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NCBI C++ ToolKit: src/objtools/data_loaders/genbank/cache/reader_cache.cpp Source File

.IsGi()?

(

.GetGi()):

.AsFastaString();

.IsGi()?

(

.GetGi()):

.AsString();

& true_subkey)

( accs.

() ) {

(

,

, it->first ) {

oss << chunk_id <<

<< split_version;

: m_BlobCache(0), m_IdCache(0)

& driver_name)

joined_blob_version = conf.

(

CParseBuffer :

{

&

,

&

);

&

,

&

,

&

,

&

,

* get_current_version);

Found(

)

m_Descr.blob_found;

FoundSome(

)

m_Descr.actual_age != unsigned(-1);

TExpirationTime GetExpirationTime(

)

m_ExpirationTime;

GotCurrentVersion(

)

m_Descr.return_current_version_supported;

CurrentVersionExpired(

)

GetExpirationTime() == TExpirationTime(-1);

(

)

ParseUint1(

)

*x_NextBytes(1);

ParseBool(

)

ParseUint4(

)

* ptr = x_NextBytes(4);

((ptr[0]&0xff)<<24)|((ptr[1]&0xff)<<16)|

((ptr[2]&0xff)<<8)|(ptr[3]&0xff);

ParseInt4(

)

ParseInt8(

)

ParseString(

);

FullString(

);

* bytes_read = 0)

*bytes_read =

;

* get_current_version,

set_expiration_time);

x_Eof(

)

;

* x_NextBytes(

);

CParseBuffer(

CParseBuffer&);

operator=(

CParseBuffer&);

TExpirationTime m_ExpirationTime;

* get_current_version,

set_expiration_time)

( set_expiration_time ) {

( get_current_version ) {

m_Descr.return_current_version =

;

( get_current_version ) {

( !get_current_version ) {

( get_current_version && GotCurrentVersion() ) {

s <<

<<m_Descr.current_version;

( get_current_version && GotCurrentVersion() ) {

s <<

<<m_Descr.current_version;

s <<

<<

(m_Descr.actual_age);

( m_Descr.actual_age > m_ExpirationTime ) {

m_ExpirationTime = TExpirationTime(-1);

m_ExpirationTime -= m_Descr.actual_age;

( get_current_version ) {

( GotCurrentVersion() ) {

*get_current_version = m_Descr.current_version;

m_ExpirationTime = TExpirationTime(-1);

*get_current_version = 0;

( Found() && !m_Descr.reader.get() ) {

m_Size = m_Descr.blob_size;

: m_Descr(m_Buffer, sizeof(m_Buffer)), m_Ptr(0), m_Size(0)

: m_Descr(m_Buffer, sizeof(m_Buffer)), m_Ptr(0), m_Size(0)

* get_current_version)

: m_Descr(m_Buffer, sizeof(m_Buffer)), m_Ptr(0), m_Size(0)

x_Init(

, cache,

,

, -1, get_current_version,

);

CParseBuffer::ParseString(

)

= ParseUint4();

ret.assign(x_NextBytes(

),

);

CParseBuffer::FullString(

)

ret.assign(m_Ptr, m_Size);

( m_Descr.reader->Read(m_Buffer,

(m_Buffer), &

) ==

) {

ret.append(m_Buffer,

);

* CParseBuffer::x_NextBytes(

)

* ret = m_Ptr;

( m_Size >=

) {

(

<=

(m_Buffer) ) {

*

= m_Buffer;

);

CParseBuffer::x_Eof(

)

* CParseBuffer::GetReader(

)

( !m_Descr.reader.get() ) {

m_Descr.reader.get();

( lock.IsLoaded() ) {

( !

.Found() ) {

(

= 0;

<

; ++

) {

.GetExpirationTime());

(

.Found() ) {

gi_num =

.ParseInt8();

( gi_num !=

(gi_num) ) {

);

.sequence_found =

;

( ids_lock.IsLoaded() ) {

.SetLoadedGiFromSeqIds(seq_id, ids_lock);

(

.Found() ) {

=

.FullString();

( !

.empty() ) {

( ids_lock.IsLoaded() ) {

.SetLoadedAccFromSeqIds(seq_id, ids_lock);

(

.Found() ) {

=

.FullString();

( ids_lock.IsLoaded() ) {

ids_lock.GetExpirationTime());

( !

.Found() ) {

( !

.Done() ) {

( !

.Found() ) {

( !seq_id.

() ) {

gi_hash.GetExpirationTime());

.sequence_found =

.ParseBool();

.hash_known =

.ParseBool();

( !

.Done() ) {

( !

.Found() ) {

( !

.Done() ) {

( !

.Found() ) {

( !

.Done() ) {

.sequence_found =

;

= ids.size();

(

= 0;

<

; ++

) {

= ids.size();

(

= 0;

<

; ++

) {

loaded[

] =

;

= ids.size();

(

= 0;

<

; ++

) {

loaded[

] =

;

= ids.size();

(

= 0;

<

; ++

) {

loaded[

] =

;

( ids.IsLoaded() ) {

, true_subkey;

( !

.Found() ) {

blob_count =

.ParseUint4();

blob_ids.reserve(blob_count);

(

= 0;

< blob_count; ++

) {

->SetSat(

.ParseInt4());

->SetSubSat(

.ParseInt4());

->SetSatKey(

.ParseInt4());

name_count =

.ParseUint4();

(

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

annots_info->AddNamedAnnotName(

.ParseString());

s =

.ParseString();

( !annots_info ) {

stream >> *annot_info;

annots_info->AddAnnotInfo(*annot_info);

( annots_info ) {

.SetAnnotInfo(annots_info);

blob_ids.push_back(

);

( !true_subkey.empty() &&

.ParseString() != true_subkey ) {

( !

.Done() ) {

.GetExpirationTime());

( !

.Found() ) {

( !

.Done() ) {

( !

.Found() ) {

( !

.Done() ) {

&

,

s <<

<<

<<

<<

<<

<<

<<

;

know_has_blobs =

;

( !

.GotCurrentVersion() ) {

);

( !

.Found() ) {

know_has_blobs =

.FoundSome();

(

.CurrentVersionExpired() ) {

<< stream.rdbuf();

( !know_has_blobs ) {

( cache_version != -1 &&

!= cache_version ) {

( !

.Found() ) {

processor_type =

(stream);

( processor_type != processor.

() ) {

<<processor_type);

processor_magic =

(stream);

( processor_magic !=

(processor.

()) ) {

<<processor_magic);

& name)

& name,

* default_value =

)

& name,

*

)

( ; values->

; ++values ) {

( driver->

().value.empty() ) {

& driver_name =

* section_name)

( src_section ) {

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

* section_name;

unique_ptr<SCacheInfo::TParams> section

( !section.get() ) {

section.release();

unique_ptr<TParams> cache_params

( !cache_params.get() ) {

manager->CreateInstanceFromKey

unique_ptr<TParams> id_params

unique_ptr<TParams> blob_params

* share_id_param =

share_id = !share_id_param ||

* share_blob_param =

share_blob = !share_blob_param ||

(share_id || share_blob) {

* cache = cache_manager.

* cache = cache_manager.

( !blob_cache ) {

( !driver.empty() && driver != m_DriverName ) {

TSatKey GetSatKey() const

TSubSat GetSubSat() const

void SetIdCache(ICache *id_cache)

void SetBlobCache(ICache *blob_cache)

CSimpleClassFactoryImpl< CReader, CCacheReader > TParent

CReader * CreateInstance(const string &driver=kEmptyStr, CVersionInfo version=NCBI_INTERFACE_VERSION(CReader), const TPluginManagerParamTree *params=0) const

Create instance of TDriver.

void x_ProcessBlob(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CNcbiIstream &stream)

ESwitch m_JoinedBlobVersion

bool LoadSeq_idSeq_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

bool LoadBlob(CReaderRequestResult &result, const TBlobId &blob_id)

bool LoadGis(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TGis &ret)

bool LoadBlobState(CReaderRequestResult &result, const TBlobId &blob_id)

bool LoadSeq_idGi(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

bool LoadBlobVersion(CReaderRequestResult &result, const TBlobId &blob_id)

bool LoadSeq_idTaxId(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

int GetRetryCount(void) const

bool LoadTaxIds(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TTaxIds &ret)

bool LoadSequenceLength(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

void x_SetBlobVersionAsCurrent(CReaderRequestResult &result, const string &key, const string &subkey, TBlobVersion version)

virtual void ResetCache(void)

int GetMaximumConnectionsLimit(void) const

bool MayBeSkippedOnErrors(void) const

bool LoadAccVers(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TIds &ret)

bool LoadSeq_idLabel(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

bool LoadLabels(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TLabels &ret)

bool LoadSeq_idAccVer(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

static bool NoNeedToSave(ECacheEntryType type)

void x_AddConnectionSlot(TConn conn)

static void GoingToLoad(ECacheEntryType type)

@ eCacheEntry_BlobVersion

bool LoadSequenceType(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

bool LoadSeq_idBlob_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel)

All LoadXxx() methods should return false if there is no requested data in the reader.

bool LoadChunk(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id)

bool ReadSeq_ids(CReaderRequestResult &result, const string &key, CLoadLockSeqIds &ids)

void x_ConnectAtSlot(TConn conn)

virtual void InitializeCache(CReaderCacheManager &cache_manager, const TPluginManagerParamTree *params)

void x_DisconnectAtSlot(TConn conn, bool failed)

bool LoadSequenceHash(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

void x_RemoveConnectionSlot(TConn conn)

In-memory stream (a la strstream or stringstream)

CID2S_Seq_annot_Info –.

static bool IsFound(const TData &data)

TData GetAccVer(void) const

static const CSeq_id_Handle & GetAcc(const TData &data)

bool IsLoadedAccVer(void) const

bool SetLoadedAccVer(const TData &data)

bool SetLoadedBlob_ids(const TData &data, TExpirationTime expiration_time)

bool IsLoadedBlobState(void) const

bool IsLoadedBlobVersion(void) const

TData GetBlobVersion(void) const

bool IsLoadedChunk(void) const

const CTSE_Split_Info & GetSplitInfo(void) const

TBlobVersion GetKnownBlobVersion(void) const

bool SetLoadedGi(const TData &data)

bool IsLoadedGi(void) const

static bool IsFound(const TData &data)

static TGi GetGi(const TData &data)

bool SetLoadedHash(const TData &data)

bool IsLoadedHash(void) const

static int GetHash(const TData &data)

bool IsLoadedLabel(void) const

bool SetLoadedLabel(const TData &data)

TData GetLabel(void) const

bool IsLoadedLength(void) const

bool SetLoadedLength(const TData &data)

TData GetSeq_ids(void) const

bool SetLoadedSeq_ids(const TData &data)

bool IsLoadedTaxId(void) const

bool SetLoadedTaxId(const TData &data)

TData GetTaxId(void) const

bool SetLoadedType(const TData &data)

bool IsLoadedType(void) const

Data loader exceptions, used by GenBank loader.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

CObjectIStreamAsnBinary –.

static bool IsExtAnnot(const TBlobId &blob_id)

virtual void ProcessStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CNcbiIstream &stream) const

virtual EType GetType(void) const =0

virtual TMagic GetMagic(void) const =0

Note about the "buf_size" parameter for streams in this API.

void LoadBlobVersion(CReaderRequestResult &result, const TBlobId &blob_id, const CReader *asking_reader=0)

const CProcessor & GetProcessor(CProcessor::EType type) const

static bool CannotProcess(const CSeq_id_Handle &sih)

virtual void RegisterCache(ICache &cache, ECacheType cache_type)=0

GBL::CInfo_Base::TExpirationTime TExpirationTime

vector< CSeq_id_Handle > TSeqIds

CReadDispatcher * m_Dispatcher

void SetAndSaveBlobVersion(CReaderRequestResult &result, const TBlobId &blob_id, TBlobVersion version) const

vector< CBlob_Info > TBlobIds

void SetAndSaveBlobState(CReaderRequestResult &result, const TBlobId &blob_id, TBlobState blob_state) const

static int ReadInt(CNcbiIstream &stream)

vector< CSeq_id_Handle > TIds

int SetMaximumConnections(int max)

Template class helps to implement one driver class factory.

TSplitVersion GetSplitVersion(void) const

definition of a Culling tree

BLOB cache read/write/maintenance interface.

virtual bool HasBlobs(const string &key, const string &subkey)=0

Check if any BLOB exists (any version)

virtual void GetBlobAccess(const string &key, TBlobVersion version, const string &subkey, SBlobAccessDescr *blob_descr)=0

Get BLOB access using BlobAccessDescr.

virtual void SetBlobVersionAsCurrent(const string &key, const string &subkey, TBlobVersion version)=0

Set current valid version for a BLOB.

A very basic data-read interface.

static CS_CONNECTION * conn

static const char * str(char *buf, int n)

#define GI_FROM(T, value)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define TAX_ID_FROM(T, value)

@ eTakeOwnership

An object can take ownership of another.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

void Read(CObjectIStream &in, TObjectPtr object, const CTypeRef &type)

bool GetBool(const string &driver_name, const string &param_name, EErrAction on_error, bool default_value, const list< string > *synonyms=NULL)

Utility function to get an integer element of parameter tree Throws an exception when mandatory param...

@ eErr_NoThrow

Return default value on error.

static CSeq_id_Handle GetGiHandle(TGi gi)

Faster way to create a handle for a gi.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

const TNamedAnnotAccessions & GetNamedAnnotAccessions(void) const

void Reset(void)

Reset reference object.

#define NCBI_PARAM_TYPE(section, name)

Generate typename for a parameter from its {section, name} attributes.

@ eParam_NoThread

Do not use per-thread values.

static void NCBI_EntryPointImpl(TDriverInfoList &info_list, EEntryPointRequest method)

Entry point implementation.

#define NCBI_INTERFACE_VERSION(iface)

Macro to construct CVersionInfo class using interface name (relies on CInterfaceVersion class)

list< SDriverInfo > TDriverInfoList

List of driver information.

EEntryPointRequest

Actions performed by the entry point.

uint8_t Uint1

1-byte (8-bit) unsigned integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

ERW_Result

Result codes for I/O operations.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

@ eRW_Eof

End of data, should be considered permanent.

@ eRW_Success

Everything is okay, I/O completed.

static bool StringToBool(const CTempString str)

Convert string to bool.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

const TTreeType * FindNode(const TKeyType &key, TNodeSearchMode sflag=eImmediateAndTop) const

Search for node.

void AddNode(TTreeType *subnode)

Add new subnode.

const TTreeType * FindSubNode(const TKeyType &key) const

Non recursive linear scan of all subnodes, with key comparison.

const TValue & GetValue(void) const

Return node's value.

EMol

molecule class in living organism

unsigned int

A callback function used to compare two keys in a database.

Interfaces for a local cache of versioned binary large objects (BLOBS).

static void hex(unsigned char c)

const string version

version string

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

const struct ncbi::grid::netcache::search::fields::KEY key

const struct ncbi::grid::netcache::search::fields::SUBKEY subkey

string s_Value(TValue value)

const GenericPointer< typename T::ValueType > T2 value

Defines: CTimeFormat - storage class for time format.

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

static const SPluginParams::SDefaultValue s_DefaultBlobParams[]

static const SPluginParams::SDefaultValue s_DefaultIdParams[]

void GenBankReaders_Register_Cache(void)

static const SPluginParams::SDefaultValue s_DefaultReaderParams[]

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

static SCacheEntryAccessCount s_CacheEntryAccessCounts[CCacheReader::eCacheEntry_Count]

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

NCBI_PARAM_DECL(int, GENBANK, CACHE_DEBUG)

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

static const SPluginParams::SDefaultValue s_DefaultParams[]

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 const SPluginParams::SDefaultValue s_DefaultWriterParams[]

static const size_t kHashLimit

#define NCBI_GBLOADER_READER_CACHE_PARAM_ID_SECTION

#define NCBI_GBLOADER_WRITER_CACHE_PARAM_SHARE

#define NCBI_GBLOADER_READER_CACHE_PARAM_DRIVER

#define NCBI_GBLOADER_READER_CACHE_PARAM_JOINED_BLOB_VERSION

#define NCBI_GBLOADER_READER_CACHE_DRIVER_NAME

#define NCBI_GBLOADER_READER_CACHE_PARAM_BLOB_SECTION

Reader-writer based streams.

static sljit_uw total_size

static int GetDebugLevel()

Better replacement of GetAccVer(), this method should be defined in data loaders, GetAccVer() is left...

Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for com...

Better replacement of GetSequenceHash(), this method should be defined in data loaders,...

Better replacement of GetSequenceType(), this method should be defined in data loaders,...

unsigned maximum_age

Set to a non-zero value to return a version not older than the specified value.

atomic< Uint8 > save_count

atomic< Uint8 > load_count

structure for common cache reader&writer implementation

static void GetBlob_idsSubkey(const SAnnotSelector *sel, string &subkey, string &true_subkey)

Id cache subkeys:

CConfig::TParamTree TParams

static ICache * CreateCache(const TParams *params, EReaderOrWriter reader_or_writer, EIdOrBlob id_or_blob)

static string GetBlobSubkey(CLoadLockBlob &blob, int chunk_id=kMain_ChunkId)

BLOB cache subkeys:

static string GetIdKey(const CSeq_id &id)

Return Id cache key string based on CSeq_id of gi.

static const char * GetAccVerSubkey(void)

static const char * GetTypeSubkey(void)

static const char * GetBlobStateSubkey(void)

static const char * GetGiSubkey(void)

static int GetDebugLevel(void)

static const char * GetHashSubkey(void)

static const char * GetLabelSubkey(void)

static const char *const BLOB_IDS_SUBKEY

static const char * GetLengthSubkey(void)

static const char * GetTaxIdSubkey(void)

static const char * GetSeq_idsSubkey(void)

static const char * GetBlobVersionSubkey(void)

static string GetBlobKey(const CBlob_id &blob_id)

Return BLOB cache key string based on Sat() and SatKey()

static const int BLOB_IDS_MAGIC

static const string & SetDefaultValue(TParams *params, const string &name, const char *value)

static const TParams * FindSubNode(const TParams *params, const string &name)

static const string & SetDefaultValue(TParams *params, const SDefaultValue &value)

static TParams * SetSubNode(TParams *params, const string &name, const char *default_value="")

static TParams * FindSubNode(TParams *params, const string &name)

SCacheInfo::TParams TParams

static TParams * SetSubSection(TParams *params, const string &name)

static void SetDefaultValues(TParams *params, const SDefaultValue *values)

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