entrez_db.cpp

来自「ncbi源码」· C++ 代码 · 共 384 行

/*
 * ===========================================================================
 * PRODUCTION $Log: entrez_db.cpp,v $
 * PRODUCTION Revision 1000.0  2004/06/01 21:26:30  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.1
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: entrez_db.cpp,v 1000.0 2004/06/01 21:26:30 gouriano Exp $
 * ===========================================================================
 *
 *                            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.
 *
 * ===========================================================================
 *
 * Authors:  Mike DiCuccio
 *
 * File Description:
 *    CDataPlugin_EntrezSearch - load sequence information form Genbank.
 */

#include <ncbi_pch.hpp>
#include "entrez_db.hpp"
#include <objects/entrez2/Entrez2_id_list.hpp>
#include <objects/entrez2/Entrez2_info.hpp>
#include <objects/entrez2/Entrez2_eval_boolean.hpp>
#include <objects/entrez2/Entrez2_boolean_reply.hpp>
#include <objects/entrez2/Entrez2_boolean_exp.hpp>
#include <objects/entrez2/Entrez2_boolean_element.hpp>
#include <objects/entrez2/Entrez2_docsum.hpp>
#include <objects/entrez2/Entrez2_docsum_list.hpp>
#include <objects/entrez2/Entrez2_docsum_data.hpp>
#include <objects/entrez2/Entrez2_db_id.hpp>
#include <objects/entrez2/Entrez2_limits.hpp>
#include <gui/core/version.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


//
// db=nucleotide or db=protein
//
class CEntrezDB_NucProt : public CEntrezDBHandler
{
public:

    CEntrezDB_NucProt(const string& db, const string& visible_db)
        : m_DB(db),
          m_VisibleDB(visible_db) {}

    string GetDbName() const
    {
        return m_DB;
    }

    string GetVisibleDbName() const
    {
        return m_VisibleDB;
    }

    void GetHeaders(vector<SHeaderInfo>& headers) const
    {
        headers.push_back(SHeaderInfo("ID", 1.0));
        headers.push_back(SHeaderInfo("Description", 4.0));
    }

    void Format(const CEntrez2_docsum& ds,
                vector<string>& cols) const
    {
        cols.push_back(ds.GetValue("Caption"));
        cols.push_back(ds.GetValue("Title"));
    }

    // retrieve seq-ids for a given set of docsums
    TIds GetSeqIds(const CEntrez2_docsum_list& ds_list,
                   TSeqIdFlags flags = fDefaults)
    {
        TIds ids;
        ITERATE (CEntrez2_docsum_list::TList, iter, ds_list.GetList()) {
            const CEntrez2_docsum& ds = **iter;
            CRef<CSeq_id> id(new CSeq_id());
            id->SetGi(ds.GetUid());
            ids.push_back(id);
        }
        return ids;
    }

    TIds GetSeqIds(const CEntrez2_docsum& ds,
                   TSeqIdFlags flags = fDefaults)
    {
        TIds ids;
        CRef<CSeq_id> id(new CSeq_id());
        id->SetGi(ds.GetUid());
        ids.push_back(id);
        return ids;
    }

private:
    string m_DB;
    string m_VisibleDB;
};


class CEntrezDB_Genome : public CEntrezDBHandler
{
public:
    string GetDbName() const
    {
        return "genome";
    }

    string GetVisibleDbName() const
    {
        return "Genome";
    }

    void GetHeaders(vector<SHeaderInfo>& headers) const
    {
        headers.push_back(SHeaderInfo("ID", 1.0));
        headers.push_back(SHeaderInfo("Description", 4.0));
    }

    void Format(const CEntrez2_docsum& ds,
                vector<string>& cols) const
    {
        cols.push_back(ds.GetValue("Caption"));
        cols.push_back(ds.GetValue("Title"));
    }

    // retrieve seq-ids for a given set of docsums
    TIds GetSeqIds(const CEntrez2_docsum_list& ds_list,
                   TSeqIdFlags flags = fDefaults)
    {
        TIds ids;
        ITERATE (CEntrez2_docsum_list::TList, iter, ds_list.GetList()) {
            string str = (*iter)->GetValue("Extra");
            CRef<CSeq_id> id(new CSeq_id(str));
            if (id->Which() != CSeq_id::e_not_set) {
                ids.push_back(id);
            }
        }

        return ids;
    }

    TIds GetSeqIds(const CEntrez2_docsum& ds,
                   TSeqIdFlags flags = fDefaults)
    {
        TIds ids;
        string str = ds.GetValue("Extra");
        CRef<CSeq_id> id(new CSeq_id(str));
        if (id->Which() != CSeq_id::e_not_set) {
            ids.push_back(id);
        }
        return ids;
    }
};


class CEntrezDB_Gene : public CEntrezDBHandler
{
public:
    string GetDbName() const
    {
        return "gene";
    }

    string GetVisibleDbName() const
    {
        return "Entrez Gene";
    }

    void GetHeaders(vector<SHeaderInfo>& headers) const
    {
        headers.push_back(SHeaderInfo("Symbol", 1.0));
        headers.push_back(SHeaderInfo("Description", 3.0));
        headers.push_back(SHeaderInfo("Organism", 3.0));
    }

    void Format(const CEntrez2_docsum& ds,
                vector<string>& cols) const
    {
        cols.push_back(ds.GetValue("Name"));
        cols.push_back(ds.GetValue("Description"));
        cols.push_back(ds.GetValue("Orgname"));
    }

    // retrieve seq-ids for a given set of docsums
    TIds GetSeqIds(const CEntrez2_docsum_list& ds_list,
                   TSeqIdFlags flags = fDefaults)
    {
        TIds ids;

        return ids;
    }

    TIds GetSeqIds(const CEntrez2_docsum& ds,
                   TSeqIdFlags flags = fDefaults)
    {
        TIds ids;

        return ids;
    }
};


class CEntrezDB_HomoloGene : public CEntrezDBHandler
{
public:
    string GetDbName() const
    {
        return "homologene";
    }

    string GetVisibleDbName() const
    {
        return "HomoloGene";
    }

    void GetHeaders(vector<SHeaderInfo>& headers) const
    {
        headers.push_back(SHeaderInfo("ID", 1.0));
        headers.push_back(SHeaderInfo("Symbol", 3.0));
        headers.push_back(SHeaderInfo("Name", 3.0));
        headers.push_back(SHeaderInfo("Organism", 3.0));
    }

    void Format(const CEntrez2_docsum& ds,
                vector<string>& cols) const
    {
        cols.push_back(ds.GetValue("GeneID"));
        cols.push_back(ds.GetValue("Symbol"));
        cols.push_back(ds.GetValue("Name"));
        cols.push_back(ds.GetValue("OrgName"));
    }

    // retrieve seq-ids for a given set of docsums
    TIds GetSeqIds(const CEntrez2_docsum_list& ds_list,
                   TSeqIdFlags flags = fDefaults)
    {
        TIds ids;

        return ids;
    }

    TIds GetSeqIds(const CEntrez2_docsum& ds,
                   TSeqIdFlags flags = fDefaults)
    {
        TIds ids;

        return ids;
    }
};


CRef<CEntrez2_docsum_list>
CEntrezDBHandler::Query(const string& terms,
                        size_t& total_uids,
                        size_t start, size_t count)
{
    try {
        CEntrez2Client& client = x_GetClient();
        CEntrez2_eval_boolean req;
        CEntrez2_boolean_exp& exp = req.SetQuery();

        // set the database we're querying
        exp.SetDb().Set(GetDbName());

        // set the query
        CRef<CEntrez2_boolean_element> elem(new CEntrez2_boolean_element());
        elem->SetStr(terms);
        exp.SetExp().push_back(elem);

        // get UIDs first, then get the docsums
        // set some limits - if num > 0, we assume it's correct
        if (start > 0) {
            exp.SetLimits().SetOffset_UIDs(start);
        }
        if (count > 0) {
            exp.SetLimits().SetMax_UIDs(count);
        }
        req.SetReturn_UIDs(true);
        CRef<CEntrez2_boolean_reply> query_res =
            x_GetClient().AskEval_boolean(req);
        if (query_res) {
            total_uids = query_res->GetCount();
            return client.AskGet_docsum(query_res->GetUids());
        }
    }
    catch (...) {
    }
    return CRef<CEntrez2_docsum_list>();
}


CEntrez2Client& CEntrezDBHandler::x_GetClient()
{
    if ( !m_Client ) {
        m_Client.Reset(new CEntrez2Client());

        string tool = "Genome Workbench v.";
        tool += NStr::IntToString(CPluginVersion::eMajor);
        tool += ".";
        tool += NStr::IntToString(CPluginVersion::eMinor);
        m_Client->SetDefaultRequest().SetTool(tool);
    }
    return *m_Client;
}


CEntrezDBManager::CEntrezDBManager()
{
    RegisterHandler(*new CEntrezDB_NucProt("nucleotide", "Nucleotide"));
    RegisterHandler(*new CEntrezDB_NucProt("protein", "Protein"));
    RegisterHandler(*new CEntrezDB_Gene());
    RegisterHandler(*new CEntrezDB_Genome());
    /*RegisterHandler(*new CEntrezDB_HomoloGene());*/
}

void CEntrezDBManager::RegisterHandler(CEntrezDBHandler& handler)
{
    m_Handlers[handler.GetVisibleDbName()] = CRef<CEntrezDBHandler>(&handler);
}


IEntrezDBHandler& CEntrezDBManager::GetHandler(const string& db) const
{
    THandlers::const_iterator iter = m_Handlers.find(db);
    if (iter != m_Handlers.end()) {
        CRef<CEntrezDBHandler> ref = iter->second;
        return *ref;
    }

    throw runtime_error(string("database not found: ") + db);
}

void CEntrezDBManager::GetDatabases(list<SDbEntry>& entries)
{
    ITERATE (THandlers, iter, m_Handlers) {
        SDbEntry entry;
        entry.db_name = iter->second->GetDbName();
        entry.visible_db_name = iter->second->GetVisibleDbName();
        entries.push_back(entry);
    }
}



END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: entrez_db.cpp,v $
 * Revision 1000.0  2004/06/01 21:26:30  gouriano
 * PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.1
 *
 * Revision 1.1  2004/05/25 17:15:38  dicuccio
 * Initial revision - moved over from old GenBank search
 *
 * ===========================================================================
 */