From 8447974821ca32031594525ac2ace6e15e41f03a Mon Sep 17 00:00:00 2001
From: nkumar2 <nkumar2@ebi.ac.uk>
Date: Tue, 30 Apr 2024 13:46:42 +0100
Subject: [PATCH] fix AccessionWriterTest

---
 .../listeners/ListenersConfiguration.java     | 20 -------------
 .../SubsnpAccessionJobExecutionListener.java  | 30 +++++++++++++++++++
 .../batch/io/AccessionWriterTest.java         | 12 +++++++-
 .../pipeline/test/BatchTestConfiguration.java |  3 +-
 4 files changed, 43 insertions(+), 22 deletions(-)
 create mode 100644 eva-accession-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/listeners/SubsnpAccessionJobExecutionListener.java

diff --git a/eva-accession-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/listeners/ListenersConfiguration.java b/eva-accession-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/listeners/ListenersConfiguration.java
index 67d47589d..bb183662d 100644
--- a/eva-accession-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/listeners/ListenersConfiguration.java
+++ b/eva-accession-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/listeners/ListenersConfiguration.java
@@ -1,13 +1,10 @@
 package uk.ac.ebi.eva.accession.pipeline.configuration.batch.listeners;
 
-import org.springframework.batch.core.JobExecution;
-import org.springframework.batch.core.JobExecutionListener;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 import org.springframework.web.client.RestTemplate;
-import uk.ac.ebi.eva.accession.pipeline.batch.io.AccessionWriter;
 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;
@@ -15,8 +12,6 @@
 import uk.ac.ebi.eva.metrics.count.CountServiceParameters;
 import uk.ac.ebi.eva.metrics.metric.MetricCompute;
 
-import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.ACCESSION_WRITER;
-import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.SUBSNP_ACCESSION_JOB_LISTENER;
 import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.SUBSNP_ACCESSION_STEP_LISTENER;
 
 @Configuration
@@ -34,19 +29,4 @@ public MetricCompute getClusteringMetricCompute(CountServiceParameters countServ
         return new AccessioningMetricCompute(countServiceParameters, restTemplate, inputParameters.getAssemblyAccession(),
                 inputParameters.getProjectAccession());
     }
-
-    @Bean(SUBSNP_ACCESSION_JOB_LISTENER)
-    public JobExecutionListener jobExecutionListener(@Qualifier(ACCESSION_WRITER) AccessionWriter accessionWriter) {
-        return new JobExecutionListener() {
-            @Override
-            public void beforeJob(JobExecution jobExecution) {
-                accessionWriter.setJobExecution(jobExecution);
-            }
-
-            @Override
-            public void afterJob(JobExecution jobExecution) {
-                // Do nothing
-            }
-        };
-    }
 }
diff --git a/eva-accession-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/listeners/SubsnpAccessionJobExecutionListener.java b/eva-accession-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/listeners/SubsnpAccessionJobExecutionListener.java
new file mode 100644
index 000000000..b4e2a53e0
--- /dev/null
+++ b/eva-accession-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/listeners/SubsnpAccessionJobExecutionListener.java
@@ -0,0 +1,30 @@
+package uk.ac.ebi.eva.accession.pipeline.configuration.batch.listeners;
+
+import org.springframework.batch.core.JobExecution;
+import org.springframework.batch.core.JobExecutionListener;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import uk.ac.ebi.eva.accession.pipeline.batch.io.AccessionWriter;
+
+import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.ACCESSION_WRITER;
+import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.SUBSNP_ACCESSION_JOB_LISTENER;
+
+@Configuration
+public class SubsnpAccessionJobExecutionListener {
+
+    @Bean(SUBSNP_ACCESSION_JOB_LISTENER)
+    public JobExecutionListener jobExecutionListener(@Qualifier(ACCESSION_WRITER) AccessionWriter accessionWriter) {
+        return new JobExecutionListener() {
+            @Override
+            public void beforeJob(JobExecution jobExecution) {
+                accessionWriter.setJobExecution(jobExecution);
+            }
+
+            @Override
+            public void afterJob(JobExecution jobExecution) {
+                // Do nothing
+            }
+        };
+    }
+}
diff --git a/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionWriterTest.java b/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionWriterTest.java
index 3176dbdd8..250f73764 100644
--- a/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionWriterTest.java
+++ b/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionWriterTest.java
@@ -23,10 +23,12 @@
 import org.junit.rules.ExpectedException;
 import org.junit.rules.TemporaryFolder;
 import org.junit.runner.RunWith;
+import org.mockito.Mockito;
 import org.springframework.batch.core.JobExecution;
 import org.springframework.batch.item.ExecutionContext;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
+import org.springframework.boot.test.mock.mockito.MockBean;
 import org.springframework.data.mongodb.core.MongoTemplate;
 import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.test.context.ContextConfiguration;
@@ -46,7 +48,9 @@
 import uk.ac.ebi.eva.accession.core.model.eva.SubmittedVariantEntity;
 import uk.ac.ebi.eva.accession.pipeline.batch.processors.VariantConverter;
 import uk.ac.ebi.eva.accession.pipeline.configuration.InputParametersConfiguration;
+import uk.ac.ebi.eva.accession.pipeline.configuration.batch.io.AccessionWriterConfiguration;
 import uk.ac.ebi.eva.accession.pipeline.configuration.batch.listeners.ListenersConfiguration;
+import uk.ac.ebi.eva.accession.pipeline.configuration.batch.listeners.SubsnpAccessionJobExecutionListener;
 import uk.ac.ebi.eva.accession.pipeline.metric.AccessioningMetric;
 import uk.ac.ebi.eva.commons.core.models.pipeline.Variant;
 import uk.ac.ebi.eva.commons.core.models.pipeline.VariantSourceEntry;
@@ -76,7 +80,8 @@
 
 @RunWith(SpringRunner.class)
 @EnableAutoConfiguration
-@ContextConfiguration(classes = {SubmittedVariantAccessioningConfiguration.class, ListenersConfiguration.class, InputParametersConfiguration.class})
+@ContextConfiguration(classes = {SubmittedVariantAccessioningConfiguration.class, ListenersConfiguration.class,
+        InputParametersConfiguration.class})
 @TestPropertySource("classpath:accession-pipeline-test.properties")
 public class AccessionWriterTest {
 
@@ -135,6 +140,9 @@ public class AccessionWriterTest {
 
     private ContigMapping contigMapping;
 
+    @MockBean
+    private JobExecution jobExecution;
+
     @Rule
     public TemporaryFolder temporaryFolderRule = new TemporaryFolder();
 
@@ -165,6 +173,8 @@ public void setUp() throws Exception {
         accessionWriter = new AccessionWriter(service, accessionReportWriter, variantConverter, metricCompute);
         accessionReportWriter.open(new ExecutionContext());
         mongoTemplate.dropCollection(SubmittedVariantEntity.class);
+        Mockito.when(jobExecution.getJobId()).thenReturn(1L);
+        accessionWriter.setJobExecution(jobExecution);
     }
 
     @After
diff --git a/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/test/BatchTestConfiguration.java b/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/test/BatchTestConfiguration.java
index 571932e82..a34916748 100644
--- a/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/test/BatchTestConfiguration.java
+++ b/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/test/BatchTestConfiguration.java
@@ -27,6 +27,7 @@
 import org.springframework.transaction.PlatformTransactionManager;
 
 import uk.ac.ebi.eva.accession.pipeline.configuration.batch.io.AccessionWriterConfiguration;
+import uk.ac.ebi.eva.accession.pipeline.configuration.batch.listeners.SubsnpAccessionJobExecutionListener;
 import uk.ac.ebi.eva.accession.pipeline.configuration.batch.policies.ChunkSizeCompletionPolicyConfiguration;
 import uk.ac.ebi.eva.accession.pipeline.configuration.batch.policies.InvalidVariantSkipPolicyConfiguration;
 import uk.ac.ebi.eva.accession.pipeline.configuration.batch.processors.VariantProcessorConfiguration;
@@ -49,7 +50,7 @@
          VcfReaderConfiguration.class, VariantProcessorConfiguration.class, AccessionWriterConfiguration.class,
          BuildReportStepConfiguration.class, AccessioningShutdownStepConfiguration.class,
          ChunkSizeCompletionPolicyConfiguration.class, InvalidVariantSkipPolicyConfiguration.class,
-        EvaAccessionJobLauncherCommandLineRunner.class})
+        EvaAccessionJobLauncherCommandLineRunner.class, SubsnpAccessionJobExecutionListener.class})
 public class BatchTestConfiguration {
 
     @Autowired