refactor code - update names

EBIvariation · Aug 8, 2024 · 5a91653 · 5a91653
1 parent 30181d0
commit 5a91653
Show file tree

Hide file tree

Showing 10 changed files with 80 additions and 80 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
@@ -26,20 +26,20 @@ public class BeanNames {
     public static final String VARIANT_ANNOTATION_READER = "variant-annotation-reader";
     public static final String VARIANT_READER = "variant-reader";
     public static final String ACCESSION_REPORT_READER = "accession-report-reader";
-    public static final String STATS_VARIANTS_READER = "stats-variants-reader";
+    public static final String VARIANT_STATS_READER = "variant-stats-reader";
 
     public static final String VEP_ANNOTATION_PROCESSOR = "vep-annotation-processor";
     public static final String ANNOTATION_PARSER_PROCESSOR = "annotation-parser-processor";
     public static final String ANNOTATION_COMPOSITE_PROCESSOR = "annotation-composite-processor";
-    public static final String STATS_VARIANTS_PROCESSOR = "stats-variants-processor";
+    public static final String VARIANT_STATS_PROCESSOR = "variant-stats-processor";
 
     public static final String GENE_WRITER = "gene-writer";
     public static final String ANNOTATION_WRITER = "annotation-writer";
     public static final String ANNOTATION_IN_VARIANT_WRITER = "annotation-in-variant-writer";
     public static final String COMPOSITE_ANNOTATION_VARIANT_WRITER = "composite-annotation-variant-writer";
     public static final String VARIANT_WRITER = "variant-writer";
     public static final String ACCESSION_IMPORTER = "accession-importer";
-    public static final String STATS_VARIANTS_WRITER = "stats-variants-writer";
+    public static final String VARIANT_STATS_WRITER = "variant-stats-writer";
 
     public static final String ANNOTATION_SKIP_STEP_DECIDER = "annotation-skip-step-decider";
     public static final String STATISTICS_SKIP_STEP_DECIDER = "statistics-skip-step-decider";
@@ -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_STATISTICS_STEP_NEW = "calculate-statistics-step-new";
+    public static final String CALCULATE_AND_LOAD_STATISTICS_STEP = "calculate-load-statistics-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_STATISTICS_JOB_NEW = "calculate-statistics-job-new";
+    public static final String CALCULATE_AND_LOAD_STATISTICS_JOB = "calculate-load-statistics-job";
 }
diff --git a/...ers/StatsVariantsReaderConfiguration.java → ...ders/VariantStatsReaderConfiguration.java b/...ers/StatsVariantsReaderConfiguration.java → ...ders/VariantStatsReaderConfiguration.java
@@ -21,23 +21,23 @@
 import org.springframework.context.annotation.Configuration;
 import org.springframework.data.mongodb.core.MongoTemplate;
 import uk.ac.ebi.eva.commons.models.mongo.entity.VariantDocument;
-import uk.ac.ebi.eva.pipeline.io.readers.StatsVariantReader;
+import uk.ac.ebi.eva.pipeline.io.readers.VariantStatsReader;
 import uk.ac.ebi.eva.pipeline.parameters.ChunkSizeParameters;
 import uk.ac.ebi.eva.pipeline.parameters.DatabaseParameters;
 import uk.ac.ebi.eva.pipeline.parameters.InputParameters;
 
-import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.STATS_VARIANTS_READER;
+import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.VARIANT_STATS_READER;
 
 @Configuration
-public class StatsVariantsReaderConfiguration {
+public class VariantStatsReaderConfiguration {
 
-    @Bean(STATS_VARIANTS_READER)
+    @Bean(VARIANT_STATS_READER)
     @StepScope
-    public ItemStreamReader<VariantDocument> statsVariantsReader(DatabaseParameters databaseParameters,
-                                                                 MongoTemplate mongoTemplate,
-                                                                 InputParameters inputParameters,
-                                                                 ChunkSizeParameters chunkSizeParameters) {
+    public ItemStreamReader<VariantDocument> variantStatsReader(DatabaseParameters databaseParameters,
+                                                                MongoTemplate mongoTemplate,
+                                                                InputParameters inputParameters,
+                                                                ChunkSizeParameters chunkSizeParameters) {
 
-        return new StatsVariantReader(databaseParameters, mongoTemplate, inputParameters.getStudyId(), chunkSizeParameters.getChunkSize());
+        return new VariantStatsReader(databaseParameters, mongoTemplate, inputParameters.getStudyId(), chunkSizeParameters.getChunkSize());
     }
 }
diff --git a/...ers/StatsVariantsWriterConfiguration.java → ...ters/VariantStatsWriterConfiguration.java b/...ers/StatsVariantsWriterConfiguration.java → ...ters/VariantStatsWriterConfiguration.java
@@ -21,17 +21,17 @@
 import org.springframework.context.annotation.Configuration;
 import org.springframework.data.mongodb.core.MongoTemplate;
 import uk.ac.ebi.eva.commons.models.mongo.entity.VariantDocument;
-import uk.ac.ebi.eva.pipeline.io.writers.StatsVariantWriter;
+import uk.ac.ebi.eva.pipeline.io.writers.VariantStatsWriter;
 import uk.ac.ebi.eva.pipeline.parameters.DatabaseParameters;
 
-import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.STATS_VARIANTS_WRITER;
+import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.VARIANT_STATS_WRITER;
 
 @Configuration
-public class StatsVariantsWriterConfiguration {
+public class VariantStatsWriterConfiguration {
 
-    @Bean(STATS_VARIANTS_WRITER)
+    @Bean(VARIANT_STATS_WRITER)
     @StepScope
-    public ItemWriter<VariantDocument> statsVariantsWriter(DatabaseParameters databaseParameters, MongoTemplate mongoTemplate) {
-        return new StatsVariantWriter(databaseParameters, mongoTemplate);
+    public ItemWriter<VariantDocument> variantStatsWriter(DatabaseParameters databaseParameters, MongoTemplate mongoTemplate) {
+        return new VariantStatsWriter(databaseParameters, mongoTemplate);
     }
 }
diff --git a/...ulationStatisticsJobConfigurationNew.java → ...ateAndLoadStatisticsJobConfiguration.java b/...ulationStatisticsJobConfigurationNew.java → ...ateAndLoadStatisticsJobConfiguration.java
@@ -27,11 +27,11 @@
 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.CalculateStatisticsStepConfigurationNew;
+import uk.ac.ebi.eva.pipeline.configuration.jobs.steps.CalculateAndLoadStatisticsStepConfiguration;
 import uk.ac.ebi.eva.pipeline.parameters.NewJobIncrementer;
 
-import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.CALCULATE_STATISTICS_JOB_NEW;
-import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.CALCULATE_STATISTICS_STEP_NEW;
+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;
 
 /**
  * Configuration to run a full Statistics job: variantStatsFlow: statsCreate --> statsLoad
@@ -40,24 +40,24 @@
  */
 @Configuration
 @EnableBatchProcessing
-@Import({CalculateStatisticsStepConfigurationNew.class})
-public class PopulationStatisticsJobConfigurationNew {
+@Import({CalculateAndLoadStatisticsStepConfiguration.class})
+public class CalculateAndLoadStatisticsJobConfiguration {
 
-    private static final Logger logger = LoggerFactory.getLogger(PopulationStatisticsJobConfigurationNew.class);
+    private static final Logger logger = LoggerFactory.getLogger(CalculateAndLoadStatisticsJobConfiguration.class);
 
     @Autowired
-    @Qualifier(CALCULATE_STATISTICS_STEP_NEW)
-    private Step calculateStatisticsStepNew;
+    @Qualifier(CALCULATE_AND_LOAD_STATISTICS_STEP)
+    private Step calculateAndLoadStatisticsStep;
 
-    @Bean(CALCULATE_STATISTICS_JOB_NEW)
+    @Bean(CALCULATE_AND_LOAD_STATISTICS_JOB)
     @Scope("prototype")
-    public Job calculateStatisticsJob(JobBuilderFactory jobBuilderFactory) {
-        logger.debug("Building '" + CALCULATE_STATISTICS_JOB_NEW + "'");
+    public Job calculateAndLoadStatisticsJob(JobBuilderFactory jobBuilderFactory) {
+        logger.debug("Building '" + CALCULATE_AND_LOAD_STATISTICS_JOB + "'");
 
         return jobBuilderFactory
-                .get(CALCULATE_STATISTICS_JOB_NEW)
+                .get(CALCULATE_AND_LOAD_STATISTICS_JOB)
                 .incrementer(new NewJobIncrementer())
-                .start(calculateStatisticsStepNew)
+                .start(calculateAndLoadStatisticsStep)
                 .build();
     }
 

diff --git a/...culateStatisticsStepConfigurationNew.java → ...teAndLoadStatisticsStepConfiguration.java b/...culateStatisticsStepConfigurationNew.java → ...teAndLoadStatisticsStepConfiguration.java
@@ -29,34 +29,34 @@
 import org.springframework.context.annotation.Import;
 import uk.ac.ebi.eva.commons.models.mongo.entity.VariantDocument;
 import uk.ac.ebi.eva.pipeline.configuration.ChunkSizeCompletionPolicyConfiguration;
-import uk.ac.ebi.eva.pipeline.configuration.io.readers.StatsVariantsReaderConfiguration;
-import uk.ac.ebi.eva.pipeline.configuration.io.writers.StatsVariantsWriterConfiguration;
-import uk.ac.ebi.eva.pipeline.configuration.jobs.steps.processors.StatsVariantsProcessorConfiguration;
+import uk.ac.ebi.eva.pipeline.configuration.io.readers.VariantStatsReaderConfiguration;
+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_STATISTICS_STEP_NEW;
-import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.STATS_VARIANTS_PROCESSOR;
-import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.STATS_VARIANTS_READER;
-import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.STATS_VARIANTS_WRITER;
+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_WRITER;
 
 
 @Configuration
 @EnableBatchProcessing
-@Import({StatsVariantsReaderConfiguration.class, StatsVariantsWriterConfiguration.class,
-        StatsVariantsProcessorConfiguration.class, ChunkSizeCompletionPolicyConfiguration.class})
-public class CalculateStatisticsStepConfigurationNew {
+@Import({VariantStatsReaderConfiguration.class, VariantStatsWriterConfiguration.class,
+        VariantStatsProcessorConfiguration.class, ChunkSizeCompletionPolicyConfiguration.class})
+public class CalculateAndLoadStatisticsStepConfiguration {
 
-    @Bean(CALCULATE_STATISTICS_STEP_NEW)
-    public Step calculateStatisticsStep(
-            @Qualifier(STATS_VARIANTS_READER) ItemStreamReader<VariantDocument> variantReader,
-            @Qualifier(STATS_VARIANTS_PROCESSOR) ItemProcessor<VariantDocument, VariantDocument> variantProcessor,
-            @Qualifier(STATS_VARIANTS_WRITER) ItemWriter<VariantDocument> variantWriter,
+    @Bean(CALCULATE_AND_LOAD_STATISTICS_STEP)
+    public Step calculateAndLoadStatisticsStep(
+            @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_STATISTICS_STEP_NEW)
+        TaskletStep step = stepBuilderFactory.get(CALCULATE_AND_LOAD_STATISTICS_STEP)
                 .<VariantDocument, VariantDocument>chunk(chunkSizeCompletionPolicy)
-                .reader(variantReader)
-                .processor(variantProcessor)
-                .writer(variantWriter)
+                .reader(variantStatsReader)
+                .processor(variantStatsProcessor)
+                .writer(variantStatsWriter)
                 .build();
         return step;
     }

diff --git a/.../StatsVariantsProcessorConfiguration.java → ...s/VariantStatsProcessorConfiguration.java b/.../StatsVariantsProcessorConfiguration.java → ...s/VariantStatsProcessorConfiguration.java
@@ -20,16 +20,16 @@
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import uk.ac.ebi.eva.commons.models.mongo.entity.VariantDocument;
-import uk.ac.ebi.eva.pipeline.io.processors.StatsVariantProcessor;
+import uk.ac.ebi.eva.pipeline.io.processors.VariantStatsProcessor;
 
-import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.STATS_VARIANTS_PROCESSOR;
+import static uk.ac.ebi.eva.pipeline.configuration.BeanNames.VARIANT_STATS_PROCESSOR;
 
 @Configuration
-public class StatsVariantsProcessorConfiguration {
+public class VariantStatsProcessorConfiguration {
 
-    @Bean(STATS_VARIANTS_PROCESSOR)
+    @Bean(VARIANT_STATS_PROCESSOR)
     @StepScope
-    public ItemProcessor<VariantDocument, VariantDocument> statsVariantsReader() {
-        return new StatsVariantProcessor();
+    public ItemProcessor<VariantDocument, VariantDocument> variantStatsProcessor() {
+        return new VariantStatsProcessor();
     }
 }
diff --git a/.../io/processors/StatsVariantProcessor.java → .../io/processors/VariantStatsProcessor.java b/.../io/processors/StatsVariantProcessor.java → .../io/processors/VariantStatsProcessor.java
@@ -9,7 +9,7 @@
 import uk.ac.ebi.eva.commons.models.mongo.entity.VariantDocument;
 import uk.ac.ebi.eva.commons.models.mongo.entity.subdocuments.VariantSourceEntryMongo;
 import uk.ac.ebi.eva.commons.models.mongo.entity.subdocuments.VariantStatsMongo;
-import uk.ac.ebi.eva.pipeline.io.readers.StatsVariantReader;
+import uk.ac.ebi.eva.pipeline.io.readers.VariantStatsReader;
 
 import java.util.Arrays;
 import java.util.Comparator;
@@ -21,21 +21,21 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
-public class StatsVariantProcessor implements ItemProcessor<VariantDocument, VariantDocument> {
-    private static final Logger logger = LoggerFactory.getLogger(StatsVariantProcessor.class);
+public class VariantStatsProcessor implements ItemProcessor<VariantDocument, VariantDocument> {
+    private static final Logger logger = LoggerFactory.getLogger(VariantStatsProcessor.class);
     private static final String GENOTYPE_COUNTS_MAP = "genotypeCountsMap";
     private static final String ALLELE_COUNTS_MAP = "alleleCountsMap";
     private static final String MISSING_GENOTYPE = "missingGenotype";
     private static final String MISSING_ALLELE = "missingAllele";
     private static final String DEFAULT_GENOTYPE = "def";
     private static final List<String> MISSING_GENOTYPE_ALLELE_REPRESENTATIONS = Arrays.asList(".", "-1");
 
-    public StatsVariantProcessor() {
+    public VariantStatsProcessor() {
     }
 
     @Override
     public VariantDocument process(VariantDocument variant) {
-        Map<String, Integer> filesIdNumberOfSamplesMap = StatsVariantReader.getFilesIdAndNumberOfSamplesMap();
+        Map<String, Integer> filesIdNumberOfSamplesMap = VariantStatsReader.getFilesIdAndNumberOfSamplesMap();
 
         String variantRef = variant.getReference();
         String variantAlt = variant.getAlternate();

diff --git a/...peline/io/readers/StatsVariantReader.java → ...peline/io/readers/VariantStatsReader.java b/...peline/io/readers/StatsVariantReader.java → ...peline/io/readers/VariantStatsReader.java
@@ -28,8 +28,8 @@
 import static com.mongodb.client.model.Projections.fields;
 import static java.util.Arrays.asList;
 
-public class StatsVariantReader implements ItemStreamReader<VariantDocument> {
-    private static final Logger logger = LoggerFactory.getLogger(StatsVariantReader.class);
+public class VariantStatsReader implements ItemStreamReader<VariantDocument> {
+    private static final Logger logger = LoggerFactory.getLogger(VariantStatsReader.class);
 
     private DatabaseParameters databaseParameters;
     private MongoTemplate mongoTemplate;
@@ -40,7 +40,7 @@ public class StatsVariantReader implements ItemStreamReader<VariantDocument> {
 
     private static Map<String, Integer> filesIdNumberOfSamplesMap = new HashMap<>();
 
-    public StatsVariantReader(DatabaseParameters databaseParameters, MongoTemplate mongoTemplate, String studyId, int chunkSize) {
+    public VariantStatsReader(DatabaseParameters databaseParameters, MongoTemplate mongoTemplate, String studyId, int chunkSize) {
         this.databaseParameters = databaseParameters;
         this.mongoTemplate = mongoTemplate;
         this.studyId = studyId;
@@ -50,10 +50,10 @@ public StatsVariantReader(DatabaseParameters databaseParameters, MongoTemplate m
     @Override
     public VariantDocument read() {
         Document nextElement = cursor.tryNext();
-        return (nextElement != null) ? getStatsVariant(nextElement) : null;
+        return (nextElement != null) ? getVariant(nextElement) : null;
     }
 
-    private VariantDocument getStatsVariant(Document variantDocument) {
+    private VariantDocument getVariant(Document variantDocument) {
         return converter.read(VariantDocument.class, new BasicDBObject(variantDocument));
     }
 
@@ -74,11 +74,11 @@ private MongoCursor<Document> initializeCursor() {
         Bson query = Filters.elemMatch(VariantDocument.FILES_FIELD, Filters.eq(VariantSourceEntryMongo.STUDYID_FIELD, studyId));
         logger.info("Issuing find: {}", query);
 
-        FindIterable<Document> statsVariantDocuments = getStatsVariants(query);
+        FindIterable<Document> statsVariantDocuments = getVariants(query);
         return statsVariantDocuments.iterator();
     }
 
-    private FindIterable<Document> getStatsVariants(Bson query) {
+    private FindIterable<Document> getVariants(Bson query) {
         return mongoTemplate.getCollection(databaseParameters.getCollectionVariantsName())
                 .find(query)
                 .noCursorTimeout(true)

diff --git a/...peline/io/writers/StatsVariantWriter.java → ...peline/io/writers/VariantStatsWriter.java b/...peline/io/writers/StatsVariantWriter.java → ...peline/io/writers/VariantStatsWriter.java
@@ -13,12 +13,12 @@
 
 import java.util.List;
 
-public class StatsVariantWriter implements ItemWriter<VariantDocument> {
-    private static final Logger logger = LoggerFactory.getLogger(StatsVariantWriter.class);
+public class VariantStatsWriter implements ItemWriter<VariantDocument> {
+    private static final Logger logger = LoggerFactory.getLogger(VariantStatsWriter.class);
     private DatabaseParameters databaseParameters;
     private MongoTemplate mongoTemplate;
 
-    public StatsVariantWriter(DatabaseParameters databaseParameters, MongoTemplate mongoTemplate) {
+    public VariantStatsWriter(DatabaseParameters databaseParameters, MongoTemplate mongoTemplate) {
         this.databaseParameters = databaseParameters;
         this.mongoTemplate = mongoTemplate;
     }