| Line | Branch | Exec | Source |
|---|---|---|---|
| 1 | /* BEGIN software license | ||
| 2 | * | ||
| 3 | * MsXpertSuite - mass spectrometry software suite | ||
| 4 | * ----------------------------------------------- | ||
| 5 | * Copyright (C) 2009--2020 Filippo Rusconi | ||
| 6 | * | ||
| 7 | * http://www.msxpertsuite.org | ||
| 8 | * | ||
| 9 | * This file is part of the MsXpertSuite project. | ||
| 10 | * | ||
| 11 | * The MsXpertSuite project is the successor of the massXpert project. This | ||
| 12 | * project now includes various independent modules: | ||
| 13 | * | ||
| 14 | * - massXpert, model polymer chemistries and simulate mass spectrometric data; | ||
| 15 | * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner; | ||
| 16 | * | ||
| 17 | * This program is free software: you can redistribute it and/or modify | ||
| 18 | * it under the terms of the GNU General Public License as published by | ||
| 19 | * the Free Software Foundation, either version 3 of the License, or | ||
| 20 | * (at your option) any later version. | ||
| 21 | * | ||
| 22 | * This program is distributed in the hope that it will be useful, | ||
| 23 | * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| 24 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| 25 | * GNU General Public License for more details. | ||
| 26 | * | ||
| 27 | * You should have received a copy of the GNU General Public License | ||
| 28 | * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| 29 | * | ||
| 30 | * END software license | ||
| 31 | */ | ||
| 32 | |||
| 33 | |||
| 34 | /////////////////////// Std lib includes | ||
| 35 | |||
| 36 | |||
| 37 | /////////////////////// Qt includes | ||
| 38 | #include <QDebug> | ||
| 39 | #include <QFileInfo> | ||
| 40 | |||
| 41 | |||
| 42 | /////////////////////// IsoSpec | ||
| 43 | |||
| 44 | |||
| 45 | /////////////////////// Local includes | ||
| 46 | #include "MsXpS/libXpertMassCore/MassDataCborBaseHandler.hpp" | ||
| 47 | |||
| 48 | namespace MsXpS | ||
| 49 | { | ||
| 50 | |||
| 51 | namespace libXpertMassCore | ||
| 52 | { | ||
| 53 | |||
| 54 | |||
| 55 | /*! | ||
| 56 | \class MsXpS::libXpertMassCore::MassDataCborBaseHandler | ||
| 57 | \inmodule libXpertMassCore | ||
| 58 | \ingroup XpertMassCoreUtilities | ||
| 59 | \inheaderfile MassDataCborBaseHandler.hpp | ||
| 60 | |||
| 61 | \brief The MassDataCborBaseHandler class provides features to handle | ||
| 62 | mass spectrometric data using the CBOR (Concise Binary Object Representation) | ||
| 63 | container streaming classes. | ||
| 64 | |||
| 65 | The data transported using CBOR is first qualified using the \l{Enums::MassDataType} | ||
| 66 | enum. The data are packed following that mass data type specification. | ||
| 67 | */ | ||
| 68 | |||
| 69 | |||
| 70 | |||
| 71 | /*! | ||
| 72 | \brief Constructs a MassDataCborBaseHandler instance setting parent to \a | ||
| 73 | parent_p. | ||
| 74 | */ | ||
| 75 | ✗ | MassDataCborBaseHandler::MassDataCborBaseHandler(QObject *parent_p) | |
| 76 | ✗ | : QObject(parent_p) | |
| 77 | { | ||
| 78 | ✗ | } | |
| 79 | |||
| 80 | /*! | ||
| 81 | \brief Destructs the MassDataCborBaseHandler instance. | ||
| 82 | */ | ||
| 83 | ✗ | MassDataCborBaseHandler::~MassDataCborBaseHandler() | |
| 84 | { | ||
| 85 | ✗ | } | |
| 86 | |||
| 87 | /*! | ||
| 88 | \brief Sets the input file name to \a file_name. | ||
| 89 | */ | ||
| 90 | void | ||
| 91 | ✗ | MassDataCborBaseHandler::setInputFileName(const QString &file_name) | |
| 92 | { | ||
| 93 | ✗ | m_inputFileName = file_name; | |
| 94 | ✗ | } | |
| 95 | |||
| 96 | /*! | ||
| 97 | \brief Sets the output file name to \a file_name. | ||
| 98 | */ | ||
| 99 | void | ||
| 100 | ✗ | MassDataCborBaseHandler::setOutputFileName(const QString &file_name) | |
| 101 | { | ||
| 102 | ✗ | m_outputFileName = file_name; | |
| 103 | ✗ | } | |
| 104 | |||
| 105 | /*! | ||
| 106 | \brief Sets the mass data type to \a mass_data_type. | ||
| 107 | */ | ||
| 108 | void | ||
| 109 | ✗ | MassDataCborBaseHandler::setMassDataType(Enums::MassDataType mass_data_type) | |
| 110 | { | ||
| 111 | ✗ | m_massDataType = mass_data_type; | |
| 112 | ✗ | } | |
| 113 | |||
| 114 | /*! | ||
| 115 | \brief Returns the mass data type. | ||
| 116 | */ | ||
| 117 | Enums::MassDataType | ||
| 118 | ✗ | MassDataCborBaseHandler::getMassDataType() const | |
| 119 | { | ||
| 120 | ✗ | return m_massDataType; | |
| 121 | } | ||
| 122 | |||
| 123 | /*! | ||
| 124 | \brief Decodes the data stream from \a reader_sp. | ||
| 125 | |||
| 126 | \note The base class does nothing and always returns false. | ||
| 127 | */ | ||
| 128 | bool | ||
| 129 | ✗ | MassDataCborBaseHandler::decodeStream( | |
| 130 | [[maybe_unused]] QCborStreamReaderSPtr &reader_sp) | ||
| 131 | { | ||
| 132 | ✗ | qDebug() << "The base class handler function does nothing."; | |
| 133 | ✗ | return false; | |
| 134 | } | ||
| 135 | |||
| 136 | /*! | ||
| 137 | \brief Decodes enough of the data streamed by \a reader_sp to determine and | ||
| 138 | return the mass data type of the streamed data. | ||
| 139 | |||
| 140 | \note Failure to decode the mass data type is fatal. | ||
| 141 | */ | ||
| 142 | Enums::MassDataType | ||
| 143 | ✗ | MassDataCborBaseHandler::readMassDataType(QCborStreamReaderSPtr &reader_sp) | |
| 144 | { | ||
| 145 | ✗ | QString current_key; | |
| 146 | |||
| 147 | // The file format starts with a quint64 that indicates the type of mass | ||
| 148 | // data (MassDataType enum to quint64). | ||
| 149 | |||
| 150 | ✗ | while(!reader_sp->lastError() && reader_sp->hasNext()) | |
| 151 | { | ||
| 152 | // The first iteration in the CBOR data structure is in a map. | ||
| 153 | |||
| 154 | ✗ | QCborStreamReader::Type type = reader_sp->type(); | |
| 155 | // qDebug() << "Type is:" << type; | ||
| 156 | |||
| 157 | ✗ | if(type != QCborStreamReader::Map) | |
| 158 | ✗ | qFatal( | |
| 159 | "The byte array does not have the expected CBOR structure for " | ||
| 160 | "mass data."); | ||
| 161 | |||
| 162 | ✗ | reader_sp->enterContainer(); | |
| 163 | |||
| 164 | ✗ | while(reader_sp->lastError() == QCborError::NoError && | |
| 165 | ✗ | reader_sp->hasNext()) | |
| 166 | { | ||
| 167 | ✗ | QCborStreamReader::Type type = reader_sp->type(); | |
| 168 | // qDebug() << "Type is:" << type; | ||
| 169 | |||
| 170 | // The very first item of the map should be a pair | ||
| 171 | // | ||
| 172 | // "DATA_TYPE / quint64 | ||
| 173 | |||
| 174 | ✗ | if(type == QCborStreamReader::String) | |
| 175 | { | ||
| 176 | // Read a CBOR string, concatenating all | ||
| 177 | // the chunks into a single string. | ||
| 178 | ✗ | QString str; | |
| 179 | ✗ | auto chunk = reader_sp->readString(); | |
| 180 | ✗ | while(chunk.status == QCborStreamReader::Ok) | |
| 181 | { | ||
| 182 | ✗ | str += chunk.data; | |
| 183 | ✗ | chunk = reader_sp->readString(); | |
| 184 | } | ||
| 185 | |||
| 186 | ✗ | if(chunk.status == QCborStreamReader::Error) | |
| 187 | { | ||
| 188 | // handle error condition | ||
| 189 | ✗ | qDebug() << "There was an error reading string chunk."; | |
| 190 | ✗ | str.clear(); | |
| 191 | } | ||
| 192 | |||
| 193 | // qDebug() << "The string that was read:" << str; | ||
| 194 | |||
| 195 | // If the current key is empty, this string value is a new key | ||
| 196 | // or tag. Otherwise, it's a value. | ||
| 197 | |||
| 198 | ✗ | if(current_key.isEmpty()) | |
| 199 | { | ||
| 200 | // qDebug() << "Setting current_key:" << str; | ||
| 201 | ✗ | current_key = str; | |
| 202 | } | ||
| 203 | else | ||
| 204 | { | ||
| 205 | // At this point we can reset current_key. | ||
| 206 | ✗ | current_key = QString(); | |
| 207 | } | ||
| 208 | ✗ | } | |
| 209 | ✗ | else if(type == QCborStreamReader::UnsignedInteger) | |
| 210 | { | ||
| 211 | ✗ | if(current_key != "DATA_TYPE") | |
| 212 | ✗ | qFatal( | |
| 213 | "The byte array does not have the expected CBOR " | ||
| 214 | "structure for " | ||
| 215 | "mass data."); | ||
| 216 | |||
| 217 | // quint64 data_type = reader_sp->toUnsignedInteger(); | ||
| 218 | // qDebug() << "The mass data type:" << data_type; | ||
| 219 | |||
| 220 | ✗ | return static_cast<Enums::MassDataType>( | |
| 221 | ✗ | reader_sp->toUnsignedInteger()); | |
| 222 | } | ||
| 223 | else | ||
| 224 | ✗ | qFatal( | |
| 225 | "The byte array does not have the expected CBOR " | ||
| 226 | "structure for mass data."); | ||
| 227 | } | ||
| 228 | } | ||
| 229 | |||
| 230 | return Enums::MassDataType::NOT_SET; | ||
| 231 | ✗ | } | |
| 232 | |||
| 233 | /*! | ||
| 234 | \overload | ||
| 235 | |||
| 236 | \brief Decodes enough of the data contained in file \a input_file_name to | ||
| 237 | determine and return the mass data type of the streamed data. | ||
| 238 | |||
| 239 | \note Failure to decode the mass data type is fatal. | ||
| 240 | |||
| 241 | \sa readMassDataType() overloads | ||
| 242 | */ | ||
| 243 | Enums::MassDataType | ||
| 244 | ✗ | MassDataCborBaseHandler::readMassDataType(const QString &input_file_name) | |
| 245 | { | ||
| 246 | ✗ | QFileInfo file_info(input_file_name); | |
| 247 | |||
| 248 | ✗ | if(!file_info.exists()) | |
| 249 | { | ||
| 250 | qDebug() << "File not found."; | ||
| 251 | return Enums::MassDataType::NOT_SET; | ||
| 252 | } | ||
| 253 | |||
| 254 | ✗ | QFile file(input_file_name); | |
| 255 | |||
| 256 | ✗ | bool res = file.open(QIODevice::ReadOnly); | |
| 257 | |||
| 258 | ✗ | if(!res) | |
| 259 | { | ||
| 260 | qDebug() << "Failed to open the file for read."; | ||
| 261 | return Enums::MassDataType::NOT_SET; | ||
| 262 | } | ||
| 263 | |||
| 264 | ✗ | QCborStreamReaderSPtr reader_sp = std::make_shared<QCborStreamReader>(&file); | |
| 265 | |||
| 266 | ✗ | return readMassDataType(reader_sp); | |
| 267 | ✗ | } | |
| 268 | |||
| 269 | /*! | ||
| 270 | \overload | ||
| 271 | |||
| 272 | \brief Decodes enough of the data contained in \a byte_array to | ||
| 273 | determine and return the mass data type of the streamed data. | ||
| 274 | |||
| 275 | \note Failure to decode the mass data type is fatal. | ||
| 276 | |||
| 277 | \sa readMassDataType() overloads | ||
| 278 | */ | ||
| 279 | Enums::MassDataType | ||
| 280 | ✗ | MassDataCborBaseHandler::readMassDataType(const QByteArray &byte_array) | |
| 281 | { | ||
| 282 | ✗ | QCborStreamReaderSPtr reader_sp = | |
| 283 | ✗ | std::make_shared<QCborStreamReader>(byte_array); | |
| 284 | |||
| 285 | ✗ | return readMassDataType(reader_sp); | |
| 286 | ✗ | } | |
| 287 | |||
| 288 | /*! | ||
| 289 | \brief Reads the data in file \a input_file_name by decoding the data stream | ||
| 290 | read from it. | ||
| 291 | |||
| 292 | \note The base class does nothing and always returns false. | ||
| 293 | */ | ||
| 294 | bool | ||
| 295 | ✗ | MassDataCborBaseHandler::readFile( | |
| 296 | [[maybe_unused]] const QString &input_file_name) | ||
| 297 | { | ||
| 298 | ✗ | qDebug() << "The base class handler function does nothing."; | |
| 299 | ✗ | return false; | |
| 300 | } | ||
| 301 | |||
| 302 | /*! | ||
| 303 | \brief Reads the data in byte array \a byte_array by decoding the data stream | ||
| 304 | read from it. | ||
| 305 | |||
| 306 | \note The base class does nothing and always returns false. | ||
| 307 | */ | ||
| 308 | bool | ||
| 309 | ✗ | MassDataCborBaseHandler::readByteArray( | |
| 310 | [[maybe_unused]] const QByteArray &byte_array) | ||
| 311 | { | ||
| 312 | ✗ | qDebug() << "The base class handler function does nothing."; | |
| 313 | ✗ | return false; | |
| 314 | } | ||
| 315 | |||
| 316 | /*! | ||
| 317 | \brief Writes member data to file \a output_file_name. | ||
| 318 | |||
| 319 | \note The base class does nothing and always returns false. | ||
| 320 | */ | ||
| 321 | bool | ||
| 322 | ✗ | MassDataCborBaseHandler::writeFile( | |
| 323 | [[maybe_unused]] const QString &output_file_name) | ||
| 324 | { | ||
| 325 | ✗ | qDebug() << "The base class handler function does nothing."; | |
| 326 | ✗ | return false; | |
| 327 | } | ||
| 328 | |||
| 329 | /*! | ||
| 330 | \brief Writes member data to byte array \a byte_array. | ||
| 331 | |||
| 332 | \note The base class does nothing and always returns false. | ||
| 333 | */ | ||
| 334 | void | ||
| 335 | ✗ | MassDataCborBaseHandler::writeByteArray([[maybe_unused]] QByteArray &byte_array) | |
| 336 | { | ||
| 337 | ✗ | qDebug() << "The base class handler function does nothing."; | |
| 338 | ✗ | } | |
| 339 | |||
| 340 | /*! | ||
| 341 | \brief Sets the \a title of the mass data entity carried by the CBOR container. | ||
| 342 | */ | ||
| 343 | void | ||
| 344 | ✗ | MassDataCborBaseHandler::setTitle(const QString &title) | |
| 345 | { | ||
| 346 | ✗ | m_title = title; | |
| 347 | ✗ | } | |
| 348 | |||
| 349 | /*! | ||
| 350 | \brief Returns the title of the mass data entity carried by the CBOR container. | ||
| 351 | */ | ||
| 352 | QString | ||
| 353 | ✗ | MassDataCborBaseHandler::getTitle() const | |
| 354 | { | ||
| 355 | ✗ | return m_title; | |
| 356 | } | ||
| 357 | |||
| 358 | |||
| 359 | } // namespace libXpertMassCore | ||
| 360 | |||
| 361 | } // namespace MsXpS | ||
| 362 |