Merge pull request #1484 from apetkau/fix/sync-old-irida

hotfix/sync old irida

CHANGELOG.md

@@ -5,6 +5,7 @@
 * [UI]: Fixed bug that caused all metadata fields to be removed when single field was removed from a template. See [PR 1482](https://github.com/phac-nml/irida/pull/1482)
 * [Developer]: Fixed bug which allowed duplicated entries in the user_group_project table which prevented the user group from being removed. Fixed bug which was preventing analyses with `html` file outputs from completing. See [PR 1483](https://github.com/phac-nml/irida/pull/1483)
 * [Developer]: Fixed flaky PipelinesPhylogenomicsPageIT test. See [PR 1482](https://github.com/phac-nml/irida/pull/1482)
+* [REST]: Fixed issues with syncing between newer IRIDA (>22.09) and older IRIDA (<=20.09) by disabling requests for `application/xml` for some of the REST requests and only requesting data as `application/json`. See [PR 1484](https://github.com/phac-nml/irida/pull/1484).
 
 
 ## [23.01.1] - 2023/03/21

src/main/java/ca/corefacility/bioinformatics/irida/repositories/remote/impl/ProjectRemoteRepositoryImpl.java

@@ -1,5 +1,6 @@
 package ca.corefacility.bioinformatics.irida.repositories.remote.impl;
 
+import com.google.common.collect.ImmutableList;
 import ca.corefacility.bioinformatics.irida.exceptions.LinkNotFoundException;
 import ca.corefacility.bioinformatics.irida.model.RemoteAPI;
 import ca.corefacility.bioinformatics.irida.model.project.Project;
@@ -11,10 +12,12 @@
 import ca.corefacility.bioinformatics.irida.service.user.UserService;
 import ca.corefacility.bioinformatics.irida.web.assembler.resource.ProjectHashResource;
 import ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController;
+import org.springframework.http.MediaType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.ParameterizedTypeReference;
 import org.springframework.hateoas.Link;
 import org.springframework.http.HttpEntity;
+import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpMethod;
 import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Repository;
@@ -64,8 +67,12 @@ public Integer readProjectHash(Project project) {
 		OAuthTokenRestTemplate restTemplate = new OAuthTokenRestTemplate(tokenService, remoteAPI);
 		Link link = project.getLink(HASH_REL).map(i -> i).orElse(null);
 
+		HttpHeaders headers = new HttpHeaders();
+		headers.setAccept(ImmutableList.of(MediaType.APPLICATION_JSON));
+		HttpEntity<Object> request = new HttpEntity<Object>(headers);
+
 		ResponseEntity<ResourceWrapper<ProjectHashResource>> exchange = restTemplate.exchange(link.getHref(),
-				HttpMethod.GET, HttpEntity.EMPTY, projectHashReference);
+				HttpMethod.GET, request, projectHashReference);
 
 		Integer projectHash = exchange.getBody().getResource().getProjectHash();
 

src/main/java/ca/corefacility/bioinformatics/irida/repositories/remote/impl/RemoteRepositoryImpl.java

@@ -2,10 +2,13 @@
 
 import java.util.List;
 
+import com.google.common.collect.ImmutableList;
+import org.springframework.http.MediaType;
 import org.springframework.core.ParameterizedTypeReference;
 import org.springframework.http.HttpEntity;
 import org.springframework.http.HttpMethod;
 import org.springframework.http.HttpStatus;
+import org.springframework.http.HttpHeaders;
 import org.springframework.http.ResponseEntity;
 import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;
 import org.springframework.security.core.Authentication;
@@ -64,7 +67,12 @@ public RemoteRepositoryImpl(RemoteAPITokenService tokenService, UserService user
 	@Override
 	public Type read(String uri, RemoteAPI remoteAPI) {
 		OAuthTokenRestTemplate restTemplate = new OAuthTokenRestTemplate(tokenService, remoteAPI);
-		ResponseEntity<ResourceWrapper<Type>> exchange = restTemplate.exchange(uri, HttpMethod.GET, HttpEntity.EMPTY,
+
+		HttpHeaders headers = new HttpHeaders();
+		headers.setAccept(ImmutableList.of(MediaType.APPLICATION_JSON));
+		HttpEntity<Object> request = new HttpEntity<Object>(headers);
+
+		ResponseEntity<ResourceWrapper<Type>> exchange = restTemplate.exchange(uri, HttpMethod.GET, request,
 				objectTypeReference);
 
 		Type resource = exchange.getBody().getResource();
@@ -79,8 +87,13 @@ public Type read(String uri, RemoteAPI remoteAPI) {
 	@Override
 	public List<Type> list(String uri, RemoteAPI remoteAPI) {
 		OAuthTokenRestTemplate restTemplate = new OAuthTokenRestTemplate(tokenService, remoteAPI);
+
+		HttpHeaders headers = new HttpHeaders();
+		headers.setAccept(ImmutableList.of(MediaType.APPLICATION_JSON));
+		HttpEntity<Object> request = new HttpEntity<Object>(headers);
+
 		ResponseEntity<ListResourceWrapper<Type>> exchange = restTemplate.exchange(uri, HttpMethod.GET,
-				HttpEntity.EMPTY, listTypeReference);
+				request, listTypeReference);
 
 		List<Type> resources = exchange.getBody().getResource().getResources();
 		for (Type r : resources) {
@@ -95,7 +108,12 @@ public List<Type> list(String uri, RemoteAPI remoteAPI) {
 	@Override
 	public boolean getServiceStatus(RemoteAPI remoteAPI) {
 		OAuthTokenRestTemplate restTemplate = new OAuthTokenRestTemplate(tokenService, remoteAPI);
-		ResponseEntity<String> forEntity = restTemplate.getForEntity(remoteAPI.getServiceURI(), String.class);
+
+		HttpHeaders headers = new HttpHeaders();
+		headers.setAccept(ImmutableList.of(MediaType.APPLICATION_JSON));
+		HttpEntity<Object> request = new HttpEntity<Object>(headers);
+
+		ResponseEntity<String> forEntity = restTemplate.exchange(remoteAPI.getServiceURI(), HttpMethod.GET, request, String.class);
 
 		return forEntity.getStatusCode() == HttpStatus.OK;
 	}

src/main/java/ca/corefacility/bioinformatics/irida/repositories/remote/impl/SampleRemoteRepositoryImpl.java

@@ -3,12 +3,15 @@
 import java.util.List;
 import java.util.Map;
 
+import com.google.common.collect.ImmutableList;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.http.MediaType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.ParameterizedTypeReference;
 import org.springframework.hateoas.Link;
 import org.springframework.http.HttpEntity;
+import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpMethod;
 import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Repository;
@@ -74,9 +77,13 @@ public Map<String, MetadataEntry> getSampleMetadata(Sample sample) {
 		// get the metadata link
 		Link metadataLink = sample.getLink(METADATA_REL).map(i -> i).orElse(null);
 
+		HttpHeaders headers = new HttpHeaders();
+		headers.setAccept(ImmutableList.of(MediaType.APPLICATION_JSON));
+		HttpEntity<Object> request = new HttpEntity<Object>(headers);
+
 		// request metadata response
 		ResponseEntity<ResourceWrapper<SampleMetadataWrapper>> exchange = restTemplate.exchange(metadataLink.getHref(),
-				HttpMethod.GET, HttpEntity.EMPTY, metadataTypeReference);
+				HttpMethod.GET, request, metadataTypeReference);
 
 		// pull metadata response from request
 		Map<String, MetadataEntry> resource = exchange.getBody().getResource().getMetadata();