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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/catch2-only-tests [mzcbor] -s
// ./tests/catch2-only-tests [mzcborindex] -s
#include <catch2/catch_test_macros.hpp>
#include <pappsomspp/core/processing/cbor/mzcbor/cvparam.h>
#include <pappsomspp/core/processing/cbor/mzcbor/converttomzml.h>
#include <pappsomspp/core/processing/cbor/mzcbor/mzmlconvert.h>
#include <pappsomspp/core/processing/cbor/mzcbor/mzcborreaderbase.h>
#include <pappsomspp/core/processing/cbor/mzcbor/mzcborindexreader.h>
#include <pappsomspp/core/processing/uimonitor/uimonitorvoid.h>
#include <QDebug>
#include <QFileInfo>
#include <QTextStream>
#include <QXmlStreamWriter>
#include "tests/tests-config.h"
#include <pappsomspp/core/msfile/msfileaccessor.h>
#include <pappsomspp/core/msrun/msrunreader.h>
#include <pappsomspp/core/msrun/private/mzcbormsrunreader.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("..:: cvParam for mzcbor::..", "[mzcbor]")
{
pappso::cbor::mzcbor::CvParam cv_param;
QByteArray byte_array;
// QTextStream xml_out(byte_array, QIODevice::WriteOnly);
QXmlStreamWriter writer(&byte_array);
cv_param.toMzml(writer);
REQUIRE(byte_array.toStdString() ==
"<cvParam cvRef=\"\" accession=\"\" value=\"\" name=\"\"/>");
}
SECTION("..:: PSM cbor features::..", "[mzcbor]")
{
pappso::UiMonitorVoid monitor;
QFileInfo mzml_file(QString(CMAKE_SOURCE_DIR).append("/tests/data/mzml/mzml_minimal.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());
REQUIRE(mzml_convert.getRunIdList().size() == 1);
REQUIRE(mzml_convert.getRunIdList().at(0).toStdString() ==
"20120906_balliau_extract_1_A01_urnb-1");
// Oddly enough works with Langella, but not with Rusconi
// REQUIRE_THAT(mzml_convert.getRunAndSpectrumOffsetList().at(0),
// Catch::Matchers::Approx(std::vector<qint64>({2868, 16265, 31614})));
REQUIRE(mzml_convert.getRunAndSpectrumIdList().at(0).at(0).toStdString() ==
"controllerType=0 controllerNumber=1 scan=1");
REQUIRE(mzml_convert.getRunAndSpectrumIdList().at(0).at(2).toStdString() ==
"controllerType=0 controllerNumber=1 scan=2716");
}
SECTION("..:: PSM cbor features::..", "[mzcbor]")
{
pappso::UiMonitorVoid monitor;
QFile mzcbor_file("mzcbor.cbor");
mzcbor_file.open(QIODevice::ReadOnly);
pappso::cbor::CborStreamWriter writer(&mzcbor_file);
pappso::cbor::mzcbor::MzcborReaderBase mzcbor_reader;
mzcbor_reader.readCbor(&mzcbor_file, monitor);
mzcbor_reader.close();
mzcbor_file.close();
}
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() == 3);
qDebug();
// msrunA01.get()->getRetentionTimeLine();
REQUIRE_THAT(
msrunA01.get()->getRetentionTimeLine(),
Catch::Matchers::Approx(std::vector<double>({0.29255299800000001, 830.33550000000002456})));
pappso::QualifiedMassSpectrum qualifiedMassSpectrum =
msrunA01.get()->qualifiedMassSpectrum(0, true);
REQUIRE(qualifiedMassSpectrum.getMsLevel() == 1);
REQUIRE(qualifiedMassSpectrum.getMassSpectrumId().getNativeId().toStdString() ==
"controllerType=0 controllerNumber=1 scan=1");
REQUIRE(qualifiedMassSpectrum.getMassSpectrumCstSPtr().get()->size() == 1552);
REQUIRE(qualifiedMassSpectrum.getMassSpectrumId().getSpectrumIndex() == 0);
qualifiedMassSpectrum = msrunA01.get()->qualifiedMassSpectrum(2, true);
REQUIRE(qualifiedMassSpectrum.getPrecursorCharge() == 3);
REQUIRE(qualifiedMassSpectrum.getMassSpectrumCstSPtr().get()->size() == 219);
REQUIRE(qualifiedMassSpectrum.getPrecursorSpectrumIndex() == 1);
pappso::MzcborMsRunReader *p_msreader =
dynamic_cast<pappso::MzcborMsRunReader *>(msrunA01.get());
// Oddly enough works with Langella, but not with Rusconi
// REQUIRE_THAT(p_msreader->getSpectrumIndexPositionInFile(),
// Catch::Matchers::Approx(std::vector<qint64>({2868, 16265, 31614})));
REQUIRE_THAT(p_msreader->getTicChromatogram().yValues(),
Catch::Matchers::Approx(
std::vector<double>({13677255.374359130859375, 607363151.728515625})));
REQUIRE_THAT(p_msreader->getRetentionTimeLine(),
Catch::Matchers::Approx(std::vector<double>({0.2925529, 830.3355000})));
}
SECTION("..:: convert to mzML ::..", "[mzcbor]")
{
pappso::UiMonitorVoid monitor;
QFile mzml_file("mzcbor.mzml");
QFile mzcbor_file("mzcbor.cbor");
mzml_file.open(QIODevice::WriteOnly);
QXmlStreamWriter writer(&mzml_file);
mzcbor_file.open(QIODevice::ReadOnly);
pappso::cbor::mzcbor::ConvertToMzml convert_mzml(&writer);
convert_mzml.readCbor(&mzcbor_file, monitor);
mzcbor_file.close();
}
}
TEST_CASE("cbor mz test suite.", "[mzcborindex]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: mz cbor features::..", "[mzcborindex]")
{
pappso::UiMonitorVoid monitor;
QFileInfo mzml_file(QString(CMAKE_SOURCE_DIR).append("/tests/data/mzml/mzml_minimal.mzML"));
QFile mzcbor_file("mzcbor_idx.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();
QFile mzcbor_index_file("mzcbor_idx.cbor.idx");
mzcbor_index_file.open(QIODevice::WriteOnly);
pappso::cbor::CborStreamWriter writer_index(&mzcbor_index_file);
mzml_convert.writeMzcborIndex(&writer_index);
mzcbor_index_file.close();
pappso::MsFileAccessor file_access("mzcbor_idx.cbor", "");
pappso::MsRunReaderSPtr msrunA01 = file_access.getMsRunReaderSPtrByRunId("", "runa01");
REQUIRE(msrunA01.get()->getMsRunId().get()->getRunId().toStdString() ==
"20120906_balliau_extract_1_A01_urnb-1");
REQUIRE(msrunA01.get()->getMsRunId().get()->getFileName().toStdString() == "mzcbor_idx.cbor");
REQUIRE(msrunA01.get()->getMsRunId().get()->getSampleName().toStdString() ==
"20120906_balliau_extract_1_A01_urnb-1");
pappso::QualifiedMassSpectrum qualifiedMassSpectrum =
msrunA01.get()->qualifiedMassSpectrum(2, true);
REQUIRE(qualifiedMassSpectrum.getPrecursorCharge() == 3);
REQUIRE(qualifiedMassSpectrum.getMassSpectrumCstSPtr().get()->size() == 219);
REQUIRE(qualifiedMassSpectrum.getPrecursorSpectrumIndex() == 1);
// QFile mzcbor_index_file("mzcbor_idx.cbor.idx");
mzcbor_index_file.open(QIODevice::ReadOnly);
pappso::cbor::mzcbor::MzcborIndexReader reader_index;
reader_index.readCbor(&mzcbor_index_file);
mzcbor_index_file.close();
REQUIRE(reader_index.getRunAndSpectrumMsLevelList().at(0) ==
std::vector<std::uint8_t>({1, 1, 2}));
REQUIRE(reader_index.getRunAndSpectrumRtList().size() == 1);
REQUIRE_THAT(reader_index.getRunAndSpectrumRtList().at(0),
Catch::Matchers::Approx(std::vector<double>({0.292552, 830.3355, 831.2315399})));
REQUIRE(reader_index.getRunAndSpectrumTotalIonCountList().size() == 1);
REQUIRE(reader_index.getRunAndSpectrumTotalIonCountList().at(0) ==
std::vector<qint64>({17377980, 622686020, 1369537}));
REQUIRE(msrunA01.get()->getMsRunId().get()->getRunId().toStdString() ==
"20120906_balliau_extract_1_A01_urnb-1");
REQUIRE_THAT(msrunA01.get()->getTicChromatogram().yValues(),
Catch::Matchers::Approx(std::vector<double>({17377980.0, 622686020.0})));
REQUIRE_THAT(msrunA01.get()->getRetentionTimeLine(),
Catch::Matchers::Approx(std::vector<double>({0.2925529, 830.3355000})));
}
}
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