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Fix unescaped ampersands in msfragger pepXML output #3154

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Merged
merged 3 commits into from
Sep 11, 2024
Merged

Fix unescaped ampersands in msfragger pepXML output #3154

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616dfd4
Fix unescaped ampersands in msfragger pepXML output
bspratt Sep 10, 2024
fe7aeca
per Brendan review, also include numeric formats in the search for fo…
bspratt Sep 10, 2024
19063e9
Merge branch 'master' into Skyline/work/20240910_fix_unescaped_xml_ms…
bspratt Sep 11, 2024
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11 changes: 11 additions & 0 deletions pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -461,13 +461,24 @@ private void FixPercolatorPepXml(string cruxOutputFilepath, string finalOutputFi
bool isBrukerSource = DataSourceUtil.GetSourceType(spectrumFilename.GetFilePath()) == DataSourceUtil.TYPE_BRUKER;
var lastPsmIdRegex = new Regex(@".* spectrum=""([^""]+?)"" .*",RegexOptions.Compiled);

// This looks for an ampersand that is NOT followed by:
// - "amp;", "lt;", "gt;", "quot;", "apos;" (predefined XML entities)
// - "&#" followed by any number of digits and a semicolon (decimal entity)
// - "&#x" followed by any number of hexadecimal digits and a semicolon (hexadecimal entity)
var unescapedAmpersandRegex = new Regex(@"&(?!amp;|lt;|gt;|quot;|apos;|#\d+;|#x[0-9A-Fa-f]+;)", RegexOptions.Compiled);

using (var pepXmlFile = new StreamReader(cruxOutputFilepath))
using (var fixedPepXmlFile = new StreamWriter(finalOutputFilepath))
{
string line;
string lastPsmId = "";
while ((line = pepXmlFile.ReadLine()) != null)
{
if (line.Contains(@"&"))
{
// Replace unescaped ampersands with the correct &
line = unescapedAmpersandRegex.Replace(line, @"&");
}
if (line.Contains(@"<spectrum_query"))
lastPsmId = lastPsmIdRegex.Replace(line, "$1");
else if (line.Contains(@"<search_score name=""hyperscore"""))
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