public static new EntryDictionary Unmarshal(TextReader reader)
{
EntryDictionary dict = new OWLReact();
try
{
XDocument doc = XDocument.Load(reader);
XElement 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();
foreach (var entry in entries)
{
if (entry.Name.NamespaceName.Equals(ownNS, StringComparison.Ordinal))
{
EntryReact dbEntry = Unmarshal(entry, ownNS);
dict.AddEntry(dbEntry);
Debug.WriteLine($"Added entry: {dbEntry}");
}
else
{
Debug.WriteLine($"Found a non-fact: {entry.Name.ToString()}");
}
}
}
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($"Due to an IOException, the parser could not check:{ex.Message}");
Debug.WriteLine(ex);
dict = null;
}
return(dict);
}
public static EntryReact Unmarshal(XElement entry, XNamespace ownNS)
{
// create a new entry by ID
XAttribute id = entry.Attribute(rdfNS + "ID");
Debug.WriteLine($"ID: {id.Value}");
EntryReact dbEntry = new EntryReact(id.Value);
// set additional, optional data
XElement label = entry.Element(rdfsNS + "label");
Debug.WriteLine($"label: {label}");
if (label != null)
{
dbEntry.Label = label.Value;
}
dbEntry.ClassName = entry.Name.LocalName;
Debug.WriteLine($"class name: {dbEntry.ClassName}");
XElement definition = entry.Element(ownNS + "definition");
if (definition != null)
{
dbEntry.Definition = definition.Value;
Debug.WriteLine($"definition name: {definition.Value}");
}
XElement description = entry.Element(ownNS + "description");
if (description != null)
{
dbEntry.Description = description.Value;
Debug.WriteLine($"description name: {description.Value}");
}
var representations = entry.Elements(ownNS + "representation");
foreach (var representation in representations)
{
// string idRepr = representations[i].GetAttributeValue("id");
string contentRepr = representation.Attribute("content")?.Value;
dbEntry.AddRepresentation(contentRepr);
}
var params_ = entry.Elements(ownNS + "parameters");
foreach (var p in params_)
{
string typeParam = p.Attribute("dataType")?.Value;
typeParam = typeParam.Substring(typeParam.IndexOf(':') + 1);
string nameParam = p.Attribute("resource")?.Value;
string value = p.Value;
dbEntry.SetParameters(nameParam, typeParam, value);
}
var paramsList = entry.Elements(ownNS + "parameterList");
foreach (var p in paramsList)
{
var params2 = p.Elements(ownNS + "parameter2");
foreach (var p2 in params2)
{
string paramClass = p2.FirstAttribute.Value;
paramClass = paramClass.Substring(paramClass.IndexOf('#') + 1);
Debug.WriteLine($"parameter class: {paramClass}");
string needsToSet = "";
string value = "";
string dataType = "";
var paramSubt1 = p2.Elements(ownNS + "IsSetParameter");
needsToSet = paramSubt1.FirstOrDefault()?.Value;
if (needsToSet == null)
{
needsToSet = "";
}
var paramSubt2 = p2.Elements(ownNS + "value");
var eparamSubt2 = paramSubt2.FirstOrDefault();
value = eparamSubt2 == null ? "" : eparamSubt2.Value;
dataType = eparamSubt2.Attribute("dataType")?.Value;
dataType = dataType.Substring(dataType.IndexOf(':') + 1);
var pp = new List <string>
{
paramClass,
needsToSet,
dataType,
value
};
dbEntry.AddParameter(pp);
}
}
var mechanismDependence = entry.Elements(ownNS + "mechanismDependence");
string mechanism = "";
foreach (var md in mechanismDependence)
{
mechanism = md.FirstAttribute.Value;
mechanism = mechanism.Substring(mechanism.IndexOf('#') + 1);
Debug.WriteLine($"mechanism name: {mechanism}");
}
dbEntry.Mechanism = mechanism;
var exampleReact = entry.Elements(ownNS + "example-Reactions");
foreach (var er in exampleReact)
{
var reaction = er.Elements(ownNS + "reaction");
foreach (var r in reaction)
{
dbEntry.AddExampleReaction(r.ToString(SaveOptions.DisableFormatting));
}
}
return(dbEntry);
}
