libpappsomspp
Library for mass spectrometry
xtandeminputsaxhandler.cpp
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1 /**
2  * \file pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.cpp
3  * \date 25/01/2020
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 
29 #include "xtandeminputsaxhandler.h"
30 #include "../../pappsoexception.h"
31 #include <QFileInfo>
32 namespace pappso
33 {
35  const QString &destinationMzXmlFile,
36  const QString &destinationTandemInputFile,
37  const QString &destinationTandemOutputFile)
38  : m_destinationTandemInputFile(destinationTandemInputFile)
39 {
40  m_destinationMzXmlFileName = destinationMzXmlFile;
41  m_destinationTandemOutputFileName = destinationTandemOutputFile;
43  QFileInfo(destinationTandemInputFile).absoluteFilePath();
44 
45  if(!m_destinationTandemInputFile.open(QIODevice::WriteOnly))
46  {
48  QObject::tr("ERROR: unable to open %1 tandem output file for write")
49  .arg(destinationTandemInputFile));
50  }
51 
52  p_writeXmlTandemInput = new QXmlStreamWriter();
54 }
55 
57 {
58  if(p_writeXmlTandemInput != nullptr)
59  {
61  delete p_writeXmlTandemInput;
62  }
63 }
64 
65 void
67  const QXmlAttributes &attributes)
68 {
69  p_writeXmlTandemInput->writeStartElement(qName);
70  for(int i = 0; i < attributes.length(); i++)
71  {
72  p_writeXmlTandemInput->writeAttribute(attributes.qName(i),
73  attributes.value(i));
74  }
75 }
76 
77 bool
79  [[maybe_unused]] const QString &namespaceURI,
80  [[maybe_unused]] const QString &localName,
81  const QString &qName,
82  const QXmlAttributes &attributes)
83 {
84  /*
85 <?xml version="1.0" encoding="UTF-8"?>
86 <bioml label="20191222_18_EF1_test_condor_22janv_third_step.xml">
87 <note type="heading">Paths</note>
88 <note type="input" label="list path, default
89 parameters">/gorgone/pappso/jouy/presets/metapappso/Lumos_04112019_PROTEOCARDIS_THIRD_STEP_AB.xml</note>
90 <note type="input" label="list path, taxonomy
91 information">/gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/params/xtandem_database_third_step_test_condor_22janv.database</note>
92 <note type="input" label="spectrum,
93 path">/gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML</note>
94 <note type="heading">Protein general</note>
95 <note type="input" label="protein, taxon">usedefined</note>
96 <note type="heading">Output</note>
97 <note type="input" label="output,
98 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>
99 </bioml>
100 */
101  m_tagStack.push_back(qName);
102  bool is_ok = true;
103 
104  try
105  {
106  m_currentText.clear();
107  //<bioml label="example api document">
108  if(m_tagStack.size() == 1)
109  {
110  if(qName != "bioml")
111  {
112  m_errorString = QObject::tr(
113  "ERROR in XtandemInputSaxHandler::startElement "
114  "root tag %1 is not <bioml>")
115  .arg(qName);
116  m_isTandemParameter = false;
117  return false;
118  }
119  else
120  {
121 
122  m_isTandemParameter = true;
123  // label="20191222_18_EF1_test_condor_22janv_third_step.xml"
124  m_labelName = attributes.value("label");
125 
126  writeOpenTag(qName, attributes);
127  }
128  }
129  // startElement_group
130 
131  if(qName == "note")
132  {
133  is_ok = startElement_note(attributes);
134  }
135  }
136  catch(pappso::PappsoException &exception_pappso)
137  {
138  m_errorString = QObject::tr(
139  "ERROR in XtandemInputSaxHandler::startElement "
140  "tag %1, PAPPSO exception:\n%2")
141  .arg(qName)
142  .arg(exception_pappso.qwhat());
143  return false;
144  }
145  catch(std::exception &exception_std)
146  {
147  m_errorString = QObject::tr(
148  "ERROR in XtandemInputSaxHandler::startElement "
149  "tag %1, std exception:\n%2")
150  .arg(qName)
151  .arg(exception_std.what());
152  return false;
153  }
154  return is_ok;
155 }
156 
157 bool
158 XtandemInputSaxHandler::endElement([[maybe_unused]] const QString &namespaceURI,
159  [[maybe_unused]] const QString &localName,
160  const QString &qName)
161 {
162 
163  bool is_ok = true;
164  // endElement_peptide_list
165  try
166  {
167 
168  if(qName == "note")
169  {
170  is_ok = endElement_note();
171  }
172  else
173  {
174  p_writeXmlTandemInput->writeCharacters(m_currentText);
175  p_writeXmlTandemInput->writeEndElement();
176  }
177  }
178  catch(pappso::PappsoException &exception_pappso)
179  {
180  m_errorString = QObject::tr(
181  "ERROR in XtandemInputSaxHandler::endElement tag "
182  "%1, PAPPSO exception:\n%2")
183  .arg(qName)
184  .arg(exception_pappso.qwhat());
185  return false;
186  }
187  catch(std::exception &exception_std)
188  {
189  m_errorString = QObject::tr(
190  "ERROR in XtandemInputSaxHandler::endElement tag "
191  "%1, std exception:\n%2")
192  .arg(qName)
193  .arg(exception_std.what());
194  return false;
195  }
196 
197  m_currentText.clear();
198  m_tagStack.pop_back();
199 
200  return is_ok;
201 }
202 
203 bool
205 {
206 
207  p_writeXmlTandemInput->setAutoFormatting(true);
208  p_writeXmlTandemInput->writeStartDocument("1.0");
209  return true;
210 }
211 
212 bool
214 {
215  p_writeXmlTandemInput->writeEndDocument();
216 
218  delete p_writeXmlTandemInput;
219  p_writeXmlTandemInput = nullptr;
220  return true;
221 }
222 
223 bool
225 {
226  m_currentText += str;
227  return true;
228 }
229 
230 
231 bool
232 XtandemInputSaxHandler::error(const QXmlParseException &exception)
233 {
234  m_errorString = QObject::tr(
235  "Parse error at line %1, column %2 :\n"
236  "%3")
237  .arg(exception.lineNumber())
238  .arg(exception.columnNumber())
239  .arg(exception.message());
240  qDebug() << m_errorString;
241  return false;
242 }
243 
244 
245 bool
246 XtandemInputSaxHandler::fatalError(const QXmlParseException &exception)
247 {
248  m_errorString = QObject::tr(
249  "Parse error at line %1, column %2 :\n"
250  "%3")
251  .arg(exception.lineNumber())
252  .arg(exception.columnNumber())
253  .arg(exception.message());
254  qDebug() << m_errorString;
255  return false;
256 }
257 
258 QString
260 {
261  return m_errorString;
262 }
263 
264 
265 bool
267 {
268  // qDebug() << "XtandemParamSaxHandler::startElement_note begin " <<
269  // <note type="input"
270  // 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>
271 
272  writeOpenTag("note", attributes);
273  m_currentLabel = "";
274 
275  if(attributes.value("type") == "input")
276  {
277  m_currentLabel = attributes.value("label");
278  }
279 
280  // qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " <<
281  // _current_label;
282  return true;
283 }
284 
285 bool
287 {
288  // qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
289  // _current_label << " " << _current_text.simplified();
290  if(m_currentLabel == "output, path")
291  {
294  }
295  else if(m_currentLabel == "list path, default parameters")
296  {
297  // <note type="input" label="list path, default parameters">
298  p_writeXmlTandemInput->writeCharacters(m_currentText);
300  QFileInfo(m_currentText).absoluteFilePath();
301  }
302  else if(m_currentLabel == "spectrum, path")
303  {
304  //<note type="input"
305  // label="spectrum,path">/gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML</note>
308  }
309  else
310  {
311  p_writeXmlTandemInput->writeCharacters(m_currentText);
312  }
313  p_writeXmlTandemInput->writeEndElement();
314  return true;
315 }
316 
317 
318 const QString &
320 {
321  return m_originMzDataFileName;
322 }
323 
324 const QString &
326 {
328 }
329 
330 const QString &
332 {
334 }
335 } // namespace pappso
pappso::XtandemInputSaxHandler::m_currentText
QString m_currentText
Definition: xtandeminputsaxhandler.h:97
pappso::XtandemInputSaxHandler::errorString
QString errorString() const
Definition: xtandeminputsaxhandler.cpp:259
xtandeminputsaxhandler.h
rewrites tandem xml input file with temporary files
pappso::XtandemInputSaxHandler::fatalError
bool fatalError(const QXmlParseException &exception) override
Definition: xtandeminputsaxhandler.cpp:246
pappso::XtandemInputSaxHandler::XtandemInputSaxHandler
XtandemInputSaxHandler(const QString &destinationMzXmlFile, const QString &destinationTandemInputFile, const QString &destinationTandemOutputFile)
Definition: xtandeminputsaxhandler.cpp:34
pappso::XtandemInputSaxHandler::m_destinationTandemInputFile
QFile m_destinationTandemInputFile
Definition: xtandeminputsaxhandler.h:92
pappso::XtandemInputSaxHandler::startDocument
bool startDocument() override
Definition: xtandeminputsaxhandler.cpp:204
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks
Definition: aa.cpp:39
pappso::XtandemInputSaxHandler::endElement_note
bool endElement_note()
Definition: xtandeminputsaxhandler.cpp:286
pappso::XtandemInputSaxHandler::startElement
bool startElement(const QString &namespaceURI, const QString &localName, const QString &qName, const QXmlAttributes &attributes) override
Definition: xtandeminputsaxhandler.cpp:78
pappso::XtandemInputSaxHandler::~XtandemInputSaxHandler
~XtandemInputSaxHandler()
Definition: xtandeminputsaxhandler.cpp:56
pappso::XtandemInputSaxHandler::m_labelName
QString m_labelName
Definition: xtandeminputsaxhandler.h:99
pappso::XtandemInputSaxHandler::m_currentLabel
QString m_currentLabel
Definition: xtandeminputsaxhandler.h:98
pappso::XtandemInputSaxHandler::p_writeXmlTandemInput
QXmlStreamWriter * p_writeXmlTandemInput
Definition: xtandeminputsaxhandler.h:93
pappso::XtandemInputSaxHandler::m_originTandemOutpuFileName
QString m_originTandemOutpuFileName
Definition: xtandeminputsaxhandler.h:90
pappso::XtandemInputSaxHandler::writeOpenTag
void writeOpenTag(const QString &qName, const QXmlAttributes &attributes)
Definition: xtandeminputsaxhandler.cpp:66
pappso::XtandemInputSaxHandler::characters
bool characters(const QString &str) override
Definition: xtandeminputsaxhandler.cpp:224
pappso::XtandemInputSaxHandler::endElement
bool endElement(const QString &namespaceURI, const QString &localName, const QString &qName) override
Definition: xtandeminputsaxhandler.cpp:158
pappso::XtandemInputSaxHandler::getOriginalTandemOutputFileName
const QString & getOriginalTandemOutputFileName() const
Definition: xtandeminputsaxhandler.cpp:325
pappso::XtandemInputSaxHandler::startElement_note
bool startElement_note(QXmlAttributes attributes)
Definition: xtandeminputsaxhandler.cpp:266
pappso::PappsoException::qwhat
virtual const QString & qwhat() const
Definition: pappsoexception.h:66
pappso::XtandemInputSaxHandler::error
bool error(const QXmlParseException &exception) override
Definition: xtandeminputsaxhandler.cpp:232
pappso::XtandemInputSaxHandler::m_destinationMzXmlFileName
QString m_destinationMzXmlFileName
Definition: xtandeminputsaxhandler.h:86
pappso::XtandemInputSaxHandler::m_originMzDataFileName
QString m_originMzDataFileName
Definition: xtandeminputsaxhandler.h:87
pappso::XtandemInputSaxHandler::getOriginalTandemPresetFileName
const QString & getOriginalTandemPresetFileName() const
Definition: xtandeminputsaxhandler.cpp:331
pappso::XtandemInputSaxHandler::endDocument
bool endDocument() override
Definition: xtandeminputsaxhandler.cpp:213
pappso::XtandemInputSaxHandler::m_originTandemPresetFileName
QString m_originTandemPresetFileName
Definition: xtandeminputsaxhandler.h:89
pappso::XtandemInputSaxHandler::m_destinationTandemInputFileName
QString m_destinationTandemInputFileName
Definition: xtandeminputsaxhandler.h:88
pappso::XtandemInputSaxHandler::m_errorString
QString m_errorString
Definition: xtandeminputsaxhandler.h:96
pappso::XtandemInputSaxHandler::getOriginalMsDataFileName
const QString & getOriginalMsDataFileName() const
Definition: xtandeminputsaxhandler.cpp:319
pappso::XtandemInputSaxHandler::m_isTandemParameter
bool m_isTandemParameter
Definition: xtandeminputsaxhandler.h:95
pappso::PappsoException
Definition: pappsoexception.h:42
pappso::XtandemInputSaxHandler::m_tagStack
std::vector< QString > m_tagStack
Definition: xtandeminputsaxhandler.h:94
pappso::XtandemInputSaxHandler::m_destinationTandemOutputFileName
QString m_destinationTandemOutputFileName
Definition: xtandeminputsaxhandler.h:91