Merge branch 'hotfix-assemblies-not-available' into release-20.09.2

CHANGELOG.md

@@ -8,6 +8,7 @@ Changes
 * [UI]: Added two additional fields to SISTR viewer describing the number of alleles found (20.09.1)
 * [UI]: Fixed bug where users could not see or connect to Remote APIs (20.09.2)
 * [UI]: Fixed bug on project page where incorrect link to Remote API was displayed. (20.09.2)
+* [REST]: Added handling for synchronizing data from older IRIDA instances.  It was failing for APIs without assembly functionality addded in 20.09. (20.09.2)
 
 20.05 to 20.09
 --------------

src/main/java/ca/corefacility/bioinformatics/irida/exceptions/LinkNotFoundException.java

@@ -0,0 +1,11 @@
+package ca.corefacility.bioinformatics.irida.exceptions;
+
+/**
+ * Exception thrown when there is no link for a given rel when reading from an API
+ */
+public class LinkNotFoundException extends RuntimeException {
+
+	public LinkNotFoundException(String message) {
+		super(message);
+	}
+}

src/main/java/ca/corefacility/bioinformatics/irida/service/remote/GenomeAssemblyRemoteService.java

@@ -1,5 +1,6 @@
 package ca.corefacility.bioinformatics.irida.service.remote;
 
+import ca.corefacility.bioinformatics.irida.exceptions.LinkNotFoundException;
 import ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly;
 import ca.corefacility.bioinformatics.irida.model.assembly.UploadedAssembly;
 import ca.corefacility.bioinformatics.irida.model.sample.Sample;
@@ -15,8 +16,9 @@ public interface GenomeAssemblyRemoteService extends RemoteService<UploadedAssem
 	 *
 	 * @param sample the Sample to get assemblies for
 	 * @return a list of {@link UploadedAssembly}
+	 * @throws LinkNotFoundException if the targeted API does not support assemblies
 	 */
-	public List<UploadedAssembly> getGenomeAssembliesForSample(Sample sample);
+	public List<UploadedAssembly> getGenomeAssembliesForSample(Sample sample) throws LinkNotFoundException;
 
 	/**
 	 * Download the given {@link UploadedAssembly} to the local server

src/main/java/ca/corefacility/bioinformatics/irida/service/remote/ProjectSynchronizationService.java

@@ -1,6 +1,7 @@
 package ca.corefacility.bioinformatics.irida.service.remote;
 
 import ca.corefacility.bioinformatics.irida.exceptions.IridaOAuthException;
+import ca.corefacility.bioinformatics.irida.exceptions.LinkNotFoundException;
 import ca.corefacility.bioinformatics.irida.exceptions.ProjectSynchronizationException;
 import ca.corefacility.bioinformatics.irida.model.MutableIridaThing;
 import ca.corefacility.bioinformatics.irida.model.RemoteAPI;
@@ -36,6 +37,8 @@
 import java.util.*;
 import java.util.stream.Collectors;
 
+import com.google.common.collect.Lists;
+
 /**
  * Service class to run a project synchornization task. Ths class will be
  * responsible for communicating with Remote IRIDA installations and pulling
@@ -371,8 +374,15 @@ public List<ProjectSynchronizationException> syncSample(Sample sample, Project p
 			}
 		}
 
-		//list the remote assemblies for the sample
-		List<UploadedAssembly> genomeAssembliesForSample = assemblyRemoteService.getGenomeAssembliesForSample(sample);
+		//list the remote assemblies for the sample.
+		List<UploadedAssembly> genomeAssembliesForSample;
+		try {
+			genomeAssembliesForSample = assemblyRemoteService.getGenomeAssembliesForSample(sample);
+		} catch (LinkNotFoundException e) {
+			//if the target IRIDA doesn't support assemblies yet, warn and ignore assemblies.
+			logger.warn("The sample on the referenced IRIDA doesn't support assemblies: " + sample.getSelfHref());
+			genomeAssembliesForSample = Lists.newArrayList();
+		}
 
 		//for each assembly
 		for (UploadedAssembly file : genomeAssembliesForSample) {

src/main/java/ca/corefacility/bioinformatics/irida/service/remote/impl/GenomeAssemblyRemoteServiceImpl.java

@@ -6,6 +6,7 @@
 import org.springframework.hateoas.Link;
 import org.springframework.stereotype.Service;
 
+import ca.corefacility.bioinformatics.irida.exceptions.LinkNotFoundException;
 import ca.corefacility.bioinformatics.irida.model.RemoteAPI;
 import ca.corefacility.bioinformatics.irida.model.assembly.UploadedAssembly;
 import ca.corefacility.bioinformatics.irida.model.sample.Sample;
@@ -42,7 +43,10 @@ public GenomeAssemblyRemoteServiceImpl(GenomeAssemblyRemoteRepository repository
 	 * {@inheritDoc}
 	 */
 	@Override
-	public List<UploadedAssembly> getGenomeAssembliesForSample(Sample sample) {
+	public List<UploadedAssembly> getGenomeAssembliesForSample(Sample sample) throws LinkNotFoundException {
+		if (!sample.hasLink(SAMPLE_ASSEMBLY_REL)) {
+			throw new LinkNotFoundException("No link for rel: " + SAMPLE_ASSEMBLY_REL);
+		}
 		Link link = sample.getLink(SAMPLE_ASSEMBLY_REL);
 		String href = link.getHref();
 

src/test/java/ca/corefacility/bioinformatics/irida/service/ProjectSynchronizationServiceTest.java

@@ -3,6 +3,8 @@
 import java.util.Date;
 
 import ca.corefacility.bioinformatics.irida.exceptions.IridaOAuthException;
+import ca.corefacility.bioinformatics.irida.exceptions.LinkNotFoundException;
+import ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly;
 import ca.corefacility.bioinformatics.irida.model.assembly.UploadedAssembly;
 import ca.corefacility.bioinformatics.irida.service.impl.TestEmailController;
 import org.junit.Before;
@@ -188,6 +190,23 @@ public void testExistingSample(){
 		verify(projectService,times(0)).addSampleToProject(expired, sample, true);
 		verify(sampleService,times(2)).update(any(Sample.class));
 	}
+
+	@Test
+	public void testSyncSampleNoAssemblies() {
+		Sample sample = new Sample();
+		RemoteStatus sampleStatus = new RemoteStatus("http://sample",api);
+		sample.setRemoteStatus(sampleStatus);
+
+		when(sampleService.create(sample)).thenReturn(sample);
+		when(assemblyRemoteService.getGenomeAssembliesForSample(sample)).thenThrow(new LinkNotFoundException("no link"));
+
+		syncService.syncSample(sample, expired, Maps.newHashMap());
+
+		verify(projectService).addSampleToProject(expired, sample, true);
+		verify(assemblyRemoteService, times(0)).mirrorAssembly(any(UploadedAssembly.class));
+
+		assertEquals(SyncStatus.SYNCHRONIZED,sample.getRemoteStatus().getSyncStatus());
+	}
 
 	@Test
 	public void testSyncFiles() {