("select distinct t.subtaxa from Taxonomy2 t where t.subtaxa like ?1 and t.genus in (?2) and t.species in (?3)")
+	@Query("select distinct t.subtaxa from Taxonomy2 t where lower(t.subtaxa) like lower(?1) and t.genus in (?2) and t.species in (?3)")
 	List<String> autocompleteSubtaxaByGenusAndSpecies(String string, List<String> genus, List<String> species, Pageable page);
 	
-	@Query("select t from Taxonomy2 t where t.genus = ?1 and t.species = ?2 and t.spAuthor = ?3 and t.subtaxa = ?4 and t.subtAuthor = ?5")
+	@Query("select t from Taxonomy2 t where lower(t.genus) = lower(?1) and lower(t.species) = lower(?2) and lower(t.spAuthor) = lower(?3) and lower(t.subtaxa) = lower(?4) and lower(t.subtAuthor) = lower(?5)")
 	Taxonomy2 findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(String genus, String species, String spAuthor, String subtaxa, String subtAuthor);
 
 	List<Taxonomy2> findByGenus(String genus);

src/main/java/org/genesys2/server/service/impl/GenesysLowlevelRepositoryCustomImpl.java

@@ -251,8 +251,6 @@ public class GenesysLowlevelRepositoryCustomImpl implements GenesysLowlevelRepos
 				final ArgumentPreparedStatementSetter apss = new ArgumentPreparedStatementSetter(directQuery.getParameters());
 				apss.setValues(stmt);
 
-				// Set mysql JConnector to stream results
-				stmt.setFetchSize(Integer.MIN_VALUE);
 				return stmt;
 			}
 		}, rowCallbackHandler);
@@ -277,8 +275,6 @@ public class GenesysLowlevelRepositoryCustomImpl implements GenesysLowlevelRepos
 				final ArgumentPreparedStatementSetter apss = new ArgumentPreparedStatementSetter(directQuery.getParameters());
 				apss.setValues(stmt);
 
-				// Set mysql JConnector to stream results
-				// stmt.setFetchSize(Integer.MIN_VALUE);
 				return stmt;
 			}
 		}, rowCallbackHandler);
@@ -305,8 +301,6 @@ public class GenesysLowlevelRepositoryCustomImpl implements GenesysLowlevelRepos
 				final ArgumentPreparedStatementSetter apss = new ArgumentPreparedStatementSetter(directQuery.getParameters());
 				apss.setValues(stmt);
 
-				// Set mysql JConnector to stream results
-				stmt.setFetchSize(Integer.MIN_VALUE);
 				return stmt;
 			}
 		}, rowCallbackHandler);
@@ -332,8 +326,6 @@ public class GenesysLowlevelRepositoryCustomImpl implements GenesysLowlevelRepos
 				final ArgumentPreparedStatementSetter apss = new ArgumentPreparedStatementSetter(directQuery.getParameters());
 				apss.setValues(stmt);
 
-				// Set mysql JConnector to stream results
-				stmt.setFetchSize(Integer.MIN_VALUE);
 				return stmt;
 			}
 		}, rowCallbackHandler);
@@ -346,8 +338,6 @@ public class GenesysLowlevelRepositoryCustomImpl implements GenesysLowlevelRepos
 			public PreparedStatement createPreparedStatement(final Connection con) throws SQLException {
 				final PreparedStatement stmt = con
 						.prepareStatement("select n.accessionId, n.instCode, n.name, n.aliasType, n.lang, n.version, n.id from accession_alias n order by n.accessionId");
-				// Set mysql JConnector to stream results
-				stmt.setFetchSize(Integer.MIN_VALUE);
 				return stmt;
 			}
 		}, rowCallbackHandler);
@@ -375,8 +365,6 @@ public class GenesysLowlevelRepositoryCustomImpl implements GenesysLowlevelRepos
 				final ArgumentPreparedStatementSetter apss = new ArgumentPreparedStatementSetter(directQuery.getParameters());
 				apss.setValues(stmt);
 
-				// Set mysql JConnector to stream results
-				stmt.setFetchSize(Integer.MIN_VALUE);
 				return stmt;
 			}
 		}, rowCallbackHandler);
@@ -390,8 +378,6 @@ public class GenesysLowlevelRepositoryCustomImpl implements GenesysLowlevelRepos
 				final PreparedStatement stmt = con
 						.prepareStatement("select distinct a.id, a.instCode, a.acceNumb, t.genus from accessiontrait at inner join accession a on a.id=at.accessionId left outer join taxonomy2 t on t.id=a.taxonomyId2 where at.metadataId = ?");
 				stmt.setLong(1, id);
-				// Set mysql JConnector to stream results
-				stmt.setFetchSize(Integer.MIN_VALUE);
 				return stmt;
 			}
 		}, rowCallbackHandler);

src/main/java/org/genesys2/server/service/impl/TraitValueRepositoryImpl.java

@@ -114,8 +114,8 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 		return this.jdbcTemplate.query(new PreparedStatementCreator() {
 			@Override
 			public PreparedStatement createPreparedStatement(Connection conn) throws SQLException {
-				final PreparedStatement pst = conn.prepareStatement("select accessionId, `" + method.getFieldName() + "` as traitvalue from `" + method.getId()
-						+ "` where metadataId=?");
+				final PreparedStatement pst = conn.prepareStatement("select accessionId, \"" + method.getFieldName().toLowerCase() + "\" as traitvalue from \"" + method.getId()
+						+ "\" where metadataId=?");
 				pst.setLong(1, metadataId);
 				return pst;
 			}
@@ -139,8 +139,8 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 		for (final AccessionTrait at : accessionTraits) {
 			final Method method = methodRepository.findOne(at.getMethodId());
 
-			final List<Map<String, Object>> rows = this.jdbcTemplate.queryForList("select metadataId, `" + method.getFieldName() + "` as traitvalue from `"
-					+ method.getId() + "` where accessionId=?", new Object[] { at.getAccession().getId() });
+			final List<Map<String, Object>> rows = this.jdbcTemplate.queryForList("select metadataid, \"" + method.getFieldName().toLowerCase() + "\" as traitvalue from \""
+					+ method.getId() + "\" where accessionId=?", new Object[] { at.getAccession().getId() });
 
 			if (rows == null || rows.size() == 0) {
 				// Skip
@@ -186,8 +186,8 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 			final long methodId = method.getId();
 			LOG.debug("MethodID={}", methodId);
 
-			this.namedJdbcTemplate.query("select accessionId, `" + method.getFieldName() + "` as traitvalue from `" + method.getId()
-					+ "` where metadataId = :metadataId and accessionId in ( :accessionIds )", paramMap, new RowCallbackHandler() {
+			this.namedJdbcTemplate.query("select accessionid, \"" + method.getFieldName().toLowerCase() + "\" as traitvalue from \"" + method.getId()
+					+ "\" where metadataId = :metadataId and accessionId in ( :accessionIds )", paramMap, new RowCallbackHandler() {
 
 				@Override
 				public void processRow(ResultSet rs) throws SQLException {
@@ -216,8 +216,8 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 
 	@Transactional
 	private void delete(final Metadata metadata, final AccessionId accession, Method method) {
-		LOG.info("Deleting trait values in methodId={} for metadataId={} and accnId={}", method.getId(), metadata.getId(), accession.getId());
-		this.jdbcTemplate.update(String.format("DELETE FROM `%s` WHERE accessionId=? AND metadataId=?", method.getId()), new PreparedStatementSetter() {
+		LOG.info("Deleting trait values in methodid={} for metadataid={} and accnid={}", method.getId(), metadata.getId(), accession.getId());
+		this.jdbcTemplate.update(String.format("DELETE FROM \"%s\" WHERE accessionid=? AND metadataid=?", method.getId()), new PreparedStatementSetter() {
 			@Override
 			public void setValues(PreparedStatement pst) throws SQLException {
 				pst.setLong(1, accession.getId());
@@ -248,7 +248,7 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 		}
 
 		this.jdbcTemplate.batchUpdate(
-				String.format("INSERT INTO `%s` (accessionId, metadataId, `%s`) VALUES (?, ?, ?)", method.getId(), method.getFieldName()),
+				String.format("INSERT INTO \"%s\" (accessionId, metadataId, \"%s\") VALUES (?, ?, ?)", method.getId(), method.getFieldName().toLowerCase()),
 				new BatchPreparedStatementSetter() {
 					@Override
 					public void setValues(PreparedStatement pst, int idx) throws SQLException {
@@ -342,7 +342,7 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 	 * @return
 	 */
 	private int countTraitAccessions(long methodId, long metadataId) {
-		return this.jdbcTemplate.queryForObject(String.format("SELECT COUNT(*) FROM `%s` WHERE metadataId=?", methodId), Integer.class, metadataId);
+		return this.jdbcTemplate.queryForObject(String.format("SELECT COUNT(*) FROM \"%s\" WHERE metadataId=?", methodId), Integer.class, metadataId);
 	}
 
 	/**
@@ -354,14 +354,14 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 	 * @return
 	 */
 	private int countTraitValues(long methodId, long metadataId, long accessionId) {
-		return this.jdbcTemplate.queryForObject(String.format("SELECT COUNT(*) FROM `%s` WHERE metadataId=? AND accessionId=?", methodId), Integer.class,
+		return this.jdbcTemplate.queryForObject(String.format("SELECT COUNT(*) FROM \"%s\" WHERE metadataId=? AND accessionId=?", methodId), Integer.class,
 				metadataId, accessionId);
 	}
 
 	@Override
 	public Map<String, Long> getStatistics(Method method) {
 		final HashMap<String, Long> stats = new HashMap<String, Long>();
-		this.jdbcTemplate.query(MessageFormat.format("SELECT `{0}`, COUNT(*) FROM `{1,number,#}` GROUP BY `{0}`", method.getFieldName(), method.getId()),
+		this.jdbcTemplate.query(MessageFormat.format("SELECT \"{0}\", COUNT(*) FROM \"{1,number,#}\" GROUP BY \"{0}\"", method.getFieldName().toLowerCase(), method.getId()),
 				new RowCallbackHandler() {
 					@Override
 					public void processRow(ResultSet rs) throws SQLException {