Dataset 2

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

+/**
+ * Copyright 2015 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 javax.persistence.Column;
+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.SequenceGenerator;
+import javax.persistence.Table;
+
+import org.genesys2.server.model.EntityId;
+import org.genesys2.server.model.genesys.Accession;
+
+/**
+ * A Descriptor represents a dimension of a sparse vector.
+ *
+ * @author mobreza
+ */
+@Entity(name = "datasetval")
+@Table(indexes = { @Index(name = "IX_datasetrow_dataset", unique = false, columnList = "datasetId, descriptorId, accessionId"),
+		@Index(name = "IX_datasetrow_accn", unique = false, columnList = "accessionId, descriptorId, datasetId") })
+@Inheritance(strategy = InheritanceType.TABLE_PER_CLASS)
+public abstract class DatasetRow<T> implements EntityId {
+	@Id
+	@GeneratedValue(strategy = GenerationType.SEQUENCE, generator = "datasetrow_seq")
+	@SequenceGenerator(name = "datasetrow_seq", sequenceName = "datasetrow_seq", allocationSize = 10)
+	@Column(name = "id", unique = true, nullable = false, length = 20)
+	protected Long id;
+
+	@ManyToOne(cascade = {}, optional = false)
+	@JoinColumn(name = "datasetId")
+	private Dataset dataset;
+
+	@ManyToOne(cascade = {}, optional = false)
+	@JoinColumn(name = "descriptorId")
+	private Descriptor descriptor;
+
+	@ManyToOne(cascade = {}, optional = true)
+	@JoinColumn(name = "accessionId")
+	private Accession accession;
+
+	@Override
+	public Long getId() {
+		return this.id;
+	}
+
+	public void setId(Long id) {
+		this.id = id;
+	}
+
+	public Dataset getDataset() {
+		return dataset;
+	}
+
+	public void setDataset(Dataset dataset) {
+		this.dataset = dataset;
+	}
+
+	public Descriptor getDescriptor() {
+		return descriptor;
+	}
+
+	public void setDescriptor(Descriptor descriptor) {
+		this.descriptor = descriptor;
+	}
+
+	public Accession getAccession() {
+		return accession;
+	}
+
+	public void setAccession(Accession accession) {
+		this.accession = accession;
+	}
+
+	public abstract T getVal();
+
+	public abstract void setVal(T val);
+}

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

+/**
+ * Copyright 2015 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 javax.persistence.Column;
+import javax.persistence.Entity;
+
+/**
+ * A Descriptor represents a dimension of a sparse vector.
+ *
+ * @author mobreza
+ */
+@Entity(name = "datasetdbl")
+public class TraitDblValue extends DatasetRow<Double> {
+
+	@Column(nullable = false, name="vald")
+	private Double val;
+
+	@Override
+	public Double getVal() {
+		return val;
+	}
+
+	@Override
+	public void setVal(Double val) {
+		this.val = val;
+	}
+
+}

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

+/**
+ * Copyright 2015 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 javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.Index;
+import javax.persistence.Table;
+
+/**
+ * A Descriptor represents a dimension of a sparse vector.
+ *
+ * @author mobreza
+ */
+@Entity(name = "datasetint")
+@Table(indexes={ @Index(name="IX_datasetint_val", unique=false, columnList="descriptorId, vali") }) 
+public class TraitIntValue extends DatasetRow<Integer> {
+	@Column(nullable = false, name="vali")
+	private Integer val;
+
+	@Override
+	public Integer getVal() {
+		return val;
+	}
+
+	@Override
+	public void setVal(Integer val) {
+		this.val=val;
+	}
+
+}

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

+/**
+ * Copyright 2015 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 javax.persistence.Column;
+import javax.persistence.Entity;
+
+/**
+ * A Descriptor represents a dimension of a sparse vector.
+ *
+ * @author mobreza
+ */
+@Entity(name = "datasetstr")
+public class TraitStrValue extends DatasetRow<String> {
+
+	@Column(nullable = false, name="vals")
+	private String val;
+
+	@Override
+	public String getVal() {
+		return val;
+	}
+
+	@Override
+	public void setVal(String val) {
+		this.val = val;
+	}
+
+}

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

+/**
+ * Copyright 2015 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.persistence.domain;
+
+import org.genesys2.server.model.impl.Dataset;
+import org.genesys2.server.model.impl.DatasetRow;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+public interface DatasetRowRepository extends JpaRepository<DatasetRow<?>, Long> {
+
+	Page<DatasetRow<?>> findByDataset(Dataset ds, Pageable page);
+}

src/main/java/org/genesys2/server/service/Dataset2Service.java

+/**
+ * Copyright 2015 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.service;
+
+public interface Dataset2Service {
+
+}

src/main/java/org/genesys2/server/service/impl/Dataset2ServiceImpl.java

+/**
+ * Copyright 2015 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.service.impl;
+
+import org.genesys2.server.service.Dataset2Service;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
+@Service
+@Transactional
+public class Dataset2ServiceImpl implements Dataset2Service {
+
+}

src/test/java/org/genesys2/server/service/impl/DatasetTest.java

+/**
+ * Copyright 2015 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.service.impl;
+
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.is;
+import static org.hamcrest.Matchers.notNullValue;
+import static org.hamcrest.Matchers.nullValue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.genesys2.server.model.impl.Dataset;
+import org.genesys2.server.model.impl.DatasetRow;
+import org.genesys2.server.model.impl.Descriptor;
+import org.genesys2.server.model.impl.TraitIntValue;
+import org.genesys2.server.model.impl.TraitStrValue;
+import org.genesys2.server.persistence.domain.DatasetRepository;
+import org.genesys2.server.persistence.domain.DatasetRowRepository;
+import org.genesys2.server.persistence.domain.DescriptorRepository;
+import org.genesys2.server.service.Dataset2Service;
+import org.genesys2.server.test.JpaDataConfig;
+import org.genesys2.server.test.PropertyPlacholderInitializer;
+import org.genesys2.spring.config.HazelcastConfig;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Import;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.test.context.ActiveProfiles;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.transaction.annotation.Transactional;
+
+import com.hazelcast.core.HazelcastInstance;
+import com.hazelcast.spring.cache.HazelcastCacheManager;
+
+@RunWith(SpringJUnit4ClassRunner.class)
+@ContextConfiguration(classes = DatasetTest.Config.class, initializers = PropertyPlacholderInitializer.class)
+@ActiveProfiles("dev")
+public class DatasetTest {
+
+	@Import({ HazelcastConfig.class, JpaDataConfig.class })
+	public static class Config {
+		@Bean
+		public HazelcastCacheManager cacheManager(HazelcastInstance hazelcastInstance) {
+			HazelcastCacheManager cm = new HazelcastCacheManager(hazelcastInstance);
+			return cm;
+		}
+
+		@Bean
+		public Dataset2Service dataset2Service() {
+			return new Dataset2ServiceImpl();
+		}
+
+	}
+
+	@Autowired
+	private Dataset2Service datasetService;
+
+	@Autowired
+	private DatasetRepository datasetRepository;
+
+	@Autowired
+	private DescriptorRepository descriptorRepository;
+	
+	@Autowired
+	private DatasetRowRepository datasetRowRepository;
+
+	@Test
+	public void test1() {
+		List<Dataset> x = datasetRepository.findAll();
+		System.err.println(x);
+	}
+	
+	@Test
+	@Transactional
+	public void test2() {
+		Dataset ds=new Dataset();
+		ds.setName("DS1");
+		datasetRepository.save(ds);
+		assertThat("Dataset ID was not assigned", ds.getId(), notNullValue());
+		
+		Dataset loaded = datasetRepository.getOne(ds.getId());
+		assertThat("Loaded ds not same as saved ds", loaded.getId(), is(ds.getId()));
+		
+		datasetRepository.delete(loaded);
+		loaded = datasetRepository.findOne(ds.getId());
+		assertThat("Expected null", loaded, nullValue());
+	}
+	
+	@Test
+	@Transactional
+	public void testInts() {
+		Dataset ds=new Dataset();
+		ds.setName("DS1");
+		datasetRepository.save(ds);
+		assertThat("Dataset ID was not assigned", ds.getId(), notNullValue());
+		
+		Descriptor intDescriptor=new Descriptor();
+		intDescriptor.setCode("INT");
+		intDescriptor.setTitle("Integer descriptor");
+		descriptorRepository.save(intDescriptor);
+		
+		List<TraitIntValue> vals=new ArrayList<TraitIntValue>();
+		for (int i=0; i<100; i++) {
+			TraitIntValue val = new TraitIntValue();
+			val.setDataset(ds);
+			val.setDescriptor(intDescriptor);
+			val.setVal(i);
+			vals.add(val);
+		}
+		datasetRowRepository.save(vals);
+		
+		Page<DatasetRow<?>> res = datasetRowRepository.findByDataset(ds, new PageRequest(0, 101));
+		assertThat("Expected non-null result", res, notNullValue());
+		assertThat("Expected 100 result entries", res.getContent(), hasSize(100));
+	
+		datasetRowRepository.delete(res);
+		descriptorRepository.delete(intDescriptor);
+		datasetRepository.delete(ds);
+		ds = datasetRepository.findOne(ds.getId());
+		assertThat("Expected null", ds, nullValue());
+	}
+	
+	
+
+	@Test
+	@Transactional
+	public void testStrs() {
+		Dataset ds=new Dataset();
+		ds.setName("DS1");
+		datasetRepository.save(ds);
+		assertThat("Dataset ID was not assigned", ds.getId(), notNullValue());
+		
+		Descriptor strDescriptor=new Descriptor();
+		strDescriptor.setCode("STR");
+		strDescriptor.setTitle("String descriptor");
+		descriptorRepository.save(strDescriptor);
+		
+		List<TraitStrValue> vals=new ArrayList<TraitStrValue>();
+		for (int i=0; i<100; i++) {
+			TraitStrValue val = new TraitStrValue();
+			val.setDataset(ds);
+			val.setDescriptor(strDescriptor);
+			val.setVal("Str " + i);
+			vals.add(val);
+		}
+		datasetRowRepository.save(vals);
+		
+		Page<DatasetRow<?>> res = datasetRowRepository.findByDataset(ds, new PageRequest(0, 101));
+		assertThat("Expected non-null result", res, notNullValue());
+		assertThat("Expected 100 result entries", res.getContent(), hasSize(100));
+	
+		datasetRowRepository.delete(res);
+		descriptorRepository.delete(strDescriptor);
+		datasetRepository.delete(ds);
+		ds = datasetRepository.findOne(ds.getId());
+		assertThat("Expected null", ds, nullValue());
+	}
+	
+
+
+	@Test
+	@Transactional
+	public void testStrsAndInts() {
+		Dataset ds=new Dataset();
+		ds.setName("DS1");
+		datasetRepository.save(ds);
+		assertThat("Dataset ID was not assigned", ds.getId(), notNullValue());
+		
+		Descriptor strDescriptor=new Descriptor();
+		strDescriptor.setCode("STR");
+		strDescriptor.setTitle("String descriptor");
+		descriptorRepository.save(strDescriptor);
+
+		List<TraitStrValue> vals=new ArrayList<TraitStrValue>();
+		for (int i=0; i<100; i++) {
+			TraitStrValue val = new TraitStrValue();
+			val.setDataset(ds);
+			val.setDescriptor(strDescriptor);
+			val.setVal("Str " + i);
+			vals.add(val);
+		}
+		datasetRowRepository.save(vals);
+		
+		Descriptor intDescriptor=new Descriptor();
+		intDescriptor.setCode("INT");
+		intDescriptor.setTitle("Integer descriptor");
+		descriptorRepository.save(intDescriptor);
+		List<TraitIntValue> iVals=new ArrayList<TraitIntValue>();
+		for (int i=0; i<100; i++) {
+			TraitIntValue val = new TraitIntValue();
+			val.setDataset(ds);
+			val.setDescriptor(intDescriptor);
+			val.setVal(i);
+			iVals.add(val);
+		}
+		datasetRowRepository.save(iVals);
+		
+		Page<DatasetRow<?>> res = datasetRowRepository.findByDataset(ds, new PageRequest(0, 201));
+		assertThat("Expected non-null result", res, notNullValue());
+		assertThat("Expected 200 result entries", res.getContent(), hasSize(200));
+
+		for (DatasetRow<?> row : res.getContent()) {
+			System.out.println(row.getId() + " " + row.getVal());
+		}
+		
+		datasetRowRepository.delete(res);
+		descriptorRepository.delete(intDescriptor);
+		descriptorRepository.delete(strDescriptor);
+		datasetRepository.delete(ds);
+		ds = datasetRepository.findOne(ds.getId());
+		assertThat("Expected null", ds, nullValue());
+	}
+}