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NCBI C++ ToolKit: include/db/bdb/bdb_split_blob.hpp Source File

this->

(

, &dim_idx);

size_split[] = {

256, 512, 2048, 4096, 8192, 16384, 32768

kMaxSize = (unsigned)(

(size_split) /

(*size_split));

(

= 0;

< kMaxSize; ++

) {

(blob_size < size_split[

]) {

rec_max = 3 * 1000000)

(

)coord[1] + 1);

(

, coord[1]) += blob_size;

vol_max = 1.5 * (1024.00*1024.00*1024.00),

rec_max = 3 * 1000000)

( !

.empty() ) {

<< e.

());

ostr <<

(

, j) <<

;

ostr <<

(

, j) <<

;

<

TBV,

TObjDeMux=CBDB_BlobDeMux,

TL=CFastMutex>

(

& storage_name,

* old_coord,

* coords,

* coords2);

* coords,

* coords,

* coords,

SLockedDb&

(

vol,

slice,

<

TBV,

TObjDeMux,

TL>

m_VolumeCacheSize(0),

m_AllProjAvail(

),

m_RevSplitOff(

)

<

TBV,

TObjDeMux,

TL>

(std::exception& e) {

<<

<< e.what());

(std::exception& e) {

<<

<< e.what());

<

TBV,

TObjDeMux,

TL>

m_RevSplitOff =

;

<

TBV,

TObjDeMux,

TL>

<

TBV,

TObjDeMux,

TL>

(

= 0;

< m_Volumes.size(); ++

) {

<

TBV,

TObjDeMux,

TL>

* coords1,

* coords2)

coords1[0] == coords2[0] &&

coords1[1] == coords2[1];

<

TBV,

TObjDeMux,

TL>

m_IdDeMux->GetIdVector(bv);

<

TBV,

TObjDeMux,

TL>

* coords)

old_coord[2];

found = m_IdDeMux->GetCoordinatesFast(

, old_coord);

(found && IsSameCoordinates(old_coord, coords)) {

m_IdDeMux->SetCoordinatesFast(

, coords);

<

TBV,

TObjDeMux,

TL>

this->Insert(

,

,

, coord);

<

TBV,

TObjDeMux,

TL>

found = m_IdDeMux->GetCoordinatesFast(

, coord);

TLockGuard

(m_ObjDeMuxLock);

m_ObjDeMux->GetCoordinates((

)

, coord);

m_IdDeMux->SetCoordinatesFast(

, coord);

SLockedDb& dbp = this->GetDb(coord[0], coord[1], eGetWrite);

TLockGuard

(*dbp.lock);

dbp.db->SetTransaction(GetTransaction());

dbp.db->Insert(

,

);

<

TBV,

TObjDeMux,

TL>

this->UpdateInsert(

,

,

, coord);

<

TBV,

TObjDeMux,

TL>

found = m_IdDeMux->GetCoordinatesFast(

, coord);

this->Insert(

,

,

, coord);

slice = m_ObjDeMux->SelectSplit(

);

(slice != coord[1]) {

TLockGuard

(m_CrossDBLock);

this->Insert(

,

,

, coord);

SLockedDb& dbp = this->GetDb(coord[0], coord[1], eGetWrite);

TLockGuard

(*(dbp.lock));

dbp.db->SetTransaction(GetTransaction());

dbp.db->UpdateInsert(

,

);

<

TBV,

TObjDeMux,

TL>

* old_coord,

found = m_IdDeMux->GetCoordinatesFast(

, coord);

(old_coord[0] != coord[0] || old_coord[1] != coord[1]) {

this->Insert(

,

,

, coord);

coord[0] = old_coord[0];

coord[1] = old_coord[1];

this->Insert(

,

,

, coord);

slice = m_ObjDeMux->SelectSplit(

);

(slice != coord[1]) {

this->Insert(

,

,

, coord);

& dbp = this->GetDb(coord[0], coord[1], eGetWrite);

dbp.

->SetTransaction(GetTransaction());

<

TBV,

TObjDeMux,

TL>

found = m_IdDeMux->GetCoordinatesFast(

, coord);

this->Delete(

, coord, on_error);

<

TBV,

TObjDeMux,

TL>

* coords,

m_IdDeMux->SetCoordinatesFast(

, coords,

);

& dbp = this->GetDb(coords[0], coords[1], eGetWrite);

dbp.

->SetTransaction(GetTransaction());

dbp.

->Delete(on_error);

<

TBV,

TObjDeMux,

TL>

found = m_IdDeMux->GetCoordinatesFast(

, coord);

this->CreateReader(

, coord);

<

TBV,

TObjDeMux,

TL>

* coords)

& dbp = this->GetDb(coords[0], coords[1], eGetRead);

db = dbp.

.

();

<

TBV,

TObjDeMux,

TL>

m_IdDeMux->FreeUnusedMem();

<

TBV,

TObjDeMux,

TL>

<

TBV,

TObjDeMux,

TL>

curr_trans = this->GetBDBTransaction();

curr_trans->

(

);

curr_trans = db_trans;

curr_trans->

(

);

<

TBV,

TObjDeMux,

TL>

(

= 0;

< m_Volumes.size(); ++

) {

(

j = 0; j < v->

.size(); ++j) {

(db && db->

) {

<

TBV,

TObjDeMux,

TL>

* coords,

& dbp = this->GetDb(coords[0], coords[1], eGetRead);

db = dbp.

.

();

ret = db->

(

, buf_size, allow_realloc);

<

TBV,

TObjDeMux,

TL>

found = m_IdDeMux->GetCoordinatesFast(

, coord);

this->Fetch(

, coord,

, buf_size, allow_realloc, blob_size);

<

TBV,

TObjDeMux,

TL>

found = m_IdDeMux->GetCoordinatesFast(

, coord);

<

TBV,

TObjDeMux,

TL>

* coords,

& dbp = this->GetDb(coords[0], coords[1], eGetRead);

db = dbp.

.

();

<

TBV,

TObjDeMux,

TL>

found = m_IdDeMux->GetCoordinatesFast(

, coord);

this->ReadRealloc(

, coord,

);

<

TBV,

TObjDeMux,

TL>

found = m_IdDeMux->GetCoordinatesFast(

, coord);

this->BlobSize(

, coord, blob_size);

<

TBV,

TObjDeMux,

TL>

* coords,

& dbp = this->GetDb(coords[0], coords[1], eGetRead);

db = dbp.

.

();

<

TBV,

TObjDeMux,

TL>

m_StorageName = storage_name;

m_OpenMode = open_mode;

m_DB_Type = db_type;

LoadIdDeMux(*m_IdDeMux, *m_DictFile);

<

TBV,

TObjDeMux,

TL>

m_DictFile.get() ?

:

;

<

TBV,

TObjDeMux,

TL>

max_split = m_ObjDeMux->GetSplitSize();

max_vol = m_ObjDeMux->GetVolumeSize();

(!max_split || !max_vol) {

(

= 0;

< max_vol; ++

) {

(

j = 0; j < max_split; ++j) {

this->GetDb(

, j, eGetRead);

m_AllProjAvail =

;

this->Save(TDeMuxStore::eNoCompact);

<

TBV,

TObjDeMux,

TL>

m_DictFile->SetEnv(*m_Env);

dict_fname(m_StorageName);

dict_fname.append(

);

m_DictFile->Open(dict_fname.c_str(), m_OpenMode);

m_IdDeMux.reset(

(2));

<

TBV,

TObjDeMux,

TL>

dim = dict_file.

;

dim_idx = dict_file.

;

<

TBV,

TObjDeMux,

TL>

( m_IdDeMux.get() && m_DictFile.get() ) {

this->SaveIdDeMux(*m_IdDeMux, *m_DictFile, 0, compact_vectors);

<

TBV,

TObjDeMux,

TL>

= de_mux.

();

(

= 0;

<

; ++

) {

(

j = 0; j < dv.size(); ++j) {

<

TBV,

TObjDeMux,

TL>

(splice < m_PageSizes.size())

m_PageSizes[splice];

<

TBV,

TObjDeMux,

TL>

m_StorageName +

+

<

TBV,

TObjDeMux,

TL>

(ldb->

.

() == 0) {

<

TBV,

TObjDeMux,

TL>

(m_AllProjAvail) {

(m_Volumes.size() > vol);

((m_Volumes[vol])->db_vect.size() > slice);

& volume = *(m_Volumes[vol]);

lp = &*volume.

[slice];

((m_Volumes.size() > vol) &&

((m_Volumes[vol])->db_vect.size() > slice)) {

& volume = *(m_Volumes[vol]);

lp = &*volume.

[slice];

(lp->

.

()) {

(m_Volumes.size() < (vol+1)) {

unique_ptr<SVolume> v(

);

v->db_vect.resize(slice+1);

(

= 0;

< v->db_vect.size(); ++

) {

( !v->db_vect[

] ) {

m_Volumes.push_back(v.release());

& volume = *(m_Volumes[vol]);

(volume.

.size() <= slice) {

volume.

.resize(slice+1);

(

= 0;

< volume.

.size(); ++

) {

lp = &*volume.

[slice];

needs_save =

;

(lp->

.

() == 0) {

fname = this->MakeDbFileName(vol, slice);

lp->

->SetEnv(*m_Env);

lp->

->SetEnv(*m_Env);

(m_VolumeCacheSize) {

lp->

->SetCacheSize(m_VolumeCacheSize);

page_size = GetPageSize(slice);

lp->

->SetPageSize(page_size);

lp->

->SetBtreeMinKeysPerPage(6);

lp->

->SetBtreeMinKeysPerPage(3);

(m_RevSplitOff) {

lp->

->RevSplitOff();

lp->

->Open(fname.c_str(), m_OpenMode);

lp->

->SetCachePriority(m_CachePriority);

lp->

->SetCachePriority(m_CachePriority);

get_mode == eGetWrite) {

this->Save(TDeMuxStore::eNoCompact);

BDB library BLOB support.

Berkeley BDB file cursor.

Wrapper around Berkeley DB transaction structure.

Split demux which can save and load state into a file Stateful (persistent) class.

Base class for page-split demultiplexers.

BLOB demultiplexer implements round-robin volume rotation.

Volume split BLOB demultiplexer.

BLOB storage based on single unsigned integer key Supports BLOB volumes and different base page size ...

Persistent storage for demux information.

Basic template class for bitvector storage.

BDB environment object a collection including support for some or all of caching, locking,...

Berkeley DB file cursor class.

Variant of BLOB storage for integer key database.

Raw file class wraps up basic Berkeley DB operations.

Id to coordinates demultiplexer.

size_t GetN() const

Get order of Multiplexer.

const TDimVector & GetDimVector(size_t i) const

Get dimension vector.

void SetProjection(size_t i, size_t idx, TBitVector *bv)

Assign projection idx for dimension i.

vector< TBitVectorPtr > TDimVector

Dimension vector.

void Resize(size_t i, size_t j, T val=T())

resize this matrix, filling the empty cells with a known value

size_t GetRows() const

get the number of rows in this matrix

size_t GetCols() const

get the number of columns in this matrix

Reallocable memory buffer (no memory copy overhead) Mimics vector<>, without the overhead of explicit...

Thread local transactional object.

A very basic data-read interface.

Include a standard set of the NCBI C++ Toolkit most basic headers.

The NCBI C++ standard methods for dealing with std::string.

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

element_type * get(void) const

Get pointer.

CBDB_Env * GetEnv(void) const

Get pointer on file environment Return NULL if no environment has been set.

void Save(CNcbiOstream &ostr)

TL::TWriteLockGuard TLockGuard

unique_ptr< TDeMuxStore > m_DictFile

Split dictionary(id demux file)

SLockedDb & GetDb(unsigned vol, unsigned slice, EGetDB_Mode get_mode)

Get database pair (method opens and mounts database if necessary)

void InitDbMutex(SLockedDb *ldb)

Init database mutex lock (mathod is protected against double init)

IReader * CreateReader(unsigned id)

Create stream oriented reader.

CBDB_RawFile::EOpenMode m_OpenMode

CBDB_BlobStoreDict< TBV > TDeMuxStore

void OpenProjections()

Try to open all storage files in all projections This is only possible when object de-mux has fixed n...

size_t LobSize() const

Get LOB size. Becomes available right after successfull Fetch.

const string & GetFileName() const

Return the base filename of the underlying split store.

void SaveIdDeMux(const TIdDeMux &de_mux, TDeMuxStore &dict_file, CBDB_Transaction *trans, typename TDeMuxStore::ECompact compact_vectors)

Store id demux (projection vectors) into the database file.

void Load(CNcbiIstream &istr)

TLock m_CrossDBLock

Lock used to sync. muli-db transactions to avoid deadlocks.

bool IsSameCoordinates(const unsigned *coords1, const unsigned *coords2)

Returns true if two sets of coordinates are the same.

EBDB_ErrCode Delete(unsigned id, CBDB_RawFile::EIgnoreError on_error=CBDB_RawFile::eThrowOnError)

Delete BLOB.

EBDB_ErrCode ReadRealloc(TBuffer &buffer)

Read BLOB into vector.

CBDB_BlobDeMux(double vol_max=1.5 *(1024.00 *1024.00 *1024.00), unsigned rec_max=3 *1000000)

EBDB_ErrCode WriteVector(const TBitVector &bv, ECompact compact)

Save a bitvector to the store.

CNcbiMatrix< unsigned > TVolumeRecs

EBDB_ErrCode Insert(unsigned id, const void *data, size_t size, unsigned *coord)

Insert BLOB into the storage.

EBDB_ErrCode BlobSize(unsigned id, const unsigned *coords, size_t *blob_size)

unique_ptr< TObjDeMux > m_ObjDeMux

Obj to coordinates mapper.

CBDB_IdBlobFile TBlobFile

CBDB_RawFile::EDBType m_DB_Type

bool m_RevSplitOff

Flag carrying reverse split status.

void Sync()

Sync the underlying stores.

CBDB_FieldUint4 dim

dimention

CBDB_RawFile::ECachePriority m_CachePriority

static unsigned SelectSplit(size_t blob_size)

LOBs are getting split into slices based on LOB size, similar BLOBs go to the compartment with more o...

virtual void SetTransaction(ITransaction *trans)

Establish transaction association.

void FreeUnusedMem()

Reclaim unused memory.

EBDB_ErrCode Insert(unsigned id, const void *data, size_t size)

vector< CRef< SLockedDb > > db_vect

void RevSplitOff()

Turn off reverse splitting on the underlying stores.

EBDB_ErrCode UpdateInsert(unsigned id, const void *data, size_t size)

CBDB_Transaction * GetBDBTransaction()

void OpenDict()

Open split storage dictionary.

CBDB_BvStore< TBV > TParent

EBDB_ErrCode ReadRealloc(unsigned id, CBDB_RawFile::TBuffer &buffer)

Read BLOB into vector.

AutoPtr< TLock > lock_ro

db lock for reads

CBDB_BlobSplitStore(TObjDeMux *de_mux)

Construction The main parameter here is object demultiplexer for splitting incoming LOBs into volumes...

EBDB_ErrCode ReadRealloc(unsigned id, const unsigned *coords, CBDB_RawFile::TBuffer &buffer)

Read BLOB into vector using provided coordinates If BLOB does not fit, method resizes the vector to a...

bool IsOpen() const

Return true if the split store has been opened.

AutoPtr< TBlobFile > db

database file

void GetCoordinates(unsigned blob_size, unsigned *coord)

coordinates:

TVolumeRecs m_RecS

Volumes record counts.

string MakeDbFileName(unsigned vol, unsigned slice)

Make BDB file name based on volume and page size split.

EBDB_ErrCode UpdateInsert(unsigned id, const unsigned *old_coord, const void *data, size_t size, unsigned *coord)

Update or insert BLOB using old coordinates.

EBDB_ErrCode Fetch()

Fetch the record corresponding to the current key value.

TBuffer & GetBuffer()

Get access to the internal buffer.

CBDB_BlobDeMuxPersistent(const string &path, double vol_max=1.5 *(1024.00 *1024.00 *1024.00), unsigned rec_max=3 *1000000)

void SetVolumeCacheSize(unsigned int cache_size)

TVolumeVect m_Volumes

Volumes.

unsigned GetVolumeSize() const

Returns total number of volumes (vertical projection) If method returns 0 - means there is no hard nu...

AutoPtr< TLock > lock

db lock

CBDB_BlobSplitStore(const CBDB_BlobSplitStore< TBV, TObjDeMux, TL > &)

forbidden

void Deserialize(TBitVector *bv, const TBufferValue *buf)

EBDB_ErrCode Delete(unsigned id, const unsigned *coords, CBDB_RawFile::EIgnoreError on_error=CBDB_RawFile::eThrowOnError)

EBDB_ErrCode UpdateInsert(unsigned id, const void *data, size_t size, unsigned *coord)

Update or insert BLOB.

void GetCoordinates(unsigned blob_size, unsigned *coord)

coordinates:

void LoadIdDeMux(TIdDeMux &de_mux, TDeMuxStore &dict_file)

void Save(typename TDeMuxStore::ECompact compact_vectors=TDeMuxStore::eCompact)

Save storage dictionary (demux disposition).

IReader * CreateReader(unsigned id, const unsigned *coords)

void SetCachePriority(CBDB_RawFile::ECachePriority)

Set the priority for this database's pages in the buffer cache This is generally a temporary adviseme...

unsigned m_RecMax

Maximum number of records.

IReader * CreateReader()

Creates stream like object to read BLOB by chunks.

void CloseVolumes()

Close volumes without saving or doing anything with id demux.

double m_VolMax

Volume max size.

TVolumeSize m_VolS

Volumes BLOB sizes.

EBDB_ErrCode Fetch(unsigned id, void **buf, size_t buf_size, CBDB_RawFile::EReallocMode allow_realloc, size_t *blob_size)

Fetch LOB record directly into the provided '*buf'.

EGetDB_Mode

Read or write operation.

vector< SVolume * > TVolumeVect

CBDB_FieldUint4 dim_idx

projection index

void SetEnv(CBDB_Env &env)

Associate with the environment. Should be called before opening.

unsigned GetVolumeSize() const

Returns total number of volumes (vertical projection) If method returns 0 - means there is no hard nu...

unsigned GetPageSize(unsigned splice) const

Select preferred page size for the specified slice.

EBDB_ErrCode BlobSize(unsigned id, size_t *blob_size)

Get size of the BLOB.

vector< unsigned > m_PageSizes

TLock m_VolumesLock

Volumes locker.

CBDB_FieldUint4 id

ID key.

EBDB_ErrCode Fetch(unsigned id, const unsigned *coords, void **buf, size_t buf_size, CBDB_RawFile::EReallocMode allow_realloc, size_t *blob_size)

unsigned m_VolumeCacheSize

CBDB_BlobDeMux_RoundRobin(unsigned volumes=0)

TLock m_DictFileLock

id demux file locker

void GetIdVector(TBitVector *bv) const

Get all id of all BLOBs stored.

CBDB_BlobSplitStore< TBV, TObjDeMux, TL > & operator=(const CBDB_BlobSplitStore< TBV, TObjDeMux, TL > &)

EBDB_ErrCode GetCoordinates(unsigned id, unsigned *coords)

Find (demux) coordinates by BLOB id.

CNcbiMatrix< double > TVolumeSize

ECompact

Compression options for vector storage.

unique_ptr< TIdDeMux > m_IdDeMux

Id to coordinates mapper.

EBDB_ErrCode FetchToBuffer(CBDB_FileCursor &cur)

Fetch the next BLOB record to the resiable buffer.

~CBDB_BlobDeMuxPersistent()

void Open(const string &storage_name, CBDB_RawFile::EOpenMode open_mode, CBDB_RawFile::EDBType db_type=CBDB_RawFile::eBtree)

Open storage (reads storage dictionary into memory)

AutoPtr< TBlobFile > db_ro

database file for reads

unsigned GetSplitSize() const

Returns total number of splits (horizontal projection) If method returns 0 - means there is no hard n...

void AssignCoordinates(unsigned id, const unsigned *coords)

Assing de-mux coordinates.

bool m_AllProjAvail

True when all proj.dbs are pre-open.

EBDB_ErrCode Delete(EIgnoreError on_error=eThrowOnError)

Delete record corresponding to the current key value.

void SetCondition(ECondition cond_from, ECondition cond_to=eNotSet)

Set search condition(type of interval)

EOpenMode

BDB file open mode.

EDBType

Berkeley DB database type.

virtual void SetTransaction(ITransaction *trans)

Establish transaction association.

void BindKey(const char *field_name, CBDB_Field *key_field, size_t buf_size=0)

EReallocMode

BLOB read mode, controld data buffer reallocation when there is not enough space in buffer.

ECachePriority

Set the priority for this database's pages in the buffer cache This is generally a temporary adviseme...

EBDB_ErrCode

BDB Return codes.

CBDB_ConditionHandle From

@ eReadWriteCreate

read-write, create if it doesn't exist

EKeepFileAssociation GetAssociationMode() const

Transaction file association mode.

virtual void Add(ITransactional *dbfile)

Add file to the list of connected files.

static CBDB_Transaction * CastTransaction(ITransaction *trans)

Downcast ITransaction.

virtual void Remove(ITransactional *dbfile)

Remove file from the list of connected files.

@ eFullAssociation

Transaction associated with files.

#define ERR_POST_XX(error_name, err_subcode, message)

Error posting with error code having given name and with given error subcode.

void Error(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

CGuard< CRWLock, SSimpleWriteLock< CRWLock > > TWriteLockGuard

virtual void SetTransaction(ITransaction *trans)

Establish transaction association.

@ BM_GAP

GAP compression is ON.

Classes and interfaces to map integer ids into multi-dimension coordinates.

Definition of all error codes used in bdb library (bdb.lib and ncbi_xcache_bdb.lib).

const struct ncbi::grid::netcache::search::fields::SIZE size

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

Multi-threading – mutexes; rw-locks; semaphore.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

static SLJIT_INLINE sljit_ins lg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

BDB Database together with the locker One database is opened twice, one regular mode,...

Volume split on optimal page size.

Abstract object demultiplexer.

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