Merge pull request #1137 from ericenns/spring-hateoas-1.0

Spring hateoas 1.0

CHANGELOG.md

@@ -11,6 +11,7 @@ Changes
 * [UI]: Refactored share/move samples between projects to use a separate page.
 * [UI]: Added capability to share/move samples between projects from the line list page.
 * [UI]: Fixed issue with dynamic pipeline parameters with only one value not rendering.
+* [Developer]: Upgraded Spring Hateoas to 1.0.3.RELEASE
 
 21.05 to 21.09
 --------------

pom.xml

@@ -1160,7 +1160,7 @@
 		<commons.fileupload.version>1.3.1</commons.fileupload.version>
 		<javax.el-api.version>3.0.0</javax.el-api.version>
 		<javax.servlet-api.version>3.1.0</javax.servlet-api.version>
-		<spring.hateoas.version>0.19.0.RELEASE</spring.hateoas.version>
+		<spring.hateoas.version>1.0.3.RELEASE</spring.hateoas.version>
 		<el.ri.version>1.0</el.ri.version>
 		<oltu.version>1.0.0</oltu.version>
 		<thymeleaf.version>3.0.9.RELEASE</thymeleaf.version>

src/main/java/ca/corefacility/bioinformatics/irida/model/IridaResourceSupport.java → src/main/java/ca/corefacility/bioinformatics/irida/model/IridaRepresentationModel.java

@@ -2,11 +2,13 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Optional;
 
 import javax.xml.bind.annotation.XmlElement;
 
+import org.springframework.hateoas.IanaLinkRelations;
 import org.springframework.hateoas.Link;
-import org.springframework.hateoas.ResourceSupport;
+import org.springframework.hateoas.RepresentationModel;
 import org.springframework.util.Assert;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
@@ -17,15 +19,15 @@
 
 /**
  * Adds a collection of {@link Link}s to extending objects. Similar to
- * {@link ResourceSupport}
+ * {@link RepresentationModel}
  * 
- * @see ResourceSupport
+ * @see RepresentationModel
  *
  */
-public class IridaResourceSupport {
+public class IridaRepresentationModel {
 	private final List<Link> links;
 
-	public IridaResourceSupport() {
+	public IridaRepresentationModel() {
 		this.links = new ArrayList<Link>();
 	}
 
@@ -98,15 +100,15 @@ public void removeLinks() {
 	 *            the String rel to get a link for
 	 * @return the link with the given rel or {@literal null} if none found.
 	 */
-	public Link getLink(String rel) {
+	public Optional<Link> getLink(String rel) {
 
 		for (Link link : links) {
-			if (link.getRel().equals(rel)) {
-				return link;
+			if (link.getRel().value().equals(rel)) {
+				return Optional.of(link);
 			}
 		}
 
-		return null;
+		return Optional.empty();
 	}
 
 	/**
@@ -131,7 +133,7 @@ public boolean equals(Object obj) {
 			return false;
 		}
 
-		IridaResourceSupport that = (IridaResourceSupport) obj;
+		IridaRepresentationModel that = (IridaRepresentationModel) obj;
 
 		return this.links.equals(that.links);
 	}
@@ -152,11 +154,8 @@ public int hashCode() {
 	 */
 	@JsonIgnore
 	public String getSelfHref() {
-		Link link = getLink(Link.REL_SELF);
-		if (link != null) {
-			return link.getHref();
-		}
-		return null;
+		Optional<Link> link = getLink(IanaLinkRelations.SELF.value());
+		return link.map(i -> i.getHref()).orElse(null);
 	}
 
 	/**

src/main/java/ca/corefacility/bioinformatics/irida/model/assembly/GenomeAssembly.java

@@ -16,7 +16,7 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.data.annotation.CreatedDate;
 
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 import ca.corefacility.bioinformatics.irida.model.IridaThing;
 import ca.corefacility.bioinformatics.irida.model.VersionedFileFields;
 import ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile;
@@ -33,7 +33,7 @@
 @Table(name = "genome_assembly")
 @Inheritance(strategy = InheritanceType.JOINED)
 @Audited
-public abstract class GenomeAssembly extends IridaResourceSupport
+public abstract class GenomeAssembly extends IridaRepresentationModel
 		implements IridaThing, IridaSequenceFile, VersionedFileFields<Long> {
 
 	private static final Logger logger = LoggerFactory.getLogger(GenomeAssembly.class);

src/main/java/ca/corefacility/bioinformatics/irida/model/project/Project.java

@@ -1,6 +1,6 @@
 package ca.corefacility.bioinformatics.irida.model.project;
 
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 import ca.corefacility.bioinformatics.irida.model.MutableIridaThing;
 import ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission;
 import ca.corefacility.bioinformatics.irida.model.event.ProjectEvent;
@@ -40,7 +40,7 @@
 @Table(name = "project")
 @Audited
 @EntityListeners(AuditingEntityListener.class)
-public class Project extends IridaResourceSupport
+public class Project extends IridaRepresentationModel
 		implements MutableIridaThing, Comparable<Project>, RemoteSynchronizable {
 
 	@Id

src/main/java/ca/corefacility/bioinformatics/irida/model/remote/resource/ListResourceWrapper.java

@@ -1,16 +1,16 @@
 package ca.corefacility.bioinformatics.irida.model.remote.resource;
 
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 
 /**
  * Object wrapping a list of returned resources from a remote IRIDA API. This
  * type will be returned when listing objects from the API. Example: "/projects"
  * 
  * @param <Type>
  *            The type of object being stored in the list extends
- *            {@link IridaResourceSupport}
+ *            {@link IridaRepresentationModel}
  */
-public class ListResourceWrapper<Type extends IridaResourceSupport> {
+public class ListResourceWrapper<Type extends IridaRepresentationModel> {
 	private ResourceList<Type> resource;
 
 	public ResourceList<Type> getResource() {

src/main/java/ca/corefacility/bioinformatics/irida/model/remote/resource/ResourceList.java

@@ -2,15 +2,15 @@
 
 import java.util.List;
 
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 
 /**
  * Class to hold a list of resources when being read from a remote Irida API
  * 
  * @param <Type>
  *            The type of object being held in this list
  */
-public class ResourceList<Type extends IridaResourceSupport> extends IridaResourceSupport{
+public class ResourceList<Type extends IridaRepresentationModel> extends IridaRepresentationModel{
 
 	private List<Type> resources;
 	private Long totalResources;
@@ -20,31 +20,31 @@ public ResourceList() {
 
 	/**
 	 * Get the list of resources
-	 * @return the {@link IridaResourceSupport} collection.
+	 * @return the {@link IridaRepresentationModel} collection.
 	 */
 	public List<Type> getResources() {
 		return resources;
 	}
 
 	/**
 	 * Set the list of resources
-	 * @param resources the {@link IridaResourceSupport} collection.
+	 * @param resources the {@link IridaRepresentationModel} collection.
 	 */
 	public void setResources(List<Type> resources) {
 		this.resources = resources;
 	}
 
 	/**
 	 * Get the total number of resources in this list
-	 * @return the total number of {@link IridaResourceSupport} in the collection.
+	 * @return the total number of {@link IridaRepresentationModel} in the collection.
 	 */
 	public Long getTotalResources() {
 		return totalResources;
 	}
 
 	/**
 	 * Set the total number of resources
-	 * @param totalResources the total number of {@link IridaResourceSupport} in the collection.
+	 * @param totalResources the total number of {@link IridaRepresentationModel} in the collection.
 	 */
 	public void setTotalResources(Long totalResources) {
 		this.totalResources = totalResources;

src/main/java/ca/corefacility/bioinformatics/irida/model/remote/resource/ResourceWrapper.java

@@ -1,21 +1,21 @@
 package ca.corefacility.bioinformatics.irida.model.remote.resource;
 
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 
 /**
  * Object wrapping a resource read from an Irida API
  * 
  * @param <Type>
  *            The type this resource will hold (extends
- *            {@link IridaResourceSupport})
+ *            {@link IridaRepresentationModel})
  */
-public class ResourceWrapper<Type extends IridaResourceSupport> {
+public class ResourceWrapper<Type extends IridaRepresentationModel> {
 	private Type resource;
 
 	/**
 	 * Get the resource
 	 * 
-	 * @return the {@link IridaResourceSupport} wrapped by this object.
+	 * @return the {@link IridaRepresentationModel} wrapped by this object.
 	 */
 	public Type getResource() {
 		return resource;
@@ -25,7 +25,7 @@ public Type getResource() {
 	 * Set the resource
 	 * 
 	 * @param resource
-	 *            the {@link IridaResourceSupport} wrapped by this object.
+	 *            the {@link IridaRepresentationModel} wrapped by this object.
 	 */
 	public void setResource(Type resource) {
 		this.resource = resource;

src/main/java/ca/corefacility/bioinformatics/irida/model/run/SequencingRun.java

@@ -1,6 +1,6 @@
 package ca.corefacility.bioinformatics.irida.model.run;
 
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 import ca.corefacility.bioinformatics.irida.model.MutableIridaThing;
 import ca.corefacility.bioinformatics.irida.model.enums.SequencingRunUploadStatus;
 import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject;
@@ -26,7 +26,7 @@
 @Audited
 @Inheritance(strategy = InheritanceType.JOINED)
 @EntityListeners(AuditingEntityListener.class)
-public class SequencingRun extends IridaResourceSupport implements MutableIridaThing, Comparable<SequencingRun> {
+public class SequencingRun extends IridaRepresentationModel implements MutableIridaThing, Comparable<SequencingRun> {
 	@Id
 	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private Long id;

src/main/java/ca/corefacility/bioinformatics/irida/model/sample/Sample.java

@@ -16,7 +16,7 @@
 import org.springframework.data.annotation.LastModifiedDate;
 import org.springframework.data.jpa.domain.support.AuditingEntityListener;
 
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 import ca.corefacility.bioinformatics.irida.model.MutableIridaThing;
 import ca.corefacility.bioinformatics.irida.model.event.SampleAddedProjectEvent;
 import ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin;
@@ -51,7 +51,7 @@
 @Audited
 @EntityListeners(AuditingEntityListener.class)
 @JsonIgnoreProperties(ignoreUnknown = true)
-public class Sample extends IridaResourceSupport
+public class Sample extends IridaRepresentationModel
 		implements MutableIridaThing, Comparable<Sample>, RemoteSynchronizable {
 
 	@Id

src/main/java/ca/corefacility/bioinformatics/irida/model/sequenceFile/SequenceFile.java

@@ -37,7 +37,7 @@
 import org.springframework.data.jpa.domain.support.AuditingEntityListener;
 
 import ca.corefacility.bioinformatics.irida.exceptions.AnalysisAlreadySetException;
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 import ca.corefacility.bioinformatics.irida.model.MutableIridaThing;
 import ca.corefacility.bioinformatics.irida.model.VersionedFileFields;
 import ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile;
@@ -58,7 +58,7 @@
 @Table(name = "sequence_file")
 @Audited
 @EntityListeners({ AuditingEntityListener.class, RelativePathTranslatorListener.class })
-public class SequenceFile extends IridaResourceSupport
+public class SequenceFile extends IridaRepresentationModel
 		implements MutableIridaThing, Comparable<SequenceFile>, VersionedFileFields<Long>, IridaSequenceFile,
 		RemoteSynchronizable {
 

src/main/java/ca/corefacility/bioinformatics/irida/model/sequenceFile/SequencingObject.java

@@ -1,7 +1,7 @@
 package ca.corefacility.bioinformatics.irida.model.sequenceFile;
 
 import ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException;
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 import ca.corefacility.bioinformatics.irida.model.MutableIridaThing;
 import ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus;
 import ca.corefacility.bioinformatics.irida.model.remote.RemoteSynchronizable;
@@ -31,7 +31,7 @@
 @EntityListeners(AuditingEntityListener.class)
 @Audited
 @Inheritance(strategy = InheritanceType.JOINED)
-public abstract class SequencingObject extends IridaResourceSupport implements MutableIridaThing, RemoteSynchronizable {
+public abstract class SequencingObject extends IridaRepresentationModel implements MutableIridaThing, RemoteSynchronizable {
 
 	@Id
 	@GeneratedValue(strategy = GenerationType.IDENTITY)

src/main/java/ca/corefacility/bioinformatics/irida/model/user/User.java

@@ -23,7 +23,7 @@
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 import ca.corefacility.bioinformatics.irida.model.MutableIridaThing;
 import ca.corefacility.bioinformatics.irida.model.RemoteAPIToken;
 import ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin;
@@ -39,7 +39,7 @@
 		@UniqueConstraint(name = User.USER_USERNAME_CONSTRAINT_NAME, columnNames = "username") })
 @Audited
 @EntityListeners(AuditingEntityListener.class)
-public class User extends IridaResourceSupport implements MutableIridaThing, Comparable<User>, UserDetails {
+public class User extends IridaRepresentationModel implements MutableIridaThing, Comparable<User>, UserDetails {
 
 	private static final long serialVersionUID = -7516211470008791995L;
 

src/main/java/ca/corefacility/bioinformatics/irida/model/workflow/analysis/Analysis.java

@@ -26,7 +26,7 @@
 import javax.persistence.UniqueConstraint;
 import javax.validation.constraints.NotNull;
 
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 import ca.corefacility.bioinformatics.irida.model.IridaThing;
 import ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType;
 
@@ -42,7 +42,7 @@
 @Entity
 @Table(name = "analysis")
 @Inheritance(strategy = InheritanceType.JOINED)
-public class Analysis extends IridaResourceSupport implements IridaThing {
+public class Analysis extends IridaRepresentationModel implements IridaThing {
 
 	@Id
 	@GeneratedValue(strategy = GenerationType.IDENTITY)

src/main/java/ca/corefacility/bioinformatics/irida/model/workflow/analysis/AnalysisOutputFile.java

@@ -28,7 +28,7 @@
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.google.common.base.Strings;
 
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 import ca.corefacility.bioinformatics.irida.model.IridaThing;
 import ca.corefacility.bioinformatics.irida.model.VersionedFileFields;
 import ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository;
@@ -43,7 +43,7 @@
 @Entity
 @Table(name = "analysis_output_file")
 @EntityListeners(RelativePathTranslatorListener.class)
-public class AnalysisOutputFile extends IridaResourceSupport implements IridaThing, VersionedFileFields<Long> {
+public class AnalysisOutputFile extends IridaRepresentationModel implements IridaThing, VersionedFileFields<Long> {
 	private static final Logger logger = LoggerFactory.getLogger(AnalysisOutputFile.class);
 
 	@Id

src/main/java/ca/corefacility/bioinformatics/irida/model/workflow/analysis/JobError.java

@@ -11,7 +11,7 @@
 import org.hibernate.envers.Audited;
 import org.springframework.data.jpa.domain.support.AuditingEntityListener;
 
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 import ca.corefacility.bioinformatics.irida.model.IridaThing;
 import ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission;
 
@@ -30,7 +30,7 @@
 @Entity
 @Table(name = "job_error")
 @EntityListeners(AuditingEntityListener.class)
-public class JobError extends IridaResourceSupport implements IridaThing, Comparable<JobError> {
+public class JobError extends IridaRepresentationModel implements IridaThing, Comparable<JobError> {
 	@Id
 	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private final Long id;

src/main/java/ca/corefacility/bioinformatics/irida/model/workflow/submission/AbstractAnalysisSubmission.java

@@ -1,6 +1,6 @@
 package ca.corefacility.bioinformatics.irida.model.workflow.submission;
 
-import ca.corefacility.bioinformatics.irida.model.IridaResourceSupport;
+import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 import ca.corefacility.bioinformatics.irida.model.MutableIridaThing;
 import ca.corefacility.bioinformatics.irida.model.project.ReferenceFile;
 import ca.corefacility.bioinformatics.irida.model.user.User;
@@ -27,7 +27,7 @@
 @Inheritance(strategy = InheritanceType.SINGLE_TABLE)
 @Audited
 @EntityListeners(AuditingEntityListener.class)
-public abstract class AbstractAnalysisSubmission extends IridaResourceSupport implements MutableIridaThing {
+public abstract class AbstractAnalysisSubmission extends IridaRepresentationModel implements MutableIridaThing {
 	@Id
 	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	@Column(name = "id")