Bug/cite 221

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

@@ -9,6 +9,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.dao.DuplicateKeyException;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
@@ -89,6 +90,9 @@ public ResponseEntity<String> getItem(@RequestHeader HttpHeaders headers,
         } catch (ZoteroHttpStatusException e) {
             logger.error("Zotero threw exception.", e);
             return new ResponseEntity<String>("{\"error\": \"" + e.getMessage() + ".\"}", HttpStatus.INTERNAL_SERVER_ERROR);
+        } catch (DuplicateKeyException e) {
+            logger.error("Duplicate key found.", e);
+            return new ResponseEntity<String>("{\"error\": \"" + e.getMessage() + ".\"}", HttpStatus.INTERNAL_SERVER_ERROR);
         }
         return new ResponseEntity<String>(output, HttpStatus.OK);
     }

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

@@ -7,6 +7,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.PropertySource;
+import org.springframework.dao.DuplicateKeyException;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
@@ -60,7 +61,7 @@ public ResponseEntity<Collections> getCollectionsByGroupId(@RequestHeader HttpHe
             @RequestParam(defaultValue = "1", required = false, value = "page") String page,
             @RequestParam(defaultValue = "20", required = false, value = "maxCollectionNumber") String maxCollections,
             @RequestParam(defaultValue = "title", required = false, value = "sort") String sort, Principal principal)
-            throws GroupDoesNotExistException {
+            throws GroupDoesNotExistException, DuplicateKeyException {
         // TODO add pagination
 
         IUser user = userManager.findByUsername(principal.getName());

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

@@ -3,6 +3,7 @@
 import java.security.Principal;
 
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.dao.DuplicateKeyException;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
@@ -37,7 +38,7 @@ public class GroupApiController extends V1Controller {
 
     @RequestMapping(value = { "/groups/{zoteroGroupId}" }, produces = { MediaType.APPLICATION_JSON_VALUE })
     public ResponseEntity<Group> getCollectionsByGroupId(@RequestHeader HttpHeaders headers,
-            @PathVariable("zoteroGroupId") String groupId, Principal principal) throws GroupDoesNotExistException {
+            @PathVariable("zoteroGroupId") String groupId, Principal principal) throws GroupDoesNotExistException, DuplicateKeyException {
 
         IUser user = userManager.findByUsername(principal.getName());
 

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

@@ -2,13 +2,13 @@
 
 import java.io.IOException;
 import java.security.Principal;
-import java.util.ArrayList;
 import java.util.List;
 import java.util.stream.Collectors;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.dao.DuplicateKeyException;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
@@ -47,7 +47,7 @@ public class ItemApiController extends V1Controller {
 
     @GetMapping(value = "/groups/{groupId}/items/{item}", produces = { MediaType.APPLICATION_JSON_VALUE })
     public ResponseEntity<String> getItem(@PathVariable("groupId") String groupId, @PathVariable("item") String itemKey,
-            Principal principal) throws GroupDoesNotExistException {
+            Principal principal) throws GroupDoesNotExistException, DuplicateKeyException {
         IUser user = userManager.findByUsername(principal.getName());
 
         ICitationGroup group = groupManager.getGroup(user, groupId);

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

@@ -8,6 +8,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.PropertySource;
+import org.springframework.dao.DuplicateKeyException;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
@@ -67,7 +68,7 @@ public ResponseEntity<String> getCollectionsByGroupId(@RequestHeader HttpHeaders
             @RequestParam(defaultValue = "1", required = false, value = "page") String page,
             @RequestParam(defaultValue = "title", required = false, value = "sort") String sort,
             @RequestParam(required = false, value = "columns") String[] columns, Principal principal)
-            throws GroupDoesNotExistException {
+            throws GroupDoesNotExistException, DuplicateKeyException {
         Integer pageInt = 1;
         try {
             pageInt = new Integer(page);
@@ -90,7 +91,9 @@ public ResponseEntity<String> getCollectionsByGroupId(@RequestHeader HttpHeaders
             return new ResponseEntity<String>(HttpStatus.FORBIDDEN);
         } catch (ZoteroHttpStatusException e1) {
             return new ResponseEntity<String>(HttpStatus.INTERNAL_SERVER_ERROR);
-        } 
+        } catch(DuplicateKeyException de) {
+            return new ResponseEntity<String>(HttpStatus.INTERNAL_SERVER_ERROR);
+        }
 
         Items itemsResponse = new Items();
         itemsResponse.setGroup(jsonUtil.createGroup(group));

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/export/impl/ExportManager.java

@@ -22,6 +22,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.PropertySource;
+import org.springframework.dao.DuplicateKeyException;
 import org.springframework.stereotype.Service;
 
 import edu.asu.diging.citesphere.core.exceptions.AccessForbiddenException;
@@ -121,7 +122,7 @@ public void init() {
     @Override
     public void export(ExportType exportType, IUser user, String groupId, String collectionId)
             throws GroupDoesNotExistException, ExportTypeNotSupportedException, ExportFailedException,
-            ExportTooBigException, ZoteroHttpStatusException, AccessForbiddenException {
+            ExportTooBigException, ZoteroHttpStatusException, AccessForbiddenException, DuplicateKeyException {
 
         ICitationGroup group = groupManager.getGroup(user, groupId);
         if (group == null) {
@@ -156,7 +157,7 @@ public void export(ExportType exportType, IUser user, String groupId, String col
     @Override
     public void distributedExport(ExportType exportType, IUser user, String groupId, String collectionId)
             throws GroupDoesNotExistException, ExportTypeNotSupportedException, ExportFailedException,
-            ExportTooBigException, ZoteroHttpStatusException, AccessForbiddenException {
+            ExportTooBigException, ZoteroHttpStatusException, AccessForbiddenException, DuplicateKeyException {
 
         ICitationGroup group = groupManager.getGroup(user, groupId);
         if (group == null) {

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

@@ -16,6 +16,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.PropertySource;
+import org.springframework.dao.DuplicateKeyException;
 import org.springframework.http.HttpEntity;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpMethod;
@@ -199,7 +200,7 @@ public void updateCitation(ICitation citation, Set<IGilesUpload> checkedUploads,
             citationManager.updateCitation(user, citation.getGroup(),
                     currentCitation);
         } catch (ZoteroConnectionException | CitationIsOutdatedException
-                | ZoteroHttpStatusException | ZoteroItemCreationFailedException e) {
+                | ZoteroHttpStatusException | ZoteroItemCreationFailedException | DuplicateKeyException e) {
             logger.error("Could not update citation.", e);
         }
     }
@@ -216,6 +217,8 @@ public ICitation getCurrentCitation(ICitation citation, IUser user) {
             logger.error("Could not get citation.", e);
         } catch (ZoteroHttpStatusException e) {
             logger.error("Could not get citation.", e);
+        } catch (DuplicateKeyException e) {
+            logger.error("Duplicate key found.", e);
         }
         return null;
     }

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

@@ -16,6 +16,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.dao.DuplicateKeyException;
 import org.springframework.scheduling.annotation.Async;
 import org.springframework.stereotype.Service;
 
@@ -206,7 +207,7 @@ private void removeDeletedItems(DeletedZoteroElements deletedElements, GroupSync
         }
     }
 
-    private long retrieveCitations(IUser user, String groupId, List<String> keysToRetrieve) throws ZoteroHttpStatusException {
+    private long retrieveCitations(IUser user, String groupId, List<String> keysToRetrieve) throws ZoteroHttpStatusException, DuplicateKeyException {
         try {
             // wait 1 second to not send too many requests to Zotero
             TimeUnit.SECONDS.sleep(1);
@@ -234,7 +235,7 @@ private long retrieveCollections(IUser user, String groupId, List<String> keysTo
         return response.getContentVersion();
     }
 
-    private void storeCitation(ICitation citation) {
+    private void storeCitation(ICitation citation) throws DuplicateKeyException {
         Optional<ICitation> optional = citationStore.findById(citation.getKey());
         if (optional.isPresent()) {
             citationStore.delete((Citation) optional.get());