refactor job names for variant steps

EBIvariation · Aug 21, 2024 · 2039708 · 2039708
1 parent 022ca8f
commit 2039708
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Showing 4 changed files with 27 additions and 32 deletions.
diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/configuration/BeanNames.java b/src/main/java/uk/ac/ebi/eva/pipeline/configuration/BeanNames.java
@@ -63,7 +63,7 @@ public class BeanNames {
     public static final String DROP_FILES_BY_STUDY_STEP = "drop-files-by-study-step";
     public static final String LOAD_ANNOTATION_METADATA_STEP = "annotation-metadata-step";
     public static final String ACCESSION_IMPORT_STEP = "accession-import-step";
-    public static final String CALCULATE_AND_LOAD_STATISTICS_STEP = "calculate-load-statistics-step";
+    public static final String VARIANT_STATS_STEP = "variant-stats-step";
 
     public static final String AGGREGATED_VCF_JOB = "aggregated-vcf-job";
     public static final String ANNOTATE_VARIANTS_JOB = "annotate-variants-job";
@@ -73,5 +73,5 @@ public class BeanNames {
     public static final String CALCULATE_STATISTICS_JOB = "calculate-statistics-job";
     public static final String DROP_STUDY_JOB = "drop-study-job";
     public static final String ACCESSION_IMPORT_JOB = "accession-import-job";
-    public static final String CALCULATE_AND_LOAD_STATISTICS_JOB = "calculate-load-statistics-job";
+    public static final String VARIANT_STATS_JOB = "variant-stats-job";
 }
diff --git a/...ateAndLoadStatisticsJobConfiguration.java → ...on/jobs/VariantStatsJobConfiguration.java b/...ateAndLoadStatisticsJobConfiguration.java → ...on/jobs/VariantStatsJobConfiguration.java
@@ -27,37 +27,32 @@
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Scope;
-import uk.ac.ebi.eva.pipeline.configuration.jobs.steps.CalculateAndLoadStatisticsStepConfiguration;
+import uk.ac.ebi.eva.pipeline.configuration.jobs.steps.VariantStatsStepConfiguration;
 import uk.ac.ebi.eva.pipeline.parameters.NewJobIncrementer;
 
-import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.CALCULATE_AND_LOAD_STATISTICS_JOB;
-import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.CALCULATE_AND_LOAD_STATISTICS_STEP;
+import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.VARIANT_STATS_JOB;
+import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.VARIANT_STATS_STEP;
 
-/**
- * Configuration to run a full Statistics job: variantStatsFlow: statsCreate --> statsLoad
- * <p>
- * TODO add a new PopulationStatisticsJobParametersValidator
- */
 @Configuration
 @EnableBatchProcessing
-@Import({CalculateAndLoadStatisticsStepConfiguration.class})
-public class CalculateAndLoadStatisticsJobConfiguration {
+@Import({VariantStatsStepConfiguration.class})
+public class VariantStatsJobConfiguration {
 
-    private static final Logger logger = LoggerFactory.getLogger(CalculateAndLoadStatisticsJobConfiguration.class);
+    private static final Logger logger = LoggerFactory.getLogger(VariantStatsJobConfiguration.class);
 
     @Autowired
-    @Qualifier(CALCULATE_AND_LOAD_STATISTICS_STEP)
-    private Step calculateAndLoadStatisticsStep;
+    @Qualifier(VARIANT_STATS_STEP)
+    private Step variantStatsStep;
 
-    @Bean(CALCULATE_AND_LOAD_STATISTICS_JOB)
+    @Bean(VARIANT_STATS_JOB)
     @Scope("prototype")
-    public Job calculateAndLoadStatisticsJob(JobBuilderFactory jobBuilderFactory) {
-        logger.debug("Building '" + CALCULATE_AND_LOAD_STATISTICS_JOB + "'");
+    public Job variantStatsJob(JobBuilderFactory jobBuilderFactory) {
+        logger.debug("Building '" + VARIANT_STATS_JOB + "'");
 
         return jobBuilderFactory
-                .get(CALCULATE_AND_LOAD_STATISTICS_JOB)
+                .get(VARIANT_STATS_JOB)
                 .incrementer(new NewJobIncrementer())
-                .start(calculateAndLoadStatisticsStep)
+                .start(variantStatsStep)
                 .build();
     }
 

diff --git a/...teAndLoadStatisticsStepConfiguration.java → .../steps/VariantStatsStepConfiguration.java b/...teAndLoadStatisticsStepConfiguration.java → .../steps/VariantStatsStepConfiguration.java
@@ -33,26 +33,26 @@
 import uk.ac.ebi.eva.pipeline.configuration.io.writers.VariantStatsWriterConfiguration;
 import uk.ac.ebi.eva.pipeline.configuration.jobs.steps.processors.VariantStatsProcessorConfiguration;
 
-import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.CALCULATE_AND_LOAD_STATISTICS_STEP;
 import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.VARIANT_STATS_PROCESSOR;
 import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.VARIANT_STATS_READER;
+import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.VARIANT_STATS_STEP;
 import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.VARIANT_STATS_WRITER;
 
 
 @Configuration
 @EnableBatchProcessing
 @Import({VariantStatsReaderConfiguration.class, VariantStatsWriterConfiguration.class,
         VariantStatsProcessorConfiguration.class, ChunkSizeCompletionPolicyConfiguration.class})
-public class CalculateAndLoadStatisticsStepConfiguration {
+public class VariantStatsStepConfiguration {
 
-    @Bean(CALCULATE_AND_LOAD_STATISTICS_STEP)
-    public Step calculateAndLoadStatisticsStep(
+    @Bean(VARIANT_STATS_STEP)
+    public Step variantStatsStep(
             @Qualifier(VARIANT_STATS_READER) ItemStreamReader<VariantDocument> variantStatsReader,
             @Qualifier(VARIANT_STATS_PROCESSOR) ItemProcessor<VariantDocument, VariantDocument> variantStatsProcessor,
             @Qualifier(VARIANT_STATS_WRITER) ItemWriter<VariantDocument> variantStatsWriter,
             StepBuilderFactory stepBuilderFactory,
             SimpleCompletionPolicy chunkSizeCompletionPolicy) {
-        TaskletStep step = stepBuilderFactory.get(CALCULATE_AND_LOAD_STATISTICS_STEP)
+        TaskletStep step = stepBuilderFactory.get(VARIANT_STATS_STEP)
                 .<VariantDocument, VariantDocument>chunk(chunkSizeCompletionPolicy)
                 .reader(variantStatsReader)
                 .processor(variantStatsProcessor)

diff --git a/...s/CalculateAndLoadStatisticsStepTest.java → ...tion/jobs/steps/VariantStatsStepTest.java b/...s/CalculateAndLoadStatisticsStepTest.java → ...tion/jobs/steps/VariantStatsStepTest.java
@@ -31,7 +31,7 @@
 import org.springframework.test.context.junit4.SpringRunner;
 import uk.ac.ebi.eva.pipeline.configuration.BeanNames;
 import uk.ac.ebi.eva.pipeline.configuration.MongoConfiguration;
-import uk.ac.ebi.eva.pipeline.configuration.jobs.CalculateAndLoadStatisticsJobConfiguration;
+import uk.ac.ebi.eva.pipeline.configuration.jobs.VariantStatsJobConfiguration;
 import uk.ac.ebi.eva.test.configuration.BatchTestConfiguration;
 import uk.ac.ebi.eva.test.configuration.TemporaryRuleConfiguration;
 import uk.ac.ebi.eva.test.rules.PipelineTemporaryFolderRule;
@@ -46,20 +46,20 @@
 import static uk.ac.ebi.eva.test.utils.TestFileUtils.getResourceUrl;
 
 /**
- * Test for {@link CalculateAndLoadStatisticsStepConfiguration}
+ * Test for {@link VariantStatsStepConfiguration}
  */
 @RunWith(SpringRunner.class)
 @TestPropertySource({"classpath:test-stats.properties"})
-@ContextConfiguration(classes = {CalculateAndLoadStatisticsJobConfiguration.class, BatchTestConfiguration.class,
+@ContextConfiguration(classes = {VariantStatsJobConfiguration.class, BatchTestConfiguration.class,
         TemporaryRuleConfiguration.class, MongoConfiguration.class})
-public class CalculateAndLoadStatisticsStepTest {
+public class VariantStatsStepTest {
     private static final String MONGO_DUMP = "/dump/VariantStatsConfigurationTest_vl";
 
     private static final String COLLECTION_VARIANTS_NAME = "variants";
 
     private static final String COLLECTION_FILES_NAME = "files";
 
-    private static final String DATABASE_NAME = "calculate_load_stats_test_db";
+    private static final String DATABASE_NAME = "variant_stats_test_db";
 
     private static final String STUDY_ID = "1";
 
@@ -85,7 +85,7 @@ public void cleanUp() {
     }
 
     @Test
-    public void calculateAndLoadStatisticsStepShouldCalculateAndLoadStats() {
+    public void variantStatsStepShouldCalculateAndLoadStats() {
         JobParameters jobParameters = new EvaJobParameterBuilder()
                 .collectionFilesName(COLLECTION_FILES_NAME)
                 .collectionVariantsName(COLLECTION_VARIANTS_NAME)
@@ -94,7 +94,7 @@ public void calculateAndLoadStatisticsStepShouldCalculateAndLoadStats() {
                 .chunkSize("100")
                 .toJobParameters();
 
-        JobExecution jobExecution = jobLauncherTestUtils.launchStep(BeanNames.CALCULATE_AND_LOAD_STATISTICS_STEP, jobParameters);
+        JobExecution jobExecution = jobLauncherTestUtils.launchStep(BeanNames.VARIANT_STATS_STEP, jobParameters);
 
         // check job completed successfully
         assertCompleted(jobExecution);