EVA3454 - Retrieve and Update Md5checksum for assemblies

pom.xml

@@ -144,7 +144,7 @@
         <dependency>
             <groupId>org.springframework.retry</groupId>
             <artifactId>spring-retry</artifactId>
-            <version>1.2.5.RELEASE</version>
+            <version>1.3.1</version>
         </dependency>
 
     </dependencies>

src/main/java/uk/ac/ebi/eva/contigalias/ContigAliasApplication.java

@@ -22,7 +22,9 @@
 import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
 import org.springframework.hateoas.config.EnableHypermediaSupport;
 import org.springframework.retry.annotation.EnableRetry;
+import org.springframework.scheduling.annotation.EnableScheduling;
 
+@EnableScheduling
 @SpringBootApplication
 @EnableRetry
 @EnableHypermediaSupport(type = EnableHypermediaSupport.HypermediaType.HAL)

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

@@ -21,16 +21,20 @@
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.DeleteMapping;
+import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.PutMapping;
 import org.springframework.web.bind.annotation.RequestBody;
 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;
 import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 @RequestMapping("/v1/admin")
 @RestController
@@ -87,6 +91,36 @@ public ResponseEntity<?> fetchAndInsertAssemblyByAccession(
         return new ResponseEntity<>("Accession Processing Result : " + accessionResult, HttpStatus.MULTI_STATUS);
     }
 
+    @ApiOperation(value = "Given an assembly accession, retrieve MD5 checksum for all chromosomes belonging to assembly and update")
+    @PutMapping(value = "assemblies/{accession}/md5checksum")
+    public ResponseEntity<String> retrieveAndInsertMd5ChecksumForAssembly(@PathVariable(name = "accession")
+                                                                          @ApiParam(value = "INSDC or RefSeq assembly accession. Eg: " +
+                                                                                  "GCA_000001405.10") String asmAccession) {
+        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 ")
+    @GetMapping(value = "assemblies/md5checksum/status")
+    public ResponseEntity<String> getMD5ChecksumUpdateTaskStatus() {
+        Map<String, Set<String>> md5ChecksumUpdateTasks = handler.getMD5ChecksumUpdateTaskStatus();
+        Set<String> runningTasks = md5ChecksumUpdateTasks.get("running");
+        Set<String> scheduledTasks = md5ChecksumUpdateTasks.get("scheduled");
+        String runningTaskRes = runningTasks == null || runningTasks.isEmpty() ? "No running MD5 checksum update tasks" :
+                runningTasks.stream().collect(Collectors.joining(","));
+        String scheduledTaskRes = scheduledTasks == null || scheduledTasks.isEmpty() ? "No scheduled MD5 checksum update tasks" :
+                scheduledTasks.stream().collect(Collectors.joining(","));
+        return ResponseEntity.ok("running: " + runningTaskRes + "\nscheduled: " + scheduledTaskRes);
+    }
+
 //    This endpoint can be enabled in the future when checksums for assemblies are added to the project.
 //    @ApiOperation(value = "Add MD5 and TRUNC512 checksums to an assembly by accession.",
 //            notes = "Given an INSDC or RefSeq accession along with a MD5 or a TRUNC512 checksum, this endpoint will

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

@@ -27,6 +27,8 @@
 import java.io.IOException;
 import java.util.List;
 import java.util.Map;
+import java.util.Optional;
+import java.util.Set;
 
 @Service
 public class AdminHandler {
@@ -46,6 +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);
     }
@@ -54,6 +60,14 @@ public Map<String, List<String>> fetchAndInsertAssemblyByAccession(List<String>
         return assemblyService.fetchAndInsertAssembly(accessions);
     }
 
+    public void retrieveAndInsertMd5ChecksumForAssembly(String accession) {
+        assemblyService.retrieveAndInsertMd5ChecksumForAssembly(accession);
+    }
+
+    public Map<String, Set<String>> getMD5ChecksumUpdateTaskStatus() {
+        return assemblyService.getMD5ChecksumUpdateTaskStatus();
+    }
+
     public void deleteAssemblyByAccession(String accession) {
         assemblyService.deleteAssemblyByAccession(accession);
     }

src/main/java/uk/ac/ebi/eva/contigalias/datasource/ENAAssemblyDataSource.java

@@ -123,20 +123,17 @@ public Optional<Path> downloadAssemblyReport(ENABrowser enaBrowser, String acces
      * @param optional {@link AssemblyEntity} to add ENA sequence names to
      * @throws IOException Passes IOException thrown by {@link #getAssemblyByAccession(String)}
      */
-    public void addENASequenceNamesToAssembly(Optional<AssemblyEntity> optional) throws IOException {
-        if (optional.isPresent()) {
-            AssemblyEntity targetAssembly = optional.get();
-            if (!hasAllEnaSequenceNames(targetAssembly)) {
-                String insdcAccession = targetAssembly.getInsdcAccession();
-                Optional<AssemblyEntity> enaAssembly = getAssemblyByAccession(insdcAccession);
-
-                if (enaAssembly.isPresent()) {
-                    AssemblyEntity sourceAssembly = enaAssembly.get();
-                    addENASequenceNames(Objects.nonNull(sourceAssembly.getChromosomes()) ?
-                                    sourceAssembly.getChromosomes() : Collections.emptyList(),
-                            Objects.nonNull(targetAssembly.getChromosomes()) ?
-                                    targetAssembly.getChromosomes() : Collections.emptyList());
-                }
+    public void addENASequenceNamesToAssembly(AssemblyEntity targetAssembly) throws IOException {
+        if (!hasAllEnaSequenceNames(targetAssembly)) {
+            String insdcAccession = targetAssembly.getInsdcAccession();
+            Optional<AssemblyEntity> enaAssembly = getAssemblyByAccession(insdcAccession);
+
+            if (enaAssembly.isPresent()) {
+                AssemblyEntity sourceAssembly = enaAssembly.get();
+                addENASequenceNames(Objects.nonNull(sourceAssembly.getChromosomes()) ?
+                                sourceAssembly.getChromosomes() : Collections.emptyList(),
+                        Objects.nonNull(targetAssembly.getChromosomes()) ?
+                                targetAssembly.getChromosomes() : Collections.emptyList());
             }
         }
     }

src/main/java/uk/ac/ebi/eva/contigalias/repo/ChromosomeRepository.java

@@ -19,11 +19,16 @@
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Modifying;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
 import org.springframework.stereotype.Repository;
 
 import uk.ac.ebi.eva.contigalias.entities.AssemblyEntity;
 import uk.ac.ebi.eva.contigalias.entities.ChromosomeEntity;
 
+import java.util.List;
+
 @Repository
 public interface ChromosomeRepository extends JpaRepository<ChromosomeEntity, Long> {
 
@@ -35,6 +40,16 @@ public interface ChromosomeRepository extends JpaRepository<ChromosomeEntity, Lo
 
     Page<ChromosomeEntity> findChromosomeEntitiesByAssembly_InsdcAccession(String asmInsdcAccession, Pageable request);
 
+    @Query("SELECT c FROM ChromosomeEntity c WHERE c.assembly.insdcAccession = :asmInsdcAccession AND (c.md5checksum IS NULL OR c.md5checksum = '')")
+    Page<ChromosomeEntity> findChromosomeEntitiesByAssembly_InsdcAccessionAndMd5checksumIsNullOrEmpty(@Param("asmInsdcAccession") String asmInsdcAccession, Pageable pageable);
+
+    @Query("SELECT distinct c.assembly.insdcAccession FROM ChromosomeEntity c WHERE c.md5checksum IS NULL OR c.md5checksum = ''")
+    List<String> findAssembliesWhereChromosomeMd5checksumIsNullOrEmpty();
+
+    @Modifying
+    @Query("UPDATE ChromosomeEntity c SET c.md5checksum = :md5Checksum WHERE c.assembly.insdcAccession= :asmInsdcAccession AND c.insdcAccession = :insdcAccession")
+    void updateMd5ChecksumByInsdcAccession(@Param("asmInsdcAccession") String asmInsdcAccession, @Param("insdcAccession") String insdcAccession, @Param("md5Checksum") String md5Checksum);
+
     Page<ChromosomeEntity> findChromosomeEntitiesByAssembly_Refseq(String asmRefseq, Pageable request);
 
     Page<ChromosomeEntity> findChromosomeEntitiesByGenbankSequenceNameAndAssembly_Taxid(String genbankName, long asmTaxid, Pageable request);

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

@@ -0,0 +1,123 @@
+package uk.ac.ebi.eva.contigalias.scheduler;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.domain.Slice;
+import org.springframework.scheduling.annotation.Scheduled;
+import org.springframework.stereotype.Component;
+import uk.ac.ebi.eva.contigalias.entities.ChromosomeEntity;
+import uk.ac.ebi.eva.contigalias.service.ChromosomeService;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ExecutionException;
+import java.util.stream.Collectors;
+
+@Component
+public class ChecksumSetter {
+    private final Logger logger = LoggerFactory.getLogger(ChecksumSetter.class);
+    private final Map<String, CompletableFuture<Void>> runningMD5ChecksumUpdateTasks = new ConcurrentHashMap<>();
+    private Set<String> scheduledToRunMD5ChecksumUpdateTasks = new HashSet<>();
+    private int DEFAULT_PAGE_SIZE = 10000;
+    private ChromosomeService chromosomeService;
+    private Md5ChecksumRetriever md5ChecksumRetriever;
+
+    @Autowired
+    public ChecksumSetter(ChromosomeService chromosomeService, Md5ChecksumRetriever md5ChecksumRetriever) {
+        this.chromosomeService = chromosomeService;
+        this.md5ChecksumRetriever = md5ChecksumRetriever;
+    }
+
+    @Scheduled(cron = "0 0 0 ? * TUE")
+    public void updateMd5CheckSumForAllAssemblies() {
+        scheduledToRunMD5ChecksumUpdateTasks = new HashSet<>();
+        List<String> assemblyList = chromosomeService.getAssembliesWhereChromosomeMd5ChecksumIsNull();
+        logger.info("List of assemblies to be updated for MD5 Checksum: " + assemblyList);
+        scheduledToRunMD5ChecksumUpdateTasks.addAll(assemblyList.stream().collect(Collectors.toSet()));
+
+        for (String assembly : assemblyList) {
+            CompletableFuture<Void> future = updateMd5CheckSumForAssemblyAsync(assembly);
+            try {
+                future.get();
+            } catch (InterruptedException | ExecutionException e) {
+                logger.error("Encountered an error when running MD5Checksum update for assembly: " + assembly);
+            } finally {
+                scheduledToRunMD5ChecksumUpdateTasks.remove(assembly);
+            }
+        }
+    }
+
+    public CompletableFuture<Void> updateMd5CheckSumForAssemblyAsync(String assembly) {
+        logger.info("Submitted job for updating MD5 Checksum for assembly (asynchronously)");
+        // Check if the async task for this assembly is already running
+        CompletableFuture<Void> existingTask = runningMD5ChecksumUpdateTasks.get(assembly);
+        if (existingTask != null && !existingTask.isDone()) {
+            logger.info("Async task is still running for assembly: " + assembly);
+            return existingTask;
+        }
+        // Start the async task (removing existing run if present)
+        runningMD5ChecksumUpdateTasks.remove(assembly);
+        CompletableFuture<Void> future = CompletableFuture.runAsync(() -> {
+            updateMD5ChecksumForAllChromosomesInAssembly(assembly);
+        });
+        // Store the future in the map for the given assembly
+        runningMD5ChecksumUpdateTasks.put(assembly, future);
+
+        // check the status of task upon completion and remove from running tasks
+        future.whenComplete((result, exception) -> {
+            if (exception != null) {
+                logger.error("Async task (MD5Checksum setter) failed for assembly: " + assembly, exception);
+            } else {
+                logger.info("Async task (MD5Checksum setter) completed successfully for assembly: " + assembly);
+            }
+            runningMD5ChecksumUpdateTasks.remove(assembly);
+        });
+
+        return future;
+    }
+
+    public void updateMD5ChecksumForAllChromosomesInAssembly(String assembly) {
+        logger.info("Trying to update md5checksum for assembly: " + assembly);
+        Slice<ChromosomeEntity> chrSlice;
+        Pageable pageable = PageRequest.of(0, DEFAULT_PAGE_SIZE);
+        long chromosomeUpdated = 0;
+        do {
+            chrSlice = chromosomeService.getChromosomesByAssemblyInsdcAccessionWhereMd5ChecksumIsNull(assembly, pageable);
+            List<ChromosomeEntity> chromosomeEntityList = chrSlice.getContent();
+            updateMd5ChecksumForChromosome(chromosomeEntityList);
+
+            chromosomeUpdated += chromosomeEntityList.size();
+            logger.info("Chromosomes Updated till now: " + chromosomeUpdated);
+        } while (chrSlice.hasNext());
+
+        logger.info("Updating md5checksum for assembly " + assembly + " completed");
+    }
+
+    public void updateMd5ChecksumForChromosome(List<ChromosomeEntity> chromosomesList) {
+        chromosomesList.parallelStream().forEach(chromosome -> {
+            try {
+                String md5Checksum = md5ChecksumRetriever.retrieveMd5Checksum(chromosome.getInsdcAccession());
+                chromosome.setMd5checksum(md5Checksum);
+            } catch (Exception e) {
+                logger.info("Could not retrieve md5Checksum for insdc accession: " + chromosome.getInsdcAccession());
+            }
+        });
+
+        chromosomeService.updateMd5ChecksumForAll(chromosomesList);
+    }
+
+    public Map<String, Set<String>> getMD5ChecksumUpdateTaskStatus() {
+        Map<String, Set<String>> taskStatus = new HashMap<>();
+        taskStatus.put("running", runningMD5ChecksumUpdateTasks.keySet());
+        taskStatus.put("scheduled", scheduledToRunMD5ChecksumUpdateTasks);
+        return taskStatus;
+    }
+}

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

@@ -0,0 +1,32 @@
+package uk.ac.ebi.eva.contigalias.scheduler;
+
+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;
+import org.springframework.web.client.RestTemplate;
+
+@Component
+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;
+
+    @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) {
+        String apiURL = INSDC_CHECKSUM_URL.replace(INSDC_ACCESSION_PLACE_HOLDER, insdcAccession);
+        JsonNode jsonResponse = restTemplate.getForObject(apiURL, JsonNode.class);
+        String md5Checksum = jsonResponse.get("metadata").get("md5").asText();
+        return md5Checksum;
+    }
+}