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/*******************************************************************************
* Copyright (c) 2025 Olivier Langella
*<Olivier.Langella@universite-paris-saclay.fr>.
*
* This file is part of the PAPPSOms++ library.
*
* PAPPSOms++ is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms++ is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
// ./tests/pappsotree/catch2-only-pappsotree [mzmlname] -s
// msconvert
// /gorgone/pappso/formation/Janvier2014/TD/mzXML/20120906_balliau_extract_1_A01_urnb-1.mzXML
// --filter "index 4291" --mgf
#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_approx.hpp>
#include <catch2/matchers/catch_matchers_vector.hpp>
#include <QString>
#include <QFile>
#include <QJsonObject>
#include <iostream>
#include "../common.h"
#include "tests/tests-config.h"
#include <pappsomspp/core/msfile/msfileaccessor.h>
#include <pappsomspp/core/msrun/msrunreader.h>
TEST_CASE("test msrun sample name in mzml.", "[mzmlname]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: Check sample name ::..", "[mzmlname]")
{
//
pappso::MsFileAccessor file_access(
"/gorgone/pappso/moulon/raw/20251015_test_hoac_precipitation/"
"20251015_test_hoac_precipitation_1_20251016185414.mzML",
"");
pappso::MsRunReaderSPtr msrunA01 = file_access.getMsRunReaderSPtrByRunId("", "runa01");
REQUIRE(msrunA01.get()->getMsRunId().get()->getSampleName().toStdString() ==
"20251015_test_hoac_precipitation_1_20251016185414");
}
//
SECTION("..:: Check sample name ::..", "[mzmlname]")
{
//
pappso::MsFileAccessor file_access(
"/gorgone/pappso/moulon/raw/20251127_yeastpep_50_51/"
"20251127_yeastpeps_51_2024E5_M_acetyl.mzML",
"");
pappso::MsRunReaderSPtr msrunA01 = file_access.getMsRunReaderSPtrByRunId("", "runa01");
std::size_t index = msrunA01.get()->scanNumber2SpectrumIndex(6587);
MassSpectrumSPtr mass_spectrum = msrunA01.get()->massSpectrumSPtr(index);
QFile jsonf(QString("20251127_yeastpeps_51_2024E5_M_acetyl_%1.json").arg(index));
if(jsonf.open(QIODevice::WriteOnly))
{
QJsonDocument doc;
QJsonObject psm_json;
QJsonObject spectrum_json;
spectrum_json.insert("mz", toJson(mass_spectrum.get()->xValues()));
spectrum_json.insert("intensity", toJson(mass_spectrum.get()->yValues()));
psm_json.insert("spectra", spectrum_json);
doc.setObject(psm_json);
jsonf.write(doc.toJson());
jsonf.close();
}
}
}
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