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EBIvariation · Feb 12, 2024 · cb4f0f4 · cb4f0f4
1 parent 3d23017
commit cb4f0f4
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Showing 8 changed files with 15 additions and 15 deletions.
diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/controller/admin/AdminController.java b/src/main/java/uk/ac/ebi/eva/contigalias/controller/admin/AdminController.java
@@ -198,7 +198,7 @@ public ResponseEntity<String> retrieveAndInsertENASequenceNameForAssembly(
     }
 
 
-    @ApiOperation(value = "Retrieve list of assemblies for which MD5 Checksum updates are running/going-to-run ")
+    @ApiOperation(value = "Retrieve list of Jobs that are running or scheduled to run")
     @GetMapping(value = "assemblies/scheduled-jobs")
     public ResponseEntity<List<String>> getMD5ChecksumUpdateTaskStatus() {
         List<String> scheduledJobStatus = handler.getScheduledJobStatus();

diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/ChromosomeUpdater.java b/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/ChromosomeUpdater.java
@@ -6,9 +6,9 @@
 import org.springframework.scheduling.annotation.Async;
 import org.springframework.stereotype.Service;
 import uk.ac.ebi.eva.contigalias.conf.ApplicationContextHolder;
-import uk.ac.ebi.eva.contigalias.scheduler.Job.Job;
-import uk.ac.ebi.eva.contigalias.scheduler.Job.JobSubmittedEvent;
-import uk.ac.ebi.eva.contigalias.scheduler.Job.JobType;
+import uk.ac.ebi.eva.contigalias.scheduler.job.Job;
+import uk.ac.ebi.eva.contigalias.scheduler.job.JobSubmittedEvent;
+import uk.ac.ebi.eva.contigalias.scheduler.job.JobType;
 
 import java.util.ArrayList;
 import java.util.List;

diff --git a/...bi/eva/contigalias/scheduler/Job/Job.java → ...bi/eva/contigalias/scheduler/job/Job.java b/...bi/eva/contigalias/scheduler/Job/Job.java → ...bi/eva/contigalias/scheduler/job/Job.java
@@ -1,4 +1,4 @@
-package uk.ac.ebi.eva.contigalias.scheduler.Job;
+package uk.ac.ebi.eva.contigalias.scheduler.job;
 
 public class Job {
     private final JobType type;

diff --git a/...lias/scheduler/Job/JobSubmittedEvent.java → ...lias/scheduler/job/JobSubmittedEvent.java b/...lias/scheduler/Job/JobSubmittedEvent.java → ...lias/scheduler/job/JobSubmittedEvent.java
@@ -1,4 +1,4 @@
-package uk.ac.ebi.eva.contigalias.scheduler.Job;
+package uk.ac.ebi.eva.contigalias.scheduler.job;
 
 
 import org.springframework.context.ApplicationEvent;

diff --git a/...heduler/Job/JobSubmittedEventHandler.java → ...heduler/job/JobSubmittedEventHandler.java b/...heduler/Job/JobSubmittedEventHandler.java → ...heduler/job/JobSubmittedEventHandler.java
@@ -1,4 +1,4 @@
-package uk.ac.ebi.eva.contigalias.scheduler.Job;
+package uk.ac.ebi.eva.contigalias.scheduler.job;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationListener;

diff --git a/...va/contigalias/scheduler/Job/JobType.java → ...va/contigalias/scheduler/job/JobType.java b/...va/contigalias/scheduler/Job/JobType.java → ...va/contigalias/scheduler/job/JobType.java
@@ -1,4 +1,4 @@
-package uk.ac.ebi.eva.contigalias.scheduler.Job;
+package uk.ac.ebi.eva.contigalias.scheduler.job;
 
 public enum JobType {
     ENA_SEQUENCE_NAME_UPDATE,

diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/service/AssemblyService.java b/src/main/java/uk/ac/ebi/eva/contigalias/service/AssemblyService.java
@@ -32,8 +32,8 @@
 import uk.ac.ebi.eva.contigalias.repo.AssemblyRepository;
 import uk.ac.ebi.eva.contigalias.repo.ChromosomeRepository;
 import uk.ac.ebi.eva.contigalias.scheduler.ChromosomeUpdater;
-import uk.ac.ebi.eva.contigalias.scheduler.Job.Job;
-import uk.ac.ebi.eva.contigalias.scheduler.Job.JobType;
+import uk.ac.ebi.eva.contigalias.scheduler.job.Job;
+import uk.ac.ebi.eva.contigalias.scheduler.job.JobType;
 
 import javax.transaction.Transactional;
 import java.io.BufferedReader;
@@ -146,17 +146,16 @@ public void parseFileAndInsertAssembly(String accession) throws IOException {
                 chrLines.add(line);
                 if (chrLines.size() == BATCH_SIZE) {
                     List<ChromosomeEntity> chromosomeEntityList = ncbiDataSource.getChromosomeEntityList(assemblyEntity, chrLines);
-                    chromosomeService.saveAllChromosomes(chromosomeEntityList);
+                    chromosomeService.insertAllChromosomes(chromosomeEntityList);
                     chromosomesSavedTillNow += chrLines.size();
                     logger.info("Number of chromosomes saved till now  : " + chromosomesSavedTillNow);
 
                     chrLines = new ArrayList<>();
                 }
             }
             if (!chrLines.isEmpty()) {
-                // add ena sequence name and save
                 List<ChromosomeEntity> chromosomeEntityList = ncbiDataSource.getChromosomeEntityList(assemblyEntity, chrLines);
-                chromosomeService.saveAllChromosomes(chromosomeEntityList);
+                chromosomeService.insertAllChromosomes(chromosomeEntityList);
                 chromosomesSavedTillNow += chrLines.size();
                 logger.info("Number of chromosomes saved till now  : " + chromosomesSavedTillNow);
             }

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
@@ -208,7 +208,7 @@ private void stripAssemblyFromChromosome(ChromosomeEntity chromosome) {
     public void putChromosomeChecksumsByAccession(String accession, String md5, String trunc512) {
         Page<ChromosomeEntity> page = repository.findChromosomeEntitiesByInsdcAccessionOrRefseq(
                 accession, accession, Pageable.unpaged());
-        if (page.isEmpty()){
+        if (page.isEmpty()) {
             throw new IllegalArgumentException(
                     "No chromosomes corresponding to accession " + accession + " found in the database");
         }
@@ -284,7 +284,7 @@ public long countChromosomeEntitiesByEnaName(String enaName) {
         return repository.countChromosomeEntitiesByEnaSequenceName(enaName);
     }
 
-    public void saveAllChromosomes(List<ChromosomeEntity> chromosomeEntityList) {
+    public void insertAllChromosomes(List<ChromosomeEntity> chromosomeEntityList) {
         String sql = "INSERT INTO chromosome (assembly_insdc_accession,contig_type,ena_sequence_name," +
                 "genbank_sequence_name,insdc_accession,md5checksum,refseq,seq_length,trunc512checksum,ucsc_name) " +
                 "VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)";
@@ -303,6 +303,7 @@ public void setValues(PreparedStatement ps, int i) throws SQLException {
                 ps.setString(9, chromosome.getTrunc512checksum());
                 ps.setString(10, chromosome.getUcscName());
             }
+
             @Override
             public int getBatchSize() {
                 return chromosomeEntityList.size();