Java Code Examples for com.mongodb.DBCursor#next()

@Override
public void importCollection() {
    DBCursor cursor = mongo.getCollection("studentCohortAssociation").find();
    while (cursor.hasNext()) {
        DBObject spa = cursor.next();
        Map<String, Object> body = (Map) spa.get("body");
        for (Vertex student : graph.getVertices("mongoid", body.get("studentId"))) {
            for (Vertex program : graph.getVertices("mongoid", body.get("cohortId"))) {
                Edge e = graph.addEdge(null, program, student, "studentCohort");
                e.setProperty("mongoid", spa.get("_id"));
                // This may not be safe.
                e.setProperty("endDate", body.get("endDate"));
            }
            
        }
        
    }
    
}
 

private void toPrivateStorageList(String collectionName, List<PrivateStorage> privatesStorage, DBCursor cursor) throws JsonProcessingException {
    try {
        while (cursor.hasNext()) {
            cursor.next();

            String content = jsonParsingService.toJsonString(cursor.curr().toMap());

            privatesStorage.add(PrivateStorage.builder()
                    .collectionName(collectionName)
                    .collectionContent(content)
                    .build());
        }
    } finally {
        cursor.close();
    }
}
 

public List<Seq> getSeqFromSeqEcOrg(String seq, String ec, String organism) {
  List<Seq> seqs = new ArrayList<>();
  BasicDBObject query = new BasicDBObject();
  query.put("seq", seq);
  query.put("ecnum", ec);
  query.put("org", organism);

  DBCursor cur = this.dbSeq.find(query, new BasicDBObject());
  try {
    while (cur.hasNext()) {
      DBObject o = cur.next();
      seqs.add(convertDBObjectToSeq(o));
    }
  } finally {
    if (cur != null) {
      cur.close();
    }
  }

  return seqs;
}
 

public List<Seq> getSeqWithSARConstraints() {
  List<Seq> seqs = new ArrayList<Seq>();
  BasicDBObject query = new BasicDBObject();
  query.put("sar_constraints", new BasicDBObject("$exists", true));

  BasicDBObject keys = new BasicDBObject();

  DBCursor cur = this.dbSeq.find(query, keys);
  while (cur.hasNext()) {
    DBObject o = cur.next();
    seqs.add( convertDBObjectToSeq(o) );
  }
  cur.close();

  return seqs;
}
 

public List<Seq> getSeqWithRxnRef(Long rxnId) {
  List<Seq> seqs = new ArrayList<>();
  BasicDBObject query = new BasicDBObject();
  query.put("rxn_refs", rxnId);

  DBCursor cur = this.dbSeq.find(query, new BasicDBObject());
  try {
    while (cur.hasNext()) {
      DBObject o = cur.next();
      seqs.add(convertDBObjectToSeq(o));
    }
  } finally {
    if (cur != null) {
      cur.close();
    }
  }

  return seqs;
}
 

@Override
public void importCollection() {
    DBCursor cursor = mongo.getCollection("studentSectionAssociation").find();
    cursor.batchSize(BATCH_SIZE);
    while (cursor.hasNext()) {
        DBObject spa = cursor.next();
        @SuppressWarnings("unchecked")
        Map<String, Object> body = (Map<String, Object>) spa.get("body");
        String studentId = (String) body.get("studentId");
        String sectionId = (String) body.get("sectionId");
        for (Vertex student : graph.getVertices("mongoid", studentId)) {
            for (Vertex section : graph.getVertices("mongoid", sectionId)) {
                Edge e = graph.addEdge(null, section, student, "studentSection");
                e.setProperty("mongoid", spa.get("_id"));

                if (body.containsKey("endDate")) {
                    e.setProperty("endDate", body.get("endDate"));
                }
                
                logger.log(Level.INFO, "Adding an edge between section: " + sectionId + " --> student: " + studentId);
            }
        }            
    }        
}
 

private List<Reaction> keywordInReaction(String in_field, String keyword) {
  List<Reaction> rxns = new ArrayList<Reaction>();
  BasicDBObject query = new BasicDBObject();
  query.put(in_field, keyword);

  BasicDBObject keys = new BasicDBObject();

  DBCursor cur = this.dbReactions.find(query, keys);
  while (cur.hasNext()) {
    DBObject o = cur.next();
    rxns.add( convertDBObjectToReaction(o) );
  }
  cur.close();

  return rxns;
}
 

@Override
public List<Content> getFeedFor(final User user, final int limit) {

    List<Content> result = new ArrayList<Content>(limit);
    DBCursor cursor = buckets.find(
            findBy(BUCKET_OWNER_KEY, user.getUserId()), getFields(BUCKET_CONTENT_KEY)).
            sort(sortByDecending(BUCKET_ID_KEY)).batchSize(config.bucket_read_batch_size);
    
    try{
        while(cursor.hasNext() && result.size() < limit){
            DBObject currentBucket = cursor.next();
            @SuppressWarnings("unchecked")
            List<DBObject> contentList = (List<DBObject>)currentBucket.get(BUCKET_CONTENT_KEY);
            int bucketSize = contentList.size();
            for(int i = bucketSize - 1; i >= 0; --i){
                result.add(new Content(contentList.get(i)));
                if(result.size() >= limit)
                    break;
            } 
        }
    } finally {
        cursor.close();
    }
    
    return result;
}
 

public Map<String, Long> constructAllInChIs() {
  Map<String, Long> chems = new HashMap<String, Long>();
  BasicDBObject keys = new BasicDBObject();
  keys.append("_id", true);
  keys.append("InChI", true);
  DBCursor cur = constructCursorForMatchingChemicals(null, null, keys);
  while (cur.hasNext()) {
    DBObject o = cur.next();
    long uuid = (Long)o.get("_id"); // checked: db type IS long
    String inchi = (String)o.get("InChI");
    chems.put(inchi, uuid);
  }

  cur.close();
  return chems;
}
 

public static void main(String[] args) throws Exception {

		MongoConnection mongo = new MongoConnection(MONGO_FT_CONNECTION);

		DBCursor it = mongo.coll.find().batchSize(1000);

		int i = 0;
		while (it.hasNext()) {
			DBObject dbObject = (DBObject) it.next();
			int pmId = Integer.parseInt(dbObject.get("_id").toString());
			// dbObject.put(MongoFieldMapping.PM_ID, pmId);
			mongo.coll.update(dbObject, new BasicDBObject("$set",
					new BasicDBObject(PM_ID, pmId)));
			// mongo.coll.apply(dbObject);
			if (i++ % 1000 == 0)
				System.err.println("updated " + pmId);
		}

	}
 

private List<Seq> keywordInSequence(String in_field, String keyword) {
  List<Seq> seqs = new ArrayList<Seq>();
  BasicDBObject query = new BasicDBObject();
  query.put(in_field, keyword);

  BasicDBObject keys = new BasicDBObject();

  DBCursor cur = this.dbSeq.find(query, keys);
  while (cur.hasNext()) {
    DBObject o = cur.next();
    seqs.add( convertDBObjectToSeq(o) );
  }
  cur.close();

  return seqs;
}
 

public List<Long> getRxnsWithSubstrate(String enzyme, Long org, List<Long> substrates) {
  BasicDBObject query = new BasicDBObject();
  query.put("organisms.id", org);
  BasicDBObject enzymeQuery = new BasicDBObject();
  enzymeQuery.put("ecnum", enzyme);
  query.put("$ne", enzymeQuery);
  for (Long substrate: substrates) {
    BasicDBList queryList = new BasicDBList();
    DBObject querySubstrate = new BasicDBObject();
    querySubstrate.put("enz_summary.substrates.pubchem", substrate);
    DBObject queryProduct = new BasicDBObject();
    queryProduct.put("enz_summary.products.pubchem", substrate);
    queryList.add(querySubstrate);
    queryList.add(queryProduct);
    query.put("$or", queryList);
  }

  DBCursor cur = this.dbReactions.find(query);
  List<Long> reactions = new ArrayList<Long>();
  while (cur.hasNext()) {
    DBObject o = cur.next();
    long id = (Integer) o.get("_id"); // checked: db type IS int
    reactions.add(id);
  }
  cur.close();
  return reactions;
}
 

/**
 * Calculates shard chunks.
 *
 * @param collection the collection
 * @return the deep partition [ ]
 */
private DeepPartition[] calculateShardChunks(DBCollection collection) {

    DBCursor chuncks = getChunks(collection);

    Map<String, String[]> shards = getShards(collection);

    MongoPartition[] deepPartitions = new MongoPartition[chuncks.count()];
    int i = 0;
    boolean keyAssigned = false;
    String key = null;
    while (chuncks.hasNext()) {

        DBObject dbObject = chuncks.next();
        if (!keyAssigned) {
            Set<String> keySet = ((DBObject) dbObject.get("min")).keySet();
            for (String s : keySet) {
                key = s;
                keyAssigned = true;
            }
        }
        deepPartitions[i] = new MongoPartition(mongoDeepJobConfig.getRddId(), i,
                new DeepTokenRange(shards.get(dbObject.get
                        ("shard")),
                        ((DBObject) dbObject.get
                                ("min")).get(key),
                        ((DBObject) dbObject.get("max")).get(key)), key);
        i++;
    }
    List<MongoPartition> mongoPartitions = Arrays.asList(deepPartitions);

    Collections.shuffle(mongoPartitions);
    return mongoPartitions.toArray(new MongoPartition[mongoPartitions.size()]);
}
 

private List<Content> getContentFromBuckets(
        final User user,  final String contentField, final int limit) {
    
    List<Content> result = new ArrayList<Content>(limit);

    // Get a cursor for looking at buckets back in time
    DBCursor cursor = buckets.find(
        findBy(subField(BUCKET_ID_KEY, BUCKET_OWNER_KEY), user.getUserId()), 
        getFields(contentField)).
        sort(sortByDecending(BUCKET_ID_KEY)).batchSize(config.bucket_read_batch_size);
    
    try{
        // Go through buckets grabbing content until limit is
        // hit or we run out of buckets
        while(cursor.hasNext() && result.size() < limit){
            DBObject currentBucket = cursor.next();
            @SuppressWarnings("unchecked")
            List<DBObject> contentList = (List<DBObject>)currentBucket.get(contentField);
            int bucketSize = contentList == null ? 0 : contentList.size();
            for(int i = bucketSize - 1; i >= 0; --i){
                result.add(new Content(contentList.get(i)));
                if(result.size() >= limit)
                    break;
            } 
        }
    } finally {
        cursor.close();
    }
    
    return result;
}
 

private List<GridFSDBFile> toFileList(DBCursor cursor){
    List<GridFSDBFile> list = new ArrayList<GridFSDBFile>();
    while(cursor.hasNext()){
        DBObject dbo = cursor.next();
        list.add((GridFSDBFile)dbo);
    }
    cursor.close();
    return list;
}
 

public List<Long> getRxnsWithEnzyme(String enzyme, Long org, List<Long> substrates) {
  BasicDBObject query = new BasicDBObject();
  query.put("ecnum", enzyme);
  query.put("organisms.id", org);
  for (Long substrate : substrates) {
    BasicDBObject mainQuery = new BasicDBObject();
    mainQuery.put("$ne", substrate);
    BasicDBList queryList = new BasicDBList();
    BasicDBObject productQuery = new BasicDBObject();
    productQuery.put("enz_summary.products.pubchem", mainQuery);
    BasicDBObject substrateQuery = new BasicDBObject();
    substrateQuery.put("enz_summary.substrates.pubchem", mainQuery);
    queryList.add(substrateQuery);
    queryList.add(productQuery);
    query.put("$or", queryList);
  }
  DBCursor cur = this.dbReactions.find(query);

  List<Long> reactions = new ArrayList<Long>();
  while (cur.hasNext()) {
    DBObject o = cur.next();
    long id = (Integer) o.get("_id"); // checked: db type IS int
    reactions.add(id);
  }
  cur.close();
  return reactions;
}
 

public List<Reaction> getRxnsWithAll(List<Long> reactants, List<Long> products) {

    if (reactants.size() == 0 && products.size() == 0) {
      throw new IllegalArgumentException("Reactants and products both empty! Query would return entire DB.");
    }
    BasicDBObject query = new BasicDBObject();

    if (!reactants.isEmpty()) {
      BasicDBList substrateIds = new BasicDBList();
      substrateIds.addAll(reactants);
      query.put("enz_summary.substrates.pubchem", new BasicDBObject("$all", substrateIds));
    }

    if (!products.isEmpty()) {
      BasicDBList productIds = new BasicDBList();
      productIds.addAll(products);
      query.put("enz_summary.products.pubchem", new BasicDBObject("$all", productIds));
    }

    DBCursor cur = this.dbReactions.find(query);
    List<Reaction> reactions = new ArrayList<Reaction>();

    try {
      while (cur.hasNext()) {
        DBObject o = cur.next();
        reactions.add(convertDBObjectToReaction(o));
      }
    } finally {
      cur.close();
    }

    return reactions;
  }
 

public static <T> List<T> toList(Class<T> clazz, DBCursor cursor, boolean withoutCascade){
    List<T> list = new ArrayList<>();
    try {
        while(cursor.hasNext()){
            DBObject dbo = cursor.next();
            list.add(fromDBObject(clazz, dbo, withoutCascade));
        }
    } finally {
        cursor.close();
    }
    return list;
}
 

@Test
public void greaterThan() throws Exception {

    UUID appId = emf.lookupApplication( "test-organization/test-app" );
    EntityManager em = emf.getEntityManager( appId );

    Map<String, Object> properties = new LinkedHashMap<String, Object>();
    properties.put( "name", "Kings of Leon" );
    properties.put( "genre", "Southern Rock" );
    properties.put( "founded", 2000 );
    em.create( "greaterthan", properties );

    properties = new LinkedHashMap<String, Object>();
    properties.put( "name", "Stone Temple Pilots" );
    properties.put( "genre", "Rock" );
    properties.put( "founded", 1986 );
    em.create( "greaterthan", properties );

    properties = new LinkedHashMap<String, Object>();
    properties.put( "name", "Journey" );
    properties.put( "genre", "Classic Rock" );
    properties.put( "founded", 1973 );
    em.create( "greaterthan", properties );

    // See http://www.mongodb.org/display/DOCS/Java+Tutorial

    Mongo m = new Mongo( "localhost", 27017 );

    DB db = m.getDB( "test-organization/test-app" );
    db.authenticate( "test", "test".toCharArray() );

    BasicDBObject query = new BasicDBObject();
    query.put( "founded", new BasicDBObject( "$gt", 1973 ) );

    DBCollection coll = db.getCollection( "greaterthans" );
    DBCursor cur = coll.find( query );

    assertTrue( cur.hasNext() );

    DBObject result = cur.next();
    assertEquals( "Stone Temple Pilots", result.get( "name" ) );
    assertEquals( "Rock", result.get( "genre" ) );

    result = cur.next();
    assertEquals( "Kings of Leon", result.get( "name" ) );
    assertEquals( "Southern Rock", result.get( "genre" ) );

    assertFalse( cur.hasNext() );
}
 

public Representation doRepresent() {
      // Ready query params
      String _page = getQueryValue("page");
      String _size = getQueryValue("size");

ProjectRepository projectRepo = platform.getProjectRepositoryManager().getProjectRepository();
       
      DBCursor cursor;
      if(_page != null && !"".equals(_page) && isInteger(_page) && _size != null && !"".equals(_size) && isInteger(_size)) {
      	int page = Integer.valueOf(_page);
      	int pageSize = Integer.valueOf(_size);
      	cursor = projectRepo.getProjects().getDbCollection().find().skip(page*pageSize).limit(pageSize);
      } else {
      	cursor = projectRepo.getProjects().getDbCollection().find();
      }
      
      ArrayNode projects = mapper.createArrayNode();
      
      while (cursor.hasNext()) {
          try {
          	DBObject p = cursor.next();
          	p.removeField("storage");
		p.removeField("metricProviderData");
		p.removeField("_superTypes");
		p.removeField("_id");
		
		// FIXME: Temporary solution
		p.removeField("licenses");
		p.removeField("persons");
		
		projects.add(mapper.readTree(p.toString()));
          } catch (Exception e) {
          	System.err.println("Error: " + e.getMessage());
		ObjectNode m = mapper.createObjectNode();
		m.put("apicall", "list-all-projects");
		return Util.generateErrorMessageRepresentation(m, e.getMessage());
          }
      }
      
      cursor.close();
      
      StringRepresentation resp = new StringRepresentation(projects.toString());
resp.setMediaType(MediaType.APPLICATION_JSON);
return resp;
  }