From 8a796ad01fcd66c8e49760f9660136b3b0f96426 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Wed, 12 Jun 2019 23:40:12 +0200
Subject: [PATCH] stronger tandem parameter file parser
---
src/core/tandem_run/tandemparameters.cpp | 181 +++++++++++++-----
src/files/tandemparametersfile.cpp | 33 ++--
src/files/tandemparametersfile.h | 5 +-
.../edittandempresetdialog.cpp | 24 ++-
src/input/xtandemparamsaxhandler.cpp | 71 +++++--
src/input/xtandemparamsaxhandler.h | 11 +-
6 files changed, 238 insertions(+), 87 deletions(-)
diff --git a/src/core/tandem_run/tandemparameters.cpp b/src/core/tandem_run/tandemparameters.cpp
index 0a64767d3..872ebb490 100644
--- a/src/core/tandem_run/tandemparameters.cpp
+++ b/src/core/tandem_run/tandemparameters.cpp
@@ -85,24 +85,32 @@ TandemParameters::equals(const TandemParameters &other) const
const QString
TandemParameters::getLabelCategory(const QString &value) const
{
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << value;
return value.split(", ").at(0);
}
const QString &
TandemParameters::getValue(const QString &label) const
{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << label;
QMap<QString, QString>::const_iterator it = _map_label_value.constFind(label);
if(it == _map_label_value.end())
{
throw pappso::ExceptionNotFound(
- QObject::tr("X!Tandem preset label %1 not found in method %2")
+ QObject::tr("X!Tandem preset label \"%1\" not found in method \"%2\"")
.arg(label)
.arg(_method_name));
}
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
return it.value();
}
void
TandemParameters::setParamLabelValue(const QString &label, const QString &value)
{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << label;
// list path
//<note type="input" label="list path, default
// parameters">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/QExactive_analysis_FDR_nosemi.xml</note>
@@ -112,40 +120,47 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
{
return;
}
- if(label == "spectrum, path")
- {
- return;
- }
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << label;
if((label == "spectrum, parent monoisotopic mass error units") ||
(label == "spectrum, fragment monoisotopic mass error units"))
{
if((value != "Da") && (value != "Daltons") && (value != "ppm"))
{
throw pappso::ExceptionNotPossible(
- QObject::tr("%1 value must be Daltons or ppm (not %2)")
+ QObject::tr("\"%1\" value must be Daltons or ppm (not \"%2\")")
.arg(label)
.arg(value));
}
}
- if((label == "spectrum, parent monoisotopic mass isotope error") ||
- (label == "spectrum, use neutral loss window") ||
- (label == "spectrum, use contrast angle") ||
- (label == "protein, cleavage semi") ||
- (label == "protein, quick acetyl") ||
- (label == "protein, quick pyrolidone") || (label == "protein, stP bias") ||
- (label == "scoring, cyclic permutation") ||
- (label == "scoring, include reverse") || (label == "scoring, y ions") ||
- (label == "scoring, b ions") || (label == "scoring, c ions") ||
- (label == "scoring, z ions") || (label == "scoring, a ions") ||
- (label == "scoring, x ions") || (label == "refine") ||
- (label == "refine, use potential modifications for full refinement") ||
- (label == "refine, cleavage semi") ||
- (label == "refine, unanticipated cleavage") ||
- (label == "refine, spectrum synthesis") ||
- (label == "refine, point mutations") || (label == "output, mzid") ||
- (label == "output, spectra") ||
- (label == "spectrum, use noise suppression"))
+ else if((label == "spectrum, parent monoisotopic mass isotope error") ||
+ (label == "spectrum, use neutral loss window") ||
+ (label == "spectrum, use contrast angle") ||
+ (label == "protein, cleavage semi") ||
+ (label == "protein, quick acetyl") ||
+ (label == "protein, quick pyrolidone") ||
+ (label == "protein, stP bias") ||
+ (label == "scoring, cyclic permutation") ||
+ (label == "scoring, include reverse") ||
+ (label == "scoring, y ions") || (label == "scoring, b ions") ||
+ (label == "scoring, c ions") || (label == "scoring, z ions") ||
+ (label == "scoring, a ions") || (label == "scoring, x ions") ||
+ (label == "refine") ||
+ (label ==
+ "refine, use potential modifications for full refinement") ||
+ (label == "refine, cleavage semi") ||
+ (label == "refine, unanticipated cleavage") ||
+ (label == "refine, spectrum synthesis") ||
+ (label == "refine, point mutations") || (label == "output, mzid") ||
+ (label == "output, spectra") || (label == "output, proteins") ||
+ (label == "output, sequences") ||
+ (label == "output, one sequence copy") ||
+ (label == "output, parameters") || (label == "output, performance") ||
+ (label == "output, histograms") ||
+ (label == "output, path hashing") ||
+ (label == "spectrum, use noise suppression")||
+ (label == "spectrum, use noise suppression"))
{
if((value != "yes") && (value != "no"))
{
@@ -154,19 +169,35 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
.arg(label)
.arg(value));
}
+ /*
+ <note label="scoring, algorithm" type="input">k-score</note>
+ <note label="spectrum, use conditioning" type="input">no</note>
+ <note label="scoring, minimum ion count" type="input">1</note>
+*/
+
}
+ else if((label == "spectrum, parent monoisotopic mass error minus") ||
+ (label == "spectrum, parent monoisotopic mass error plus") ||
+ (label == "spectrum, dynamic range") ||
+ (label == "spectrum, minimum parent m+h") ||
+ (label == "protein, cleavage C-terminal mass change") ||
+ (label == "protein, cleavage N-terminal mass change") ||
+ (label == "protein, C-terminal residue modification mass") ||
+ (label == "protein, N-terminal residue modification mass") ||
+ (label == "refine, maximum valid expectation value") ||
+ (label == "spectrum, fragment monoisotopic mass error") ||
+ (label == "spectrum, neutral loss mass") ||
+ (label == "spectrum, neutral loss window") ||
+ (label == "spectrum, minimum fragment mz") ||
+ (label == "output, maximum valid expectation value") ||
+ (label == "output, maximum valid protein expectation value")
+
+
+ )
- if((label == "spectrum, parent monoisotopic mass error minus") ||
- (label == "spectrum, parent monoisotopic mass error plus") ||
- (label == "spectrum, dynamic range") ||
- (label == "spectrum, minimum parent m+h") ||
- (label == "protein, cleavage C-terminal mass change") ||
- (label == "protein, cleavage N-terminal mass change") ||
- (label == "protein, C-terminal residue modification mass") ||
- (label == "protein, N-terminal residue modification mass") ||
- (label == "refine, maximum valid expectation value"))
{
+
bool ok;
QString value_bis = value.simplified();
if(value_bis.isEmpty())
@@ -177,49 +208,105 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
if(!ok)
{ // not an integer
throw pappso::ExceptionNotPossible(
- QObject::tr("%1 value must be a number (not %2)")
+ QObject::tr("\"%1\" value must be a number (not \"%2\")")
.arg(label)
.arg(value));
}
}
-
-
- if((label == "spectrum, maximum parent charge") ||
- (label == "spectrum, total peaks") ||
- (label == "spectrum, minimum peaks") ||
- (label == "spectrum, sequence batch size") ||
- (label == "spectrum, threads") ||
- (label == "scoring, minimum ion count") ||
- (label == "scoring, maximum missed cleavage sites"))
+ else if((label == "protein, cleavage site") ||
+ (label == "protein, modified residue mass file") ||
+ (label == "residue, modification mass") ||
+ (label == "residue, modification mass 1") ||
+ (label == "residue, modification mass 2") ||
+ (label == "residue, potential modification mass") ||
+ (label == "residue, potential modification mass 1") ||
+ (label == "residue, potential modification mass 2") ||
+ (label == "residue, potential modification motif") ||
+ (label == "residue, potential modification motif 1") ||
+ (label == "residue, potential modification motif 2") ||
+ (label == "refine, potential N-terminus modifications") ||
+ (label == "refine, potential C-terminus modifications") ||
+ (label == "refine, modification mass") ||
+ (label == "refine, modification mass 1") ||
+ (label == "refine, modification mass 2") ||
+ (label == "refine, potential modification mass") ||
+ (label == "refine, potential modification mass 1") ||
+ (label == "refine, potential modification mass 2") ||
+ (label == "refine, potential modification motif") ||
+ (label == "refine, potential modification motif 1") ||
+ (label == "refine, potential modification motif 2") ||
+ (label == "output, sort results by") ||
+ (label == "output, xsl path")||
+ (label == "spectrum, path"))
+ {
+ // string
+ }
+ else if((label == "spectrum, maximum parent charge") ||
+ (label == "spectrum, total peaks") ||
+ (label == "spectrum, minimum peaks") ||
+ (label == "spectrum, sequence batch size") ||
+ (label == "spectrum, threads") ||
+ (label == "scoring, minimum ion count") ||
+ (label == "scoring, maximum missed cleavage sites")||
+ (label == "output, histogram column width"))
{
+
bool ok;
value.toInt(&ok);
if(!ok)
{ // not an integer
throw pappso::ExceptionNotPossible(
- QObject::tr("%1 value must be an integer (not %2)")
+ QObject::tr("\"%1\" value must be an integer (not \"%2\")")
.arg(label)
.arg(value));
}
}
- if(label == "spectrum, fragment mass type")
+ else if(label == "spectrum, fragment mass type")
{
if((value != "monoisotopic") && (value != "average"))
{
throw pappso::ExceptionNotPossible(
- QObject::tr("%1 value must be monoisotopic or average (not %2)")
+ QObject::tr(
+ "\"%1\" value must be monoisotopic or average (not \"%2\")")
.arg(label)
.arg(value));
}
}
+ // tandem input parameter label "output, results" for value "valid" not known.
+
+ else if(label == "output, results")
+ {
+ /*
+ if((value != "all") && (value != "valid"))
+ {
+ throw pappso::ExceptionNotPossible(
+ QObject::tr("\"%1\" value must be valid or all (not \"%2\")")
+ .arg(label)
+ .arg(value));
+ }
+ */
+ }
+ else
+ {
+
+ throw pappso::ExceptionNotPossible(
+ QObject::tr(
+ "tandem input parameter label \"%1\" for value \"%2\" not known.")
+ .arg(label)
+ .arg(value));
+ }
+
// text "protein, cleavage site" "protein, modified residue mass file"
// "residue, modification mass" || (label == "refine, potential N-terminus
// modifications") || (label == "refine, potential C-terminus modifications")
// spectrum, neutral loss mass
// spectrum, neutral loss window
-
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << label;
_map_label_value.insert(label, value);
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << label;
}
void
TandemParameters::setMethodName(const QString &method)
diff --git a/src/files/tandemparametersfile.cpp b/src/files/tandemparametersfile.cpp
index 68c82d692..65545954e 100644
--- a/src/files/tandemparametersfile.cpp
+++ b/src/files/tandemparametersfile.cpp
@@ -39,7 +39,9 @@
TandemParametersFile::TandemParametersFile(const QString &fasta_source)
: _param_source(fasta_source)
{
- qDebug() << "TandemParametersFile::TandemParametersFile " << fasta_source;
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << fasta_source;
}
TandemParametersFile::TandemParametersFile(const QFileInfo &fasta_source)
: _param_source(fasta_source)
@@ -143,17 +145,17 @@ TandemParametersFile::setTandemParameters(const TandemParameters ¶meters)
}
TandemParameters
-TandemParametersFile::getTandemParameters() const
+TandemParametersFile::getTandemParameters()
{
- qDebug() << "TandemParametersFile::getTandemParameters begin";
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
TandemParameters parameters;
XtandemParamSaxHandler *parser = new XtandemParamSaxHandler(¶meters);
QXmlSimpleReader simplereader;
simplereader.setContentHandler(parser);
simplereader.setErrorHandler(parser);
-
- qDebug() << "TandemParametersFile::getTandemParameters '"
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< _param_source.absoluteFilePath() << "'";
parameters.setMethodName(getMethodName());
@@ -162,14 +164,18 @@ TandemParametersFile::getTandemParameters() const
if(simplereader.parse(xmlInputSource))
{
- qDebug() << "TandemParametersFile::getTandemParameters parse ok";
+ m_isTandemParameterFile = parser->isTandemParameter();
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << m_isTandemParameterFile;
+ // parameters.getValue("spectrum, parent monoisotopic mass error units");
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
qfile.close();
delete parser;
}
else
{
-
- qDebug() << "TandemParametersFile::getTandemParameters parse error";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ m_isTandemParameterFile = parser->isTandemParameter();
qfile.close();
throw pappso::PappsoException(
@@ -182,7 +188,7 @@ TandemParametersFile::getTandemParameters() const
}
bool
-TandemParametersFile::isTandemPresetFile() const
+TandemParametersFile::isTandemPresetFile()
{
if(this->exists())
@@ -191,15 +197,20 @@ TandemParametersFile::isTandemPresetFile() const
try
{
TandemParameters param = getTandemParameters();
+
+ if(!m_isTandemParameterFile)
+ return false;
param.getValue("spectrum, threads");
}
catch(pappso::ExceptionNotFound &error)
{
- return false;
+ if(!m_isTandemParameterFile)
+ return false;
}
catch(pappso::PappsoException &error)
{
- return false;
+ if(!m_isTandemParameterFile)
+ return false;
}
return true;
}
diff --git a/src/files/tandemparametersfile.h b/src/files/tandemparametersfile.h
index ae2e2f58f..cdd6e2b1d 100644
--- a/src/files/tandemparametersfile.h
+++ b/src/files/tandemparametersfile.h
@@ -52,11 +52,11 @@ class TandemParametersFile
/** @brief tells if this file is really a tandem preset file
*/
- bool isTandemPresetFile() const;
+ bool isTandemPresetFile();
/** @brief read tandem parameters from XML file
*/
- TandemParameters getTandemParameters() const;
+ TandemParameters getTandemParameters();
/** @brief write tandem parameters to XML file
*/
@@ -72,6 +72,7 @@ class TandemParametersFile
private:
QFileInfo _param_source;
+ bool m_isTandemParameterFile = false;
};
#endif // TANDEMPARAMETERSFILE_H
diff --git a/src/gui/edit/edit_tandem_preset_dialog/edittandempresetdialog.cpp b/src/gui/edit/edit_tandem_preset_dialog/edittandempresetdialog.cpp
index e9128c4b9..2f73aa430 100644
--- a/src/gui/edit/edit_tandem_preset_dialog/edittandempresetdialog.cpp
+++ b/src/gui/edit/edit_tandem_preset_dialog/edittandempresetdialog.cpp
@@ -167,6 +167,7 @@ EditTandemPresetDialog::doLoad()
int index = ui->preset_combo_box->currentIndex();
if(index != -1)
{ // -1 for not found
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
TandemParametersFile *p_tandem_preset_file = new TandemParametersFile(
ui->preset_combo_box->itemData(index).value<QString>());
if(p_tandem_preset_file->isTandemPresetFile())
@@ -182,8 +183,23 @@ EditTandemPresetDialog::doLoad()
}
_p_tandem_preset_file = p_tandem_preset_file;
- _tandem_params = _p_tandem_preset_file->getTandemParameters();
- populate();
+ try
+ {
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _tandem_params = _p_tandem_preset_file->getTandemParameters();
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ populate();
+ }
+ catch(pappso::PappsoException &error)
+ {
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ QMessageBox::warning(
+ this,
+ tr("Error :"),
+ tr("Error reading %1 X!Tandem parameter file:\n %2")
+ .arg(p_tandem_preset_file->getAbsoluteFilePath())
+ .arg(error.qwhat()));
+ }
}
else
{
@@ -834,7 +850,7 @@ EditTandemPresetDialog::readUi()
void
EditTandemPresetDialog::populate()
{
- qDebug() << "EditTandemPresetDialog::populate begin";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
try
{
ui->method_name_line_edit->setText(_tandem_params.getMethodName());
@@ -1314,7 +1330,7 @@ EditTandemPresetDialog::populate()
{
QMessageBox::warning(this, tr("Error in parameters :"), error.qwhat());
}
- qDebug() << "EditTandemPresetDialog::populate end";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
diff --git a/src/input/xtandemparamsaxhandler.cpp b/src/input/xtandemparamsaxhandler.cpp
index 08b9feed0..cdbfe4fe8 100644
--- a/src/input/xtandemparamsaxhandler.cpp
+++ b/src/input/xtandemparamsaxhandler.cpp
@@ -48,7 +48,11 @@ XtandemParamSaxHandler::~XtandemParamSaxHandler()
{
}
-
+bool
+XtandemParamSaxHandler::isTandemParameter() const
+{
+ return m_isTandemParameter;
+}
bool
XtandemParamSaxHandler::startElement(const QString &namespaceURI,
const QString &localName,
@@ -67,12 +71,18 @@ XtandemParamSaxHandler::startElement(const QString &namespaceURI,
{
if(qName != "bioml")
{
- _errorStr =
- QObject::tr("ERROR in XtandemParamSaxHandler::startElement "
+ _errorStr = QObject::tr(
+ "ERROR in XtandemParamSaxHandler::startElement "
"root tag %1 is not <bioml>")
- .arg(qName);
+ .arg(qName);
+ m_isTandemParameter = false;
return false;
}
+ else
+ {
+
+ m_isTandemParameter = true;
+ }
}
// startElement_group
@@ -84,16 +94,18 @@ XtandemParamSaxHandler::startElement(const QString &namespaceURI,
}
catch(pappso::PappsoException exception_pappso)
{
- _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::startElement "
- "tag %1, PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtandemParamSaxHandler::startElement "
+ "tag %1, PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
}
catch(std::exception exception_std)
{
- _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::startElement "
- "tag %1, std exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtandemParamSaxHandler::startElement "
+ "tag %1, std exception:\n%2")
.arg(qName)
.arg(exception_std.what());
return false;
@@ -119,16 +131,18 @@ XtandemParamSaxHandler::endElement(const QString &namespaceURI,
}
catch(pappso::PappsoException exception_pappso)
{
- _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::endElement tag "
- "%1, PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtandemParamSaxHandler::endElement tag "
+ "%1, PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
}
catch(std::exception exception_std)
{
- _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::endElement tag "
- "%1, std exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtandemParamSaxHandler::endElement tag "
+ "%1, std exception:\n%2")
.arg(qName)
.arg(exception_std.what());
return false;
@@ -144,12 +158,14 @@ XtandemParamSaxHandler::endElement(const QString &namespaceURI,
bool
XtandemParamSaxHandler::error(const QXmlParseException &exception)
{
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3")
+ _errorStr = QObject::tr(
+ "Parse error at line %1, column %2 :\n"
+ "%3")
.arg(exception.lineNumber())
.arg(exception.columnNumber())
.arg(exception.message());
- qDebug() << "XtandemParamSaxHandler::error " << _errorStr;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << _errorStr;
return false;
}
@@ -157,12 +173,14 @@ XtandemParamSaxHandler::error(const QXmlParseException &exception)
bool
XtandemParamSaxHandler::fatalError(const QXmlParseException &exception)
{
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3")
+ _errorStr = QObject::tr(
+ "Parse error at line %1, column %2 :\n"
+ "%3")
.arg(exception.lineNumber())
.arg(exception.columnNumber())
.arg(exception.message());
- qDebug() << "XtandemParamSaxHandler::fatalError " << _errorStr;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << _errorStr;
return false;
}
@@ -223,8 +241,21 @@ XtandemParamSaxHandler::endElement_note()
// _current_label << " " << _current_text.simplified();
if(!_current_label.isEmpty())
{
- _p_tandem_parameters->setParamLabelValue(_current_label,
- _current_text.simplified());
+ try
+ {
+ _p_tandem_parameters->setParamLabelValue(_current_label,
+ _current_text.simplified());
+ }
+ catch(pappso::PappsoException &exception)
+ {
+ _errorStr =
+ QObject::tr("Error reading tandem input parameter \"%1\" :\n%2")
+ .arg(_current_label)
+ .arg(exception.qwhat());
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << _errorStr;
+ return false;
+ }
}
return true;
}
diff --git a/src/input/xtandemparamsaxhandler.h b/src/input/xtandemparamsaxhandler.h
index 398f516ca..a15489998 100644
--- a/src/input/xtandemparamsaxhandler.h
+++ b/src/input/xtandemparamsaxhandler.h
@@ -41,10 +41,13 @@ class XtandemParamSaxHandler : public QXmlDefaultHandler
XtandemParamSaxHandler(TandemParameters *p_tandem_parameters);
~XtandemParamSaxHandler();
- bool startElement(const QString &namespaceURI, const QString &localName,
- const QString &qName, const QXmlAttributes &attributes);
+ bool startElement(const QString &namespaceURI,
+ const QString &localName,
+ const QString &qName,
+ const QXmlAttributes &attributes);
- bool endElement(const QString &namespaceURI, const QString &localName,
+ bool endElement(const QString &namespaceURI,
+ const QString &localName,
const QString &qName);
bool startDocument();
@@ -58,6 +61,7 @@ class XtandemParamSaxHandler : public QXmlDefaultHandler
QString errorString() const;
+ bool isTandemParameter() const;
private:
bool startElement_note(QXmlAttributes attributes);
bool endElement_note();
@@ -70,6 +74,7 @@ class XtandemParamSaxHandler : public QXmlDefaultHandler
QString _current_text;
QString _current_label;
+ bool m_isTandemParameter = false;
};
#endif // XTANDEMPARAMSAXHANDLER_H
--
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