Merge pull request #464 from apriltuesday/EVA-3719

EVA-3719: Retry MissingUnsavedAccessionsException
EBIvariation · Dec 19, 2024 · c76ddcc · c76ddcc
2 parents 8fd081a + 87ef5fe
commit c76ddcc
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Showing 2 changed files with 8 additions and 1 deletion.
diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -14,7 +14,7 @@ jobs:
       matrix:
         mongodb-version: [4.0.18]
         java-version: [1.8]
-        python-version: [3.7]
+        python-version: [3.8]
 
     steps:
       - uses: actions/checkout@v2

diff --git a/...accession/pipeline/configuration/batch/steps/CreateSubsnpAccessionsStepConfiguration.java b/...accession/pipeline/configuration/batch/steps/CreateSubsnpAccessionsStepConfiguration.java
@@ -28,6 +28,8 @@
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.retry.backoff.ExponentialBackOffPolicy;
+import uk.ac.ebi.ampt2d.commons.accession.core.exceptions.MissingUnsavedAccessionsException;
 
 import uk.ac.ebi.eva.accession.pipeline.batch.io.AccessionWriter;
 import uk.ac.ebi.eva.accession.pipeline.batch.policies.InvalidVariantSkipPolicy;
@@ -72,6 +74,11 @@ public Step createSubsnpAccessionStep(StepBuilderFactory stepBuilderFactory,
                 .processor(variantProcessor)
                 .writer(accessionWriter)
                 .faultTolerant()
+                // Exception can arise from running parallel accessioning jobs for a single study, hence the retry.
+                // See EVA-3719 for details.
+                .retry(MissingUnsavedAccessionsException.class)
+                .retryLimit(3)
+                .backOffPolicy(new ExponentialBackOffPolicy())
                 .skipPolicy(invalidVariantSkipPolicy)
                 .listener(stepListener)
                 .build();