Subsets model and API

pom.xml

@@ -566,6 +566,7 @@
 							<includes>
 								<!-- List packages to be processed -->
 								<include>org.genesys2.server.model</include>
+								<include>org.genesys2.server.model.*</include>
 							</includes>
 							<outputDirectory>target/generated-sources/querydsl</outputDirectory>
 							<processor>com.querydsl.apt.jpa.JPAAnnotationProcessor</processor>

src/main/java/org/genesys2/server/service/worker/InvalidApiUsageException.java → src/main/java/org/genesys2/server/exception/InvalidApiUsageException.java

-/*
- * Copyright 2017 Global Crop Diversity Trust
+/**
+ * Copyright 2018 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.
@@ -12,8 +12,8 @@
  * 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.worker;
+ **/
+package org.genesys2.server.exception;
 
 /**
  * Parent exception for cases where data does not match business logic.

src/main/java/org/genesys2/server/exception/NotFoundElement.java

+/**
+ * Copyright 2018 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.exception;
+
+/**
+ * This exception should generate when some element not found somewhere.
+ * Example: some element not found in DB by ID or UUId.
+ *
+ * @author Andrey Lugovskoy.
+ */
+public class NotFoundElement extends InvalidApiUsageException {
+
+	private static final long serialVersionUID = 6621976491018091330L;
+
+	/**
+	 * Instantiates a new not found element.
+	 */
+	public NotFoundElement() {
+	}
+
+	/**
+	 * Instantiates a new not found element.
+	 *
+	 * @param message the message
+	 */
+	public NotFoundElement(final String message) {
+		super(message);
+	}
+
+	/**
+	 * Instantiates a new not found element.
+	 *
+	 * @param message the message
+	 * @param cause the cause
+	 */
+	public NotFoundElement(final String message, final Throwable cause) {
+		super(message, cause);
+	}
+
+	/**
+	 * Instantiates a new not found element.
+	 *
+	 * @param cause the cause
+	 */
+	public NotFoundElement(final Throwable cause) {
+		super(cause);
+	}
+
+}

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

+/**
+ * Copyright 2018 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 org.genesys.blocks.model.AuditedVersionedModel;
+import org.genesys.blocks.security.model.AclAwareModel;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.Lob;
+import javax.persistence.ManyToMany;
+import javax.persistence.PrePersist;
+import javax.persistence.Table;
+import java.util.List;
+import java.util.UUID;
+
+import org.genesys2.server.model.genesys.AccessionId;
+import org.hibernate.annotations.Type;
+
+@Entity
+@Table
+public class Subset extends AuditedVersionedModel implements AclAwareModel {
+
+    /** The Constant serialVersionUID. */
+    private static final long serialVersionUID = 7021405309572916429L;
+
+    @Column(unique = true, updatable = false, nullable = false, columnDefinition = "binary(16)")
+    protected UUID uuid;
+
+    @Column
+    protected boolean published;
+
+    @Column
+    protected String title;
+
+    @Column
+    @Lob
+    @Type(type = "org.hibernate.type.TextType")
+    protected String description;
+
+    @Column
+    protected String publisher;
+
+    @Column
+    protected String dateCreated;
+
+    @Column
+    protected String rights;
+
+    @ManyToMany(cascade = {}, fetch = FetchType.LAZY)
+    @JoinTable(name = "SubsetAccessions", joinColumns = @JoinColumn(name = "subsetId"), inverseJoinColumns = @JoinColumn(name = "acceId"))
+    private List<AccessionId> accessionIds;
+
+    /**
+     * Generate UUID if missing
+     */
+    @PrePersist
+    protected void prepersist() {
+        if (this.uuid == null) {
+            this.uuid = UUID.randomUUID();
+        }
+    }
+
+    /**
+     * Gets the uuid.
+     *
+     * @return the uuid
+     */
+    public UUID getUuid() {
+        return uuid;
+    }
+
+    /**
+     * Sets the uuid.
+     *
+     * @param uuid the new uuid
+     */
+    public void setUuid(final UUID uuid) {
+        this.uuid = uuid;
+    }
+
+    /**
+     * Checks if published.
+     *
+     * @return the published
+     */
+    public boolean isPublished() {
+        return published;
+    }
+
+    /**
+     * Sets the published.
+     *
+     * @param published the new published
+     */
+    public void setPublished(final boolean published) {
+        this.published = published;
+    }
+
+    /**
+     * Gets the subset title.
+     *
+     * @return the subset title
+     */
+    public String getTitle() {
+        return title;
+    }
+
+    /**
+     * Sets the subset title.
+     *
+     * @param title the new subset title
+     */
+    public void setTitle(final String title) {
+        this.title = title;
+    }
+
+    /**
+     * Gets the subset description.
+     *
+     * @return the subset description
+     */
+    public String getDescription() {
+        return description;
+    }
+
+    /**
+     * Sets the subset description.
+     *
+     * @param description the new descriptor list
+     */
+    public void setDescription(final String description) {
+        this.description = description;
+    }
+
+    /**
+     * Gets the subset publisher.
+     *
+     * @return the subset publisher
+     */
+    public String getPublisher() {
+        return publisher;
+    }
+
+    /**
+     * Sets the subset publisher.
+     *
+     * @param publisher the new subset publisher
+     */
+    public void setPublisher(final String publisher) {
+        this.publisher = publisher;
+    }
+
+    /**
+     * Gets the subset date created.
+     *
+     * @return the date created
+     */
+    public String getDateCreated() {
+        return dateCreated;
+    }
+
+    /**
+     * Sets the date created.
+     *
+     * @param dateCreated the new date created
+     */
+    public void setDateCreated(final String dateCreated) {
+        this.dateCreated = dateCreated;
+    }
+
+    /**
+     * Gets the subset rights.
+     *
+     * @return the subset rights
+     */
+    public String getRights() {
+        return rights;
+    }
+
+    /**
+     * Sets the subset rights.
+     *
+     * @param rights the new subset rights
+     */
+    public void setRights(final String rights) {
+        this.rights = rights;
+    }
+
+    /**
+     * Gets the accessionIds list.
+     *
+     * @return the accessionIds list
+     */
+    public List<AccessionId> getAccessionIds() {
+        return accessionIds;
+    }
+
+    /**
+     * Sets the accessionIds list.
+     *
+     * @param accessionIds the new accessionIds list
+     */
+    public void setAccessionIds(final List<AccessionId> accessionIds) {
+        this.accessionIds = accessionIds;
+    }
+}

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

@@ -18,6 +18,7 @@ package org.genesys2.server.persistence.domain;
 
 import java.util.Collection;
 import java.util.List;
+import java.util.UUID;
 
 import org.genesys2.server.model.genesys.AccessionId;
 import org.springframework.data.domain.Pageable;
@@ -35,4 +36,6 @@ public interface AccessionIdRepository extends JpaRepository<AccessionId, Long>
 	@Query("select id from AccessionId")
 	Collection<Long> findAllIds();
 
+	AccessionId findByUuid(UUID uuid);
+
 }

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

+/**
+ * Copyright 2018 Global Crop Diversity Trust
+ * <p/>
+ * 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
+ * <p/>
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * <p/>
+ * 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 java.util.UUID;
+
+import org.genesys2.server.model.impl.Subset;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.querydsl.QueryDslPredicateExecutor;
+import org.springframework.stereotype.Repository;
+
+/**
+ * The Class SubsetRepository.
+ *
+ * @author Maxym Borodenko
+ */
+@Repository
+public interface SubsetRepository extends JpaRepository<Subset, Long>, QueryDslPredicateExecutor<Subset> {
+
+    /**
+     * Gets the subset by uuid.
+     *
+     * @param uuid the uuid
+     * @return the subset by uuid
+     */
+    Subset getByUuid(UUID uuid);
+
+    /**
+     * Gets the record by uuid and version.
+     *
+     * @param uuid the uuid
+     * @param version the version
+     * @return the by uuid and version
+     */
+    Subset getByUuidAndVersion(UUID uuid, int version);
+}

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

+/**
+ * Copyright 2018 Global Crop Diversity Trust
+ * <p/>
+ * 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
+ * <p/>
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * <p/>
+ * 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;
+
+import java.util.Set;
+import java.util.UUID;
+
+import org.genesys2.server.model.impl.Subset;
+import org.genesys2.server.service.filter.SubsetFilter;
+import org.genesys2.server.servlet.controller.rest.model.AccessionHeaderJson;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
+
+/**
+ * @author Maxym Borodenko
+ */
+public interface SubsetService {
+
+    /**
+     * List published subsets matching the filter.
+     *
+     * @param filter filter data
+     * @param page Pageable
+     * @return list of Subset
+     */
+    Page<Subset> list(SubsetFilter filter, Pageable page);
+
+    /**
+     * Method creating Subset.
+     *
+     * @param subset new Subset
+     * @return saved Subset in db.
+     */
+    Subset create(Subset subset);
+
+    /**
+     * Load subset based on identifiers and version provided in the input.
+     *
+     * @param input query by example
+     * @return subset loaded from the database
+     */
+    Subset loadSubset(Subset input);
+
+    /**
+     * Load Subset.
+     *
+     * @param uuid the uuid
+     * @return the subset
+     */
+    Subset get(UUID uuid);
+
+    /**
+     * Load Subset.
+     *
+     * @param uuid the uuid
+     * @param version the version
+     * @return the subset
+     */
+    Subset get(UUID uuid, int version);
+
+    /**
+     * Method updating Subset.
+     *
+     * @param subset new Subset
+     * @return updated Subset in db.
+     */
+    Subset update(Subset subset);
+
+    /**
+     * Remove subset.
+     *
+     * @param subset subset
+     * @return removed subset
+     */
+    Subset delete(Subset subset);
+
+    /**
+     * Method removing preserved accessionIds from Subset.
+     *
+     * @param input current Subset
+     * @param accesionsUuid the accessions UUIDs
+     * @return updated Subset in db.
+     */
+    Subset removeAccessions(Subset input, Set<UUID> accesionsUuid);
+
+    /**
+     * Method adding new accessionId to Subset.
+     *
+     * @param input current Subset
+     * @param accessionIds the accessions IDs
+     * @return updated Subset in db.
+     */
+    Subset addAccessions(Subset input, Set<AccessionHeaderJson> accessionIds);
+
+}

src/main/java/org/genesys2/server/service/filter/SubsetFilter.java

+/**
+ * Copyright 2018 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.filter;
+
+import static org.genesys2.server.model.impl.QSubset.subset;
+
+import java.util.Set;
+
+import com.querydsl.core.BooleanBuilder;
+import com.querydsl.core.types.Predicate;
+import org.genesys.blocks.model.filters.AuditedVersionedModelFilter;
+import org.genesys.blocks.model.filters.StringFilter;
+
+/**
+ * The Class SubsetFilter.
+ *
+ * @author Maxym Borodenko
+ */
+public class SubsetFilter extends AuditedVersionedModelFilter {
+
+    /** The published. */
+    public Boolean published;
+
+    /** The title. */
+    public StringFilter title;
+
+    /** The description. */
+    public StringFilter description;
+
+    /** The publisher. */
+    public Set<String> publisher;
+
+    /** The date created. */
+    public StringFilter dateCreated;
+
+    /** The rights. */
+    public Set<String> rights;
+
+    /**
+     * Builds the query.
+     *
+     * @return the predicate
+     */
+    public Predicate buildQuery() {
+        final BooleanBuilder and = new BooleanBuilder();
+        super.buildQuery(subset._super, and);
+
+        if (published != null) {
+            and.and(subset.published.eq(published));
+        }
+        if (title != null) {
+            and.and(title.buildQuery(subset.title));
+        }
+        if (description != null) {
+            and.and(description.buildQuery(subset.description));
+        }
+        if ((publisher != null) && !publisher.isEmpty()) {
+            and.and(subset.publisher.in(publisher));
+        }
+        if (dateCreated != null) {
+            and.and(dateCreated.buildQuery(subset.dateCreated));
+        }
+        if ((rights != null) && !rights.isEmpty()) {
+            and.and(subset.rights.in(rights));
+        }
+        return and;
+    }
+}

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

+/**
+ * Copyright 2018 Global Crop Diversity Trust
+ * <p/>
+ * 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
+ * <p/>
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * <p/>
+ * 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 java.util.List;
+import java.util.Objects;
+import java.util.Set;
+import java.util.UUID;
+import java.util.stream.Collectors;
+
+import org.genesys.blocks.model.BasicModel;
+import org.genesys2.server.exception.NotFoundElement;
+import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.impl.Subset;
+import org.genesys2.server.persistence.domain.AccessionIdRepository;
+import org.genesys2.server.persistence.domain.AccessionRepository;
+import org.genesys2.server.persistence.domain.FaoInstituteRepository;
+import org.genesys2.server.persistence.domain.SubsetRepository;
+import org.genesys2.server.service.SubsetService;
+import org.genesys2.server.service.filter.SubsetFilter;
+import org.genesys2.server.servlet.controller.rest.model.AccessionHeaderJson;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.dao.ConcurrencyFailureException;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
+/**
+ * The Class SubsetServiceImpl.
+ *
+ * @author Maxym Borodenko
+ */
+@Service
+@Transactional(readOnly = true)
+public class SubsetServiceImpl implements SubsetService {
+
+	private static final Logger LOG = LoggerFactory.getLogger(SubsetServiceImpl.class);
+
+	@Autowired