#include <ncbi_pch.hpp>
#include <objtools/data_loaders/genbank/cache/reader_cache.hpp>
#include <objtools/data_loaders/genbank/cache/reader_cache_entry.hpp>
#include <objtools/data_loaders/genbank/cache/reader_cache_params.h>
#include <objtools/data_loaders/genbank/readers.hpp>
#include <objtools/data_loaders/genbank/impl/dispatcher.hpp>
#include <objtools/data_loaders/genbank/impl/processors.hpp>
#include <objtools/data_loaders/genbank/impl/request_result.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <corelib/ncbitime.hpp>
#include <corelib/rwstream.hpp>
#include <corelib/plugin_manager_store.hpp>
#include <util/cache/icache.hpp>
#include <connect/ncbi_conn_stream.hpp>
#include <objmgr/objmgr_exception.hpp>
#include <objmgr/impl/tse_split_info.hpp>
#include <objmgr/impl/tse_chunk_info.hpp>
#include <objmgr/annot_selector.hpp>
#include <serial/objistrasnb.hpp>
#include <serial/serial.hpp>
#include <objects/seqloc/Seq_id.hpp>

Include dependency graph for reader_cache.cpp:

Go to the SVN repository for this file.

Classes
struct	SCacheEntryAccessCount

struct	SPluginParams

struct	SPluginParams::SDefaultValue

class	CCacheReaderCF

Macros
#define	FIX_BAD_ID2S_REPLY_DATA 1

Functions
	NCBI_PARAM_DECL (int, GENBANK, CACHE_DEBUG)

	NCBI_PARAM_DEF_EX (int, GENBANK, CACHE_DEBUG, 0, eParam_NoThread, GENBANK_CACHE_DEBUG)

static bool	IsDisabledCache (const SCacheInfo::TParams *params)

static SCacheInfo::TParams *	GetDriverParams (SCacheInfo::TParams *params)

static SCacheInfo::TParams *	GetCacheParamsCopy (const SCacheInfo::TParams src_params, const char section_name)

SCacheInfo::TParams *	GetCacheParams (const SCacheInfo::TParams *src_params, SCacheInfo::EReaderOrWriter reader_or_writer, SCacheInfo::EIdOrBlob id_or_blob)

void	NCBI_EntryPoint_CacheReader (CPluginManager< CReader >::TDriverInfoList &info_list, CPluginManager< CReader >::EEntryPointRequest method)

void	NCBI_EntryPoint_xreader_cache (CPluginManager< CReader >::TDriverInfoList &info_list, CPluginManager< CReader >::EEntryPointRequest method)

void	GenBankReaders_Register_Cache (void)

Macro Definition Documentation

◆ FIX_BAD_ID2S_REPLY_DATA

#define FIX_BAD_ID2S_REPLY_DATA 1

Definition at line 56 of file reader_cache.cpp.

Function Documentation

◆ GenBankReaders_Register_Cache()

void GenBankReaders_Register_Cache ( void )

Definition at line 1796 of file reader_cache.cpp.

References NCBI_EntryPoint_CacheReader().

Referenced by CGBDataLoader_Native::x_GetReaderManager().

◆ GetCacheParams()

SCacheInfo::TParams* GetCacheParams	(	const SCacheInfo::TParams *	src_params,
		SCacheInfo::EReaderOrWriter	reader_or_writer,
		SCacheInfo::EIdOrBlob	id_or_blob
	)

Definition at line 1620 of file reader_cache.cpp.

References SCacheInfo::eCacheReader, SCacheInfo::eIdCache, GetCacheParamsCopy(), GetDriverParams(), NCBI_GBLOADER_READER_CACHE_PARAM_BLOB_SECTION, NCBI_GBLOADER_READER_CACHE_PARAM_ID_SECTION, s_DefaultBlobParams, s_DefaultIdParams, s_DefaultParams, s_DefaultReaderParams, s_DefaultWriterParams, and SPluginParams::SetDefaultValues().

Referenced by SCacheInfo::CreateCache(), CCacheReader::InitializeCache(), and CCacheWriter::InitializeCache().

◆ GetCacheParamsCopy()

static SCacheInfo::TParams* GetCacheParamsCopy	(	const SCacheInfo::TParams *	src_params,
		const char *	section_name
	)

static

Definition at line 1548 of file reader_cache.cpp.

References SPluginParams::FindSubNode(), and IsDisabledCache().

Referenced by GetCacheParams().

◆ GetDriverParams()

static SCacheInfo::TParams* GetDriverParams ( SCacheInfo::TParams * params )

static

Definition at line 1536 of file reader_cache.cpp.

References NCBI_GBLOADER_READER_CACHE_PARAM_DRIVER, SPluginParams::SetDefaultValue(), and SPluginParams::SetSubSection().

Referenced by GetCacheParams().

◆ IsDisabledCache()

static bool IsDisabledCache ( const SCacheInfo::TParams * params )

static

Definition at line 1520 of file reader_cache.cpp.

References SPluginParams::FindSubNode(), CTreeNode< TValue, TKeyGetterP >::GetValue(), and NCBI_GBLOADER_READER_CACHE_PARAM_DRIVER.

Referenced by GetCacheParamsCopy().

◆ NCBI_EntryPoint_CacheReader()

void NCBI_EntryPoint_CacheReader	(	CPluginManager< CReader >::TDriverInfoList &	info_list,
		CPluginManager< CReader >::EEntryPointRequest	method
	)

Definition at line 1779 of file reader_cache.cpp.

References CHostEntryPointImpl< TClassFactory >::NCBI_EntryPointImpl().

Referenced by GenBankReaders_Register_Cache(), and NCBI_EntryPoint_xreader_cache().

◆ NCBI_EntryPoint_xreader_cache()

void NCBI_EntryPoint_xreader_cache	(	CPluginManager< CReader >::TDriverInfoList &	info_list,
		CPluginManager< CReader >::EEntryPointRequest	method
	)

Definition at line 1788 of file reader_cache.cpp.

References NCBI_EntryPoint_CacheReader().

◆ NCBI_PARAM_DECL()

NCBI_PARAM_DECL	(	int	,
		GENBANK	,
		CACHE_DEBUG
	)

◆ NCBI_PARAM_DEF_EX()

NCBI_PARAM_DEF_EX	(	int	,
		GENBANK	,
		CACHE_DEBUG	,
		0	,
		eParam_NoThread	,
		GENBANK_CACHE_DEBUG
	)

Variable Documentation

◆ kHashLimit

const size_t kHashLimit = 100

static

Definition at line 105 of file reader_cache.cpp.

Referenced by SCacheInfo::GetBlob_idsSubkey().

◆ s_CacheEntryAccessCounts

SCacheEntryAccessCount s_CacheEntryAccessCounts[CCacheReader::eCacheEntry_Count]

static

Definition at line 1165 of file reader_cache.cpp.

Referenced by CCacheReader::GoingToLoad(), and CCacheReader::NoNeedToSave().

◆ s_DefaultBlobParams

const SPluginParams::SDefaultValue s_DefaultBlobParams[]

static

Initial value:

= {
    
    { "name", "blobs" },
    { "timeout", "432000" }, 
    { "timestamp", "onread expire_not_used"  },
 
    { 0, 0 }
}

Definition at line 1598 of file reader_cache.cpp.

Referenced by GetCacheParams().

◆ s_DefaultIdParams

const SPluginParams::SDefaultValue s_DefaultIdParams[]

static

Initial value:

= {
    
    { "name", "ids" },
    { "timeout", "172800" }, 
    { "timestamp", "subkey check_expiration"  },
    
    { "page_size", "small" },
 
    { 0, 0 }
}

Definition at line 1588 of file reader_cache.cpp.

Referenced by GetCacheParams().

◆ s_DefaultParams

const SPluginParams::SDefaultValue s_DefaultParams[]

static

Initial value:

= {
    
    { "keep_versions", "all" },
    { "write_sync", "no" },
    
    { "path", ".genbank_cache" },
    { "mem_size", "20M" },
    { "log_file_max", "20M" },
    { "purge_batch_sleep", "500" }, 
    { "purge_thread_delay", "3600" }, 
    { "purge_clean_log", "16" },
    
    { "connection_max_retries", "0" },
    { "connection_timeout", "0.3" },
    { "communication_timeout", "0.1" },
    { "max_connection_pool_size", "30" },
    { "max_find_lbname_retries", "2" },
    { "retry_delay", "0.001" },
 
    { 0, 0 }
}

Definition at line 1567 of file reader_cache.cpp.

Referenced by GetCacheParams().

◆ s_DefaultReaderParams

const SPluginParams::SDefaultValue s_DefaultReaderParams[]

static

Initial value:

= {
    
    { "purge_thread", "yes" },
 
    { 0, 0 }
}

Definition at line 1606 of file reader_cache.cpp.

Referenced by GetCacheParams().

◆ s_DefaultWriterParams

const SPluginParams::SDefaultValue s_DefaultWriterParams[]

static

Initial value:

= {
    
    { "purge_thread", "no" },
 
    { 0, 0 }
}

Definition at line 1612 of file reader_cache.cpp.

Referenced by GetCacheParams().

Variables
static const size_t	kHashLimit = 100

static SCacheEntryAccessCount	s_CacheEntryAccessCounts [CCacheReader::eCacheEntry_Count]

static const SPluginParams::SDefaultValue	s_DefaultParams []

static const SPluginParams::SDefaultValue	s_DefaultIdParams []

static const SPluginParams::SDefaultValue	s_DefaultBlobParams []

static const SPluginParams::SDefaultValue	s_DefaultReaderParams []

static const SPluginParams::SDefaultValue	s_DefaultWriterParams []

Classes

Macros

Functions

Variables

Macro Definition Documentation

◆ FIX_BAD_ID2S_REPLY_DATA

Function Documentation

◆ GenBankReaders_Register_Cache()

◆ GetCacheParams()

◆ GetCacheParamsCopy()

◆ GetDriverParams()

◆ IsDisabledCache()

◆ NCBI_EntryPoint_CacheReader()

◆ NCBI_EntryPoint_xreader_cache()

◆ NCBI_PARAM_DECL()

◆ NCBI_PARAM_DEF_EX()

Variable Documentation

◆ kHashLimit

◆ s_CacheEntryAccessCounts

◆ s_DefaultBlobParams

◆ s_DefaultIdParams

◆ s_DefaultParams

◆ s_DefaultReaderParams

◆ s_DefaultWriterParams