fix eva-pipeline tests

EBIvariation · Apr 18, 2024 · 66e080f · 66e080f
1 parent e1fd1be
commit 66e080f
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Showing 7 changed files with 18 additions and 9 deletions.
diff --git a/...batch/steps/AccessioningShutdownStep.java → ...ccessioningShutdownStepConfiguration.java b/...batch/steps/AccessioningShutdownStep.java → ...ccessioningShutdownStepConfiguration.java
@@ -13,7 +13,7 @@
 
 @Configuration
 @EnableBatchProcessing
-public class AccessioningShutdownStep {
+public class AccessioningShutdownStepConfiguration {
     @Autowired
     private SubmittedVariantAccessioningService submittedVariantAccessioningService;
 
@@ -22,7 +22,7 @@ public class AccessioningShutdownStep {
 
     @Bean(ACCESSIONING_SHUTDOWN_STEP)
     public Step accessioningShutDownStep(StepBuilderFactory stepBuilderFactory) {
-        return stepBuilderFactory.get("accessioningShutdownStep")
+        return stepBuilderFactory.get(ACCESSIONING_SHUTDOWN_STEP)
                 .tasklet((contribution, chunkContext) -> {
                     submittedVariantAccessioningService.shutDownAccessionGenerator();
                     clusteredVariantAccessioningService.shutDownAccessionGenerator();

diff --git a/...batch/steps/AccessioningShutdownStep.java → ...ccessioningShutdownStepConfiguration.java b/...batch/steps/AccessioningShutdownStep.java → ...ccessioningShutdownStepConfiguration.java
@@ -12,13 +12,13 @@
 
 @Configuration
 @EnableBatchProcessing
-public class AccessioningShutdownStep {
+public class AccessioningShutdownStepConfiguration {
     @Autowired
     private SubmittedVariantAccessioningService submittedVariantAccessioningService;
 
     @Bean(ACCESSIONING_SHUTDOWN_STEP)
     public Step accessioningShutDownStep(StepBuilderFactory stepBuilderFactory) {
-        return stepBuilderFactory.get("accessioningShutdownStep")
+        return stepBuilderFactory.get(ACCESSIONING_SHUTDOWN_STEP)
                 .tasklet((contribution, chunkContext) -> {
                     submittedVariantAccessioningService.shutDownAccessionGenerator();
                     return null;

diff --git a/...onfiguration/batch/jobs/CreateSeveralIntervalsOfSubsnpAccessionsJobConfigurationTest.java b/...onfiguration/batch/jobs/CreateSeveralIntervalsOfSubsnpAccessionsJobConfigurationTest.java
@@ -52,6 +52,7 @@
 import java.util.TreeSet;
 
 import static org.junit.Assert.assertEquals;
+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_STEP;
@@ -111,9 +112,10 @@ public void executeJob() throws Exception {
     }
 
     private void assertStepNames(Collection<StepExecution> stepExecutions) {
-        assertEquals(3, stepExecutions.size());
+        assertEquals(4, stepExecutions.size());
         Iterator<StepExecution> iterator = stepExecutions.iterator();
         assertEquals(CREATE_SUBSNP_ACCESSION_STEP, iterator.next().getStepName());
+        assertEquals(ACCESSIONING_SHUTDOWN_STEP, iterator.next().getStepName());
         assertEquals(BUILD_REPORT_STEP, iterator.next().getStepName());
         assertEquals(CHECK_SUBSNP_ACCESSION_STEP, iterator.next().getStepName());
     }

diff --git a/...cession/pipeline/configuration/batch/jobs/CreateSubsnpAccessionsJobConfigurationTest.java b/...cession/pipeline/configuration/batch/jobs/CreateSubsnpAccessionsJobConfigurationTest.java
@@ -51,6 +51,7 @@
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
+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_STEP;
@@ -128,9 +129,10 @@ private static int getVariantLineNumberByPosition(File output, String position)
     }
 
     private void assertStepNames(Collection<StepExecution> stepExecutions) {
-        assertEquals(3, stepExecutions.size());
+        assertEquals(4, stepExecutions.size());
         Iterator<StepExecution> iterator = stepExecutions.iterator();
         assertEquals(CREATE_SUBSNP_ACCESSION_STEP, iterator.next().getStepName());
+        assertEquals(ACCESSIONING_SHUTDOWN_STEP, iterator.next().getStepName());
         assertEquals(BUILD_REPORT_STEP, iterator.next().getStepName());
         assertEquals(CHECK_SUBSNP_ACCESSION_STEP, iterator.next().getStepName());
     }

diff --git a/...a/accession/pipeline/configuration/batch/jobs/CreateSubsnpAccessionsRecoverStateTest.java b/...a/accession/pipeline/configuration/batch/jobs/CreateSubsnpAccessionsRecoverStateTest.java
@@ -67,6 +67,7 @@
 import static org.springframework.test.web.client.match.MockRestRequestMatchers.method;
 import static org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo;
 import static org.springframework.test.web.client.response.MockRestResponseCreators.withStatus;
+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_STEP;
@@ -249,9 +250,10 @@ private void runAccessioningJob() throws Exception {
     }
 
     private void assertStepNames(Collection<StepExecution> stepExecutions) {
-        assertEquals(3, stepExecutions.size());
+        assertEquals(4, stepExecutions.size());
         Iterator<StepExecution> iterator = stepExecutions.iterator();
         assertEquals(CREATE_SUBSNP_ACCESSION_STEP, iterator.next().getStepName());
+        assertEquals(ACCESSIONING_SHUTDOWN_STEP, iterator.next().getStepName());
         assertEquals(BUILD_REPORT_STEP, iterator.next().getStepName());
         assertEquals(CHECK_SUBSNP_ACCESSION_STEP, iterator.next().getStepName());
     }

diff --git a/...e/configuration/batch/jobs/CreateSubsnpAccessionsRecoveringStateJobConfigurationTest.java b/...e/configuration/batch/jobs/CreateSubsnpAccessionsRecoveringStateJobConfigurationTest.java
@@ -65,6 +65,7 @@
 import static org.springframework.test.web.client.match.MockRestRequestMatchers.method;
 import static org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo;
 import static org.springframework.test.web.client.response.MockRestResponseCreators.withStatus;
+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_STEP;
@@ -172,9 +173,10 @@ private void runJob() throws Exception {
     }
 
     private void assertStepNames(Collection<StepExecution> stepExecutions) {
-        assertEquals(3, stepExecutions.size());
+        assertEquals(4, stepExecutions.size());
         Iterator<StepExecution> iterator = stepExecutions.iterator();
         assertEquals(CREATE_SUBSNP_ACCESSION_STEP, iterator.next().getStepName());
+        assertEquals(ACCESSIONING_SHUTDOWN_STEP, iterator.next().getStepName());
         assertEquals(BUILD_REPORT_STEP, iterator.next().getStepName());
         assertEquals(CHECK_SUBSNP_ACCESSION_STEP, iterator.next().getStepName());
     }

diff --git a/...-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/test/BatchTestConfiguration.java b/...-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/test/BatchTestConfiguration.java
@@ -32,6 +32,7 @@
 import uk.ac.ebi.eva.accession.pipeline.configuration.batch.processors.VariantProcessorConfiguration;
 import uk.ac.ebi.eva.accession.pipeline.configuration.batch.io.VcfReaderConfiguration;
 import uk.ac.ebi.eva.accession.pipeline.configuration.batch.jobs.CreateSubsnpAccessionsJobConfiguration;
+import uk.ac.ebi.eva.accession.pipeline.configuration.batch.steps.AccessioningShutdownStepConfiguration;
 import uk.ac.ebi.eva.accession.pipeline.configuration.batch.steps.BuildReportStepConfiguration;
 import uk.ac.ebi.eva.accession.pipeline.configuration.batch.steps.CheckSubsnpAccessionsStepConfiguration;
 import uk.ac.ebi.eva.accession.pipeline.configuration.batch.steps.CreateSubsnpAccessionsStepConfiguration;
@@ -46,7 +47,7 @@
 @Import({CreateSubsnpAccessionsJobConfiguration.class,
          CreateSubsnpAccessionsStepConfiguration.class, CheckSubsnpAccessionsStepConfiguration.class,
          VcfReaderConfiguration.class, VariantProcessorConfiguration.class, AccessionWriterConfiguration.class,
-         BuildReportStepConfiguration.class,
+         BuildReportStepConfiguration.class, AccessioningShutdownStepConfiguration.class,
          ChunkSizeCompletionPolicyConfiguration.class, InvalidVariantSkipPolicyConfiguration.class,
         EvaAccessionJobLauncherCommandLineRunner.class})
 public class BatchTestConfiguration {