Java Code Examples for com.mongodb.BasicDBList#addAll()

public void updateDatabase(DBCollection reachables) {
  for (String product : products) {
    // The query object for this product
    BasicDBObject newProductQuery = new BasicDBObject().append(INCHI_KEY, product);

    // DB list of the substrates of this projection
    BasicDBList substrateList = new BasicDBList();
    substrateList.addAll(substrates);

    // DB list of the one RO associated with this projection
    BasicDBList roList = new BasicDBList();
    roList.addAll(ros);

    // The full entry to be added to the product's precursor list
    BasicDBObject precursorEntry = new BasicDBObject()
        .append(SUBSTRATES_KEY, substrateList)
        .append(RO_KEY, roList);

    // The command to push the precursor entry onto the precursor list
    BasicDBObject precursors = new BasicDBObject();
    precursors.append("$push", new BasicDBObject(PRECURSOR_KEY, precursorEntry));

    // Do the update!
    reachables.update(newProductQuery, precursors, UPSERT, NO_MULTI);
  }
}
 

public BasicDBObject createCofactorDoc(Cofactor c, Long ID) {
  BasicDBObject doc = new BasicDBObject();

  doc.put("_id", ID);
  doc.put("InChI", c.getInChI());

  BasicDBList names = new BasicDBList();
  names.addAll(c.getNames());
  doc.put("names", names);

  return doc;
}
 

public void updateChemicalWithRoBinningInformation(long id, List<Integer> matchedROs) {
  BasicDBObject query = new BasicDBObject("_id", id);
  BasicDBObject createDerivedDataContainer = new BasicDBObject("$set", new BasicDBObject("derived_data", new BasicDBObject()));
  this.dbChemicals.update(query, createDerivedDataContainer);

  BasicDBList listOfRos = new BasicDBList();
  listOfRos.addAll(matchedROs);

  BasicDBObject updateDerivedDataContainerWithMatchedRos =
      new BasicDBObject("$set", new BasicDBObject("derived_data.matched_ros", listOfRos));
  this.dbChemicals.update(query, updateDerivedDataContainerWithMatchedRos);
}
 

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 void updateReferences(Seq seq) {
  BasicDBObject query = new BasicDBObject().append("_id", seq.getUUID());
  DBObject obj = this.dbSeq.findOne(query);
  BasicDBList refs = new BasicDBList();

  List<DBObject> newReferences = new ArrayList<>();
  for (JSONObject ref : seq.getReferences()) {
    newReferences.add(MongoDBToJSON.conv(ref));
  }

  refs.addAll(newReferences);
  obj.put("references", refs);
  this.dbSeq.update(query, obj);
}
 

public DBCursor fetchNamesAndUsageForInchis(Set<String> inchis) {
  BasicDBList inchiList = new BasicDBList();
  inchiList.addAll(inchis);
  BasicDBObject inClause = new BasicDBObject("$in", inchiList);
  BasicDBObject whereQuery = new BasicDBObject("InChI", inClause);
  whereQuery.put("xref.BING", new BasicDBObject("$exists", true));
  BasicDBObject fields = new BasicDBObject();
  fields.put("InChI", true);
  fields.put("names.brenda", true);
  fields.put("xref", true);
  DBCursor cursor = dbChemicals.find(whereQuery, fields);
  return cursor;
}
 

@GET
@Path("/{product}/{major}.{minor}.{servicePack}/{build}")
@Produces(MediaType.APPLICATION_JSON)
public Response getSearchResults(@BeanParam final Coordinates coordinates, @QueryParam("keywords") final String keyword) {
	final String[] searchCategories = { "name", "description", "tags.name", "elements.name", "elements.description",
			"elements.steps.name", "elements.tags.name" };
	final List<String> searchWords = Arrays.asList(keyword.split("\\s+"));
	final DBCollection collection = this.mongoLegacyDb.getCollection("features");
	final List<DBObject> searchResults = new ArrayList<>();

	final QueryBuilder queryBuilder = QueryBuilder.getInstance();
	final DBCursor results = collection.find(queryBuilder.getSearchQuery(searchWords, coordinates, searchCategories));

	while (results.hasNext()) {
		final DBObject doc = results.next();
		searchResults.add(doc);
	}

	searchResults.sort(new DBObjectComparator(searchWords));

	while (searchResults.size() > SEARCH_LIMIT) {
		searchResults.remove(searchResults.size() - 1);
	}

	final BasicDBList basicDBList = new BasicDBList();
	basicDBList.addAll(searchResults);

	return Response.ok(SerializerUtil.serialise(basicDBList)).build();
}
 

private BasicDBList constructEditStepChanges(final DBObject currentVersion, final DBObject previousVersion) {
	final BasicDBList stepChanges = new BasicDBList();
	final BasicDBList scenarios = (BasicDBList) currentVersion.get("elements");
	final BasicDBList prevScenarios = (BasicDBList) previousVersion.get("elements");
	if (scenarios != null) {
		for (int i = 0; i < scenarios.size(); i++) {
			stepChanges.addAll(updateScenarioSteps((BasicDBObject) scenarios.get(i), (BasicDBObject) prevScenarios.get(i)));
		}
	}
	return stepChanges;
}
 

public void cloneStack(final StackId fromStackId,
                       final StackId toStackId,
                       final List<Double> zValues,
                       final Boolean skipTransforms)
        throws IllegalArgumentException, IllegalStateException {

    MongoUtil.validateRequiredParameter("fromStackId", fromStackId);
    MongoUtil.validateRequiredParameter("toStackId", toStackId);

    if ((skipTransforms == null) || (! skipTransforms)) {
        final MongoCollection<Document> fromTransformCollection = getTransformCollection(fromStackId);
        final MongoCollection<Document> toTransformCollection = getTransformCollection(toStackId);
        cloneCollection(fromTransformCollection, toTransformCollection, new Document());
    }

    final Document filterQuery = new Document();
    if ((zValues != null) && (zValues.size() > 0)) {
        final BasicDBList list = new BasicDBList();
        list.addAll(zValues);
        final Document zFilter = new Document(QueryOperators.IN, list);
        filterQuery.append("z", zFilter);
    }

    final MongoCollection<Document> fromTileCollection = getTileCollection(fromStackId);
    final MongoCollection<Document> toTileCollection = getTileCollection(toStackId);
    cloneCollection(fromTileCollection, toTileCollection, filterQuery);
}
 

private static BasicDBList compare(BasicDBList l, BasicDBList refl, boolean listsAreSet) {
  boolean different = false;
  BasicDBList diff = new BasicDBList();

  if (!listsAreSet) {
    // lists are to be treated as ordered sets and so we can compare element by element
    for (int i = 0; i < l.size(); i++){
      Object val = l.get(i);
      Object refv = refl.get(i);
      Object d;
      if ((d = compare(val, refv, listsAreSet)) != null) {
        different = true;
        diff.add(d);
      } else {
        // elements at this index are identical, but we don't want to muck up the order
        // in case future elements are not identical... so add a null to the diff,
        // BUT IMP: do not set the flag that the list is different
        diff.add(null);
      }
    }
  } else {
    // lists are to be treated as unordered sets: we try to match each element best
    // effort to any one of the list elements, and if it does proceed greedily

    // we keep this as a list as opposed to a true set because the original (ref)
    // and the current (new) might have (identical) replicates, and so should not
    // be flagged different because of that.
    List<Object> refset = new ArrayList<Object>();
    refset.addAll(refl);

    for (Object e : l) {
      boolean matches_some = false;
      for (Object eref : refset) {
        if (compare(e, eref, listsAreSet) == null) {
          // this object matches something, great, lets move to the next object
          // also remove the matched object from the ref list, so that we have
          // a 1-1 mapping between this and the ref list object
          matches_some = true;
          refset.remove(eref);
          break;
        }
      }
      if (!matches_some) {
        // if this object in new list could not be matched against something,
        // the lists are different
        different = true;
        diff.add(e);
      }
    }

    if (refset.size() != 0) {
      // still some elements remain in the ref list, i.e., sets different
      different = true;
      diff.addAll(refset);
    }

  }

  return different ? diff : null;
}
 

public static BasicDBObject createChemicalDoc(Chemical c, Long ID) {
  BasicDBObject doc = new BasicDBObject();

  doc.put("_id", ID);

  doc.put("canonical", c.getCanon());

  doc.put("SMILES", c.getSmiles());
  doc.put("InChI", c.getInChI());
  doc.put("InChIKey", c.getInChIKey());

  doc.put("isCofactor", c.isCofactor());
  doc.put("isNative", c.isNative());

  BasicDBObject names = new BasicDBObject();
  BasicDBList synonyms = new BasicDBList();
  synonyms.addAll(c.getSynonyms());
  names.put("synonyms", synonyms);

  BasicDBList pubchemNames = new BasicDBList();

  for (String type : c.getPubchemNameTypes()) {
    String[] temp = c.getPubchemNames(type);
    BasicDBList dbNames = new BasicDBList();
    for (String t : temp) {
      dbNames.add(t);
    }
    BasicDBObject dbNameObj = new BasicDBObject();
    dbNameObj.put("type", type);
    dbNameObj.put("values", dbNames);
    pubchemNames.add(dbNameObj);
  }
  names.put("pubchem", pubchemNames);
  BasicDBList brendaNames = new BasicDBList(); // will really get its fields later if initial install
  brendaNames.addAll(c.getBrendaNames()); // but for cases where we call it post install, we construct full chem entry
  names.put("brenda", brendaNames);

  doc.put("names", names);

  BasicDBObject xrefs = new BasicDBObject();
  xrefs.put("pubchem", c.getPubchemID());
  int cnt = 0;
  for (REFS xrefTyp : Chemical.REFS.values()) {
    if (c.getRef(xrefTyp) != null) {
      xrefs.put(xrefTyp.name(), MongoDBToJSON.conv((JSONObject)c.getRef(xrefTyp)));
      cnt++;
    }
  }
  doc.put("xref", xrefs);

  doc.put("estimateEnergy", c.getEstimatedEnergy());

  doc.put("keywords", c.getKeywords());
  doc.put("keywords_case_insensitive", c.getCaseInsensitiveKeywords());

  doc.put("csid", c.getChemSpiderID());
  doc.put("num_vendors", c.getChemSpiderNumUniqueVendors());
  doc.put("vendors", MongoDBToJSON.conv(c.getChemSpiderVendorXrefs()));

  return doc;
}
 

<X> BasicDBList to_dblist(Set<X> set) {
  BasicDBList dblist = new BasicDBList();
  if (set != null) dblist.addAll(set);
  return dblist;
}
 

private void updateBatch(BasicDBList sample) {
	
	// The batch may span collection splits, so maintain
	// a current collection and batch operation
	BulkWriteOperation currentOp = null;
	int currentOpOffset = 0;
	int sampleIdx = 0;
	DBCollection currentColl = null;	
	
	logger.debug("Received batch of size : {}", sample.size());
	
	try{
		for(; sampleIdx < sample.size(); ++sampleIdx){
			
			// prepare the sample to batch
			BasicDBObject doc = (BasicDBObject) (sample.get(sampleIdx));
			long timestamp = this.rollupPeriod * (doc.getLong(Sample.TS_KEY) / this.rollupPeriod);			
			DBCollection collection = collectionAllocator.getCollection(timestamp);
			
			// if the collection has changed, commit the current
			// batch to the collection and start new
			if(collection.equals(currentColl) == false){
				executeBatchUpdate(currentOp, sample);
				currentColl = collection;
				currentOp = collection.initializeUnorderedBulkOperation();
				currentOpOffset = sampleIdx;
			}
			
			// put the doc insert into the batch
			// Ask the id allocator for the query
			BasicDBObject query = this.idFactory.getQuery(doc.get(Sample.SOURCE_KEY), timestamp);
			
			// Build the update clause using the ops list
			BasicDBObject update = new BasicDBObject();
			for(RollupOperation rollupOp : this.rollupOps){
				
				DBObject updateClause = rollupOp.getUpdateClause(doc);
				
				// Check for top level operators that already exist so they dont overwrite
				for(String key : updateClause.keySet()){
					BasicDBObject existingClause = (BasicDBObject) update.get(key);
					if(existingClause != null){
						// Merge the arguments to the top level op
						existingClause.putAll((DBObject)updateClause.get(key));
					} else {
						update.put(key, updateClause.get(key));
					}
				}
			}
			
			currentOp.find(query).upsert().updateOne(update);
		}		
		
		// Finalize the last batch
		executeBatchUpdate(currentOp, sample);		
		
	} catch(Exception ex){
		
		// One of the bulk writes has failed
		BasicDBList failedDocs = new BasicDBList();
		if(ex instanceof BulkWriteException){
			
			// We need to figure out the failures and remove the writes
			// that worked from the batch
			int batchSize = sampleIdx - currentOpOffset;
			BulkWriteException bwex = (BulkWriteException)ex;
			int errorCount = bwex.getWriteErrors().size(); 
			if(errorCount < batchSize){
				
				for(BulkWriteError we : bwex.getWriteErrors()){
					failedDocs.add(sample.get(currentOpOffset + we.getIndex()));
				}
				
				// since we have accounted for the failures in the current
				// batch, move the offset forward to the last sample
				currentOpOffset = sampleIdx;					
			}
		}
		
		// If this happened part way through the batch, send remaining 
		// docs to failed list and update sample to contain only failed docs
		if(currentOpOffset > 0){
			for(; currentOpOffset < sample.size(); ++currentOpOffset)
				failedDocs.add(sample.get(currentOpOffset));
			sample.clear();
			sample.addAll(failedDocs);	
		}
		
		throw ex;
	}
}
 

private void storeBatch(BasicDBList sample, BasicDBList resultList) {
	
	// The batch may span collection splits, so maintain
	// a current collection and batch operation
	BulkWriteOperation currentOp = null;
	int currentOpOffset = 0;
	int sampleIdx = 0;
	DBCollection currentColl = null;	
	
	logger.debug("Received batch of size : {}", sample.size());
	
	try{
		for(; sampleIdx < sample.size(); ++sampleIdx){
			
			// prepare the sample to batch
			BasicDBObject doc = (BasicDBObject) (sample.get(sampleIdx));
			SampleId _id = this.idFactory.createId(doc);
			doc.put(Sample.ID_KEY, _id.toObject());
			resultList.add(_id.toObject());
			long timestamp = doc.getLong(Sample.TS_KEY);
			DBCollection collection = collectionAllocator.getCollection(timestamp);
			
			// if the collection has changed, commit the current
			// batch to the collection and start new
			if(collection.equals(currentColl) == false){
				executeBatchWrite(currentOp, sample);
				currentColl = collection;
				currentOp = collection.initializeUnorderedBulkOperation();
				currentOpOffset = sampleIdx;
			}
			
			// put the doc insert into the batch
			currentOp.insert(doc);
		}		
		
		// Finalize the last batch
		executeBatchWrite(currentOp, sample);		
		
	} catch(Exception ex){
		
		// One of the bulk writes has failed
		BasicDBList failedDocs = new BasicDBList();
		if(ex instanceof BulkWriteException){
			
			// We need to figure out the failures and remove the writes
			// that worked from the batch
			int batchSize = sampleIdx - currentOpOffset;
			BulkWriteException bwex = (BulkWriteException)ex;
			int errorCount = bwex.getWriteErrors().size(); 
			if(errorCount < batchSize){
				
				for(BulkWriteError we : bwex.getWriteErrors()){
					failedDocs.add(sample.get(currentOpOffset + we.getIndex()));
				}
				
				// since we have accounted for the failures in the current
				// batch, move the offset forward to the last sample
				currentOpOffset = sampleIdx;					
			}
		}
		
		// If this happened part way through the batch, send remaining 
		// docs to failed list and update sample to contain only failed docs
		if(currentOpOffset > 0){
			for(; currentOpOffset < sample.size(); ++currentOpOffset)
				failedDocs.add(sample.get(currentOpOffset));
			sample.clear();
			sample.addAll(failedDocs);	
		}
		
		// TODO : we also need to handle the result Ids here as well,
		// the failed doc Ids must be pulled from the resultList
		throw ex;
	}
}