#include <ncbi_pch.hpp>
#include <numeric>
#include <unordered_set>
#include <unordered_map>
#include <connect/impl/connect_misc.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqsplit/ID2S_Split_Info.hpp>
#include <objects/seqsplit/ID2S_Chunk.hpp>
#include <serial/enumvalues.hpp>
#include <serial/objcopy.hpp>
#include <serial/objistr.hpp>
#include <serial/objostr.hpp>
#include <util/checksum.hpp>
#include <util/compress/zlib.hpp>
#include <util/compress/stream.hpp>
#include "performance.hpp"
#include "processing.hpp"

Include dependency graph for processing.cpp:

Go to the SVN repository for this file.

Classes
struct	SNewRequestContext

struct	SInteractiveNewRequestStart

struct	SInteractiveNewRequestStart::SExtra

struct	SDataOnlyCopy

struct	SNonVerboseBase< TArgs >

struct	SNonVerbose< TArgs >

struct	SNonVerboseBase< SBatchResolveParams >

Typedefs
using	verbose = true_type

using	no_verbose = false_type

using	testing = true_type

using	no_testing = false_type

using	server_mode = true_type

using	no_server_mode = false_type

Enumerations
enum	EJsonRpcErrors { eJsonRpc_ParseError = -32700 , eJsonRpc_InvalidRequest = -32600 , eJsonRpc_ExceptionOnRead = -32000 }

Functions
string	s_GetId (const CJson_Document &req_doc)

CRequestStatus::ECode	s_PsgStatusToRequestStatus (EPSG_Status psg_status)

const char *	s_StrStatus (EPSG_Status status)

const char *	s_GetItemName (CPSG_ReplyItem::EType type, bool trouble=true)

auto	s_IsRawRequest (shared_ptr< const CPSG_Request > &request)

auto	s_IsRawResponse (const CPSG_BlobId *blob_id)

string	s_ReasonToString (CPSG_SkippedBlob::EReason reason)

string	s_ProgressStatusToString (CPSG_Processor::EProgressStatus progress_status)

ESerialDataFormat	s_GetInputFormat (const string &format)

TTypeInfo	s_GetInputType (const shared_ptr< CPSG_BlobData > &blob_data)

template<class... TArgs>
void	s_ItemComplete (SJsonOut &json_out, EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item)

template<class... TArgs>
void	s_ReplyComplete (SJsonOut &json_out, EPSG_Status status, const shared_ptr< CPSG_Reply > &reply)

template<>
void	s_ReplyComplete< SOneRequestParams > (SJsonOut &json_out, EPSG_Status status, const shared_ptr< CPSG_Reply > &reply)

template<class... TArgs>
void	s_NewItem (SJsonOut &, const shared_ptr< CPSG_ReplyItem > &)

template<>
void	s_NewItem< SOneRequestParams > (SJsonOut &json_out, const shared_ptr< CPSG_ReplyItem > &reply_item)

template<>
void	s_ItemComplete< no_verbose > (SJsonOut &json_out, EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item)

template<>
void	s_ReplyComplete< no_verbose > (SJsonOut &json_out, EPSG_Status status, const shared_ptr< CPSG_Reply > &reply)

template<>
void	s_ReplyComplete< SInteractiveParams, testing, server_mode > (SJsonOut &json_out, EPSG_Status status, const shared_ptr< CPSG_Reply > &reply)

template<>
void	s_ReplyComplete< SInteractiveParams, testing, no_server_mode > (SJsonOut &json_out, EPSG_Status status, const shared_ptr< CPSG_Reply > &reply)

template<>
void	s_ReplyComplete< SInteractiveParams, no_testing, server_mode > (SJsonOut &json_out, EPSG_Status status, const shared_ptr< CPSG_Reply > &reply)

template<>
void	s_ReplyComplete< SInteractiveParams, no_testing, no_server_mode > (SJsonOut &json_out, EPSG_Status status, const shared_ptr< CPSG_Reply > &reply)

template<>
void	s_ItemComplete< SInteractiveParams > (SJsonOut &json_out, EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item)

template<>
void	s_NewItem< SInteractiveParams, verbose > (SJsonOut &json_out, const shared_ptr< CPSG_ReplyItem > &item)

shared_ptr< CPSG_Reply >	s_GetReply (shared_ptr< CPSG_ReplyItem > &item)

shared_ptr< CPSG_Reply >	s_GetReply (shared_ptr< CPSG_Reply > &reply)

Variables
const initializer_list< SDataFlag >	kDataFlags

const initializer_list< SInfoFlag >	kInfoFlags

Typedef Documentation

◆ no_server_mode

using no_server_mode = false_type

Definition at line 1014 of file processing.cpp.

◆ no_testing

using no_testing = false_type

Definition at line 1012 of file processing.cpp.

◆ no_verbose

using no_verbose = false_type

Definition at line 891 of file processing.cpp.

◆ server_mode

using server_mode = true_type

Definition at line 1013 of file processing.cpp.

◆ testing

using testing = true_type

Definition at line 1011 of file processing.cpp.

◆ verbose

using verbose = true_type

Definition at line 890 of file processing.cpp.

Enumeration Type Documentation

◆ EJsonRpcErrors

enum EJsonRpcErrors

Enumerator
eJsonRpc_ParseError
eJsonRpc_InvalidRequest
eJsonRpc_ExceptionOnRead

Definition at line 57 of file processing.cpp.

Function Documentation

◆ s_GetId()

string s_GetId ( const CJson_Document & req_doc )

Definition at line 1162 of file processing.cpp.

References CJson_ConstNode::GetObject(), CJson_ConstValue::GetString(), CJson_ConstNode::GetValue(), and CJson_ConstNode::IsObject().

Referenced by CProcessing::ReadCommands(), and CParallelProcessing< TParams >::SImpl::Submitter().

◆ s_GetInputFormat()

ESerialDataFormat s_GetInputFormat ( const string & format )

Definition at line 629 of file processing.cpp.

References eSerial_AsnBinary, eSerial_AsnText, eSerial_Json, eSerial_Xml, and format.

Referenced by SDataOnlyCopy::Process().

◆ s_GetInputType()

TTypeInfo s_GetInputType ( const shared_ptr< CPSG_BlobData > & blob_data )

Definition at line 638 of file processing.cpp.

Referenced by SDataOnlyCopy::Process().

◆ s_GetItemName()

const char* s_GetItemName	(	CPSG_ReplyItem::EType	type,
		bool	trouble = `true`
	)

Definition at line 226 of file processing.cpp.

References _TROUBLE, CPSG_ReplyItem::eBioseqInfo, CPSG_ReplyItem::eBlobData, CPSG_ReplyItem::eBlobInfo, CPSG_ReplyItem::eEndOfReply, CPSG_ReplyItem::eIpgInfo, CPSG_ReplyItem::eNamedAnnotInfo, CPSG_ReplyItem::eNamedAnnotStatus, CPSG_ReplyItem::eProcessor, CPSG_ReplyItem::ePublicComment, and CPSG_ReplyItem::eSkippedBlob.

Referenced by CJsonResponse::Fill(), CJsonResponse::NewItem(), and SMetrics::OutputItems().

◆ s_GetReply() [1/2]

shared_ptr<CPSG_Reply> s_GetReply ( shared_ptr< CPSG_Reply > & reply )

Definition at line 1143 of file processing.cpp.

◆ s_GetReply() [2/2]

shared_ptr<CPSG_Reply> s_GetReply ( shared_ptr< CPSG_ReplyItem > & item )

Definition at line 1138 of file processing.cpp.

Referenced by CJsonResponse::AddRequestID().

◆ s_IsRawRequest()

auto s_IsRawRequest ( shared_ptr< const CPSG_Request > & request )

Definition at line 311 of file processing.cpp.

References CPSG_Request::eBlob.

Referenced by CJsonResponse::Fill().

◆ s_IsRawResponse()

auto s_IsRawResponse ( const CPSG_BlobId * blob_id )

Definition at line 316 of file processing.cpp.

References CPSG_BlobId::GetLastModified(), and min().

Referenced by CJsonResponse::Fill().

◆ s_ItemComplete()

template<class... TArgs>

void s_ItemComplete	(	SJsonOut &	json_out,
		EPSG_Status	status,
		const shared_ptr< CPSG_ReplyItem > &	item
	)

Definition at line 780 of file processing.cpp.

◆ s_ItemComplete< no_verbose >()

template<>

void s_ItemComplete< no_verbose >	(	SJsonOut &	json_out,
		EPSG_Status	status,
		const shared_ptr< CPSG_ReplyItem > &	item
	)

Definition at line 894 of file processing.cpp.

References _ASSERT, and context.

Referenced by CParallelProcessing< TParams >::SImpl::GetItemComplete().

◆ s_ItemComplete< SInteractiveParams >()

template<>

void s_ItemComplete< SInteractiveParams >	(	SJsonOut &	json_out,
		EPSG_Status	status,
		const shared_ptr< CPSG_ReplyItem > &	item
	)

Definition at line 1055 of file processing.cpp.

References CJsonResponse::eDoNotAddRequestID.

Referenced by CParallelProcessing< TParams >::SImpl::GetItemComplete().

◆ s_NewItem()

template<class... TArgs>

void s_NewItem	(	SJsonOut &	,
		const shared_ptr< CPSG_ReplyItem > &
	)

Definition at line 800 of file processing.cpp.

◆ s_NewItem< SInteractiveParams, verbose >()

template<>

void s_NewItem< SInteractiveParams, verbose >	(	SJsonOut &	json_out,
		const shared_ptr< CPSG_ReplyItem > &	item
	)

Definition at line 1091 of file processing.cpp.

References CJsonResponse::NewItem().

Referenced by CParallelProcessing< TParams >::SImpl::GetNewItem().

◆ s_NewItem< SOneRequestParams >()

template<>

void s_NewItem< SOneRequestParams >	(	SJsonOut &	json_out,
		const shared_ptr< CPSG_ReplyItem > &	reply_item
	)

Definition at line 805 of file processing.cpp.

References CJsonResponse::NewItem().

Referenced by CProcessing::OneRequest().

◆ s_ProgressStatusToString()

string s_ProgressStatusToString ( CPSG_Processor::EProgressStatus progress_status )

Definition at line 437 of file processing.cpp.

References _TROUBLE, CPSG_Processor::eCanceled, CPSG_Processor::eDone, CPSG_Processor::eError, CPSG_Processor::eInProgress, CPSG_Processor::eNotFound, CPSG_Processor::eStart, CPSG_Processor::eTimeout, CPSG_Processor::eUnauthorized, and CPSG_Processor::eUnknown.

Referenced by CJsonResponse::Fill().

◆ s_PsgStatusToRequestStatus()

CRequestStatus::ECode s_PsgStatusToRequestStatus ( EPSG_Status psg_status )

Definition at line 1148 of file processing.cpp.

References _TROUBLE, CRequestStatus::e200_Ok, CRequestStatus::e400_BadRequest, CRequestStatus::e403_Forbidden, CRequestStatus::e404_NotFound, CRequestStatus::e499_BrokenConnection, CRequestStatus::e500_InternalServerError, eCanceled, eError, eForbidden, eInProgress, eNotFound, and eSuccess.

Referenced by s_ReplyComplete< SInteractiveParams, no_testing, no_server_mode >(), and s_ReplyComplete< SInteractiveParams, no_testing, server_mode >().

◆ s_ReasonToString()

string s_ReasonToString ( CPSG_SkippedBlob::EReason reason )

Definition at line 374 of file processing.cpp.

References _TROUBLE, CPSG_SkippedBlob::eExcluded, CPSG_SkippedBlob::eInProgress, CPSG_SkippedBlob::eSent, and CPSG_SkippedBlob::eUnknown.

Referenced by CJsonResponse::Fill().

◆ s_ReplyComplete()

template<class... TArgs>

void s_ReplyComplete	(	SJsonOut &	json_out,
		EPSG_Status	status,
		const shared_ptr< CPSG_Reply > &	reply
	)

Definition at line 786 of file processing.cpp.

◆ s_ReplyComplete< no_verbose >()

template<>

void s_ReplyComplete< no_verbose >	(	SJsonOut &	json_out,
		EPSG_Status	status,
		const shared_ptr< CPSG_Reply > &	reply
	)

Definition at line 908 of file processing.cpp.

References _ASSERT, and context.

Referenced by CParallelProcessing< TParams >::SImpl::GetReplyComplete().

◆ s_ReplyComplete< SInteractiveParams, no_testing, no_server_mode >()

template<>

void s_ReplyComplete< SInteractiveParams, no_testing, no_server_mode >	(	SJsonOut &	json_out,
		EPSG_Status	status,
		const shared_ptr< CPSG_Reply > &	reply
	)

Definition at line 1045 of file processing.cpp.

References s_PsgStatusToRequestStatus(), s_ReplyComplete< SInteractiveParams, testing, no_server_mode >(), and CRequestContextGuard_Base::SetStatus().

Referenced by CParallelProcessing< TParams >::SImpl::GetReplyComplete().

◆ s_ReplyComplete< SInteractiveParams, no_testing, server_mode >()

template<>

void s_ReplyComplete< SInteractiveParams, no_testing, server_mode >	(	SJsonOut &	json_out,
		EPSG_Status	status,
		const shared_ptr< CPSG_Reply > &	reply
	)

Definition at line 1035 of file processing.cpp.

References s_PsgStatusToRequestStatus(), s_ReplyComplete< SInteractiveParams, testing, server_mode >(), and CRequestContextGuard_Base::SetStatus().

Referenced by CParallelProcessing< TParams >::SImpl::GetReplyComplete().

◆ s_ReplyComplete< SInteractiveParams, testing, no_server_mode >()

template<>

void s_ReplyComplete< SInteractiveParams, testing, no_server_mode >	(	SJsonOut &	json_out,
		EPSG_Status	status,
		const shared_ptr< CPSG_Reply > &	reply
	)

Definition at line 1027 of file processing.cpp.

References eSuccess, and s_ReplyComplete< SInteractiveParams, testing, server_mode >().

Referenced by CParallelProcessing< TParams >::SImpl::GetReplyComplete(), and s_ReplyComplete< SInteractiveParams, no_testing, no_server_mode >().

◆ s_ReplyComplete< SInteractiveParams, testing, server_mode >()

template<>

void s_ReplyComplete< SInteractiveParams, testing, server_mode >	(	SJsonOut &	json_out,
		EPSG_Status	status,
		const shared_ptr< CPSG_Reply > &	reply
	)

Definition at line 1017 of file processing.cpp.

References CJsonResponse::eDoNotAddRequestID.

Referenced by CParallelProcessing< TParams >::SImpl::GetReplyComplete(), s_ReplyComplete< SInteractiveParams, no_testing, server_mode >(), and s_ReplyComplete< SInteractiveParams, testing, no_server_mode >().

◆ s_ReplyComplete< SOneRequestParams >()

template<>

void s_ReplyComplete< SOneRequestParams >	(	SJsonOut &	json_out,
		EPSG_Status	status,
		const shared_ptr< CPSG_Reply > &	reply
	)

Definition at line 792 of file processing.cpp.

References eSuccess.

Referenced by CProcessing::OneRequest().

◆ s_StrStatus()

const char* s_StrStatus ( EPSG_Status status )

Definition at line 128 of file processing.cpp.

References eCanceled, eError, eForbidden, eInProgress, eNotFound, and eSuccess.

Referenced by CJsonResponse::Fill(), CJsonResponse::NewItem(), SMetrics::OutputItems(), and SDataOnlyCopy::ReportErrors().

Variable Documentation

◆ kDataFlags

const initializer_list<SDataFlag> kDataFlags

Initial value:

=
{
    { "no-tse",    "Return only the info",                                  CPSG_Request_Biodata::eNoTSE    },
    { "slim-tse",  "Return split info blob if available, or nothing",       CPSG_Request_Biodata::eSlimTSE  },
    { "smart-tse", "Return split info blob if available, or original blob", CPSG_Request_Biodata::eSmartTSE },
    { "whole-tse", "Return all split blobs if available, or original blob", CPSG_Request_Biodata::eWholeTSE },
    { "orig-tse",  "Return original blob",                                  CPSG_Request_Biodata::eOrigTSE  },
}

Definition at line 1638 of file processing.cpp.

Referenced by SRequestBuilder::GetDataFlags().

◆ kInfoFlags

const initializer_list<SInfoFlag> kInfoFlags

Initial value:

=
{
    { "all-info-except", "Return all info except explicitly specified by other flags", CPSG_Request_Resolve::fAllInfo },
    { "canonical-id",    "Return canonical ID info",                    CPSG_Request_Resolve::fCanonicalId  },
    { "name",            "Use name for canonical ID info, if returned", CPSG_Request_Resolve::fName         },
    { "other-ids",       "Return other IDs info",                       CPSG_Request_Resolve::fOtherIds     },
    { "molecule-type",   "Return molecule type info",                   CPSG_Request_Resolve::fMoleculeType },
    { "length",          "Return length info",                          CPSG_Request_Resolve::fLength       },
    { "chain-state",     "Return chain state info (in seq_state pair)", CPSG_Request_Resolve::fChainState   },
    { "state",           "Return state info",                           CPSG_Request_Resolve::fState        },
    { "blob-id",         "Return blob ID info",                         CPSG_Request_Resolve::fBlobId       },
    { "tax-id",          "Return tax ID info",                          CPSG_Request_Resolve::fTaxId        },
    { "hash",            "Return hash info",                            CPSG_Request_Resolve::fHash         },
    { "date-changed",    "Return date changed info",                    CPSG_Request_Resolve::fDateChanged  },
    { "gi",              "Return GI",                                   CPSG_Request_Resolve::fGi           },
}

Definition at line 1652 of file processing.cpp.

Referenced by SRequestBuilder::GetInfoFlags().

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ no_server_mode

◆ no_testing

◆ no_verbose

◆ server_mode

◆ testing

◆ verbose

Enumeration Type Documentation

◆ EJsonRpcErrors

Function Documentation

◆ s_GetId()

◆ s_GetInputFormat()

◆ s_GetInputType()

◆ s_GetItemName()

◆ s_GetReply() [1/2]

◆ s_GetReply() [2/2]

◆ s_IsRawRequest()

◆ s_IsRawResponse()

◆ s_ItemComplete()

◆ s_ItemComplete< no_verbose >()

◆ s_ItemComplete< SInteractiveParams >()

◆ s_NewItem()

◆ s_NewItem< SInteractiveParams, verbose >()

◆ s_NewItem< SOneRequestParams >()

◆ s_ProgressStatusToString()

◆ s_PsgStatusToRequestStatus()

◆ s_ReasonToString()

◆ s_ReplyComplete()

◆ s_ReplyComplete< no_verbose >()

◆ s_ReplyComplete< SInteractiveParams, no_testing, no_server_mode >()

◆ s_ReplyComplete< SInteractiveParams, no_testing, server_mode >()

◆ s_ReplyComplete< SInteractiveParams, testing, no_server_mode >()

◆ s_ReplyComplete< SInteractiveParams, testing, server_mode >()

◆ s_ReplyComplete< SOneRequestParams >()

◆ s_StrStatus()

Variable Documentation

◆ kDataFlags

◆ kInfoFlags