CRef<CGC_Assembly> CGenomicCollectionsService::GetAssembly(const string& acc_,
int level,
int asmAttrFlags,
int chrAttrFlags,
int scafAttrFlags,
int compAttrFlags)
{
string acc = NStr::TruncateSpaces(acc_);
ValidateAsmAccession(acc);
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);
LogRequest(req);
try {
return AskGet_assembly(req, &reply);
} catch (CException& ex) {
if(reply.IsSrvr_error()) {
NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
}
throw;
}
}
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;
}
}
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);
LogRequest(req);
try {
return AskGet_assembly(req, &reply);
} catch (CException& ex) {
if(reply.IsSrvr_error()) {
NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
}
throw;
}
}
string CGenomicCollectionsService::ValidateChrType(const string& chrType, const string& chrLoc)
{
CGCClient_ValidateChrTypeLocRequest req;
CGCClientResponse reply;
req.SetType(chrType);
req.SetLocation(chrLoc);
LogRequest(req);
try {
return AskGet_chrtype_valid(req, &reply);
} catch (CException& ex) {
if(reply.IsSrvr_error()) {
NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
}
throw;
}
}
CRef<CGC_Assembly> CGenomicCollectionsService::GetAssembly(int releaseId, const string& mode)
{
CGCClient_GetAssemblyBlobRequest req;
CGCClientResponse reply;
req.SetRelease_id(releaseId);
req.SetMode(mode);
LogRequest(req);
try {
return CCachedAssembly(AskGet_assembly_blob(req, &reply)).Assembly();
} catch (CException& ex) {
if(reply.IsSrvr_error()) {
NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
}
throw;
}
}
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;
}
}
CRef<CGC_Assembly> CGenomicCollectionsService::GetAssembly(const string& acc_, const string& mode)
{
string acc = NStr::TruncateSpaces(acc_);
ValidateAsmAccession(acc);
CGCClient_GetAssemblyBlobRequest req;
CGCClientResponse reply;
req.SetAccession(acc);
req.SetMode(mode);
LogRequest(req);
try {
return CCachedAssembly(AskGet_assembly_blob(req, &reply)).Assembly();
} catch (CException& ex) {
if(reply.IsSrvr_error()) {
NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
}
throw;
}
}