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NCBI C++ ToolKit: src/misc/data_loaders_util/data_loaders_util.cpp Source File

63

arg_desc.SetCurrentGroup(

"Data source and object manager options"

);

66 if

(loaders & fLDS2) {

67

arg_desc.AddOptionalKey(

"lds2"

"LDSDatabases"

68 "Comma-separated list of LDS2 databases to use."

74 if

(loaders & fBLAST) {

75

arg_desc.AddOptionalKey(

"blastdb"

"BlastDatabases"

76 "Comma-separated list of BLAST databases to use. " 77 "Use na: prefix for nucleotide, " 78 "or aa: for protein."

81 if

(!arg_desc.Exist(

"d"

)) arg_desc.AddAlias(

"d"

"blastdb"

);

85 if

(loaders & fAsnCache) {

86

arg_desc.AddOptionalKey(

"asn-cache"

"AsnCache"

87 "Comma-separated list of ASN Cache databases to use."

95 if

(((loaders & fGenbank) && (loaders & fGenbankOffByDefault)) ||

98 if

(!arg_desc.Exist(

"r"

)) {

99

arg_desc.AddFlag(

"r"

100 "Enable remote data retrieval"

);

104 if

(loaders & fGenbank) {

105 if

(loaders & fGenbankOffByDefault) {

106 if

( !arg_desc.Exist(

"genbank"

)) {

107

arg_desc.AddFlag(

"genbank"

108 "Enable remote data retrieval using the Genbank data loader"

);

112 if

(!arg_desc.Exist(

"nogenbank"

)) {

113

arg_desc.AddFlag(

"nogenbank"

114 "Do not use GenBank data loader."

);

117

arg_desc.AddOptionalKey(

"gb-method"

"GBMethod"

118 "Semicolon-separated list of Genbank loader method(s)"

121

arg_desc.AddOptionalKey(

"gb-snp"

"enable"

122 "Genbank SNP processor"

124

arg_desc.AddOptionalKey(

"gb-wgs"

"enable"

125 "Genbank WGS processor"

127

arg_desc.AddOptionalKey(

"gb-cdd"

"enable"

128 "Genbank SNP processor"

131 string

dep_arg = loaders & fGenbankOffByDefault ?

"genbank"

"nogenbank"

;

132

arg_desc.SetDependency(

"gb-method"

, dep_type, dep_arg);

133

arg_desc.SetDependency(

"gb-snp"

, dep_type, dep_arg);

134

arg_desc.SetDependency(

"gb-wgs"

, dep_type, dep_arg);

135

arg_desc.SetDependency(

"gb-cdd"

, dep_type, dep_arg);

139 if

(loaders & fVDB) {

140 if

(loaders & fVDBOnByDefault) {

141

arg_desc.AddFlag(

"vdb"

"Use VDB data loader."

146

arg_desc.AddFlag(

"vdb"

"Use VDB data loader."

);

148

arg_desc.AddFlag(

"novdb"

"Do not use VDB data loader."

);

149

arg_desc.SetDependency(

"vdb"

152

arg_desc.AddOptionalKey(

"vdb-path"

"Path"

153 "Root path for VDB look-up"

158 if

(loaders & fSRA) {

159

arg_desc.AddFlag(

"sra"

"Add the SRA data loader with no options."

);

161

arg_desc.AddOptionalKey(

"sra-acc"

"AddSra"

"Add the SRA data loader, specifying an accession."

164

arg_desc.AddOptionalKey(

"sra-file"

"AddSra"

"Add the SRA data loader, specifying an sra file."

173 if

(loaders & fVDB) {

174

arg_desc.AddFlag(

"novdb"

"Do not use VDB data loader."

);

182

arg_desc.SetCurrentGroup(

"General application arguments"

);

191 bool

nogenbank = args.

Exist

(

"nogenbank"

) && args[

"nogenbank"

];

193 if

((args.

Exist

(

"genbank"

) && args[

"genbank"

]) ||

194

(args.

Exist

(

"r"

) && args[

"r"

])) {

205 if

(args.

Exist

(

"gb-method"

) && args[

"gb-method"

]) {

206

methods = args[

"gb-method"

].GetStringList();

210 if

(!gb_methods.empty()) gb_methods +=

";"

;

213 if

(!gb_methods.empty()) {

217 if

(args.

Exist

(

"gb-snp"

) && args[

"gb-snp"

]) {

220 if

(args.

Exist

(

"gb-wgs"

) && args[

"gb-wgs"

]) {

223 if

(args.

Exist

(

"gb-cdd"

) && args[

"gb-cdd"

]) {

230 #ifdef HAVE_PUBSEQ_OS 240

priority =

max

(priority, 16000);

247

" ("

<< priority <<

")"

);

261

(args.

Exist

(

"vdb"

) && args[

"vdb"

]);

262 if

( !use_vdb_loader ) {

263 string

vdbEnabled = reg.

Get

(

"Gpipe"

"enable_vdb"

);

264 if

(vdbEnabled ==

"Y"

) {

265

use_vdb_loader =

true

;

269 if

(!use_vdb_loader) {

270 if

(args.

Exist

(

"r"

) && args[

"r"

]) {

271

use_vdb_loader =

true

;

275 if

(args.

Exist

(

"novdb"

) && args[

"novdb"

]) {

276

use_vdb_loader =

false

;

279 if

(use_vdb_loader) {

280 string

vdbpath = reg.

Get

(

"Gpipe"

"VDB_PATH"

);

281 if

(args.

Exist

(

"vdb-path"

) && args[

"vdb-path"

]) {

282

vdbpath = args[

"vdb-path"

].AsString();

284 if

(vdbpath.empty()){

303 if

((args.

Exist

(

"sra"

) && args[

"sra"

]) || (args.

Exist

(

"r"

) && args[

"r"

])) {

308 else if

(args.

Exist

(

"sra-acc"

) && args[

"sra-acc"

]) {

310

args[

"sra-acc"

].AsString(),

314 else if

(args.

Exist

(

"sra-file"

) && args[

"sra-file"

]) {

315 CDirEntry

file_entry(args[

"sra-file"

].AsString());

330 typedef

vector<string> TDbs;

333 if

(args.

Exist

(

"blastdb"

) && args[

"blastdb"

]) {

334

blastdbstr = args[

"blastdb"

].GetStringList();

361

" ("

<< priority <<

")"

);

371 typedef

vector<string> TDbs;

374 if

(args.

Exist

(

"lds2"

) && args[

"lds2"

]) {

375

lds2dbstr = args[

"lds2"

].GetStringList();

388 if

( !

CFile

(db).Exists() ) {

393 string

alias(

"lds2_"

);

401

" ("

<< priority <<

")"

);

411 typedef

vector<string> TDbs;

415 string

cachePaths = reg.

Get

(

"ASN_CACHE"

"ASN_CACHE_PATH"

);

416 if

(cachePaths.size() > 0) {

417

asn_cache_str.push_back(cachePaths);

418 LOG_POST

(

Info

"From config: ASNCache:ASN_CACHE_PATH "

<< cachePaths);

421 if

(args.

Exist

(

"asn-cache"

) && args[

"asn-cache"

]) {

422

asn_cache_str = args[

"asn-cache"

].GetStringList();

432 if

(

CDir

(db).Exists()) {

439

" ("

<< priority <<

")"

);

483 if

(loaders &

fLDS2

) {

511 if

(loaders &

fSRA

) {

542

scope->AddDefaults();

Data loader implementation that uses the blast databases.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const string &db_path, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const string &dbname="nr", const EDbType dbtype=eUnknown, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

EDbType

Describes the type of blast database to use.

@ eNucleotide

nucleotide database

@ eProtein

protein database

@ eUnknown

protein is attempted first, then nucleotide

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const SLoaderParams &params, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

static void x_SetupLDS2DataLoader(const CArgs &args, objects::CObjectManager &obj_mgr, int &priority)

static void SetupObjectManager(const CArgs &args, objects::CObjectManager &obj_mgr, TLoaders loaders=fDefault)

Set up the standard object manager data loaders according to the arguments provided above.

static void x_SetupSRADataLoader(const CArgs &args, objects::CObjectManager &obj_mgr, int &priority)

static void x_SetupVDBDataLoader(const CArgs &args, objects::CObjectManager &obj_mgr, int &priority, TLoaders loaders)

static CRef< objects::CScope > GetDefaultScope(const CArgs &args)

static void x_SetupBlastDataLoader(const CArgs &args, objects::CObjectManager &obj_mgr, int &priority)

static void x_SetupGenbankDataLoader(const CArgs &args, objects::CObjectManager &obj_mgr, int &priority, TLoaders loaders)

static void x_SetupASNCacheDataLoader(const CArgs &args, objects::CObjectManager &obj_mgr, int &priority)

static void SetupGenbankDataLoader(const CArgs &args, objects::CObjectManager &obj_mgr)

Set up just the GenBank data loader.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

void SetEnableSNP(bool enable)

void SetLoaderMethod(const string &loader_method)

void SetEnableWGS(bool enable)

void SetEnableCDD(bool enable)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

Argument-less loader - for compatibility only, unusable.

static CNcbiApplication * Instance(void)

Singleton method.

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

bool Exist(const string &name) const

Check existence of argument description.

EDependency

Dependencies between arguments.

vector< string > TStringArray

Some values types can contain several value lists.

@ fAllowMultiple

Repeated key arguments are legal (use with AddKey)

@ fHidden

Hide it in Usage.

@ eRequires

One argument requires another.

@ eExcludes

One argument excludes another.

@ eBoolean

{'true', 't', 'false', 'f'}, case-insensitive

@ eString

An arbitrary string.

void DBAPI_RegisterDriver_FTDS(void)

#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...

void Error(CExceptionArgs_Base &args)

void Warning(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

static string NormalizePath(const string &path, EFollowLinks follow_links=eIgnoreLinks)

Normalize a path.

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

string GetDir(EIfEmptyPath mode=eIfEmptyPath_Current) const

Get the directory component for this directory entry.

string GetName(void) const

Get the base entry name with extension (if any).

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

#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.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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 TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ eNocase

Case insensitive compare.

void GenBankReaders_Register_Pubseq2(void)

void GenBankReaders_Register_Pubseq(void)

Defines CRequestContext class for NCBI C++ diagnostic API.

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Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/data__loaders__util_8cpp_source.html below:

NCBI C++ ToolKit: src/misc/data_loaders_util/data_loaders_util.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/dataloadersutil_8cpp_source.html below: