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Deal with an unhandled exception in small molecule transition list reader… #2741

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merged 3 commits into from
Oct 10, 2023
Merged

Deal with an unhandled exception in small molecule transition list reader… #2741

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bd948e0
Deal with an unhandled exception in small molecule transition list re…
bspratt Oct 10, 2023
8af7a16
tidier multi-catch implementation
bspratt Oct 10, 2023
4b0e914
Merge branch 'master' into Skyline/work/20231009_small_mol_transition…
bspratt Oct 10, 2023
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39 changes: 18 additions & 21 deletions pwiz_tools/Skyline/Model/SmallMoleculeTransitionListReader.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -254,6 +254,15 @@ private bool ErrorAddingToExistingMoleculeGroup(ref SrmDocument document, Parsed
return false;
}

// Check for the various kinds of exceptions that may be thrown in the course of
// parsing sometimes-wonky user data
private bool IsParserException(Exception exception)
{
return exception is InvalidOperationException
|| exception is InvalidDataException
|| exception is ArgumentException;
}

// Returns true on error
private bool ErrorFindingTransitionGroupForPrecursor(ref SrmDocument document, ParsedIonInfo precursor, Row row,
PeptideGroupDocNode pepGroup, Adduct adduct, double precursorMonoMz, double precursorAverageMz,
Expand Down Expand Up @@ -296,13 +305,9 @@ private bool ErrorFindingTransitionGroupForPrecursor(ref SrmDocument document, P
_firstAddedPathPepGroup = _firstAddedPathPepGroup ?? pathGroup;
}
}
catch (InvalidDataException x)
{
errmsg = x.Message;
}
catch (InvalidOperationException x) // Adduct handling code can throw these
catch (Exception exception) when (IsParserException(exception))
{
errmsg = x.Message;
errmsg = exception.Message;
}

if (errmsg != null)
Expand Down Expand Up @@ -1357,7 +1362,7 @@ private ParsedIonInfo ReadPrecursorOrProductColumns(SrmDocument document,
adduct = DetermineAdductFromFormulaChargeAndMz(formula, charge.Value, mz);
}
}
catch (Exception e)
catch (Exception e) when (IsParserException(e))
{
ShowTransitionError(new PasteError
{
Expand Down Expand Up @@ -1511,13 +1516,9 @@ private ParsedIonInfo ReadPrecursorOrProductColumns(SrmDocument document,
}
}
}
catch (InvalidDataException x)
catch (Exception exception) when (IsParserException(exception))
{
massErrMsg = x.Message;
}
catch (InvalidOperationException x) // Adduct handling code can throw these
{
massErrMsg = x.Message;
massErrMsg = exception.Message;
}
if (massErrMsg != null)
{
Expand Down Expand Up @@ -1704,7 +1705,7 @@ private bool ProcessAdduct(Row row, int indexAdduct, int indexFormula, bool getP
adduct = Adduct.FromStringAssumeChargeOnly(adductText);
IonInfo.ApplyAdductToFormula(formula ?? string.Empty, adduct); // Just to see if it throws
}
catch (Exception x) when ((x is InvalidOperationException) || (x is ArgumentException))
catch (Exception x) when (IsParserException(x))
{
ShowTransitionError(new PasteError
{
Expand Down Expand Up @@ -1831,7 +1832,7 @@ private PeptideDocNode GetMoleculePeptide(SrmDocument document, Row row, Peptide
molecule = new CustomMolecule(parsedIonInfo.MonoMass, parsedIonInfo.AverageMass, shortName, parsedIonInfo.MoleculeID.AccessionNumbers);
}
}
catch (ArgumentException e)
catch (Exception e) when (IsParserException(e))
{
ShowTransitionError(new PasteError
{
Expand All @@ -1849,7 +1850,7 @@ private PeptideDocNode GetMoleculePeptide(SrmDocument document, Row row, Peptide
return null;
return new PeptideDocNode(pep, document.Settings, null, null, parsedIonInfo.ExplicitRetentionTime, new[] { tranGroup }, false);
}
catch (InvalidOperationException e)
catch (Exception e) when (IsParserException(e))
{
ShowTransitionError(new PasteError
{
Expand Down Expand Up @@ -1908,11 +1909,7 @@ private TransitionGroupDocNode GetMoleculeTransitionGroup(SrmDocument document,
return new TransitionGroupDocNode(group, document.Annotations, document.Settings, null,
null, moleculeInfo.ExplicitTransitionGroupValues, null, new[] { tran }, false);
}
catch (InvalidDataException x)
{
errmsg = x.Message;
}
catch (InvalidOperationException x) // Adduct handling code can throw these
catch (Exception x) when (IsParserException(x))
{
errmsg = x.Message;
}
Expand Down