public new static EntryDictionary Unmarshal(TextReader reader)
{
EntryDictionary dict = new OWLFile();
try
{
var text = reader.ReadToEnd();
var doc = XDocument.Parse(text);
var root = doc.Root;
Debug.WriteLine($"Found root element: {root.Name}");
// Extract ownNS from root element
// final string ownNS = root.GetBaseURI();
string ownNS = root.Attribute("xmlns").Value;
dict.NS = ownNS;
Debug.WriteLine($"Found ontology namespace: {ownNS}");
// process the defined facts
var entries = root.Elements();
//Trace.TraceInformation("Found #elements in OWL dict:", entries.Count());
foreach (var entry in entries)
{
if (entry.Name.NamespaceName.Equals(ownNS, StringComparison.Ordinal))
{
Entry dbEntry = Unmarshal(entry, ownNS);
dict.AddEntry(dbEntry);
Debug.WriteLine($"Added entry: {dbEntry}");
}
else
{
Debug.WriteLine($"Found a non-fact: {entry.Name}");
}
}
}
catch (XmlException ex)
{
Trace.TraceError($"Dictionary is not well-formed: {ex.Message}");
Debug.WriteLine("Error at line " + ex.LineNumber, ", column " + ex.LinePosition);
dict = null;
}
catch (IOException ex)
{
Trace.TraceError($"Due to an IOException, the parser could not check:{ex.Message}");
Debug.WriteLine(ex);
dict = null;
}
return(dict);
}
private static EntryDictionary ReadDictionary(string databaseLocator, string type, Dictionary <string, EntryDictionary> cache)
{
EntryDictionary dictionary;
// to distinguish between OWL: QSAR & REACT
if (type.Contains("_React"))
{
databaseLocator += "." + type.Substring(0, type.Length - 6);
}
else
{
databaseLocator += "." + type;
}
if (cache.ContainsKey(databaseLocator))
{
return(cache[databaseLocator]);
}
else
{
Trace.TraceInformation($"Reading dictionary from {databaseLocator}");
try
{
var reader = new StreamReader(ResourceLoader.GetAsStream(databaseLocator));
switch (type)
{
case "owl":
dictionary = OWLFile.Unmarshal(reader);
break;
case "owl_React":
dictionary = OWLReact.Unmarshal(reader);
break;
default:
// assume XML using Castor
dictionary = EntryDictionary.Unmarshal(reader);
break;
}
}
catch (Exception exception)
{
dictionary = null;
Trace.TraceError($"Could not read dictionary {databaseLocator}");
Debug.WriteLine(exception);
}
cache[databaseLocator] = dictionary;
return(dictionary);
}
}