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;
42  m_destinationTandemInputFileName =
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();
53  p_writeXmlTandemInput->setDevice(&m_destinationTandemInputFile);
54 }
55 
57 {
58  if(p_writeXmlTandemInput != nullptr)
59  {
61  delete p_writeXmlTandemInput;
62  }
63 }
64 
65 void
66 XtandemInputSaxHandler::writeOpenTag(const QString &qName,
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
78 XtandemInputSaxHandler::startElement([[maybe_unused]] const QString &namespaceURI,
79  [[maybe_unused]] const QString &localName,
80  const QString &qName,
81  const QXmlAttributes &attributes)
82 {
83  /*
84 <?xml version="1.0" encoding="UTF-8"?>
85 <bioml label="20191222_18_EF1_test_condor_22janv_third_step.xml">
86 <note type="heading">Paths</note>
87 <note type="input" label="list path, default
88 parameters">/gorgone/pappso/jouy/presets/metapappso/Lumos_04112019_PROTEOCARDIS_THIRD_STEP_AB.xml</note>
89 <note type="input" label="list path, taxonomy
90 information">/gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/params/xtandem_database_third_step_test_condor_22janv.database</note>
91 <note type="input" label="spectrum,
92 path">/gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML</note>
93 <note type="heading">Protein general</note>
94 <note type="input" label="protein, taxon">usedefined</note>
95 <note type="heading">Output</note>
96 <note type="input" label="output,
97 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>
98 </bioml>
99 */
100  m_tagStack.push_back(qName);
101  bool is_ok = true;
102 
103  try
104  {
105  m_currentText.clear();
106  //<bioml label="example api document">
107  if(m_tagStack.size() == 1)
108  {
109  if(qName != "bioml")
110  {
111  m_errorString = QObject::tr(
112  "ERROR in XtandemInputSaxHandler::startElement "
113  "root tag %1 is not <bioml>")
114  .arg(qName);
115  m_isTandemParameter = false;
116  return false;
117  }
118  else
119  {
120 
121  m_isTandemParameter = true;
122  // label="20191222_18_EF1_test_condor_22janv_third_step.xml"
123  m_labelName = attributes.value("label");
124 
125  writeOpenTag(qName, attributes);
126  }
127  }
128  // startElement_group
129 
130  if(qName == "note")
131  {
132  is_ok = startElement_note(attributes);
133  }
134  }
135  catch(pappso::PappsoException &exception_pappso)
136  {
137  m_errorString = QObject::tr(
138  "ERROR in XtandemInputSaxHandler::startElement "
139  "tag %1, PAPPSO exception:\n%2")
140  .arg(qName)
141  .arg(exception_pappso.qwhat());
142  return false;
143  }
144  catch(std::exception &exception_std)
145  {
146  m_errorString = QObject::tr(
147  "ERROR in XtandemInputSaxHandler::startElement "
148  "tag %1, std exception:\n%2")
149  .arg(qName)
150  .arg(exception_std.what());
151  return false;
152  }
153  return is_ok;
154 }
155 
156 bool
157 XtandemInputSaxHandler::endElement([[maybe_unused]] const QString &namespaceURI,
158  [[maybe_unused]] const QString &localName,
159  const QString &qName)
160 {
161 
162  bool is_ok = true;
163  // endElement_peptide_list
164  try
165  {
166 
167  if(qName == "note")
168  {
169  is_ok = endElement_note();
170  }
171  else
172  {
173  p_writeXmlTandemInput->writeCharacters(m_currentText);
174  p_writeXmlTandemInput->writeEndElement();
175  }
176  }
177  catch(pappso::PappsoException &exception_pappso)
178  {
179  m_errorString = QObject::tr(
180  "ERROR in XtandemInputSaxHandler::endElement tag "
181  "%1, PAPPSO exception:\n%2")
182  .arg(qName)
183  .arg(exception_pappso.qwhat());
184  return false;
185  }
186  catch(std::exception &exception_std)
187  {
188  m_errorString = QObject::tr(
189  "ERROR in XtandemInputSaxHandler::endElement tag "
190  "%1, std exception:\n%2")
191  .arg(qName)
192  .arg(exception_std.what());
193  return false;
194  }
195 
196  m_currentText.clear();
197  m_tagStack.pop_back();
198 
199  return is_ok;
200 }
201 
202 bool
204 {
205 
206  p_writeXmlTandemInput->setAutoFormatting(true);
207  p_writeXmlTandemInput->writeStartDocument("1.0");
208  return true;
209 }
210 
211 bool
213 {
214  p_writeXmlTandemInput->writeEndDocument();
215 
217  delete p_writeXmlTandemInput;
218  p_writeXmlTandemInput = nullptr;
219  return true;
220 }
221 
222 bool
223 XtandemInputSaxHandler::characters(const QString &str)
224 {
225  m_currentText += str;
226  return true;
227 }
228 
229 
230 bool
231 XtandemInputSaxHandler::error(const QXmlParseException &exception)
232 {
233  m_errorString = QObject::tr(
234  "Parse error at line %1, column %2 :\n"
235  "%3")
236  .arg(exception.lineNumber())
237  .arg(exception.columnNumber())
238  .arg(exception.message());
239  qDebug() << m_errorString;
240  return false;
241 }
242 
243 
244 bool
245 XtandemInputSaxHandler::fatalError(const QXmlParseException &exception)
246 {
247  m_errorString = QObject::tr(
248  "Parse error at line %1, column %2 :\n"
249  "%3")
250  .arg(exception.lineNumber())
251  .arg(exception.columnNumber())
252  .arg(exception.message());
253  qDebug() << m_errorString;
254  return false;
255 }
256 
257 QString
259 {
260  return m_errorString;
261 }
262 
263 
264 bool
265 XtandemInputSaxHandler::startElement_note(QXmlAttributes attributes)
266 {
267  // qDebug() << "XtandemParamSaxHandler::startElement_note begin " <<
268  // <note type="input"
269  // 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>
270 
271  writeOpenTag("note", attributes);
272  m_currentLabel = "";
273 
274  if(attributes.value("type") == "input")
275  {
276  m_currentLabel = attributes.value("label");
277  }
278 
279  // qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " <<
280  // _current_label;
281  return true;
282 }
283 
284 bool
286 {
287  // qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
288  // _current_label << " " << _current_text.simplified();
289  if(m_currentLabel == "output, path")
290  {
293  }
294  else if(m_currentLabel == "list path, default parameters")
295  {
296  // <note type="input" label="list path, default parameters">
297  p_writeXmlTandemInput->writeCharacters(m_currentText);
299  QFileInfo(m_currentText).absoluteFilePath();
300  }
301  else if(m_currentLabel == "spectrum, path")
302  {
303  //<note type="input"
304  // label="spectrum,path">/gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML</note>
307  }
308  else
309  {
310  p_writeXmlTandemInput->writeCharacters(m_currentText);
311  }
312  p_writeXmlTandemInput->writeEndElement();
313  return true;
314 }
315 
316 
317 const QString &
319 {
320  return m_originMzDataFileName;
321 }
322 
323 const QString &
325 {
327 }
328 
329 const QString &
331 {
333 }
334 } // namespace pappso
pappso::XtandemInputSaxHandler::m_currentText
QString m_currentText
Definition: xtandeminputsaxhandler.h:133
pappso::XtandemInputSaxHandler::errorString
QString errorString() const
Definition: xtandeminputsaxhandler.cpp:276
xtandeminputsaxhandler.h
rewrites tandem xml input file with temporary files
pappso::XtandemInputSaxHandler::fatalError
bool fatalError(const QXmlParseException &exception) override
Definition: xtandeminputsaxhandler.cpp:263
pappso::XtandemInputSaxHandler::XtandemInputSaxHandler
XtandemInputSaxHandler(const QString &destinationMzXmlFile, const QString &destinationTandemInputFile, const QString &destinationTandemOutputFile)
Definition: xtandeminputsaxhandler.cpp:52
pappso::XtandemInputSaxHandler::m_destinationTandemInputFile
QFile m_destinationTandemInputFile
Definition: xtandeminputsaxhandler.h:128
pappso::XtandemInputSaxHandler::startDocument
bool startDocument() override
Definition: xtandeminputsaxhandler.cpp:221
pappso
Definition: aa.cpp:38
pappso::XtandemInputSaxHandler::endElement_note
bool endElement_note()
Definition: xtandeminputsaxhandler.cpp:303
pappso::XtandemInputSaxHandler::startElement
bool startElement(const QString &namespaceURI, const QString &localName, const QString &qName, const QXmlAttributes &attributes) override
Definition: xtandeminputsaxhandler.cpp:96
pappso::XtandemInputSaxHandler::~XtandemInputSaxHandler
~XtandemInputSaxHandler()
Definition: xtandeminputsaxhandler.cpp:74
pappso::XtandemInputSaxHandler::m_labelName
QString m_labelName
Definition: xtandeminputsaxhandler.h:135
pappso::XtandemInputSaxHandler::m_currentLabel
QString m_currentLabel
Definition: xtandeminputsaxhandler.h:134
pappso::XtandemInputSaxHandler::p_writeXmlTandemInput
QXmlStreamWriter * p_writeXmlTandemInput
Definition: xtandeminputsaxhandler.h:129
pappso::XtandemInputSaxHandler::m_originTandemOutpuFileName
QString m_originTandemOutpuFileName
Definition: xtandeminputsaxhandler.h:126
pappso::XtandemInputSaxHandler::writeOpenTag
void writeOpenTag(const QString &qName, const QXmlAttributes &attributes)
Definition: xtandeminputsaxhandler.cpp:84
pappso::XtandemInputSaxHandler::characters
bool characters(const QString &str) override
Definition: xtandeminputsaxhandler.cpp:241
pappso::XtandemInputSaxHandler::endElement
bool endElement(const QString &namespaceURI, const QString &localName, const QString &qName) override
Definition: xtandeminputsaxhandler.cpp:175
pappso::XtandemInputSaxHandler::getOriginalTandemOutputFileName
const QString & getOriginalTandemOutputFileName() const
Definition: xtandeminputsaxhandler.cpp:342
pappso::XtandemInputSaxHandler::startElement_note
bool startElement_note(QXmlAttributes attributes)
Definition: xtandeminputsaxhandler.cpp:283
pappso::PappsoException::qwhat
virtual const QString & qwhat() const
Definition: pappsoexception.h:108
pappso::XtandemInputSaxHandler::error
bool error(const QXmlParseException &exception) override
Definition: xtandeminputsaxhandler.cpp:249
pappso::XtandemInputSaxHandler::m_destinationMzXmlFileName
QString m_destinationMzXmlFileName
Definition: xtandeminputsaxhandler.h:122
pappso::XtandemInputSaxHandler::m_originMzDataFileName
QString m_originMzDataFileName
Definition: xtandeminputsaxhandler.h:123
pappso::XtandemInputSaxHandler::getOriginalTandemPresetFileName
const QString & getOriginalTandemPresetFileName() const
Definition: xtandeminputsaxhandler.cpp:348
pappso::XtandemInputSaxHandler::endDocument
bool endDocument() override
Definition: xtandeminputsaxhandler.cpp:230
pappso::XtandemInputSaxHandler::m_originTandemPresetFileName
QString m_originTandemPresetFileName
Definition: xtandeminputsaxhandler.h:125
pappso::XtandemInputSaxHandler::m_errorString
QString m_errorString
Definition: xtandeminputsaxhandler.h:132
pappso::XtandemInputSaxHandler::getOriginalMsDataFileName
const QString & getOriginalMsDataFileName() const
Definition: xtandeminputsaxhandler.cpp:336
pappso::XtandemInputSaxHandler::m_isTandemParameter
bool m_isTandemParameter
Definition: xtandeminputsaxhandler.h:131
pappso::PappsoException
Definition: pappsoexception.h:62
pappso::XtandemInputSaxHandler::m_tagStack
std::vector< QString > m_tagStack
Definition: xtandeminputsaxhandler.h:130
pappso::XtandemInputSaxHandler::m_destinationTandemOutputFileName
QString m_destinationTandemOutputFileName
Definition: xtandeminputsaxhandler.h:127