virtual void* Main(void) {
//for (int i = 0; i < 10; ++i) {
for (;;) {
try {
CDatabase db("MSDEV");
db.Connect();
CQuery q = db.NewQuery("select serverproperty('servername')");
q.Execute();
LOG_POST("Thread " << m_Num << " connected to " << q.begin()[1].AsString());
try {
q.SetSql("drop table #t");
q.Execute();
}
catch (CSDB_Exception&) {
//
}
q.SetSql("create table #t (tt varchar(100))");
q.Execute();
q.SetSql("insert into #t values (@tt)");
for (int i = 0; i < 500; ++i) {
q.SetParameter("@tt", i, eSDB_String);
q.Execute();
}
SleepMilliSec(100);
}
catch (CSDB_Exception& ex) {
LOG_POST("Error from SDBAPI in thread " << m_Num << ": " << ex);
}
}
return NULL;
}
void SNS_Parameters::CheckAffinityGarbageCollectorSettings(void)
{
bool well_formed = true;
if (affinity_high_mark_percentage >= 100) {
LOG_POST(Message << Warning <<
"INI file sets affinity_high_mark_percentage >= 100. "
"All the affinity garbage collector settings are reset to default.");
well_formed = false;
}
if (well_formed && affinity_low_mark_percentage >= affinity_high_mark_percentage) {
LOG_POST(Message << Warning <<
"INI file sets affinity_low_mark_percentage >= affinity_high_mark_percentage. "
"All the affinity garbage collector settings are reset to default.");
well_formed = false;
}
if (well_formed && affinity_dirt_percentage >= affinity_low_mark_percentage) {
LOG_POST(Message << Warning <<
"INI file sets affinity_dirt_percentage >= affinity_low_mark_percentage. "
"All the affinity garbage collector settings are reset to default.");
well_formed = false;
}
if (well_formed == false) {
affinity_high_mark_percentage = default_affinity_high_mark_percentage;
affinity_low_mark_percentage = default_affinity_low_mark_percentage;
affinity_high_removal = default_affinity_high_removal;
affinity_low_removal = default_affinity_low_removal;
affinity_dirt_percentage = default_affinity_dirt_percentage;
}
return;
}
void CTest::x_TestSeverity()
{
SetDiagPostLevel(eDiag_Info);
SetDiagFilter(eDiagFilter_All, "[Error]module [Info]!module");
LOG_POST(Warning << MDiagModule("module") << "Test error 1");
LOG_POST(Error << MDiagModule("module") << "Test error 2");
LOG_POST(Warning << MDiagModule("module2") << "Test error 3");
LOG_POST(Info << MDiagModule("module3") << "Test error 4");
}
void SequenceTable::dump(string filename)
{
CNcbiOfstream outStream(filename.c_str(), IOS_BASE::out | IOS_BASE::binary);
string err;
if (!outStream) {
err = "Cannot open file for writing";
}
SeqidToBioseqMap::iterator sit = m_table.begin();
for (; sit != m_table.end(); sit++)
{
if (!WriteASNToStream(outStream, *(sit->first), false,&err))
LOG_POST("Failed to write to "<<filename<<" because of "<<err);
if (!WriteASNToStream(outStream, *(sit->second), false,&err))
LOG_POST("Failed to write to "<<filename<< "because of "<<err);
}
}
void CSampleJobCleanupListener::HandleEvent(
EWorkerNodeCleanupEvent cleanup_event)
{
LOG_POST(m_CleanupType << (cleanup_event ==
IWorkerNodeCleanupEventListener::eRegularCleanup ?
" regular clean-up" : " clean-up during force exit"));
}
CRef<CGC_Assembly> CGenomicCollectionsService::GetAssembly(string acc,
int level,
int asmAttrFlags,
int chrAttrFlags,
int scafAttrFlags,
int compAttrFlags)
{
CGCClient_GetAssemblyRequest req;
CGCClientResponse reply;
req.SetAccession(acc);
req.SetLevel(level);
req.SetAssm_flags(asmAttrFlags);
req.SetChrom_flags(chrAttrFlags);
req.SetScaf_flags(scafAttrFlags);
req.SetComponent_flags(compAttrFlags);
#ifdef _DEBUG
ostringstream ostrstrm;
ostrstrm << "Making request - " << MSerial_AsnText << req;
LOG_POST(Info << ostrstrm.str());
#endif
try {
return AskGet_assembly(req, &reply);
} catch (CException& ex) {
if(reply.Which() == CGCClientResponse::e_Srvr_error) {
ERR_POST(Error << " at Server side (will be propagated) ...\nErrId:"
<< reply.GetSrvr_error().GetError_id() << ": "
<< reply.GetSrvr_error().GetDescription());
NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
}
throw;
}
}
CRef<CGC_Assembly> CGenomicCollectionsService::GetAssembly(int releaseId,
int level,
int asmAttrFlags,
int chrAttrFlags,
int scafAttrFlags,
int compAttrFlags)
{
CGCClient_GetAssemblyRequest req;
CGCClientResponse reply;
req.SetRelease_id(releaseId);
req.SetLevel(level);
req.SetAssm_flags(asmAttrFlags);
req.SetChrom_flags(chrAttrFlags);
req.SetScaf_flags(scafAttrFlags);
req.SetComponent_flags(compAttrFlags);
#ifdef _DEBUG
ostringstream ostrstrm;
ostrstrm << "Making request -" << MSerial_AsnText << req;
LOG_POST(Info << ostrstrm.str());
#endif
try {
return AskGet_assembly(req, &reply);
} catch (CException& ex) {
if(reply.Which() == CGCClientResponse::e_Srvr_error) {
NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
}
throw;
}
}
string CGenomicCollectionsService::ValidateChrType(string chrType, string chrLoc)
{
CGCClient_ValidateChrTypeLocRequest req;
CGCClientResponse reply;
req.SetType(chrType);
req.SetLocation(chrLoc);
#ifdef _DEBUG
ostringstream ostrstrm;
ostrstrm << "Making request -" << MSerial_AsnText << req;
LOG_POST(Info << ostrstrm.str());
#endif
try {
return AskGet_chrtype_valid(req, &reply);
} catch (CException& ex) {
if(reply.Which() == CGCClientResponse::e_Srvr_error) {
ERR_POST(Error << " at Server side (will be propagated) ...\n"
<< reply.GetSrvr_error().GetError_id() << ": "
<< reply.GetSrvr_error().GetDescription());
NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
}
throw;
}
}
NCBITEST_INIT_TREE()
{
if ( s_Random.GetSeed() == 0 ) {
s_Random.Randomize();
LOG_POST("Random seed: "<<s_Random.GetSeed());
}
}
/*********************************************************************
* @brief : REST API handler to clear the bst stats
*
* @param[in] cookie : pointer to the cookie
* @param[in] asicId : asic id
* @param[in] id : unit id
* @param[in] pCommand : pointer to the input command structure
*
* @retval : BVIEW_STATUS_SUCCESS : the message is successfully posted to bst queue.
* @retval : BVIEW_STATUS_FAILURE : failed to post the message to bst.
* @retval : BVIEW_STATUS_INVALID_PARAMETER : invalid parameter.
*
* @note : This api posts the request to bst application to clear stats.
*
*********************************************************************/
BVIEW_STATUS bstjson_clear_bst_statistics_impl (void *cookie, int asicId,
int id,
BSTJSON_CLEAR_BST_STATISTICS_t *
pCommand)
{
BVIEW_BST_REQUEST_MSG_t msg_data;
BVIEW_STATUS rv;
/* copy the params from the request */
memset (&msg_data, 0, sizeof (BVIEW_BST_REQUEST_MSG_t));
msg_data.unit = asicId;
msg_data.cookie = cookie;
msg_data.id = id;
msg_data.msg_type = BVIEW_BST_CMD_API_CLEAR_STATS;
/* send message to bst application */
rv = bst_send_request (&msg_data);
if (BVIEW_STATUS_SUCCESS != rv)
{
_BST_LOG(_BST_DEBUG_ERROR, "bstjson_clear_bst_statistics_impl: failed to post clear bst stats request to bst queue. err = %d.\r\n",rv);
LOG_POST (BVIEW_LOG_ERROR,
"failed to post clear bst stats request to bst queue. err = %d.\r\n",rv);
}
return rv;
}
/*********************************************************************
* @brief : REST API handler to configure the bst track params
*
* @param[in] cookie : pointer to the cookie
* @param[in] asicId : asic id
* @param[in] id : unit id
* @param[in] pCommand : pointer to the input command structure
*
* @retval : BVIEW_STATUS_SUCCESS : the message is successfully posted to bst queue.
* @retval : BVIEW_STATUS_FAILURE : failed to post the message to bst.
* @retval : BVIEW_STATUS_INVALID_PARAMETER : invalid parameter.
*
* @note : This api posts the request to bst application to set the track params.
*
* @end
*********************************************************************/
BVIEW_STATUS bstjson_configure_bst_tracking_impl (void *cookie, int asicId,
int id,
BSTJSON_CONFIGURE_BST_TRACKING_t
* pCommand)
{
BVIEW_BST_REQUEST_MSG_t msg_data;
BVIEW_STATUS rv;
if (NULL == pCommand)
return BVIEW_STATUS_INVALID_PARAMETER;
memset (&msg_data, 0, sizeof (BVIEW_BST_REQUEST_MSG_t));
msg_data.unit = asicId;
msg_data.cookie = cookie;
msg_data.msg_type = BVIEW_BST_CMD_API_SET_TRACK;
msg_data.id = id;
msg_data.request.track = *pCommand;
/* send message to bst application */
rv = bst_send_request (&msg_data);
if (BVIEW_STATUS_SUCCESS != rv)
{
LOG_POST (BVIEW_LOG_ERROR,
"failed to post configure bst tracking to bst queue. err = %d.\r\n",rv);
}
return rv;
}
/*********************************************************************
* @brief : REST API handler to get the bst threshold
*
* @param[in] cookie : pointer to the cookie
* @param[in] asicId : asic id
* @param[in] id : unit id
* @param[in] pCommand : pointer to the input command structure
*
* @retval : BVIEW_STATUS_SUCCESS : the message is successfully posted to bst queue.
* @retval : BVIEW_STATUS_FAILURE : failed to post the message to bst.
* @retval : BVIEW_STATUS_INVALID_PARAMETER : invalid parameter.
*
* @note : This api posts the request to bst application to get the bst thresholds.
*
*********************************************************************/
BVIEW_STATUS bstjson_get_bst_thresholds_impl (void *cookie, int asicId, int id,
BSTJSON_GET_BST_THRESHOLDS_t *
pCommand)
{
BVIEW_BST_REQUEST_MSG_t msg_data;
BVIEW_STATUS rv;
if (NULL == pCommand)
return BVIEW_STATUS_INVALID_PARAMETER;
memset (&msg_data, 0, sizeof (BVIEW_BST_REQUEST_MSG_t));
msg_data.unit = asicId;
msg_data.cookie = cookie;
msg_data.msg_type = BVIEW_BST_CMD_API_GET_THRESHOLD;
msg_data.id = id;
memcpy (&msg_data.request.collect, pCommand, sizeof(BSTJSON_GET_BST_THRESHOLDS_t));
/* send message to bst application */
rv = bst_send_request (&msg_data);
if (BVIEW_STATUS_SUCCESS != rv)
{
LOG_POST (BVIEW_LOG_ERROR,
"failed to post get bst thresholds to bst queue. err = %d.\r\n",rv);
}
return rv;
}
inline void add_step()
{
CAtomicCounter::TValue c = current_step.Add(1);
if ( c % 1000000 == 0 ) {
LOG_POST("step "<<c<<" of "<<total_steps);
}
}
void LogRequest(const TReq& req)
{
#ifdef _DEBUG
ostringstream ostrstrm;
ostrstrm << "Making request -" << MSerial_AsnText << req;
LOG_POST(Info << ostrstrm.str());
#endif
}
void Dump(void) const
{
unsigned total_locks = 0;
ITERATE ( TLocks, it, m_Locks ) {
++total_locks;
LOG_POST("Locked<"<<sx_MonitorType->name()<<">"
"("<<it->first<<","<<m_Object<<")"
" @ " << *it->second);
}
bool CTestTlsObjectApp::TestApp_Exit(void)
{
check_cnts(~0u);
LOG_POST("Max memory VS: " << (double)max_total/(1024*1024.) << " MB" <<
" RSS: " << (double)max_resident/(1024*1024.) << " MB" <<
" SHR: " << (double)max_shared/(1024*1024.) << " MB");
NcbiCout << "Test completed." << NcbiEndl;
return true;
}
void CNetCacheServerListener::OnWarning(const string& warn_msg,
SNetServerImpl* server)
{
if (m_EventHandler)
m_EventHandler->OnWarning(warn_msg, server);
else {
LOG_POST(Warning << server->m_ServerInPool->m_Address.AsString() <<
": " << warn_msg);
}
}
bool CCSRATestApp::TestApp_Exit(void)
{
if ( m_ErrorCount ) {
ERR_POST("Errors found: "<<m_ErrorCount);
}
else {
LOG_POST("Done.");
}
return !m_ErrorCount;
}
//------------------------------------------------------------------------------
int CWinMaskCountsConverter::operator()()
{
CRef< CSeqMaskerOstat > ostat( 0 );
if( os == 0 ) {
ostat = CSeqMaskerOstatFactory::create( oformat, ofname, true );
}
else ostat = CSeqMaskerOstatFactory::create( oformat, *os, true );
Uint4 unit_size = istat->UnitSize();
_TRACE( "set unit size to " << unit_size );
ostat->setUnitSize( unit_size );
Uint8 num_units = (unit_size < 16) ? (1ULL<<(2*unit_size))
: 0x100000000ULL;
LOG_POST( "converting counts..." );
for( Uint8 i = 0; i < num_units; ++i ) {
Uint4 ri = CSeqMaskerUtil::reverse_complement( i, unit_size );
if( i <= ri ) {
Uint4 count = istat->trueat( i );
if( count != 0 ) ostat->setUnitCount( i, count );
}
}
LOG_POST( "converting parameters..." );
ostat->setBlank();
ostat->setBlank();
Uint4 t_low = istat->get_min_count();
Uint4 t_extend = istat->get_textend();
Uint4 t_threshold = istat->get_threshold();
Uint4 t_high = istat->get_max_count();
ostat->setParam( "t_low ", t_low );
ostat->setParam( "t_extend ", t_extend );
ostat->setParam( "t_threshold", t_threshold );
ostat->setParam( "t_high ", t_high );
ostat->setBlank();
LOG_POST( "final processing..." );
ostat->finalize();
return 0;
}
//----------------------------------------------------------------------------
void CWinMaskUtil::CIdSet_SeqId::insert( const string & id_str )
{
try {
CRef<CSeq_id> id(new CSeq_id(id_str));
idset.insert(CSeq_id_Handle::GetHandle(*id));
} catch (CSeqIdException& e) {
LOG_POST(Error
<< "CWinMaskConfig::FillIdList(): can't understand id: "
<< id_str << ": " << e.what() << ": ignoring");
}
}
void x_Init(const string& NC_registry_section)
{
LOG_POST(Trace << "NS queue NC: " << NC_registry_section);
m_NC_api = CNetCacheAPI(CNetCacheAPI::eAppRegistry, NC_registry_section);
m_Grid_cli.reset(new CGridClient(m_NS_api.GetSubmitter(),
m_NC_api,
CGridClient::eManualCleanup,
CGridClient::eProgressMsgOn
)
);
}
int
CSeqDBPerfApp::x_ScanDatabase()
{
CStopWatch sw;
sw.Start();
Uint8 num_letters = m_BlastDb->GetTotalLength();
const bool kScanUncompressed = GetArgs()["scan_uncompressed"];
vector<int> oids2iterate;
for (int oid = 0; m_DbHandles.front()->CheckOrFindOID(oid); oid++) {
oids2iterate.push_back(oid);
}
LOG_POST(Info << "Will go over " << oids2iterate.size() << " sequences");
#pragma omp parallel default(none) num_threads(m_DbHandles.size()) \
shared(oids2iterate) if(m_DbHandles.size() > 1)
{
int thread_id = 0;
#ifdef _OPENMP
thread_id = omp_get_thread_num();
#endif
#pragma omp for schedule(static, (oids2iterate.size()/m_DbHandles.size())) nowait
for (size_t i = 0; i < oids2iterate.size(); i++) {
int oid = oids2iterate[i];
const char* buffer = NULL;
int seqlen = 0;
if (m_DbIsProtein || kScanUncompressed) {
int encoding = m_DbIsProtein ? 0 : kSeqDBNuclBlastNA8;
m_DbHandles[thread_id]->GetAmbigSeq(oid, &buffer, encoding);
seqlen = m_DbHandles[thread_id]->GetSeqLength(oid);
} else {
m_DbHandles[thread_id]->GetSequence(oid, &buffer);
seqlen = m_DbHandles[thread_id]->GetSeqLength(oid) / 4;
}
for (int i = 0; i < seqlen; i++) {
char base = buffer[i];
base = base; // dummy statement
}
if (m_DbIsProtein || kScanUncompressed) {
m_DbHandles[thread_id]->RetAmbigSeq(&buffer);
} else {
m_DbHandles[thread_id]->RetSequence(&buffer);
}
}
x_UpdateMemoryUsage(thread_id);
} // end of omp parallel
sw.Stop();
Uint8 bases = static_cast<Uint8>(num_letters / sw.Elapsed());
cout << "Scanning rate: "
<< NStr::NumericToString(bases, NStr::fWithCommas)
<< " bases/second" << endl;
return 0;
}
bool CTestRegApp::TestApp_Init(void)
{
LOG_POST("Testing NCBITIME " +
NStr::UIntToString(s_NumThreads) + " threads...");
// Set err.-posting and tracing to maximum
SetDiagTrace(eDT_Enable);
SetDiagPostFlag(eDPF_All);
SetDiagPostLevel(eDiag_Info);
return true;
}
void CGenomicCollectionsService::x_Connect()
{
#ifdef _DEBUG
LOG_POST(Info << "Connecting to url:" << x_GetURL().c_str());
#endif
STimeout to5Min;
to5Min.sec=600;
to5Min.usec=0;
SetTimeout(&to5Min);
x_ConnectURL(x_GetURL());
}
int CNetCacheBlobFetchApp::ProcessRequest(CCgiContext& ctx)
{
const CCgiRequest& request = ctx.GetRequest();
CCgiResponse& reply = ctx.GetResponse();
bool is_found;
string key = request.GetEntry("key", &is_found);
if (key.empty() || !is_found) {
NCBI_THROW(CArgException, eNoArg, "CGI entry 'key' is missing");
}
string fmt = request.GetEntry("fmt", &is_found);
if (fmt.empty() || !is_found)
fmt = "image/png";
string filename(request.GetEntry("filename", &is_found));
if (is_found && !filename.empty()) {
string is_inline(request.GetEntry("inline", &is_found));
reply.SetHeaderValue("Content-Disposition",
(is_found && NStr::StringToBool(is_inline) ?
"inline; filename=" : "attachment; filename=") +
filename);
}
reply.SetContentType(fmt);
reply.WriteHeader();
CNetStorageObject netstorage_object(m_NetStorage.Open(key));
char buffer[NETSTORAGE_IO_BUFFER_SIZE];
size_t total_bytes_written = 0;
while (!netstorage_object.Eof()) {
size_t bytes_read = netstorage_object.Read(buffer, sizeof(buffer));
reply.out().write(buffer, bytes_read);
total_bytes_written += bytes_read;
if (bytes_read < sizeof(buffer))
break;
}
netstorage_object.Close();
LOG_POST(Info << "retrieved data: " << total_bytes_written << " bytes");
return 0;
}
void message(const char* msg,
const char* msg1, double t1,
const char* msg2, double t2,
size_t COUNT)
{
if ( 0 ) {
LOG_POST(msg
<<'\n'<<setw(40) << msg1 << ": "<< t1 * 1e9/(double)COUNT << " usec"
<<'\n'<<setw(40) << msg2 << ": "<< t2 * 1e9/(double)COUNT << " usec");
}
size_t total, resident, shared;
if ( GetMemoryUsage(&total, &resident, &shared) ) {
max_total = max(max_total, total);
max_resident = max(max_resident, resident);
max_shared = max(max_shared, shared);
if ( 0 ) {
LOG_POST("Alloc: "<<alloc_count.Get()<<
" "<<object_count.Get()<<'\n'<<
"Current memory: "<<total<<" "<<resident<<" "<<shared);
}
}
}
//------------------------------------------------------------------------------
CWinMaskCountsConverter::CWinMaskCountsConverter(
const string & input_fname, CNcbiOstream & out_stream,
const string & counts_oformat )
: istat( 0 ), ofname( "" ), oformat( counts_oformat ), os( &out_stream )
{
if( input_fname == "-" ) {
NCBI_THROW(
Exception, eBadOption, "input file name must be non-empty" );
}
LOG_POST( "reading counts..." );
istat = CSeqMaskerIstatFactory::create(
input_fname, 0, 0, 0, 0, 0, 0, true );
}
//Use it for testing
CRef <CSeq_annot> createAnnot(string rid)
{
CRef <CSeq_annot> m_Annot(new CSeq_annot);
string path_cgi = CNcbiApplication::Instance()->GetProgramExecutablePath();
string path_base = CDirEntry(path_cgi).GetDir();
string ASN1FilePath = CDirEntry::MakePath(path_base, "testSeqAnnot.txt");
LOG_POST(path_cgi);
LOG_POST(path_base);
LOG_POST(ASN1FilePath);
try {
auto_ptr<CObjectIStream> in
(CObjectIStream::Open(eSerial_AsnText,ASN1FilePath));
*in >> *m_Annot;
}
catch (CException& e) {
cerr << "Exception reading SeqAnnot exception message: " + e.GetMsg() << endl;
}
cerr << MSerial_AsnText << *m_Annot;
return m_Annot;
}
//------------------------------------------------------------------------------
void tracker::report_match( Uint4 queryseq, Uint4 match_count,
string::size_type s_off,
string::size_type q_off )
{
string query_id( table.seqid( queryseq ) );
LOG_POST( Warning <<
"Possible duplication of sequences:\n"
<< "subject: " << subject_id << " and query: " << query_id << "\n"
<< "at intervals\n"
<< "subject: " << s_off - match_count*SAMPLE_SKIP
<< " --- " << s_off - SAMPLE_SKIP << "\n"
<< "query : " << q_off - match_count*SAMPLE_SKIP
<< " --- " << q_off - SAMPLE_SKIP << "\n" );
}
/*********************************************************************
* @brief Function used to initialize various system components
* Each component is initialized using a proper API
*
* @param[in] NA
*
* @retval NA
*
* @note NA
*
* @end
*********************************************************************/
void system_init()
{
/* Initialize platform */
VENDOR_PLATFORM_INIT();
/*Initialize logging, Not handling error as openlog() does not return anything*/
logging_init();
/*Initialize Module manager*/
if (modulemgr_init() != BVIEW_STATUS_SUCCESS)
{
LOG_POST (BVIEW_LOG_CRITICAL, "Failed to initialize Module Manager\r\n");
}
/*Initialize south-bound plugin*/
if (sb_redirector_init() != BVIEW_STATUS_SUCCESS)
{
LOG_POST (BVIEW_LOG_CRITICAL, "Failed to initialize south-bound plugin\r\n");
}
/*Initialize south-bound BST plugin*/
if (sbplugin_common_init() != BVIEW_STATUS_SUCCESS)
{
LOG_POST (BVIEW_LOG_CRITICAL, "Failed to initialize south-bound BST plugin r\n");
}
/*Initialize BST application*/
if (bst_main() != BVIEW_STATUS_SUCCESS)
{
LOG_POST (BVIEW_LOG_CRITICAL, "Failed to initialize BST application\r\n");
}
/*Initialize REST*/
if (rest_init() != BVIEW_STATUS_SUCCESS)
{
LOG_POST (BVIEW_LOG_CRITICAL, "Failed to initialize REST \n All components must be De-initialized\r\n");
system_deinit();
}
}