Rtirabassi uid map oom

dcm4chee-arc-audit/pom.xml

@@ -82,12 +82,6 @@
       <version>${project.version}</version>
       <scope>provided</scope>
     </dependency>
-    <dependency>
-      <groupId>org.dcm4che.dcm4chee-arc</groupId>
-      <artifactId>dcm4chee-arc-keycloak</artifactId>
-      <version>${project.version}</version>
-      <scope>provided</scope>
-    </dependency>
     <dependency>
       <groupId>org.dcm4che.dcm4chee-arc</groupId>
       <artifactId>dcm4chee-arc-patient</artifactId>

dcm4chee-arc-delete/src/main/java/org/dcm4chee/arc/delete/impl/DeletionServiceEJB.java

@@ -516,6 +516,14 @@ private boolean hasSeriesWithOtherRejectionState(Study study, RejectionState rej
                 .getSingleResult() > 0;
     }
 
+    public boolean hasInUseFile(String storageID, String storagePath) {
+        return em.createNamedQuery(Location.COUNT_IN_USE_FILES, Long.class)
+                .setParameter(1, storageID)
+                .setParameter(2, Location.Status.OK)
+                .setParameter(3, storagePath)
+                .getSingleResult() > 0;
+    }
+
     private long countStudiesOfPatient(Patient patient) {
         return em.createNamedQuery(Study.COUNT_STUDIES_OF_PATIENT, Long.class).setParameter(1, patient)
                 .getSingleResult();

dcm4chee-arc-delete/src/main/java/org/dcm4chee/arc/delete/impl/PurgeStorageScheduler.java

@@ -502,7 +502,13 @@ private void deleteObjectsFromStorage(ArchiveDeviceExtension arcDev, StorageDesc
     private void deleteLocation(Storage storage, Location location, AtomicInteger success, AtomicInteger skipped) {
         try {
             if (ejb.claimDeleteObject(location)) {
-                storage.deleteObject(location.getStoragePath());
+                if ( !ejb.hasInUseFile(location.getStorageID(), location.getStoragePath()) ) {
+                    // File can actually be removed since not used in any other valid location
+                    storage.deleteObject(location.getStoragePath());
+                }
+                else {
+                    LOG.debug("Location {} deleted from {}, but file is still in use", location, storage);
+                }
                 ejb.removeLocation(location);
                 LOG.debug("Successfully delete {} from {}", location, storage);
                 success.getAndIncrement();

dcm4chee-arc-entity/src/main/java/org/dcm4chee/arc/entity/Location.java

@@ -57,6 +57,8 @@
     @Index(columnList = "multi_ref")
 })
 @NamedQueries({
+        @NamedQuery(name = Location.COUNT_IN_USE_FILES,
+                query = "select count(l) from Location l where l.storageID=?1 and l.status=?2 and l.storagePath=?3"),
         @NamedQuery(name = Location.FIND_BY_STORAGE_ID_AND_STATUS,
                 query = "select l from Location l where l.storageID=?1 and l.status=?2"),
         @NamedQuery(name = Location.FIND_BY_STUDY_PK,
@@ -125,6 +127,7 @@
 })
 public class Location {
 
+    public static final String COUNT_IN_USE_FILES = "Location.CountInUseFiles";
     public static final String FIND_BY_STORAGE_ID_AND_STATUS = "Location.FindByStorageIDAndStatus";
     public static final String FIND_BY_STUDY_PK = "Location.FindByStudyPk";
     public static final String FIND_BY_SERIES_PK = "Location.FindBySeriesPk";

dcm4chee-arc-retrieve/src/main/java/org/dcm4chee/arc/retrieve/RetrieveService.java

@@ -53,8 +53,9 @@
 import org.dcm4chee.arc.conf.ArchiveAEExtension;
 import org.dcm4chee.arc.conf.ArchiveDeviceExtension;
 import org.dcm4chee.arc.entity.Series;
-import org.dcm4chee.arc.metrics.MetricsService;
+import org.dcm4chee.arc.entity.UIDMap;
 import org.dcm4chee.arc.keycloak.HttpServletRequestInfo;
+import org.dcm4chee.arc.metrics.MetricsService;
 import org.dcm4chee.arc.storage.Storage;
 import org.dcm4chee.arc.store.InstanceLocations;
 import org.dcm4chee.arc.store.StoreService;
@@ -85,7 +86,7 @@ RetrieveContext newRetrieveContextGET(ArchiveAEExtension arcAE,
                                           Association as, Attributes cmd, QueryRetrieveLevel2 qrLevel, Attributes keys);
 
     RetrieveContext newRetrieveContextMOVE(ArchiveAEExtension arcAE,
-            Association as, Attributes cmd, QueryRetrieveLevel2 qrLevel, Attributes keys)
+                                           Association as, Attributes cmd, QueryRetrieveLevel2 qrLevel, Attributes keys)
             throws ConfigurationException;
 
     RetrieveContext newRetrieveContextWADO(
@@ -149,4 +150,6 @@ LocationInputStream openLocationInputStream(RetrieveContext ctx, InstanceLocatio
     Date getLastModifiedFromMatches(RetrieveContext ctx);
 
     Date getLastModified(RetrieveContext ctx);
+
+    UIDMap getUIDMap(Long uidMapPk, Map<Long, UIDMap> uidMapCache);
 }

dcm4chee-arc-retrieve/src/main/java/org/dcm4chee/arc/retrieve/impl/LocationQuery.java

@@ -55,7 +55,6 @@
 import org.hibernate.engine.spi.SessionFactoryImplementor;
 
 import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
 import javax.persistence.Tuple;
 import javax.persistence.criteria.*;
 import java.util.ArrayList;
@@ -82,6 +81,8 @@ class LocationQuery {
     private final Path<byte[]> instanceAttrBlob;
     private final List<Predicate> predicates = new ArrayList<>();
     private Predicate[] iuidPredicates;
+    private final HashMap<Long, UIDMap> uidMapCache = new HashMap<>();
+
 
     public LocationQuery(EntityManager em, CriteriaBuilder cb, RetrieveContext ctx, CodeCache codeCache) {
         this.em = em;
@@ -138,6 +139,7 @@ public LocationQuery(EntityManager em, CriteriaBuilder cb, RetrieveContext ctx,
                 locationPath.get(Location_.digest),
                 locationPath.get(Location_.size),
                 locationPath.get(Location_.status),
+                locationPath.get(Location_.multiReference),
                 series.get(Series_.pk),
                 instance.get(Instance_.pk),
                 instance.get(Instance_.retrieveAETs),
@@ -146,7 +148,6 @@ public LocationQuery(EntityManager em, CriteriaBuilder cb, RetrieveContext ctx,
                 instance.get(Instance_.createdTime),
                 instance.get(Instance_.updatedTime),
                 uidMap.get(UIDMap_.pk),
-                uidMap.get(UIDMap_.encodedMap),
                 instanceAttrBlob
         );
     }
@@ -171,7 +172,7 @@ public void execute(Map<Long, StudyInfo> studyInfoMap) {
     }
 
     private void execute(Map<Long, StudyInfo> studyInfoMap, Predicate[] predicates) {
-        HashMap<Long,InstanceLocations> instMap = new HashMap<>();
+        HashMap<Long, InstanceLocations> instMap = new HashMap<>();
         HashMap<Long,Attributes> seriesAttrsMap = new HashMap<>();
         HashMap<Long,Map<String, CodeEntity>> rejectedInstancesOfSeriesMap = new HashMap<>();
         for (Tuple tuple : em.createQuery(q.where(predicates)).getResultList()) {
@@ -240,9 +241,10 @@ private void addLocation(InstanceLocations match, Tuple tuple) {
                 .size(tuple.get(locationPath.get(Location_.size)))
                 .status(tuple.get(locationPath.get(Location_.status)))
                 .build();
+        location.setMultiReference(tuple.get(locationPath.get(Location_.multiReference))) ;
         Long uidMapPk = tuple.get(uidMap.get(UIDMap_.pk));
         if (uidMapPk != null) {
-            location.setUidMap(new UIDMap(uidMapPk, tuple.get(uidMap.get(UIDMap_.encodedMap))));
+            location.setUidMap(ctx.getRetrieveService().getUIDMap(uidMapPk, uidMapCache));
         }
         match.getLocations().add(location);
     }

dcm4chee-arc-retrieve/src/main/java/org/dcm4chee/arc/retrieve/impl/RetrieveContextImpl.java

@@ -52,9 +52,12 @@
 import org.dcm4chee.arc.conf.*;
 import org.dcm4chee.arc.entity.Location;
 import org.dcm4chee.arc.entity.Series;
-import org.dcm4chee.arc.retrieve.*;
-import org.dcm4chee.arc.storage.Storage;
 import org.dcm4chee.arc.keycloak.HttpServletRequestInfo;
+import org.dcm4chee.arc.retrieve.RetrieveContext;
+import org.dcm4chee.arc.retrieve.RetrieveService;
+import org.dcm4chee.arc.retrieve.SeriesInfo;
+import org.dcm4chee.arc.retrieve.StudyInfo;
+import org.dcm4chee.arc.storage.Storage;
 import org.dcm4chee.arc.store.InstanceLocations;
 import org.dcm4chee.arc.store.UpdateLocation;
 

dcm4chee-arc-retrieve/src/main/java/org/dcm4chee/arc/retrieve/impl/RetrieveServiceEJB.java

@@ -43,11 +43,13 @@
 import org.dcm4chee.arc.entity.Completeness;
 import org.dcm4chee.arc.entity.Series;
 import org.dcm4chee.arc.entity.Study;
+import org.dcm4chee.arc.entity.UIDMap;
 import org.dcm4chee.arc.retrieve.RetrieveContext;
 
 import javax.ejb.Stateless;
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
+import java.util.Map;
 
 /**
  * @author Gunter Zeilinger <[email protected]>
@@ -87,6 +89,15 @@ public void updateCompleteness(RetrieveContext ctx, Completeness completeness) {
         }
     }
 
+    public UIDMap getUIDMapReference(Long uidMapPk, Map<Long, UIDMap> uidMapCache) {
+        UIDMap uidMap = uidMapCache.get(uidMapPk) ;
+        if ( null == uidMap ) {
+            uidMap = em.find(UIDMap.class, uidMapPk) ;
+            uidMapCache.put(uidMapPk, uidMap) ;
+        }
+        return uidMap;
+    }
+
     private void setCompletenessOfStudy(String studyInstanceUID, Completeness completeness) {
         em.createNamedQuery(completeness == Completeness.PARTIAL
                 ? Study.INCREMENT_FAILED_RETRIEVES

dcm4chee-arc-retrieve/src/main/java/org/dcm4chee/arc/retrieve/impl/RetrieveServiceImpl.java

@@ -58,8 +58,8 @@
 import org.dcm4chee.arc.code.CodeCache;
 import org.dcm4chee.arc.conf.*;
 import org.dcm4chee.arc.entity.*;
-import org.dcm4chee.arc.metrics.MetricsService;
 import org.dcm4chee.arc.keycloak.HttpServletRequestInfo;
+import org.dcm4chee.arc.metrics.MetricsService;
 import org.dcm4chee.arc.query.scu.CFindSCU;
 import org.dcm4chee.arc.query.scu.CFindSCUAttributeCoercion;
 import org.dcm4chee.arc.query.util.QueryBuilder;
@@ -153,7 +153,7 @@ public ArchiveDeviceExtension getArchiveDeviceExtension() {
 
     @Override
     public RetrieveContext newRetrieveContextGET(ArchiveAEExtension arcAE,
-            Association as, Attributes rqCmd, QueryRetrieveLevel2 qrLevel, Attributes keys) {
+                                                 Association as, Attributes rqCmd, QueryRetrieveLevel2 qrLevel, Attributes keys) {
         RetrieveContext ctx = newRetrieveContext(arcAE, as, qrLevel, keys);
         ctx.setPriority(rqCmd.getInt(Tag.Priority, 0));
         ctx.setDestinationAETitle(as.getRemoteAET());
@@ -162,7 +162,7 @@ public RetrieveContext newRetrieveContextGET(ArchiveAEExtension arcAE,
 
     @Override
     public RetrieveContext newRetrieveContextMOVE(ArchiveAEExtension arcAE,
-            Association as, Attributes rqCmd, QueryRetrieveLevel2 qrLevel, Attributes keys)
+                                                  Association as, Attributes rqCmd, QueryRetrieveLevel2 qrLevel, Attributes keys)
             throws ConfigurationException {
         RetrieveContext ctx = newRetrieveContext(arcAE, as, qrLevel, keys);
         ctx.setPriority(rqCmd.getInt(Tag.Priority, 0));
@@ -321,7 +321,7 @@ public boolean calculateMatches(RetrieveContext ctx) throws DicomServiceExceptio
         Collection<InstanceLocations> matches = ctx.getMatches();
         matches.clear();
         try {
-            HashMap<Long,StudyInfo> studyInfoMap = new HashMap<>();
+            HashMap<Long, StudyInfo> studyInfoMap = new HashMap<>();
             Series.MetadataUpdate metadataUpdate = ctx.getSeriesMetadataUpdate();
             if (metadataUpdate != null && metadataUpdate.instancePurgeState == Series.InstancePurgeState.PURGED) {
                 SeriesAttributes seriesAttributes = new SeriesAttributes(em, cb, metadataUpdate.seriesPk);
@@ -982,4 +982,9 @@ public BulkData createBulkData(DicomInputStream dis) throws IOException {
         }
         return attrs;
     }
+
+    @Override
+    public UIDMap getUIDMap(Long uidMapPk, Map<Long, UIDMap> uidMapCache) {
+        return ejb.getUIDMapReference(uidMapPk, uidMapCache);
+    }
 }

dcm4chee-arc-store/src/main/java/org/dcm4chee/arc/store/impl/StoreServiceEJB.java

@@ -1503,7 +1503,13 @@ private Location copyLocation(StoreSession session,
             Location prevLocation, Instance instance, Map<String, String> uidMap, Map<Long, UIDMap> uidMapCache) {
         if (prevLocation.getMultiReference() == null) {
             prevLocation = em.find(Location.class, prevLocation.getPk());
-            prevLocation.setMultiReference(idService.newLocationMultiReference());
+            // Since Location members could have been populated by a query result, not containing multiReference value,
+            // the location itself is now reloaded.
+            // This means that prevLocation.getMultiReference() can now return a non null value.
+            // That's why check must be done again before assigning a new value.
+            if (prevLocation.getMultiReference() == null) {
+                prevLocation.setMultiReference(idService.newLocationMultiReference());
+            }
         }
         Location newLocation = new Location(prevLocation);
         newLocation.setUidMap(createUIDMap(uidMap, prevLocation.getUidMap(), uidMapCache));