Bug/cite 221

citesphere/pom.xml

@@ -410,27 +410,27 @@
         <dependency>
             <groupId>org.apache.tiles</groupId>
             <artifactId>tiles-template</artifactId>
-            <version>3.0.1</version>
+            <version>3.0.8</version>
         </dependency>
         <dependency>
             <groupId>org.apache.tiles</groupId>
             <artifactId>tiles-core</artifactId>
-            <version>3.0.1</version>
+            <version>3.0.8</version>
         </dependency>
         <dependency>
             <groupId>org.apache.tiles</groupId>
             <artifactId>tiles-api</artifactId>
-            <version>3.0.1</version>
+            <version>3.0.8</version>
         </dependency>
         <dependency>
             <groupId>org.apache.tiles</groupId>
             <artifactId>tiles-servlet</artifactId>
-            <version>3.0.1</version>
+            <version>3.0.8</version>
         </dependency>
         <dependency>
             <groupId>org.apache.tiles</groupId>
             <artifactId>tiles-jsp</artifactId>
-            <version>3.0.1</version>
+            <version>3.0.8</version>
         </dependency>
 
         <dependency>
@@ -563,7 +563,7 @@
         <dependency>
             <groupId>commons-io</groupId>
             <artifactId>commons-io</artifactId>
-            <version>2.7</version>
+            <version>2.14.0</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/io.jsonwebtoken/jjwt -->
@@ -651,8 +651,8 @@
             <plugin>
                 <artifactId>maven-compiler-plugin</artifactId>
                 <configuration>
-                    <source>11</source>
-                    <target>11</target>
+                    <source>1.8</source>
+                    <target>1.8</target>
                     <encoding>UTF-8</encoding>
                 </configuration>
             </plugin>

citesphere/src/main/java/edu/asu/diging/citesphere/api/v1/user/GroupApiController.java

@@ -11,14 +11,11 @@
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestHeader;
 import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestParam;
 
 import edu.asu.diging.citesphere.api.v1.V1Controller;
-import edu.asu.diging.citesphere.api.v1.model.impl.Collections;
 import edu.asu.diging.citesphere.api.v1.model.impl.Group;
 import edu.asu.diging.citesphere.core.exceptions.GroupDoesNotExistException;
 import edu.asu.diging.citesphere.core.service.IGroupManager;
-import edu.asu.diging.citesphere.core.service.jobs.ISyncJobManager;
 import edu.asu.diging.citesphere.core.user.IUserManager;
 import edu.asu.diging.citesphere.model.bib.ICitationGroup;
 import edu.asu.diging.citesphere.user.IUser;

citesphere/src/main/java/edu/asu/diging/citesphere/api/v1/user/ItemApiController.java

@@ -2,7 +2,6 @@
 
 import java.io.IOException;
 import java.security.Principal;
-import java.util.ArrayList;
 import java.util.List;
 import java.util.stream.Collectors;
 

citesphere/src/main/java/edu/asu/diging/citesphere/config/core/MongoConfig.java

@@ -5,18 +5,23 @@
 import java.time.ZoneOffset;
 import java.util.Arrays;
 
+import org.springframework.beans.factory.InitializingBean;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.PropertySource;
 import org.springframework.core.convert.converter.Converter;
 import org.springframework.data.convert.ReadingConverter;
 import org.springframework.data.convert.WritingConverter;
+import org.springframework.data.domain.Sort;
 import org.springframework.data.mongodb.MongoDatabaseFactory;
 import org.springframework.data.mongodb.core.MongoTemplate;
 import org.springframework.data.mongodb.core.SimpleMongoClientDatabaseFactory;
 import org.springframework.data.mongodb.core.convert.DefaultDbRefResolver;
 import org.springframework.data.mongodb.core.convert.MappingMongoConverter;
+import org.springframework.data.mongodb.core.index.Index;
+import org.springframework.data.mongodb.core.index.IndexOperations;
 import org.springframework.data.mongodb.core.mapping.MongoMappingContext;
 import org.springframework.data.mongodb.repository.config.EnableMongoRepositories;
 import org.springframework.stereotype.Component;
@@ -28,6 +33,10 @@
 import com.mongodb.client.MongoClient;
 import com.mongodb.client.MongoClients;
 
+import edu.asu.diging.citesphere.model.bib.impl.Citation;
+import edu.asu.diging.citesphere.model.bib.impl.CitationCollection;
+import edu.asu.diging.citesphere.model.bib.impl.CitationGroup;
+
 @Configuration
 @PropertySource({ "classpath:config.properties", "${appConfigFile:classpath:}/app.properties" })
 @EnableMongoRepositories({ "edu.asu.diging.citesphere.core.mongo", "edu.asu.diging.citesphere.data.bib" })
@@ -98,4 +107,21 @@ public OffsetDateTime convert(String source) {
             return OffsetDateTime.parse(source);
         }
     }
+
+    @Configuration
+    public static class MongoIndex implements InitializingBean {
+
+        @Autowired
+        private MongoTemplate mongoTemplate;
+
+        @Override
+        public void afterPropertiesSet() throws Exception {
+            IndexOperations citationIndexOps = mongoTemplate.indexOps(Citation.class);
+            citationIndexOps.ensureIndex(new Index().on("key", Sort.Direction.ASC).unique());
+            IndexOperations citationCollectionIndexOps = mongoTemplate.indexOps(CitationCollection.class);
+            citationCollectionIndexOps.ensureIndex(new Index().on("key", Sort.Direction.ASC).unique());
+            IndexOperations citationGorupIndexOps = mongoTemplate.indexOps(CitationGroup.class);
+            citationGorupIndexOps.ensureIndex(new Index().on("groupId", Sort.Direction.ASC).unique());
+        }
+    }
 }

citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java

@@ -14,6 +14,9 @@
 import javax.annotation.PostConstruct;
 import javax.transaction.Transactional;
 
+import org.bson.types.ObjectId;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.PropertySource;
@@ -181,15 +184,15 @@ public void updateCitation(IUser user, String groupId, ICitation citation)
             throws ZoteroConnectionException, CitationIsOutdatedException, ZoteroHttpStatusException, ZoteroItemCreationFailedException {
         long citationVersion = zoteroManager.getGroupItemVersion(user, groupId, citation.getKey());
         Optional<ICitation> storedCitationOptional = citationStore.findById(citation.getKey());
+        ICitation updatedCitation = zoteroManager.updateCitation(user, groupId, citation);
         if (storedCitationOptional.isPresent()) {
             ICitation storedCitation = storedCitationOptional.get();
             if (storedCitation.getVersion() != citationVersion) {
                 throw new CitationIsOutdatedException();
             }
-            citationStore.delete(storedCitation);
+            updatedCitation.setId(storedCitation.getId());
         }
 
-        ICitation updatedCitation = zoteroManager.updateCitation(user, groupId, citation);
         citationStore.save(updatedCitation);
     }
 
@@ -251,7 +254,7 @@ public ICitation updateCitationFromZotero(IUser user, String groupId, String ite
 
             Optional<ICitation> oldCitation = citationStore.findById(itemKey);
             if (oldCitation.isPresent()) {
-                citationStore.delete(oldCitation.get());
+                citation.setId(oldCitation.get().getId());
             }
             citationStore.save(citation);
             return citation;
@@ -326,8 +329,9 @@ public List<ICitationGroup> getGroups(IUser user) {
             if (groupOptional.isPresent()) {
                 ICitationGroup group = groupOptional.get();
                 if (group.getMetadataVersion() != groupVersions.get(id)) {
-                    groupRepository.delete((CitationGroup) group);
+                    ObjectId groupID = group.getId();
                     group = zoteroManager.getGroup(user, id + "", true);
+                    group.setId(groupID);
                     group.setUpdatedOn(OffsetDateTime.now().toString());
                 }
                 addUserToGroup(group, user);
@@ -382,6 +386,9 @@ public CitationResults getGroupItems(IUser user, String groupId, String collecti
         if (!groupOptional.isPresent() || !groupOptional.get().getUsers().contains(user.getUsername())) {
             group = zoteroManager.getGroup(user, groupId, false);
             if (group != null) {
+                if (groupOptional.isPresent()){
+                    group.setId(groupOptional.get().getId());
+                }
                 group.getUsers().add(user.getUsername());
                 groupRepository.save((CitationGroup) group);
             }
@@ -399,13 +406,14 @@ public CitationResults getGroupItems(IUser user, String groupId, String collecti
             long previousVersion = group.getContentVersion();
             // first update the group info
             // if we are using a previously stored group, delete it
+            ICitationGroup zoteroGroup = null;
             if (group.getId() != null) {
-                groupRepository.delete((CitationGroup) group);
-                group = zoteroManager.getGroup(user, groupId + "", true);
+                zoteroGroup = zoteroManager.getGroup(user, groupId + "", true);
+                zoteroGroup.setId(group.getId());
             }
-            group.setUpdatedOn(OffsetDateTime.now().toString());
-            addUserToGroup(group, user);
-            group = groupRepository.save((CitationGroup) group);
+            zoteroGroup.setUpdatedOn(OffsetDateTime.now().toString());
+            addUserToGroup(zoteroGroup, user);
+            group = groupRepository.save((CitationGroup) zoteroGroup);
 
             // then update content
             results.setNotModified(false);

citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/GroupManager.java

@@ -6,7 +6,6 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
-import edu.asu.diging.citesphere.core.exceptions.GroupDoesNotExistException;
 import edu.asu.diging.citesphere.core.service.ICitationCollectionManager;
 import edu.asu.diging.citesphere.core.service.ICitationManager;
 import edu.asu.diging.citesphere.core.service.IGroupManager;
@@ -44,9 +43,11 @@ public ICitationGroup getGroup(IUser user, String groupId) {
         if (groupOptional.isPresent() && groupOptional.get().getUsers().contains(user.getUsername())) {
             return (ICitationGroup) groupOptional.get();
         }
-
         ICitationGroup group = zoteroManager.getGroup(user, groupId, false);
         if (group != null) {
+            if (groupOptional.isPresent()) {
+                group.setId(groupOptional.get().getId()); 
+            }
             group.getUsers().add(user.getUsername());
             groupRepository.save((CitationGroup) group);
             return group;

citesphere/src/main/java/edu/asu/diging/citesphere/core/service/jobs/impl/UploadFileJobManager.java

@@ -18,15 +18,11 @@
 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.kafka.IKafkaRequestProducer;
-import edu.asu.diging.citesphere.core.repository.jobs.UploadFileJobRepository;
 import edu.asu.diging.citesphere.core.service.ICitationManager;
 import edu.asu.diging.citesphere.core.service.IGroupManager;
 import edu.asu.diging.citesphere.core.service.giles.GilesUploadChecker;
 import edu.asu.diging.citesphere.core.service.giles.GilesUploadService;
 import edu.asu.diging.citesphere.core.service.jobs.IUploadFileJobManager;
-import edu.asu.diging.citesphere.core.service.jwt.IJwtTokenService;
-import edu.asu.diging.citesphere.core.service.upload.IFileStorageManager;
 import edu.asu.diging.citesphere.model.bib.ICitation;
 import edu.asu.diging.citesphere.model.bib.ICitationGroup;
 import edu.asu.diging.citesphere.model.bib.IGilesUpload;

citesphere/src/main/java/edu/asu/diging/citesphere/web/user/DownloadGilesFileController.java

@@ -12,15 +12,13 @@
 import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestParam;
 
 import edu.asu.diging.citesphere.core.exceptions.CannotFindCitationException;
 import edu.asu.diging.citesphere.core.exceptions.GroupDoesNotExistException;
 import edu.asu.diging.citesphere.core.exceptions.ZoteroHttpStatusException;
 import edu.asu.diging.citesphere.core.service.ICitationManager;
 import edu.asu.diging.citesphere.model.bib.ICitation;
 import edu.asu.diging.citesphere.model.bib.IGilesUpload;
-import edu.asu.diging.citesphere.model.bib.impl.IGilesFile;
 import edu.asu.diging.citesphere.user.IUser;
 
 @Controller

citesphere/src/main/java/edu/asu/diging/citesphere/web/user/SyncItemController.java

@@ -7,7 +7,6 @@
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.servlet.mvc.support.RedirectAttributes;
 
 import edu.asu.diging.citesphere.core.exceptions.CannotFindCitationException;
 import edu.asu.diging.citesphere.core.exceptions.GroupDoesNotExistException;

citesphere/src/test/java/edu/asu/diging/citesphere/core/service/impl/CitationManagerTest.java

@@ -481,12 +481,15 @@ public void test_addCitationToReferences_citationFound() throws SelfCitationExce
         String referenceCitationKey = "referenceCitationKey";
         citation.getReferences().add(reference);
         citation.setVersion(1L);
+        citation.setId(new ObjectId("507f1f77bcf86cd799439011"));
 
-        Mockito.when(zoteroManager.getGroupItemVersion(user, GROUP_ID, CITATION_KEY)).thenReturn(currentVersion);
+        when(zoteroManager.getGroupItemVersion(user, GROUP_ID, CITATION_KEY)).thenReturn(currentVersion);
         ICitation updatedCitation = new Citation();
         updatedCitation.setKey(CITATION_KEY);
         updatedCitation.setVersion(new Long(2));
-        Mockito.when(zoteroManager.updateCitation(user, GROUP_ID, citation)).thenReturn(updatedCitation);
+
+        when(zoteroManager.updateCitation(Mockito.eq(user), Mockito.eq(GROUP_ID), Mockito.any(ICitation.class)))
+            .thenReturn(updatedCitation);
 
         when(citationStore.save(citation)).thenReturn(updatedCitation);
         when(citationStore.findById(citation.getKey())).thenReturn(Optional.of(citation));
@@ -502,13 +505,16 @@ public void test_addCitationToReferences_nullReferences() throws SelfCitationExc
         String referenceCitationKey = "referenceCitationKey";
         citation.setReferences(null);
         citation.setVersion(1L);
+        citation.setId(new ObjectId("507f1f77bcf86cd799439011"));
 
-        Mockito.when(zoteroManager.getGroupItemVersion(user, GROUP_ID, CITATION_KEY)).thenReturn(currentVersion);
+        when(zoteroManager.getGroupItemVersion(user, GROUP_ID, CITATION_KEY)).thenReturn(1L);
         ICitation updatedCitation = new Citation();
         updatedCitation.setKey(CITATION_KEY);
-        updatedCitation.setVersion(new Long(2));
-        Mockito.when(zoteroManager.updateCitation(user, GROUP_ID, citation)).thenReturn(updatedCitation);
-
+        updatedCitation.setVersion(2L);
+
+        when(zoteroManager.updateCitation(Mockito.eq(user), Mockito.eq(GROUP_ID), Mockito.any(ICitation.class)))
+            .thenReturn(updatedCitation);
+
         when(citationStore.save(citation)).thenReturn(updatedCitation);
         when(citationStore.findById(citation.getKey())).thenReturn(Optional.of(citation));
         doNothing().when(citationStore).delete(any(ICitation.class));