Merge pull request #170 from EBISPOT/develop

Develop
EBISPOT · Dec 6, 2022 · 9b237cc · 9b237cc
2 parents f3f2c8e + 92a6d5f
commit 9b237cc
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Showing 19 changed files with 326 additions and 87 deletions.
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/curation/repository/AssociationRepository.java b/src/main/java/uk/ac/ebi/spot/gwas/curation/repository/AssociationRepository.java
@@ -13,6 +13,7 @@
 public interface AssociationRepository extends MongoRepository<Association, String> {
 
     Stream<Association> readBySubmissionId(String submissionId);
+    Stream<Association> readByIdIn(List<String> ids);
     Integer countByIsValidAndSubmissionId(Boolean isValid, String submissionId);
     Integer countByIsApprovedAndSubmissionId(Boolean isApproved, String submissionId);
 }
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/curation/repository/SampleRepository.java b/src/main/java/uk/ac/ebi/spot/gwas/curation/repository/SampleRepository.java
@@ -16,5 +16,6 @@ public interface SampleRepository extends MongoRepository<Sample, String> {
 
     Page<Sample> findBySubmissionId(String submissionId, Pageable page);
 
-    List<Sample> findByIdIn(List<String> ids);
+
+    Stream<Sample> findByIdIn(List<String> ids);
 }
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/curation/rest/SubmissionDiffController.java b/src/main/java/uk/ac/ebi/spot/gwas/curation/rest/SubmissionDiffController.java
@@ -22,6 +22,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
+import java.util.Set;
 
 @RestController
 @RequestMapping(value = GeneralCommon.API_V1 + DepositionCurationConstants.API_SUBMISSIONS)
@@ -49,9 +50,14 @@ public List<VersionSummary> diffVersionSubmissions(@PathVariable String submissi
         if(changeList != null && !changeList.isEmpty()) {
             Optional<Map<Double, List<JaversChangeWrapper>>> convertedEntityOptional = conversionService.filterJaversResponse(changeList);
             List<Double> versionMapTobeDeleted = conversionService.removeInvalidSumstatsEntries(changeList);
+            Optional<Set<Double>> versionMapMetaDataDuplicated = conversionService.removeDuplicateMetaDataVersions(convertedEntityOptional);
             if(versionMapTobeDeleted != null && !versionMapTobeDeleted.isEmpty())
                 conversionService.removeVersionMap(convertedEntityOptional, versionMapTobeDeleted );
-            summaries = conversionService.filterStudiesFromJavers(convertedEntityOptional);
+           if(versionMapMetaDataDuplicated.isPresent()) {
+                conversionService.removeVersionMap(convertedEntityOptional,versionMapMetaDataDuplicated.get() );
+            }
+
+            summaries = conversionService.buiildVersionSummary(convertedEntityOptional);
             Optional<List<FileUpload>> fileUploadsOptional = conversionService.filterJaversResponseForFiles(responseEntity.getBody());
             summaries = fileUploadsOptional.isPresent()?conversionService.mapFilesToVersionSummary(summaries, fileUploadsOptional.get()):null;
         }

diff --git a/src/main/java/uk/ac/ebi/spot/gwas/curation/service/AssociationJaversService.java b/src/main/java/uk/ac/ebi/spot/gwas/curation/service/AssociationJaversService.java
@@ -17,5 +17,5 @@ public interface AssociationJaversService {
 
     public AddedRemoved getAssociationVersionStats(List<Association> prevAscns, List<Association> newAscns);
 
-    public Association processAssociationTag(ElementChange elementChange);
+    public String processAssociationTag(ElementChange elementChange);
 }
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/curation/service/AssociationsService.java b/src/main/java/uk/ac/ebi/spot/gwas/curation/service/AssociationsService.java
@@ -4,12 +4,15 @@
 import uk.ac.ebi.spot.gwas.deposition.dto.curation.SnpStatusReportDto;
 
 import java.util.List;
+import java.util.stream.Stream;
 
 public interface AssociationsService {
 
 
     Association getAssociation(String associationId);
 
+    Stream<Association> readBySeqIds(List<String> ids);
+
     List<Association> getAssociations(String submissionId);
 
     byte[] getSnpValidationReportTsv(String submissionId);

diff --git a/src/main/java/uk/ac/ebi/spot/gwas/curation/service/ConversionJaversService.java b/src/main/java/uk/ac/ebi/spot/gwas/curation/service/ConversionJaversService.java
@@ -7,6 +7,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
+import java.util.Set;
 
 public interface ConversionJaversService {
 
@@ -17,9 +18,14 @@ public interface ConversionJaversService {
     public void removeVersionMap(Optional<Map<Double, List<JaversChangeWrapper>>> javersChangeWrapperMap,
                                  List<Double> versionsTobeRemoved );
 
+    public void removeVersionMap(Optional<Map<Double, List<JaversChangeWrapper>>> javersChangeWrapperMap,
+                                 Set<Double> versionsTobeRemoved );
+
+    public Optional<Set<Double>> removeDuplicateMetaDataVersions(Optional<Map<Double, List<JaversChangeWrapper>>> javersChangeWrapperMap);
+
     public Optional<List<FileUpload>> filterJaversResponseForFiles(List<JaversChangeWrapper> javersChangeWrapperList);
 
-    public List<VersionSummary> filterStudiesFromJavers(Optional<Map<Double, List<JaversChangeWrapper>>> javersChangeWrapperList);
+    public List<VersionSummary> buiildVersionSummary(Optional<Map<Double, List<JaversChangeWrapper>>> javersChangeWrapperList);
 
     public List<VersionSummary> mapFilesToVersionSummary(List<VersionSummary> summaries, List<FileUpload> fileUploads);
 }
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/curation/service/SampleJaversService.java b/src/main/java/uk/ac/ebi/spot/gwas/curation/service/SampleJaversService.java
@@ -17,7 +17,7 @@ public interface SampleJaversService {
 
     public AddedRemoved getSampleVersionStats(List<Sample> prevSamples, List<Sample> newSamples);
 
-    public Sample processSampleTag(ElementChange elementChange);
+    public String processSampleTag(ElementChange elementChange);
 
 
 }
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/curation/service/SamplesService.java b/src/main/java/uk/ac/ebi/spot/gwas/curation/service/SamplesService.java
@@ -6,10 +6,13 @@
 import uk.ac.ebi.spot.gwas.deposition.domain.Submission;
 
 import java.util.List;
+import java.util.stream.Stream;
 
 public interface SamplesService {
 
 
     Sample getSample(String sampleId);
 
+    Stream<Sample> findByIdIn(List<String> ids);
+
 }
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/curation/service/StudiesService.java b/src/main/java/uk/ac/ebi/spot/gwas/curation/service/StudiesService.java
@@ -9,12 +9,15 @@
 import uk.ac.ebi.spot.gwas.deposition.dto.curation.*;
 
 import java.util.List;
+import java.util.stream.Stream;
 
 public interface StudiesService {
 
 
     Study getStudy(String studyId);
 
+    Stream<Study> getStudies(List<String> ids);
+
     Study getStudyByAccession(String accessionId, String submissionId);
 
     Study updateStudies(Study study);

diff --git a/src/main/java/uk/ac/ebi/spot/gwas/curation/service/StudyJaversService.java b/src/main/java/uk/ac/ebi/spot/gwas/curation/service/StudyJaversService.java
@@ -21,6 +21,6 @@ public interface StudyJaversService {
 
     public AddedRemoved getReportedEfoVersionStats(List<Study> prevStudies, List<Study> newStudies);
 
-    public Study processStudyTag(ElementChange elementChange);
+    public String processStudyTag(ElementChange elementChange);
 
 }
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/curation/service/impl/AssociationJaversServiceImpl.java b/src/main/java/uk/ac/ebi/spot/gwas/curation/service/impl/AssociationJaversServiceImpl.java
@@ -42,7 +42,7 @@ public VersionDiffStats findAssociationChanges(String tag, List<Association> pre
             diffStats.setAssociations(new ArrayList<>());
 
         prevAscns.forEach((asscn) -> {
-            log.info("VariantId*****"+asscn.getVariantId());
+            //log.info("VariantId*****"+asscn.getVariantId());
             List<AssociationDto> newAsscnsDto = newAscns.stream()
                     .filter((ascn) -> ascn.getVariantId().equals(asscn.getVariantId()))
                     .map(AssociationDtoAssembler::assemble)
@@ -70,8 +70,8 @@ public VersionDiffStats findAssociationChanges(String tag, List<Association> pre
     public List<ValueChangeWrapper> diffAssociations(AssociationDto dto1, AssociationDto dto2) {
         Javers javers = JaversBuilder.javers().build();
         Diff diff = javers.compare(dto1, dto2);
-        log.info("************");
-        log.info("Diff Asscn"+ diff);
+        //log.info("************");
+        //log.info("Diff Asscn"+ diff);
         List<ValueChange> valChanges = diff.getChangesByType(ValueChange.class);
         try {
             ValueChangeWrapper[]  changes = new ObjectMapper().readValue(
@@ -84,7 +84,7 @@ public List<ValueChangeWrapper> diffAssociations(AssociationDto dto1, Associatio
     }
 
     public AddedRemoved getAssociationVersionStats(List<Association> prevAscns, List<Association> newAscns) {
-        log.info("Inside getAssociationVersionStats() ");
+        //log.info("Inside getAssociationVersionStats() ");
 
         List<String> newAscnsTags = newAscns.stream()
                 .map(asscn -> asscn.getStudyTag() + asscn.getVariantId())
@@ -102,10 +102,10 @@ public AddedRemoved getAssociationVersionStats(List<Association> prevAscns, List
                 .filter(asscn -> !prevAscnsTags.contains(asscn.getStudyTag() + asscn.getVariantId()))
                 .collect(Collectors.toList());
 
-        log.info("newAscnsTags****"+newAscnsTags);
-        log.info("prevAscnsTags****"+prevAscnsTags);
-        log.info("asscnsRemoved****"+asscnsRemoved);
-        log.info("asscnsAdded****"+asscnsAdded);
+        //log.info("newAscnsTags****"+newAscnsTags);
+       // log.info("prevAscnsTags****"+prevAscnsTags);
+       // log.info("asscnsRemoved****"+asscnsRemoved);
+        //log.info("asscnsAdded****"+asscnsAdded);
 
         AddedRemoved addedRemoved = new AddedRemoved();
         addedRemoved.setAdded(asscnsAdded.size());
@@ -114,9 +114,10 @@ public AddedRemoved getAssociationVersionStats(List<Association> prevAscns, List
         return addedRemoved;
     }
 
-    public Association processAssociationTag(ElementChange elementChange){
+    public String processAssociationTag(ElementChange elementChange){
         if (elementChange.getElementChangeType().equals("ValueAdded")){
-            return associationsService.getAssociation(elementChange.getValue().toString() );
+            //return associationsService.getAssociation(elementChange.getValue().toString() );
+            return elementChange.getValue().toString();
         }
         return null;
     }

diff --git a/src/main/java/uk/ac/ebi/spot/gwas/curation/service/impl/AssociationsServiceImpl.java b/src/main/java/uk/ac/ebi/spot/gwas/curation/service/impl/AssociationsServiceImpl.java
@@ -20,6 +20,7 @@
 import java.util.*;
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 @Service
 public class AssociationsServiceImpl implements AssociationsService {
@@ -39,10 +40,10 @@ public class AssociationsServiceImpl implements AssociationsService {
 
     @Override
     public Association getAssociation(String associationId) {
-        log.info("Retrieving association: {}", associationId);
+        //log.info("Retrieving association: {}", associationId);
         Optional<Association> associationOptional = associationRepository.findById(associationId);
         if (associationOptional.isPresent()) {
-            log.info("Found association: {}", associationOptional.get().getStudyTag());
+            //log.info("Found association: {}", associationOptional.get().getStudyTag());
             return associationOptional.get();
         }
         log.error("Unable to find association: {}", associationId);
@@ -100,4 +101,9 @@ public SnpStatusReportDto getSnpStatus(String submissionId) {
         snpStatusReportDto.setNoValidSnps(associationRepository.countByIsValidAndSubmissionId(true, submissionId));
         return snpStatusReportDto;
     }
+
+    @Override
+    public Stream<Association> readBySeqIds(List<String> ids) {
+       return  associationRepository.readByIdIn(ids);
+    }
 }