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//
// File: test_mzcbor.cpp
// Created by: Olivier Langella
// Created on: 19/11/2025
//
/*******************************************************************************
* 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 [mzcbor] -s
#include <catch2/catch_test_macros.hpp>
#include <pappsomspp/core/processing/cbor/mzcbor/mzmlconvert.h>
#include <pappsomspp/core/processing/uimonitor/uimonitorvoid.h>
#include <QDebug>
#include <QFileInfo>
#include "tests/tests-config.h"
#include <pappsomspp/core/msfile/msfileaccessor.h>
#include <catch2/matchers/catch_matchers_vector.hpp>
TEST_CASE("cbor psm map test suite.", "[mzcbor]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: PSM cbor features::..", "[mzcbor]")
{
pappso::MsFileAccessor file_access(
"/gorgone/pappso/moulon/raw/20250521_proteobench_dda_astral/mzcbor/"
"LFQ_Astral_DDA_15min_50ng_Condition_A_REP3.mzcbor",
"");
pappso::MsRunReaderSPtr msrunA01 = file_access.getMsRunReaderSPtrByRunId("", "runa01");
REQUIRE(msrunA01.get()->getMsRunId().get()->getSampleName().toStdString() ==
"LFQ_Astral_DDA_15min_50ng_Condition_A_REP3");
pappso::QualifiedMassSpectrum qualifiedMassSpectrum =
msrunA01.get()->qualifiedMassSpectrum(2, true);
REQUIRE(qualifiedMassSpectrum.getRtInSeconds() == 0.76824700000000201);
REQUIRE(qualifiedMassSpectrum.getMsLevel() == 1);
REQUIRE(qualifiedMassSpectrum.getMassSpectrumCstSPtr().get()->size() == 1140);
qualifiedMassSpectrum = msrunA01.get()->qualifiedMassSpectrum(77766, true);
REQUIRE(qualifiedMassSpectrum.getRtInSeconds() == 933.30781799999999748);
REQUIRE(qualifiedMassSpectrum.getMsLevel() == 2);
REQUIRE(qualifiedMassSpectrum.getMassSpectrumCstSPtr().get()->size() == 1102);
qDebug();
// msrunA01.get()->getRetentionTimeLine();
}
SECTION("..:: PSM cbor features::..", "[mzcbor]")
{
pappso::MsFileAccessor file_access(
"/gorgone/pappso/data_extraction_pappso/mzcbor/20120906_balliau_extract_1_A01_urnb-1.mzcbor",
"");
pappso::MsRunReaderSPtr msrunA01 = file_access.getMsRunReaderSPtrByRunId("", "runa01");
REQUIRE(msrunA01.get()->getMsRunId().get()->getSampleName().toStdString() ==
"20120906_balliau_extract_1_A01_urnb-1");
}
SECTION("..:: PSM cbor features::..", "[mzcbor]")
{
pappso::UiMonitorVoid monitor;
QFileInfo mzml_file(
"/gorgone/pappso/data_extraction_pappso/mzML/20120906_balliau_extract_1_A01_urnb-1.mzML");
QFile mzcbor_file("mzcbor.cbor");
mzcbor_file.open(QIODevice::WriteOnly);
pappso::cbor::CborStreamWriter writer(&mzcbor_file);
pappso::cbor::mzcbor::MzmlConvert mzml_convert(&monitor, &writer);
mzml_convert.readFile(mzml_file.absoluteFilePath());
mzcbor_file.close();
REQUIRE(mzml_convert.errorString().isEmpty());
}
SECTION("..:: PSM cbor features::..", "[mzcbor]")
{
pappso::MsFileAccessor file_access("mzcbor.cbor", "");
pappso::MsRunReaderSPtr msrunA01 = file_access.getMsRunReaderSPtrByRunId("", "runa01");
REQUIRE(msrunA01.get()->getMsRunId().get()->getSampleName().toStdString() ==
"20120906_balliau_extract_1_A01_urnb-1");
REQUIRE(msrunA01.get()->spectrumListSize() == 16576);
qDebug();
// msrunA01.get()->getRetentionTimeLine();
}
}
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