query.cpp

来自「ncbi源码」· C++ 代码 · 共 231 行

/*
 * ===========================================================================
 * PRODUCTION $Log: query.cpp,v $
 * PRODUCTION Revision 1000.3  2004/06/01 20:56:52  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: query.cpp,v 1000.3 2004/06/01 20:56:52 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:
 *
 */

#include <ncbi_pch.hpp>
#include "query.hpp"
#include "utils.hpp"

#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginRequest.hpp>
#include <gui/plugin/PluginCommand.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginArgSet.hpp>
#include <gui/plugin/PluginArg.hpp>
#include <gui/core/version.hpp>
#include <gui/core/idocument.hpp>
#include <gui/core/plugin_utils.hpp>
#include <gui/utils/app_popup.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbireg.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seqfeat/Org_ref.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(ncbi::objects);


// standard info boilerplate
void CAlgoLinkOut_Query::x_AddStandardArgs(CPluginCommand& command)
{
    // database to search
    command.AddDefaultArgument("db", "Database", CPluginArg::eString,
                               "PubMed");
    command.SetConstraint("db",
        (*CPluginValueConstraint::CreateSet(),
         "3D Domains",
         "Books",
         "GEO Data Sets",
         "GEO",
         "Genome",
         "Journals",
         "MeSH",
         "NCBI Web Site",
         "Nucleotide",
         "Online Mendelian Inheritance in Man (OMIM)",
         "Population Studies (PopSet)",
         "Protein",
         "PubMed Central (PMC)",
         "PubMed",
         "Structure",
         "Taxonomy",
         "UniGene",
         "UniSTS"
         "dbSNP"));

    command.AddArgument("org", "Limit to organism", CPluginArg::eBoolean);
}


// run our plugin
void CAlgoLinkOut_Query::x_RunCommand(CPluginMessage& msg)
{
    const CPluginCommand& args = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();

    // retrieve the default link for Query
    CNcbiApplication* app = CNcbiApplication::Instance();
    _ASSERT(app);
    const CNcbiRegistry& reg = app->GetConfig();

    string query_url =
        reg.GetString("LINKOUT", "Query",
                      "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
                      "?cmd=<cmd>&db=<db>&term=<term>");

    string terms;
    string org;
    bool org_limit = args["org"].AsBoolean();

    //
    // were we called with args = seq-id?
    //
    if (args.HasArgument("seq-id")) {
        // retrieve the seq-id
        plugin_args::TIdList ids;
        GetArgValue(args["seq-id"], ids);
        const CSeq_id&   id  = *ids.front().second;
        const IDocument& doc = *ids.front().first;

        // get a title from the sequence and use that as the terms
        CBioseq_Handle handle = doc.GetScope().GetBioseqHandle(id);
        if ( !handle ) {
            reply.SetStatus(eMessageStatus_failed);
            return;
        }

        terms = sequence::GetTitle(handle);
        if (org_limit) {
            CConstRef<COrg_ref> ref = GetOrganism(handle);
            if (ref) {
                ref->GetLabel(&org);
            }
        }
    }

    //
    // were we called with args = feat?
    //
    if (args.HasArgument("feat")) {
        // retrieve the feature
        plugin_args::TFeatList feats;
        GetArgValue(args["feat"], feats);
        const CSeq_feat& feat = *feats.front().second;
        const IDocument& doc  = *feats.front().first;

        // get a label from the feature and use that as the terms
        feature::GetLabel(feat, &terms, feature::eContent, &doc.GetScope());
        if (org_limit) {
            CBioseq_Handle handle = doc.GetScope().GetBioseqHandle(feat.GetLocation());
            CConstRef<COrg_ref> ref = GetOrganism(handle);
            if (ref) {
                ref->GetLabel(&org);
            }
        }
    }

    //
    // encode our white-space
    if ( !org.empty() ) {
        org = " AND \"" + org + "\" [ORGN]";
        terms += org;
    }
    string::size_type pos = 0;
    while ( (pos = terms.find_first_of(" ", pos)) != string::npos) {
        terms[pos] = '+';
    }

    //
    // retrieve the database
    //
    string db = args["db"].AsString();

    //
    // what command do we run?
    //
    string cmd = "search";

    //
    // finalize our URL and launch!
    //
    query_url = NStr::Replace(query_url, "<db>",   db);
    query_url = NStr::Replace(query_url, "<term>", terms);
    query_url = NStr::Replace(query_url, "<cmd>",  cmd);

    if ( !CAppPopup::PopupURL(query_url) ) {
        reply.SetStatus(eMessageStatus_failed);
    } else {
        reply.SetStatus(eMessageStatus_success);
    }
}



END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: query.cpp,v $
 * Revision 1000.3  2004/06/01 20:56:52  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
 *
 * Revision 1.6  2004/05/21 22:27:48  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.5  2004/01/27 18:45:27  dicuccio
 * Added missing header files
 *
 * Revision 1.4  2003/11/04 17:49:24  dicuccio
 * Changed calling parameters for plugins - pass CPluginMessage instead of paired
 * CPluginCommand/CPluginReply
 *
 * Revision 1.3  2003/10/07 13:47:04  dicuccio
 * Renamed CPluginURL* to CPluginValue*
 *
 * Revision 1.2  2003/09/25 17:49:17  dicuccio
 * Cleaned up handling of org-refs - implemented private function to return the
 * apporpriate COrg_ref.  Added virtual destructors where necessary
 *
 * Revision 1.1  2003/09/23 19:45:45  dicuccio
 * Initial revision
 *
 * ===========================================================================
 */