external.cpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: external.cpp,v $
 * PRODUCTION Revision 1000.5  2004/06/01 20:56:05  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.25
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: external.cpp,v 1000.5 2004/06/01 20:56:05 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:  Josh Cherry
 *
 * File Description:
 *
 */

#include <ncbi_pch.hpp>
#include "external.hpp"
#include <gui/utils/exec.hpp>
#include "../basic/output_dlg.hpp"

#include <gui/core/idocument.hpp>
#include <gui/core/plugin_utils.hpp>
#include <gui/plugin/PluginRequest.hpp>
#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginValueConstraint.hpp>
#include <gui/core/version.hpp>

#include <objmgr/util/sequence.hpp>

#include <objmgr/scope.hpp>
#include <objmgr/seq_vector.hpp>

#include <objects/seqloc/Seq_loc.hpp>
#include <connect/ncbi_pipe.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);

// stuff for running external apps
void CExternal::GetInfo(CPluginInfo& info)
{
    info.Reset();

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CExternal", "Run external executable",
                 "A crude interface for running external executables",
                 "");

    // command info
    CPluginCommandSet& cmds = info.SetCommands();
    CPluginCommand&    args = cmds.AddAlgoCommand(eAlgoCommand_run);
    args.AddArgument("locs", "Sequences to evaluate",
                     CSeq_loc::GetTypeInfo(),
                     CPluginArg::TData::e_Array);
    args.SetConstraint("locs",
                       *CPluginValueConstraint::CreateSeqSameMol());
    args.AddArgument("path", "path name to executable",
                     CPluginArg::eString);
}


void CExternal::RunCommand(CPluginMessage& msg)
{
    const CPluginCommand& args = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();
    _TRACE("CExternal::Run()");
    if ( !m_OutputDlg.get() ) {
        m_OutputDlg.reset(new COutputDlg());
    }
    m_OutputDlg->SetTitle("Results of executing external app");

    string str;
    vector<string> seqs;


    /****************************************/
    CPluginArg::TValues seq_list;
    args["path"];
    args["locs"].AsList(seq_list);

    CRef<CScope> new_scope;

    vector<string> seq_labels;
    vector<int>    seq_gis;

    plugin_args::TLocList locs;
    GetArgValue(args["seqs"], locs);
    ITERATE (plugin_args::TLocList, iter, locs) {
        const CSeq_loc&  loc = *iter->second;
        const IDocument& doc = *iter->first;

        CScope& scope = doc.GetScope();
        if ( !new_scope ) {
            new_scope.Reset(&scope);
        }

        if ( !sequence::IsOneBioseq(loc, &scope) ) {
            string str = CPluginUtils::GetLabel(loc, &doc.GetScope());
            LOG_POST(Info << "CExternal: "
                     "location on multiple bioseqs ignored: " << str);
            continue;
        }

        CBioseq_Handle handle =
            scope.GetBioseqHandle(sequence::GetId(loc, &scope));

        CSeqVector vec =
            handle.GetSequenceView(loc,
                                   CBioseq_Handle::eViewConstructed,
                                   CBioseq_Handle::eCoding_Iupac);

        // save our sequence
        seqs.push_back(string());
        vec.GetSeqData(0, vec.size(), seqs.back());
        NStr::ToUpper(seqs.back());

        // save a label for this sequence
        seq_labels.push_back(CPluginUtils::GetLabel(loc, &doc.GetScope()));

        // save the gi for this sequence
        const CSeq_id& gi_id =
            sequence::GetId(handle, sequence::eGetId_ForceGi);
        _TRACE("gi = " << gi_id.GetGi());
        seq_gis.push_back(gi_id.GetGi());
    }

    /***************************************/

    // stdin will contain all sequences, separated by spaces
    string std_in;
    for(size_t i = 0;  i < seqs.size(); i++) {
        std_in += seqs[i];
        if (i != seqs.size() - 1) {
            std_in += ' ';
        } 
    }

    string std_out, std_err;
    vector<string> arguments;

    CExecute::Exec(args["path"].AsString().c_str(), arguments,
                   std_in, std_out, std_err );

    if ( !str.empty() ) {
        str += "\n";
    }

    str += "standard output:\n\n";
    str += std_out + "\n\n";

    str += "standard error:\n\n";
    str += std_err + "\n\n";
    //
    // prepare our dialog box
    //
    if (str.empty()) {
        str = "No output";
    }

    m_OutputDlg->SetText(str);
    m_OutputDlg->Show();
    reply.SetStatus(eMessageStatus_success);
}


END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: external.cpp,v $
 * Revision 1000.5  2004/06/01 20:56:05  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.25
 *
 * Revision 1.25  2004/05/21 22:27:47  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.24  2004/03/11 17:40:36  dicuccio
 * Use sequence::GetId() instead of CSeq_id::GetStringDescr()
 *
 * Revision 1.23  2004/01/27 18:45:23  dicuccio
 * Added missing header files
 *
 * Revision 1.22  2004/01/07 15:50:39  dicuccio
 * Adjusted for API change in CPluginUtils::GetLabel().  Standardized exception
 * reporting in algorithms.
 *
 * Revision 1.21  2003/11/24 15:45:29  dicuccio
 * Renamed CVersion to CPluginVersion
 *
 * Revision 1.20  2003/11/06 21:17:19  ucko
 * Adjust for scope fixes in public headers.
 *
 * Revision 1.19  2003/11/04 21:17:46  dicuccio
 * Changed calling semantics to match new plugin API
 *
 * Revision 1.18  2003/10/07 15:31:17  ucko
 * Fixed fallout from URL -> Value conversion
 *
 * Revision 1.17  2003/10/07 13:47:04  dicuccio
 * Renamed CPluginURL* to CPluginValue*
 *
 * Revision 1.16  2003/09/25 19:10:30  jcherry
 * Moved exec.?pp to gui/utils
 *
 * Revision 1.15  2003/09/25 17:36:27  jcherry
 * Renamed CExec to CExecute to avoid name conflict.  Made Exec()
 * really return the process's exit status.
 *
 * Revision 1.14  2003/09/04 17:34:04  ucko
 * Really use IDocument instead of CDocument.
 *
 * Revision 1.13  2003/09/04 14:05:24  dicuccio
 * Use IDocument instead of CDocument
 *
 * Revision 1.12  2003/09/03 14:46:53  rsmith
 * change namespace name from args to plugin_args to avoid clashes with variable names.
 *
 * Revision 1.11  2003/09/02 23:12:02  jcherry
 * Partial accommodation of changes to CPipe
 *
 * Revision 1.10  2003/08/21 12:03:08  dicuccio
 * Make use of new typedef in plugin_utils.hpp for argument values.
 *
 * Revision 1.9  2003/07/28 18:17:04  jcherry
 * Moved code for actually executing a program to a separate
 * class (CExec).  Moved 'external' into a new project.
 *
 * Revision 1.8  2003/07/22 15:32:16  dicuccio
 * Changed to make use of new API in plugin_utils.hpp - GetArgValue()
 *
 * Revision 1.7  2003/07/14 11:12:28  shomrat
 * Plugin messageing system related changes
 *
 * Revision 1.6  2003/07/01 15:08:41  jcherry
 * Moved a bunch of stuff into CNucProp and CProtProp
 * Put these in c++/{src,include}/algo/sequence
 *
 * Revision 1.5  2003/06/26 15:33:40  dicuccio
 * Moved GetURLValue() from PluginURL.hpp to plugin_utils.hpp.  Fixed compilation
 * errors relating to missing #includes
 *
 * Revision 1.4  2003/06/25 17:02:57  dicuccio
 * Split CPluginHandle into a handle (pointer-to-implementation) and
 * implementation file.  Lots of #include file clean-ups.
 *
 * Revision 1.3  2003/06/20 14:52:36  dicuccio
 * Revised plugin registration - moved GetInfo() into the plugin handler
 *
 * Revision 1.2  2003/06/19 20:20:25  jcherry
 * Corrected minor error
 *
 * Revision 1.1  2003/06/19 19:12:42  jcherry
 * Initial version of interface for running external executables
 * from gbench.  For now this just passes sequences on stdin.
 *
 * ===========================================================================
 */