Java tutorial
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You further acknowledge and agree that * Stanford shall have no liability arising in connection with claims resulting from your breach of any of the terms of * this Agreement. * 6. YOU WARRANT THAT TO THE BEST OF YOUR KNOWLEDGE YOUR CONTRIBUTION DOES NOT CONTAIN ANY CODE OBTAINED BY YOU UNDER AN * OPEN SOURCE LICENSE THAT REQUIRES OR PRESCRIBES DISTRBUTION OF DERIVATIVE WORKS UNDER SUCH OPEN SOURCE LICENSE. (By way * of non-limiting example, you will not contribute any code obtained by you under the GNU General Public License or other * so-called "reciprocal" license.) *******************************************************************************/ package edu.stanford.epad.common.util; import java.util.Arrays; import org.json.XML; import com.mongodb.BasicDBObject; import com.mongodb.DB; import com.mongodb.DBCollection; import com.mongodb.DBCursor; import com.mongodb.DBObject; import com.mongodb.MongoClient; import com.mongodb.MongoCredential; import com.mongodb.ServerAddress; import com.mongodb.util.JSON; /** * Class for jsonAnnotations operations in MongoDB * The class is here instead of epad-ws, because plugins may need to call it * * @author Dev Gude * */ public class MongoDBOperations { private static final EPADLogger log = EPADLogger.getInstance(); private static DB mongoDB; /** * Connection to mongo database * @return */ public static DB getMongoDB() { if (mongoDB == null) { try { String mongoHost = EPADConfig.mongoHostname; if (mongoHost == null) return null; MongoClient mongoClient = null; if (EPADConfig.mongoUser == null) { mongoClient = new MongoClient(mongoHost); } else { MongoCredential credential = MongoCredential.createCredential(EPADConfig.mongoUser, EPADConfig.mongoDB, EPADConfig.mongoPassword.toCharArray()); mongoClient = new MongoClient(new ServerAddress(), Arrays.asList(credential)); } mongoDB = mongoClient.getDB(EPADConfig.mongoDB); } catch (Exception e) { log.warning("Error connecting to MongoDB", e); } } return mongoDB; } /** * Saves a json doc to mongoDB * @param jsonString * @param collection * @throws Exception */ public static void saveJsonToMongo(String jsonString, String collection) throws Exception { try { DB db = MongoDBOperations.getMongoDB(); if (db == null) { log.warning("No connection to Mongo DB"); return; } DBCollection coll = db.getCollection(collection); DBObject dbObject = (DBObject) JSON.parse(jsonString); //TODO: Check if document exists and replace instead of insert coll.insert(dbObject); } catch (Exception e) { log.warning("Error saving to mongodb:", e); throw e; } } /** * Get number of documents in mongoDB * @param jsonQuery * @param collection * @return * @throws Exception */ public static int getNumberOfDocuments(String jsonQuery, String collection) throws Exception { try { int count = 0; DB db = MongoDBOperations.getMongoDB(); if (db == null) { log.warning("No connection to Mongo DB"); return count; } DBCollection dbColl = db.getCollection(collection); if (jsonQuery != null && jsonQuery.trim().length() > 0) { DBObject dbQuery = (DBObject) JSON.parse(jsonQuery); return dbColl.find(dbQuery).count(); } else { return dbColl.find().count(); } } catch (Exception e) { log.warning("Error querying mongodb:", e); throw e; } } /** * Create indexes (only if they don't already exist) * @param collection * @throws Exception */ public static void createIndexes(String collection) throws Exception { try { int count = 0; DB db = MongoDBOperations.getMongoDB(); if (db == null) { log.warning("No connection to Mongo DB"); return; } DBCollection dbColl = db.getCollection(collection); BasicDBObject dbObj = new BasicDBObject("ImageAnnotationCollection.uniqueIdentifier.root", 1); dbColl.createIndex(dbObj, "uid_idx", true); // Does not create index, if it already exists dbObj = new BasicDBObject("ImageAnnotationCollection.person.name.value", 1); dbColl.createIndex(dbObj, "patientname_idx", false); // Does not create index, if it already exists dbObj = new BasicDBObject("ImageAnnotationCollection.person.id.value", 1); dbColl.createIndex(dbObj, "patientid_idx", false); // Does not create index, if it already exists } catch (Exception e) { log.warning("Error querying mongodb:", e); throw e; } } /** * Converts and saves an annotation to mongoDB * @param annotationID * @param aimXML * @param collection * @throws Exception */ public static void saveAnnotationToMongo(String annotationID, String aimXML, String collection) throws Exception { try { DB db = MongoDBOperations.getMongoDB(); if (db == null) { log.warning("No connection to Mongo DB"); return; } if (aimXML == null || aimXML.trim().length() == 0) return; String jsonString = XML.toJSONObject(aimXML).toString(0); ; if (jsonString == null) throw new Exception("Error converting to json"); DBCollection dbColl = db.getCollection(collection); BasicDBObject dbObj = new BasicDBObject("ImageAnnotationCollection.uniqueIdentifier.root", 1); dbColl.createIndex(dbObj, "uid_idx", true); // Does not create index, if it already exists BasicDBObject query = new BasicDBObject(); query.put("ImageAnnotationCollection.uniqueIdentifier.root", annotationID); DBObject dbObject = (DBObject) JSON.parse(jsonString); DBCursor cursor = dbColl.find(query); if (cursor.count() > 0) { log.info("Updating existing annotation in mongoDB:" + annotationID + " in " + collection); dbColl.update(query, dbObject, true, false); } else { log.info("Creating new annotation in mongoDB:" + annotationID + " in " + collection); dbColl.insert(dbObject); } } catch (Exception e) { log.warning("Error saving AIM to mongodb:", e); throw e; } } /** * Deletes json annotation from mongoDB * * @param annotationID * @param collection * @throws Exception */ public static void deleteAnotationInMongo(String annotationID, String collection) throws Exception { try { DB db = MongoDBOperations.getMongoDB(); if (db == null) { log.warning("No connection to Mongo DB"); return; } DBCollection dbColl = db.getCollection(collection); BasicDBObject query = new BasicDBObject(); query.put("ImageAnnotationCollection.uniqueIdentifier.root", annotationID); DBCursor cursor = dbColl.find(query); if (cursor.count() > 0) { log.info("Deleting annotation in mongoDB:" + annotationID + " in " + collection); DBObject annotation = cursor.next(); dbColl.remove(annotation); } else { log.info("Annotation not found in mongoDB:" + annotationID + " in " + collection); } } catch (Exception e) { log.warning("Error deleting AIM from mongodb:", e); throw e; } } }