CEutilsClient Class Reference

Search Toolkit Book for CEutilsClient

Class for querying via E-Utils. More...

#include <misc/eutils_client/eutils_client.hpp>

Inheritance diagram for CEutilsClient:

Collaboration diagram for CEutilsClient:

Classes
class	CMessageHandler
	Subclass this to override how messages (warnings and errors) are handled. More...

Public Types
enum	EUseHistory { eUseHistoryDisabled = 1 , eUseHistoryEnabled }
enum	EContentType {   eContentType_default = 1 , eContentType_xml , eContentType_text , eContentType_html ,   eContentType_asn1 }

Public Member Functions
	CEutilsClient ()
	CEutilsClient (const string &host)
void	SetMessageHandlerDefault (void)
	Default is to log all messages at informational level. More...
void	SetMessageHandlerDiagPost (void)
	Equivalent to: ERR_POST(Warning|Error << ...). More...
void	SetMessageHandlerThrowOnError (void)
	Equivalent to: NCBI_THROW, ERR_POST, LOG_POST as appropriate. More...
void	SetMessageHandler (CMessageHandler &message_handler)
	Set custom message handler. More...
void	SetUserTag (const string &tag)
void	SetMaxReturn (int ret_max)
void	SetLinkName (const string &link_name)
void	ClearAddedParameters ()
void	AddParameter (const string &name, const string &value)
Uint8	Count (const string &db, const string &term)
Uint8	Search (const string &db, const string &term, vector< objects::CSeq_id_Handle > &uids, const string &xml_path=kEmptyStr)
Uint8	Search (const string &db, const string &term, vector< string > &uids, const string &xml_path=kEmptyStr)
Uint8	Search (const string &db, const string &term, vector< TEntrezId > &uids, const string &xml_path=kEmptyStr)
void	Search (const string &db, const string &term, CNcbiOstream &ostr, EUseHistory use_history=eUseHistoryDisabled)
void	SearchHistory (const string &db, const string &term, const string &web_env, Int8 query_key, int retstart, CNcbiOstream &ostr)
void	SearchHistory (const string &db, const string &term, const string &web_env, objects::CSeq_id_Handle query_key, int retstart, CNcbiOstream &ostr)
void	SearchHistory (const string &db, const string &term, const string &web_env, const string &query_key, int retstart, CNcbiOstream &ostr)
void	Link (const string &db_from, const string &db_to, const vector< objects::CSeq_id_Handle > &uids_from, vector< objects::CSeq_id_Handle > &uids_to, const string &xml_path=kEmptyStr, const string &command="neighbor")
void	Link (const string &db_from, const string &db_to, const vector< string > &uids_from, vector< string > &uids_to, const string &xml_path=kEmptyStr, const string &command="neighbor")
void	Link (const string &db_from, const string &db_to, const vector< TEntrezId > &uids_from, vector< TEntrezId > &uids_to, const string &xml_path=kEmptyStr, const string &command="neighbor")
void	Link (const string &db_from, const string &db_to, const vector< TEntrezId > &uids_from, vector< objects::CSeq_id_Handle > &uids_to, const string &xml_path=kEmptyStr, const string &command="neighbor")
void	Link (const string &db_from, const string &db_to, const vector< objects::CSeq_id_Handle > &uids_from, vector< TEntrezId > &uids_to, const string &xml_path=kEmptyStr, const string &command="neighbor")
void	Link (const string &db_from, const string &db_to, const vector< objects::CSeq_id_Handle > &uids_from, CNcbiOstream &ostr, const string &command="neighbor")
void	Link (const string &db_from, const string &db_to, const vector< string > &uids_from, CNcbiOstream &ostr, const string &command="neighbor")
void	Link (const string &db_from, const string &db_to, const vector< TEntrezId > &uids_from, CNcbiOstream &ostr, const string &command="neighbor")
void	LinkHistory (const string &db_from, const string &db_to, const string &web_env, Int8 query_key, CNcbiOstream &ostr)
void	LinkHistory (const string &db_from, const string &db_to, const string &web_env, objects::CSeq_id_Handle query_key, CNcbiOstream &ostr)
void	LinkHistory (const string &db_from, const string &db_to, const string &web_env, const string &query_key, CNcbiOstream &ostr)
void	LinkOut (const string &db, const vector< objects::CSeq_id_Handle > &uids, xml::document &docsums, const string &cmd="llinks")
void	LinkOut (const string &db, const vector< string > &uids, xml::document &docsums, const string &cmd="llinks")
void	LinkOut (const string &db, const vector< TEntrezId > &uids, xml::document &docsums, const string &cmd="llinks")
void	Summary (const string &db, const vector< objects::CSeq_id_Handle > &uids, xml::document &docsums, const string &version="")
void	Summary (const string &db, const vector< string > &uids, xml::document &docsums, const string &version="")
void	Summary (const string &db, const vector< TEntrezId > &uids, xml::document &docsums, const string &version="")
void	SummaryHistory (const string &db, const string &web_env, Int8 query_key, int retstart, const string &version, CNcbiOstream &ostr)
void	SummaryHistory (const string &db, const string &web_env, objects::CSeq_id_Handle query_key, int retstart, const string &version, CNcbiOstream &ostr)
void	SummaryHistory (const string &db, const string &web_env, const string &query_key, int retstart, const string &version, CNcbiOstream &ostr)
void	Fetch (const string &db, const vector< objects::CSeq_id_Handle > &uids, CNcbiOstream &ostr, const string &retmode="xml")
void	Fetch (const string &db, const vector< string > &uids, CNcbiOstream &ostr, const string &retmode="xml")
void	Fetch (const string &db, const vector< TEntrezId > &uids, CNcbiOstream &ostr, const string &retmode="xml")
void	FetchHistory (const string &db, const string &web_env, Int8 query_key, int retstart, EContentType content_type, CNcbiOstream &ostr)
void	FetchHistory (const string &db, const string &web_env, objects::CSeq_id_Handle query_key, int retstart, EContentType content_type, CNcbiOstream &ostr)
void	FetchHistory (const string &db, const string &web_env, const string &query_key, int retstart, EContentType content_type, CNcbiOstream &ostr)
const list< string >	GetUrl (void) const
const list< CTime >	GetTime (void) const
void	SetWaitTime (const CIncreasingTime &wait_time)
void	SetMaxRetries (unsigned int max_retries)
void	SetConnTimeout (const CTimeout &timeout)

Protected Types
typedef map< string, string >	TParamList

Protected Member Functions
Uint8	ParseSearchResults (CNcbiIstream &istr, vector< objects::CSeq_id_Handle > &uids)
Uint8	ParseSearchResults (CNcbiIstream &istr, vector< string > &uids)
Uint8	ParseSearchResults (CNcbiIstream &istr, vector< TEntrezId > &uids)
Uint8	ParseSearchResults (const string &xml_file, vector< objects::CSeq_id_Handle > &uids)
Uint8	ParseSearchResults (const string &xml_file, vector< string > &uids)
Uint8	ParseSearchResults (const string &xml_file, vector< TEntrezId > &uids)
const string &	x_GetHostName (void) const
void	x_Get (string const &path, string const &params, CNcbiOstream &ostr)
void	x_AddAdditionalParameters (string &params)
template<class T >
Uint8	x_Search (const string &db, const string &term, vector< T > &uids, const string &xml_path=kEmptyStr)
template<class T1 , class T2 >
void	x_Link (const string &db_from, const string &db_to, const vector< T1 > &uids_from, vector< T2 > &uids_to, const string &xml_path, const string &command)
template<class T >
void	x_Link (const string &db_from, const string &db_to, const vector< T > &uids_from, CNcbiOstream &ostr, const string &command)
template<class T >
void	x_LinkOut (const string &db, const vector< T > &uids, xml::document &doc, const string &cmd)
template<class T >
void	x_Summary (const string &db, const vector< T > &uids, xml::document &docsums, const string &version="")
template<class T >
void	x_Fetch (const string &db, const vector< T > &uids, CNcbiOstream &ostr, const string &retmode="xml")
template<class T >
Uint8	x_ParseSearchResults (const string &xml_file, vector< T > &uids)
template<class T >
Uint8	x_ParseSearchResults (CNcbiIstream &istr, vector< T > &uids)
template<class Call >
std::invoke_result< Call >::type	CallWithRetry (Call &&call, const char *name)

Static Protected Member Functions
static string	x_BuildUrl (const string &host, const string &path, const string &params)

Protected Attributes
CRef< CMessageHandler >	m_MessageHandler
int	m_CachedHostNameCount
string	m_CachedHostName
string	m_HostName
string	m_UrlTag
TParamList	m_AdditionalParams
int	m_RetMax
string	m_LinkName
list< string >	m_Url
list< CTime >	m_Time

Private Member Functions
void	x_InitParams (void)
Uint8	x_CountOnce (const string &params)
template<class T >
Uint8	x_SearchOnce (const string &params, vector< T > &uids, const string &xml_path)
void	x_GetOnce (string const &path, string const &extra_params, CNcbiOstream &ostr)
template<class T >
void	x_LinkOnceT (const string &db_from, const string &db_to, vector< T > &uids_to, const string &xml_path, const string &params)
void	x_LinkOnce (CNcbiOstream &ostr, const string &params)
void	x_LinkOutOnce (xml::document &doc, const string &params)
void	x_SummaryOnce (xml::document &docsums, const string &params)
void	x_FetchOnce (CNcbiOstream &ostr, const string &params)

Private Attributes
unsigned int	m_MaxRetries
CIncreasingTime	m_WaitTime
unsigned int	m_Attempt = 0
CTimeout	m_Timeout

Detailed Description

Class for querying via E-Utils.

Definition at line 76 of file eutils_client.hpp.

Member Typedef Documentation

TParamList

typedef map<string,string> CEutilsClient::TParamList

protected

Definition at line 443 of file eutils_client.hpp.

Member Enumeration Documentation

EContentType

enum CEutilsClient::EContentType

Enumerator
eContentType_default
eContentType_xml
eContentType_text
eContentType_html
eContentType_asn1

Definition at line 102 of file eutils_client.hpp.

EUseHistory

enum CEutilsClient::EUseHistory

Enumerator
eUseHistoryDisabled
eUseHistoryEnabled

Definition at line 97 of file eutils_client.hpp.

Constructor & Destructor Documentation

CEutilsClient() [1/2]

CEutilsClient::CEutilsClient

(

)

Definition at line 527 of file eutils_client.cpp.

References SetMessageHandlerDefault(), and x_InitParams().

CEutilsClient() [2/2]

CEutilsClient::CEutilsClient

(

const string &

host

)

Definition at line 537 of file eutils_client.cpp.

References SetMessageHandlerDefault(), and x_InitParams().

Member Function Documentation

AddParameter()

void CEutilsClient::AddParameter	(	const string &	name,
		const string &	value
	)

Definition at line 581 of file eutils_client.cpp.

References m_AdditionalParams, NStr::URLEncode(), and rapidjson::value.

CallWithRetry()

template<class Call >

std::invoke_result< Call >::type CEutilsClient::CallWithRetry ( Call &&  call, const char *  name  )

protected

Definition at line 631 of file eutils_client.cpp.

References CIncreasingTime::GetTime(), LOG_POST, m_Attempt, m_MaxRetries, m_WaitTime, SleepMilliSec(), Warning(), and CException::what().

Referenced by Count(), x_Fetch(), x_Get(), x_Link(), x_LinkOut(), x_Search(), and x_Summary().

ClearAddedParameters()

void CEutilsClient::ClearAddedParameters

(

)

Definition at line 576 of file eutils_client.cpp.

References map_checker< Container >::clear(), and m_AdditionalParams.

Count()

Uint8 CEutilsClient::Count	(	const string &	db,
		const string &	term
	)

Definition at line 654 of file eutils_client.cpp.

References CallWithRetry(), eUnknown, LOG_POST, m_Time, m_Url, m_UrlTag, NCBI_THROW, Trace(), NStr::URLEncode(), x_AddAdditionalParameters(), and x_CountOnce().

Referenced by pub_report::CSkipPubJournalHook::IsJournalMissing(), and CAssemblyInfo::x_ValidateTaxId().

Fetch() [1/3]

void CEutilsClient::Fetch	(	const string &	db,
		const vector< objects::CSeq_id_Handle > &	uids,
		CNcbiOstream &	ostr,
		const string &	retmode = "xml"
	)

Referenced by CEntrezDB::CreateGene_Gene(), CEntrezDB::CreateGeneSet_Gene(), pub_report::CUnpublishedReport::FetchPub(), CReloadPublications::LookUpByPmid(), and CMacroFunction_LookupPub::s_GetArticleFromEntrezById().

Fetch() [2/3]

void CEutilsClient::Fetch	(	const string &	db,
		const vector< string > &	uids,
		CNcbiOstream &	ostr,
		const string &	retmode = "xml"
	)

Definition at line 1668 of file eutils_client.cpp.

References x_Fetch().

Fetch() [3/3]

void CEutilsClient::Fetch	(	const string &	db,
		const vector< TEntrezId > &	uids,
		CNcbiOstream &	ostr,
		const string &	retmode = "xml"
	)

Definition at line 1676 of file eutils_client.cpp.

References x_Fetch().

FetchHistory() [1/3]

void CEutilsClient::FetchHistory	(	const string &	db,
		const string &	web_env,
		const string &	query_key,
		int	retstart,
		EContentType	content_type,
		CNcbiOstream &	ostr
	)

Definition at line 1792 of file eutils_client.cpp.

References m_RetMax, s_FetchHistoryQuery(), and x_Get().

FetchHistory() [2/3]

void CEutilsClient::FetchHistory	(	const string &	db,
		const string &	web_env,
		Int8	query_key,
		int	retstart,
		EContentType	content_type,
		CNcbiOstream &	ostr
	)

Definition at line 1763 of file eutils_client.cpp.

References m_RetMax, s_FetchHistoryQuery(), and x_Get().

Referenced by BOOST_AUTO_TEST_CASE().

FetchHistory() [3/3]

void CEutilsClient::FetchHistory	(	const string &	db,
		const string &	web_env,
		objects::CSeq_id_Handle	query_key,
		int	retstart,
		EContentType	content_type,
		CNcbiOstream &	ostr
	)

GetTime()

const list< CTime > CEutilsClient::GetTime

(

void

)

const

Definition at line 1812 of file eutils_client.cpp.

References m_Time.

GetUrl()

const list< string > CEutilsClient::GetUrl

(

void

)

const

Definition at line 1807 of file eutils_client.cpp.

References m_Url.

Link() [1/8]

void CEutilsClient::Link	(	const string &	db_from,
		const string &	db_to,
		const vector< objects::CSeq_id_Handle > &	uids_from,
		CNcbiOstream &	ostr,
		const string &	command = "neighbor"
	)

Link() [2/8]

void CEutilsClient::Link	(	const string &	db_from,
		const string &	db_to,
		const vector< objects::CSeq_id_Handle > &	uids_from,
		vector< objects::CSeq_id_Handle > &	uids_to,
		const string &	xml_path = kEmptyStr,
		const string &	command = "neighbor"
	)

Referenced by BOOST_AUTO_TEST_CASE(), and s_ELinkQuery().

Link() [3/8]

void CEutilsClient::Link	(	const string &	db_from,
		const string &	db_to,
		const vector< objects::CSeq_id_Handle > &	uids_from,
		vector< TEntrezId > &	uids_to,
		const string &	xml_path = kEmptyStr,
		const string &	command = "neighbor"
	)

Link() [4/8]

void CEutilsClient::Link	(	const string &	db_from,
		const string &	db_to,
		const vector< string > &	uids_from,
		CNcbiOstream &	ostr,
		const string &	command = "neighbor"
	)

Definition at line 1293 of file eutils_client.cpp.

References command, and x_Link().

Link() [5/8]

void CEutilsClient::Link	(	const string &	db_from,
		const string &	db_to,
		const vector< string > &	uids_from,
		vector< string > &	uids_to,
		const string &	xml_path = kEmptyStr,
		const string &	command = "neighbor"
	)

Definition at line 1127 of file eutils_client.cpp.

References command, and x_Link().

Link() [6/8]

void CEutilsClient::Link	(	const string &	db_from,
		const string &	db_to,
		const vector< TEntrezId > &	uids_from,
		CNcbiOstream &	ostr,
		const string &	command = "neighbor"
	)

Definition at line 1302 of file eutils_client.cpp.

References command, and x_Link().

Link() [7/8]

void CEutilsClient::Link	(	const string &	db_from,
		const string &	db_to,
		const vector< TEntrezId > &	uids_from,
		vector< objects::CSeq_id_Handle > &	uids_to,
		const string &	xml_path = kEmptyStr,
		const string &	command = "neighbor"
	)

Link() [8/8]

void CEutilsClient::Link	(	const string &	db_from,
		const string &	db_to,
		const vector< TEntrezId > &	uids_from,
		vector< TEntrezId > &	uids_to,
		const string &	xml_path = kEmptyStr,
		const string &	command = "neighbor"
	)

Definition at line 1137 of file eutils_client.cpp.

References command, and x_Link().

LinkHistory() [1/3]

void CEutilsClient::LinkHistory	(	const string &	db_from,
		const string &	db_to,
		const string &	web_env,
		const string &	query_key,
		CNcbiOstream &	ostr
	)

Definition at line 1391 of file eutils_client.cpp.

References NStr::URLEncode(), and x_Get().

LinkHistory() [2/3]

void CEutilsClient::LinkHistory	(	const string &	db_from,
		const string &	db_to,
		const string &	web_env,
		Int8	query_key,
		CNcbiOstream &	ostr
	)

Definition at line 1356 of file eutils_client.cpp.

References NStr::URLEncode(), and x_Get().

LinkHistory() [3/3]

void CEutilsClient::LinkHistory	(	const string &	db_from,
		const string &	db_to,
		const string &	web_env,
		objects::CSeq_id_Handle	query_key,
		CNcbiOstream &	ostr
	)

LinkOut() [1/3]

void CEutilsClient::LinkOut	(	const string &	db,
		const vector< objects::CSeq_id_Handle > &	uids,
		xml::document &	docsums,
		const string &	cmd = "llinks"
	)

Definition at line 1420 of file eutils_client.cpp.

References cmd, and x_LinkOut().

Referenced by BOOST_AUTO_TEST_CASE().

LinkOut() [2/3]

void CEutilsClient::LinkOut	(	const string &	db,
		const vector< string > &	uids,
		xml::document &	docsums,
		const string &	cmd = "llinks"
	)

Definition at line 1428 of file eutils_client.cpp.

References cmd, and x_LinkOut().

LinkOut() [3/3]

void CEutilsClient::LinkOut	(	const string &	db,
		const vector< TEntrezId > &	uids,
		xml::document &	docsums,
		const string &	cmd = "llinks"
	)

Definition at line 1436 of file eutils_client.cpp.

References cmd, and x_LinkOut().

ParseSearchResults() [1/6]

Uint8 CEutilsClient::ParseSearchResults ( CNcbiIstream &  istr, vector< objects::CSeq_id_Handle > &  uids  )

protected

Referenced by x_GetOnce(), x_ParseSearchResults(), and x_SearchOnce().

ParseSearchResults() [2/6]

Uint8 CEutilsClient::ParseSearchResults ( CNcbiIstream &  istr, vector< string > &  uids  )

protected

Definition at line 722 of file eutils_client.cpp.

References x_ParseSearchResults().

ParseSearchResults() [3/6]

Uint8 CEutilsClient::ParseSearchResults ( CNcbiIstream &  istr, vector< TEntrezId > &  uids  )

protected

Definition at line 728 of file eutils_client.cpp.

References x_ParseSearchResults().

ParseSearchResults() [4/6]

Uint8 CEutilsClient::ParseSearchResults ( const string &  xml_file, vector< objects::CSeq_id_Handle > &  uids  )

protected

ParseSearchResults() [5/6]

Uint8 CEutilsClient::ParseSearchResults ( const string &  xml_file, vector< string > &  uids  )

protected

Definition at line 774 of file eutils_client.cpp.

References x_ParseSearchResults().

ParseSearchResults() [6/6]

Uint8 CEutilsClient::ParseSearchResults ( const string &  xml_file, vector< TEntrezId > &  uids  )

protected

Definition at line 780 of file eutils_client.cpp.

References x_ParseSearchResults().

Search() [1/4]

void CEutilsClient::Search	(	const string &	db,
		const string &	term,
		CNcbiOstream &	ostr,
		EUseHistory	use_history = eUseHistoryDisabled
	)

Definition at line 917 of file eutils_client.cpp.

References eUseHistoryEnabled, m_RetMax, NStr::URLEncode(), and x_Get().

Search() [2/4]

Uint8 CEutilsClient::Search	(	const string &	db,
		const string &	term,
		vector< objects::CSeq_id_Handle > &	uids,
		const string &	xml_path = kEmptyStr
	)

Referenced by BOOST_AUTO_TEST_CASE(), pub_report::DoEUtilsSearch(), CIdfetchApplication::Run(), s_ESearchQuery(), CAssemblyInfo::x_FilterTaxIds(), CNAUtils::x_GetNAId(), CRelaxedLookupDlg::x_GetPubIds(), and CAssemblyInfo::x_SearchIds().

Search() [3/4]

Uint8 CEutilsClient::Search	(	const string &	db,
		const string &	term,
		vector< string > &	uids,
		const string &	xml_path = kEmptyStr
	)

Definition at line 816 of file eutils_client.cpp.

References x_Search().

Search() [4/4]

Uint8 CEutilsClient::Search	(	const string &	db,
		const string &	term,
		vector< TEntrezId > &	uids,
		const string &	xml_path = kEmptyStr
	)

Definition at line 825 of file eutils_client.cpp.

References x_Search().

SearchHistory() [1/3]

void CEutilsClient::SearchHistory	(	const string &	db,
		const string &	term,
		const string &	web_env,
		const string &	query_key,
		int	retstart,
		CNcbiOstream &	ostr
	)

Definition at line 993 of file eutils_client.cpp.

References m_RetMax, s_SearchHistoryQuery(), and x_Get().

SearchHistory() [2/3]

void CEutilsClient::SearchHistory	(	const string &	db,
		const string &	term,
		const string &	web_env,
		Int8	query_key,
		int	retstart,
		CNcbiOstream &	ostr
	)

Definition at line 962 of file eutils_client.cpp.

References m_RetMax, s_SearchHistoryQuery(), and x_Get().

Referenced by BOOST_AUTO_TEST_CASE(), and CSeqUtils::ESearchQuery().

SearchHistory() [3/3]

void CEutilsClient::SearchHistory	(	const string &	db,
		const string &	term,
		const string &	web_env,
		objects::CSeq_id_Handle	query_key,
		int	retstart,
		CNcbiOstream &	ostr
	)

SetConnTimeout()

void CEutilsClient::SetConnTimeout ( const CTimeout &  timeout )

inline

Definition at line 412 of file eutils_client.hpp.

References m_Timeout.

SetLinkName()

void CEutilsClient::SetLinkName

(

const string &

link_name

)

Definition at line 586 of file eutils_client.cpp.

References m_LinkName.

SetMaxRetries()

void CEutilsClient::SetMaxRetries ( unsigned int  max_retries )

inline

Definition at line 411 of file eutils_client.hpp.

References m_MaxRetries.

SetMaxReturn()

void CEutilsClient::SetMaxReturn

(

int

ret_max

)

Definition at line 591 of file eutils_client.cpp.

References m_RetMax.

Referenced by BOOST_AUTO_TEST_CASE(), CNADocSumIterator::CNADocSumIterator(), CSeqUtils::ESearchQuery(), CSeqUtils::GetAssmAccs_Gi(), CSeqUtils::GetAssmIds_GI(), CSeqUtils::GetAssmIds_GIChr(), CReloadPublications::LookUpByPmid(), CDoiLookup::LookupIsojta(), CEntrezDB::Query(), s_ELinkQuery(), s_ESearchQuery(), CMacroFunction_LookupPub::s_GetArticleFromEntrezById(), CAssemblyInfo::x_FilterTaxIds(), CAssemblyInfo::x_GetAssmInfo(), CNAUtils::x_GetNAId(), CRelaxedLookupDlg::x_GetPubIds(), and CAssemblyInfo::x_SearchIds().

SetMessageHandler()

void CEutilsClient::SetMessageHandler

(

CMessageHandler &

message_handler

)

Set custom message handler.

Definition at line 566 of file eutils_client.cpp.

References m_MessageHandler.

SetMessageHandlerDefault()

void CEutilsClient::SetMessageHandlerDefault

(

void

)

Default is to log all messages at informational level.

Equivalent to: LOG_POST(Info << ...).

Definition at line 551 of file eutils_client.cpp.

References m_MessageHandler.

Referenced by CEutilsClient().

SetMessageHandlerDiagPost()

void CEutilsClient::SetMessageHandlerDiagPost

(

void

)

Equivalent to: ERR_POST(Warning|Error << ...).

Definition at line 556 of file eutils_client.cpp.

References m_MessageHandler.

SetMessageHandlerThrowOnError()

void CEutilsClient::SetMessageHandlerThrowOnError

(

void

)

Equivalent to: NCBI_THROW, ERR_POST, LOG_POST as appropriate.

Definition at line 561 of file eutils_client.cpp.

References m_MessageHandler.

SetUserTag()

void CEutilsClient::SetUserTag

(

const string &

tag

)

Definition at line 571 of file eutils_client.cpp.

References m_UrlTag, and tag.

SetWaitTime()

void CEutilsClient::SetWaitTime ( const CIncreasingTime &  wait_time )

inline

Definition at line 410 of file eutils_client.hpp.

References m_WaitTime.

Summary() [1/3]

void CEutilsClient::Summary	(	const string &	db,
		const vector< objects::CSeq_id_Handle > &	uids,
		xml::document &	docsums,
		const string &	version = ""
	)

Referenced by CNADocSumIterator::CNADocSumIterator(), CSeqUtils::GetAssmAccs_Gi(), CSeqUtils::GetAssmIds_GIChr(), CDoiLookup::LookupIsojta(), CEntrezDB::Query(), and CAssemblyInfo::x_GetAssmInfo().

Summary() [2/3]

void CEutilsClient::Summary	(	const string &	db,
		const vector< string > &	uids,
		xml::document &	docsums,
		const string &	version = ""
	)

Definition at line 1513 of file eutils_client.cpp.

References dtl::version, and x_Summary().

Summary() [3/3]

void CEutilsClient::Summary	(	const string &	db,
		const vector< TEntrezId > &	uids,
		xml::document &	docsums,
		const string &	version = ""
	)

Definition at line 1521 of file eutils_client.cpp.

References dtl::version, and x_Summary().

SummaryHistory() [1/3]

void CEutilsClient::SummaryHistory	(	const string &	db,
		const string &	web_env,
		const string &	query_key,
		int	retstart,
		const string &	version,
		CNcbiOstream &	ostr
	)

Definition at line 1636 of file eutils_client.cpp.

References m_RetMax, s_SummaryHistoryQuery(), dtl::version, and x_Get().

SummaryHistory() [2/3]

void CEutilsClient::SummaryHistory	(	const string &	db,
		const string &	web_env,
		Int8	query_key,
		int	retstart,
		const string &	version,
		CNcbiOstream &	ostr
	)

Definition at line 1609 of file eutils_client.cpp.

References m_RetMax, s_SummaryHistoryQuery(), dtl::version, and x_Get().

Referenced by BOOST_AUTO_TEST_CASE().

SummaryHistory() [3/3]

void CEutilsClient::SummaryHistory	(	const string &	db,
		const string &	web_env,
		objects::CSeq_id_Handle	query_key,
		int	retstart,
		const string &	version,
		CNcbiOstream &	ostr
	)

x_AddAdditionalParameters()

void CEutilsClient::x_AddAdditionalParameters ( string &  params )

inlineprotected

Definition at line 1827 of file eutils_client.cpp.

References map_checker< Container >::empty(), and m_AdditionalParams.

Referenced by Count(), x_Fetch(), x_Get(), x_Link(), x_LinkOut(), x_Search(), and x_Summary().

x_BuildUrl()

string CEutilsClient::x_BuildUrl ( const string &  host, const string &  path, const string &  params  )

staticprotected

Definition at line 1817 of file eutils_client.cpp.

Referenced by x_CountOnce(), x_FetchOnce(), x_GetOnce(), x_LinkOnce(), x_LinkOnceT(), x_LinkOutOnce(), x_SearchOnce(), and x_SummaryOnce().

x_CountOnce()

Uint8 CEutilsClient::x_CountOnce ( const string &  params )

private

Definition at line 681 of file eutils_client.cpp.

References CTime::eCurrent, eUnknown, fHTTP_AutoReconnect, g_CTimeoutToSTimeout(), CESearchParser< T >::GetCount(), xml::error_messages::has_errors(), xml::error_messages::has_fatal_errors(), kEmptyStr, m_MessageHandler, m_Time, m_Timeout, m_Url, NCBI_THROW, xml::event_parser::parse_stream(), xml::error_messages::print(), CESearchParser< T >::ProcessMessages(), x_BuildUrl(), and x_GetHostName().

Referenced by Count().

x_Fetch()

template<class T >

void CEutilsClient::x_Fetch ( const string &  db, const vector< T > &  uids, CNcbiOstream &  ostr, const string &  retmode = "xml"  )

protected

Definition at line 1685 of file eutils_client.cpp.

References CallWithRetry(), eUnknown, m_Time, m_Url, NCBI_THROW, s_FormatIds(), NStr::URLEncode(), x_AddAdditionalParameters(), and x_FetchOnce().

Referenced by Fetch().

x_FetchOnce()

void CEutilsClient::x_FetchOnce ( CNcbiOstream &  ostr, const string &  params  )

private

Definition at line 1710 of file eutils_client.cpp.

References CTime::eCurrent, eUnknown, fHTTP_AutoReconnect, g_CTimeoutToSTimeout(), CConn_HttpStream_Base::GetStatusCode(), kEmptyStr, m_Time, m_Timeout, m_Url, NCBI_THROW, NcbiStreamCopy(), x_BuildUrl(), and x_GetHostName().

Referenced by x_Fetch().

x_Get()

void CEutilsClient::x_Get ( string const &  path, string const &  params, CNcbiOstream &  ostr  )

protected

Definition at line 1055 of file eutils_client.cpp.

References CallWithRetry(), eUnknown, m_Time, m_Url, msg(), NCBI_THROW, x_AddAdditionalParameters(), and x_GetOnce().

Referenced by FetchHistory(), LinkHistory(), Search(), SearchHistory(), and SummaryHistory().

x_GetHostName()

const string & CEutilsClient::x_GetHostName ( void  ) const

protected

Definition at line 1010 of file eutils_client.cpp.

References _ASSERT, buf, ConnNetInfo_Create(), ConnNetInfo_Destroy(), ConnNetInfo_GetValue(), free(), fSERV_Dns, HOST_NAME_REFRESH_FREQ, info, m_CachedHostName, m_CachedHostNameCount, m_HostName, CSocketAPI::ntoa(), REG_CONN_HOST, SERV_ANYHOST, SERV_GetInfo(), and string.

Referenced by x_CountOnce(), x_FetchOnce(), x_GetOnce(), x_LinkOnce(), x_LinkOnceT(), x_LinkOutOnce(), x_SearchOnce(), and x_SummaryOnce().

x_GetOnce()

void CEutilsClient::x_GetOnce ( string const &  path, string const &  extra_params, CNcbiOstream &  ostr  )

private

Definition at line 1077 of file eutils_client.cpp.

References CTime::eCurrent, eUnknown, fHTTP_AutoReconnect, g_CTimeoutToSTimeout(), CConn_HttpStream_Base::GetStatusCode(), kEmptyStr, m_Time, m_Timeout, m_Url, NCBI_THROW, NcbiStreamCopy(), ParseSearchResults(), x_BuildUrl(), and x_GetHostName().

Referenced by x_Get().

x_InitParams()

void CEutilsClient::x_InitParams ( void  )

private

Definition at line 599 of file eutils_client.cpp.

References DEFAULT_MAX_RETRIES, CTimeout::eDefault, ERR_POST, EUTILS_CLIENT_SECTION, NStr::fDecimalPosixOrLocal, CNcbiApplicationAPI::GetConfig(), IRegistry::GetString(), CIncreasingTime::Init(), CNcbiApplicationAPI::InstanceGuard(), m_MaxRetries, m_Timeout, m_WaitTime, s_WaitTimeParams, CTimeout::Set(), and NStr::StringToDouble().

Referenced by CEutilsClient().

x_Link() [1/2]

template<class T >

void CEutilsClient::x_Link ( const string &  db_from, const string &  db_to, const vector< T > &  uids_from, CNcbiOstream &  ostr, const string &  command  )

protected

Definition at line 1312 of file eutils_client.cpp.

References CallWithRetry(), command, eUnknown, m_Time, m_Url, NCBI_THROW, s_FormatIds(), NStr::URLEncode(), x_AddAdditionalParameters(), and x_LinkOnce().

x_Link() [2/2]

template<class T1 , class T2 >

void CEutilsClient::x_Link ( const string &  db_from, const string &  db_to, const vector< T1 > &  uids_from, vector< T2 > &  uids_to, const string &  xml_path, const string &  command  )

protected

Definition at line 1190 of file eutils_client.cpp.

References CallWithRetry(), command, eUnknown, m_Time, m_Url, NCBI_THROW, s_FormatIds(), NStr::URLEncode(), and x_AddAdditionalParameters().

Referenced by Link().

x_LinkOnce()

void CEutilsClient::x_LinkOnce ( CNcbiOstream &  ostr, const string &  params  )

private

Definition at line 1340 of file eutils_client.cpp.

References CTime::eCurrent, eUnknown, fHTTP_AutoReconnect, g_CTimeoutToSTimeout(), CConn_HttpStream_Base::GetStatusCode(), kEmptyStr, m_Time, m_Timeout, m_Url, NCBI_THROW, NcbiStreamCopy(), x_BuildUrl(), and x_GetHostName().

Referenced by x_Link().

x_LinkOnceT()

template<class T >

void CEutilsClient::x_LinkOnceT ( const string &  db_from, const string &  db_to, vector< T > &  uids_to, const string &  xml_path, const string &  params  )

private

Definition at line 1222 of file eutils_client.cpp.

References CTime::eCurrent, ERR_POST, Error(), eUnknown, fHTTP_AutoReconnect, g_CTimeoutToSTimeout(), CConn_HttpStream_Base::GetStatusCode(), xml::error_messages::has_errors(), xml::error_messages::has_fatal_errors(), kEmptyStr, m_Attempt, m_LinkName, m_Time, m_Timeout, m_Url, NCBI_THROW, NcbiStreamCopy(), NStr::NumericToString(), xml::event_parser::parse_file(), xml::event_parser::parse_stream(), xml::error_messages::print(), CELinkParser< T >::SetLinkName(), x_BuildUrl(), and x_GetHostName().

x_LinkOut()

template<class T >

void CEutilsClient::x_LinkOut ( const string &  db, const vector< T > &  uids, xml::document &  doc, const string &  cmd  )

protected

Definition at line 1444 of file eutils_client.cpp.

References CallWithRetry(), cmd, eUnknown, m_Time, m_Url, NCBI_THROW, s_FormatIds(), NStr::URLEncode(), x_AddAdditionalParameters(), and x_LinkOutOnce().

Referenced by LinkOut().

x_LinkOutOnce()

void CEutilsClient::x_LinkOutOnce ( xml::document &  doc, const string &  params  )

private

Definition at line 1469 of file eutils_client.cpp.

References CTime::eCurrent, eUnknown, fHTTP_AutoReconnect, g_CTimeoutToSTimeout(), CConn_HttpStream_Base::GetStatusCode(), kEmptyStr, LOG_POST, m_Time, m_Timeout, m_Url, NCBI_THROW, xml::document::swap(), Trace(), x_BuildUrl(), and x_GetHostName().

Referenced by x_LinkOut().

x_ParseSearchResults() [1/2]

template<class T >

Uint8 CEutilsClient::x_ParseSearchResults ( CNcbiIstream &  istr, vector< T > &  uids  )

protected

Definition at line 735 of file eutils_client.cpp.

References eUnknown, CESearchParser< T >::GetCount(), CEUtilsParser::GetErrors(), xml::error_messages::has_errors(), xml::error_messages::has_fatal_errors(), CEUtilsParser::HasError(), NStr::Join(), m_MessageHandler, msg(), NCBI_THROW, xml::event_parser::parse_stream(), xml::error_messages::print(), and CESearchParser< T >::ProcessMessages().

x_ParseSearchResults() [2/2]

template<class T >

Uint8 CEutilsClient::x_ParseSearchResults ( const string &  xml_file, vector< T > &  uids  )

protected

Definition at line 787 of file eutils_client.cpp.

References eUnknown, NCBI_THROW, and ParseSearchResults().

Referenced by ParseSearchResults().

x_Search()

template<class T >

Uint8 CEutilsClient::x_Search ( const string &  db, const string &  term, vector< T > &  uids, const string &  xml_path = kEmptyStr  )

protected

Definition at line 834 of file eutils_client.cpp.

References CallWithRetry(), eUnknown, LOG_POST, m_RetMax, m_Time, m_Url, m_UrlTag, NCBI_THROW, NStr::NumericToString(), Trace(), NStr::URLEncode(), rapidjson::value, and x_AddAdditionalParameters().

Referenced by Search().

x_SearchOnce()

template<class T >

Uint8 CEutilsClient::x_SearchOnce ( const string &  params, vector< T > &  uids, const string &  xml_path  )

private

Definition at line 873 of file eutils_client.cpp.

References count, CTime::eCurrent, ERR_POST, Error(), eUnknown, fHTTP_AutoReconnect, g_CTimeoutToSTimeout(), CConn_HttpStream_Base::GetStatusCode(), kEmptyStr, m_Attempt, m_Time, m_Timeout, m_Url, NCBI_THROW, NcbiStreamCopy(), NStr::NumericToString(), ParseSearchResults(), x_BuildUrl(), and x_GetHostName().

x_Summary()

template<class T >

void CEutilsClient::x_Summary ( const string &  db, const vector< T > &  uids, xml::document &  docsums, const string &  version = ""  )

protected

Definition at line 1530 of file eutils_client.cpp.

References CallWithRetry(), eUnknown, m_Time, m_Url, NCBI_THROW, s_FormatIds(), NStr::URLEncode(), dtl::version, x_AddAdditionalParameters(), and x_SummaryOnce().

Referenced by Summary().

x_SummaryOnce()

void CEutilsClient::x_SummaryOnce ( xml::document &  docsums, const string &  params  )

private

Definition at line 1558 of file eutils_client.cpp.

References CTime::eCurrent, eUnknown, fHTTP_AutoReconnect, g_CTimeoutToSTimeout(), CConn_HttpStream_Base::GetStatusCode(), kEmptyStr, LOG_POST, m_Time, m_Timeout, m_Url, NCBI_THROW, xml::document::swap(), Trace(), x_BuildUrl(), and x_GetHostName().

Referenced by x_Summary().

Member Data Documentation

m_AdditionalParams

TParamList CEutilsClient::m_AdditionalParams

protected

Definition at line 450 of file eutils_client.hpp.

Referenced by AddParameter(), ClearAddedParameters(), and x_AddAdditionalParameters().

m_Attempt

unsigned int CEutilsClient::m_Attempt = 0

private

Definition at line 543 of file eutils_client.hpp.

Referenced by CallWithRetry(), x_LinkOnceT(), and x_SearchOnce().

m_CachedHostName

string CEutilsClient::m_CachedHostName

mutableprotected

Definition at line 447 of file eutils_client.hpp.

Referenced by x_GetHostName().

m_CachedHostNameCount

int CEutilsClient::m_CachedHostNameCount

mutableprotected

Definition at line 446 of file eutils_client.hpp.

Referenced by x_GetHostName().

m_HostName

string CEutilsClient::m_HostName

protected

Definition at line 448 of file eutils_client.hpp.

Referenced by x_GetHostName().

m_LinkName

string CEutilsClient::m_LinkName

protected

Definition at line 452 of file eutils_client.hpp.

Referenced by SetLinkName(), and x_LinkOnceT().

m_MaxRetries

unsigned int CEutilsClient::m_MaxRetries

private

Definition at line 541 of file eutils_client.hpp.

Referenced by CallWithRetry(), SetMaxRetries(), and x_InitParams().

m_MessageHandler

CRef<CMessageHandler> CEutilsClient::m_MessageHandler

protected

Definition at line 445 of file eutils_client.hpp.

Referenced by SetMessageHandler(), SetMessageHandlerDefault(), SetMessageHandlerDiagPost(), SetMessageHandlerThrowOnError(), x_CountOnce(), and x_ParseSearchResults().

m_RetMax

int CEutilsClient::m_RetMax

protected

Definition at line 451 of file eutils_client.hpp.

Referenced by FetchHistory(), Search(), SearchHistory(), SetMaxReturn(), SummaryHistory(), and x_Search().

m_Time

list<CTime> CEutilsClient::m_Time

protected

Definition at line 460 of file eutils_client.hpp.

Referenced by Count(), GetTime(), x_CountOnce(), x_Fetch(), x_FetchOnce(), x_Get(), x_GetOnce(), x_Link(), x_LinkOnce(), x_LinkOnceT(), x_LinkOut(), x_LinkOutOnce(), x_Search(), x_SearchOnce(), x_Summary(), and x_SummaryOnce().

m_Timeout

CTimeout CEutilsClient::m_Timeout

private

Definition at line 544 of file eutils_client.hpp.

Referenced by SetConnTimeout(), x_CountOnce(), x_FetchOnce(), x_GetOnce(), x_InitParams(), x_LinkOnce(), x_LinkOnceT(), x_LinkOutOnce(), x_SearchOnce(), and x_SummaryOnce().

m_Url

list<string> CEutilsClient::m_Url

protected

Definition at line 456 of file eutils_client.hpp.

Referenced by Count(), GetUrl(), x_CountOnce(), x_Fetch(), x_FetchOnce(), x_Get(), x_GetOnce(), x_Link(), x_LinkOnce(), x_LinkOnceT(), x_LinkOut(), x_LinkOutOnce(), x_Search(), x_SearchOnce(), x_Summary(), and x_SummaryOnce().

m_UrlTag

string CEutilsClient::m_UrlTag

protected

Definition at line 449 of file eutils_client.hpp.

Referenced by Count(), SetUserTag(), and x_Search().

m_WaitTime

CIncreasingTime CEutilsClient::m_WaitTime

private

Definition at line 542 of file eutils_client.hpp.

Referenced by CallWithRetry(), SetWaitTime(), and x_InitParams().

---

The documentation for this class was generated from the following files:

• include/misc/eutils_client/eutils_client.hpp
• src/misc/eutils_client/eutils_client.cpp