Merge pull request #1208 from phac-nml/fix-sync-without-project-hash-rel

hotfix: Fixed syncing remote projects from version 20.09 and older.

CHANGELOG.md

@@ -5,6 +5,7 @@ Changes
 --------------
 * [REST]: Corrected behaviour of date fields in REST API to return epoch instead of textual string. (22.01.1)
 * [Documentation]: Fixed issue that prevented a user from saving analysis results back to a sample and concatenating sequence files. Fixed date format in Swagger REST API documentation. (22.01.2)
+* [REST]: Fixed bug that was preventing syncing remote projects from versions 20.09 and older. (22.01.3)
 
 21.09 to 22.01
 --------------

pom.xml

@@ -1,15 +1,16 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+		 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<parent>
 		<groupId>org.springframework.boot</groupId>
 		<artifactId>spring-boot-starter-parent</artifactId>
 		<version>2.6.3</version>
-		<relativePath />
+		<relativePath/>
 	</parent>
 	<groupId>ca.corefacility.bioinformatics</groupId>
 	<artifactId>irida</artifactId>
 	<packaging>war</packaging>
-	<version>22.01.2</version>
+	<version>22.01.3</version>
 	<name>irida</name>
 	<url>http://www.irida.ca</url>
 
@@ -587,7 +588,8 @@
 							<!--suppress UnresolvedMavenProperty -->
 							<argLine>${failsafeArgLine}</argLine>
 							<systemPropertyVariables>
-								<junit.platform.execution.listeners.deactivate>${exclude.test.listeners}</junit.platform.execution.listeners.deactivate>
+								<junit.platform.execution.listeners.deactivate>${exclude.test.listeners}
+								</junit.platform.execution.listeners.deactivate>
 								<spring.profiles.active>test</spring.profiles.active>
 								<irida.db.profile>it</irida.db.profile>
 							</systemPropertyVariables>
@@ -939,7 +941,8 @@
 		<liquibase.config.url>jdbc:mysql://localhost:3306/irida_test</liquibase.config.url>
 		<liquibase.config.username>test</liquibase.config.username>
 		<liquibase.config.password>test</liquibase.config.password>
-		<liquibase.config.changeLogFile>ca/corefacility/bioinformatics/irida/database/all-changes.xml</liquibase.config.changeLogFile>
+		<liquibase.config.changeLogFile>ca/corefacility/bioinformatics/irida/database/all-changes.xml
+		</liquibase.config.changeLogFile>
 
 		<!-- URL to a pre-populated SQLite database for Galaxy -->
 		<!-- Set to 'local' to use the local version stored in irida-api, or set 

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

@@ -19,13 +19,11 @@
 import ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus;
 
 /**
- * Adds a collection of {@link Link}s to extending objects. Similar to
- * {@link RepresentationModel}
- * 
- * @see RepresentationModel
+ * Adds a collection of {@link Link}s to extending objects. Similar to {@link RepresentationModel}
  *
+ * @see RepresentationModel
  */
-@JsonIgnoreProperties(ignoreUnknown = true, value = {"hibernateLazyInitializer"})
+@JsonIgnoreProperties(ignoreUnknown = true, value = { "hibernateLazyInitializer" })
 public class IridaRepresentationModel {
 	private final List<Link> links;
 
@@ -35,9 +33,8 @@ public IridaRepresentationModel() {
 
 	/**
 	 * Adds the given link to the resource.
-	 * 
-	 * @param link
-	 *            The link to add to the resource
+	 *
+	 * @param link The link to add to the resource
 	 */
 	public void add(Link link) {
 		Assert.notNull(link, "Link must not be null!");
@@ -46,9 +43,8 @@ public void add(Link link) {
 
 	/**
 	 * Adds all given {@link Link}s to the resource.
-	 * 
-	 * @param links
-	 *            The list of links to add to the resource
+	 *
+	 * @param links The list of links to add to the resource
 	 */
 	public void add(Iterable<Link> links) {
 		Assert.notNull(links, "Given links must not be null!");
@@ -59,7 +55,7 @@ public void add(Iterable<Link> links) {
 
 	/**
 	 * Returns whether the resource contains {@link Link}s at all.
-	 * 
+	 *
 	 * @return true/false whether the resource contains the link
 	 */
 	public boolean hasLinks() {
@@ -68,18 +64,17 @@ public boolean hasLinks() {
 
 	/**
 	 * Returns whether the resource contains a {@link Link} with the given rel.
-	 * 
-	 * @param rel
-	 *            The rel name to test
+	 *
+	 * @param rel The rel name to test
 	 * @return true/false if it has a link with the given rel
 	 */
 	public boolean hasLink(String rel) {
-		return getLink(rel) != null;
+		return getLink(rel).isPresent();
 	}
 
 	/**
 	 * Returns all {@link Link}s contained in this resource.
-	 * 
+	 *
 	 * @return The list of links for this resource
 	 */
 	@XmlElement(name = "link", namespace = Link.ATOM_NAMESPACE)
@@ -97,9 +92,8 @@ public void removeLinks() {
 
 	/**
 	 * Returns the link with the given rel.
-	 * 
-	 * @param rel
-	 *            the String rel to get a link for
+	 *
+	 * @param rel the String rel to get a link for
 	 * @return the link with the given rel or {@literal null} if none found.
 	 */
 	public Optional<Link> getLink(String rel) {
@@ -149,9 +143,8 @@ public int hashCode() {
 	}
 
 	/**
-	 * Convenience method for getting the self rel href for an object read from
-	 * a remote site
-	 * 
+	 * Convenience method for getting the self rel href for an object read from a remote site
+	 *
 	 * @return String href if available, null otherwise
 	 */
 	@JsonIgnore
@@ -161,21 +154,18 @@ public String getSelfHref() {
 	}
 
 	/**
-	 * Set the {@link RemoteStatus} for this object if it was read from a remote
-	 * source
-	 * 
-	 * @param status
-	 *            the {@link RemoteStatus} object
+	 * Set the {@link RemoteStatus} for this object if it was read from a remote source
+	 *
+	 * @param status the {@link RemoteStatus} object
 	 */
 	// TODO: Make these abstract
 	public void setRemoteStatus(RemoteStatus status) {
 
 	}
 
 	/**
-	 * Get the {@link RemoteStatus} for this object if it was read from a remote
-	 * source
-	 * 
+	 * Get the {@link RemoteStatus} for this object if it was read from a remote source
+	 *
 	 * @return a {@link RemoteStatus}
 	 */
 	@JsonIgnore

src/test/java/ca/corefacility/bioinformatics/irida/repositories/remote/impl/ProjectRemoteRepositoryImplTest.java

@@ -0,0 +1,40 @@
+package ca.corefacility.bioinformatics.irida.repositories.remote.impl;
+
+import java.util.Optional;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import ca.corefacility.bioinformatics.irida.exceptions.LinkNotFoundException;
+import ca.corefacility.bioinformatics.irida.model.project.Project;
+import ca.corefacility.bioinformatics.irida.repositories.remote.ProjectRemoteRepository;
+import ca.corefacility.bioinformatics.irida.service.RemoteAPITokenService;
+import ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController;
+
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+public class ProjectRemoteRepositoryImplTest {
+
+	private ProjectRemoteRepository projectRemoteRepository;
+	private RemoteAPITokenService tokenService;
+	private static final String PROJECT_HASH_REL = RESTProjectsController.PROJECT_HASH_REL;
+
+	@BeforeEach
+	public void setUp() {
+		tokenService = mock(RemoteAPITokenService.class);
+		projectRemoteRepository = new ProjectRemoteRepositoryImpl(tokenService);
+	}
+
+	@Test
+	public void testReadProjectHashWithoutProjectHashRel() {
+		Project remoteProject = mock(Project.class);
+
+		when(remoteProject.getLink(PROJECT_HASH_REL)).thenReturn(Optional.empty());
+
+		assertThrows(LinkNotFoundException.class, () -> {
+			projectRemoteRepository.readProjectHash(remoteProject);
+		});
+	}
+}