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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/reader__pubseq2_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/data_loaders/genbank/pubseq2/reader_pubseq2.cpp Source File

65 #define BINARY_REQUESTS 1 66 #define LONG_REQUESTS 1 70 #define CRequestSerializer CObjectOStreamAsnBinary 73 #define CRequestSerializer CObjectOStreamAsn 76 # define MAX_ASN_IN (20*1024) 78 # define MAX_ASN_IN 255 81 #define DEFAULT_DB_SERVER "PUBSEQ_OS_PUBLIC_GI64" 82 #define DEFAULT_DB_USER "anyone" 83 #define DEFAULT_DB_PASSWORD "allowed" 84 #define DEFAULT_DB_DRIVER "ftds;ctlib" 85 #define DEFAULT_NUM_CONN 2 86 #define MAX_MT_CONN 256 87 #define DEFAULT_EXCL_WGS_MASTER false 88 #define DEFAULT_TIMEOUT 40 89 #define DEFAULT_OPEN_TIMEOUT 20 91 #define NCBI_USE_ERRCODE_X Objtools_Rd_Pubseq2 98 const string

& server,

101 const string

& dbapi_driver)

102

: m_Server(server) , m_User(user), m_Password(pswd),

103

m_DbapiDriver(dbapi_driver),

104

m_Context(

nullptr

106

m_SetCubbyUser(

false

)

108 if

( m_Server.empty() ) {

111 if

( m_User.empty() ) {

114 if

( m_Password.empty() ) {

117 if

( m_DbapiDriver.empty() ) {

126 const string

& driver_name)

129

m_SetCubbyUser(

false

)

190 #if defined(NCBI_THREADS) 250 "CPubseq2Reader: no active command"

);

252 return

*iter->second.m_Result;

263 "CPubseq2Reader: no active connection"

);

265

iter->second.m_Result =

result

;

277 bool

excl_wgs_master)

280

m_ExclWGSMaster(excl_wgs_master)

285 if

( m_ExclWGSMaster ) {

287

(

conn

.LangCmd(

"set exclude_wgs_master on"

));

291

m_Reader->x_InitConnection(

conn

, m_Conn);

295 virtual string

GetName(

void

)

const

{

296 return "CPubseq2Validator"

;

302 bool

m_ExclWGSMaster;

307 while

(

result

.Fetch() ) {

308 for

(

unsigned

pos = 0; pos <

result

.NofItems(); ++pos ) {

309 if

(

result

.ItemName(pos) == name ) {

339 if

( !sx_FetchNextItem(*

m_DB_Result

"asnout"

) ) {

340

m_DB_RPCCmd->DumpResults();

362 static const char

* kEMyNCBIURL =

363 "https://www.ncbi.nlm.nih.gov/entrez/eutils/emyncbi.cgi?cmd=whoami&WebCubbyUser="

;

365 if

(!web_cookie.empty()) {

367 int

response_timeout = 40;

369

session.

Get

(

CUrl

(kEMyNCBIURL + web_cookie),

CTimeout

(response_timeout), 0);

376 if

(

result

.GetUE().IsUU() &&

result

.GetUE().GetUU().IsSetUserName())

377

cubby_user =

result

.GetUE().GetUU().GetUserName();

385 if

(cubby_user.empty())

402

args[

"packet"

"3584"

;

403

args[

"version"

"125"

;

404

vector<string> driver_list;

406 size_t

driver_count = driver_list.size();

407

vector<string> errmsg(driver_count);

408 for

(

size_t i

= 0;

< driver_count; ++

) {

411

&errmsg[

], &args);

417

errmsg[

] = exc.

what

();

421 for

(

size_t i

= 0;

< driver_count; ++

) {

422 ERR_POST_X

(2,

"Failed to create dbapi context with driver '" 423

<<driver_list[

]<<

"': "

<<errmsg[

]);

426 "Cannot create dbapi context with driver '"

441 if

( !

conn

.get() ) {

456 NcbiCout

"CPubseq2Reader::Connected to "

conn

->ServerName()

471

packet.

Set

().push_back(

Ref

(&req));

489

s <<

" ID2-Request-Packet"

;

498 "failed to send init request"

);

502

s <<

"Sent ID2-Request-Packet."

;

511

s <<

"Receiving ID2-Reply..."

;

529 "bad init reply: 'discard' is set"

);

533 "bad init reply: 'error' is set"

);

537 "bad init reply: 'end-of-reply' is not set"

);

541 "bad init reply: 'reply' is not 'init'"

);

543 if

(

result

->HaveMoreData() ) {

574 ERR_POST_X

(4,

"CPubseq2Reader: extra blob data"

);

597 "CPubseq2Reader: packet size overflow"

);

599 size

= mem_str.pcount();

614 cmd

->SetParam(

"@service"

, &service);

615 cmd

->SetParam(

"@asnin"

, &short_asn);

616 cmd

->SetParam(

"@text"

, &text_in);

617 cmd

->SetParam(

"@out_text"

, &text_out);

618 cmd

->SetParam(

"@asnin_long"

, &long_asn);

622 while

(

cmd

->HasMoreResults() ) {

623 if

(

cmd

->HasFailed() ) {

625 "CPubseq2Reader: failed RPC"

);

627

dbr =

cmd

->Result();

628 if

( !dbr.

get

() ) {

633 while

( dbr->

Fetch

() )

637 if

( sx_FetchNextItem(*dbr,

"asnout"

) ) {

648 "CPubseq2Reader: no more results"

);

653 const string

& web_cookie)

678

objects::CPubseq2Reader>

695

objects::CReader* drv = 0;

701

drv =

new

objects::CPubseq2Reader(params, driver);

User-defined methods of the data storage class.

ERW_Result PendingCount(size_t *)

Via parameter "count" (which is guaranteed to be supplied non-NULL) return the number of bytes that a...

ERW_Result Read(void *buf, size_t count, size_t *bytes_read)

Read as many as "count" bytes into a buffer pointed to by the "buf" argument.

CDB_Result_Reader(CDB_Result *db_result)

virtual void x_ReceiveReply(TConn conn, CID2_Reply &reply)=0

void x_SetContextData(CID2_Request &request)

void x_DisableProcessors()

static int GetDebugLevel(void)

Data loader exceptions, used by GenBank loader.

CObjectIStreamAsnBinary â.

Class factory for Pubseq reader.

CSimpleClassFactoryImpl< objects::CReader, objects::CPubseq2Reader > TParent

objects::CReader * CreateInstance(const string &driver=kEmptyStr, CVersionInfo version=NCBI_INTERFACE_VERSION(objects::CReader), const TPluginManagerParamTree *params=0) const

Create instance of TDriver.

virtual void x_ReceiveReply(TConn conn, CID2_Reply &reply) override

virtual void x_AddConnectionSlot(TConn conn) override

virtual void x_RemoveConnectionSlot(TConn conn) override

void x_InitConnection(CDB_Connection &db_conn, TConn conn)

CPubseq2Reader(int max_connections=0, const string &server=kEmptyStr, const string &user=kEmptyStr, const string &pswd=kEmptyStr, const string &dbapi_driver=kEmptyStr)

virtual void SetIncludeHUP(bool include_hup=true, const string &web_cookie=NcbiEmptyString) override

void x_SetCurrentResult(TConn conn, AutoPtr< CObjectIStream > result)

TConnections m_Connections

atomic< I_DriverContext * > m_Context

virtual string x_ConnDescription(TConn conn) const override

virtual void x_DisconnectAtSlot(TConn conn, bool failed) override

virtual void x_EndOfPacket(TConn conn) override

CObjectIStream & x_GetCurrentResult(TConn conn)

virtual int GetMaximumConnectionsLimit(void) const override

CDB_Connection & x_GetConnection(TConn conn)

virtual void x_ConnectAtSlot(TConn conn) override

virtual void x_SendPacket(TConn conn, const CID2_Request_Packet &packet) override

virtual ~CPubseq2Reader() override

Note about the "buf_size" parameter for streams in this API.

void x_SetIncludeHUP(bool include_hup)

void x_ReportDisconnect(const char *reader, const char *server, TConn conn, bool failed) const

virtual void OpenConnection(TConn conn)

void InitParams(CConfig &conf, const string &driver_name, int default_max_conn)

Template class helps to implement one driver class factory.

static string GetUserName(void)

Get actual user name for the current process.

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

CTimeout â Timeout interval.

definition of a Culling tree

A very basic data-read interface.

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

#define DBLB_INSTALL_DEFAULT()

Easy-to-use macro to install the default DBAPI service mapper.

static CS_CONNECTION * conn

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

element_type * get(void) const

Get pointer.

element_type * release(void)

Release will release ownership of pointer to caller.

@ eTakeOwnership

An object can take ownership of another.

I_DriverContext * GetDriverContext(const string &driver_name, string *err_msg=0, const map< string, string > *attr=0)

virtual EDB_ResType ResultType() const

Get type of the result.

virtual size_t ReadItem(void *buffer, size_t buffer_size, bool *is_null=0)

Read a result item body (for BLOB columns, mostly).

virtual CDB_RPCCmd * RPC(const string &rpc_name)

Make remote procedure call command.

virtual void SetTimeout(size_t nof_secs)

Set connection timeout.

virtual bool Fetch()

Fetch next row.

void SetValue(const void *v, size_t v_size)

CDB_VarChar & SetValue(const string &s, EEncoding enc=eEncoding_Unknown)

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

#define NCBI_RETHROW(prev_exception, exception_class, err_code, message)

Generic macro to re-throw an exception.

#define MSerial_AsnText

I/O stream manipulators â.

CHttpResponse Get(const CUrl &url, const CTimeout &timeout=CTimeout(CTimeout::eDefault), THttpRetries retries=null)

Shortcut for GET requests.

CNcbiIstream & ContentStream(void) const

Get input stream.

int GetStatusCode(void) const

Get response status code.

int GetInt(const string &driver_name, const string &param_name, EErrAction on_error, int default_value, const list< string > *synonyms=NULL)

Utility function to get an integer element of parameter tree Throws an exception when mandatory param...

string GetString(const string &driver_name, const string &param_name, EErrAction on_error, const string &default_value, const list< string > *synonyms=NULL)

Utility function to get an element of parameter tree Throws an exception when mandatory parameter is ...

bool GetBool(const string &driver_name, const string &param_name, EErrAction on_error, bool default_value, const list< string > *synonyms=NULL)

Utility function to get an integer element of parameter tree Throws an exception when mandatory param...

@ eErr_NoThrow

Return default value on error.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

static void NCBI_EntryPointImpl(TDriverInfoList &info_list, EEntryPointRequest method)

Entry point implementation.

#define NCBI_INTERFACE_VERSION(iface)

Macro to construct CVersionInfo class using interface name (relies on CInterfaceVersion class)

list< SDriverInfo > TDriverInfoList

List of driver information.

EEntryPointRequest

Actions performed by the entry point.

#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.

ERW_Result

Result codes for I/O operations.

@ eRW_NotImplemented

Action / information is not available.

@ eRW_Eof

End of data, should be considered permanent.

@ eRW_Success

Everything is okay, I/O completed.

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 CStringUTF8 SQLEncode(const CStringUTF8 &str, ESqlEncode flag)

SQL-encode string.

@ eSqlEnc_TagNonASCII

Produce N'...' when input's not pure ASCII.

#define DEFINE_STATIC_FAST_MUTEX(id)

Define static fast mutex and initialize it.

@ eNonCompatible

major, minor does not match

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetDiscard(void) const

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

const TReply & GetReply(void) const

Get the Reply member data.

Tdata & Set(void)

Assign a value to data member.

bool IsSetError(void) const

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

void SetRequest(TRequest &value)

Assign a value to Request data member.

bool IsSetEnd_of_reply(void) const

true if this reply is the last one for the request false if more replies will follow Check if a value...

const string version

version string

const struct ncbi::grid::netcache::search::fields::SIZE size

Helper classes and templates to implement plugins.

#define DEFAULT_DB_PASSWORD

#define DEFAULT_DB_DRIVER

void GenBankReaders_Register_Pubseq2(void)

void NCBI_EntryPoint_xreader_pubseqos2(CPluginManager< objects::CReader >::TDriverInfoList &info_list, CPluginManager< objects::CReader >::EEntryPointRequest method)

#define DEFAULT_EXCL_WGS_MASTER

#define DEFAULT_DB_SERVER

void NCBI_EntryPoint_ReaderPubseqos2(CPluginManager< objects::CReader >::TDriverInfoList &info_list, CPluginManager< objects::CReader >::EEntryPointRequest method)

#define CRequestSerializer

#define DEFAULT_OPEN_TIMEOUT

static string s_GetCubbyUserName(const string &web_cookie)

#define NCBI_GBLOADER_READER_PUBSEQ2_PARAM_OPEN_TIMEOUT

#define NCBI_GBLOADER_READER_PUBSEQ2_PARAM_EXCL_WGS_MASTER

#define NCBI_GBLOADER_READER_PUBSEQ2_PARAM_SERVER

#define NCBI_GBLOADER_READER_PUBSEQ2_DRIVER_NAME

#define NCBI_GBLOADER_READER_PUBSEQ2_PARAM_DRIVER

#define NCBI_GBLOADER_READER_PUBSEQ2_PARAM_TIMEOUT

#define NCBI_GBLOADER_READER_PUBSEQ2_PARAM_PASSWORD

#define NCBI_GBLOADER_READER_PUBSEQ2_PARAM_USER

Reader-writer based streams.

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

AutoPtr< CDB_Connection > m_Connection

AutoPtr< CObjectIStream > m_Result

static CS_CONTEXT * context

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