/// <summary>
/// Triggers the XML parsing of the data file and returns the read Isotopes.
/// It turns of XML validation before parsing.
/// </summary>
/// <returns>a List of Isotope's. Returns an empty list is some reading error occurred.</returns>
public IReadOnlyList <IIsotope> ReadIsotopes()
{
var reader = new XReader();
var handler = new IsotopeHandler();
reader.Handler = handler;
try
{
var settings = new XmlReaderSettings
{
ValidationType = ValidationType.None,
ValidationFlags = System.Xml.Schema.XmlSchemaValidationFlags.None
};
var xreader = XmlReader.Create(input, settings);
var doc = XDocument.Load(xreader);
reader.Read(doc);
return(handler.Isotopes);
}
catch (Exception exception)
{
Trace.TraceError($"{exception.GetType().Name}: {exception.Message}");
Debug.WriteLine(exception);
}
return(Array.Empty <IIsotope>());
}
// private functions
/// <summary>
/// Reads a ChemFile object from input.
/// </summary>
/// <returns>ChemFile with the content read from the input</returns>
private IChemFile ReadChemFile(IChemObjectBuilder bldr)
{
IChemFile cf = null;
XmlReaderSettings setting = new XmlReaderSettings
{
ValidationFlags = XmlSchemaValidationFlags.None
};
InChIHandler handler = new InChIHandler(bldr);
try
{
var r = new XReader
{
Handler = handler
};
XDocument doc = XDocument.Load(input);
r.Read(doc);
cf = handler.ChemFile;
}
catch (IOException e)
{
Trace.TraceError($"IOException: {e.Message}");
Debug.WriteLine(e);
}
catch (XmlException saxe)
{
Trace.TraceError($"SAXException: {saxe.Message}");
Debug.WriteLine(saxe);
}
return(cf);
}
/// <summary>
/// Reads the atom type mappings from the data file.
/// </summary>
/// <returns>a <see cref="IReadOnlyDictionary{TKey, TValue}"/> with atom type mappings. <see langword="null"/>, if some reading error occurred.</returns>
public IReadOnlyDictionary <string, string> ReadAtomTypeMappings()
{
IReadOnlyDictionary <string, string> mappings = null;
var setting = new XmlReaderSettings
{
DtdProcessing = DtdProcessing.Parse,
ValidationFlags = XmlSchemaValidationFlags.None
};
var handler = new OWLAtomTypeMappingHandler();
var parser = XmlReader.Create(input, setting);
var reader = new XReader
{
Handler = handler
};
try
{
var doc = XDocument.Load(parser);
reader.Read(doc);
mappings = handler.GetAtomTypeMappings();
}
catch (IOException exception)
{
Trace.TraceError(nameof(IOException) + ": " + exception.Message);
Debug.WriteLine(exception);
}
catch (XmlException saxe)
{
Trace.TraceError(nameof(XmlException) + ": " + saxe.Message);
Debug.WriteLine(saxe);
}
return(mappings ?? Dictionaries.Empty <string, string>());
}
// private functions
private IChemFile ReadChemFile(IChemFile file)
{
Debug.WriteLine("Started parsing from input...");
var setting = new XmlReaderSettings
{
DtdProcessing = DtdProcessing.Parse,
ValidationFlags = XmlSchemaValidationFlags.None,
XmlResolver = new CMLResolver()
};
XmlReader parser;
if (input == null)
{
Debug.WriteLine($"Parsing from URL: {url}");
parser = XmlReader.Create(url, setting);
}
else
{
Debug.WriteLine("Parsing from Reader");
parser = XmlReader.Create(input, setting);
}
CMLHandler handler = new CMLHandler(file);
// copy the manually added conventions
foreach (var conv in userConventions.Keys)
{
handler.RegisterConvention(conv, userConventions[conv]);
}
var reader = new XReader {
Handler = handler
};
try
{
var doc = XDocument.Load(parser);
reader.Read(doc);
}
catch (IOException e)
{
var error = "Error while reading file: " + e.Message;
Trace.TraceError(error);
Debug.WriteLine(e);
throw new CDKException(error, e);
}
catch (XmlException saxe)
{
string error = "Error while parsing XML: " + saxe.Message;
Trace.TraceError(error);
Debug.WriteLine(saxe);
throw new CDKException(error, saxe);
}
return(file);
}
public static EntryDictionary Unmarshal(TextReader reader)
{
var handler = new DictionaryHandler();
var r = new XReader
{
Handler = handler
};
var doc = XDocument.Load(reader);
r.Read(doc);
return(handler.Dictionary);
}
