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NCBI C++ ToolKit: src/gui/objutils/macro_engine_parallel.cpp Source File

(

<< identifier);

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);

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);

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);

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(

<< res);

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sRTVarRoot, sRTVarFields;

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message +=

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(

std::exception& e) {

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name = iter.first;

do_funcs.push_back(name);

where_funcs.push_back(name);

do_funcs.push_back(name);

where_funcs.push_back(name);

(!line_reader->

()) {

vector<CRef<CMacroRep>> parsed_vec;

(parser.

(

)) {

parsed_vec.push_back(mr);

lib.reserve(lib.size() + parsed_vec.size());

lib.insert(lib.end(), parsed_vec.begin(), parsed_vec.end());

(!line_reader->

()) {

macro_list.resize(0);

(parser.

(

)) {

macro_list.push_back(mr);

macro_list.resize(0);

(macro_text.empty()) {

= (ex.GetMsg().empty()) ? ex.what() : ex.GetMsg();

exec_info.

=

;

(throw_on_error) {

=

;

=

;

evaluateDo =

;

(!data_iter->IsEnd()) {

,

->GetQueryTree());

data_iter->BuildEditedObject();

(data_iter->IntendToDelete()) {

data_iter->RunDeleteCommand(CmdComposite);

(data_iter->IsModified()) {

data_iter->RunEditCommand(CmdComposite);

nr_nonmatched = 0;

= data_iter->GetUnMatchedTableEntries(nr_nonmatched);

oss <<

<< exec_info.

<<

<< exec_info.

;

exec_info.

=

;

(throw_on_error) {

=

;

=

;

resolver(macro_rep, data_iter, CmdComposite, func_context, *stat);

evaluateDo =

;

(!data_iter->IsEnd()) {

,

->GetQueryTree());

data_iter->BuildEditedObject();

(data_iter->IntendToDelete()) {

data_iter->RunDeleteCommand(CmdComposite);

(data_iter->IsModified()) {

data_iter->RunEditCommand(CmdComposite);

oss <<

<< exec_info.

<<

<< exec_info.

;

(thread_count == 1) {

is_data_bioseq =

.GetTSE().IsSeq();

(!is_data_bioseq) {

exec_info.

=

;

(!is_feat_selector) {

exec_info.

=

;

((total_range.

() == total_range.

()) && (total_range.

() == 0)) {

vector<future<stringstream>> futures(thread_count);

vector<thread> threads(thread_count);

vector<CRef<CMacroStat>>

;

.reserve(thread_count);

(

= 0;

< thread_count; ++

) {

vector<CRef<CMacroRep>> reps_for_threads;

reps_for_threads.reserve(thread_count);

(

= 0;

< thread_count; ++

) {

(

= 0;

< thread_count; ++

) {

(start == total_range.

()) {

(

<<

<<

<<

<< start <<

<< stop <<

);

(

<<

<<

<<

<< start <<

<< stop <<

);

futures[

] = task.get_future();

threads[

] = thread(move(task), cref(reps_for_threads[

].GetObject()), cref(

), feat_int,

ref(CmdComposite), ref(

[

]), throw_on_error);

stringstream result_stream;

(

&& it : futures) {

result_stream << it.get().str();

*ostream << result_stream.str();

(

&& stat_it :

) {

report = stat_it->GetMacroReport();

(!report.GetLog().empty()) {

(

<< report.GetName() <<

<< report.GetLog());

thread_count = 0;

((total_range.

() == total_range.

()) && (total_range.

() == 0)) {

(

<<

);

(feat_nrs < 100'000) {

(feat_nrs <= 5'000'000) {

(

<<

<< feat_nrs);

(

<<

<< thread_count);

(

<<

<< thread_count);

thread_count;

Subclass of the IQueryParseUserObject which is held as the user-defined object in each CQueryParseNod...

The following asn-selectors are defined to be used in the FOR EACH statement:

class CMacroExecException

class CMacroExecException

Subclass of CQueryExec that adds: 1) Macro identifiers resolution 2) Where clause evaluation.

Class provides macro language interface for bulk bio-editing.

Class for parsed macro representation.

CMacroResolver Variable and function resolver Provides interfaces for:

CMacroStat - collecting statistics about a single macro.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

Query tree and associated utility methods.

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

definition of a Culling tree

Base class for any user function that performs editing operations on ASN.1 data.

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

static const int chunk_size

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define DIAG_COMPILE_INFO

Make compile time diagnostic information object to use in CNcbiDiag and CException.

#define ERR_POST(message)

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

#define LOG_POST(message)

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

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

static const char * sm_BsrcForSeq

static CTempString GetFuncName()

static const char * sm_Stop

vector< CRef< CMacroRep > > TMacroLibrary

void GetFunctionNames(CMacroParser::TFunctionNamesList &where_funcs, CMacroParser::TFunctionNamesList &do_funcs) const

static const char * sm_Automatic

static CTempString GetFuncName()

static const char * sm_Contain

static CTempString GetFuncName()

static CTempString GetFuncName()

CRef< CMacroCmdComposite > m_CmdComposite

SMacroInfo m_ParsingInfo

Status, error message related to parsing a macro.

virtual void ResetTmpRTVarObjects()

static const char * sm_Lower

static CTempString GetFuncName()

static CTempString GetFuncName()

bool Parse(bool bSingleMacroMode=true, CQueryExec *exec=NULL)

Parse the macro and build its representation Function throws CMacroException if parsing is unsuccessf...

static const char * sm_BsrcForSeqdesc

static const char * sm_PubIssue

static const char * sm_SeqNa

class CMacroFunction_LocationSeqType IS_SEQ_AA(["location"]) - returns true if the sequence identifie...

static CTempString GetFuncName()

EScopeEnum GetFuncScope()

bool GetNodeValue(const string &name, IQueryMacroUserObject &v) const

Function fills in IQueryMacroUserObject-derived node out of stored variable.

void AddToReport(const string &report)

function gradually builds the log report

void x_SetFunctions(CMacroParser &parser)

Initialize do/where lists of functions in parser.

void x_InitSetOfBuiltInFunctions()

void GatherUnMatchedTableEntries(const string &report, const int count)

Used when applying a table to the entry: it stores the values and number of table entries that were n...

static CTempString GetFuncName()

static stringstream s_ExecuteInParallel(const CMacroRep &macro_rep, const CMacroBioData &data, const SFeatInterval &feat_interval, CRef< CMacroCmdComposite > CmdComposite, CRef< CMacroStat > &stat, bool throw_on_error)

static const char * sm_SeqForFeat

static CTempString GetFuncName()

void ThrowCMacroExecException(const CDiagCompileInfo &info, CMacroExecException::EErrCode code, const string &message, const CQueryParseTree::TNode *treeNode, const CException *previous=nullptr)

Throws CMacroExecException with the specified message and error location from the TNode.

void SetSource(const char *sMacroText)

Reset the parser and sets macro text to be parsed.

virtual bool ResolveIdentifier(const string &identifier, CMQueryNodeValue &val, const CQueryParseTree::TNode *parent)

Resolve identifier and store the value in @val.

static CTempString GetFuncName()

virtual ~IMacroFunctionContext()

static CTempString GetFuncName()

void SetError(const string &message, Uint4 line, Uint4 column)

static const char * sm_FunctionName

class CMacroFunction_SetPubField SetPub_Date(year, month, day, season, hour, minute,...

bool m_Status

status of the activity (parsing or execution)

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

const string & GetForEachString() const

Return "for each" string.

static CTempString GetFuncName()

static const char * sm_FunctionName

class CMacroFunction_ApplyPublication SetPub_Sub(author_field_name, author_field_value) Apply new pub...

static CTempString GetFuncName()

static CTempString GetFuncName()

void EvaluateTree(CQueryParseTree &Qtree, IResolver &resolver, bool query_tree, bool case_sensitive=false)

Evaluates tree.

static const char * sm_InList

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_PubJournal

static const char * sm_Equal

static const char * sm_Last

const string & GetErrorReport() const

static const char * sm_SeqForDescr

class CMacroFunction_Sequence_For_Seqdesc SEQUENCE_FOR_SEQDESC(field_name) SEQUENCE_FOR_SEQFEAT(field...

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

CMacroRep * DetachMacroRep()

Detach macro representation for futher processing Caller is responsible for deletion of returned obje...

static const char * sm_PartialStart

class CMacroFunction_LocPartialTest - tests whether the location is 5'/3' partial ISPARTIALSTART() - ...

list< SResolvedField > TObs

static CTempString GetFuncName()

static const char * sm_SeqAa

Uint4 m_Column

location of problem within the macro script

static CTempString GetFuncName()

static const char * sm_PubSerialNumber

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_MolinfoForFeat

bool GetSimpleTypeValue(CObjectInfo &oi, const string &field_name, CMQueryNodeValue &value)

Get single node data from the node specified by parameter of type CObjectInfo and additionally field ...

static const char * sm_UpperAll

static const char * sm_FuncVolume

class CMacroFunction_SetPubVolIssuePages SetPubVolume(newValue, existing_text, delimiter,...

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

const TObs & GetObjects() const

unsigned x_GetThreadCount(const CMacroRep &macro_rep, const CMacroBioData &data)

static const char * sm_PubAuthors

void LogStart(const string &macro_name)

log start of macro execution

CIRef< IMacroBioDataIter > m_DataIter

bool ResolveIdentToObjects(const CObjectInfo &oi, const string &identifier, CMQueryNodeValue &v)

Resolve name to the list of objects.

static CTempString GetFuncName()

static CTempString GetFuncName()

string m_ErrorMessage

error message

static CTempString GetFuncName()

static const char * sm_FromStart

class CMacroFunction_LocationDistConstraint DISTFROMSTART() [>][=][<] distance DISTFROMSTOP()

static const char * sm_PartialStop

static CTempString GetFuncName()

CConstIRef< IMacroFunctionContext > m_FuncContext

unsigned GetColumnNo(void) const

Returns the column number where error occurred.

static CTempString GetFuncName()

static CTempString GetFuncName()

bool ReadAndParseMacros(const string &filename, vector< CRef< CMacroRep >> &macro_list)

Parse a file containing macros and store them in a vector.

bool Exec(const CMacroRep &macro_rep, const CMacroBioData &data, CRef< CMacroCmdComposite > CmdComposite, bool throw_on_error=false, CNcbiOstream *ostream=nullptr)

Execute a macro.

static const char * sm_PunctAll

static const char * sm_Punct

static const char * sm_Upper

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

void LogStop(bool status, const string &err_message)

log end of macro execution this includes time of execution, status, count of changed qualifiers and a...

CQueryParseTree * GetAssignmentWhereClause(int index) const

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_SNP

EType GetDataType() const

static CTempString GetFuncName()

static const char * sm_First

CMacroFunction_FirstItem FIRSTOF(objects) - returns the first item from the list of objects LASTOF(ob...

CQueryParseTree::TFunctionNames TFunctionNamesList

Type for the list of functions in Where/Do clauses.

static const char * sm_FunctionName

void SetFunctionNames(const TFunctionNamesList &wh_funcs, const TFunctionNamesList &do_funcs)

initializes lists of known functions that should be recognized by the parser when going through WHERE...

static CTempString GetFuncName()

static CTempString GetFuncName()

const TSeqRange & GetSeqRange() const

Return sequence range.

static const char * sm_BsrcForFeat

const string & GetNamedAnnot() const

Return "from" named annotation.

static CTempString GetFuncName()

static CTempString GetFuncName()

virtual bool GetTmpRTVarObject(const string &name, CObjectInfo &oi)

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_PubVolume

virtual bool ExistRTVar(const string &name)

Return true if the run-time variable, identified by its name, is defined.

static CTempString GetFuncName()

static CTempString GetFuncName()

virtual CQueryParseTree * GetAssignmentWhereClause(int index) const

Return the "where" sub-query from the DO-DONE section identified by the index in the main parsed tree...

const string & GetName() const

Return macro name.

static CTempString GetFuncName()

virtual CRef< CMQueryNodeValue > GetOrCreateRTVar(const string &name)

Get or create run-time variable.

static CTempString GetFuncName()

CMacroStat m_MacroStat

Most recent executed macro statistics.

bool IsNotSetType() const

Check/get functions result from the top node after calculation.

static CTempString GetFuncName()

CRef< CMQueryNodeValue > x_LocateRTVar(const string &identifier)

Return data associated with the RT variable based on its name.

static CTempString GetFuncName()

static CTempString GetFuncName()

CConstRef< CMacroRep > m_MacroRep

bool ResolveIdentToSimple(const CObjectInfo &oi, const string &identifier, CMQueryNodeValue &v)

Resolve name to simple types value.

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_FuncPages

static CTempString GetFuncName()

static const char * sm_PubStatus

static CTempString GetFuncName()

void SetNestedState(ENestedFunc type)

const string & GetFuncReport() const

Function extracts statistic from the object.

static CTempString GetFuncName()

static CMacroEngineParallel::SMacroInfo s_ExecuteSingleThread(const CMacroRep &macro_rep, const CMacroBioData &data, CRef< CMacroCmdComposite > CmdComposite, CConstIRef< IMacroFunctionContext > context, CMacroStat &stat, bool throw_on_error, CNcbiOstream *ostream)

static CTempString GetFuncName()

static CTempString GetFuncName()

bool x_AppendToLibrary(const string &filename, CMacroLib::TMacroLibrary &lib)

static CTempString GetFuncName()

static const char * sm_PubTitle

class CMacroFunction_PubFields PUB_TITLE(), PUB_ISSUE(), PUB_AFFIL(subfield) - returns a list of CObj...

static const char * sm_PubDOI

static CTempString GetFuncName()

static CTempString GetFuncName()

CIRef< IMacroFunctionContext > m_EngineFuncContext

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_End

TBuiltInFunctionsMap m_BuiltInFunctions

unsigned GetLineNo(void) const

Returns the line number where error occurred.

static CTempString GetFuncName()

static const char * sm_LowerAll

virtual void CallFunction(const string &name, CQueryParseTree::TNode &qnode)

Function call the function specified by name, passing args as parameters and it can update nv as a re...

static const char * sm_PubPMID

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_PubDate

static const char * sm_PubAffil

CMacroRep * Parse(const string &macro_text)

Parse the macro script into its binary representation.

static CTempString GetFuncName()

CQueryParseTree * GetDoTree() const

Return "do" clause.

static CTempString GetFuncName()

static const char * sm_BsrcForMolinfo

class CMacroFunction_GetSeqdesc BIOSOURCE_FOR_MOLINFO(field_name) or BIOSOURCE_FOR_MOLINFO(container,...

static const char * sm_PubCit

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_FromStop

static CTempString GetFuncName()

void Reset()

reset the macro name, qualifier and iteration counts

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_Start

static const char * sm_FunctionName

EditRelatedFeatureQual(feat_type, field_name, find_text, repl_text, location, case_sensitive,...

TTempRTVarsMap m_TempRTVars

bool GetBoolValue() const

static CTempString GetFuncName()

static const char * sm_PubPages

static CTempString GetFuncName()

IEditMacroFunction * ResolveFunctionName(const string &name) const

Return pointer to macro function identified by its name.

bool AppendToLibrary(const string &filename, CMacroLib::TMacroLibrary &lib)

Parse a file containing macros and append the results to the map that stores these macros.

static CTempString GetFuncName()

static CTempString GetFuncName()

CQueryParseTree * GetWhereClause() const

Return "where" clause.

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_FuncIssue

static CTempString GetFuncName()

void AddToErrorReport(const string &error)

store encountered errors

static CTempString GetFuncName()

static const char * sm_PubClass

const string & GetSource() const

bool x_ResolveRTVar(const string &identifier, CMQueryNodeValue &val, const CQueryParseTree::TNode *parent)

Return the value of Run-Time (RT) variable.

virtual void AddTmpRTVarObject(const string &name, CObjectInfo &oi)

used together with the Assignment Operator (CMQueryFunctionAssignment)

static const char * sm_Start

class CMacroFunction_LocEnd Start() and Stop() - return the positional extremes of a location

static CTempString GetFuncName()

void x_InitSetOfBuiltInFunctions()

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

const string & GetThreadCount() const

Return number of threads.

static const char * sm_MolinfoForBsrc

@ eFunctionNotImplemented

static size_t EstimateSNPCount(const TSeqRange &range, const string &sAnnotName, CBioseq_Handle &Handle)

CTempString GetCurrentLine(void) const

static CRef< ILineReader > New(const string &filename)

Return a new ILineReader object corresponding to the given filename, taking "-" (but not "....

virtual bool AtEOF(void) const =0

Indicates (negatively) whether there is any more input.

TSeqPos GetBioseqLength(void) const

TObjectType * GetNCPointerOrNull(void) const THROWS_NONE

Get pointer value.

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

TObjectType & GetNCObject(void) const

Get object.

unsigned pos

Position in the src line.

unsigned line

Src line number.

position_type GetLength(void) const

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

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

Convert string to int.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

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

Case-insensitive equality of a substring with another string.

const TValue & GetValue(void) const

Return node's value.

const TTreeType * GetParent(void) const

Get node's parent.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

@ ePublication_field_affiliation

@ ePublication_field_pages

@ ePublication_field_pmid

@ ePublication_field_pub_class

@ ePublication_field_issue

@ ePublication_field_date

@ ePublication_field_title

@ ePublication_field_serial_number

@ ePublication_field_authors

@ ePublication_field_volume

@ ePublication_field_journal

@ eSeqtype_constraint_prot

@ eSeqtype_constraint_nuc

@ e_Molinfo

info on the molecule and techniques

@ e_Source

source of materials, includes Org-ref

Lightweight interface for getting lines of data with minimal memory copying.

Functions that resolve field names described in asn format.

Interface class for macro function implementation.

Functions used in the DO/DONE section affecting the top seq-entry.

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

Source location (points to the position in the original src) All positions are 0 based.

static CS_CONTEXT * context

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