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NCBI C++ ToolKit: src/app/pubseq_gateway/server/wgs_client.cpp Source File

(

.empty() ||

[0] != c ) {

c ==

|| (c >=

&& c <=

);

<

Int>

=

.substr(int_size);

( !

(s,

) ) {

& db = dbtag.

();

( num_letters = 0; num_letters <

; ++num_letters ) {

( !

(acc[num_letters]&0xff) ) {

(

= num_letters;

< prefix_len; ++

) {

( acc[row_pos] ) {

row_digits = acc.size() - row_pos;

(

= row_pos;

< acc.size(); ++

) {

( c < '0' || c >

) {

& acc =

.GetAccession();

(

.IsSetName() ) {

( !

.IsSetAccession() ) {

& acc =

.GetAccession();

(

);

(

<< exc);

( exception& exc ) {

(

<< exc.

());

m_WGSDbCache(

.m_CacheSize,

.m_FileReopenTime,

.m_FileRecheckTime)

seq_id_type = -1;

( req_type ) {

seq_id = resolve_request.

;

seq_id_type = resolve_request.m_SeqIdType;

seq_id = blob_sid_request.

;

seq_id_type = blob_sid_request.m_SeqIdType;

( !seq_id.empty() ) {

(seq_id_type, seq_id);

shared_ptr<SWGSData> ret;

( !seq )

ret;

shared_ptr<SWGSData> ret;

( !seq )

ret;

( find(excluded.begin(), excluded.end(), ret->m_BlobId) != excluded.end() ) {

shared_ptr<SWGSData> ret;

( !id2_blob_id )

ret;

( !seq )

ret;

shared_ptr<SWGSData> ret;

( !parsed_id2info.

)

ret;

( !seq0 )

ret;

ret = make_shared<SWGSData>();

ret->m_Id2BlobId.Reset(&

(seq0));

ret->m_Id2BlobState = id2_blob_state;

ret = make_shared<SWGSData>();

ret->m_Id2BlobId.Reset(&

(seq0));

ret->m_Id2BlobState = id2_blob_state;

( !ret->m_Data ) {

GetTiming().Register(

,

, status, start, 0);

(

<< prefix <<

);

(

<< prefix <<

<< exc);

(

<< prefix <<

<< exc);

( exception& exc ) {

(

<< prefix <<

<< exc.what());

->m_WGSDb = wgs_db;

slot->SetObject(

);

wgs_db =

->m_WGSDb;

(

<< prefix <<

);

(

<< prefix);

( !it.

() ) {

project_state = seq.

->GetProjectGBState();

(project_state) {

project_state == special_state;

( !it.

() ) {

project_state = seq.

->GetProjectGBState();

(project_state) {

(

.Which() ) {

& db = dbtag.

();

is_tsa =

;

(

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

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

( object_id.

() ) {

gi == wgs_db->GetMasterGi() ) {

( !prefixes.empty() ) {

wgs_resolver->

(gi, prefixes);

(

.IsSetName() ) {

( !

.IsSetAccession() ||

( !

.IsSetAccession() ) {

& acc =

.GetAccession();

& acc =

.GetAccession();

ask_version =

.IsSetVersion()?

.GetVersion(): -1;

(

= wgs_db.GetProtAccRowId(acc, ask_version) ) {

( !prefixes.empty() ) {

wgs_resolver->

(acc, prefixes);

( num_letters = 0; num_letters <

; ++num_letters ) {

( !

(acc[num_letters]&0xff) ) {

(

= num_letters;

< prefix_len; ++

) {

seq.

= acc.substr(0, prefix_len);

( acc[row_pos] ) {

row_digits = acc.size() - row_pos;

(

= row_pos;

< acc.size(); ++

) {

( c < '0' || c >

) {

=

.IsSetVersion()?

.GetVersion(): 1;

( acc[num_letters+

] !=

) {

( seq.

->GetIdRowDigits() != row_digits ) {

subsat = unsigned(

.GetSub_sat());

( seq_type ) {

seq.

+= char(

+subsat%26);

seq.

+= char(

+subsat%10);

(skip_lookup ||

(seq)) {

seq.

=

.GetSat_key();

(

= 0;

< 6; ++

) {

(

= 0;

< 2; ++

) {

(skip_lookup ||

(seq)) {

seq.

=

.GetSat_key();

(

= 0;

< seq.

.size(); ++

) {

->SetSub_sat(subsat);

->SetSat_key(

(seq.

));

(

= 0;

< seq.

.size(); ++

) {

subsat |= (seq.

[

]-

) << bit;

subsat |= (seq.

[

]-

) << bit;

(

= 0;

< seq.

.size(); ++

) {

subsat += (seq.

[

]-

)*mul;

subsat += (seq.

[

]-

)*mul;

->SetSub_sat(

(subsat));

->SetSat_key(

(seq.

));

( gb_state ) {

(seq)->GetMasterSeq_id();

ids.push_back(

);

ids.push_back(gi_id);

(seq_id_type <= 0) {

( !seq )

;

= make_shared<SWGSData>();

->m_BioseqInfo = make_shared<CBioseqInfoRecord>();

list< CRef<CSeq_id> > wgs_ids;

(

&

: wgs_ids ) {

(

text_id = id->GetTextseq_Id() ) {

text_id->IsSetAccession() && text_id->IsSetVersion() ) {

.SetSeqIdType(id->Which());

.SetAccession(text_id->GetAccession());

.SetVersion(text_id->GetVersion());

( text_id->IsSetName() ) {

.SetName(text_id->GetName());

->m_BioseqInfoFlags |=

psg_ids.

(make_tuple(id->Which(), std::move(content)));

.SetAccession(content);

.SetVersion(0);

->m_BioseqInfoFlags |=

psg_ids.

(make_tuple(gi_id.

(), std::move(content)));

.SetSeqIds(std::move(psg_ids));

->m_BioseqInfoFlags |=

->m_BioseqInfoFlags |=

->m_BioseqInfoFlags |=

->m_BioseqInfoFlags |=

->m_BioseqInfoFlags |=

( wgs->HasCommonTaxId() ) {

.SetTaxId(wgs->GetCommonTaxId());

( root_seq.IsContig() ) {

( root_seq.IsProtein() ) {

(

->m_Id2BlobId->IsSetVersion() ) {

.SetDateChanged(

->m_Id2BlobId->GetVersion()*60000);

.SetState(

->GetPSGBioseqState());

= make_shared<SWGSData>();

(

->IsForbidden() )

;

( asn_data.first ) {

->m_SplitVersion = asn_data.second;

( !asn_data.first ) {

( !asn_data.first ) {

->m_Data = asn_data.first;

(

->m_Data ) {

id_str = blob_id.

();

->SetSub_sat(subsat);

->SetSat_key(satkey);

->SetSub_sat(subsat);

->SetSat_key(satkey);

->SetVersion(tse_version);

(

, seq_id_type, seq_id);

(

.IsGeneral() ) {

(

text_id =

.GetTextseq_Id() ) {

( exception&

) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

virtual void DoJob(void)

Payload function.

CIndexUpdateThread(unsigned update_delay, CRef< CWGSResolver > resolver)

CRef< CWGSResolver > m_Resolver

EPSGS_Type GetRequestType(void) const

@ ePSGS_BlobBySatSatKeyRequest

@ ePSGS_BlobBySeqIdRequest

TRequest & GetRequest(void)

static CPubseqGatewayApp * GetInstance(void)

@ eProtectedDb

DB is protected.

@ eNotFoundDb

DB main file not found.

virtual TErrCode GetErrCode(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.

CRef< CSlot > GetSlot(const string &acc_or_path)

static void SetSeqId(CSeq_id &id, int seq_id_type, const string &seq_id)

shared_ptr< SWGSData > GetChunk(const string &id2info, int64_t chunk_id)

bool GetCompress(SWGSProcessor_Config::ECompressData comp, const SWGSSeqInfo &seq, const objects::CAsnBinData &data) const

SWGSSeqInfo ResolveBlobId(const objects::CID2_Blob_Id &id, bool skip_lookup=false)

SWGSSeqInfo ResolveGi(TGi gi, bool skip_lookup=false)

static bool IsOSGBlob(const CID2_Blob_Id &blob_id)

shared_ptr< SWGSData > GetBlobByBlobId(const string &blob_id)

bool IsCorrectVersion(SWGSSeqInfo &seq, int version)

void ResetIteratorCache(SWGSSeqInfo &seq)

void GetWGSData(shared_ptr< SWGSData > &data, SWGSSeqInfo &seq0)

static string GetPSGBlobId(const CID2_Blob_Id &blob_id)

CRef< objects::CSeq_id > GetAccVer(SWGSSeqInfo &seq)

CWGSClient(const SWGSProcessor_Config &config)

CFastMutex m_ResolverMutex

SWGSSeqInfo & GetRootSeq(SWGSSeqInfo &seq0)

static bool CanBeWGS(int seq_id_type, const string &seq_id)

objects::CWGSScaffoldIterator & GetScaffoldIterator(SWGSSeqInfo &seq)

shared_ptr< SWGSData > ResolveSeqId(const objects::CSeq_id &seq_id)

TGi GetGi(SWGSSeqInfo &seq)

shared_ptr< SWGSData > GetSeqInfoBySeqId(const objects::CSeq_id &seq_id, SWGSSeqInfo &seq, const TBlobIds &excluded)

CRef< objects::CWGSResolver > m_Resolver

bool IsValidRowId(SWGSSeqInfo &seq)

CRef< objects::CWGSResolver > GetWGSResolver(void)

SWGSSeqInfo ResolveAcc(const objects::CTextseq_id &id, bool skip_lookup=false)

SWGSSeqInfo Resolve(const objects::CSeq_id &id, bool skip_lookup=false)

bool HasMigrated(SWGSSeqInfo &seq)

objects::CID2_Blob_Id & GetBlobId(SWGSSeqInfo &id)

static SParsedId2Info ParsePSGId2Info(const string &idsss2_info)

objects::CWGSDb GetWGSDb(const string &prefix)

CRef< objects::CSeq_id > GetGeneral(SWGSSeqInfo &seq)

bool CanProcessRequest(CPSGS_Request &request)

int GetID2BlobState(SWGSSeqInfo &seq)

objects::CWGSSeqIterator & GetContigIterator(SWGSSeqInfo &seq)

vector< string > TBlobIds

NCBI_gb_state GetGBState(SWGSSeqInfo &seq0)

void GetBioseqInfo(shared_ptr< SWGSData > &data, SWGSSeqInfo &seq)

objects::CWGSProteinIterator & GetProteinIterator(SWGSSeqInfo &seq)

static CRef< CID2_Blob_Id > ParsePSGBlobId(const SPSGS_BlobId &blob_id)

void x_RegisterTiming(psg_time_point_t start, EPSGOperation operation, EPSGOperationStatus status)

SWGSSeqInfo ResolveWGSAcc(const string &acc, const objects::CTextseq_id &id, TAllowSeqType allow_seq_type, bool skip_lookup=false)

bool HasSpecialState(SWGSSeqInfo &seq, NCBI_gb_state special_state)

SWGSSeqInfo ResolveGeneral(const objects::CDbtag &dbtag, bool skip_lookup=false)

SWGSSeqInfo ResolveProtAcc(const objects::CTextseq_id &id, bool skip_lookup=false)

SWGSProcessor_Config m_Config

void GetSeqIds(SWGSSeqInfo &seq, list< CRef< objects::CSeq_id > > &ids)

CRef< CThreadNonStop > m_IndexUpdateThread

TVDBRowId GetContigNameRowId(const string &name) const

TVDBRowId GetProteinNameRowId(const string &name) const

bool LoadMasterDescr(EDescrFilter filter=eDescrDefaultFilter) const

TVDBRowId GetScaffoldNameRowId(const string &name) const

TVDBRowId GetLocRowId(void) const

NCBI_WGS_seqtype GetLocSeqType(void) const

ESeqType GetSeqType(void) const

TVDBRowId GetRowId(void) const

NCBI_gb_state GetGBState(void) const

bool HasTaxId(void) const

TSeqPos GetSeqLength(void) const

CSeq_id::TGi GetGi(void) const

THash GetSeqHash(void) const

CRef< CSeq_entry > GetSeq_entry(TFlags flags=fDefaultFlags) const

int GetAccVersion(void) const

bool HasSeqHash(void) const

TTaxId GetTaxId(void) const

virtual TWGSPrefixes GetPrefixes(TGi gi)=0

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

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< CSeq_entry > GetSeq_entry(TFlags flags=fDefaultFlags) const

TSeqPos GetSeqLength(void) const

CRef< CAsnBinData > GetSeq_entryData(TFlags flags=fDefaultFlags) const

CRef< CAsnBinData > GetChunkDataForVersion(TChunkId chunk_id, TSplitVersion split_version) const

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

TTaxId GetTaxId(void) const

CSeq_id::TGi GetGi(void) const

THash GetSeqHash(void) const

pair< CRef< CAsnBinData >, TSplitVersion > GetSplitInfoDataAndVersion(TFlags flags=fDefaultFlags) const

bool HasTaxId(void) const

TSeqPos GetSeqLength(EClipType clip_type=eDefaultClip) const

bool HasAccVersion(int version) const

CRef< CSeq_entry > GetSeq_entry(TFlags flags=fDefaultFlags) const

iterator_bool insert(const value_type &val)

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

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...

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

EAccessionInfo

For IdentifyAccession (below)

@ eFasta_AsTypeAndContent

@ eFastaContent

Like eFasta, but without any tag.

void Reset(void)

Reset reference object.

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.

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

uint64_t Uint8

8-byte (64-bit) unsigned integer

NCBI_NS_STD::string::size_type SIZE_TYPE

static TNumeric StringToNumeric(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to a numeric value.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

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.

size_type find(const CTempString match, size_type pos=0) const

Find the first instance of the entire matching string within the current string, beginning at an opti...

static string & ToUpper(string &str)

Convert string to upper case – string& version.

@ fConvErr_NoErrMessage

Set errno, but do not set CNcbiError message on error.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ eNocase

Case insensitive compare.

bool Run(TRunMode flags=fRunDefault)

Run the thread.

CGuard< CRWLock, SSimpleWriteLock< CRWLock > > TWriteLockGuard

void Join(void **exit_data=0)

Wait for the thread termination.

operation

Bit operations.

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.

TSat_key GetSat_key(void) const

Get the Sat_key member data.

TSub_sat GetSub_sat(void) const

Get the Sub_sat member data.

TSat GetSat(void) const

Get the Sat member data.

@ eID2_Blob_State_suppressed

@ eID2_Blob_State_protected

@ eID2_Blob_State_withdrawn

E_Choice Which(void) const

Which variant is currently selected.

TGi & SetGi(void)

Select the variant.

TVersion GetVersion(void) const

Get the Version member data.

E_Choice

Choice variants.

bool IsSetVersion(void) const

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

@ 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.

unsigned int

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

const string version

version string

const GenericPointer< typename T::ValueType > T2 value

const CConstRef< CSeq_id > GetAccession(const CSeq_id_Handle &id_handle)

#define PSG_ERROR(message)

#define PSG_INFO(message)

psg_clock_t::time_point psg_time_point_t

#define row(bind, expected)

TID2SplitVersion split_version

CRef< CID2_Blob_Id > tse_id

AutoPtr< SWGSSeqInfo > m_RootSeq

objects::CWGSProteinIterator m_ProteinIter

bool IsProtein(void) const

bool IsMaster(void) const

objects::CWGSScaffoldIterator m_ScaffoldIter

objects::CWGSSeqIterator m_ContigIter

objects::TVDBRowId m_RowId

CRef< objects::CID2_Blob_Id > m_BlobId

bool IsContig(void) const

bool IsScaffold(void) const

int GetPSGBioseqState() const

unsigned m_IndexUpdateDelay

ECompressData m_CompressData

static EAddMasterDescr s_AddMasterDescrLevel(void)

static bool s_AddMasterDescrScaffold()

static bool s_ParseInt(CTempString &str, Int &v)

static const size_t kNumLettersV1

static bool s_Skip(CTempString &str, char c)

static const size_t kMaxRowDigitsV2

static const int kOSG_Sat_CDD_max

static const EResolveMaster kResolveMaster

static bool s_IsValidIntChar(char c)

static int s_GBStateToID2(NCBI_gb_state gb_state)

static const size_t kMinRowDigitsV2

static bool s_MarkMasterDescr(void)

static bool IsWGSProtAccession(const CTextseq_id &id)

static bool s_IsEnabledOSGSat(CWGSClient::TEnabledFlags enabled_flags, Int4 sat)

static const size_t kNumLettersV2

NCBI_PARAM_DEF_EX(bool, WGS, FILTER_ALL, false, eParam_NoThread, WGS_FILTER_ALL)

NCBI_PARAM_DEF(bool, WGS, SPLIT_FEATURES, true)

static const int kOSG_Sat_WGS_max

static bool s_KeepReplaced(void)

static bool s_ParseOSGBlob(CTempString &s, Int4 &sat, Int4 &subsat, Int4 &satkey)

static const size_t kVersionDigits

static const int kBlobIdV2VersionContig

static const int kBlobIdV2SatMax

static const int kBlobIdV2SatMin

static const size_t kTypePrefixLen

static bool s_AddMasterDescrContig()

static bool s_SplitFeatures(void)

static const size_t kMaxRowDigitsV1

static const size_t kPrefixLenV2

static bool IsWGSGeneral(const CDbtag &dbtag)

static const int kBlobIdV2VersionScaffold

@ eAddMasterDescr_detached

NCBI_PARAM_DECL(bool, WGS, FILTER_ALL)

static EAddMasterDescr s_ProcessAddMasterDescr(void)

static bool s_IsOSGSat(Int4 sat)

static const int kBlobIdV1Sat

static bool s_KeepMigrated(void)

static const size_t kMaxProtAccLen

static const int kBlobIdV2VersionProtein

static const int kOSG_Sat_CDD_min

static const int kOSG_Sat_WGS_min

static bool s_IsOSGBlob(Int4 sat, Int4, Int4)

static const char kSubSatSeparator

static const size_t kMinRowDigitsV1

static bool s_AddMasterDescrProtein()

static const int kOSG_Sat_SNP_min

static const size_t kMinProtAccLen

@ eResolveMaster_without_gi

static const int kOSG_Sat_SNP_max

static bool IsWGSAccession(const string &acc, const CTextseq_id &id, TAllowSeqType allow_seq_type)

static void s_FormatBlobId(ostream &s, const CID2_Blob_Id &blob_id)

static const size_t kPrefixLenV1

@ NCBI_gb_state_eWGSGenBankUnverified

@ NCBI_gb_state_eWGSGenBankReplaced

@ NCBI_gb_state_eWGSGenBankSuppressed

@ NCBI_gb_state_eWGSGenBankMigrated

@ NCBI_gb_state_eWGSGenBankLive

@ NCBI_gb_state_eWGSGenBankWithdrawn

@ NCBI_WGS_seqtype_scaffold

@ NCBI_WGS_seqtype_contig

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