Merge pull request #168 from EBISPOT/develop

Develop

.gitlab-ci.yml

@@ -106,7 +106,7 @@ deploy-fallback:
   - mkdir -p /root/.kube
   - echo ${PFALLBACK_KUBECONFIG} | base64 -d > /root/.kube/config
   - helm init --stable-repo-url https://charts.helm.sh/stable
-  - helm delete --purge gwas-curation-service || true
+  #- helm delete --purge gwas-curation-service || true
   - helm install --name gwas-curation-service --set k8Namespace=gwas,replicaCount=1,image.env.envName=prod-fallback,image.repository=$BACKEND_REGISTRY_IMAGE,image.tag=$CI_COMMIT_SHA,image.env.dbUser=gwasdepo,image.env.secretsName=prod-secrets,image.env.secretsKey=db-backend,image.env.rabbitSecretsName=prod-secrets,image.env.rabbitSecretsKey=rabbitmq-password ./k8chart/ --wait
   environment:
     name: prod
@@ -121,7 +121,7 @@ deploy-live:
   - mkdir -p /root/.kube
   - echo ${PLIVE_KUBECONFIG} | base64 -d > /root/.kube/config
   - helm init --stable-repo-url https://charts.helm.sh/stable
-  - helm delete --purge gwas-curation-service || true
+  #- helm delete --purge gwas-curation-service || true
   - helm install --name gwas-curation-service --set k8Namespace=gwas,replicaCount=1,image.env.envName=prod,image.repository=$BACKEND_REGISTRY_IMAGE,image.tag=$CI_COMMIT_SHA,image.env.dbUser=gwasdepo,image.env.secretsName=prod-secrets,image.env.secretsKey=db-backend,image.env.rabbitSecretsName=prod-secrets,image.env.rabbitSecretsKey=rabbitmq-password ./k8chart/ --wait
   environment:
     name: prod

src/main/java/uk/ac/ebi/spot/gwas/curation/rabbitmq/StudyIngestConsumer.java

@@ -29,7 +29,11 @@ public class StudyIngestConsumer {
     @RabbitListener(queues = { DepositionCurationConstants.QUEUE_NAME_SANDBOX,
             DepositionCurationConstants.QUEUE_NAME_PROD } )
      public void listen(StudyDto studyDto) {
-        log.info("Consuming message for"+studyDto.getSubmissionId()+":"+studyDto.getAccession());
-        studySolrIndexerService.syncSolrWithStudies(studyDto);
+        try {
+            log.info("Consuming message for" + studyDto.getSubmissionId() + ":" + studyDto.getAccession());
+            studySolrIndexerService.syncSolrWithStudies(studyDto);
+        } catch(Exception ex) {
+            log.error("Error in consuming message"+ex.getMessage(),ex);
+        }
     }
 }

src/main/java/uk/ac/ebi/spot/gwas/curation/service/impl/StudiesServiceImpl.java

@@ -1,6 +1,7 @@
 package uk.ac.ebi.spot.gwas.curation.service.impl;
 
 //import com.querydsl.core.types.Predicate;
+import com.mongodb.bulk.BulkWriteResult;
 import org.apache.commons.lang3.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -345,6 +346,8 @@ public Study getStudyByAccession(String accessionId, String submissionId) {
 
     @Override
     public UploadReportWrapper updateMultiTraitsForStudies(List<MultiTraitStudyMappingDto> multiTraitStudyMappingDtos, String submissionId) {
+        log.info("Inside updateMultiTraitsForStudies()");
+
         Set<String> shortForms = new HashSet<>();
         Set<String> backgroundShortForms = new HashSet<>();
         Set<String> reportedTraits = new HashSet<>();
@@ -353,6 +356,9 @@ public UploadReportWrapper updateMultiTraitsForStudies(List<MultiTraitStudyMappi
             backgroundShortForms.addAll(Arrays.asList(StringUtils.deleteWhitespace(multiTraitStudyMappingDto.getBackgroundEfoShortForm()).split("\\|")));
             reportedTraits.add(multiTraitStudyMappingDto.getReportedTrait());
         });
+
+
+
         Map<String, EfoTrait> retrievedEfoTraits = efoTraitRepository.findByShortFormIn(shortForms).collect(Collectors.toMap(EfoTrait::getShortForm, e -> e));
         Map<String, EfoTrait> retrievedBackgroundEfoTraits = efoTraitRepository.findByShortFormIn(backgroundShortForms).collect(Collectors.toMap(EfoTrait::getShortForm, e -> e));
         Map<String, DiseaseTrait> retrievedReportedTraits = diseaseTraitRepository.findByTraitIgnoreCaseIn(reportedTraits).collect(Collectors.toMap(DiseaseTrait::getTrait, d -> d));
@@ -370,10 +376,12 @@ public UploadReportWrapper updateMultiTraitsForStudies(List<MultiTraitStudyMappi
             }
             else {
                 if(!multiTraitStudyMappingDto.getStudyTag().trim().equalsIgnoreCase(study.getStudyTag())) {
+                    //log.info("Inside invalidStudyTag block()"+study.getStudyTag());
                     invalidStudyTag = true;
                 }
 
                 if (!invalidStudyTag) {
+                    //log.info("Inside validStudyTag block()"+study.getStudyTag());
                     String efoTraitComments = "";
                     HashSet<String> newStudyEfos = new HashSet<>(Arrays.asList(StringUtils.deleteWhitespace(multiTraitStudyMappingDto.getEfoTraitShortForm().trim()).split("\\|")));
                     ArrayList<String> studyEfoTraitsIds = new ArrayList<>();
@@ -412,7 +420,10 @@ public UploadReportWrapper updateMultiTraitsForStudies(List<MultiTraitStudyMappi
 
                     String reportedTraitComments = "";
                     if (retrievedReportedTraits.containsKey(multiTraitStudyMappingDto.getReportedTrait().trim())) {
+                        //log.info("Reported Trait in file:"+multiTraitStudyMappingDto.getReportedTrait().trim());
+                        //log.info("GCST currently being analysed:"+study.getAccession());
                         DiseaseTrait diseaseTrait = retrievedReportedTraits.get(multiTraitStudyMappingDto.getReportedTrait().trim());
+                        //log.info("Disease Trait Id being assigned :"+diseaseTrait.getId());
                         study.setDiseaseTrait(diseaseTrait.getId());
                         studiesToSave.put(study.getId(), study);
                         reportedTraitComments = reportedTraitComments.concat("Reported trait set to: " + diseaseTrait.getTrait());
@@ -430,7 +441,9 @@ public UploadReportWrapper updateMultiTraitsForStudies(List<MultiTraitStudyMappi
         });
         BulkOperations bulkOps = mongoTemplate.bulkOps(BulkOperations.BulkMode.UNORDERED, Study.class);
         for (Study study: studiesToSave.values()) {
-            Query query = new Query().addCriteria(new Criteria("id  ").is(study.getId()));
+            //log.info("Study GCST which are bulkuploaded -:"+study.getAccession());
+            //log.info("Disease Trait Id being assigned to study is :"+study.getDiseaseTrait());
+            Query query = new Query().addCriteria(new Criteria("id").is(study.getId()));
             Update update = new Update()
                     .set("efoTraits", study.getEfoTraits())
                     .set("backgroundEfoTraits", study.getBackgroundEfoTraits())
@@ -440,6 +453,7 @@ public UploadReportWrapper updateMultiTraitsForStudies(List<MultiTraitStudyMappi
         }
         if (!studiesToSave.isEmpty()) {
             bulkOps.execute();
+            //log.info("Bule write Result"+bulkWriteResult.getUpserts());
         }
         uploadReportWrapper.setUploadReport(fileHandler.serializePojoToTsv(report));
         return uploadReportWrapper;