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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/DB/DBConnection.h>
#include <OpenMS/FORMAT/DB/DBAdapter.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
using namespace OpenMS;
using namespace std;
/**
@page TOPP_DBExporter DBExporter
@brief Extracts MS data from a %OpenMS database.
@deprecated Deprecated in OpenMS 1.9
[Tool is no longer supported and will be removed in OpenMS 2.0]
Extracts arbitrary MS data (MS, LC-MS, MS/MS) from a %OpenMS database.
A single dataset can be exported by giving one id contained in the 'MSExperiment' table.
A query that returns several ids of the 'MSExperiment' table can be used to export several datasets at a time.
If only one dataset is exported, it is stored with the given name.
If several datasets are exported, the given name is prefixed with the DB id and an underscore.
In order to create a new %OpenMS database, use the @ref TOPP_DBImporter.
<B>The command line parameters of this tool are:</B>
@verbinclude TOPP_DBExporter.cli
<B>INI file documentation of this tool:</B>
@htmlinclude TOPP_DBExporter.html
*/
// We do not want this class to show up in the docu -> cond
/// @cond TOPPCLASSES
class TOPPDBExporter :
public TOPPBase
{
public:
TOPPDBExporter() :
TOPPBase("DBExporter", "Exports data from an OpenMS database to a file.")
{
}
protected:
void registerOptionsAndFlags_()
{
registerStringOption_("user", "<user>", "", "user/login of the DB");
registerStringOption_("host", "<host>", "localhost", "host name of the DB server", false);
registerStringOption_("password", "<password>", "", "password for the user");
registerIntOption_("port", "<port>", 3306, "port the DB server is running on", false);
registerStringOption_("db", "<name>", "", "DB name");
registerIntOption_("id", "<DB id>", 0, "id of the the map to export", false);
registerStringOption_("query", "<query>", "", "a SQL query that returns one or several DB ids of the MSExperiment table", false);
registerStringOption_("out", "<file>", "", "output file in mzML format (prefixed with DB id and '_' if several files are exported)");
}
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
//varaibles
String db, user, password, host, query, out;
UInt port;
UID id;
out = getStringOption_("out");
db = getStringOption_("db");
user = getStringOption_("user");
password = getStringOption_("password");
host = getStringOption_("host");
port = getIntOption_("port");
query = getStringOption_("query");
id = getIntOption_("id");
if (id == 0 && query == "")
{
writeLog_("Error: You have to give weither the 'id' option or the 'query' option! Aborting.");
return ILLEGAL_PARAMETERS;
}
//-------------------------------------------------------------
// reading input
//-------------------------------------------------------------
vector<UID> ids;
if (id != 0)
{
ids.push_back(id);
}
if (query != "")
{
DBConnection con;
con.connect(db, user, password, host, port);
QSqlQuery result = con.executeQuery(query);
while (result.isValid())
{
ids.push_back(result.value(0).toInt());
result.next();
}
}
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
if (ids.size() >= 1)
{
writeDebug_("Opening DB connection ...", 1);
DBConnection con;
con.connect(db, user, password, host, port);
DBAdapter a(con);
MzMLFile f;
f.setLogType(log_type_);
MSExperiment<Peak1D> exp;
if (ids.size() == 1)
{
writeDebug_("Writing single file...", 1);
//load from db
a.loadExperiment(*(ids.begin()), exp);
//annotate output with data processing info
addDataProcessing_(exp, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
//write to file
f.store(out, exp);
}
else
{
writeDebug_("Writing multiple files...", 1);
for (vector<UID>::iterator it = ids.begin(); it != ids.end(); ++it)
{
//load from db
a.loadExperiment(*it, exp);
//annotate output with data processing info
addDataProcessing_(exp, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
//write to file
stringstream ss;
ss << *it;
ss << "_" << out;
f.store(ss.str(), exp);
}
}
}
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPDBExporter tool;
return tool.main(argc, argv);
}
/// @endcond
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