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remove dependency on member variable which is being accessed by multi…
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…ple threads (race condition)
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@cbielow
cbielow committed Aug 14, 2023
1 parent ef37a65 commit 331436c
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Showing 3 changed files with 23 additions and 31 deletions.
6 changes: 0 additions & 6 deletions src/openms/include/OpenMS/FORMAT/HANDLERS/XMLHandler.h
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Original file line number Diff line number Diff line change
Expand Up @@ -390,9 +390,6 @@ namespace OpenMS
/// Writes the contents to a stream.
virtual void writeTo(std::ostream & /*os*/);

/// Returns the last error description
String errorString();

/// handler which support partial loading, implement this method
virtual LOADDETAIL getLoadDetail() const;

Expand Down Expand Up @@ -469,9 +466,6 @@ namespace OpenMS
void checkUniqueIdentifiers_(const std::vector<ProteinIdentification>& prot_ids) const;

protected:
/// Error message of the last error
mutable String error_message_;

/// File name
String file_;

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10 changes: 5 additions & 5 deletions src/openms/source/FORMAT/HANDLERS/MzMLHandlerHelper.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -43,20 +43,20 @@ namespace OpenMS::Internal

void MzMLHandlerHelper::warning(int mode, const String & msg, UInt line, UInt column)
{
String error_message_;
String error_message;
if (mode == 0)
{
error_message_ = String("While loading '") + "': " + msg;
error_message = String("While loading '") + "': " + msg;
}
else if (mode == 1)
{
error_message_ = String("While storing '") + "': " + msg;
error_message = String("While storing '") + "': " + msg;
}
if (line != 0 || column != 0)
{
error_message_ += String("( in line ") + line + " column " + column + ")";
error_message += String("( in line ") + line + " column " + column + ")";
}
OPENMS_LOG_WARN << error_message_ << std::endl;
OPENMS_LOG_WARN << error_message << std::endl;
}

String MzMLHandlerHelper::getCompressionTerm_(const PeakFileOptions& opt, MSNumpressCoder::NumpressConfig np, const String& indent, bool use_numpress)
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38 changes: 18 additions & 20 deletions src/openms/source/FORMAT/HANDLERS/XMLHandler.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -104,70 +104,73 @@ namespace OpenMS::Internal

void XMLHandler::fatalError(ActionMode mode, const String & msg, UInt line, UInt column) const
{
String error_message;
if (mode == LOAD)
{
error_message_ = String("While loading '") + file_ + "': " + msg;
error_message = String("While loading '") + file_ + "': " + msg;
// test if file has the wrong extension and is therefore passed to the wrong parser
// only makes sense if we are loading/parsing a file
FileTypes::Type ft_name = FileHandler::getTypeByFileName(file_);
FileTypes::Type ft_content = FileHandler::getTypeByContent(file_);
if (ft_name != ft_content)
{
error_message_ += String("\nProbable cause: The file suffix (") + FileTypes::typeToName(ft_name)
error_message += String("\nProbable cause: The file suffix (") + FileTypes::typeToName(ft_name)
+ ") does not match the file content (" + FileTypes::typeToName(ft_content) + "). "
+ "Rename the file to fix this.";
}
}
else if (mode == STORE)
{
error_message_ = String("While storing '") + file_ + "': " + msg;
error_message = String("While storing '") + file_ + "': " + msg;
}
if (line != 0 || column != 0)
{
error_message_ += String("( in line ") + line + " column " + column + ")";
error_message += String("( in line ") + line + " column " + column + ")";
}

OPENMS_LOG_FATAL_ERROR << error_message_ << std::endl;
throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, file_, error_message_);
OPENMS_LOG_FATAL_ERROR << error_message << std::endl;
throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, file_, error_message);
}

void XMLHandler::error(ActionMode mode, const String & msg, UInt line, UInt column) const
{
String error_message;
if (mode == LOAD)
{
error_message_ = String("Non-fatal error while loading '") + file_ + "': " + msg;
error_message = String("Non-fatal error while loading '") + file_ + "': " + msg;
}
else if (mode == STORE)
{
error_message_ = String("Non-fatal error while storing '") + file_ + "': " + msg;
error_message = String("Non-fatal error while storing '") + file_ + "': " + msg;
}
if (line != 0 || column != 0)
{
error_message_ += String("( in line ") + line + " column " + column + ")";
error_message += String("( in line ") + line + " column " + column + ")";
}
OPENMS_LOG_ERROR << error_message_ << std::endl;
OPENMS_LOG_ERROR << error_message << std::endl;
}

void XMLHandler::warning(ActionMode mode, const String & msg, UInt line, UInt column) const
{
String error_message;
if (mode == LOAD)
{
error_message_ = String("While loading '") + file_ + "': " + msg;
error_message = String("While loading '") + file_ + "': " + msg;
}
else if (mode == STORE)
{
error_message_ = String("While storing '") + file_ + "': " + msg;
error_message = String("While storing '") + file_ + "': " + msg;
}
if (line != 0 || column != 0)
{
error_message_ += String("( in line ") + line + " column " + column + ")";
error_message += String("( in line ") + line + " column " + column + ")";
}

// warn only in Debug mode but suppress warnings in release mode (more happy users)
#ifdef OPENMS_ASSERTIONS
OPENMS_LOG_WARN << error_message_ << std::endl;
OPENMS_LOG_WARN << error_message << std::endl;
#else
OPENMS_LOG_DEBUG << error_message_ << std::endl;
OPENMS_LOG_DEBUG << error_message << std::endl;
#endif

}
Expand All @@ -188,11 +191,6 @@ namespace OpenMS::Internal
{
}

String XMLHandler::errorString()
{
return error_message_;
}

SignedSize XMLHandler::cvStringToEnum_(const Size section, const String & term, const char * message, const SignedSize result_on_error)
{
OPENMS_PRECONDITION(section < cv_terms_.size(), "cvStringToEnum_: Index overflow (section number too large)");
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