Added support to link submissions to PMIDs from body of works.

EBISPOT · May 27, 2020 · ae15549 · ae15549
1 parent ab79096
commit ae15549
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Showing 7 changed files with 40 additions and 7 deletions.
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/deposition/components/BodyOfWorkListener.java b/src/main/java/uk/ac/ebi/spot/gwas/deposition/components/BodyOfWorkListener.java
@@ -7,7 +7,9 @@
 import uk.ac.ebi.spot.gwas.deposition.domain.BodyOfWorkWatch;
 import uk.ac.ebi.spot.gwas.deposition.domain.Submission;
 import uk.ac.ebi.spot.gwas.deposition.repository.BodyOfWorkWatchRepository;
+import uk.ac.ebi.spot.gwas.deposition.repository.SubmissionRepository;
 
+import java.util.List;
 import java.util.Optional;
 
 @Component
@@ -16,14 +18,27 @@ public class BodyOfWorkListener {
     @Autowired
     private BodyOfWorkWatchRepository bodyOfWorkWatchRepository;
 
+    @Autowired
+    private SubmissionRepository submissionRepository;
+
     @Async
-    public void update(BodyOfWork bodyOfWork) {
+    public void update(BodyOfWork bodyOfWork, String publicationId) {
         Optional<BodyOfWorkWatch> bodyOfWorkWatchOptional = bodyOfWorkWatchRepository.findByBowId(bodyOfWork.getBowId());
         if (bodyOfWorkWatchOptional.isPresent()) {
             BodyOfWorkWatch bodyOfWorkWatch = bodyOfWorkWatchOptional.get();
             bodyOfWorkWatch.setVisited(false);
             bodyOfWorkWatchRepository.save(bodyOfWorkWatch);
         }
+
+        if (publicationId != null) {
+            List<Submission> submissionList = submissionRepository.findByBodyOfWorksContainsAndArchived(bodyOfWork.getBowId(), false);
+            for (Submission submission : submissionList) {
+                if (submission.getPublicationId() == null) {
+                    submission.setPublicationId(publicationId);
+                    submissionRepository.save(submission);
+                }
+            }
+        }
     }
 
     public void update(Submission submission) {

diff --git a/src/main/java/uk/ac/ebi/spot/gwas/deposition/repository/StudyRepository.java b/src/main/java/uk/ac/ebi/spot/gwas/deposition/repository/StudyRepository.java
@@ -12,6 +12,8 @@ public interface StudyRepository extends MongoRepository<Study, String> {
 
     Page<Study> findBySubmissionId(String submissionId, Pageable page);
 
+    Stream<Study> readByIdIn(List<String> ids);
+
     Stream<Study> readBySubmissionId(String submissionId);
 
     List<Study> findByIdIn(List<String> ids);

diff --git a/src/main/java/uk/ac/ebi/spot/gwas/deposition/repository/SubmissionRepository.java b/src/main/java/uk/ac/ebi/spot/gwas/deposition/repository/SubmissionRepository.java
@@ -28,6 +28,8 @@ public interface SubmissionRepository extends MongoRepository<Submission, String
 
     Page<Submission> findByBodyOfWorksContainsAndArchived(String bodyOfWorkId, boolean archived, Pageable page);
 
+    List<Submission> findByBodyOfWorksContainsAndArchived(String bodyOfWorkId, boolean archived);
+
     Page<Submission> findByPublicationIdAndArchived(String publicationId, boolean archived, Pageable page);
 
     Page<Submission> findByPublicationIdAndArchivedAndCreated_UserId(String publicationId, boolean b, String userId, Pageable page);

diff --git a/src/main/java/uk/ac/ebi/spot/gwas/deposition/service/impl/BodyOfWorkServiceImpl.java b/src/main/java/uk/ac/ebi/spot/gwas/deposition/service/impl/BodyOfWorkServiceImpl.java
@@ -8,12 +8,10 @@
 import org.springframework.data.domain.Pageable;
 import org.springframework.stereotype.Service;
 import uk.ac.ebi.spot.gwas.deposition.components.BodyOfWorkListener;
-import uk.ac.ebi.spot.gwas.deposition.domain.BodyOfWork;
-import uk.ac.ebi.spot.gwas.deposition.domain.Provenance;
-import uk.ac.ebi.spot.gwas.deposition.domain.Study;
-import uk.ac.ebi.spot.gwas.deposition.domain.User;
+import uk.ac.ebi.spot.gwas.deposition.domain.*;
 import uk.ac.ebi.spot.gwas.deposition.exception.EntityNotFoundException;
 import uk.ac.ebi.spot.gwas.deposition.repository.BodyOfWorkRepository;
+import uk.ac.ebi.spot.gwas.deposition.repository.PublicationRepository;
 import uk.ac.ebi.spot.gwas.deposition.repository.StudyRepository;
 import uk.ac.ebi.spot.gwas.deposition.service.BodyOfWorkService;
 import uk.ac.ebi.spot.gwas.deposition.service.CuratorAuthService;
@@ -47,6 +45,9 @@ public class BodyOfWorkServiceImpl implements BodyOfWorkService {
     @Autowired
     private BodyOfWorkListener bodyOfWorkListener;
 
+    @Autowired
+    private PublicationRepository publicationRepository;
+
     @Override
     public BodyOfWork createBodyOfWork(BodyOfWork bodyOfWork) {
         log.info("Creating body of work: {}", bodyOfWork.getTitle());
@@ -150,6 +151,7 @@ public BodyOfWork updateBodyOfWork(String bodyofworkId, BodyOfWork bodyOfWork, U
         existing.setTitle(bodyOfWork.getTitle());
         existing.setUrl(bodyOfWork.getUrl());
 
+        String publicationId = null;
         if (existing.getPmids() != null) {
             if (!existing.getPmids().isEmpty()) {
                 List<Study> studyList = studyRepository.findByBodyOfWorkListContains(bodyofworkId);
@@ -164,11 +166,16 @@ public BodyOfWork updateBodyOfWork(String bodyofworkId, BodyOfWork bodyOfWork, U
                     study.setPmids(pmids);
                     studyRepository.save(study);
                 }
+
+                Optional<Publication> publicationOptional = publicationRepository.findByPmid(existing.getPmids().get(0));
+                if (publicationOptional.isPresent()) {
+                    publicationId = publicationOptional.get().getId();
+                }
             }
         }
 
         existing = bodyOfWorkRepository.save(existing);
-        bodyOfWorkListener.update(bodyOfWork);
+        bodyOfWorkListener.update(bodyOfWork, publicationId);
         return existing;
     }
 }
diff --git a/src/main/java/uk/ac/ebi/spot/gwas/deposition/service/impl/TemplatePrefillServiceImpl.java b/src/main/java/uk/ac/ebi/spot/gwas/deposition/service/impl/TemplatePrefillServiceImpl.java
@@ -78,7 +78,8 @@ public FileObject prefillGCST(String submissionId, User user) {
         log.info("Pre-filling GCST list: {}", submissionId);
         Submission submission = submissionService.getSubmission(submissionId, user);
         StudyCollector studyCollector = new StudyCollector();
-        Stream<Study> studyStream = studyRepository.readBySubmissionId(submission.getId());
+        Stream<Study> studyStream = studyRepository.readByIdIn(submission.getStudies());
+//        Stream<Study> studyStream = studyRepository.readBySubmissionId(submission.getId());
         studyStream.forEach(study -> studyCollector.add(study));
         studyStream.close();
 

diff --git a/src/main/resources/application-prod-fallback.yml b/src/main/resources/application-prod-fallback.yml
@@ -25,6 +25,9 @@ spring:
           starttls:
             enable: true
 
+audit:
+  enabled: true
+
 quartz:
   scheduler:
     dbName: gwasdepo

diff --git a/src/main/resources/application-prod.yml b/src/main/resources/application-prod.yml
@@ -25,6 +25,9 @@ spring:
           starttls:
             enable: true
 
+audit:
+  enabled: true
+
 quartz:
   scheduler:
     dbName: gwasdepo