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NCBI C++ ToolKit: src/sra/data_loaders/wgs/wgsloader_impl.cpp Source File

=

=

=

=

: m_WGSPrefix(

.

->GetWGSPrefix()),

m_SeqType(

.seq_type),

m_RowId(

.row_id),

( slash ==

) {

<<

);

=

.substr(slash+1);

(

[pos] ==

||

[pos] ==

) {

= NStr::StringToNumeric<int>(

.substr(dot+1));

=

.substr(0, dot);

= NStr::StringToNumeric<Uint8>(

);

( resolver.

() ) {

<<exc);

( exception& exc ) {

<<exc.

());

: m_WGSVolPath(params.m_WGSVolPath),

m_FileReopenTime, m_FileRecheckTime),

m_ResolverCreated(

)

info_slot)).second ) {

<<

->GetWGSPrefix());

( !resolver->IsValid() ) {

<<

.AsFastaString());

(22,

<<*rit);

( !prefix.empty() ) {

(23,

<<prefix);

prefixes.push_back(prefix);

<

Call>

retry_count)

( retry_count == 0 ) {

(

= 1;

< retry_count; ++

) {

(

<<

<<name<<

<<

<<

<<exc);

( exception& exc ) {

(

<<

<<name<<

<<

<<

<<exc.

());

(

<<

<<name<<

<<

<<

);

(

<<

<<wait_sec<<

);

& prefix)

ref(info_slot), cref(prefix)),

& prefix)

(

&& m_IndexUpdateDeadline->IsExpired() ) {

info_slot = it->second;

(11,

<<prefix<<

);

& prefix)

<<prefix);

<<gi<<

<<gi);

<<gi<<

<<

->GetWGSPrefix());

(

->FindGi(ret, gi) ) {

( !prefixes.empty() ) {

<<acc<<

<<acc);

<<acc<<

<<

->GetWGSPrefix());

(

->FindProtAcc(ret, text_id) ) {

( !prefixes.empty() ) {

prefix = acc.substr(0, prefix_len);

( acc[row_pos] ==

|| acc[row_pos] ==

) {

( acc.size() <= row_pos ) {

ret.

= NStr::StringToNumeric<Uint8>(acc.substr(row_pos),

row_digits = acc.size() - row_pos;

(

->m_WGSDb->GetIdRowDigits() == row_digits ) {

& db = dbtag.

();

( db.size() != 8

&&

is_tsa =

;

wgs_acc = db.substr(4);

(

(wgs_acc.back()&0xff) ) {

( wgs_db->IsTSA() != is_tsa ) {

( object_id.

() ) {

( idh.

() ) {

* text_id =

->GetTextseq_Id();

(IsContig() && row_id != 0);

(IsScaffold() && row_id != 0);

(IsProtein() && row_id != 0);

data_source, cref(blob_id)),

data_source, cref(idh), choice),

+idh.

(),

GetFileInfo(blob_id)->LoadBlob(blob_id, load_lock);

cref(blob_id), ref(chunk_info)),

GetFileInfo(blob_id)->LoadChunk(blob_id, chunk_info);

cref(idh), ref(ids)),

(

.seq_type ) {

.GetScaffoldIterator().GetIds(ids2);

.GetProteinIterator().GetIds(ids2);

.GetContigIterator().GetIds(ids2);

(

.seq_type ) {

acc_id = it.GetAccSeq_id();

acc_id = it.GetAccSeq_id();

acc_id = it.GetAccSeq_id();

(

.IsContig() ) {

ret.

= it.GetGi();

(

.IsProtein() ) {

ret.

= it.GetGi();

& vdb =

.file->GetDb();

( vdb->HasCommonTaxId() ) {

vdb->GetCommonTaxId();

(

.IsContig() ) {

.GetContigIterator().GetTaxId();

(

.IsProtein() ) {

(

root =

.GetRootFileInfo() ) {

( root.IsContig() ) {

root.GetContigIterator().GetTaxId();

( root.IsProtein() ) {

root.GetProteinIterator().GetTaxId();

.GetProteinIterator().GetTaxId();

);

(

.seq_type ) {

it.GetSeqLength();

it.GetSeqLength();

it.GetSeqLength();

);

(

.seq_type ) {

( it.HasSeqHash() ) {

ret.

= it.GetSeqHash();

( it.HasSeqHash() ) {

ret.

= it.GetSeqHash();

);

(

.seq_type ) {

ret.

=

.file->GetDb()->GetScaffoldMolType();

ret.

=

.file->GetDb()->GetProteinMolType();

ret.

=

.file->GetDb()->GetContigMolType();

& prefix)

& prefix)

<<prefix<<

<<exc);

<<prefix<<

<<exc);

<<prefix);

& prefix)

mgr =

.m_Mgr;

<<prefix<<

<<

(

.GetAddWGSMasterDescr() ) {

( !real_seq_id ) {

!real_text_id->IsSetVersion() ) {

real_text_id->GetVersion() == asked_text_id.

();

( !iter.

() ) {

project_state =

->GetDb()->GetProjectGBState();

(project_state) {

( row_id == 0 ) {

( IsScaffold() ) {

( IsProtein() ) {

( IsMigrated(iter) ) {

( !iter.HasAccVersion(

) ) {

iter.SelectAccVersion(

);

= iter.GetLatestAccVersion();

( row_id == 0 ) {

( IsScaffold() ) {

( IsProtein() ) {

( IsMigrated(iter) ) {

(11,

<<gi<<

);

iter.GetGi() == gi;

( iter.GetGi() == gi ) {

= iter.GetLatestAccVersion();

( !

.ValidateGi(gi) ) {

.row_id = row_id;

.seq_type =

;

( !

.ValidateAcc(text_id) ) {

( gb_state ) {

entry = it.GetSeq_entry();

entry = it.GetSeq_entry();

CWGSSeqIterator::TFlags

= it.fDefaultFlags;

&= ~it.fSplitQualityGraph;

&= ~it.fSplitSeqData;

&= ~it.fSplitFeatures;

( !

.first ) {

entry = it.GetSeq_entry(

);

( !entry && !

.first ) {

(

.first ) {

<<

.second<<

(

.first ) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

std::invoke_result< Call >::type CallWithRetry(Call &&call, const char *name, int retry_count=0)

bool IsSetDescr(void) const

const TDescr & GetDescr(void) const

Blob state exceptions, used by GenBank loader.

CTSE_LoadLock GetTSE_LoadLock(const TBlobId &blob_id)

virtual void DoJob(void)

Payload function.

CIndexUpdateThread(unsigned update_delay, CRef< CWGSResolver > resolver)

CRef< CWGSResolver > m_Resolver

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

static void Attach(CTSE_Info &tse, const CID2S_Split_Info &split)

static void Load(CTSE_Chunk_Info &chunk, const CID2S_Chunk &data)

@ eProtectedDb

DB is protected.

@ eNotFoundDb

DB main file not found.

void SetParam(const string &param)

const string & GetParam(void) const

virtual TErrCode GetErrCode(void) const

void SetLoaded(CObject *obj=0)

TChunkId GetChunkId(void) const

const CTSE_Split_Info & GetSplitInfo(void) const

TBlobState GetBlobState(void) const

void SetBlobState(TBlobState state)

CTSE_Split_Info & GetSplitInfo(void)

void SetSeq_entry(CSeq_entry &entry, CTSE_SetObjectInfo *set_info=0)

bool IsLoaded(void) const

void SetSplitVersion(TSplitVersion version)

TSplitVersion GetSplitVersion(void) const

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

Adaptation of CThread class repeatedly running some job.

void RequestStop()

Schedule thread Stop.

TSlotMutex & GetSlotMutex()

void UpdateExpiration(const CVDBCacheWithExpiration &cache, const string &acc_or_path)

void SetObject(CObject *object)

bool IsExpired(const CVDBCacheWithExpiration &cache, const string &acc_or_path) const

CRef< Object > GetObject() const

CRef< CSlot > GetSlot(const string &acc_or_path)

CWGSBlobId(const string &str)

string ToString(void) const

Get string representation of blob id.

bool operator<(const CBlobId &id) const

void FromString(CTempString str)

bool operator==(const CBlobId &id) const

CWGSResolver & GetResolver(void)

CWGSDataLoader_Impl(const CWGSDataLoader::SLoaderParams &params)

CDataLoader::TTSE_LockSet GetRecordsOnce(CDataSource *data_source, const CSeq_id_Handle &idh, CDataLoader::EChoice choice)

CDataLoader::SHashFound GetSequenceHash(const CSeq_id_Handle &idh)

CDataLoader::TTSE_LockSet GetRecords(CDataSource *data_source, const CSeq_id_Handle &idh, CDataLoader::EChoice choice)

TTaxId GetTaxIdOnce(const CSeq_id_Handle &idh)

vector< CSeq_id_Handle > TIds

TTaxId GetTaxId(const CSeq_id_Handle &idh)

CDataLoader::STypeFound GetSequenceTypeOnce(const CSeq_id_Handle &idh)

unsigned m_IndexUpdateDelay

CRef< CThreadNonStop > m_IndexUpdateThread

CRef< CWGSFileInfo > OpenWGSFile(SWGSFileInfoSlot &slot, const string &prefix)

CRef< CWGSFileInfo > GetWGSFile(const string &acc)

CDataLoader::SAccVerFound GetAccVerOnce(const CSeq_id_Handle &idh)

CRef< CWGSBlobId > GetBlobIdOnce(const CSeq_id_Handle &idh)

SAccFileInfo GetFileInfoByProtAcc(const CTextseq_id &text_id)

friend class CWGSFileInfo

std::invoke_result< Call >::type CallWithRetry(Call &&call, const char *name, unsigned retry_count=0)

SAccFileInfo GetFileInfoByAcc(const CTextseq_id &text_id)

CDataLoader::STypeFound GetSequenceType(const CSeq_id_Handle &idh)

CDataLoader::SGiFound GetGi(const CSeq_id_Handle &idh)

void GetChunkOnce(const CWGSBlobId &blob_id, CTSE_Chunk_Info &chunk)

CDataLoader::SHashFound GetSequenceHashOnce(const CSeq_id_Handle &idh)

CDataLoader::SGiFound GetGiOnce(const CSeq_id_Handle &idh)

CRef< CWGSFileInfo > x_GetFileInfo(SWGSFileInfoSlot &info_slot, const string &prefix)

CRef< CWGSFileInfo > OpenWGSFileOnce(SWGSFileInfoSlot &slot, const string &prefix)

SAccFileInfo GetFileInfoByGi(TGi gi)

CTSE_LoadLock GetBlobById(CDataSource *data_source, const CWGSBlobId &blob_id)

CRef< CWGSBlobId > GetBlobId(const CSeq_id_Handle &idh)

void GetChunk(const CWGSBlobId &blob_id, CTSE_Chunk_Info &chunk)

atomic< bool > m_ResolverCreated

CDataLoader::SAccVerFound GetAccVer(const CSeq_id_Handle &idh)

TSeqPos GetSequenceLengthOnce(const CSeq_id_Handle &idh)

CTSE_LoadLock GetBlobByIdOnce(CDataSource *data_source, const CWGSBlobId &blob_id)

void GetIds(const CSeq_id_Handle &idh, TIds &ids)

CWGSFileInfo::SAccFileInfo SAccFileInfo

CFastMutex m_ResolverMutex

CRef< CWGSResolver > m_Resolver

SAccFileInfo GetFileInfoByGeneral(const CDbtag &dbtag)

TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

CRef< CWGSFileInfo > GetFileInfo(const CWGSBlobId &blob_id)

~CWGSDataLoader_Impl(void)

void LoadBlob(const CWGSBlobId &blob_id, CTSE_LoadLock &load_lock)

void GetIdsOnce(const CSeq_id_Handle &idh, TIds &ids)

static string NormalizePathOrAccession(CTempString path_or_acc, CTempString vol_path=CTempString())

const string & GetWGSPath(void) const

TVDBRowId GetContigNameRowId(const string &name) const

void SetMasterDescr(const TMasterDescr &descr, EDescrFilter filter=eDescrDefaultFilter) const

TVDBRowId GetProteinNameRowId(const string &name) const

TVDBRowId GetProtAccRowId(const string &acc, int version=-1) const

bool LoadMasterDescr(EDescrFilter filter=eDescrDefaultFilter) const

TVDBRowId GetScaffoldNameRowId(const string &name) const

TVDBRowId GetLocRowId(void) const

NCBI_WGS_seqtype GetLocSeqType(void) const

bool FindProtAcc(SAccFileInfo &info, const CTextseq_id &text_id)

void x_Initialize(const CWGSDataLoader_Impl &impl, const string &prefix)

void Open(const CWGSDataLoader_Impl &impl, const string &prefix)

CWGSFileInfo(const CWGSDataLoader_Impl &impl, const string &prefix)

CWGSProteinIterator GetProteinIterator(const CWGSBlobId &blob_id) const

CWGSSeqIterator GetContigIterator(const CWGSBlobId &blob_id) const

bool FindGi(SAccFileInfo &info, TGi gi)

void LoadChunk(const CWGSBlobId &blob_id, CTSE_Chunk_Info &chunk) const

void LoadBlob(const CWGSBlobId &blob_id, CTSE_LoadLock &load_lock) const

CWGSScaffoldIterator GetScaffoldIterator(const CWGSBlobId &blob_id) const

const string & GetWGSPrefix(void) const

const CWGSDb & GetDb(void) const

void x_InitMasterDescr(void)

ESeqType GetSeqType(void) const

TVDBRowId GetRowId(void) const

NCBI_gb_state GetGBState(void) const

TVDBRowId GetBestProductFeatRowId(void) const

CWGSResolver_DL(CDataLoader *loader)

CRef< CDataLoader > m_Loader

static CRef< CWGSResolver > CreateResolver(void)

static CRef< CWGSResolver > CreateResolver(CDataLoader *loader)

virtual TWGSPrefixes GetPrefixes(const CSeq_id &id)

string ParseWGSPrefix(const CDbtag &dbtag) const

virtual TWGSPrefixes GetPrefixes(TGi gi)=0

virtual void SetNonWGS(TGi gi, const TWGSPrefixes &prefixes)

static bool s_DebugEnabled(EDebugLevel level)

vector< string > TWGSPrefixes

virtual bool Update(void)

static CRef< CWGSResolver > CreateResolver(const CVDBMgr &mgr)

virtual void SetWGSPrefix(TGi gi, const TWGSPrefixes &prefixes, const string &prefix)

CRef< CID2S_Chunk > GetChunkForVersion(TChunkId chunk_id, TSplitVersion split_version) const

void SelectAccVersion(int version)

container_type::iterator iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

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

std::ofstream out("events_result.xml")

main entry point for tests

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

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.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define LOG_POST_X(err_subcode, message)

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_RETHROW_FMT(prev_exception, exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

#define NCBI_THROW_FMT(exception_class, err_code, message)

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

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

#define MSerial_AsnText

I/O stream manipulators –.

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

CConstRef< CSeq_id > GetSeqId(void) const

EAccessionInfo

For IdentifyAccession (below)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

string AsString(void) const

CSeq_id::E_Choice Which(void) const

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

vector< CSeq_id_Handle > TIds

CDataLoader * FindDataLoader(const string &loader_name) const

Try to find a registered data loader by name.

virtual void GetIds(const CSeq_id_Handle &idh, TIds &ids)

Request for a list of all Seq-ids of a sequence.

EChoice

main blob is blob with sequence all other blobs are external and contain external annotations

TTSE_LockSet GetRecordsNoBlobState(const CSeq_id_Handle &idh, EChoice choice)

The same as GetRecords() but always returns empty TSE lock set instead of throwing CBlobStateExceptio...

@ eExtFeatures

external features

@ eExtAnnot

all external annotations

@ eExtAlign

external aligns

@ eOrphanAnnot

all external annotations if no Bioseq exists

@ eBioseqCore

main blob with bioseq core (no seqdata and annots)

@ eExtGraph

external graph annotations

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Swap(TThisType &ref)

Swaps the pointer with another reference.

#define NCBI_PARAM_TYPE(section, name)

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

@ eParam_NoThread

Do not use per-thread values.

unsigned char Uchar

Alias for unsigned char.

uint32_t Uint4

4-byte (32-bit) unsigned 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.

NCBI_NS_STD::string::size_type SIZE_TYPE

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

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.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ eNocase

Case insensitive compare.

bool Run(TRunMode flags=fRunDefault)

Run the thread.

CMutexGuard TWriteLockGuard

Define Write Lock Guard.

void Join(void **exit_data=0)

Wait for the thread termination.

bool IsStr(void) const

Check if variant Str is selected.

const TTag & GetTag(void) const

Get the Tag member data.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

TId GetId(void) const

Get the variant data.

bool IsSetAccession(void) const

Check if a value has been assigned to Accession data member.

TVersion GetVersion(void) const

Get the Version member data.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsSetVersion(void) const

Check if a value has been assigned to Version data member.

const TAccession & GetAccession(void) const

Get the Accession member data.

@ e_Gibbmt

Geninfo backbone moltype.

@ e_Giim

Geninfo import id.

@ e_Gibbsq

Geninfo backbone seqid.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_not_set

No variant selected.

const Tdata & Get(void) const

Get the member data.

list< CRef< CSeq_id > > TId

User-defined methods of the data storage class.

Definition of all error codes used in SRA C++ support libraries.

const string version

version string

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

string s_Value(TValue value)

const GenericPointer< typename T::ValueType > T2 value

void SleepMilliSec(unsigned long ml_sec, EInterruptOnSignal onsignal=eRestartOnSignal)

void split(std::vector< std::string > *strVec, const std::string &str_, const std::string &split_)

Helper classes and templates to implement plugins.

#define row(bind, expected)

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,...

vector< string > m_WGSFiles

CWGSProteinIterator GetProteinIterator(void) const

CWGSSeqIterator GetContigIterator(void) const

bool ValidateAcc(const CTextseq_id &text_id)

bool IsMigrated(const CWGSProteinIterator &iter) const

SAccFileInfo GetRootFileInfo(void) const

CRef< CWGSFileInfo > file

CWGSScaffoldIterator GetScaffoldIterator(void) const

void sx_Update(CWGSResolver &resolver)

static bool s_ValidateAcc(const CConstRef< CSeq_id > &real_seq_id, const CTextseq_id &asked_text_id)

static bool GetSplitFeaturesParam(void)

static bool GetSplitQualityGraphParam(void)

static string GetWGSVolPath(void)

static unsigned GetRetryCountParam(void)

static bool GetResolveGIsParam(void)

static bool GetKeepMigratedParam(void)

static CBioseq_Handle::TBioseqStateFlags s_GBStateToOM(NCBI_gb_state gb_state)

static bool GetKeepReplacedParam(void)

static int GetDebugLevel(void)

static unsigned GetFileRecheckTimeParam(void)

static const size_t kMaxWGSPrefixLetters

static bool GetResolveProtAccsParam(void)

static bool GetMasterDescrParam(void)

static unsigned GetIndexUpdateTimeParam(void)

NCBI_PARAM_DEF_EX(int, WGS_LOADER, DEBUG, 0, eParam_NoThread, WGS_LOADER_DEBUG)

static const size_t kMinWGSPrefixLetters

static unsigned GetFileReopenTimeParam(void)

static const size_t kWGSPrefixDigits

static size_t GetGCSizeParam(void)

NCBI_DEFINE_ERR_SUBCODE_X(23)

NCBI_PARAM_DECL(int, WGS_LOADER, DEBUG)

NCBI_PARAM_DEF(bool, WGS_LOADER, MASTER_DESCR, true)

static bool GetSplitSequenceParam(void)

static const size_t kMaxWGSProteinAccLen

@ NCBI_gb_state_eWGSGenBankReplaced

@ NCBI_gb_state_eWGSGenBankSuppressed

@ NCBI_gb_state_eWGSGenBankMigrated

@ NCBI_gb_state_eWGSGenBankWithdrawn

@ NCBI_WGS_seqtype_scaffold

@ NCBI_WGS_seqtype_contig

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