libpappsomspp
Library for mass spectrometry
xtandemoutputsaxhandler.cpp
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1 /**
2  * \file pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.cpp
3  * \date 01/02/2020
4  * \author Olivier Langella
5  * \brief rewrites tandem xml input file with temporary files
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2020 Olivier Langella <Olivier.Langella@u-psud.fr>.
10  *
11  * This file is part of PAPPSOms-tools.
12  *
13  * PAPPSOms-tools is free software: you can redistribute it and/or modify
14  * it under the terms of the GNU General Public License as published by
15  * the Free Software Foundation, either version 3 of the License, or
16  * (at your option) any later version.
17  *
18  * PAPPSOms-tools is distributed in the hope that it will be useful,
19  * but WITHOUT ANY WARRANTY; without even the implied warranty of
20  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21  * GNU General Public License for more details.
22  *
23  * You should have received a copy of the GNU General Public License
24  * along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
25  *
26  ******************************************************************************/
27 
28 
30 #include "../../pappsoexception.h"
31 #include <QFileInfo>
32 
33 namespace pappso
34 {
36  const QString &final_tandem_output, const QString &original_msdata_file_name)
37  : m_destinationTandemOutputFile(final_tandem_output)
38 {
39  qDebug() << final_tandem_output;
41  QFileInfo(original_msdata_file_name).absoluteFilePath();
42  if(!m_destinationTandemOutputFile.open(QIODevice::WriteOnly))
43  {
45  QObject::tr("ERROR: unable to open %1 to write XML output")
46  .arg(final_tandem_output));
47  }
48  p_writeXmlTandemOutput = new QXmlStreamWriter();
49  p_writeXmlTandemOutput->setAutoFormatting(true);
51 }
52 
54 {
55  if(p_writeXmlTandemOutput != nullptr)
56  {
59  }
60 }
61 
62 void
64  const QXmlAttributes &attributes)
65 {
66  p_writeXmlTandemOutput->writeStartElement(qName);
67  for(int i = 0; i < attributes.length(); i++)
68  {
69  p_writeXmlTandemOutput->writeAttribute(attributes.qName(i),
70  attributes.value(i));
71  }
72 }
73 
74 bool
75 XtandemOutputSaxHandler::startElement([[maybe_unused]] const QString &namespaceURI,
76  [[maybe_unused]] const QString &localName,
77  const QString &qName,
78  const QXmlAttributes &attributes)
79 {
80  m_tagStack.push_back(qName);
81  bool is_ok = true;
82 
83  try
84  {
85  m_currentText.clear();
86  //<bioml label="example api document">
87  if(m_tagStack.size() == 1)
88  {
89  if(qName != "bioml")
90  {
92  QObject::tr(
93  "ERROR in XtandemOutputSaxHandler::startElement "
94  "root tag %1 is not <bioml>")
95  .arg(qName);
96  m_isTandemParameter = false;
97  return false;
98  }
99  else
100  {
101 
102  m_isTandemParameter = true;
103 
104  // <bioml xmlns:GAML="http://www.bioml.com/gaml/" label="models
105  // from '/tmp/msdata.mzxml'">
106  p_writeXmlTandemOutput->writeStartElement("bioml");
107  p_writeXmlTandemOutput->writeAttribute(
108  "xmlns:GAML", attributes.value("xmlns:GAML"));
109  p_writeXmlTandemOutput->writeAttribute(
110  "label",
111  QString("models from '%1'").arg(m_originalMsDataFileName));
112  return true;
113  }
114  }
115  // startElement_group
116 
117  if(qName == "note")
118  {
119  is_ok = startElement_note(attributes);
120  }
121  else
122  {
123  writeOpenTag(qName, attributes);
124  }
125  }
126  catch(const pappso::PappsoException &exception_pappso)
127  {
128  m_errorString = QObject::tr(
129  "ERROR in XtandemOutputSaxHandler::startElement "
130  "tag %1, PAPPSO exception:\n%2")
131  .arg(qName)
132  .arg(exception_pappso.qwhat());
133  return false;
134  }
135  catch(const std::exception &exception_std)
136  {
137  m_errorString = QObject::tr(
138  "ERROR in XtandemOutputSaxHandler::startElement "
139  "tag %1, std exception:\n%2")
140  .arg(qName)
141  .arg(exception_std.what());
142  return false;
143  }
144  return is_ok;
145 }
146 
147 bool
148 XtandemOutputSaxHandler::endElement([[maybe_unused]] const QString &namespaceURI,
149  [[maybe_unused]] const QString &localName,
150  const QString &qName)
151 {
152 
153  bool is_ok = true;
154  // endElement_peptide_list
155  try
156  {
157 
158  if(qName == "note")
159  {
160  is_ok = endElement_note();
161  }
162  else
163  {
164  p_writeXmlTandemOutput->writeEndElement();
165  }
166  }
167  catch(const pappso::PappsoException &exception_pappso)
168  {
169  m_errorString = QObject::tr(
170  "ERROR in XtandemOutputSaxHandler::endElement tag "
171  "%1, PAPPSO exception:\n%2")
172  .arg(qName)
173  .arg(exception_pappso.qwhat());
174  return false;
175  }
176  catch(const std::exception &exception_std)
177  {
178  m_errorString = QObject::tr(
179  "ERROR in XtandemOutputSaxHandler::endElement tag "
180  "%1, std exception:\n%2")
181  .arg(qName)
182  .arg(exception_std.what());
183  return false;
184  }
185 
186  m_currentText.clear();
187  m_tagStack.pop_back();
188 
189  return is_ok;
190 }
191 
192 bool
194 {
195 
196  p_writeXmlTandemOutput->setAutoFormatting(true);
197  p_writeXmlTandemOutput->writeStartDocument("1.0");
198  return true;
199 }
200 
201 bool
203 {
204  p_writeXmlTandemOutput->writeEndDocument();
205 
207  delete p_writeXmlTandemOutput;
208  p_writeXmlTandemOutput = nullptr;
209  return true;
210 }
211 
212 bool
214 {
215  m_currentText += str;
216  if(m_tagStack.back() != "note")
217  {
218  p_writeXmlTandemOutput->writeCharacters(str);
219  }
220  return true;
221 }
222 
223 
224 bool
225 XtandemOutputSaxHandler::error(const QXmlParseException &exception)
226 {
227  m_errorString = QObject::tr(
228  "Parse error at line %1, column %2 :\n"
229  "%3")
230  .arg(exception.lineNumber())
231  .arg(exception.columnNumber())
232  .arg(exception.message());
233  qDebug() << m_errorString;
234  return false;
235 }
236 
237 
238 bool
239 XtandemOutputSaxHandler::fatalError(const QXmlParseException &exception)
240 {
241  m_errorString = QObject::tr(
242  "Parse error at line %1, column %2 :\n"
243  "%3")
244  .arg(exception.lineNumber())
245  .arg(exception.columnNumber())
246  .arg(exception.message());
247  qDebug() << m_errorString;
248  return false;
249 }
250 
251 QString
253 {
254  return m_errorString;
255 }
256 
257 
258 bool
260 {
261  // qDebug() << "XtandemParamSaxHandler::startElement_note begin " <<
262  // <note type="input"
263  // label="output,path">/gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/test_run/20191222_18_EF1_third_step_test_condor_22janv.xml</note>
264 
265  writeOpenTag("note", attributes);
266  m_currentLabel = "";
267 
268  if(attributes.value("type") == "input")
269  {
270  m_currentLabel = attributes.value("label");
271  }
272 
273  // qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " <<
274  // _current_label;
275  return true;
276 }
277 
278 bool
280 {
281  // qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
282  // <note type="input" label="spectrum,
283  // path">/tmp/tandemwrapper-IehrEL/msdata.mzxml</note>
284 
285  if(m_currentLabel == "spectrum, path")
286  {
287  //<note type="input"
288  // label="spectrum,path">/gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML</note>
289  // m_originMzDataFileName = m_currentText;
290  // p_writeXmlTandemOutput->writeCharacters(m_destinationMzXmlFileName);
292  p_writeXmlTandemOutput->writeEndElement();
293 
294 
295  for(auto pair_input : m_mapTandemInputParameters)
296  {
297  p_writeXmlTandemOutput->writeStartElement("note");
298  p_writeXmlTandemOutput->writeAttribute("type", "input");
299  p_writeXmlTandemOutput->writeAttribute("label", pair_input.first);
300  p_writeXmlTandemOutput->writeCharacters(pair_input.second);
301  p_writeXmlTandemOutput->writeEndElement();
302  }
303  }
304  else if(m_currentLabel == "output, path")
305  {
306  //<note type="input" label="output,
307  // path">/tmp/tandemwrapper-sSGxtE/output_tandem.xml</note>
308  p_writeXmlTandemOutput->writeCharacters(
309  QFileInfo(m_destinationTandemOutputFile).absoluteFilePath());
310  p_writeXmlTandemOutput->writeEndElement();
311  }
312  else
313  {
314  p_writeXmlTandemOutput->writeCharacters(m_currentText);
315  p_writeXmlTandemOutput->writeEndElement();
316  }
317  return true;
318 }
319 
320 void
321 XtandemOutputSaxHandler::setInputParameters(const QString &label_name_attribute,
322  const QString &input_value)
323 {
325  std::pair<QString, QString>(label_name_attribute, input_value));
326 }
327 } // namespace pappso
pappso::XtandemOutputSaxHandler::m_destinationTandemOutputFile
QFile m_destinationTandemOutputFile
Definition: xtandemoutputsaxhandler.h:84
pappso::XtandemOutputSaxHandler::characters
bool characters(const QString &str) override
Definition: xtandemoutputsaxhandler.cpp:213
pappso::XtandemOutputSaxHandler::error
bool error(const QXmlParseException &exception) override
Definition: xtandemoutputsaxhandler.cpp:225
pappso::XtandemOutputSaxHandler::m_originalMsDataFileName
QString m_originalMsDataFileName
Definition: xtandemoutputsaxhandler.h:90
pappso::XtandemOutputSaxHandler::m_currentLabel
QString m_currentLabel
Definition: xtandemoutputsaxhandler.h:89
pappso::XtandemOutputSaxHandler::startElement_note
bool startElement_note(QXmlAttributes attributes)
Definition: xtandemoutputsaxhandler.cpp:259
pappso::XtandemOutputSaxHandler::errorString
QString errorString() const
Definition: xtandemoutputsaxhandler.cpp:252
xtandemoutputsaxhandler.h
rewrites tandem xml output file with temporary files
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks
Definition: aa.cpp:39
pappso::XtandemOutputSaxHandler::endElement_note
bool endElement_note()
Definition: xtandemoutputsaxhandler.cpp:279
pappso::XtandemOutputSaxHandler::m_mapTandemInputParameters
std::map< QString, QString > m_mapTandemInputParameters
Definition: xtandemoutputsaxhandler.h:82
pappso::XtandemOutputSaxHandler::m_isTandemParameter
bool m_isTandemParameter
Definition: xtandemoutputsaxhandler.h:88
pappso::XtandemOutputSaxHandler::fatalError
bool fatalError(const QXmlParseException &exception) override
Definition: xtandemoutputsaxhandler.cpp:239
pappso::XtandemOutputSaxHandler::endElement
bool endElement(const QString &namespaceURI, const QString &localName, const QString &qName) override
Definition: xtandemoutputsaxhandler.cpp:148
pappso::XtandemOutputSaxHandler::m_errorString
QString m_errorString
Definition: xtandemoutputsaxhandler.h:86
pappso::XtandemOutputSaxHandler::p_writeXmlTandemOutput
QXmlStreamWriter * p_writeXmlTandemOutput
Definition: xtandemoutputsaxhandler.h:85
pappso::XtandemOutputSaxHandler::writeOpenTag
void writeOpenTag(const QString &qName, const QXmlAttributes &attributes)
Definition: xtandemoutputsaxhandler.cpp:63
pappso::XtandemOutputSaxHandler::XtandemOutputSaxHandler
XtandemOutputSaxHandler(const QString &final_tandem_output, const QString &original_msdata_file_name)
Definition: xtandemoutputsaxhandler.cpp:35
pappso::XtandemOutputSaxHandler::endDocument
bool endDocument() override
Definition: xtandemoutputsaxhandler.cpp:202
pappso::XtandemOutputSaxHandler::m_currentText
QString m_currentText
Definition: xtandemoutputsaxhandler.h:87
pappso::PappsoException::qwhat
virtual const QString & qwhat() const
Definition: pappsoexception.h:66
pappso::XtandemOutputSaxHandler::m_tagStack
std::vector< QString > m_tagStack
Definition: xtandemoutputsaxhandler.h:83
pappso::XtandemOutputSaxHandler::setInputParameters
void setInputParameters(const QString &label_name_attribute, const QString &input_value)
Definition: xtandemoutputsaxhandler.cpp:321
pappso::XtandemOutputSaxHandler::startElement
bool startElement(const QString &namespaceURI, const QString &localName, const QString &qName, const QXmlAttributes &attributes) override
Definition: xtandemoutputsaxhandler.cpp:75
pappso::XtandemOutputSaxHandler::~XtandemOutputSaxHandler
~XtandemOutputSaxHandler()
Definition: xtandemoutputsaxhandler.cpp:53
pappso::PappsoException
Definition: pappsoexception.h:42
pappso::XtandemOutputSaxHandler::startDocument
bool startDocument() override
Definition: xtandemoutputsaxhandler.cpp:193