taxon3.cpp

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/* $Id: taxon3.cpp 94765 2021-09-09 15:09:43Z stakhovv $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Author:  Colleen Bollin, based on work by Vladimir Soussov, Michael Domrachev
 *
 * File Description:
 *     NCBI Taxonomy 3 service library implementation
 *
 */
 
#include <ncbi_pch.hpp>
#include <corelib/ncbistr.hpp>
#include <corelib/ncbienv.hpp>
#include <objects/taxon3/taxon3.hpp>
#include <objects/seqfeat/seqfeat__.hpp>
#include <objects/misc/error_codes.hpp>
#include <connect/ncbi_conn_stream.hpp>
#include <serial/serial.hpp>
#include <serial/enumvalues.hpp>
#include <serial/objistr.hpp>
#include <serial/objostr.hpp>
 
#include <algorithm>
 
 
#define NCBI_USE_ERRCODE_X   Objects_Taxonomy
 
 
BEGIN_NCBI_SCOPE
BEGIN_objects_SCOPE // namespace ncbi::objects::
 
 
CTaxon3::CTaxon3(initialize init)
{
    if (init == initialize::yes) {
        CTaxon3::Init();
    }
}
 
CTaxon3::CTaxon3(const STimeout& timeout, unsigned reconnect_attempts, bool exponential)
  : m_exponential(exponential)
{
    CTaxon3::Init(&timeout, reconnect_attempts);
}
 
CTaxon3::~CTaxon3()
{
}
 
 
void
CTaxon3::Init()
{
    static const STimeout def_timeout = { 20, 0 };
    CTaxon3::Init(&def_timeout);
}
 
 
void
CTaxon3::Init(const STimeout* timeout, unsigned reconnect_attempts)
{
    SetLastError(nullptr);
 
    if ( timeout ) {
        m_timeout_value = *timeout;
        m_timeout = &m_timeout_value;
    } else {
        m_timeout = kInfiniteTimeout;
    }
 
    m_nReconnectAttempts = reconnect_attempts;
 
    CNcbiEnvironment env;
    bool bFound = false;
 
    m_sService = env.Get("NI_SERVICE_NAME_TAXON3", &bFound);
    if( !bFound ) {
        m_sService = env.Get("NI_TAXON3_SERVICE_NAME", &bFound);
        if( !bFound ) {
            m_sService = "TaxService3";
        }
    }
 
#ifdef USE_TEXT_ASN
    m_eDataFormat = eSerial_AsnText;
#else
    m_eDataFormat = eSerial_AsnBinary;
#endif
}
 
 
CRef< CTaxon3_reply >
CTaxon3::SendRequest(const CTaxon3_request& request)
{
    SetLastError(nullptr);
 
    unsigned reconnect_attempts = 0;
    const STimeout* pTimeout = m_timeout;
    STimeout to;
    if (m_exponential) {
        to = m_timeout_value;
        pTimeout = &to;
    }
 
    while (reconnect_attempts < m_nReconnectAttempts) {
        try {
            unique_ptr<CObjectOStream> pOut;
            unique_ptr<CObjectIStream> pIn;
            unique_ptr<CConn_ServiceStream> pServer(
              new CConn_ServiceStream( m_sService, fSERV_Any, nullptr, nullptr, pTimeout) );
 
            pOut.reset( CObjectOStream::Open(m_eDataFormat, *pServer) );
            pIn.reset( CObjectIStream::Open(m_eDataFormat, *pServer) );
 
            CObjectIStream* ppIn = pIn.release();
            CObjectOStream* ppOut = pOut.release();
 
            try {
                *ppOut << request;
                ppOut->Flush();
                ppOut->Close();
 
                try {
                    CRef< CTaxon3_reply > response(new CTaxon3_reply);
                    *ppIn >> *response;
 
                    delete ppIn;
                    delete ppOut;
 
                    return response;
                } catch (exception& e) {
                    SetLastError( e.what() );
                }
            } catch (exception& e) {
                SetLastError( e.what() );
            }
 
        } catch( exception& e ) {
            SetLastError( e.what() );
        }
        reconnect_attempts++;
        if (m_exponential) {
            // double the value
            to.sec <<= 1;
            to.usec <<= 1;
            if (to.usec >= 1'000'000) {
                to.sec++;
                to.usec -= 1'000'000;
            }
        }
    }
 
    // return NULL
    CRef<CTaxon3_reply> reply;
    return reply;
}
 
void
CTaxon3::SetLastError( const char* pchErr )
{
    if( pchErr )
        m_sLastError.assign( pchErr );
    else
        m_sLastError.erase();
}
 
 
CRef<CTaxon3_reply> CTaxon3::SendOrgRefList(const vector<CRef< COrg_ref> >& list,
                                            COrg_ref::fOrgref_parts result_parts,
                                            fT3reply_parts t3reply_parts)
{
    CTaxon3_request request;
    if( result_parts != COrg_ref::eOrgref_default ||
        t3reply_parts != eT3reply_default ) {
        CRef<CT3Request> rq(new CT3Request);
        rq->SetJoin().Set().push_back( -int(result_parts) );
        rq->SetJoin().Set().push_back( -int(t3reply_parts) ); // set return parts
        request.SetRequest().push_back(rq);
    }
    for (CRef<COrg_ref> it : list) {
        CRef<CT3Request> rq(new CT3Request);
        CRef<COrg_ref> org(new COrg_ref);
        org->Assign(*it);
        rq->SetOrg(*org);
        request.SetRequest().push_back(rq);
    }
    return SendRequest(request);
}
 
CRef< CTaxon3_reply >
CTaxon3::SendNameList(const vector<std::string>& list,
                      COrg_ref::fOrgref_parts result_parts,
                      fT3reply_parts t3reply_parts)
{
    CTaxon3_request request;
    if( result_parts != COrg_ref::eOrgref_default ||
        t3reply_parts != eT3reply_default ) {
        CRef<CT3Request> rq(new CT3Request);
        rq->SetJoin().Set().push_back( -int(result_parts) );
        rq->SetJoin().Set().push_back( -int(t3reply_parts) ); // set return parts
        request.SetRequest().push_back(rq);
    }
    for (const std::string& it : list) {
        CRef<CT3Request> rq(new CT3Request);
        rq->SetName(it);
        request.SetRequest().push_back(rq);
    }
    return SendRequest(request);
}
 
CRef< CTaxon3_reply >
CTaxon3::SendTaxidList(const vector<TTaxId>& list,
                       COrg_ref::fOrgref_parts result_parts,
                       fT3reply_parts t3reply_parts)
{
    CTaxon3_request request;
    if( result_parts != COrg_ref::eOrgref_default ||
        t3reply_parts != eT3reply_default ) {
        CRef<CT3Request> rq(new CT3Request);
        rq->SetJoin().Set().push_back( -int(result_parts) );
        rq->SetJoin().Set().push_back( -int(t3reply_parts) ); // set return parts
        request.SetRequest().push_back(rq);
    }
    for (TTaxId it : list) {
        CRef<CT3Request> rq(new CT3Request);
        rq->SetTaxid(TAX_ID_TO(int, it));
        request.SetRequest().push_back(rq);
    }
    return SendRequest(request);
}
 
 
END_objects_SCOPE
END_NCBI_SCOPE