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 index a954cf56..e35a6ab7 100644 --- 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 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> getMD5ChecksumUpdateTaskStatus() { List 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 index 62c100dd..f39ad94b 100644 --- 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/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/Job/Job.java b/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/job/Job.java similarity index 89% rename from src/main/java/uk/ac/ebi/eva/contigalias/scheduler/Job/Job.java rename to src/main/java/uk/ac/ebi/eva/contigalias/scheduler/job/Job.java index 77bd78b6..715381ba 100644 --- a/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/Job/Job.java +++ b/src/main/java/uk/ac/ebi/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/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/Job/JobSubmittedEvent.java b/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/job/JobSubmittedEvent.java similarity index 79% rename from src/main/java/uk/ac/ebi/eva/contigalias/scheduler/Job/JobSubmittedEvent.java rename to src/main/java/uk/ac/ebi/eva/contigalias/scheduler/job/JobSubmittedEvent.java index 1a86340b..464af04e 100644 --- a/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/Job/JobSubmittedEvent.java +++ b/src/main/java/uk/ac/ebi/eva/contigalias/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/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/Job/JobSubmittedEventHandler.java b/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/job/JobSubmittedEventHandler.java similarity index 93% rename from src/main/java/uk/ac/ebi/eva/contigalias/scheduler/Job/JobSubmittedEventHandler.java rename to src/main/java/uk/ac/ebi/eva/contigalias/scheduler/job/JobSubmittedEventHandler.java index 2b1dfb89..e0df9888 100644 --- a/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/Job/JobSubmittedEventHandler.java +++ b/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/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/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/Job/JobType.java b/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/job/JobType.java similarity index 61% rename from src/main/java/uk/ac/ebi/eva/contigalias/scheduler/Job/JobType.java rename to src/main/java/uk/ac/ebi/eva/contigalias/scheduler/job/JobType.java index 6bf8f58b..47397dd4 100644 --- a/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/Job/JobType.java +++ b/src/main/java/uk/ac/ebi/eva/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 index 5b630c22..c5a9e2e9 100644 --- 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; @@ -146,7 +146,7 @@ public void parseFileAndInsertAssembly(String accession) throws IOException { chrLines.add(line); if (chrLines.size() == BATCH_SIZE) { List chromosomeEntityList = ncbiDataSource.getChromosomeEntityList(assemblyEntity, chrLines); - chromosomeService.saveAllChromosomes(chromosomeEntityList); + chromosomeService.insertAllChromosomes(chromosomeEntityList); chromosomesSavedTillNow += chrLines.size(); logger.info("Number of chromosomes saved till now : " + chromosomesSavedTillNow); @@ -154,9 +154,8 @@ public void parseFileAndInsertAssembly(String accession) throws IOException { } } if (!chrLines.isEmpty()) { - // add ena sequence name and save List 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 index 77e2564e..9fd11976 100644 --- 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 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 chromosomeEntityList) { + public void insertAllChromosomes(List 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();