CRef<CGCClient_AssembliesForSequences> CGenomicCollectionsService::FindAssembliesBySequences(const list<string>& sequence_acc, int filter, CGCClient_GetAssemblyBySequenceRequest::ESort sort, bool top_only)
{
CGCClient_GetAssemblyBySequenceRequest req;
CGCClientResponse reply;
for(auto acc : sequence_acc)
if(acc.length() > 30) {
NCBI_THROW(CException, eUnknown, "Accession is longer than 30 characters: " + acc);
}
req.SetSequence_acc().assign(sequence_acc.begin(), sequence_acc.end());
req.SetFilter(filter);
req.SetSort(sort);
req.SetTop_assembly_only(top_only ? 1 : 0);
LogRequest(req);
try {
CRef<CGCClient_AssembliesForSequences> assm = AskGet_assembly_by_sequence(req, &reply);
return assm;
} catch (const CException& ex) {
if(reply.IsSrvr_error()) {
NCBI_REPORT_EXCEPTION(reply.GetSrvr_error().GetDescription(), ex);
}
throw;
}
return CRef<CGCClient_AssembliesForSequences>();
}
CRef<CGCClient_AssemblySequenceInfo> CGenomicCollectionsService::FindBestAssembly(const list<string>& seq_id, int filter_type, int sort_type)
{
CGCClient_FindBestAssemblyRequest req;
CGCClientResponse reply;
req.SetSeq_id_acc().assign(seq_id.begin(), seq_id.end());
req.SetFilter(filter_type);
req.SetSort(sort_type);
req.SetAssembly_return_limit(1);
LogRequest(req);
try {
CRef<CGCClient_AssembliesForSequences> assm = AskGet_best_assembly(req, &reply);
return assm->CanGetAssemblies() && !assm->GetAssemblies().empty() ?
CRef<CGCClient_AssemblySequenceInfo>(assm->SetAssemblies().front()) :
CRef<CGCClient_AssemblySequenceInfo>();
} catch (const CException& ex) {
if(reply.IsSrvr_error()) {
NCBI_REPORT_EXCEPTION(reply.GetSrvr_error().GetDescription().c_str(), ex);
}
throw;
}
}
int CNetCacheBlobFetchApp::OnException(std::exception& e, CNcbiOstream& os)
{
union {
CArgException* arg_exception;
CNetCacheException* nc_exception;
};
string status_str;
string message;
if ((arg_exception = dynamic_cast<CArgException*>(&e)) != NULL) {
status_str = "400 Bad Request";
message = arg_exception->GetMsg();
SetHTTPStatus(CRequestStatus::e400_BadRequest);
} else if ((nc_exception = dynamic_cast<CNetCacheException*>(&e)) != NULL) {
switch (nc_exception->GetErrCode()) {
case CNetCacheException::eAccessDenied:
status_str = "403 Forbidden";
message = nc_exception->GetMsg();
SetHTTPStatus(CRequestStatus::e403_Forbidden);
break;
case CNetCacheException::eBlobNotFound:
status_str = "404 Not Found";
message = nc_exception->GetMsg();
SetHTTPStatus(CRequestStatus::e404_NotFound);
break;
default:
return CCgiApplication::OnException(e, os);
}
} else
return CCgiApplication::OnException(e, os);
// Don't try to write to a broken output
if (!os.good()) {
return -1;
}
try {
// HTTP header
os << "Status: " << status_str << HTTP_EOL <<
"Content-Type: text/plain" HTTP_EOL HTTP_EOL <<
"ERROR: " << status_str << " " HTTP_EOL HTTP_EOL <<
message << HTTP_EOL;
// Check for problems in sending the response
if (!os.good()) {
ERR_POST("CNetCacheBlobFetchApp::OnException() "
"failed to send error page back to the client");
return -1;
}
}
catch (exception& e) {
NCBI_REPORT_EXCEPTION("(CGI) CNetCacheBlobFetchApp::OnException", e);
}
return 0;
}
CTMS_CreateUserTrack_Client::TReplyRef
CTMS_CreateUserTrack_Client::Fetch(const TRequest& request) const
{
CRef<TReply> reply;
try {
reply.Reset(new TReply());
TBaseClient::Ask(request, *reply);
}
catch (const CException& e) {
NCBI_REPORT_EXCEPTION("Exception communicating with TMS-CreateUserTrack service ", e);
reply.Reset();
}
return reply;
}
CRef<CGCClient_EquivalentAssemblies> CGenomicCollectionsService::GetEquivalentAssemblies(const string& acc, int equivalency)
{
CGCClient_GetEquivalentAssembliesRequest req;
CGCClientResponse reply;
req.SetAccession(acc);
req.SetEquivalency(equivalency);
LogRequest(req);
try {
CRef<CGCClient_EquivalentAssemblies> assm = AskGet_equivalent_assemblies(req, &reply);
return assm;
} catch (const CException& ex) {
if(reply.IsSrvr_error()) {
NCBI_REPORT_EXCEPTION(reply.GetSrvr_error().GetDescription(), ex);
}
throw;
}
}
void CTestDiagApp::x_PrintMessages(int test_number,
int idx,
const char* module,
const char* nclass,
const char* function)
{
string location = string(module) + "::" + nclass + "::" +
function + "()";
string postmsg = location + " in ERR_POST";
string exceptmsg = location + " in the one level exception";
string secondmsg = location + " in the two levels exception";
if (idx == 0) {
m_Messages[ TCase( test_number, 0 ) ] = postmsg;
m_Messages[ TCase( test_number, 1 ) ] = exceptmsg;
m_Messages[ TCase( test_number, 2 ) ] = secondmsg;
}
// ERR_POST
ERR_POST(x_MakeMessage(postmsg, idx, TCase(test_number,0))
<< MDiagModule(module)
<< MDiagClass(nclass)
<< MDiagFunction(function));
// one level exception
try {
NCBI_EXCEPTION_VAR(expt, CException, eUnknown, "exception");
expt.SetModule(module);
expt.SetClass(nclass);
expt.SetFunction(function);
NCBI_EXCEPTION_THROW(expt);
}
catch (const CException& ex) {
NCBI_REPORT_EXCEPTION(x_MakeMessage(exceptmsg,
idx,
TCase(test_number, 1)), ex);
}
#if defined(NCBI_COMPILER_WORKSHOP)
# if NCBI_COMPILER_VERSION == 530 || NCBI_COMPILER_VERSION == 550
// Workshop 5.3 and 5.5 have MT-unsafe throw. To avoid test failures
// use mutex.
DEFINE_STATIC_FAST_MUTEX(s_ThrowMutex);
CFastMutexGuard guard(s_ThrowMutex);
# endif
#endif
// two level exceptions
try {
try {
NCBI_EXCEPTION_VAR(expt, CException, eUnknown, "exception1");
expt.SetModule(module);
expt.SetClass(nclass);
expt.SetFunction(function);
NCBI_EXCEPTION_THROW(expt);
}
catch (const CException& ex) {
NCBI_EXCEPTION_VAR_EX(e2, &ex, CException, eUnknown, "exception2");
e2.SetModule(module);
e2.SetClass(nclass);
e2.SetFunction(function);
NCBI_EXCEPTION_THROW(e2);
}
}
catch (const CException& ex) {
NCBI_REPORT_EXCEPTION(x_MakeMessage(secondmsg,
idx,
TCase(test_number, 2)), ex);
}
}
