Merge branch '255-rename-model' into 'master'

Resolve "Rename model"

Closes #255

See merge request genesys-pgr/genesys-server!150

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

@@ -3,6 +3,7 @@ package org.genesys2.server.model.dataset;
 import java.util.List;
 import java.util.UUID;
 
+import javax.persistence.CascadeType;
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.OneToMany;
@@ -23,12 +24,12 @@ public class DS extends BasicModel {
 	private UUID uuid;
 
 	@OrderBy("index")
-	@OneToMany(mappedBy = "dataset")
+	@OneToMany(mappedBy = "dataset", cascade = { CascadeType.ALL })
 	private List<DSQualifier> qualifiers;
 
 	@OrderBy("index")
-	@OneToMany(mappedBy = "dataset")
-	private List<DSDescriptor> descriptors;
+	@OneToMany(mappedBy = "dataset", cascade = { CascadeType.ALL })
+	private List<DSColumn> columns;
 
 	/**
 	 * Generate UUID if missing
@@ -56,11 +57,11 @@ public class DS extends BasicModel {
 		this.qualifiers = qualifiers;
 	}
 
-	public List<DSDescriptor> getDescriptors() {
-		return descriptors;
+	public List<DSColumn> getColumns() {
+		return columns;
 	}
 
-	public void setDescriptors(List<DSDescriptor> descriptors) {
-		this.descriptors = descriptors;
+	public void setColumns(List<DSColumn> columns) {
+		this.columns = columns;
 	}
 }

src/main/java/org/genesys2/server/model/dataset/DSColumn.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.genesys.blocks.model.BasicModel;
+
+/**
+ * Dataset column.
+ */
+@Entity
+@Table(name = "ds2column")
+public class DSColumn extends BasicModel {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -7693331325536594367L;
+
+	@Column(name="idx")
+	private float index = 1.0f;
+
+	@ManyToOne(optional = false)
+	@JoinColumn(name="ds")
+	private DS dataset;
+
+	@ManyToOne(optional = false)
+	@JoinColumn(name="d")
+	private DSDescriptor 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 DSDescriptor getDescriptor() {
+		return descriptor;
+	}
+
+	public void setDescriptor(DSDescriptor descriptor) {
+		this.descriptor = descriptor;
+	}
+	
+	@Override
+	public String toString() {
+		return "DSD " + this.getId();
+	}
+}

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

+/**
+ * Copyright 2014 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ **/
+
 package org.genesys2.server.model.dataset;
 
+import java.text.MessageFormat;
+import java.util.UUID;
+
 import javax.persistence.Column;
 import javax.persistence.Entity;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
+import javax.persistence.Lob;
+import javax.persistence.PrePersist;
 import javax.persistence.Table;
 
 import org.genesys.blocks.model.BasicModel;
-import org.genesys2.server.model.impl.Descriptor;
+import org.hibernate.annotations.Type;
 
 /**
- * Dataset descriptor
+ * A DSDescriptor represents a dimension of a sparse vector.
+ *
+ * @author mobreza
  */
 @Entity
 @Table(name = "ds2descriptor")
 public class DSDescriptor extends BasicModel {
+	private static final long serialVersionUID = 3832200593904442940L;
+
+	@Column(unique = true, nullable=false, updatable = false)
+	@Type(type = "uuid-binary")
+	private UUID uuid;
+
+	@Lob
+	@Type(type = "org.hibernate.type.TextType")
+	private String title;
+
+	@Column(nullable = false, length = 200)
+	private String code;
+
+	@Lob
+	@Type(type = "org.hibernate.type.TextType")
+	private String description;
+
+	@Column(length = 20)
+	private String uom;
 
 	/**
-	 * 
+	 * Generate UUID if missing
 	 */
-	private static final long serialVersionUID = -7693331325536594367L;
+	@PrePersist
+	protected void prepersist() {
+		if (this.uuid == null) {
+			this.uuid = UUID.randomUUID();
+		}
+	}
 
-	@Column(name="idx")
-	private float index = 1.0f;
+	public UUID getUuid() {
+		return uuid;
+	}
+
+	public void setUuid(UUID uuid) {
+		this.uuid = uuid;
+	}
 
-	@ManyToOne(optional = false)
-	@JoinColumn(name="ds")
-	private DS dataset;
+	
+	public String getTitle() {
+		return title;
+	}
 
-	@ManyToOne(optional = false)
-	@JoinColumn(name="d")
-	private Descriptor descriptor;
+	public void setTitle(String title) {
+		this.title = title;
+	}
 
-	public float getIndex() {
-		return index;
+	public String getCode() {
+		return code;
 	}
 
-	public void setIndex(float index) {
-		this.index = index;
+	public void setCode(String code) {
+		this.code = code;
 	}
 
-	public DS getDataset() {
-		return dataset;
+	public String getDescription() {
+		return description;
 	}
 
-	public void setDataset(DS dataset) {
-		this.dataset = dataset;
+	public void setDescription(final String description) {
+		this.description = description;
 	}
 
-	public Descriptor getDescriptor() {
-		return descriptor;
+	public String getUom() {
+		return uom;
 	}
 
-	public void setDescriptor(Descriptor descriptor) {
-		this.descriptor = descriptor;
+	public void setUom(String uom) {
+		this.uom = uom;
 	}
-	
+
 	@Override
 	public String toString() {
-		return "DSD " + this.getId();
+		return MessageFormat.format("DSDescriptor id={0,number,#} name={1}", getId(), code);
 	}
 }

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

@@ -7,10 +7,9 @@ import javax.persistence.ManyToOne;
 import javax.persistence.Table;
 
 import org.genesys.blocks.model.BasicModel;
-import org.genesys2.server.model.impl.Descriptor;
 
 /**
- * Dataset qualifier specification
+ * The dataset qualifier is a key lookup component for dataset rows. 
  */
 @Entity
 @Table(name = "ds2qualifier")
@@ -30,7 +29,7 @@ public class DSQualifier extends BasicModel {
 
 	@ManyToOne(optional = false)
 	@JoinColumn(name="d")
-	private Descriptor descriptor;
+	private DSDescriptor descriptor;
 
 	public float getIndex() {
 		return index;
@@ -48,11 +47,11 @@ public class DSQualifier extends BasicModel {
 		this.dataset = dataset;
 	}
 
-	public Descriptor getDescriptor() {
+	public DSDescriptor getDescriptor() {
 		return descriptor;
 	}
 
-	public void setDescriptor(Descriptor descriptor) {
+	public void setDescriptor(DSDescriptor descriptor) {
 		this.descriptor = descriptor;
 	}
 	

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

 package org.genesys2.server.model.dataset;
 
+import java.nio.ByteBuffer;
 import java.util.List;
 
 import javax.persistence.CascadeType;
@@ -12,23 +13,36 @@ import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.OneToMany;
+import javax.persistence.PrePersist;
+import javax.persistence.PreUpdate;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
+import org.apache.commons.codec.digest.DigestUtils;
 import org.genesys.blocks.model.EntityId;
 
+/**
+ * Represents a row in a DS2 dataset. The row has a unique {@link #id} and
+ * groups together different {@link DSValue} values (column values).
+ *
+ * The row is qualified by a list of row qualifiers ({@link DSRowQualifier})
+ * that represent the "keys" of the row. Their SHA-1 and MD5 sums are calculated
+ * and stored in {@link #sha1} and {@link #md5} respectively.
+ * 
+ * @author Matija Obreza
+ */
 @Entity
 @Table(name = "ds2row", uniqueConstraints = { @UniqueConstraint(columnNames = { "md5", "sha1" }) })
 public class DSRow implements EntityId {
 
-	@ManyToOne(fetch=FetchType.LAZY, optional = false)
-	@JoinColumn(name="ds")
+	@ManyToOne(fetch = FetchType.LAZY, optional = false)
+	@JoinColumn(name = "ds")
 	private DS dataset;
-	
-	@OneToMany(fetch = FetchType.LAZY, mappedBy = "row", cascade = { CascadeType.REMOVE })
+
+	@OneToMany(fetch = FetchType.LAZY, mappedBy = "row", cascade = { CascadeType.ALL })
 	private List<DSRowQualifier<?>> rowQualifiers;
 
-	@OneToMany(fetch = FetchType.LAZY, mappedBy = "row")
+	@OneToMany(fetch = FetchType.LAZY, mappedBy = "row", cascade = { CascadeType.ALL })
 	private List<DSValue<?>> values;
 
 	@Id
@@ -41,6 +55,19 @@ public class DSRow implements EntityId {
 	@Column(columnDefinition = "binary(20)", updatable = false)
 	private byte[] sha1;
 
+	@PrePersist
+	@PreUpdate
+	private void prePersist() {
+		ByteBuffer keyBuffer = ByteBuffer.allocate(500);
+		for (DSRowQualifier<?> dsq : this.getRowQualifiers()) {
+			dsq.putKey(keyBuffer);
+		}
+
+		byte[] array = keyBuffer.array();
+		this.md5 = DigestUtils.md5(array);
+		this.sha1 = DigestUtils.sha1(array);
+	}
+
 	@Override
 	public Long getId() {
 		return this.id;
@@ -53,11 +80,11 @@ public class DSRow implements EntityId {
 	public DS getDataset() {
 		return dataset;
 	}
-	
+
 	public void setDataset(DS dataset) {
 		this.dataset = dataset;
 	}
-	
+
 	public List<DSRowQualifier<?>> getRowQualifiers() {
 		return rowQualifiers;
 	}

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

 package org.genesys2.server.model.dataset;
 
+import java.nio.ByteBuffer;
+
 import javax.persistence.DiscriminatorColumn;
 import javax.persistence.DiscriminatorType;
 import javax.persistence.Entity;
@@ -14,6 +16,16 @@ import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
 
+/**
+ * Abstract class {@link DSRowQualifier} represents the "columns" of a
+ * {@link DSRow} that serve as "keys" or qualifying columns to a row. A row may
+ * have more than one qualifier and are not necessarily unique, but provide a
+ * fast mechanism to look up values in a row ({@link DSValue}).
+ * 
+ * @author Matija Obreza
+ *
+ * @param <T> type of qualifier value
+ */
 @Entity
 @Table(name = "ds2rowqualifier", indexes = { @Index(columnList = "dsq, vall") })
 @Inheritance(strategy = InheritanceType.SINGLE_TABLE)
@@ -70,4 +82,5 @@ public abstract class DSRowQualifier<T> {
 		return null;
 	}
 
+	public abstract void putKey(ByteBuffer keyBuffer);
 }

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

 package org.genesys2.server.model.dataset;
 
+import java.nio.ByteBuffer;
+
 import javax.persistence.Column;
 import javax.persistence.DiscriminatorValue;
 import javax.persistence.Entity;
@@ -20,5 +22,9 @@ public class DSRowQualifierLong extends DSRowQualifier<Long> {
 	public void setValue(Long value) {
 		this.value = value;
 	}
-
+	
+	@Override
+	public void putKey(ByteBuffer keyBuffer) {
+		keyBuffer.putLong(this.value);	
+	}
 }

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

@@ -15,7 +15,7 @@ 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") })
+@Table(name = "ds2value", indexes = { @Index(columnList = "r,dsc"), @Index(columnList = "dsc,vall"), @Index(columnList = "dsc,vald") })
 @Inheritance(strategy = InheritanceType.SINGLE_TABLE)
 @DiscriminatorColumn(discriminatorType = DiscriminatorType.INTEGER, name = "typ")
 public abstract class DSValue<T> {
@@ -28,8 +28,8 @@ public abstract class DSValue<T> {
 	private DSRow row;
 
 	@ManyToOne(fetch=FetchType.LAZY, optional = false)
-	@JoinColumn(name = "dsd")
-	private DSDescriptor datasetDescriptor;
+	@JoinColumn(name = "dsc")
+	private DSColumn datasetColumn;
 
 	public abstract T getValue();
 
@@ -51,12 +51,12 @@ public abstract class DSValue<T> {
 		this.row = row;
 	}
 
-	public DSDescriptor getDatasetDescriptor() {
-		return datasetDescriptor;
+	public DSColumn getDatasetColumn() {
+		return datasetColumn;
 	}
 
-	public void setDatasetDescriptor(DSDescriptor datasetDescriptor) {
-		this.datasetDescriptor = datasetDescriptor;
+	public void setDatasetColumn(DSColumn datasetColumn) {
+		this.datasetColumn = datasetColumn;
 	}
 
 	public static DSValue<?> make(Object v) {

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

@@ -21,12 +21,15 @@ import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.JoinColumn;
 import javax.persistence.OneToOne;
+import javax.persistence.PrePersist;
+import javax.persistence.PreUpdate;
 import javax.persistence.Table;
 import javax.persistence.Version;
 
 import org.apache.commons.lang.StringUtils;
 import org.genesys.blocks.auditlog.annotations.Audited;
 import org.genesys.blocks.model.BasicModel;
+import org.genesys.worldclim.WorldClimUtil;
 import org.genesys2.server.model.impl.GeoReferencedEntity;
 
 @Entity
@@ -57,6 +60,15 @@ public class AccessionGeo extends BasicModel implements GeoReferencedEntity, Acc
 
 	private Long tileIndex;
 
+	/**
+	 * Recalculate {@link #tileIndex} on insert and update
+	 */
+	@PrePersist
+	@PreUpdate
+	private void prePersist() {
+		tileIndex = WorldClimUtil.getTileIndex(5, this.longitude, this.latitude);
+	}
+	
 	public long getVersion() {
 		return version;
 	}

src/main/java/org/genesys2/server/model/impl/Descriptor.java

-/**
- * Copyright 2014 Global Crop Diversity Trust
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- **/
-
-package org.genesys2.server.model.impl;
-
-import java.text.MessageFormat;
-import java.util.UUID;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.Lob;
-import javax.persistence.PrePersist;
-import javax.persistence.Table;
-
-import org.genesys.blocks.model.BasicModel;
-import org.hibernate.annotations.Type;
-
-/**
- * A Descriptor represents a dimension of a sparse vector.
- *
- * @author mobreza
- */
-@Entity
-@Table(name = "descriptor")
-public class Descriptor extends BasicModel {
-	private static final long serialVersionUID = 3832200593904442940L;
-
-	@Column(unique = true, nullable=false, updatable = false)
-	@Type(type = "uuid-binary")
-	private UUID uuid;
-
-	@Lob
-	@Type(type = "org.hibernate.type.TextType")
-	private String title;
-
-	@Column(nullable = false, length = 200)
-	private String code;
-
-	@Lob
-	@Type(type = "org.hibernate.type.TextType")
-	private String description;
-
-	@Column(length = 20)
-	private String uom;
-
-	/**
-	 * 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 String getTitle() {
-		return title;
-	}
-
-	public void setTitle(String title) {
-		this.title = title;
-	}
-
-	public String getCode() {
-		return code;
-	}
-
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public String getDescription() {
-		return description;
-	}
-
-	public void setDescription(final String description) {
-		this.description = description;
-	}
-
-	public String getUom() {
-		return uom;
-	}
-
-	public void setUom(String uom) {
-		this.uom = uom;
-	}
-
-	@Override
-	public String toString() {
-		return MessageFormat.format("Descriptor id={0,number,#} name={1}", getId(), code);