GRIN taxonomy model and initial tests

pom.xml

@@ -497,6 +497,12 @@
 			<artifactId>spring-data-jpa</artifactId>
 			<version>1.4.4.RELEASE</version>
 		</dependency>
+		<dependency>
+			<groupId>org.jamel.dbf</groupId>
+			<artifactId>dbf-reader</artifactId>
+			<version>0.1.0</version>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 
 	<build>

src/main/java/org/genesys2/server/model/VersionedModel.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;
+
+import javax.persistence.MappedSuperclass;
+import javax.persistence.Version;
+
+@MappedSuperclass
+public abstract class VersionedModel extends BusinessModel {
+	private static final long serialVersionUID = 8415401512360230669L;
+
+	@Version
+	private long version = 0;
+
+	public long getVersion() {
+		return version;
+	}
+
+	public void setVersion(long version) {
+		this.version = version;
+	}
+}

src/main/java/org/genesys2/server/model/impl/GrinTaxonomy.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.util.Date;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+import org.genesys2.server.model.VersionedModel;
+
+/**
+ * GRIN taxonomy based on "species 2.dbf" from
+ * http://www.ars-grin.gov/misc/tax/species.zip
+ * 
+ * @author matijaobreza
+ */
+@Entity
+public class GrinTaxonomy extends VersionedModel {
+
+	@Column(unique = true, nullable = false)
+	private Long taxno;
+
+	@Column(nullable = true)
+	private Long validTaxNo;
+
+	@Column(length = 30)
+	private String genus;
+	private Character sHybrid;
+	@Column(length = 30)
+	private String species;
+	@Column(length = 100)
+	private String sAuthor;
+	private Character sSpHybrid;
+
+	@Column(length = 30)
+	private String subSp;
+	@Column(length = 100)
+	private String subSpAuthor;
+	private Character varHybrid;
+	@Column(length = 30)
+	private String var;
+	@Column(length = 100)
+	private String varAuthor;
+	private Character svHybrid;
+	@Column(length = 30)
+	private String subVar;
+	@Column(length = 100)
+	private String svAuthor;
+	private Character fHybrid;
+	@Column(length = 30)
+	private String forma;
+	@Column(length = 100)
+	private String fAuthor;
+
+	@Column(length = 240)
+	private String protologue;
+	@Column(length = 254)
+	private String taxcmt;
+
+	@Temporal(TemporalType.DATE)
+	private Date createdDate;
+	@Temporal(TemporalType.DATE)
+	private Date modifiedDate;
+	@Temporal(TemporalType.DATE)
+	private Date verifiedDate;
+
+	public Long getTaxno() {
+		return taxno;
+	}
+
+	public void setTaxno(Long taxno) {
+		this.taxno = taxno;
+	}
+
+	public Long getValidTaxNo() {
+		return validTaxNo;
+	}
+
+	public void setValidTaxNo(Long validTaxNo) {
+		this.validTaxNo = validTaxNo;
+	}
+
+	public String getGenus() {
+		return genus;
+	}
+
+	public void setGenus(String genus) {
+		this.genus = genus;
+	}
+
+	public Character getsHybrid() {
+		return sHybrid;
+	}
+
+	public void setsHybrid(Character sHybrid) {
+		this.sHybrid = sHybrid;
+	}
+
+	public String getSpecies() {
+		return species;
+	}
+
+	public void setSpecies(String species) {
+		this.species = species;
+	}
+
+	public String getsAuthor() {
+		return sAuthor;
+	}
+
+	public void setsAuthor(String sAuthor) {
+		this.sAuthor = sAuthor;
+	}
+
+	public Character getsSpHybrid() {
+		return sSpHybrid;
+	}
+
+	public void setsSpHybrid(Character sSpHybrid) {
+		this.sSpHybrid = sSpHybrid;
+	}
+
+	public String getSubSp() {
+		return subSp;
+	}
+
+	public void setSubSp(String subSp) {
+		this.subSp = subSp;
+	}
+
+	public String getSubSpAuthor() {
+		return subSpAuthor;
+	}
+
+	public void setSubSpAuthor(String subSpAuthor) {
+		this.subSpAuthor = subSpAuthor;
+	}
+
+	public Character getVarHybrid() {
+		return varHybrid;
+	}
+
+	public void setVarHybrid(Character varHybrid) {
+		this.varHybrid = varHybrid;
+	}
+
+	public String getVar() {
+		return var;
+	}
+
+	public void setVar(String var) {
+		this.var = var;
+	}
+
+	public String getVarAuthor() {
+		return varAuthor;
+	}
+
+	public void setVarAuthor(String varAuthor) {
+		this.varAuthor = varAuthor;
+	}
+
+	public Character getSvHybrid() {
+		return svHybrid;
+	}
+
+	public void setSvHybrid(Character svHybrid) {
+		this.svHybrid = svHybrid;
+	}
+
+	public String getSubVar() {
+		return subVar;
+	}
+
+	public void setSubVar(String subVar) {
+		this.subVar = subVar;
+	}
+
+	public String getSvAuthor() {
+		return svAuthor;
+	}
+
+	public void setSvAuthor(String svAuthor) {
+		this.svAuthor = svAuthor;
+	}
+
+	public Character getfHybrid() {
+		return fHybrid;
+	}
+
+	public void setfHybrid(Character fHybrid) {
+		this.fHybrid = fHybrid;
+	}
+
+	public String getForma() {
+		return forma;
+	}
+
+	public void setForma(String forma) {
+		this.forma = forma;
+	}
+
+	public String getfAuthor() {
+		return fAuthor;
+	}
+
+	public void setfAuthor(String fAuthor) {
+		this.fAuthor = fAuthor;
+	}
+
+	public String getProtologue() {
+		return protologue;
+	}
+
+	public void setProtologue(String protologue) {
+		this.protologue = protologue;
+	}
+
+	public String getTaxcmt() {
+		return taxcmt;
+	}
+
+	public void setTaxcmt(String taxcmt) {
+		this.taxcmt = taxcmt;
+	}
+
+	public Date getCreatedDate() {
+		return createdDate;
+	}
+
+	public void setCreatedDate(Date createdDate) {
+		this.createdDate = createdDate;
+	}
+
+	public Date getModifiedDate() {
+		return modifiedDate;
+	}
+
+	public void setModifiedDate(Date modifiedDate) {
+		this.modifiedDate = modifiedDate;
+	}
+
+	public Date getVerifiedDate() {
+		return verifiedDate;
+	}
+
+	public void setVerifiedDate(Date verifiedDate) {
+		this.verifiedDate = verifiedDate;
+	}
+
+}

src/test/java/org/genesys2/server/test/GRINTaxonomyTest.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.test;
+
+import java.io.File;
+import java.util.Date;
+
+import org.jamel.dbf.processor.DbfProcessor;
+import org.jamel.dbf.processor.DbfRowProcessor;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Value;
+
+/**
+ * Test DBF reader of GRIN Taxonomy data from http://www.ars-grin.gov/misc/tax/
+ * 
+ * @author matijaobreza
+ */
+@Ignore
+public class GRINTaxonomyTest {
+
+	@Value("${download.files.dir}")
+	private String filesDir = "./data";
+
+	// @Test
+	public void dbInfoTest() {
+		String dbfInfo = DbfProcessor.readDbfInfo(new File("genusno.dbf"));
+		System.out.println(dbfInfo);
+	}
+
+	/**
+	 * Common names
+	 */
+	// @Test
+	public void testCommon() {
+		File dbf = new File("common.dbf");
+		String dbfInfo = DbfProcessor.readDbfInfo(dbf);
+		System.out.println(dbfInfo);
+
+		DbfProcessor.processDbf(dbf, new DbfRowProcessor() {
+			@Override
+			public void processRow(Object[] row) {
+				System.out.print(new String((byte[]) row[0]).trim());
+				System.out.print(", ");
+				System.out.print(((Number) row[1]).longValue());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[2]).trim());
+				System.out.println();
+			}
+		});
+	}
+
+	@Test
+	public void testSpecies() {
+		File dbf = new File(filesDir, "species 2.dbf");
+		String dbfInfo = DbfProcessor.readDbfInfo(dbf);
+		System.out.println(dbfInfo);
+
+		DbfProcessor.processDbf(dbf, new DbfRowProcessor() {
+			@Override
+			public void processRow(Object[] row) {
+				// if (! "Zea".equals(new String((byte[]) row[3]).trim())) {
+				// return;
+				// }
+				// if ("".equals(new String((byte[]) row[4]).trim()) ||
+				// "".equals(new String((byte[]) row[8]).trim()) ) {
+				// return;
+				// }
+				System.out.print(((Number) row[0]).longValue());
+				System.out.print(", ");
+				System.out.print(((Number) row[1]).longValue());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[3]).trim());
+				System.out.print(", 4=");
+				System.out.print(new String((byte[]) row[4]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[5]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[6]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[7]).trim());
+				System.out.print(", SUB >> ");
+				System.out.print(new String((byte[]) row[8]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[9]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[10]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[11]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[12]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[13]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[14]).trim());
+				System.out.print(", ");
+
+				System.out.print(new String((byte[]) row[15]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[16]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[17]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[18]).trim());
+				System.out.print(", ");
+
+				System.out.print(new String((byte[]) row[20]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[21]).trim());
+				System.out.print(", ");
+
+				System.out.print((Date) row[24]);
+				System.out.print(", ");
+				System.out.print((Date) row[25]);
+				System.out.println();
+			}
+		});
+	}
+
+	// @Test
+	public void testGenusno() {
+		File dbf = new File("genusno.dbf");
+		String dbfInfo = DbfProcessor.readDbfInfo(dbf);
+		System.out.println(dbfInfo);
+
+		DbfProcessor.processDbf(dbf, new DbfRowProcessor() {
+			@Override
+			public void processRow(Object[] row) {
+				System.out.print(new String((byte[]) row[0]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[1]).trim());
+				System.out.print(", ");
+				System.out.print(((Number) row[2]).longValue());
+				System.out.print(", ");
+				System.out.print(((Number) row[3]).longValue());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[4]).trim());
+				System.out.println();
+			}
+		});
+	}
+
+	// @Test
+	public void testTaxonno() {
+		File dbf = new File("taxonno.dbf");
+		String dbfInfo = DbfProcessor.readDbfInfo(dbf);
+		System.out.println(dbfInfo);
+
+		DbfProcessor.processDbf(dbf, new DbfRowProcessor() {
+			@Override
+			public void processRow(Object[] row) {
+				System.out.print(new String((byte[]) row[0]).trim());
+				System.out.print(", ");
+				System.out.print(new String((byte[]) row[1]).trim());
+				System.out.print(", ");
+				System.out.print(((Number) row[2]).longValue());
+				System.out.print(", ");
+				System.out.print(((Number) row[3]).longValue());
+				System.out.println();
+			}
+		});
+	}
+}