DS2

pom.xml

@@ -152,6 +152,12 @@
 			<artifactId>commons-logging</artifactId>
 			<version>${commons.logging.version}</version>
 		</dependency>
+		
+		<dependency>
+		 	<groupId>commons-codec</groupId>
+		 	<artifactId>commons-codec</artifactId>
+		 	<version>1.10</version>
+		 </dependency>
 
 		<!-- Logging dependencies -->
 		<dependency>

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

+package org.genesys2.server.model.dataset;
+
+import java.util.List;
+import java.util.UUID;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.OneToMany;
+import javax.persistence.OrderBy;
+import javax.persistence.PrePersist;
+import javax.persistence.Table;
+
+import org.genesys2.server.model.BusinessModel;
+
+@Entity
+@Table(name = "ds2")
+public class DS extends BusinessModel {
+	@Column(columnDefinition = "binary(16)")
+	private UUID uuid;
+
+	@OrderBy("index")
+	@OneToMany(mappedBy = "dataset")
+	private List<DSQualifier> qualifiers;
+
+	@OrderBy("index")
+	@OneToMany(mappedBy = "dataset")
+	private List<DSDescriptor> descriptors;
+
+	/**
+	 * Generate UUID if missing
+	 */
+	@PrePersist
+	protected void prepersist() {
+		if (this.uuid == null) {
+			this.uuid = UUID.randomUUID();
+		}
+	}
+
+	public UUID getUuid() {
+		return uuid;
+	}
+
+	public void setUuid(UUID uuid) {
+		this.uuid = uuid;
+	}
+
+	public List<DSQualifier> getQualifiers() {
+		return qualifiers;
+	}
+
+	public void setQualifiers(List<DSQualifier> qualifiers) {
+		this.qualifiers = qualifiers;
+	}
+
+	public List<DSDescriptor> getDescriptors() {
+		return descriptors;
+	}
+
+	public void setDescriptors(List<DSDescriptor> descriptors) {
+		this.descriptors = descriptors;
+	}
+}

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

+package org.genesys2.server.model.dataset;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import org.genesys2.server.model.BusinessModel;
+import org.genesys2.server.model.impl.Descriptor;
+
+/**
+ * Dataset descriptor
+ */
+@Entity
+@Table(name = "ds2descriptor")
+public class DSDescriptor extends BusinessModel {
+
+	@Column(name="idx")
+	private float index = 1.0f;
+
+	@ManyToOne(optional = false)
+	@JoinColumn(name="ds")
+	private DS dataset;
+
+	@ManyToOne(optional = false)
+	@JoinColumn(name="d")
+	private Descriptor descriptor;
+
+	public float getIndex() {
+		return index;
+	}
+
+	public void setIndex(float index) {
+		this.index = index;
+	}
+
+	public DS getDataset() {
+		return dataset;
+	}
+
+	public void setDataset(DS dataset) {
+		this.dataset = dataset;
+	}
+
+	public Descriptor getDescriptor() {
+		return descriptor;
+	}
+
+	public void setDescriptor(Descriptor descriptor) {
+		this.descriptor = descriptor;
+	}
+	
+	@Override
+	public String toString() {
+		return "DSD " + this.getId();
+	}
+}

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

+package org.genesys2.server.model.dataset;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import org.genesys2.server.model.BusinessModel;
+import org.genesys2.server.model.impl.Descriptor;
+
+/**
+ * Dataset qualifier specification
+ */
+@Entity
+@Table(name = "ds2qualifier")
+public class DSQualifier extends BusinessModel {
+
+	@Column(name="idx")
+	private float index = 1.0f;
+
+	@ManyToOne(optional = false)
+	@JoinColumn(name="ds")
+	private DS dataset;
+
+	@ManyToOne(optional = false)
+	@JoinColumn(name="d")
+	private Descriptor descriptor;
+
+	public float getIndex() {
+		return index;
+	}
+
+	public void setIndex(float index) {
+		this.index = index;
+	}
+
+	public DS getDataset() {
+		return dataset;
+	}
+
+	public void setDataset(DS dataset) {
+		this.dataset = dataset;
+	}
+
+	public Descriptor getDescriptor() {
+		return descriptor;
+	}
+
+	public void setDescriptor(Descriptor descriptor) {
+		this.descriptor = descriptor;
+	}
+	
+	@Override
+	public String toString() {
+		return "DSQ " + this.id + " [" + this.getId() + "]";
+	}
+}

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

+package org.genesys2.server.model.dataset;
+
+import java.util.List;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.OneToMany;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import org.genesys2.server.model.EntityId;
+
+@Entity
+@Table(name = "ds2row", uniqueConstraints = { @UniqueConstraint(columnNames = { "md5", "sha1" }) })
+public class DSRow implements EntityId {
+	@OneToMany(mappedBy = "row")
+	private List<DSRowQualifier<?>> rowQualifiers;
+
+	@OneToMany(mappedBy = "row")
+	private List<DSValue<?>> values;
+
+	@Id
+	@GeneratedValue(strategy = GenerationType.TABLE)
+	private Long id;
+
+	@Column(columnDefinition="binary(16)")
+	private byte[] md5;
+
+	@Column(columnDefinition="binary(20)")
+	private byte[] sha1;
+
+	@Override
+	public Long getId() {
+		return this.id;
+	}
+
+	public void setId(Long id) {
+		this.id = id;
+	}
+
+	public List<DSRowQualifier<?>> getRowQualifiers() {
+		return rowQualifiers;
+	}
+
+	public void setRowQualifiers(List<DSRowQualifier<?>> rowQualifiers) {
+		this.rowQualifiers = rowQualifiers;
+	}
+
+	public List<DSValue<?>> getValues() {
+		return values;
+	}
+
+	public void setValues(List<DSValue<?>> values) {
+		this.values = values;
+	}
+
+	@Override
+	public String toString() {
+		return "DSR " + id;
+	}
+
+	public void setMd5(byte[] md5) {
+		this.md5 = md5;
+	}
+
+	public byte[] getMd5() {
+		return md5;
+	}
+
+	public void setSha1(byte[] sha1) {
+		this.sha1 = sha1;
+	}
+
+	public byte[] getSha1() {
+		return sha1;
+	}
+}

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

+package org.genesys2.server.model.dataset;
+
+import javax.persistence.DiscriminatorColumn;
+import javax.persistence.DiscriminatorType;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Index;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+@Entity
+@Table(name = "ds2rowqualifier", indexes = { @Index(columnList = "dsq, vall") })
+@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
+@DiscriminatorColumn(discriminatorType = DiscriminatorType.INTEGER, name = "typ")
+public abstract class DSRowQualifier<T> {
+	@Id
+	@GeneratedValue(strategy = GenerationType.TABLE)
+	private Long id;
+
+	@ManyToOne(optional = false)
+	@JoinColumn(name = "r")
+	private DSRow row;
+
+	@ManyToOne(optional = false)
+	@JoinColumn(name = "dsq")
+	private DSQualifier datasetQualifier;
+
+	public abstract T getValue();
+
+	public abstract void setValue(T value);
+
+	public Long getId() {
+		return id;
+	}
+
+	public void setId(Long id) {
+		this.id = id;
+	}
+
+	public DSRow getRow() {
+		return row;
+	}
+
+	public void setRow(DSRow row) {
+		this.row = row;
+	}
+
+	public DSQualifier getDatasetQualifier() {
+		return datasetQualifier;
+	}
+
+	public void setDatasetQualifier(DSQualifier datasetQualifier) {
+		this.datasetQualifier = datasetQualifier;
+	}
+
+	public static DSRowQualifier<?> make(Object qualifier) {
+		if (qualifier == null) {
+			return null;
+		} else if (qualifier instanceof Long) {
+			DSRowQualifierLong dsrq = new DSRowQualifierLong();
+			dsrq.setValue((Long) qualifier);
+			return dsrq;
+		}
+		return null;
+	}
+
+}

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

+package org.genesys2.server.model.dataset;
+
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+@Entity
+@DiscriminatorValue("1")
+public class DSRowQualifierLong extends DSRowQualifier<Long> {
+
+	@Column(name = "vall")
+	private Long value;
+
+	@Override
+	public Long getValue() {
+		return this.value;
+	}
+
+	@Override
+	public void setValue(Long value) {
+		this.value = value;
+	}
+
+}

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

+package org.genesys2.server.model.dataset;
+
+import javax.persistence.DiscriminatorColumn;
+import javax.persistence.DiscriminatorType;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Index;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+@Entity
+@Table(name = "ds2value", indexes = { @Index(columnList = "r,dsd"), @Index(columnList = "dsd,vall"), @Index(columnList = "dsd,vald") })
+@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
+@DiscriminatorColumn(discriminatorType = DiscriminatorType.INTEGER, name = "typ")
+public abstract class DSValue<T> {
+	@Id
+	@GeneratedValue(strategy = GenerationType.TABLE)
+	private Long id;
+
+	@ManyToOne(optional = false)
+	@JoinColumn(name = "r")
+	private DSRow row;
+
+	@ManyToOne(optional = false)
+	@JoinColumn(name = "dsd")
+	private DSDescriptor datasetDescriptor;
+
+	public abstract T getValue();
+
+	public abstract void setValue(T value);
+
+	public Long getId() {
+		return id;
+	}
+
+	public void setId(Long id) {
+		this.id = id;
+	}
+
+	public DSRow getRow() {
+		return row;
+	}
+
+	public void setRow(DSRow row) {
+		this.row = row;
+	}
+
+	public DSDescriptor getDatasetDescriptor() {
+		return datasetDescriptor;
+	}
+
+	public void setDatasetDescriptor(DSDescriptor datasetDescriptor) {
+		this.datasetDescriptor = datasetDescriptor;
+	}
+
+	public static DSValue<?> make(Object v) {
+		if (v instanceof Long) {
+			return new DSValueLong();
+		} else if (v instanceof Double) {
+			return new DSValueDouble();
+		} else if (v instanceof String) {
+			return new DSValueString();
+		}
+		return null;
+	}
+
+	public void setValue2(Object v) {
+		setValue((T) v);
+	}
+}

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

+package org.genesys2.server.model.dataset;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+@Entity
+@DiscriminatorValue("2")
+public class DSValueDouble extends DSValue<Double> {
+
+	private Double vald;
+
+	@Override
+	public Double getValue() {
+		return this.vald;
+	}
+
+	@Override
+	public void setValue(Double value) {
+		this.vald = value;
+	}
+
+}

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

+package org.genesys2.server.model.dataset;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+@Entity
+@DiscriminatorValue("1")
+public class DSValueLong extends DSValue<Long> {
+
+	private Long vall;
+
+	@Override
+	public Long getValue() {
+		return vall;
+	}
+
+	@Override
+	public void setValue(Long value) {
+		this.vall = value;
+	}
+}

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

+package org.genesys2.server.model.dataset;
+
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+@Entity
+@DiscriminatorValue("3")
+public class DSValueString extends DSValue<String> {
+
+	@Column(length=500)
+	private String vals;
+
+	@Override
+	public String getValue() {
+		return vals;
+	}
+
+	@Override
+	public void setValue(String value) {
+		this.vals = value;
+	}
+}

src/main/java/org/genesys2/server/model/genesys/AccessionGeo.java

@@ -55,6 +55,8 @@ public class AccessionGeo extends BusinessModel implements GeoReferencedEntity,
 	private String datum;
 	private String method;
 
+	private Long tileIndex;
+
 	public long getVersion() {
 		return version;
 	}
@@ -128,6 +130,14 @@ public class AccessionGeo extends BusinessModel implements GeoReferencedEntity,
 		return method;
 	}
 
+	public Long getTileIndex() {
+		return tileIndex;
+	}
+
+	public void setTileIndex(Long tileIndex) {
+		this.tileIndex = tileIndex;
+	}
+
 	public boolean isEmpty() {
 		if (StringUtils.isNotBlank(datum))
 			return false;

src/main/java/org/genesys2/server/model/json/WorldclimJson.java

@@ -12,7 +12,7 @@ import com.fasterxml.jackson.annotation.JsonIgnore;
  */
 public class WorldclimJson {
 	// Monthlies
-	private Integer[] precipitation = new Integer[12];
+	private Long[] precipitation = new Long[12];
 	private Double[] tempMin = new Double[12];
 	private Double[] tempMean = new Double[12];
 	private Double[] tempMax = new Double[12];
@@ -20,7 +20,7 @@ public class WorldclimJson {
 	@JsonIgnore
 	private Map<Descriptor, Object> other = new HashMap<Descriptor, Object>();
 
-	public Integer[] getPrecipitation() {
+	public Long[] getPrecipitation() {
 		return precipitation;
 	}
 

src/main/java/org/genesys2/server/persistence/domain/AccessionGeoRepository.java

@@ -40,4 +40,7 @@ public interface AccessionGeoRepository extends JpaRepository<AccessionGeo, Long
 	@Query("from AccessionGeo ag where ag.accession.id in ?1")
 	List<AccessionGeo> findAllFor(Collection<Long> accessionIds);
 
+	@Query("select distinct(ag.tileIndex) from AccessionGeo ag where ag.tileIndex is not null")
+	Collection<Long> getTileIndexes();
+
 }

src/main/java/org/genesys2/server/persistence/domain/dataset/DSDescriptorRepository.java

+package org.genesys2.server.persistence.domain.dataset;
+
+import org.genesys2.server.model.dataset.DSDescriptor;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+public interface DSDescriptorRepository extends JpaRepository<DSDescriptor, Long> {
+
+}

src/main/java/org/genesys2/server/persistence/domain/dataset/DSQualifierRepository.java

+package org.genesys2.server.persistence.domain.dataset;
+
+import org.genesys2.server.model.dataset.DSQualifier;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+public interface DSQualifierRepository extends JpaRepository<DSQualifier, Long> {
+
+}

src/main/java/org/genesys2/server/persistence/domain/dataset/DSRepository.java

+package org.genesys2.server.persistence.domain.dataset;
+