Merge pull request #131 from diging/develop

CITE-138
diging · Feb 4, 2021 · c48358e · c48358e
2 parents 22638f6 + 9a10f6d
commit c48358e
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Showing 8 changed files with 112 additions and 36 deletions.
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/search/service/Indexer.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/search/service/Indexer.java
@@ -6,4 +6,6 @@ public interface Indexer {
 
     void indexCitation(ICitation citation);
 
+    void deleteCitation(ICitation citation);
+
 }
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/search/service/impl/IndexerImpl.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/search/service/impl/IndexerImpl.java
@@ -44,6 +44,11 @@ public void indexCitation(ICitation citation) {
         referenceRepo.save(reference);        
     }
 
+    @Override
+    public void deleteCitation(ICitation citation) {
+        referenceRepo.deleteById(citation.getKey());
+    }
+
     private void mapCitation(ICitation citation, Reference reference) {
         reference.setAbstractNote(citation.getAbstractNote());
         reference.setAccessDate(citation.getAccessDate());

diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/ICitationStore.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/ICitationStore.java
@@ -0,0 +1,22 @@
+package edu.asu.diging.citesphere.core.service;
+
+import java.util.Optional;
+
+import edu.asu.diging.citesphere.model.bib.ICitation;
+
+public interface ICitationStore {
+
+    /**
+     * Method to save citations. This method will also index 
+     * the citation before saving.
+     * 
+     * @param citation Citation to be saved.
+     * @return the saved Citation
+     */
+    ICitation save(ICitation citation);
+
+    Optional<ICitation> findById(String id);
+
+    void delete(ICitation citation);
+
+}
diff --git a/...ere/src/main/java/edu/asu/diging/citesphere/core/service/impl/AsyncCitationProcessor.java b/...ere/src/main/java/edu/asu/diging/citesphere/core/service/impl/AsyncCitationProcessor.java
@@ -2,6 +2,7 @@
 
 import java.time.OffsetDateTime;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
@@ -11,7 +12,6 @@
 import java.util.stream.Collectors;
 
 import javax.annotation.PostConstruct;
-import javax.management.RuntimeErrorException;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -22,16 +22,15 @@
 import edu.asu.diging.citesphere.core.model.jobs.JobStatus;
 import edu.asu.diging.citesphere.core.model.jobs.impl.GroupSyncJob;
 import edu.asu.diging.citesphere.core.repository.jobs.JobRepository;
-import edu.asu.diging.citesphere.core.search.service.Indexer;
 import edu.asu.diging.citesphere.core.service.IAsyncCitationProcessor;
+import edu.asu.diging.citesphere.core.service.ICitationStore;
 import edu.asu.diging.citesphere.core.service.jobs.ISyncJobManager;
 import edu.asu.diging.citesphere.core.zotero.DeletedZoteroElements;
 import edu.asu.diging.citesphere.core.zotero.IZoteroManager;
 import edu.asu.diging.citesphere.core.zotero.ZoteroCollectionsResponse;
 import edu.asu.diging.citesphere.core.zotero.ZoteroGroupItemsResponse;
 import edu.asu.diging.citesphere.data.bib.CitationCollectionRepository;
 import edu.asu.diging.citesphere.data.bib.CitationGroupRepository;
-import edu.asu.diging.citesphere.data.bib.CitationRepository;
 import edu.asu.diging.citesphere.model.bib.ICitation;
 import edu.asu.diging.citesphere.model.bib.ICitationCollection;
 import edu.asu.diging.citesphere.model.bib.ICitationGroup;
@@ -49,7 +48,7 @@ public class AsyncCitationProcessor implements IAsyncCitationProcessor {
     private IZoteroManager zoteroManager;
 
     @Autowired
-    private CitationRepository citationRepo;
+    private ICitationStore citationStore;
 
     @Autowired
     private CitationGroupRepository groupRepo;
@@ -63,14 +62,11 @@ public class AsyncCitationProcessor implements IAsyncCitationProcessor {
     @Autowired
     private ISyncJobManager jobManager;
 
-    @Autowired
-    private Indexer indexer;
-
     private List<JobStatus> inactiveJobStatuses;
 
     @PostConstruct
     public void init() {
-        inactiveJobStatuses = new ArrayList<>();
+        inactiveJobStatuses = Collections.synchronizedList(new ArrayList<JobStatus>());
         inactiveJobStatuses.add(JobStatus.CANCELED);
         inactiveJobStatuses.add(JobStatus.DONE);
         inactiveJobStatuses.add(JobStatus.FAILURE);
@@ -145,7 +141,7 @@ private void syncCitations(IUser user, String groupId, GroupSyncJob job, Map<Str
             AtomicInteger counter) {
         List<String> keysToRetrieve = new ArrayList<>();
         for (String key : versions.keySet()) {
-            Optional<ICitation> citation = citationRepo.findByKey(key);
+            Optional<ICitation> citation = citationStore.findById(key);
 
             if (citation.isPresent()) {
                 if (citation.get().getVersion() != versions.get(key)) {
@@ -198,9 +194,9 @@ private void syncCollections(IUser user, String groupId, GroupSyncJob job, Map<S
     private void removeDeletedItems(DeletedZoteroElements deletedElements, GroupSyncJob job) {
         if (deletedElements.getItems() != null) {
             for (String key : deletedElements.getItems()) {
-                Optional<ICitation> citation = citationRepo.findByKey(key);
+                Optional<ICitation> citation = citationStore.findById(key);
                 if (citation.isPresent()) {
-                    citationRepo.delete((Citation) citation.get());
+                    citationStore.delete((Citation) citation.get());
                 }
                 job.setCurrent(job.getCurrent() + 1);
                 jobRepo.save(job);
@@ -235,12 +231,12 @@ private long retrieveCollections(IUser user, String groupId, List<String> keysTo
     }
 
     private void storeCitation(ICitation citation) {
-        Optional<ICitation> optional = citationRepo.findByKey(citation.getKey());
+        Optional<ICitation> optional = citationStore.findById(citation.getKey());
         if (optional.isPresent()) {
-            citationRepo.delete((Citation) optional.get());
+            citationStore.delete((Citation) optional.get());
         }
-        citationRepo.save((Citation) citation);
-        indexer.indexCitation(citation);
+
+        citationStore.save((Citation) citation);
     }
 
     private void storeCitationCollection(ICitationCollection collection) {

diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
@@ -31,17 +31,16 @@
 import edu.asu.diging.citesphere.core.service.IAsyncCitationProcessor;
 import edu.asu.diging.citesphere.core.service.ICitationCollectionManager;
 import edu.asu.diging.citesphere.core.service.ICitationManager;
+import edu.asu.diging.citesphere.core.service.ICitationStore;
 import edu.asu.diging.citesphere.core.service.IGroupManager;
 import edu.asu.diging.citesphere.core.zotero.IZoteroManager;
 import edu.asu.diging.citesphere.data.bib.CitationGroupRepository;
-import edu.asu.diging.citesphere.data.bib.CitationRepository;
 import edu.asu.diging.citesphere.data.bib.ICitationDao;
 import edu.asu.diging.citesphere.model.bib.ICitation;
 import edu.asu.diging.citesphere.model.bib.ICitationCollection;
 import edu.asu.diging.citesphere.model.bib.ICitationGroup;
 import edu.asu.diging.citesphere.model.bib.ItemType;
 import edu.asu.diging.citesphere.model.bib.impl.BibField;
-import edu.asu.diging.citesphere.model.bib.impl.Citation;
 import edu.asu.diging.citesphere.model.bib.impl.CitationGroup;
 import edu.asu.diging.citesphere.model.bib.impl.CitationResults;
 import edu.asu.diging.citesphere.user.IUser;
@@ -67,8 +66,8 @@ public class CitationManager implements ICitationManager {
     private CitationGroupRepository groupRepository;
 
     @Autowired
-    private CitationRepository citationRepository;
-
+    private ICitationStore citationStore;
+    
     @Autowired
     private ICitationDao citationDao;
 
@@ -96,7 +95,7 @@ public void init() {
     @Override
     public ICitation getCitation(IUser user, String groupId, String key)
             throws GroupDoesNotExistException, CannotFindCitationException, ZoteroHttpStatusException {
-        Optional<ICitation> optional = citationRepository.findByKey(key);
+        Optional<ICitation> optional = citationStore.findById(key);
         if (optional.isPresent()) {
             ICitation citation = optional.get();
             ICitationGroup group = groupManager.getGroup(user, groupId);
@@ -138,17 +137,17 @@ public ICitation getCitationFromZotero(IUser user, String groupId, String key) t
     public void updateCitation(IUser user, String groupId, ICitation citation)
             throws ZoteroConnectionException, CitationIsOutdatedException, ZoteroHttpStatusException {
         long citationVersion = zoteroManager.getGroupItemVersion(user, groupId, citation.getKey());
-        Optional<ICitation> storedCitationOptional = citationRepository.findByKey(citation.getKey());
+        Optional<ICitation> storedCitationOptional = citationStore.findById(citation.getKey());
         if (storedCitationOptional.isPresent()) {
             ICitation storedCitation = storedCitationOptional.get();
             if (storedCitation.getVersion() != citationVersion) {
                 throw new CitationIsOutdatedException();
             }
-            citationRepository.delete((Citation) storedCitationOptional.get());
+            citationStore.delete(storedCitationOptional.get());
         }
 
         ICitation updatedCitation = zoteroManager.updateCitation(user, groupId, citation);
-        citationRepository.save((Citation) updatedCitation);
+        citationStore.save(updatedCitation);
     }
 
     @Override
@@ -161,7 +160,7 @@ public ICitation createCitation(IUser user, String groupId, List<String> collect
         }
 
         ICitation newCitation = zoteroManager.createCitation(user, groupId, collectionIds, citation);
-        return citationRepository.save((Citation) newCitation);
+        return citationStore.save(newCitation);
 
         // mark group outdated, so it'll be updated on the next loading
 //        ICitationGroup group = groupOptional.get();
@@ -182,11 +181,11 @@ public ICitation updateCitationFromZotero(IUser user, String groupId, String ite
             ICitation citation = zoteroManager.getGroupItem(user, groupId, itemKey);
             citation.setGroup(groupOptional.get().getGroupId() + "");
 
-            Optional<ICitation> oldCitation = citationRepository.findByKey(itemKey);
+            Optional<ICitation> oldCitation = citationStore.findById(itemKey);
             if(oldCitation.isPresent()) {
-                citationRepository.delete((Citation)oldCitation.get());
+                citationStore.delete(oldCitation.get());
             }
-            citationRepository.save((Citation) citation);
+            citationStore.save(citation);
             return citation;
         } catch (HttpClientErrorException ex) {
             throw new CannotFindCitationException(ex);

diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationStore.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationStore.java
@@ -0,0 +1,51 @@
+package edu.asu.diging.citesphere.core.service.impl;
+
+import java.util.Optional;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import edu.asu.diging.citesphere.core.search.service.Indexer;
+import edu.asu.diging.citesphere.core.service.ICitationStore;
+import edu.asu.diging.citesphere.data.bib.CitationRepository;
+import edu.asu.diging.citesphere.model.bib.ICitation;
+import edu.asu.diging.citesphere.model.bib.impl.Citation;
+
+/**
+ * Service class to store and retrieve {@link ICitation}s.
+ * 
+ * @author Julia Damerow
+ *
+ */
+@Service
+public class CitationStore implements ICitationStore {
+
+    @Autowired
+    private CitationRepository citationRepository;
+
+    @Autowired 
+    private Indexer indexer;
+
+    /* (non-Javadoc)
+     * @see edu.asu.diging.citesphere.core.service.impl.ICitationStore#save(edu.asu.diging.citesphere.model.bib.ICitation)
+     */
+    @Override
+    public ICitation save(ICitation citation) {
+        indexer.indexCitation(citation);
+        return citationRepository.save((Citation) citation);
+    }
+
+    /* (non-Javadoc)
+     * @see edu.asu.diging.citesphere.core.service.impl.ICitationStore#findById(java.lang.String)
+     */
+    @Override
+    public Optional<ICitation> findById(String id) {
+        return citationRepository.findByKey(id);
+    }
+
+    @Override
+    public void delete(ICitation citation) {
+        indexer.deleteCitation(citation);
+        citationRepository.delete((Citation) citation);
+    }
+}
diff --git a/citesphere/src/main/resources/log4j.xml b/citesphere/src/main/resources/log4j.xml
@@ -40,10 +40,10 @@
         <level value="${log.level}" />
     </logger>
     <logger name="org.springframework.data">
-        <level value="debug" />
+        <level value="${log.level}" />
     </logger>
     <logger name="org.elasticsearch">
-        <level value="debug" />
+        <level value="${log.level}" />
     </logger>
 
     <logger name="org.hibernate.SQL">

diff --git a/...sphere/src/test/java/edu/asu/diging/citesphere/core/service/impl/CitationManagerTest.java b/...sphere/src/test/java/edu/asu/diging/citesphere/core/service/impl/CitationManagerTest.java
@@ -21,6 +21,7 @@
 import edu.asu.diging.citesphere.core.exceptions.GroupDoesNotExistException;
 import edu.asu.diging.citesphere.core.exceptions.ZoteroHttpStatusException;
 import edu.asu.diging.citesphere.core.exceptions.ZoteroItemCreationFailedException;
+import edu.asu.diging.citesphere.core.service.ICitationStore;
 import edu.asu.diging.citesphere.core.service.IGroupManager;
 import edu.asu.diging.citesphere.core.zotero.IZoteroManager;
 import edu.asu.diging.citesphere.data.bib.CitationGroupRepository;
@@ -44,7 +45,7 @@ public class CitationManagerTest {
     private CitationGroupRepository groupRepository;
 
     @Mock
-    private CitationRepository citationRepository;
+    private ICitationStore citationStore;
 
     @Mock
     private IGroupManager groupManager;
@@ -87,11 +88,11 @@ public void setUp() throws ZoteroHttpStatusException {
         existingCitation.setKey(EXISTING_ID);
         existingCitation.setVersion(currentVersion);
         existingCitation.setGroup(GROUP_ID);
-        Mockito.when(citationRepository.findByKey(EXISTING_ID)).thenReturn(Optional.of(existingCitation));
+        Mockito.when(citationStore.findById(EXISTING_ID)).thenReturn(Optional.of(existingCitation));
 
         zoteroCitation.setKey(ZOTERO_CITATION_ID);
         Mockito.when(zoteroManager.getGroupItem(user, GROUP_ID, ZOTERO_CITATION_ID)).thenReturn(zoteroCitation);
-        Mockito.when(citationRepository.findByKey(ZOTERO_CITATION_ID)).thenReturn(Optional.empty());
+        Mockito.when(citationStore.findById(ZOTERO_CITATION_ID)).thenReturn(Optional.empty());
 
         group1 = new CitationGroup();
         group1.setGroupId(GROUP1_ID);
@@ -146,7 +147,7 @@ public void test_updateCitation_success() throws ZoteroConnectionException, Cita
         Mockito.when(zoteroManager.updateCitation(user, GROUP_ID, existingCitation)).thenReturn(updatedCitation);
 
         managerToTest.updateCitation(user, GROUP_ID, existingCitation);
-        Mockito.verify(citationRepository).save((Citation)updatedCitation);
+        Mockito.verify(citationStore).save(updatedCitation);
     }
 
     @Test(expected=CitationIsOutdatedException.class)
@@ -162,7 +163,7 @@ public void test_updateCitationFromZotero_success() throws GroupDoesNotExistExce
         updatedCitation.setVersion(new Long(2));
         Mockito.when(zoteroManager.getGroupItem(user, GROUP_ID, EXISTING_ID)).thenReturn(updatedCitation);
         ICitation actual = managerToTest.updateCitationFromZotero(user, GROUP_ID, EXISTING_ID);
-        Mockito.verify(citationRepository).save((Citation)updatedCitation);
+        Mockito.verify(citationStore).save(updatedCitation);
         Assert.assertEquals(updatedCitation, actual);
     }
 
@@ -238,10 +239,10 @@ public void test_createCitation_success() throws ZoteroConnectionException, Zote
 
         Citation newCitation = new Citation();
         Mockito.when(zoteroManager.createCitation(user, GROUP_ID, new ArrayList<>(), newCitation)).thenReturn(createdCitation);
-        Mockito.when(citationRepository.save(createdCitation)).thenReturn(createdCitation);
+        Mockito.when(citationStore.save(createdCitation)).thenReturn(createdCitation);
 
         ICitation actual = managerToTest.createCitation(user, GROUP_ID, new ArrayList<>(), newCitation);
-        Mockito.verify(citationRepository).save((Citation)createdCitation);
+        Mockito.verify(citationStore).save(createdCitation);
         Assert.assertEquals(createdCitation, actual);
     }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -6,4 +6,6 @@ public interface Indexer {

		void indexCitation(ICitation citation);

		void deleteCitation(ICitation citation);

		}