creating new step for shutting down acession generator

EBIvariation · Apr 18, 2024 · e1fd1be · e1fd1be
1 parent 691e87f
commit e1fd1be
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Showing 12 changed files with 90 additions and 11 deletions.
diff --git a/...-clustering/src/main/java/uk/ac/ebi/eva/accession/clustering/configuration/BeanNames.java b/...-clustering/src/main/java/uk/ac/ebi/eva/accession/clustering/configuration/BeanNames.java
@@ -55,6 +55,8 @@ public class BeanNames {
 
     public static final String PROGRESS_LISTENER = "PROGRESS_LISTENER";
 
+    public static final String ACCESSIONING_SHUTDOWN_STEP = "ACCESSIONING_SHUTDOWN_STEP";
+
     public static final String CLUSTERING_FROM_VCF_STEP = "CLUSTERING_FROM_VCF_STEP";
 
     public static final String CLUSTERING_CLUSTERED_VARIANTS_FROM_MONGO_STEP = "CLUSTERING_CLUSTERED_VARIANTS_FROM_MONGO_STEP";

diff --git a/...ssion/clustering/configuration/batch/jobs/ClusterUnclusteredVariantsJobConfiguration.java b/...ssion/clustering/configuration/batch/jobs/ClusterUnclusteredVariantsJobConfiguration.java
@@ -24,6 +24,7 @@
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
+import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.ACCESSIONING_SHUTDOWN_STEP;
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.CLEAR_RS_MERGE_AND_SPLIT_CANDIDATES_STEP;
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.CLUSTERING_NON_CLUSTERED_VARIANTS_FROM_MONGO_STEP;
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.CLUSTER_UNCLUSTERED_VARIANTS_JOB;
@@ -42,13 +43,15 @@ public Job clusteringFromMongoJob(
             @Qualifier(PROCESS_RS_SPLIT_CANDIDATES_STEP) Step processRSSplitCandidatesStep,
             @Qualifier(CLEAR_RS_MERGE_AND_SPLIT_CANDIDATES_STEP) Step clearRSMergeAndSplitCandidatesStep,
             @Qualifier(CLUSTERING_NON_CLUSTERED_VARIANTS_FROM_MONGO_STEP) Step clusteringNonClusteredVariantsFromMongoStep,
+            @Qualifier(ACCESSIONING_SHUTDOWN_STEP) Step accessioningShutdownStep,
             JobBuilderFactory jobBuilderFactory) {
         return jobBuilderFactory.get(CLUSTER_UNCLUSTERED_VARIANTS_JOB)
                                 .incrementer(new RunIdIncrementer())
                                 .start(processRSMergeCandidatesStep)
                                 .next(processRSSplitCandidatesStep)
                                 .next(clearRSMergeAndSplitCandidatesStep)
                                 .next(clusteringNonClusteredVariantsFromMongoStep)
+                                .next(accessioningShutdownStep)
                                 .build();
     }
 }
diff --git a/...va/accession/clustering/configuration/batch/jobs/ClusteringFromMongoJobConfiguration.java b/...va/accession/clustering/configuration/batch/jobs/ClusteringFromMongoJobConfiguration.java
@@ -40,6 +40,7 @@
 
 import uk.ac.ebi.eva.accession.clustering.parameters.InputParameters;
 
+import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.ACCESSIONING_SHUTDOWN_STEP;
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.BACK_PROPAGATE_NEW_RS_STEP;
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.BACK_PROPAGATE_SPLIT_OR_MERGED_RS_STEP;
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.CLEAR_RS_MERGE_AND_SPLIT_CANDIDATES_STEP;
@@ -79,6 +80,7 @@ public Job clusteringFromMongoJob(@Qualifier(CLUSTERING_CLUSTERED_VARIANTS_FROM_
                                       @Qualifier(PROCESS_RS_SPLIT_CANDIDATES_STEP) Step processRSSplitCandidatesStep,
                                       @Qualifier(CLEAR_RS_MERGE_AND_SPLIT_CANDIDATES_STEP) Step clearRSMergeAndSplitCandidatesStep,
                                       @Qualifier(CLUSTERING_NON_CLUSTERED_VARIANTS_FROM_MONGO_STEP) Step clusteringNonClusteredVariantsFromMongoStep,
+                                      @Qualifier(ACCESSIONING_SHUTDOWN_STEP) Step accessioningShutdownStep,
                                       // Back-propagate RS that were newly created in the remapped assembly
                                       @Qualifier(BACK_PROPAGATE_NEW_RS_STEP) Step backPropagateNewRSStep,
                                       // Back-propagate RS in the remapped assembly that were split or merged
@@ -101,12 +103,14 @@ public Job clusteringFromMongoJob(@Qualifier(CLUSTERING_CLUSTERED_VARIANTS_FROM_
                             .next(processRSSplitCandidatesStep)
                             .next(clearRSMergeAndSplitCandidatesStep)
                             .next(clusteringNonClusteredVariantsFromMongoStep)
+                            .next(accessioningShutdownStep)
                             .next(backPropagateNewRSStep)
                             .next(backPropagateSplitMergedRSStep).build())
                     .on("*").end()
                 .from(jobExecutionDecider)
                     .on("FALSE")
                     .to(clusteringNonClusteredVariantsFromMongoStep)
+                    .next(accessioningShutdownStep)
                     .on("*").end()
                 .end().build();
     }

diff --git a/...bi/eva/accession/clustering/configuration/batch/jobs/StudyClusteringJobConfiguration.java b/...bi/eva/accession/clustering/configuration/batch/jobs/StudyClusteringJobConfiguration.java
@@ -24,6 +24,7 @@
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
+import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.ACCESSIONING_SHUTDOWN_STEP;
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.STUDY_CLUSTERING_JOB;
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.STUDY_CLUSTERING_STEP;
 
@@ -33,10 +34,12 @@ public class StudyClusteringJobConfiguration {
 
     @Bean(STUDY_CLUSTERING_JOB)
     public Job studyClusteringJob(@Qualifier(STUDY_CLUSTERING_STEP) Step clusteringStep,
+                                  @Qualifier(ACCESSIONING_SHUTDOWN_STEP) Step accessioningShutdownStep,
                                   JobBuilderFactory jobBuilderFactory) {
         return jobBuilderFactory.get(STUDY_CLUSTERING_JOB)
                                 .incrementer(new RunIdIncrementer())
                                 .start(clusteringStep)
+                                .next(accessioningShutdownStep)
                                 .build();
     }
 }
diff --git a/...k/ac/ebi/eva/accession/clustering/configuration/batch/steps/AccessioningShutdownStep.java b/...k/ac/ebi/eva/accession/clustering/configuration/batch/steps/AccessioningShutdownStep.java
@@ -0,0 +1,33 @@
+package uk.ac.ebi.eva.accession.clustering.configuration.batch.steps;
+
+import org.springframework.batch.core.Step;
+import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
+import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import uk.ac.ebi.eva.accession.core.service.nonhuman.ClusteredVariantAccessioningService;
+import uk.ac.ebi.eva.accession.core.service.nonhuman.SubmittedVariantAccessioningService;
+
+import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.ACCESSIONING_SHUTDOWN_STEP;
+
+@Configuration
+@EnableBatchProcessing
+public class AccessioningShutdownStep {
+    @Autowired
+    private SubmittedVariantAccessioningService submittedVariantAccessioningService;
+
+    @Autowired
+    private ClusteredVariantAccessioningService clusteredVariantAccessioningService;
+
+    @Bean(ACCESSIONING_SHUTDOWN_STEP)
+    public Step accessioningShutDownStep(StepBuilderFactory stepBuilderFactory) {
+        return stepBuilderFactory.get("accessioningShutdownStep")
+                .tasklet((contribution, chunkContext) -> {
+                    submittedVariantAccessioningService.shutDownAccessionGenerator();
+                    clusteredVariantAccessioningService.shutDownAccessionGenerator();
+                    return null;
+                })
+                .build();
+    }
+}
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
@@ -30,7 +30,7 @@ public class DbsnpMonotonicAccessionGenerator<MODEL> extends MonotonicAccessionG
 
     public DbsnpMonotonicAccessionGenerator(String categoryId, String applicationInstanceId,
                                             ContiguousIdBlockService contiguousIdBlockService) {
-        super(categoryId, applicationInstanceId, contiguousIdBlockService, (long[])null);
+        super(categoryId, applicationInstanceId, contiguousIdBlockService, null);
     }
 
     @Override

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
@@ -243,4 +243,9 @@ public AccessionWrapper<IClusteredVariant, String, Long> getLastInactive(Long ac
         }
     }
 
+    public void shutDownAccessionGenerator(){
+        accessioningService.shutDownAccessioning();
+        accessioningServiceDbsnp.shutDownAccessioning();
+    }
+
 }
diff --git a/...n/java/uk/ac/ebi/eva/accession/pipeline/batch/listeners/SubsnpAccessionsStepListener.java b/...n/java/uk/ac/ebi/eva/accession/pipeline/batch/listeners/SubsnpAccessionsStepListener.java
@@ -4,26 +4,21 @@
 import org.springframework.batch.core.StepExecution;
 import uk.ac.ebi.eva.accession.core.batch.listeners.GenericProgressListener;
 import uk.ac.ebi.eva.accession.core.model.eva.SubmittedVariantEntity;
-import uk.ac.ebi.eva.accession.core.service.nonhuman.SubmittedVariantAccessioningService;
 import uk.ac.ebi.eva.accession.pipeline.parameters.InputParameters;
 import uk.ac.ebi.eva.commons.core.models.pipeline.Variant;
 import uk.ac.ebi.eva.metrics.metric.MetricCompute;
 
 public class SubsnpAccessionsStepListener extends GenericProgressListener<Variant, SubmittedVariantEntity> {
     private final MetricCompute metricCompute;
-    private final SubmittedVariantAccessioningService submittedVariantAccessioningService;
 
-    public SubsnpAccessionsStepListener(InputParameters inputParameters, MetricCompute metricCompute,
-                                        SubmittedVariantAccessioningService submittedVariantAccessioningService) {
+    public SubsnpAccessionsStepListener(InputParameters inputParameters, MetricCompute metricCompute) {
         super(inputParameters.getChunkSize());
         this.metricCompute = metricCompute;
-        this.submittedVariantAccessioningService = submittedVariantAccessioningService;
     }
 
     @Override
     public ExitStatus afterStep(StepExecution stepExecution) {
         ExitStatus status = super.afterStep(stepExecution);
-        submittedVariantAccessioningService.shutDownAccessionGenerator();
         metricCompute.saveMetricsCountsInDB();
         return status;
     }

diff --git a/...sion-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/configuration/BeanNames.java b/...sion-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/configuration/BeanNames.java
@@ -35,4 +35,6 @@ public class BeanNames {
     public static final String CREATE_SUBSNP_ACCESSION_JOB = "CREATE_SUBSNP_ACCESSION_JOB";
 
     public static final String SUBSNP_ACCESSION_STEP_LISTENER = "SUBSNP_ACCESSION_STEP_LISTENER";
+
+    public static final String ACCESSIONING_SHUTDOWN_STEP = "ACCESSIONING_SHUTDOWN_STEP";
 }
diff --git a/...a/accession/pipeline/configuration/batch/jobs/CreateSubsnpAccessionsJobConfiguration.java b/...a/accession/pipeline/configuration/batch/jobs/CreateSubsnpAccessionsJobConfiguration.java
@@ -26,6 +26,7 @@
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
+import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.ACCESSIONING_SHUTDOWN_STEP;
 import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.BUILD_REPORT_STEP;
 import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.CHECK_SUBSNP_ACCESSION_STEP;
 import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.CREATE_SUBSNP_ACCESSION_JOB;
@@ -47,11 +48,16 @@ public class CreateSubsnpAccessionsJobConfiguration {
     @Qualifier(BUILD_REPORT_STEP)
     private Step buildReportStep;
 
+    @Autowired
+    @Qualifier(ACCESSIONING_SHUTDOWN_STEP)
+    private Step accessioningShutdownStep;
+
     @Bean(CREATE_SUBSNP_ACCESSION_JOB)
     public Job createSubsnpAccessionJob(JobBuilderFactory jobBuilderFactory) {
         return jobBuilderFactory.get(CREATE_SUBSNP_ACCESSION_JOB)
                                 .incrementer(new RunIdIncrementer())
                                 .start(createSubsnpAccessionStep)
+                                .next(accessioningShutdownStep)
                                 .next(buildReportStep)
                                 .next(checkSubsnpAccessionStep)
                                 .build();

diff --git a/...k/ac/ebi/eva/accession/pipeline/configuration/batch/listeners/ListenersConfiguration.java b/...k/ac/ebi/eva/accession/pipeline/configuration/batch/listeners/ListenersConfiguration.java
@@ -5,7 +5,6 @@
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 import org.springframework.web.client.RestTemplate;
-import uk.ac.ebi.eva.accession.core.service.nonhuman.SubmittedVariantAccessioningService;
 import uk.ac.ebi.eva.accession.pipeline.batch.listeners.SubsnpAccessionsStepListener;
 import uk.ac.ebi.eva.accession.pipeline.metric.AccessioningMetricCompute;
 import uk.ac.ebi.eva.accession.pipeline.parameters.InputParameters;
@@ -19,9 +18,8 @@
 @Import({MetricConfiguration.class})
 public class ListenersConfiguration {
     @Bean(SUBSNP_ACCESSION_STEP_LISTENER)
-    public SubsnpAccessionsStepListener clusteringProgressListener(InputParameters parameters, MetricCompute metricCompute,
-                                                                   SubmittedVariantAccessioningService submittedVariantAccessioningService) {
-        return new SubsnpAccessionsStepListener(parameters, metricCompute, submittedVariantAccessioningService);
+    public SubsnpAccessionsStepListener clusteringProgressListener(InputParameters parameters, MetricCompute metricCompute) {
+        return new SubsnpAccessionsStepListener(parameters, metricCompute);
     }
 
     @Bean

diff --git a/.../uk/ac/ebi/eva/accession/pipeline/configuration/batch/steps/AccessioningShutdownStep.java b/.../uk/ac/ebi/eva/accession/pipeline/configuration/batch/steps/AccessioningShutdownStep.java
@@ -0,0 +1,28 @@
+package uk.ac.ebi.eva.accession.pipeline.configuration.batch.steps;
+
+import org.springframework.batch.core.Step;
+import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
+import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import uk.ac.ebi.eva.accession.core.service.nonhuman.SubmittedVariantAccessioningService;
+
+import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.ACCESSIONING_SHUTDOWN_STEP;
+
+@Configuration
+@EnableBatchProcessing
+public class AccessioningShutdownStep {
+    @Autowired
+    private SubmittedVariantAccessioningService submittedVariantAccessioningService;
+
+    @Bean(ACCESSIONING_SHUTDOWN_STEP)
+    public Step accessioningShutDownStep(StepBuilderFactory stepBuilderFactory) {
+        return stepBuilderFactory.get("accessioningShutdownStep")
+                .tasklet((contribution, chunkContext) -> {
+                    submittedVariantAccessioningService.shutDownAccessionGenerator();
+                    return null;
+                })
+                .build();
+    }
+}