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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/eutils__sample_8cpp_source.html below:

NCBI C++ ToolKit: src/sample/app/eutils/eutils_sample.cpp Source File

74 virtual void Init

(

void

);

75 virtual int Run

(

void

);

76 virtual void Exit

(

void

);

119

arg_desc->AddFlag(

"einfo"

"Call einfo utility"

true

);

120

arg_desc->AddFlag(

"efetch"

"Call efetch utility"

true

);

122

arg_desc->AddFlag(

"esearch"

"Call esearch utility"

true

);

123

arg_desc->AddFlag(

"epost"

"Call epost utility"

true

);

124

arg_desc->AddFlag(

"elink"

"Call elink utility"

true

);

125

arg_desc->AddFlag(

"egquery"

"Call egquery utility"

true

);

126

arg_desc->AddFlag(

"esummary"

"Call esummary utility"

true

);

127

arg_desc->AddFlag(

"espell"

"Call espell utility"

true

);

128

arg_desc->AddFlag(

"ehistory"

"Call ehistory utility"

true

);

131

arg_desc->AddDefaultKey(

"http"

"Method"

132 "HTTP method used to send requests"

139

arg_desc->AddFlag(

"dump"

"Print raw incoming data"

true

);

142

arg_desc->AddOptionalKey(

"webenv"

"WebEnv"

"Web environment"

144

arg_desc->AddOptionalKey(

"query_key"

"Query key"

147

arg_desc->AddFlag(

"skip_query_key"

"Do not send query_key"

true

);

148

arg_desc->AddOptionalKey(

"tool"

"Client tool"

150

arg_desc->AddOptionalKey(

"email"

"Client e-mail"

154

arg_desc->AddOptionalKey(

"db"

"Database name"

156

arg_desc->AddOptionalKey(

"id"

"ID to fetch"

158

arg_desc->AddOptionalKey(

"term"

"Term to search for"

160

arg_desc->AddOptionalKey(

"retstart"

"RetStart"

"First item to fetch"

163

arg_desc->AddOptionalKey(

"retmax"

"RetMax"

"Number of items to fetch"

166

arg_desc->AddDefaultKey(

"retmode"

"RetMode"

"Data format"

169 "text"

"xml"

"asn"

"html"

));

170

arg_desc->AddOptionalKey(

"rettype"

"RetType"

"Fetched data type"

174 "uilist"

"abstract"

"citation"

"medline"

"full"

176 "native"

"fasta"

"gb"

"gbc"

"gbwithparts"

"est"

"gss"

177 "gp"

"gpc"

"seqid"

"acc"

"chr"

"flt"

"rsr"

"brief"

"docset"

180 "count"

"uilist"

));

181

arg_desc->AddOptionalKey(

"reldate"

"RelDate"

"Age of date in days"

184

arg_desc->AddOptionalKey(

"report"

"Report"

"Taxonomy data format"

187 "uilist"

"brief"

"docsum"

"xml"

));

189

arg_desc->AddOptionalKey(

"usehistory"

"UseHistory"

"Use history"

191

arg_desc->AddOptionalKey(

"sort"

"Sort"

"Sort order or 'none'"

216

arg_desc->AddOptionalKey(

"dbfrom"

"origination db for elink"

219

arg_desc->AddOptionalKey(

"cmd"

"Command"

"elink command"

222 "prlinks"

"llinks"

"llinkslib"

"lcheck"

"ncheck"

223 "neighbor"

"neighbor_history"

"acheck"

));

225

arg_desc->AddOptionalKey(

"linkname"

"Linkname"

"elink linkname"

228

arg_desc->AddOptionalKey(

"holding"

"elink holding"

231

arg_desc->AddOptionalKey(

"version"

"Version"

"elink DTD version"

235 string

prog_description =

236 "Test loading data from EUtils"

;

237

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

238

prog_description,

false

);

247 if

( args[

"http"

].AsString() ==

"get"

) {

257

cout <<

data

<< endl;

263 string

db = args[

"db"

] ? args[

"db"

].AsString() :

kEmptyStr

;

277 if

(

result

->IsDbList() ) {

278 for

(

const auto

& name :

result

->GetDbList().GetDbName()) {

295

req.

SetTerm

(args[

"term"

].AsString());

296 if

( args[

"usehistory"

] ) {

299 if

( args[

"sort"

] ) {

302 if

( args[

"reldate"

] ) {

303

req.

SetRelDate

(args[

"reldate"

].AsInteger());

306 if

( args[

"retmax"

] ) {

307

req.

SetRetMax

(args[

"retmax"

].AsInteger());

310 string

rettype = args[

"rettype"

] ? args[

"rettype"

].AsString() :

kEmptyStr

;

311 if

(rettype ==

"count"

) {

314 else if

(rettype ==

"uilist"

) {

317 else if

( !rettype.empty() ) {

319 " is incompatible with e-search request."

);

346

req.

SetTerm

(args[

"term"

].AsString());

394 if

( args[

"dbfrom"

] ) {

395

req.

SetDbFrom

(args[

"dbfrom"

].AsString());

402 if

( args[

"cmd"

] ) {

403 string cmd

= args[

"cmd"

].AsString();

404 if

(

cmd

"prlinks"

) {

407 else if

(

cmd

"llinks"

) {

410 else if

(

cmd

"llinkslib"

) {

413 else if

(

cmd

"lcheck"

) {

416 else if

(

cmd

"ncheck"

) {

419 else if

(

cmd

"neighbor"

) {

422 else if

(

cmd

"neighbor_history"

) {

425 else if

(

cmd

"acheck"

) {

432 if

( args[

"linkname"

] ) {

435 if

( args[

"holding"

] ) {

436

req.

SetHolding

(args[

"holding"

].AsString());

438 if

( args[

"version"

] ) {

439

req.

SetHolding

(args[

"version"

].AsString());

441 if

( args[

"reldate"

] ) {

442

req.

SetRelDate

(args[

"reldate"

].AsInteger());

463 string

db = args[

"db"

] ? args[

"db"

].AsString() :

kEmptyStr

;

472 if

( args[

"retstart"

] ) {

475 if

( args[

"retmax"

] ) {

476

req.

SetRetMax

(args[

"retmax"

].AsInteger());

497

cout <<

"Deserialization error: "

<< ex.

what

() << endl;

505 string

db = args[

"db"

] ? args[

"db"

].AsString() :

kEmptyStr

;

509

req.

SetTerm

(args[

"term"

].AsString());

530 if

( args[

"db"

] ) {

531

db = args[

"db"

].AsString();

554 string

db = args[

"db"

].AsString();

556 if

(db ==

"pubmed"

) {

559 else if

(db ==

"pmc"

) {

562 else if

(db ==

"journals"

) {

565 else if

(db ==

"omim"

) {

571

unique_ptr<CEFetch_Literature_Request> lit_req(

574 string

rettype = args[

"rettype"

] ? args[

"rettype"

].AsString() :

kEmptyStr

;

575 if

(rettype ==

"uilist"

) {

578 else if

(rettype ==

"abstract"

) {

581 else if

(rettype ==

"citation"

) {

584 else if

(rettype ==

"medline"

) {

587 else if

(rettype ==

"full"

) {

590 else if

( !rettype.empty() ) {

592 " is incompatible with the selected database "

<< db);

596 return

lit_req.release();

603 string

db = args[

"db"

].AsString();

608 else if

(db ==

"genome"

) {

611 else if

(db ==

"nucleotide"

) {

614 else if

(db ==

"nuccore"

) {

617 else if

(db ==

"nucest"

) {

620 else if

(db ==

"nucgss"

) {

623 else if

(db ==

"protein"

) {

626 else if

(db ==

"popset"

) {

629 else if

(db ==

"snp"

) {

632 else if

(db ==

"sequences"

) {

638

unique_ptr<CEFetch_Sequence_Request> seq_req(

641 string

rettype = args[

"rettype"

] ? args[

"rettype"

].AsString() :

kEmptyStr

;

642 if

(rettype ==

"native"

) {

645 else if

(rettype ==

"fasta"

) {

648 else if

(rettype ==

"gb"

) {

651 else if

(rettype ==

"gbc"

) {

654 else if

(rettype ==

"gbwithparts"

) {

657 else if

(rettype ==

"est"

) {

660 else if

(rettype ==

"gss"

) {

663 else if

(rettype ==

"gp"

) {

666 else if

(rettype ==

"gpc"

) {

669 else if

(rettype ==

"seqid"

) {

672 else if

(rettype ==

"acc"

) {

675 else if

(rettype ==

"chr"

) {

678 else if

(rettype ==

"flt"

) {

681 else if

(rettype ==

"rsr"

) {

684 else if

(rettype ==

"brief"

) {

687 else if

(rettype ==

"docset"

) {

690 else if

(rettype ==

"gi2acc"

) {

693 else if

( !rettype.empty() ) {

695 " is incompatible with the selected database "

<< db);

699 return

seq_req.release();

706 string

db = args[

"db"

].AsString();

707 if

(db !=

"taxonomy"

) {

710

unique_ptr<CEFetch_Taxonomy_Request> tax_req(

713 if

( args[

"report"

] ) {

714 string

report = args[

"report"

].AsString();

715 if

(report ==

"uilist"

) {

718 else if

(report ==

"brief"

) {

721 else if

(report ==

"docsum"

) {

724 else if

(report ==

"xml"

) {

728 ERR_POST

(

Error

"Unsupported taxonomy report: "

<< report);

732 return

tax_req.release();

751

<< args[

"db"

].AsString() <<

" using the specified arguments."

);

758 if

( req->GetConnContext()->GetWebEnv().empty() && args[

"id"

] ) {

759

req->GetId().SetIds(args[

"id"

].AsString());

762 string

retmode_str = args[

"retmode"

].AsString();

764 if

(retmode_str ==

"text"

) {

767 else if

(retmode_str ==

"xml"

) {

770 else if

(retmode_str ==

"html"

) {

773 else if

(retmode_str ==

"asn"

) {

779

req->SetRetMode(retmode);

781 if

( args[

"retmax"

] ) {

782

req->SetRetMax(args[

"retmax"

].AsInteger());

785

cout << req->GetScriptName() <<

"?"

<< req->GetQueryString() << endl;

795

cout << content << endl;

807 if

(args[

"webenv"

]) {

810 if

(args[

"query_key"

]) {

813 if

(args[

"skip_query_key"

]) {

816 if

(args[

"tool"

]) {

819 if

(args[

"email"

]) {

822 if

(args[

"base_url"

]) {

827 if

( args[

"einfo"

] ) {

830 if

( args[

"egquery"

] ) {

833 if

( args[

"espell"

] ) {

836 if

( args[

"esearch"

] ) {

839 if

( args[

"epost"

] ) {

842 if

( args[

"elink"

] ) {

845 if

( args[

"esummary"

] ) {

848 if

( args[

"efetch"

] ) {

852 if

( args[

"ehistory"

] ) {

CEFetch_Literature_Request.

CEFetch_Sequence_Request.

CEFetch_Taxonomy_Request.

void x_SetHttpMethod(CEUtils_Request &req, const CArgs &args)

void CallEInfo(const CArgs &args)

void CallESpell(const CArgs &args)

virtual void Init(void)

Initialize the application.

void CallEGQuery(const CArgs &args)

virtual void Exit(void)

Cleanup on application exit.

void x_DumpRequest(CEUtils_Request &req)

void CallEPost(const CArgs &args)

CRef< CEUtils_ConnContext > & x_GetCtx(void)

CEFetch_Request * x_CreateSeqRequest(const CArgs &args)

void CallESearch(const CArgs &args)

void CallELink(const CArgs &args)

void CallEHistory(const CArgs &args)

void CallESummary(const CArgs &args)

virtual int Run(void)

Run the application.

CEFetch_Request * x_CreateLitRequest(const CArgs &args)

CEFetch_Request * x_CreateTaxRequest(const CArgs &args)

void CallEFetch(const CArgs &args)

CRef< CEUtils_ConnContext > m_Ctx

Root class for all serialization exceptions.

int NcbiSys_main(int argc, ncbi::TXChar *argv[])

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ eRequires

One argument requires another.

@ eBoolean

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

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

#define ERR_POST(message)

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

virtual string GetQueryString(void) const

Get CGI script query string.

ERetMode

Output format for efetch requests.

void SetDatabase(const string &database)

Setting new database disconnects the request.

const CEUtils_IdGroupSet & GetIdGroups(void) const

Multiple ID groups.

void SetSortOrderName(CTempString name)

Set sort order. Empty string indicates no sorting (or the default one).

void SetRetStart(int retstart)

const CEUtils_IdGroup & GetId(void) const

Group of ids required if history is not used.

ESequenceDB

Sequence databases.

CRef< elink::CELinkResult > GetELinkResult(void)

Get search result.

void SetRequestMethod(ERequestMethod method)

Set HTTP method.

void SetRetMax(int retmax)

virtual string GetQueryString(void) const

Get CGI script query string.

virtual string GetQueryString(void) const

Get CGI script query string.

ELiteratureDB

Literature databases.

CRef< espell::CESpellResult > GetESpellResult(void)

Get search results.

void SetTool(const string &tool)

CRef< CEUtils_ConnContext > & GetConnContext(void) const

Get current request context.

void SetGroups(const string &groups)

Parse a set of id groups from a single string ('id=12,34&id=56,78').

CRef< einfo::CEInfoResult > GetEInfoResult(void)

Get result.

const string & GetScriptName(void) const

Get CGI script name (e.g. efetch.fcgi).

void SetTerm(const string &term)

virtual string GetQueryString(void) const

Get CGI script query string.

CRef< ehistory::CEHistoryResult > GetEHistoryResult(void)

Get request history.

CRef< epost::CEPostResult > GetEPostResult(void)

Get search results.

const CEUtils_IdGroup & GetId(void) const

Group of ids to be added to the search history.

void SetLinkName(const string &linkname)

void SetTerm(const string &term)

void SetRelDate(int days)

void SetEmail(const string &email)

CRef< esearch::CESearchResult > GetESearchResult(void)

Get search results.

CRef< esummary::CESummaryResult > GetESummaryResult(void)

Get search result.

virtual string GetQueryString(void) const

Get CGI script query string.

void Read(string *content)

Read the whole stream into the string.

void SetRetType(ERetType rettype)

CRef< egquery::CResult > GetResult(void)

Get search results.

const string & GetWebEnv(void) const

Get WebEnv.

const string & GetQueryKey(void) const

Get query_key.

void SetUseHistory(bool value)

void SetRetMax(int retmax)

void SetDbFrom(const string &dbfrom)

static void SetBaseURL(const string &url)

Set new base url for all e-utils requests.

void SetQueryKey(const string &query_key)

Set query_key.

void SetHolding(const string &holding)

void SetWebEnv(const string &webenv)

Set WebEnv.

void SetTerm(const string &term)

void SetIds(const string &ids)

Parse all ids from a string (e.g. 'id=123,456,78').

void SetRelDate(int days)

void SetCommand(ECommand cmd)

virtual string GetQueryString(void) const

Get CGI script query string.

void SetSendQueryKey(bool value)

Set SendQueryKey flag.

virtual string GetQueryString(void) const

Get CGI script query string.

@ eRetMode_text

Return data as plain text.

@ eRetMode_xml

Return data as XML.

@ eRetMode_html

Return data as HTML.

@ eRetMode_asn

Return data as text ASN.1.

@ eCmd_llinks

LinkOut URLs, except PubMed libraries.

@ eCmd_ncheck

Check for the existence of neighbor links.

@ eCmd_lcheck

Check for the existence of external links.

@ eCmd_prlinks

Links to the primary provider.

@ eCmd_acheck

Entrez databases links.

@ eCmd_neighbor

Display neighbors within a database (default)

@ eCmd_llinkslib

LinkOut URLs and Attributes.

@ eCmd_neighbor_history

Create history for use in other EUtils.

void Error(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Reset(void)

Reset reference object.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

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