added tests

src/main/java/uk/ac/ebi/eva/contigalias/conf/ContigAliasConfiguration.java

@@ -0,0 +1,14 @@
+package uk.ac.ebi.eva.contigalias.conf;
+
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.web.client.RestTemplate;
+
+@Configuration
+public class ContigAliasConfiguration {
+
+    @Bean
+    public RestTemplate getRestTemplate() {
+        return new RestTemplate();
+    }
+}

src/main/java/uk/ac/ebi/eva/contigalias/controller/admin/AdminController.java

@@ -28,6 +28,7 @@
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.RestController;
+import uk.ac.ebi.eva.contigalias.exception.AssemblyNotFoundException;
 
 import java.io.IOException;
 import java.util.List;
@@ -95,10 +96,16 @@ public ResponseEntity<?> fetchAndInsertAssemblyByAccession(
     public ResponseEntity<String> retrieveAndInsertMd5ChecksumForAssembly(@PathVariable(name = "accession")
                                                                           @ApiParam(value = "INSDC or RefSeq assembly accession. Eg: " +
                                                                                   "GCA_000001405.10") String asmAccession) {
-        handler.retrieveAndInsertMd5ChecksumForAssembly(asmAccession);
-        return ResponseEntity.ok("A task has been submitted for updating md5checksum for all chromosomes " +
-                "in assembly " + asmAccession + ". Depending upon the number of chromosomes present in assembly, " +
-                "this might take some time to complete");
+        try {
+            handler.getAssemblyByAccession(asmAccession);
+            handler.retrieveAndInsertMd5ChecksumForAssembly(asmAccession);
+            return ResponseEntity.ok("A task has been submitted for updating md5checksum for all chromosomes " +
+                    "in assembly " + asmAccession + ". Depending upon the number of chromosomes present in assembly, " +
+                    "this might take some time to complete");
+        } catch (AssemblyNotFoundException e) {
+            return ResponseEntity.ok("Could not find assembly " + asmAccession +
+                    ". Please insert the assembly first (md5checksum will be updated as part of the insertion process");
+        }
     }
 
     @ApiOperation(value = "Retrieve list of assemblies for which MD5 Checksum updates are running/going-to-run ")

src/main/java/uk/ac/ebi/eva/contigalias/controller/admin/AdminHandler.java

@@ -27,6 +27,7 @@
 import java.io.IOException;
 import java.util.List;
 import java.util.Map;
+import java.util.Optional;
 import java.util.Set;
 
 @Service
@@ -47,6 +48,10 @@ public AdminHandler(AssemblyService assemblyService,
         this.assemblyAssembler = assemblyAssembler;
     }
 
+    public Optional<AssemblyEntity> getAssemblyByAccession(String accession) {
+        return assemblyService.getAssemblyByAccession(accession);
+    }
+
     public void fetchAndInsertAssemblyByAccession(String accession) throws IOException {
         assemblyService.fetchAndInsertAssembly(accession);
     }

src/main/java/uk/ac/ebi/eva/contigalias/scheduler/Md5ChecksumRetriever.java

@@ -3,6 +3,7 @@
 import com.fasterxml.jackson.databind.JsonNode;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.retry.annotation.Backoff;
 import org.springframework.retry.annotation.Retryable;
 import org.springframework.stereotype.Component;
@@ -13,7 +14,13 @@ public class Md5ChecksumRetriever {
     private final Logger logger = LoggerFactory.getLogger(Md5ChecksumRetriever.class);
     private String INSDC_ACCESSION_PLACE_HOLDER = "INSDC_ACCESSION_PLACE_HOLDER";
     private String INSDC_CHECKSUM_URL = "https://www.ebi.ac.uk/ena/cram/sequence/insdc:" + INSDC_ACCESSION_PLACE_HOLDER + "/metadata";
-    private RestTemplate restTemplate = new RestTemplate();
+
+    private RestTemplate restTemplate;
+
+    @Autowired
+    public Md5ChecksumRetriever(RestTemplate restTemplate) {
+        this.restTemplate = restTemplate;
+    }
 
     @Retryable(value = Exception.class, maxAttempts = 5, backoff = @Backoff(delay = 2000, multiplier = 2))
     public String retrieveMd5Checksum(String insdcAccession) {

src/test/java/uk/ac/ebi/eva/contigalias/datasource/RetryTest.java

@@ -1,16 +1,20 @@
 package uk.ac.ebi.eva.contigalias.datasource;
 
+import com.fasterxml.jackson.databind.JsonNode;
 import org.apache.commons.net.ftp.FTPFile;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 import org.mockito.Mock;
 import org.mockito.Mockito;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
 import org.springframework.retry.annotation.EnableRetry;
 import org.springframework.test.context.TestPropertySource;
+import org.springframework.web.client.RestTemplate;
 import uk.ac.ebi.eva.contigalias.dus.NCBIBrowser;
 import uk.ac.ebi.eva.contigalias.exception.DownloadFailedException;
+import uk.ac.ebi.eva.contigalias.scheduler.Md5ChecksumRetriever;
 
 import java.io.IOException;
 import java.nio.file.Path;
@@ -20,6 +24,8 @@
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.eq;
 import static org.mockito.Mockito.times;
 import static org.mockito.Mockito.verify;
 import static org.mockito.Mockito.when;
@@ -38,6 +44,12 @@ public class RetryTest {
     @Autowired
     private NCBIAssemblyDataSource dataSource;
 
+    @Autowired
+    private Md5ChecksumRetriever md5ChecksumRetriever;
+
+    @MockBean
+    private RestTemplate restTemplate;
+
 
     @Test
     public void fileDownloadSuccessfulTest() throws IOException {
@@ -108,4 +120,20 @@ public void fileDownloadFailedRetryTest2() throws IOException {
         verify(ncbiBrowser, times(5)).getGenomeReportDirectory(mockAccession);
     }
 
+
+    @Test
+    public void retrieveMd5ChecksumRetry() {
+        String insdcAccession = "TEST_ACCESSION";
+        when(restTemplate.getForObject(anyString(), eq(JsonNode.class)))
+                .thenThrow(new RuntimeException("Simulated network issue"));
+
+        Md5ChecksumRetriever anotherObjSpy = Mockito.spy(md5ChecksumRetriever);
+        RuntimeException thrown = Assertions.assertThrows(RuntimeException.class, () -> {
+            anotherObjSpy.retrieveMd5Checksum(insdcAccession);
+        });
+
+        assertEquals("Simulated network issue", thrown.getMessage());
+        verify(restTemplate, times(5)).getForObject(anyString(), eq(JsonNode.class));
+    }
+
 }

src/test/java/uk/ac/ebi/eva/contigalias/entitygenerator/ChromosomeGenerator.java

@@ -40,7 +40,7 @@ public static ChromosomeEntity generate(long id) {
                 .setRefseq("refseq" + id)
                 .setUcscName("ucsc" + id)
                 .setEnaSequenceName("ena" + id)
-                .setMd5checksum("md5" + id)
+                .setMd5checksum(null)
                 .setTrunc512checksum("trunc512" + id)
                 .setAssembly(null);
     }
@@ -80,7 +80,7 @@ void generateTest() {
         assertTrue(entity.getInsdcAccession().endsWith(sId));
         assertTrue(entity.getRefseq().endsWith(sId));
         assertTrue(entity.getUcscName().endsWith(sId));
-        assertTrue(entity.getMd5checksum().endsWith(sId));
+        assertEquals(null, entity.getMd5checksum());
         assertTrue(entity.getTrunc512checksum().endsWith(sId));
         assertNull(entity.getAssembly());
     }

src/test/java/uk/ac/ebi/eva/contigalias/service/ChromosomeServiceIntegrationTest.java

@@ -22,13 +22,17 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.data.domain.Page;
+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.ChromosomeEntity;
 import uk.ac.ebi.eva.contigalias.entitygenerator.AssemblyGenerator;
 import uk.ac.ebi.eva.contigalias.entitygenerator.ChromosomeGenerator;
 
+import java.util.Collections;
+import java.util.List;
+
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
@@ -80,6 +84,31 @@ void putChromosomeChecksumsByAccession() {
         });
     }
 
+    @Test
+    void testGetAssemblyWhereChromosomeMd5ChecksumIsNullOrEmpty() {
+        List<String> asmList = service.getAssembliesWhereChromosomeMd5ChecksumIsNull();
+        assertEquals(entity.getAssembly().getInsdcAccession(), asmList.get(0));
+    }
+
+    @Test
+    void testGetChromosomesByAssemblyInsdcAccessionWhereMd5ChecksumIsNull() {
+        Page<ChromosomeEntity> chrPage = service.getChromosomesByAssemblyInsdcAccessionWhereMd5ChecksumIsNull(entity.getAssembly().getInsdcAccession(), PageRequest.of(0, 100));
+        assertChromosomePageIdenticalToEntity(chrPage);
+        assertEquals(null, chrPage.getContent().get(0).getMd5checksum());
+    }
+
+    @Test
+    void testUpdateMD5ChecksumForAllChromosomesInAssembly() {
+        String testMD5Checksum = "testmd5checksum";
+        entity.setMd5checksum(testMD5Checksum);
+        service.updateMd5ChecksumForAll(Collections.singletonList(entity));
+
+        Page<ChromosomeEntity> chrPage = service.getChromosomesByInsdcAccession(entity.getInsdcAccession(), Pageable.unpaged());
+        assertChromosomePageIdenticalToEntity(chrPage);
+        assertEquals(testMD5Checksum, chrPage.getContent().get(0).getMd5checksum());
+
+    }
+
     void assertChromosomePageIdenticalToEntity(Page<ChromosomeEntity> page) {
         assertNotNull(page);
         assertTrue(page.getTotalElements() > 0);