pass application instance id

EBIvariation · Apr 29, 2024 · 509b2ae · 509b2ae
1 parent 1348569
commit 509b2ae
Show file tree

Hide file tree

Showing 22 changed files with 84 additions and 49 deletions.
diff --git a/...lustering/src/main/java/uk/ac/ebi/eva/accession/clustering/batch/io/ClusteringWriter.java b/...lustering/src/main/java/uk/ac/ebi/eva/accession/clustering/batch/io/ClusteringWriter.java
@@ -17,6 +17,7 @@
 
 import com.mongodb.MongoBulkWriteException;
 import htsjdk.samtools.util.StringUtil;
+import org.springframework.batch.core.JobExecution;
 import org.springframework.batch.item.ItemWriter;
 import org.springframework.data.mongodb.core.BulkOperations;
 import org.springframework.data.mongodb.core.MongoTemplate;
@@ -116,14 +117,17 @@ public class ClusteringWriter implements ItemWriter<SubmittedVariantEntity> {
 
     private Map<Long, SubmittedVariantOperationEntity> rsSplitCandidateSVOE;
 
+    private JobExecution jobExecution;
+
     public ClusteringWriter(MongoTemplate mongoTemplate,
                             String assembly,
                             ClusteredVariantAccessioningService clusteredVariantAccessioningService,
                             Long accessioningMonotonicInitSs,
                             Long accessioningMonotonicInitRs,
                             MetricCompute metricCompute,
                             boolean processClusteredRemappedVariants,
-                            File rsReportFile) throws IOException {
+                            File rsReportFile,
+                            JobExecution jobExecution) throws IOException {
         this.mongoTemplate = mongoTemplate;
         this.assembly = assembly;
         this.clusteredService = clusteredVariantAccessioningService;
@@ -135,6 +139,7 @@ public ClusteringWriter(MongoTemplate mongoTemplate,
         this.metricCompute = metricCompute;
         this.processClusteredRemappedVariants = processClusteredRemappedVariants;
         this.rsReportFile = rsReportFile;
+        this.jobExecution = jobExecution;
         getSVOEWithMergeAndRSSplitCandidates();
     }
 
@@ -194,7 +199,7 @@ private void getOrCreateClusteredVariantAccessions(List<? extends SubmittedVaria
                                                                                .collect(Collectors.toList());
             if (!clusteredVariants.isEmpty()) {
                 List<GetOrCreateAccessionWrapper<IClusteredVariant, String, Long>> accessionWrappers =
-                        clusteredService.getOrCreate(clusteredVariants);
+                        clusteredService.getOrCreate(clusteredVariants, jobExecution.getJobId().toString());
                 for (GetOrCreateAccessionWrapper<IClusteredVariant, String, Long> result : accessionWrappers) {
                     if (result.isNewAccession()) {
                         ClusteringWriter.writeRSReportEntry(this.rsReportFileWriter, result.getAccession(),

diff --git a/...n-clustering/src/main/java/uk/ac/ebi/eva/accession/clustering/batch/io/RSSplitWriter.java b/...n-clustering/src/main/java/uk/ac/ebi/eva/accession/clustering/batch/io/RSSplitWriter.java
@@ -21,6 +21,7 @@
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.batch.core.JobExecution;
 import org.springframework.batch.item.ItemWriter;
 import org.springframework.data.mongodb.core.MongoTemplate;
 
@@ -96,18 +97,22 @@ public class RSSplitWriter implements ItemWriter<SubmittedVariantOperationEntity
 
     private FileWriter rsReportFileWriter;
 
+    private JobExecution jobExecution;
+
     public RSSplitWriter(ClusteringWriter clusteringWriter,
                          ClusteredVariantAccessioningService clusteredVariantAccessioningService,
                          SubmittedVariantAccessioningService submittedVariantAccessioningService,
                          MongoTemplate mongoTemplate,
                          MetricCompute<ClusteringMetric> metricCompute,
-                         File rsReportFile) throws IOException {
+                         File rsReportFile,
+                         JobExecution jobExecution) throws IOException {
         this.clusteringWriter = clusteringWriter;
         this.clusteredVariantAccessioningService = clusteredVariantAccessioningService;
         this.submittedVariantAccessioningService = submittedVariantAccessioningService;
         this.mongoTemplate = mongoTemplate;
         this.metricCompute = metricCompute;
         this.rsReportFile = rsReportFile;
+        this.jobExecution = jobExecution;
     }
 
     @Override
@@ -194,7 +199,8 @@ private void issueNewRSForHashes(List<String> hashesThatShouldGetNewRS,
                         rsHashAndAssociatedSS.get(rsHash).get(0));
                 Long newRSAccession =
                         this.clusteredVariantAccessioningService.getOrCreate(
-                                Collections.singletonList(clusteredVariantEntity)).get(0).getAccession();
+                                Collections.singletonList(clusteredVariantEntity), jobExecution.getJobId().toString())
+                                .get(0).getAccession();
                 ClusteringWriter.writeRSReportEntry(this.rsReportFileWriter, newRSAccession, rsHash);
                 metricCompute.addCount(ClusteringMetric.CLUSTERED_VARIANTS_CREATED, 1);
                 List<SubmittedVariantEntity> associatedSSEntries = rsHashAndAssociatedSS.get(rsHash);

diff --git a/...n-clustering/src/main/java/uk/ac/ebi/eva/accession/clustering/batch/io/SSSplitWriter.java b/...n-clustering/src/main/java/uk/ac/ebi/eva/accession/clustering/batch/io/SSSplitWriter.java
@@ -19,6 +19,7 @@
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.batch.core.JobExecution;
 import org.springframework.batch.item.ItemWriter;
 import org.springframework.data.mongodb.core.MongoTemplate;
 
@@ -71,14 +72,18 @@ public class SSSplitWriter implements ItemWriter<SubmittedVariantEntity> {
 
     private final MetricCompute<ClusteringMetric> metricCompute;
 
+    private JobExecution jobExecution;
+
     public SSSplitWriter(String assembly, ClusteringWriter clusteringWriter,
                          SubmittedVariantAccessioningService submittedVariantAccessioningService,
-                         MongoTemplate mongoTemplate, MetricCompute<ClusteringMetric> metricCompute) {
+                         MongoTemplate mongoTemplate, MetricCompute<ClusteringMetric> metricCompute,
+                         JobExecution jobExecution) {
         this.assembly = assembly;
         this.clusteringWriter = clusteringWriter;
         this.submittedVariantAccessioningService = submittedVariantAccessioningService;
         this.mongoTemplate = mongoTemplate;
         this.metricCompute = metricCompute;
+        this.jobExecution = jobExecution;
     }
 
     @Override
@@ -127,7 +132,8 @@ protected void processSplitCandidates(List<SubmittedVariantOperationEntity> spli
         excludeSSWithAlreadyUpdatedIDs(svesToCreateWithNewIDs);
         removeCurrentSSEntriesInDBForSplitCandidates(svesToCreateWithNewIDs.keySet());
         List<GetOrCreateAccessionWrapper<ISubmittedVariant, String, Long>> newlyCreatedSVEs =
-                this.submittedVariantAccessioningService.getOrCreate(new ArrayList<>(svesToCreateWithNewIDs.values()));
+                this.submittedVariantAccessioningService.getOrCreate(new ArrayList<>(svesToCreateWithNewIDs.values()),
+                        jobExecution.getJobId().toString());
         this.metricCompute.addCount(ClusteringMetric.SUBMITTED_VARIANTS_SS_SPLIT, newlyCreatedSVEs.size());
         this.metricCompute.saveMetricsCountsInDB();
         recordSplitOperation(svesToCreateWithNewIDs, newlyCreatedSVEs);

diff --git a/...ac/ebi/eva/accession/clustering/configuration/batch/io/ClusteringWriterConfiguration.java b/...ac/ebi/eva/accession/clustering/configuration/batch/io/ClusteringWriterConfiguration.java
@@ -17,6 +17,7 @@
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.batch.core.JobExecution;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
@@ -49,11 +50,12 @@ public ClusteringWriter clusteredClusteringWriter(MongoTemplate mongoTemplate,
                                                       Long accessioningMonotonicInitSs,
                                                       Long accessioningMonotonicInitRs,
                                                       MetricCompute metricCompute,
-                                                      File rsReportFile) throws IOException {
+                                                      File rsReportFile,
+                                                      JobExecution jobExecution) throws IOException {
         return new ClusteringWriter(mongoTemplate, inputParameters.getAssemblyAccession(),
                                     clusteredVariantAccessioningService, accessioningMonotonicInitSs,
                                     accessioningMonotonicInitRs, metricCompute, true,
-                                    rsReportFile);
+                                    rsReportFile, jobExecution);
     }
 
     @Bean(NON_CLUSTERED_CLUSTERING_WRITER)
@@ -64,10 +66,11 @@ public ClusteringWriter nonClusteredClusteringWriter(MongoTemplate mongoTemplate
                                                          Long accessioningMonotonicInitSs,
                                                          Long accessioningMonotonicInitRs,
                                                          MetricCompute metricCompute,
-                                                         File rsReportFile) throws IOException {
+                                                         File rsReportFile,
+                                                         JobExecution jobExecution) throws IOException {
         return new ClusteringWriter(mongoTemplate, inputParameters.getAssemblyAccession(),
                                     clusteredVariantAccessioningService, accessioningMonotonicInitSs,
                                     accessioningMonotonicInitRs, metricCompute, false,
-                                    rsReportFile);
+                                    rsReportFile, jobExecution);
     }
 }
diff --git a/...i/eva/accession/clustering/configuration/batch/io/RSMergeAndSplitWriterConfiguration.java b/...i/eva/accession/clustering/configuration/batch/io/RSMergeAndSplitWriterConfiguration.java
@@ -15,6 +15,7 @@
  */
 package uk.ac.ebi.eva.accession.clustering.configuration.batch.io;
 
+import org.springframework.batch.core.JobExecution;
 import org.springframework.batch.item.ItemWriter;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
@@ -67,9 +68,10 @@ public ItemWriter<SubmittedVariantOperationEntity> rsSplitWriter(
             SubmittedVariantAccessioningService submittedVariantAccessioningService,
             MongoTemplate mongoTemplate,
             MetricCompute metricCompute,
-            File rsReportFile) throws IOException {
+            File rsReportFile,
+            JobExecution jobExecution) throws IOException {
         return new RSSplitWriter(clusteringWriter, clusteredVariantAccessioningService,
                                  submittedVariantAccessioningService, mongoTemplate, metricCompute,
-                                 rsReportFile);
+                                 rsReportFile, jobExecution);
     }
 }
diff --git a/...uk/ac/ebi/eva/accession/clustering/configuration/batch/io/SSSplitWriterConfiguration.java b/...uk/ac/ebi/eva/accession/clustering/configuration/batch/io/SSSplitWriterConfiguration.java
@@ -15,6 +15,7 @@
  */
 package uk.ac.ebi.eva.accession.clustering.configuration.batch.io;
 
+import org.springframework.batch.core.JobExecution;
 import org.springframework.batch.item.ItemWriter;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.context.annotation.Bean;
@@ -44,8 +45,8 @@ public ItemWriter<SubmittedVariantEntity> ssSplitWriter(
             InputParameters inputParameters,
             @Qualifier(CLUSTERED_CLUSTERING_WRITER) ClusteringWriter clusteringWriter,
             SubmittedVariantAccessioningService submittedVariantAccessioningService,
-            MongoTemplate mongoTemplate, MetricCompute metricCompute) {
+            MongoTemplate mongoTemplate, MetricCompute metricCompute, JobExecution jobExecution) {
         return new SSSplitWriter(inputParameters.getAssemblyAccession(), clusteringWriter,
-                                 submittedVariantAccessioningService, mongoTemplate, metricCompute);
+                                 submittedVariantAccessioningService, mongoTemplate, metricCompute, jobExecution);
     }
 }
diff --git a/.../test/java/uk/ac/ebi/eva/accession/clustering/runner/ClusteringCommandLineRunnerTest.java b/.../test/java/uk/ac/ebi/eva/accession/clustering/runner/ClusteringCommandLineRunnerTest.java
@@ -127,6 +127,7 @@
 @ContextConfiguration(classes={BatchTestConfiguration.class})
 @TestPropertySource("classpath:clustering-pipeline-test.properties")
 public class ClusteringCommandLineRunnerTest {
+    private static String TEST_APPLICATION_INSTANCE_ID = "test-application-instance-id";
 
     private static final String TEST_DB = "test-db";
 
@@ -843,7 +844,7 @@ private void setupRSAndSS() throws AccessionCouldNotBeGeneratedException {
         // This is the easiest way to exhaust the accessions because
         // the monotonic accession generator will only create accessions in the EVA collection (ClusteredVariantEntity)
         // and not the dbSNP collection (DbsnpClusteredVariantEntity)
-        clusteredVariantAccessionGenerator.generateAccessions(10);
+        clusteredVariantAccessionGenerator.generateAccessions(10, TEST_APPLICATION_INSTANCE_ID);
     }
 
     private void createEVASS8InASM1WithUnassignedRS() {

diff --git a/.../eva/accession/core/configuration/nonhuman/ClusteredVariantAccessioningConfiguration.java b/.../eva/accession/core/configuration/nonhuman/ClusteredVariantAccessioningConfiguration.java
@@ -122,7 +122,6 @@ public MonotonicAccessionGenerator<IClusteredVariant> clusteredVariantAccessionG
         logger.debug("Using application properties: " + properties.toString());
         return new MonotonicAccessionGenerator<>(
                 properties.getClustered().getCategoryId(),
-                properties.getInstanceId(),
                 blockService,
                 clusteredVariantAccessioningDatabaseService());
     }

diff --git a/.../eva/accession/core/configuration/nonhuman/SubmittedVariantAccessioningConfiguration.java b/.../eva/accession/core/configuration/nonhuman/SubmittedVariantAccessioningConfiguration.java
@@ -121,7 +121,6 @@ public MonotonicAccessionGenerator<ISubmittedVariant> submittedVariantAccessionG
         logger.debug("Using application properties: " + properties.toString());
         return new MonotonicAccessionGenerator<>(
                 properties.getSubmitted().getCategoryId(),
-                properties.getInstanceId(),
                 blockService,
                 submittedVariantAccessioningDatabaseService());
     }

diff --git a/...c/main/java/uk/ac/ebi/eva/accession/core/generators/DbsnpMonotonicAccessionGenerator.java b/...c/main/java/uk/ac/ebi/eva/accession/core/generators/DbsnpMonotonicAccessionGenerator.java
@@ -30,11 +30,11 @@ public class DbsnpMonotonicAccessionGenerator<MODEL> extends MonotonicAccessionG
 
     public DbsnpMonotonicAccessionGenerator(String categoryId, String applicationInstanceId,
                                             ContiguousIdBlockService contiguousIdBlockService) {
-        super(categoryId, applicationInstanceId, contiguousIdBlockService, null);
+        super(categoryId, contiguousIdBlockService, null);
     }
 
     @Override
-    public synchronized long[] generateAccessions(int numAccessionsToGenerate) {
+    public synchronized long[] generateAccessions(int numAccessionsToGenerate, String applicationInstanceId) {
         throw new UnsupportedOperationException("New accessions cannot be issued for dbSNP variants");
     }
 
@@ -59,7 +59,8 @@ public synchronized void postSave(SaveResponse response) {
     }
 
     @Override
-    public <HASH> List<AccessionWrapper<MODEL, HASH, Long>> generateAccessions(Map<HASH, MODEL> messages) {
+    public <HASH> List<AccessionWrapper<MODEL, HASH, Long>> generateAccessions(Map<HASH, MODEL> messages,
+                                                                               String applicationInstanceId) {
         throw new UnsupportedOperationException("New accessions cannot be issued for dbSNP variants");
     }
 }
diff --git a/...va/uk/ac/ebi/eva/accession/core/service/nonhuman/ClusteredVariantAccessioningService.java b/...va/uk/ac/ebi/eva/accession/core/service/nonhuman/ClusteredVariantAccessioningService.java
@@ -68,7 +68,7 @@ public ClusteredVariantAccessioningService(ClusteredVariantMonotonicAccessioning
 
     @Override
     public List<GetOrCreateAccessionWrapper<IClusteredVariant, String, Long>> getOrCreate(
-            List<? extends IClusteredVariant> variants)
+            List<? extends IClusteredVariant> variants, String applicationInstanceId)
             throws AccessionCouldNotBeGeneratedException {
         List<GetOrCreateAccessionWrapper<IClusteredVariant, String, Long>> dbsnpVariants =
                 accessioningServiceDbsnp.get(variants).stream()
@@ -81,7 +81,7 @@ public List<GetOrCreateAccessionWrapper<IClusteredVariant, String, Long>> getOrC
             return dbsnpVariants;
         } else {
             List<GetOrCreateAccessionWrapper<IClusteredVariant, String, Long>> clusteredVariants =
-                    accessioningService.getOrCreate(variantsNotInDbsnp);
+                    accessioningService.getOrCreate(variantsNotInDbsnp, applicationInstanceId);
 
             List<GetOrCreateAccessionWrapper<IClusteredVariant, String, Long>> allClusteredVariants = new ArrayList<>();
             allClusteredVariants.addAll(dbsnpVariants);

diff --git a/...va/uk/ac/ebi/eva/accession/core/service/nonhuman/SubmittedVariantAccessioningService.java b/...va/uk/ac/ebi/eva/accession/core/service/nonhuman/SubmittedVariantAccessioningService.java
@@ -67,7 +67,7 @@ public SubmittedVariantAccessioningService(SubmittedVariantMonotonicAccessioning
 
     @Override
     public List<GetOrCreateAccessionWrapper<ISubmittedVariant, String, Long>> getOrCreate(
-            List<? extends ISubmittedVariant> variants)
+            List<? extends ISubmittedVariant> variants, String applicationInstanceId)
             throws AccessionCouldNotBeGeneratedException {
         List<AccessionWrapper<ISubmittedVariant, String, Long>> dbsnpVariants = accessioningServiceDbsnp.get(variants);
         List<ISubmittedVariant> variantsNotInDbsnp = removeFromList(variants, dbsnpVariants);
@@ -80,7 +80,7 @@ public List<GetOrCreateAccessionWrapper<ISubmittedVariant, String, Long>> getOrC
                      d.getData(), false)).collect(Collectors.toList());
         } else {
             List<AccessionWrapper<ISubmittedVariant, String, Long>> submittedVariants = new ArrayList<>();
-            accessioningService.getOrCreate(variantsNotInDbsnp)
+            accessioningService.getOrCreate(variantsNotInDbsnp, applicationInstanceId)
                                .forEach(getOrCreateAccessionWrapperObj -> submittedVariants.add(
                                        new AccessionWrapper<ISubmittedVariant, String, Long>
                                                (getOrCreateAccessionWrapperObj.getAccession(),

diff --git a/...k/ac/ebi/eva/accession/core/service/nonhuman/ClusteredVariantAccessioningServiceTest.java b/...k/ac/ebi/eva/accession/core/service/nonhuman/ClusteredVariantAccessioningServiceTest.java
@@ -60,6 +60,8 @@
 @ContextConfiguration(classes = {ClusteredVariantAccessioningConfiguration.class, MongoTestConfiguration.class})
 public class ClusteredVariantAccessioningServiceTest {
 
+    private static String TEST_APPLICATION_INSTANCE_ID = "test-application-instance-id";
+
     //Required by nosql-unit
     @Autowired
     private ApplicationContext applicationContext;
@@ -91,9 +93,9 @@ public void sameAccessionsAreReturnedForIdenticalVariants() throws Exception {
                 new ClusteredVariant("assembly", 1111, "contig_1", 200, VariantType.SNV, false, null));
 
         List<GetOrCreateAccessionWrapper<IClusteredVariant, String, Long>> generatedAccessions =
-                service.getOrCreate(variants);
+                service.getOrCreate(variants, TEST_APPLICATION_INSTANCE_ID);
         List<GetOrCreateAccessionWrapper<IClusteredVariant, String, Long>> retrievedAccessions =
-                service.getOrCreate(variants);
+                service.getOrCreate(variants, TEST_APPLICATION_INSTANCE_ID);
 
         assertEquals(new HashSet<>(generatedAccessions), new HashSet<>(retrievedAccessions));
     }