/*it extracts servers address from the message if the server is new server it assignes new server address for the server*/
void getSrvId(char *msg,char *strSrvId,int type){
char *srvId;
if(type==IPV4 && savedIpv4<MAX_SRV_CONN){
srvId=parseTocken(msg,2,DELIMITER,strlen(msg));
if(srvId){
if(strcmp(srvId,NEWSERVER)==0)
assignId(srvId);
strcpy(strSrvId,srvId);
free(srvId);
}
}
else if(type==IPV6 && savedIpv6<MAX_SRV_CONN){
srvId=parseTocken(msg,2,DELIMITER,strlen(msg));
if(srvId){
if(strcmp(srvId,NEWSERVER)==0)
assignId(srvId);
strcpy(strSrvId,srvId);
free(srvId);
}
}
else
strcpy(strSrvId,NEWSERVER);
}
bool DataSourceInterface::executeInsertInternal(Query& query, void* entity) {
DataSourceEntityMapping dsemp = mapping->getDataSourceEntityMapping(query.getClassName());
ClassInfo clas = reflector->getClassInfo(query.getClassName(), appName);
if(dsemp.isIdGenerate() && dsemp.getIdgendbEntityType()!="identity") {
assignId(dsemp, clas, entity);
}
bool flag = executeInsert(query, entity);
if(flag && dsemp.isIdGenerate() && dsemp.getIdgendbEntityType()=="identity") {
assignId(dsemp, clas, entity);
}
return flag;
}
void Ellipse::appendAsXml(SvgElement& parent, Drawing& drawing) {
SvgElement element = parent.createElement("ellipse");
assignId(element);
Point mapped = drawing.map(m_centre);
element.setAttribute("cx", NumberUtil::formatFloat(mapped.getX()));
element.setAttribute("cy", NumberUtil::formatFloat(mapped.getY()));
element.setAttribute("rx", NumberUtil::formatFloat(m_radius));
element.setAttribute("ry", NumberUtil::formatFloat(m_radius * m_eccentricity));
if (m_inclination != 0) {
element.setAttribute("transform", "rotate(" + NumberUtil::formatFloat((float) (m_inclination * 180.0 / M_PI)) + ")");
}
setStrokeAndFill(element, drawing);
parent.appendChild(element);
}
// add GeneId as RelationshipXref to Protein or ProteinReference with unipax_id id
bool UniPAX::mysql::MySQLManager::addGeneId(UnipaxId id, std::string external_protein_id,
std::map<std::string, boost::shared_ptr<UniPAX::RelationshipXref> > & rxref_map,
KernelCollector& manager, UniProtReader& reader)
{
if (DBManager::isType(id, UniPAX::ClassType::idProtein)) //UniPAX::Protein
{
boost::shared_ptr<UniPAX::Protein> protein = boost::dynamic_pointer_cast<UniPAX::Protein>(super::getObjectByID(id));
std::string::size_type found = external_protein_id.find("-");
if (found != std::string::npos)
{
std::cout << "shorten id '" << external_protein_id << "' to '" << external_protein_id.substr(0,found) << "'" << std::endl;
external_protein_id = external_protein_id.substr(0, found);
}
std::vector<std::string> ids;
// change standardName of Protein
ids = reader.getMappedId(external_protein_id,"UniProtKB-ID");
if (!ids.empty())
{
protein->setStandardName(ids[0]);
}
ids.clear();
ids = reader.getMappedId(external_protein_id,"GeneID");
// if no corresponding GeneId found ... continue
if (ids.empty())
{
std::cout << "no corresponding GeneId found for '" << external_protein_id << "'" << std::endl;
return false;
}
std::string search_string = std::string("EntrezGene")+"||"+ids[0];
boost::shared_ptr<UniPAX::RelationshipXref> rxref;
UnipaxId rxid = getRelationshipXrefId("EntrezGene", ids[0]);
UnipaxId help = db_ids["RelationshipTypeVocabulary"];
help++;
if (rxid == 0)
{
if (rxref_map.find(search_string) == rxref_map.end())
{
rxref = boost::shared_ptr<UniPAX::RelationshipXref>(new UniPAX::RelationshipXref());
rxref->setDb("EntrezGene");
rxref->setId(ids[0]);
assignId(rxref, false);
boost::shared_ptr<UniPAX::RelationshipTypeVocabulary> rtv = boost::shared_ptr<UniPAX::RelationshipTypeVocabulary>(new UniPAX::RelationshipTypeVocabulary);
rtv->setTerm("Coding gene");
rxref->addRelationshipType(rtv);
rtv->setUnipaxId(help);
rxref_map[search_string] = rxref;
}
else
{
rxref = rxref_map.find(search_string)->second;
}
}
else
{
rxref = boost::dynamic_pointer_cast<UniPAX::RelationshipXref>(super::getObjectByID(rxid));
}
protein->addXref(rxref);
manager.collect(protein);
}
else if (DBManager::isType(id, UniPAX::ClassType::idProteinReference)) //UniPAX::ProteinReference
{
boost::shared_ptr<UniPAX::ProteinReference> proteinref = boost::dynamic_pointer_cast<UniPAX::ProteinReference>(super::getObjectByID(id));
size_t found = external_protein_id.find("-");
if (found != std::string::npos)
{
std::cout << "shorten id '" << external_protein_id << "' to '" << external_protein_id.substr(0,found) << "'" << std::endl;
external_protein_id = external_protein_id.substr(0,found);
}
std::vector<std::string> ids;
// change standardName of ProteinReference
ids = reader.getMappedId(external_protein_id,"UniProtKB-ID");
if (!ids.empty())
{
proteinref->setStandardName(ids[0]);
}
ids.clear();
ids = reader.getMappedId(external_protein_id,"GeneID");
// if no corresponding GeneId found ... continue
if (ids.empty())
{
std::cout << "no corresponding GeneId found for '" << external_protein_id << "'" << std::endl;
return false;
}
std::string search_string = std::string("EntrezGene")+"||"+ids[0];
boost::shared_ptr<UniPAX::RelationshipXref> rxref;
UnipaxId rxid = getRelationshipXrefId("EntrezGene", ids[0]);
UnipaxId help = db_ids["RelationshipTypeVocabulary"];
help++;
if (rxid == 0)
{
if (rxref_map.find(search_string) == rxref_map.end())
{
rxref = boost::shared_ptr<UniPAX::RelationshipXref>(new UniPAX::RelationshipXref());
rxref->setDb("EntrezGene");
rxref->setId(ids[0]);
assignId(rxref, false);
boost::shared_ptr<UniPAX::RelationshipTypeVocabulary> rtv = boost::shared_ptr<UniPAX::RelationshipTypeVocabulary>(new UniPAX::RelationshipTypeVocabulary);
rtv->setTerm("Coding gene");
rxref->addRelationshipType(rtv);
rtv->setUnipaxId(help);
rxref_map[search_string] = rxref;
}
else
{
rxref = rxref_map.find(search_string)->second;
}
}
else
{
rxref = boost::dynamic_pointer_cast<UniPAX::RelationshipXref>(super::getObjectByID(rxid));
}
proteinref->addXref(rxref);
manager.collect(proteinref);
}
return true;
}
bool UniPAX::mysql::MySQLManager::assignId(boost::shared_ptr<UniPAX::UPBase> object)
{
return assignId(object, true);
}
