Enabled deletion of non-loaded agms and their linked disease annotati…

…ons on bulk load, SCRUM-1396
alliance-genome · Apr 26, 2022 · ae6e697 · ae6e697
1 parent 1eabf9b
commit ae6e697
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Showing 6 changed files with 116 additions and 45 deletions.
diff --git a/src/main/java/org/alliancegenome/curation_api/dao/AffectedGenomicModelDAO.java b/src/main/java/org/alliancegenome/curation_api/dao/AffectedGenomicModelDAO.java
@@ -1,6 +1,9 @@
 package org.alliancegenome.curation_api.dao;
 
+import java.util.List;
+
 import javax.enterprise.context.ApplicationScoped;
+import javax.persistence.Query;
 
 import org.alliancegenome.curation_api.base.dao.BaseSQLDAO;
 import org.alliancegenome.curation_api.model.entities.AffectedGenomicModel;
@@ -11,4 +14,10 @@ public class AffectedGenomicModelDAO extends BaseSQLDAO<AffectedGenomicModel> {
     protected AffectedGenomicModelDAO() {
         super(AffectedGenomicModel.class);
     }
+
+    public List<String> findAllAnnotationIds(String taxonID) {
+        Query jpqlQuery = entityManager.createQuery("SELECT annotation.curie FROM AffectedGenomicModel annotation WHERE annotation.taxon.curie=:taxonId");
+        jpqlQuery.setParameter("taxonId", taxonID);
+        return (List<String>) jpqlQuery.getResultList();
+    }
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/AgmFmsExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/AgmFmsExecutor.java
@@ -1,25 +1,32 @@
 package org.alliancegenome.curation_api.jobs.executors;
 
 import java.io.FileInputStream;
+import java.util.*;
+import java.util.stream.Collectors;
 import java.util.zip.GZIPInputStream;
 
 import javax.enterprise.context.ApplicationScoped;
 import javax.inject.Inject;
 
+import org.alliancegenome.curation_api.dao.AffectedGenomicModelDAO;
 import org.alliancegenome.curation_api.exceptions.ObjectUpdateException;
 import org.alliancegenome.curation_api.exceptions.ObjectUpdateException.ObjectUpdateExceptionData;
+import org.alliancegenome.curation_api.model.entities.AffectedGenomicModel;
 import org.alliancegenome.curation_api.model.entities.bulkloads.*;
 import org.alliancegenome.curation_api.model.ingest.fms.dto.*;
 import org.alliancegenome.curation_api.response.*;
 import org.alliancegenome.curation_api.services.AffectedGenomicModelService;
 import org.alliancegenome.curation_api.util.ProcessDisplayHelper;
+import org.apache.commons.collections4.ListUtils;
 
 import lombok.extern.jbosslog.JBossLog;
 
 @JBossLog
 @ApplicationScoped
 public class AgmFmsExecutor extends LoadFileExecutor {
 
+    @Inject AffectedGenomicModelDAO affectedGenomicModelDAO;
+
     @Inject AffectedGenomicModelService affectedGenomicModelService;
 
     public void runLoad(BulkLoadFile bulkLoadFile) {
@@ -38,25 +45,55 @@ public void runLoad(BulkLoadFile bulkLoadFile) {
 
     // Gets called from the API directly
     public APIResponse runLoad(AffectedGenomicModelMetaDataFmsDTO agmData) {
+        List<String> taxonIDs = agmData.getData().stream()
+                                 .map( agmDTO -> agmDTO.getTaxonId() ).distinct().collect( Collectors.toList() );
+
+        List<String> annotationsIdsBefore = new ArrayList<String>();
+        for(String taxonID: taxonIDs) {
+            List<String> annotationIds = affectedGenomicModelDAO.findAllAnnotationIds(taxonID);
+            log.debug("runLoad: Before: taxonID " + taxonID + " " + annotationIds.size());
+            annotationsIdsBefore.addAll(annotationIds);
+        }
+
+        log.debug("runLoad: Before: total " + annotationsIdsBefore.size());
+        List<String> annotationsIdsLoaded = new ArrayList<>();
 
         BulkLoadFileHistory history = new BulkLoadFileHistory(agmData.getData().size());
 
         ProcessDisplayHelper ph = new ProcessDisplayHelper(10000);
         ph.startProcess("AGM FMS DTO Update", agmData.getData().size());
-        for(AffectedGenomicModelFmsDTO agm: agmData.getData()) {
+        for(AffectedGenomicModelFmsDTO agmDTO: agmData.getData()) {
             try {
-                affectedGenomicModelService.processUpdate(agm);
+                AffectedGenomicModel annotation = affectedGenomicModelService.processUpdate(agmDTO);
                 history.incrementCompleted();
+                annotationsIdsLoaded.add(annotation.getCurie());
             } catch (ObjectUpdateException e) {
                 addException(history, e.getData());
             } catch (Exception e) {
-                addException(history, new ObjectUpdateExceptionData(agm, e.getMessage()));
+                addException(history, new ObjectUpdateExceptionData(agmDTO, e.getMessage()));
             }
 
             ph.progressProcess();
         }
         ph.finishProcess();
-
+
+        log.debug("runLoad: Loaded: " + taxonIDs.toString() + " " + annotationsIdsLoaded.size());
+
+        List<String> distinctLoaded = annotationsIdsLoaded.stream().distinct().collect(Collectors.toList());
+        log.debug("runLoad: Distinct loaded: " + taxonIDs.toString() + " " + distinctLoaded.size());
+
+        List<String> curiesToRemove = ListUtils.subtract(annotationsIdsBefore, distinctLoaded);
+        log.debug("runLoad: Remove: " + taxonIDs.toString() + " " + curiesToRemove.size());
+
+        for (String curie : curiesToRemove) {
+            SearchResponse<AffectedGenomicModel> agm = affectedGenomicModelDAO.findByField("curie", curie);
+            if (agm != null && agm.getTotalResults() == 1) {
+                affectedGenomicModelDAO.remove(agm.getResults().get(0).getCurie());
+            } else {
+                log.error("Failed getting annotation: " + curie);
+            }
+        }
+
         return new LoadHistoryResponce(history);
     }
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/AGMDiseaseAnnotation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/AGMDiseaseAnnotation.java
@@ -23,7 +23,9 @@ public class AGMDiseaseAnnotation extends DiseaseAnnotation {
 
     @IndexedEmbedded(includeDepth = 1)
     @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
-    @ManyToOne
+    @ManyToOne(cascade = {})
+    @org.hibernate.annotations.OnDelete(action = org.hibernate.annotations.OnDeleteAction.CASCADE)
+    @JoinColumn(foreignKey = @ForeignKey(name="fk_agmdasubject"))
     @JsonView({View.FieldsOnly.class})
     private AffectedGenomicModel subject;
 

diff --git a/src/main/java/org/alliancegenome/curation_api/services/AffectedGenomicModelService.java b/src/main/java/org/alliancegenome/curation_api/services/AffectedGenomicModelService.java
@@ -87,7 +87,7 @@ public ObjectResponse<AffectedGenomicModel> update(AffectedGenomicModel uiEntity
 
 
     @Transactional
-    public void processUpdate(AffectedGenomicModelFmsDTO agm) throws ObjectUpdateException {
+    public AffectedGenomicModel processUpdate(AffectedGenomicModelFmsDTO agm) throws ObjectUpdateException {
         // TODO: add loading of components
         // TODO: add loading of sequenceTargetingReagents
         // TODO: add loading of parentalPopulations
@@ -114,6 +114,8 @@ public void processUpdate(AffectedGenomicModelFmsDTO agm) throws ObjectUpdateExc
         handleSecondaryIds(agm, dbAgm);
 
         affectedGenomicModelDAO.persist(dbAgm);
+
+        return dbAgm;
     }
 
     private void handleCrossReference(AffectedGenomicModelFmsDTO agm, AffectedGenomicModel dbAgm) {

diff --git a/src/main/resources/db/migration/v0.4.0.1__agr_curation_api.sql b/src/main/resources/db/migration/v0.4.0.1__agr_curation_api.sql
@@ -2,3 +2,5 @@
 -- This change does require the application to be restarted after initial start-up (so hibernate would create the new constraint)!
 ALTER TABLE "genediseaseannotation"
 	DROP CONSTRAINT "fk8xs26m9hfc38nmy7gvu3cec3t";
+ALTER TABLE "agmdiseaseannotation"
+	DROP CONSTRAINT "fklvr4o1waqclvbktjmyg6x25ls";