NCBI C++ ToolKit
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#include <connect/services/json_over_uttp.hpp>
#include <objtools/pubseq_gateway/impl/cassandra/blob_record.hpp>
#include <objtools/pubseq_gateway/impl/cassandra/bioseq_info/record.hpp>
#include <objtools/pubseq_gateway/impl/cassandra/nannot/record.hpp>
#include <objtools/pubseq_gateway/impl/cassandra/si2csi/record.hpp>
#include <objtools/pubseq_gateway/impl/cassandra/request.hpp>
#include <objtools/pubseq_gateway/impl/cassandra/nannot_task/fetch.hpp>
#include <objtools/pubseq_gateway/impl/cassandra/blob_task/load_blob.hpp>
#include <objtools/pubseq_gateway/impl/cassandra/blob_task/fetch_split_history.hpp>
#include <objtools/pubseq_gateway/impl/cassandra/status_history/get_public_comment.hpp>
#include <objtools/pubseq_gateway/impl/cassandra/acc_ver_hist/record.hpp>
#include <objtools/pubseq_gateway/impl/cassandra/acc_ver_hist/tasks.hpp>
#include <objtools/pubseq_gateway/impl/ipg/fetch_ipg_report.hpp>
#include "pubseq_gateway_types.hpp"
#include "pubseq_gateway_utils.hpp"
#include <string>
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Variables | |
USING_NCBI_SCOPE | |
USING_IDBLOB_SCOPE | |
string ToBioseqProtobuf | ( | const CBioseqInfoRecord & | bioseq_info | ) |
Definition at line 99 of file pubseq_gateway_convert_utils.cpp.
References ncbi::psg::retrieval::BioseqInfoValue::add_seq_ids(), CBioseqInfoRecord::GetAccession(), CBioseqInfoRecord::GetDateChanged(), CBioseqInfoRecord::GetGI(), CBioseqInfoRecord::GetHash(), CBioseqInfoRecord::GetLength(), CBioseqInfoRecord::GetMol(), CBioseqInfoRecord::GetName(), CBioseqInfoRecord::GetSat(), CBioseqInfoRecord::GetSatKey(), CBioseqInfoRecord::GetSeqIds(), CBioseqInfoRecord::GetSeqIdType(), CBioseqInfoRecord::GetSeqState(), CBioseqInfoRecord::GetState(), CBioseqInfoRecord::GetTaxId(), CBioseqInfoRecord::GetVersion(), ncbi::psg::retrieval::BioseqInfoValue::mutable_blob_key(), ncbi::psg::retrieval::BioseqInfoReply::mutable_key(), ncbi::psg::retrieval::BioseqInfoReply::mutable_status(), ncbi::psg::retrieval::BioseqInfoReply::mutable_value(), ncbi::psg::retrieval::BioseqInfoKey::set_accession(), ncbi::psg::retrieval::BioseqInfoValue::set_date_changed(), ncbi::psg::retrieval::BioseqInfoKey::set_gi(), ncbi::psg::retrieval::BioseqInfoValue::set_hash(), ncbi::psg::retrieval::BioseqInfoValue::set_length(), ncbi::psg::retrieval::BioseqInfoValue::set_mol(), ncbi::psg::retrieval::BioseqInfoValue::set_name(), ncbi::psg::retrieval::BlobPropKey::set_sat(), ncbi::psg::retrieval::BlobPropKey::set_sat_key(), ncbi::psg::retrieval::BioseqInfoValue_SecondaryId::set_sec_seq_id(), ncbi::psg::retrieval::BioseqInfoValue_SecondaryId::set_sec_seq_id_type(), ncbi::psg::retrieval::BioseqInfoKey::set_seq_id_type(), ncbi::psg::retrieval::BioseqInfoValue::set_seq_state(), ncbi::psg::retrieval::BioseqInfoValue::set_state(), ncbi::psg::retrieval::ReplyStatus::set_status_code(), ncbi::psg::retrieval::BioseqInfoValue::set_tax_id(), ncbi::psg::retrieval::BioseqInfoKey::set_version(), and ncbi::psg::retrieval::STATUS_SUCCESS.
Referenced by CPSGS_ResolveProcessor::x_SendBioseqInfo(), and CPSGS_WGSProcessor::x_SendBioseqInfo().
string ToJsonString | ( | const CBioseqInfoFetchRequest & | request | ) |
Definition at line 510 of file pubseq_gateway_convert_utils.cpp.
References buf, CBioseqInfoFetchRequest::eAccession, CBioseqInfoFetchRequest::eGI, CBioseqInfoFetchRequest::eSeqIdType, CBioseqInfoFetchRequest::eVersion, CBioseqInfoFetchRequest::GetAccession(), CBioseqInfoFetchRequest::GetGI(), CBioseqInfoFetchRequest::GetSeqIdType(), CBioseqInfoFetchRequest::GetVersion(), CBioseqInfoFetchRequest::HasField(), NStr::JsonEncode(), kAccessionItem, kGiItem, kRequestItem, kSep, kSeqIdTypeItem, kVersionItem, len, and PSGToString().
string ToJsonString | ( | const CBioseqInfoRecord & | bioseq_info, |
SPSGS_ResolveRequest::TPSGS_BioseqIncludeData | include_data_flags, | ||
const string & | custom_blob_id = "" |
||
) |
Definition at line 156 of file pubseq_gateway_convert_utils.cpp.
References buf, SPSGS_ResolveRequest::fPSGS_BlobId, SPSGS_ResolveRequest::fPSGS_CanonicalId, SPSGS_ResolveRequest::fPSGS_DateChanged, SPSGS_ResolveRequest::fPSGS_Gi, SPSGS_ResolveRequest::fPSGS_Hash, SPSGS_ResolveRequest::fPSGS_Length, SPSGS_ResolveRequest::fPSGS_MoleculeType, SPSGS_ResolveRequest::fPSGS_Name, SPSGS_ResolveRequest::fPSGS_SeqIds, SPSGS_ResolveRequest::fPSGS_SeqState, SPSGS_ResolveRequest::fPSGS_State, SPSGS_ResolveRequest::fPSGS_TaxId, CBioseqInfoRecord::GetAccession(), CBioseqInfoRecord::GetDateChanged(), CBioseqInfoRecord::GetGI(), CBioseqInfoRecord::GetHash(), CBioseqInfoRecord::GetLength(), CBioseqInfoRecord::GetMol(), CBioseqInfoRecord::GetName(), CBioseqInfoRecord::GetSat(), CBioseqInfoRecord::GetSatKey(), CBioseqInfoRecord::GetSeqIds(), CBioseqInfoRecord::GetSeqIdType(), CBioseqInfoRecord::GetSeqState(), CBioseqInfoRecord::GetState(), CBioseqInfoRecord::GetTaxId(), CBioseqInfoRecord::GetVersion(), NStr::JsonEncode(), kAccessionItem, kBlobIdItem, kDateChangedItem, kGiItem, kHashItem, kLengthItem, kMolItem, kNameItem, kSatItem, kSatKeyItem, kSep, kSeqIdsItem, kSeqIdTypeItem, kSeqStateItem, kStateItem, kTaxIdItem, kVersionItem, len, and PSGToString().
Referenced by CPSGS_TSEChunkProcessor::OnGetBlobProp(), CBlobPropCallback::operator()(), CPSGS_Dispatcher::x_ConcludeIDGetNARequestStatus(), CPSGS_GetProcessor::x_GetBlobFinalStage(), CPSGS_IPGResolveProcessor::x_InitiateIPGFetch(), CPSGCache::x_LookupBioseqInfo(), CPSGCache::x_LookupBlobProp(), CPSGCache::x_LookupINSDCBioseqInfo(), CPSGCache::x_LookupSi2csi(), CPSGS_AsyncBioseqInfoBase::x_MakeRequest(), CPSGS_AccessionVersionHistoryProcessor::x_OnAccVerHistData(), CPSGS_AsyncBioseqInfoBase::x_OnBioseqInfo(), CPSGS_AsyncResolveBase::x_OnBioseqInfo(), CPSGS_AsyncBioseqInfoBase::x_OnBioseqInfoWithoutSeqIdType(), CPSGS_AsyncResolveBase::x_OnBioseqInfoWithoutSeqIdType(), CPSGS_IPGResolveProcessor::x_OnIPGResolveData(), CPSGS_AccessionVersionHistoryProcessor::x_OnSeqIdResolveFinished(), CPSGS_AnnotProcessor::x_OnSeqIdResolveFinished(), CPSGS_AsyncResolveBase::x_OnSi2csiRecord(), CPSGS_CassBlobBase::x_PrepareBlobPropData(), CPSGS_AsyncResolveBase::x_PreparePrimaryBioseqInfoQuery(), CPSGS_AsyncResolveBase::x_PrepareSi2csiQuery(), CPSGS_GetBlobProcessor::x_Process(), CPSGS_TSEChunkProcessor::x_ProcessIdModVerId2InfoFinalStage(), CPSGS_TSEChunkProcessor::x_ProcessSatInfoChunkVerId2InfoFinalStage(), CPSGS_AnnotProcessor::x_RequestBlobProp(), CPSGS_CassBlobBase::x_RequestID2BlobChunks(), CPSGS_CassBlobBase::x_RequestOriginalBlobChunks(), CPSGS_TSEChunkProcessor::x_RequestTSEChunk(), CPSGS_CDDProcessor::x_SendAnnot(), CPSGS_AnnotProcessor::x_SendAnnotDataToClient(), CPSGS_AccessionVersionHistoryProcessor::x_SendBioseqInfo(), CPSGS_AnnotProcessor::x_SendBioseqInfo(), CPSGS_GetProcessor::x_SendBioseqInfo(), CPSGS_ResolveProcessor::x_SendBioseqInfo(), CPSGS_WGSProcessor::x_SendBioseqInfo(), CPSGS_SNPProcessor::x_SendBlobProps(), CPSGS_WGSProcessor::x_SendBlobProps(), CPSGS_SNPProcessor::x_SendChunkBlobProps(), and CPSGS_WGSProcessor::x_SendChunkBlobProps().
string ToJsonString | ( | const CBlobFetchRequest & | request | ) |
Definition at line 604 of file pubseq_gateway_convert_utils.cpp.
References buf, CBlobFetchRequest::eLastModified, CBlobFetchRequest::eSat, CBlobFetchRequest::eSatKey, CBlobFetchRequest::GetLastModified(), CBlobFetchRequest::GetSat(), CBlobFetchRequest::GetSatKey(), CBlobFetchRequest::HasField(), kLastModifiedItem, kRequestItem, kSatItem, kSatKeyItem, kSep, len, and PSGToString().
string ToJsonString | ( | const CBlobRecord & | blob | ) |
Definition at line 324 of file pubseq_gateway_convert_utils.cpp.
References buf, CBlobRecord::GetClass(), CBlobRecord::GetDateAsn1(), CBlobRecord::GetDiv(), CBlobRecord::GetFlags(), CBlobRecord::GetHupDate(), CBlobRecord::GetId2Info(), CBlobRecord::GetKey(), CBlobRecord::GetModified(), CBlobRecord::GetNChunks(), CBlobRecord::GetOwner(), CBlobRecord::GetSize(), CBlobRecord::GetSizeUnpacked(), CBlobRecord::GetUserName(), NStr::JsonEncode(), kClassItem, kDateAsn1Item, kDivItem, kFlagsItem, kHupDateItem, kId2InfoItem, kKeyItem, kLastModifiedItem, kNChunksItem, kOwnerItem, kSep, kSizeItem, kSizeUnpackedItem, kUserNameItem, len, and PSGToString().
string ToJsonString | ( | const CCassAccVerHistoryTaskFetch & | request | ) |
Definition at line 868 of file pubseq_gateway_convert_utils.cpp.
References buf, CCassAccVerHistoryTaskFetch::GetAccession(), CCassBlobWaiter::GetKeySpace(), CCassAccVerHistoryTaskFetch::GetSeqIdType(), CCassAccVerHistoryTaskFetch::GetVersion(), NStr::JsonEncode(), kAccessionItem, kRequestItem, kSatNameItem, kSep, kSeqIdTypeItem, kVersionItem, len, and PSGToString().
string ToJsonString | ( | const CCassBlobTaskFetchSplitHistory & | request | ) |
Definition at line 752 of file pubseq_gateway_convert_utils.cpp.
References buf, CCassBlobWaiter::GetKey(), CCassBlobWaiter::GetKeySpace(), CCassBlobTaskFetchSplitHistory::GetSplitVersion(), CCassBlobTaskFetchSplitHistory::kAllVersions, kRequestItem, kSatKeyItem, kSatNameItem, kSep, kSplitVersionItem, len, and PSGToString().
string ToJsonString | ( | const CCassBlobTaskLoadBlob & | request | ) |
Definition at line 700 of file pubseq_gateway_convert_utils.cpp.
References CCassBlobTaskLoadBlob::BlobPropsProvided(), buf, CCassBlobWaiter::GetKeySpace(), CCassBlobTaskLoadBlob::GetModified(), CCassBlobTaskLoadBlob::GetSatKey(), CCassBlobTaskLoadBlob::kAnyModified, kBlopPropProvidedItem, kChunksRequestedItem, kLastModifiedItem, kRequestItem, kSatKeyItem, kSatNameItem, kSep, len, CCassBlobTaskLoadBlob::LoadChunks(), and PSGToString().
string ToJsonString | ( | const CCassNAnnotTaskFetch & | request | ) |
Definition at line 790 of file pubseq_gateway_convert_utils.cpp.
References buf, CCassNAnnotTaskFetch::GetAccession(), CCassNAnnotTaskFetch::GetAnnotNames(), CCassBlobWaiter::GetKeySpace(), CCassNAnnotTaskFetch::GetSeqIdType(), CCassNAnnotTaskFetch::GetVersion(), NStr::JsonEncode(), kAccessionItem, kAnnotNamesItem, kRequestItem, kSatNameItem, kSep, kSeqIdTypeItem, kVersionItem, len, and PSGToString().
string ToJsonString | ( | const CCassStatusHistoryTaskGetPublicComment & | request | ) |
Definition at line 842 of file pubseq_gateway_convert_utils.cpp.
References buf, CCassBlobWaiter::GetKey(), CCassBlobWaiter::GetKeySpace(), kRequestItem, kSatKeyItem, kSatNameItem, kSep, len, and PSGToString().
string ToJsonString | ( | const CIpgStorageReportEntry & | ipg_entry | ) |
Definition at line 1002 of file pubseq_gateway_convert_utils.cpp.
References buf, CIpgStorageReportEntry::GetAccession(), CIpgStorageReportEntry::GetAssembly(), CIpgStorageReportEntry::GetBioProject(), CIpgStorageReportEntry::GetDiv(), CIpgStorageReportEntry::GetGbState(), CIpgStorageReportEntry::GetIpg(), CIpgStorageReportEntry::GetLength(), CIpgStorageReportEntry::GetNucAccession(), CIpgStorageReportEntry::GetProductName(), CIpgStorageReportEntry::GetStrain(), CIpgStorageReportEntry::GetTaxid(), NStr::JsonEncode(), kAssemblyItem, kBioProjectItem, kDivisionItem, kGBStateItem, kIPGItem, kLengthItem, kNucleotideItem, kProductNameItem, kProteinItem, kSep, kStrainItem, kTaxIdItem, len, and PSGToString().
string ToJsonString | ( | const CNAnnotRecord & | annot_record, |
int32_t | sat, | ||
const string & | custom_blob_id = "" |
||
) |
Definition at line 396 of file pubseq_gateway_convert_utils.cpp.
References NStr::Base64Encode(), buf, CNAnnotRecord::GetAccession(), CNAnnotRecord::GetModified(), CNAnnotRecord::GetSatKey(), CNAnnotRecord::GetSeqAnnotInfo(), CNAnnotRecord::GetSeqIdType(), CNAnnotRecord::GetStart(), CNAnnotRecord::GetStop(), CNAnnotRecord::GetVersion(), NStr::JsonEncode(), kAccessionItem, kAnnotInfoItem, kBlobIdItem, kLastModifiedItem, kSatItem, kSatKeyItem, kSep, kSeqAnnotInfoItem, kSeqIdTypeItem, kStartItem, kStopItem, kVersionItem, len, and PSGToString().
string ToJsonString | ( | const CPubseqGatewayFetchIpgReportRequest & | request | ) |
Definition at line 905 of file pubseq_gateway_convert_utils.cpp.
References buf, CPubseqGatewayFetchIpgReportRequest::GetIpg(), CPubseqGatewayFetchIpgReportRequest::GetNucleotide(), CPubseqGatewayFetchIpgReportRequest::GetProtein(), CPubseqGatewayFetchIpgReportRequest::HasIpg(), CPubseqGatewayFetchIpgReportRequest::HasNucleotide(), CPubseqGatewayFetchIpgReportRequest::HasProtein(), NStr::JsonEncode(), kIPGItem, kNucleotideItem, kProteinItem, kRequestItem, kSep, len, PSGToString(), and SanitizeInputValue().
string ToJsonString | ( | const CSi2CsiFetchRequest & | request | ) |
Definition at line 569 of file pubseq_gateway_convert_utils.cpp.
References buf, CSi2CsiFetchRequest::eSecSeqId, CSi2CsiFetchRequest::eSecSeqIdType, CSi2CsiFetchRequest::GetSecSeqId(), CSi2CsiFetchRequest::GetSecSeqIdType(), CSi2CsiFetchRequest::HasField(), NStr::JsonEncode(), kRequestItem, kSecSeqIdItem, kSecSeqIdTypeItem, kSep, len, and PSGToString().
string ToJsonString | ( | const CSI2CSIRecord & | record | ) |
Definition at line 652 of file pubseq_gateway_convert_utils.cpp.
References buf, CSI2CSIRecord::GetAccession(), CSI2CSIRecord::GetGI(), CSI2CSIRecord::GetSecSeqId(), CSI2CSIRecord::GetSecSeqIdType(), CSI2CSIRecord::GetSecSeqState(), CSI2CSIRecord::GetSeqIdType(), CSI2CSIRecord::GetVersion(), NStr::JsonEncode(), kAccessionItem, kGiItem, kSecSeqIdItem, kSecSeqIdTypeItem, kSecSeqStateItem, kSep, kSeqIdTypeItem, kVersionItem, len, and PSGToString().
Definition at line 483 of file pubseq_gateway_convert_utils.cpp.
References buf, NStr::JsonEncode(), kDictValueSep, kSep, len, and PSGToString().
string ToJsonString | ( | const SAccVerHistRec & | history_record | ) |
Definition at line 949 of file pubseq_gateway_convert_utils.cpp.
References SAccVerHistRec::accession, buf, SAccVerHistRec::chain, SAccVerHistRec::date, SAccVerHistRec::gi, NStr::JsonEncode(), kAccessionItem, kChainItem, kDateItem, kGiItem, kSatItem, kSatKeyItem, kSep, kSeqIdTypeItem, kVersionItem, len, PSGToString(), SAccVerHistRec::sat, SAccVerHistRec::sat_key, SAccVerHistRec::seq_id_type, and SAccVerHistRec::version.
USING_IDBLOB_SCOPE |
Definition at line 55 of file pubseq_gateway_convert_utils.hpp.
USING_NCBI_SCOPE |
Definition at line 54 of file pubseq_gateway_convert_utils.hpp.