EVA-3503 Created new endpoint to search contig by MD5 checksum (#127)

* add end-point for getting chromosomes using md5checksum
EBIvariation · Feb 15, 2024 · 7b23066 · 7b23066
1 parent edd5c2e
commit 7b23066
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diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/controller/contigalias/ContigAliasController.java b/src/main/java/uk/ac/ebi/eva/contigalias/controller/contigalias/ContigAliasController.java
@@ -322,6 +322,21 @@ public ResponseEntity<PagedModel<EntityModel<SequenceEntity>>> getSequencesBySeq
 
     }
 
+    @ApiOperation(value = "Get a list of chromosomes using their MD5 checksum. ",
+            notes = "Given a chromosome's MD5 checksum, this endpoint will return a list of chromosomes that are " +
+                    "associated with the MD5 checksum provided. This endpoint returns a list containing one or more chromosomes. " +
+                    "It also accepts two additional parameters (page and size) to control pagination of results. " +
+                    "If the page number and/or page size are invalid then an HTTP status code of 416 is returned by this endpoint.")
+    @GetMapping(value = "chromosomes/md5checksum/{md5Checksum}", produces = "application/json")
+    public ResponseEntity<PagedModel<EntityModel<SequenceEntity>>> getSequencesByMD5Checksum(
+            @PathVariable @ApiParam(value = "MD5 Checksum of chromosome Eg: 7b6e06758e53927330346e9e7cc00cce") String md5Checksum,
+            @RequestParam(required = false, name = "page") @ApiParam(value = PAGE_NUMBER_DESCRIPTION) Integer pageNumber,
+            @RequestParam(required = false, name = "size") @ApiParam(value = PAGE_SIZE_DESCRIPTION) Integer pageSize) {
+        PageRequest pageRequest = createPageRequest(pageNumber, pageSize);
+        PagedModel<EntityModel<SequenceEntity>> pagedModel = handler.getSequencesByMD5Checksum(md5Checksum, pageRequest);
+        return createAppropriateResponseEntity(pagedModel);
+    }
+
     private void linkPagedModelGetAssemblyByAuthority(
             String accession, String authority, PagedModel pagedModel) {
         ResponseEntity<PagedModel<EntityModel<AssemblyEntity>>> method;

diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/controller/contigalias/ContigAliasHandler.java b/src/main/java/uk/ac/ebi/eva/contigalias/controller/contigalias/ContigAliasHandler.java
@@ -165,6 +165,11 @@ public PagedModel<EntityModel<SequenceEntity>> getSequencesByName(
         return generatePagedModelFromPage(createSequencePage(chrPage), sequenceAssembler);
     }
 
+    public PagedModel<EntityModel<SequenceEntity>> getSequencesByMD5Checksum(String md5Checksum, Pageable request) {
+        Page<ChromosomeEntity> chrPage = chromosomeService.getChromosomesByMD5Checksum(md5Checksum, request);
+        return generatePagedModelFromPage(createSequencePage(chrPage), sequenceAssembler);
+    }
+
     private Page<SequenceEntity> createSequencePage(Page<? extends SequenceEntity> page) {
         return new PageImpl<>(page.getContent().stream().map(e -> (SequenceEntity)e)
                 .collect(Collectors.toList()), page.getPageable(), page.getTotalElements());

diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/repo/ChromosomeRepository.java b/src/main/java/uk/ac/ebi/eva/contigalias/repo/ChromosomeRepository.java
@@ -88,6 +88,8 @@ Page<ChromosomeEntity> findChromosomeEntitiesByAssemblyInsdcAccessionOrAssemblyR
 
     Page<ChromosomeEntity> findChromosomeEntitiesByUcscName(String ucscName, Pageable request);
 
+    Page<ChromosomeEntity> findChromosomeEntitiesByMd5checksumOrderByInsdcAccession(String md5Checksum, Pageable request);
+
     long countChromosomeEntitiesByInsdcAccession(String insdcAccession);
 
     long countChromosomeEntitiesByRefseq(String refseq);

diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/service/ChromosomeService.java b/src/main/java/uk/ac/ebi/eva/contigalias/service/ChromosomeService.java
@@ -173,6 +173,11 @@ public Page<ChromosomeEntity> getChromosomesByEnaNameAndAssembly(
         return injectAssemblyIntoChromosomes(page, assembly);
     }
 
+    public Page<ChromosomeEntity> getChromosomesByMD5Checksum(String md5Checksum, Pageable request) {
+        Page<ChromosomeEntity> chrPage = repository.findChromosomeEntitiesByMd5checksumOrderByInsdcAccession(md5Checksum, request);
+        return stripChromosomesAndScaffoldsFromAssembly(chrPage);
+    }
+
     private Page<ChromosomeEntity> injectAssemblyIntoChromosomes(Page<ChromosomeEntity> page, AssemblyEntity assembly) {
         if (page != null && page.getTotalElements() > 0) {
             page.forEach(it -> it.setAssembly(assembly));

diff --git a/src/test/java/uk/ac/ebi/eva/contigalias/service/ChromosomeServiceIntegrationTest.java b/src/test/java/uk/ac/ebi/eva/contigalias/service/ChromosomeServiceIntegrationTest.java
@@ -25,14 +25,16 @@
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.test.context.ActiveProfiles;
-
+import uk.ac.ebi.eva.contigalias.entities.AssemblyEntity;
 import uk.ac.ebi.eva.contigalias.entities.ChromosomeEntity;
 import uk.ac.ebi.eva.contigalias.entitygenerator.AssemblyGenerator;
 import uk.ac.ebi.eva.contigalias.entitygenerator.ChromosomeGenerator;
 import uk.ac.ebi.eva.contigalias.repo.ChromosomeRepository;
 
 import java.util.Collections;
+import java.util.Comparator;
 import java.util.List;
+import java.util.stream.Collectors;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -115,6 +117,58 @@ void testUpdateMD5ChecksumForAllChromosomesInAssembly() {
 
     }
 
+    @Test
+    void testGetChromosomesByMD5Checksum() {
+        String testMD5Checksum = "test-MD5-checksum";
+
+        AssemblyEntity assemblyEntity = AssemblyGenerator.generate();
+        ChromosomeEntity chromosomeWithMD5 = ChromosomeGenerator.generate(assemblyEntity);
+        chromosomeWithMD5.setMd5checksum(testMD5Checksum);
+        chromosomeRepository.save(chromosomeWithMD5);
+
+        Page<ChromosomeEntity> chrPage = service.getChromosomesByMD5Checksum(testMD5Checksum, Pageable.unpaged());
+        List<ChromosomeEntity> chromosomeList = chrPage.getContent();
+
+        assertEquals(1, chromosomeList.size());
+        assertChromosomesIdentical(chromosomeWithMD5, chromosomeList.get(0));
+        assertEquals(testMD5Checksum, chromosomeList.get(0).getMd5checksum());
+        assertEquals(assemblyEntity.getInsdcAccession(), chromosomeList.get(0).getAssembly().getInsdcAccession());
+    }
+
+    @Test
+    void testGetMultipleChromosomesByMD5ChecksumInDifferentAssemblies() {
+        String testMD5Checksum = "test-MD5-checksum";
+
+        AssemblyEntity assemblyEntity1 = AssemblyGenerator.generate();
+        assemblyEntity1.setInsdcAccession("assembly1");
+        ChromosomeEntity chromosomeWithMD51 = ChromosomeGenerator.generate(assemblyEntity1);
+        chromosomeWithMD51.setInsdcAccession("chromosome1");
+        chromosomeWithMD51.setMd5checksum(testMD5Checksum);
+        chromosomeRepository.save(chromosomeWithMD51);
+
+        AssemblyEntity assemblyEntity2 = AssemblyGenerator.generate();
+        assemblyEntity2.setInsdcAccession("assembly2");
+        ChromosomeEntity chromosomeWithMD52 = ChromosomeGenerator.generate(assemblyEntity2);
+        chromosomeWithMD52.setInsdcAccession("chromosome2");
+        chromosomeWithMD52.setMd5checksum(testMD5Checksum);
+        chromosomeRepository.save(chromosomeWithMD52);
+
+        Page<ChromosomeEntity> chrPage = service.getChromosomesByMD5Checksum(testMD5Checksum, Pageable.unpaged());
+
+        List<ChromosomeEntity> chromosomeList = chrPage.getContent().stream()
+                .sorted(Comparator.comparing(c -> c.getInsdcAccession()))
+                .collect(Collectors.toList());
+        assertEquals(2, chromosomeList.size());
+
+        assertEquals(testMD5Checksum, chromosomeList.get(0).getMd5checksum());
+        assertChromosomesIdentical(chromosomeWithMD51, chromosomeList.get(0));
+        assertEquals("assembly1", chromosomeList.get(0).getAssembly().getInsdcAccession());
+
+        assertEquals(testMD5Checksum, chromosomeList.get(1).getMd5checksum());
+        assertChromosomesIdentical(chromosomeWithMD52, chromosomeList.get(1));
+        assertEquals("assembly2", chromosomeList.get(1).getAssembly().getInsdcAccession());
+    }
+
     void assertChromosomePageIdenticalToEntity(Page<ChromosomeEntity> page) {
         assertNotNull(page);
         assertTrue(page.getTotalElements() > 0);
@@ -129,4 +183,12 @@ void assertChromosomeIdenticalToEntity(ChromosomeEntity chromosomeEntity) {
         assertEquals(entity.getEnaSequenceName(), chromosomeEntity.getEnaSequenceName());
     }
 
+    void assertChromosomesIdentical(ChromosomeEntity chromosomeEntity1, ChromosomeEntity chromosomeEntity2) {
+        assertEquals(chromosomeEntity1.getGenbankSequenceName(), chromosomeEntity2.getGenbankSequenceName());
+        assertEquals(chromosomeEntity1.getInsdcAccession(), chromosomeEntity2.getInsdcAccession());
+        assertEquals(chromosomeEntity1.getRefseq(), chromosomeEntity2.getRefseq());
+        assertEquals(chromosomeEntity1.getUcscName(), chromosomeEntity2.getUcscName());
+        assertEquals(chromosomeEntity1.getEnaSequenceName(), chromosomeEntity2.getEnaSequenceName());
+    }
+
 }