std::string CjsonExporter::toCjson(const mongo::BSONObj &mongoChemObj)
{
// Follow the database link and convert to CJSON.
MongoDatabase *db = MongoDatabase::instance();
if (!db)
return "";
mongo::BSONObj structure = mongoChemObj.getObjectField("3dStructure");
if (!structure.hasField("$ref") || !structure.hasField("$id")
|| !structure.getField("$id").isSimpleType()) {
return "";
}
std::auto_ptr<mongo::DBClientCursor> cursor =
db->query(db->databaseName() + "." + structure.getStringField("$ref"),
QUERY("_id" << structure.getField("$id").OID()), 1);
mongo::BSONObj object;
if (cursor->more())
object = cursor->next();
else
return "";
std::vector<std::string> toCopy;
toCopy.push_back("name");
toCopy.push_back("inchi");
toCopy.push_back("formula");
toCopy.push_back("properties");
mongo::BSONObjBuilder builder;
for (size_t i = 0; i < toCopy.size(); i++) {
mongo::BSONElement field = mongoChemObj.getField(toCopy[i]);
if (!field.eoo())
builder.append(field);
}
toCopy.clear();
toCopy.push_back("atoms");
toCopy.push_back("bonds");
for (size_t i = 0; i < toCopy.size(); i++) {
mongo::BSONElement field = object.getField(toCopy[i]);
if (!field.eoo())
builder.append(field);
}
// Add the chemical JSON version field.
builder.append("chemical json", 0);
mongo::BSONObj obj = builder.obj();
return obj.jsonString(mongo::Strict);
}
void ComputationalResultsModel::setQuery(const mongo::Query &query)
{
beginInsertRows(QModelIndex(), 0, rowCount(QModelIndex()));
m_objects.clear();
MongoDatabase *db = MongoDatabase::instance();
try {
std::string collection = db->databaseName();
std::auto_ptr<mongo::DBClientCursor> cursor =
db->connection()->query(collection + ".quantum", query);
// Let's read in the results, but limit to 1000 in case of bad queries.
int i(0);
while (cursor->more() && ++i < 1000)
m_objects.push_back(cursor->next().copy());
}
catch (mongo::SocketException &e) {
std::cerr << "Failed to query MongoDB: " << e.what() << std::endl;
}
endInsertRows();
}