review comments - name changes

EBIvariation · May 14, 2024 · c29770b · c29770b
1 parent 852cc97
commit c29770b
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Showing 22 changed files with 155 additions and 145 deletions.
diff --git a/...essionRecoveryAgentCategoryRSService.java → .../recovery/RSAccessionRecoveryService.java b/...essionRecoveryAgentCategoryRSService.java → .../recovery/RSAccessionRecoveryService.java
@@ -5,14 +5,14 @@
 
 import java.time.LocalDateTime;
 
-public class MonotonicAccessionRecoveryAgentCategoryRSService {
+public class RSAccessionRecoveryService {
     private final static String CATEGORY_ID = "rs";
     private MonotonicAccessionRecoveryAgent monotonicAccessionRecoveryAgent;
     private JobExecution jobExecution;
     private long recoveryCutOffDays;
 
-    public MonotonicAccessionRecoveryAgentCategoryRSService(MonotonicAccessionRecoveryAgent monotonicAccessionRecoveryAgent,
-                                                            long recoveryCutOffDays) {
+    public RSAccessionRecoveryService(MonotonicAccessionRecoveryAgent monotonicAccessionRecoveryAgent,
+                                      long recoveryCutOffDays) {
         this.monotonicAccessionRecoveryAgent = monotonicAccessionRecoveryAgent;
         this.recoveryCutOffDays = recoveryCutOffDays;
     }

diff --git a/...-clustering/src/main/java/uk/ac/ebi/eva/accession/clustering/configuration/BeanNames.java b/...-clustering/src/main/java/uk/ac/ebi/eva/accession/clustering/configuration/BeanNames.java
@@ -98,11 +98,11 @@ public class BeanNames {
 
     public static final String RS_SPLIT_WRITER_JOB_EXECUTION_SETTER = "RS_SPLIT_WRITER_JOB_EXECUTION_SETTER";
 
-    public static final String MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_SERVICE = "MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_SERVICE";
+    public static final String RS_ACCESSION_RECOVERY_SERVICE = "RS_ACCESSION_RECOVERY_SERVICE";
 
-    public static final String MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_STEP = "MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_STEP";
+    public static final String RS_ACCESSION_RECOVERY_STEP = "RS_ACCESSION_RECOVERY_STEP";
 
-    public static final String MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_JOB = "MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_JOB";
+    public static final String RS_ACCESSION_RECOVERY_JOB = "RS_ACCESSION_RECOVERY_JOB";
 
-    public static final String MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_JOB_LISTENER = "MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_JOB_LISTENER";
+    public static final String RS_ACCESSION_RECOVERY_JOB_LISTENER = "RS_ACCESSION_RECOVERY_JOB_LISTENER";
 }
diff --git a/...overyAgentCategoryRSJobConfiguration.java → .../RSAccessionRecoveryJobConfiguration.java b/...overyAgentCategoryRSJobConfiguration.java → .../RSAccessionRecoveryJobConfiguration.java
@@ -11,25 +11,25 @@
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
-import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_JOB;
-import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_JOB_LISTENER;
-import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_STEP;
+import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.RS_ACCESSION_RECOVERY_JOB;
+import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.RS_ACCESSION_RECOVERY_JOB_LISTENER;
+import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.RS_ACCESSION_RECOVERY_STEP;
 
 @Configuration
 @EnableBatchProcessing
-public class MonotonicAccessionRecoveryAgentCategoryRSJobConfiguration {
+public class RSAccessionRecoveryJobConfiguration {
 
     @Autowired
-    @Qualifier(MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_STEP)
+    @Qualifier(RS_ACCESSION_RECOVERY_STEP)
     private Step monotonicAccessionRecoveryAgentCategoryRSStep;
 
     @Autowired
-    @Qualifier(MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_JOB_LISTENER)
+    @Qualifier(RS_ACCESSION_RECOVERY_JOB_LISTENER)
     private JobExecutionListener monotonicAccessionRecoveryAgentCategoryRSJobListener;
 
-    @Bean(MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_JOB)
+    @Bean(RS_ACCESSION_RECOVERY_JOB)
     public Job createMonotonicAccessionRecoveryAgentCategoryRSJob(JobBuilderFactory jobBuilderFactory) {
-        return jobBuilderFactory.get(MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_JOB)
+        return jobBuilderFactory.get(RS_ACCESSION_RECOVERY_JOB)
                 .incrementer(new RunIdIncrementer())
                 .start(monotonicAccessionRecoveryAgentCategoryRSStep)
                 .listener(monotonicAccessionRecoveryAgentCategoryRSJobListener)

diff --git a/...ntCategoryRSJobListenerConfiguration.java → ...sionRecoveryJobListenerConfiguration.java b/...ntCategoryRSJobListenerConfiguration.java → ...sionRecoveryJobListenerConfiguration.java
@@ -5,20 +5,20 @@
 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.clustering.batch.recovery.MonotonicAccessionRecoveryAgentCategoryRSService;
+import uk.ac.ebi.eva.accession.clustering.batch.recovery.RSAccessionRecoveryService;
 
-import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_JOB_LISTENER;
-import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_SERVICE;
+import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.RS_ACCESSION_RECOVERY_JOB_LISTENER;
+import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.RS_ACCESSION_RECOVERY_SERVICE;
 
 @Configuration
-public class MonotonicAccessionRecoveryAgentCategoryRSJobListenerConfiguration {
-    @Bean(MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_JOB_LISTENER)
-    public JobExecutionListener jobExecutionListener(@Qualifier(MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_SERVICE)
-                                                     MonotonicAccessionRecoveryAgentCategoryRSService monotonicAccessionRecoveryAgentCategoryRSService) {
+public class RSAccessionRecoveryJobListenerConfiguration {
+    @Bean(RS_ACCESSION_RECOVERY_JOB_LISTENER)
+    public JobExecutionListener jobExecutionListener(@Qualifier(RS_ACCESSION_RECOVERY_SERVICE)
+                                                     RSAccessionRecoveryService RSAccessionRecoveryService) {
         return new JobExecutionListener() {
             @Override
             public void beforeJob(JobExecution jobExecution) {
-                monotonicAccessionRecoveryAgentCategoryRSService.setJobExecution(jobExecution);
+                RSAccessionRecoveryService.setJobExecution(jobExecution);
             }
 
             @Override

diff --git a/...yAgentCategoryRSServiceConfiguration.java → ...ccessionRecoveryServiceConfiguration.java b/...yAgentCategoryRSServiceConfiguration.java → ...ccessionRecoveryServiceConfiguration.java
@@ -6,13 +6,13 @@
 import org.springframework.context.annotation.Configuration;
 import uk.ac.ebi.ampt2d.commons.accession.generators.monotonic.MonotonicAccessionRecoveryAgent;
 import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.monotonic.service.ContiguousIdBlockService;
-import uk.ac.ebi.eva.accession.clustering.batch.recovery.MonotonicAccessionRecoveryAgentCategoryRSService;
+import uk.ac.ebi.eva.accession.clustering.batch.recovery.RSAccessionRecoveryService;
 import uk.ac.ebi.eva.accession.core.service.nonhuman.eva.ClusteredVariantAccessioningDatabaseService;
 
-import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_SERVICE;
+import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.RS_ACCESSION_RECOVERY_SERVICE;
 
 @Configuration
-public class MonotonicAccessionRecoveryAgentCategoryRSServiceConfiguration {
+public class RSAccessionRecoveryServiceConfiguration {
     @Autowired
     private ContiguousIdBlockService blockService;
     @Autowired
@@ -21,9 +21,9 @@ public class MonotonicAccessionRecoveryAgentCategoryRSServiceConfiguration {
     @Value("${recovery.cutoff.days}")
     private long recoveryCutOffDays;
 
-    @Bean(MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_SERVICE)
-    public MonotonicAccessionRecoveryAgentCategoryRSService getMonotonicAccessionRecoveryAgentCategoryRSService() {
-        return new MonotonicAccessionRecoveryAgentCategoryRSService(getMonotonicAccessionRecoveryAgent(), recoveryCutOffDays);
+    @Bean(RS_ACCESSION_RECOVERY_SERVICE)
+    public RSAccessionRecoveryService getMonotonicAccessionRecoveryAgentCategoryRSService() {
+        return new RSAccessionRecoveryService(getMonotonicAccessionRecoveryAgent(), recoveryCutOffDays);
     }
 
     private MonotonicAccessionRecoveryAgent getMonotonicAccessionRecoveryAgent() {

diff --git a/...veryAgentCategoryRSStepConfiguration.java → ...RSAccessionRecoveryStepConfiguration.java b/...veryAgentCategoryRSStepConfiguration.java → ...RSAccessionRecoveryStepConfiguration.java
@@ -7,23 +7,23 @@
 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.clustering.batch.recovery.MonotonicAccessionRecoveryAgentCategoryRSService;
+import uk.ac.ebi.eva.accession.clustering.batch.recovery.RSAccessionRecoveryService;
 
-import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_SERVICE;
-import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_STEP;
+import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.RS_ACCESSION_RECOVERY_SERVICE;
+import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.RS_ACCESSION_RECOVERY_STEP;
 
 @Configuration
 @EnableBatchProcessing
-public class MonotonicAccessionRecoveryAgentCategoryRSStepConfiguration {
+public class RSAccessionRecoveryStepConfiguration {
     @Autowired
-    @Qualifier(MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_SERVICE)
-    private MonotonicAccessionRecoveryAgentCategoryRSService monotonicAccessionRecoveryAgentCategoryRSService;
+    @Qualifier(RS_ACCESSION_RECOVERY_SERVICE)
+    private RSAccessionRecoveryService RSAccessionRecoveryService;
 
-    @Bean(MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_STEP)
+    @Bean(RS_ACCESSION_RECOVERY_STEP)
     public Step monotonicAccessionRecoveryAgentCategoryRSStep(StepBuilderFactory stepBuilderFactory) {
-        return stepBuilderFactory.get(MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_STEP)
+        return stepBuilderFactory.get(RS_ACCESSION_RECOVERY_STEP)
                 .tasklet((contribution, chunkContext) -> {
-                    monotonicAccessionRecoveryAgentCategoryRSService.runRecoveryForCategoryRS();
+                    RSAccessionRecoveryService.runRecoveryForCategoryRS();
                     return null;
                 })
                 .build();

diff --git a/.../accession/clustering/configuration/batch/jobs/ClusteringVariantJobConfigurationTest.java b/.../accession/clustering/configuration/batch/jobs/ClusteringVariantJobConfigurationTest.java
@@ -71,15 +71,15 @@
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.CLUSTERING_CLUSTERED_VARIANTS_FROM_MONGO_STEP;
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.CLUSTERING_FROM_VCF_STEP;
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.CLUSTERING_NON_CLUSTERED_VARIANTS_FROM_MONGO_STEP;
-import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_STEP;
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.PROCESS_RS_MERGE_CANDIDATES_STEP;
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.PROCESS_RS_SPLIT_CANDIDATES_STEP;
+import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.RS_ACCESSION_RECOVERY_STEP;
 import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.STUDY_CLUSTERING_STEP;
 import static uk.ac.ebi.eva.accession.clustering.configuration.batch.io.RSMergeAndSplitCandidatesReaderConfiguration.MERGE_CANDIDATE_ID_PREFIX;
 import static uk.ac.ebi.eva.accession.clustering.configuration.batch.io.RSMergeAndSplitCandidatesReaderConfiguration.SPLIT_CANDIDATE_ID_PREFIX;
 import static uk.ac.ebi.eva.accession.clustering.test.configuration.BatchTestConfiguration.JOB_LAUNCHER_FROM_MONGO;
 import static uk.ac.ebi.eva.accession.clustering.test.configuration.BatchTestConfiguration.JOB_LAUNCHER_FROM_VCF;
-import static uk.ac.ebi.eva.accession.clustering.test.configuration.BatchTestConfiguration.JOB_LAUNCHER_MONOTONIC_ACCESSION_RECOVERY_AGENT;
+import static uk.ac.ebi.eva.accession.clustering.test.configuration.BatchTestConfiguration.JOB_LAUNCHER_RS_ACCESSION_RECOVERY;
 import static uk.ac.ebi.eva.accession.clustering.test.configuration.BatchTestConfiguration.JOB_LAUNCHER_STUDY_FROM_MONGO;
 
 @RunWith(SpringRunner.class)
@@ -102,7 +102,7 @@ public class ClusteringVariantJobConfigurationTest {
     private JobLauncherTestUtils jobLauncherTestUtilsStudyFromMongo;
 
     @Autowired
-    @Qualifier(JOB_LAUNCHER_MONOTONIC_ACCESSION_RECOVERY_AGENT)
+    @Qualifier(JOB_LAUNCHER_RS_ACCESSION_RECOVERY)
     private JobLauncherTestUtils jobLauncherTestUtilsMonotonicAccessionRecoveryAgent;
 
     @Autowired
@@ -227,10 +227,10 @@ public void assertDataThatExceedsChunkSizeIsFullyProcessed() throws Exception {
 
     @Test
     @DirtiesContext
-    public void testJobMonotonicAccessionRecoveryAgent() throws Exception{
+    public void testJobRSAccessionRecovery() throws Exception {
         JobExecution jobExecution = jobLauncherTestUtilsMonotonicAccessionRecoveryAgent.launchJob();
         List<String> expectedSteps = new ArrayList<>();
-        expectedSteps.add(MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS_STEP);
+        expectedSteps.add(RS_ACCESSION_RECOVERY_STEP);
         assertStepsExecuted(expectedSteps, jobExecution);
         assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());
     }

diff --git a/...AccessionRecoveryAgentCategoryRSTest.java → ...n/batch/jobs/RSAccessionRecoveryTest.java b/...AccessionRecoveryAgentCategoryRSTest.java → ...n/batch/jobs/RSAccessionRecoveryTest.java
@@ -30,7 +30,7 @@
 import org.springframework.test.context.junit4.SpringRunner;
 import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.monotonic.entities.ContiguousIdBlock;
 import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.monotonic.repositories.ContiguousIdBlockRepository;
-import uk.ac.ebi.eva.accession.clustering.test.configuration.RecoveryAgentCategoryRSTestConfiguration;
+import uk.ac.ebi.eva.accession.clustering.test.configuration.RSAccessionRecoveryTestConfiguration;
 import uk.ac.ebi.eva.accession.core.model.ClusteredVariant;
 import uk.ac.ebi.eva.accession.core.model.eva.ClusteredVariantEntity;
 import uk.ac.ebi.eva.accession.core.repository.nonhuman.eva.ClusteredVariantAccessioningRepository;
@@ -42,30 +42,30 @@
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
-import static uk.ac.ebi.eva.accession.clustering.test.configuration.RecoveryAgentCategoryRSTestConfiguration.JOB_LAUNCHER_MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS;
+import static uk.ac.ebi.eva.accession.clustering.test.configuration.RSAccessionRecoveryTestConfiguration.JOB_LAUNCHER_RS_ACCESSION_RECOVERY;
 
 @RunWith(SpringRunner.class)
-@ContextConfiguration(classes = {RecoveryAgentCategoryRSTestConfiguration.class,})
-@TestPropertySource("classpath:monotonic-accession-recovery-agent-category-rs.properties")
+@ContextConfiguration(classes = {RSAccessionRecoveryTestConfiguration.class,})
+@TestPropertySource("classpath:rs-accession-recovery.properties")
 @SpringBatchTest
-public class MonotonicAccessionRecoveryAgentCategoryRSTest {
+public class RSAccessionRecoveryTest {
     @Autowired
     private ContiguousIdBlockRepository blockRepository;
 
     @Autowired
     private ClusteredVariantAccessioningRepository mongoRepository;
 
     @Autowired
-    @Qualifier(JOB_LAUNCHER_MONOTONIC_ACCESSION_RECOVERY_AGENT_CATEGORY_RS)
+    @Qualifier(JOB_LAUNCHER_RS_ACCESSION_RECOVERY)
     private JobLauncherTestUtils jobLauncherTestUtilsMonotonicAccessionRecoveryAgent;
 
     @Test
     @DirtiesContext
-    public void testContiguousBlocksAreReleasedInCaseOfJobFailures() throws Exception {
+    public void testContiguousBlocksForCategoryRSAreRecovered() throws Exception {
         initializeMongoDbWithUncommittedAccessions();
         verifyInitialDBState();
 
-        // recovery cut off time is -14 days (provided in monotonic-accession-recovery-agent-category-rs.properties)
+        // recovery cut off time is -14 days (provided in rs-accession-recovery.properties)
         JobExecution jobExecution = jobLauncherTestUtilsMonotonicAccessionRecoveryAgent.launchJob();
         assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());
 
@@ -119,7 +119,7 @@ private void initializeMongoDbWithUncommittedAccessions() {
 
     private void verifyInitialDBState() {
         // Initial state of Contiguous Id Block DB is 5 blocks are present but their "last_committed" is not updated
-        // (Initialized using "resources/test-data/monotonic_accession_recovery_agent_category_rs_test_data.sql")
+        // (Initialized using "resources/test-data/rs_accession_recovery_test_data.sql")
 
         // block id  first value  last value  last committed  reserved  last_updated_timestamp | remarks
         //  1        3000000000   3000000029  2999999999      true      1970-01-01 00:00:00    | should be recovered