Merge pull request #1465 from phac-nml/get_sample_by_name

deprecated getSampleBySequencerId, added getSampleBySampleName

CHANGELOG.md

@@ -14,6 +14,7 @@
 * [Developer/UI]: Fix for updating sample modified date when metadata is deleted. See [PR 1457](https://github.com/phac-nml/irida/pull/1457).
 * [Developer]: Added support for cloud based storage. Currently, Microsoft Azure Blob and Amazon AWS S3 are supported. [See PR 1194](https://github.com/phac-nml/irida/pull/1194)
 * [Developer]: Updated metadata uploader to use react-router-dom Outlet. [See PR 1464](https://github.com/phac-nml/irida/pull/1464)
+* [Developer]: Deprecated "/api/projects/{projectId}/samples/bySequencerId/{seqeuncerId}" in favour of "/api/projects/{projectId}/samples/bySampleName", which accepts a json property "sampleName"
 
 ## [22.09.7] - 2022/01/24
 * [UI]: Fixed bugs on NCBI Export page preventing the NCBI `submission.xml` file from being properly written. See [PR 1451](https://github.com/phac-nml/irida/pull/1451)

src/main/java/ca/corefacility/bioinformatics/irida/web/controller/api/projects/RESTProjectSamplesController.java

@@ -243,6 +243,7 @@ public ResponseResource<ResourceCollection<Sample>> getProjectSamples(@PathVaria
 	 * @param seqeuncerId the string id of the sample
 	 * @return The found sample
 	 */
+	@Deprecated()
 	@RequestMapping(value = "/api/projects/{projectId}/samples/bySequencerId/{seqeuncerId}", method = RequestMethod.GET)
 	public ModelAndView getProjectSampleBySequencerId(@PathVariable Long projectId, @PathVariable String seqeuncerId) {
 		Project p = projectService.read(projectId);
@@ -258,6 +259,28 @@ public ModelAndView getProjectSampleBySequencerId(@PathVariable Long projectId,
 		return new ModelAndView(redirectView);
 	}
 
+	/**
+	 * Get samples by a given string name
+	 *
+	 * @param projectId   the Project to get samples from
+	 * @param sampleName  String containing sample name
+	 * @return The found sample
+	 */
+	@RequestMapping(value = "/api/projects/{projectId}/samples/bySampleName", method = RequestMethod.GET)
+	public ModelAndView getProjectSampleBySampleName(@PathVariable Long projectId, @RequestParam String sampleName) {
+		Project p = projectService.read(projectId);
+
+		Sample sampleBySampleName = sampleService.getSampleBySampleName(p, sampleName);
+
+		Link withSelfRel = linkTo(
+				methodOn(RESTProjectSamplesController.class).getSample(sampleBySampleName.getId())).withSelfRel();
+		String href = withSelfRel.getHref();
+
+		RedirectView redirectView = new RedirectView(href);
+
+		return new ModelAndView(redirectView);
+	}
+
 	/**
 	 * Get the representation of a specific sample that's associated with the
 	 * project.

src/test/java/ca/corefacility/bioinformatics/irida/web/controller/test/integration/project/ProjectSamplesIT.java

@@ -1,9 +1,6 @@
 package ca.corefacility.bioinformatics.irida.web.controller.test.integration.project;
 
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Random;
+import java.util.*;
 import java.util.concurrent.*;
 
 import org.apache.http.HttpResponse;
@@ -388,4 +385,31 @@ public void testReadSamplesAsSequencer() {
 				.when()
 				.get(projectSamplesUri);
 	}
+
+	@Test
+	public void testReadSampleByName() {
+		String rootUri = uriTemplateHandler.getRootUri() + "/api";
+		String projectUri = rootUri + "/projects/5";
+		String sampleByNameUri = projectUri + "/samples/bySampleName?sampleName=sample1";
+		String expectedSampleUri = rootUri + "/samples/1";
+
+		final Response r = asAdmin().expect()
+				.body("resource.links.rel", hasItems("self", "sample/sequenceFiles"))
+				.when()
+				.get(sampleByNameUri);
+		final String responseBody = r.getBody().asString();
+		final String selfUri = from(responseBody).get("resource.links.find{it.rel == 'self'}.href");
+		assertEquals(expectedSampleUri, selfUri);
+	}
+
+	@Test
+	public void testReadSampleByNameError() {
+		String projectUri = uriTemplateHandler.getRootUri() + "/api/projects/5";
+		String sampleByNameUri = projectUri + "/samples/bySampleName?sampleName=not_a_sample";
+
+		asAdmin().expect()
+				.statusCode(equalTo(404))
+				.when()
+				.get(sampleByNameUri);
+	}
 }

src/test/java/ca/corefacility/bioinformatics/irida/web/controller/test/unit/projects/RESTProjectSamplesControllerTest.java

@@ -34,6 +34,8 @@
 import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
 import com.google.common.net.HttpHeaders;
+import org.springframework.web.servlet.ModelAndView;
+import org.springframework.web.servlet.view.RedirectView;
 
 import static org.junit.jupiter.api.Assertions.*;
 import static org.mockito.Mockito.*;
@@ -190,6 +192,25 @@ public void testGetProjectSample() throws IOException {
 
 	}
 
+	@Test
+	public void testGetProjectSampleByName() throws IOException {
+		Project p = TestDataFactory.constructProject();
+		Sample s = TestDataFactory.constructSample();
+
+		// mock out the service calls
+		when(projectService.read(p.getId())).thenReturn(p);
+		when(sampleService.getSampleBySampleName(p, s.getSampleName())).thenReturn(s);
+
+		String sampleLocation = "http://localhost/api/samples/" + s.getId();
+
+		ModelAndView responseObject = controller.getProjectSampleBySampleName(p.getId(), s.getSampleName());
+
+		verify(sampleService).getSampleBySampleName(p, s.getSampleName());
+
+		RedirectView rv = (RedirectView) responseObject.getView();
+		assertEquals(sampleLocation, rv.getUrl());
+	}
+
 	@Test
 	public void testUpdateSample() {
 		Sample s = TestDataFactory.constructSample();