private List <AopNetwork> GetAopNetworks(string id = null)
{
var queryString = new SparqlParameterizedString();
queryString.Namespaces.AddNamespace("dc", new Uri("http://purl.org/dc/elements/1.1/"));
queryString.Namespaces.AddNamespace("aopo", new Uri("http://aopkb.org/aop_ontology#"));
queryString.Namespaces.AddNamespace("rdfs", new Uri("http://www.w3.org/2000/01/rdf-schema#"));
if (!string.IsNullOrEmpty(id))
{
queryString.SetUri("id", new Uri($@"http://identifiers.org/aop/{id}"));
queryString.CommandText = (@"
SELECT *
WHERE {
?Aop a aopo:AdverseOutcomePathway ;
dc:title ?AopName ;
rdfs:label ?AopId .
FILTER (?Aop = @id)
}
");
}
else
{
queryString.CommandText = (@"
SELECT *
WHERE {
?Aop a aopo:AdverseOutcomePathway ;
dc:title ?AopName ;
rdfs:label ?AopId .
}
");
}
queryString.SetUri("value", new Uri("http://aopwiki-rdf.prod.openrisknet.org/sparql/"));
var parser = new SparqlQueryParser();
var processor = new RemoteQueryProcessor(new SparqlRemoteEndpoint(Endpoint));
var query = parser.ParseFromString(queryString);
var resultSet = processor.ProcessQuery(query);
if (resultSet is SparqlResultSet)
{
var result = new List <AopNetwork>();
foreach (var resultRow in (resultSet as SparqlResultSet))
{
var recordId = ((ILiteralNode)resultRow["AopId"]).Value;
var record = new AopNetwork()
{
Id = recordId.Replace("AOP ", ""),
Name = recordId,
Description = ((ILiteralNode)resultRow["AopName"]).Value,
};
result.Add(record);
}
return(result);
}
else
{
return(null);
}
}
/// <summary>
/// Gets sequential layers of the AOP network.
/// </summary>
/// <param name="aopNetwork"></param>
/// <returns></returns>
public static IList <AopNetworkLayer> GetAopNetworkLayers(this AopNetwork aopNetwork)
{
var cyclicKers = aopNetwork.FindFeedbackRelationships();
var kers = aopNetwork.KeyEventRelationships.Except(cyclicKers);
var toNodesLookup = kers.ToLookup(r => r.ToNode, r => r.FromNode);
var fromNodesLookup = kers.ToLookup(r => r.FromNode, r => r.ToNode);
var rootNodes = aopNetwork.KeyEvents.Where(r => !toNodesLookup.Contains(r)).ToList();
return(GetAopNetworkLayersRecursive(rootNodes, toNodesLookup, fromNodesLookup, new HashSet <KeyEvent>()));
}
/// <summary>
/// Finds key-event relationships that feed-back to earlier key events, and therewith
/// cause cycles.
/// </summary>
/// <param name="aopNetwork"></param>
/// <returns></returns>
public static ICollection <KeyEventRelationship> FindFeedbackRelationships(this AopNetwork aopNetwork)
{
var toNodesLookup = aopNetwork.KeyEventRelationships.ToLookup(r => r.ToNode, r => r.FromNode);
var fromNodesLookup = aopNetwork.KeyEventRelationships.ToLookup(r => r.FromNode);
var rootNodes = aopNetwork.KeyEvents.Where(r => !toNodesLookup.Contains(r)).ToList();
var result = aopNetwork.KeyEventRelationships
.Where(r => rootNodes.Contains(r.FromNode))
.SelectMany(r => FindFeedbackRelationshipsRecursive(r, fromNodesLookup, new HashSet <KeyEventRelationship>()))
.Distinct()
.ToList();
return(result);
}
/// <summary>
/// Creates an svg of the AOP network graph and writes it to the specified file.
/// </summary>
/// <param name="aopNetwork"></param>
/// <param name="fileName"></param>
public void Create(AopNetwork aopNetwork, string fileName)
{
var layers = aopNetwork.GetAopNetworkLayers();
var title = !string.IsNullOrEmpty(aopNetwork.Name) ? aopNetwork.Name : null;
var showTitle = title != null;
var offsetX = 10D;
var offsetY = showTitle ? 40D : 20D;
var width = offsetX + layers.Count * (BlockWidth + HorizontalMargin) - HorizontalMargin + 1;
var height = offsetY + layers.Max(r => r.KeyEvents.Count) * (BlockHeight + VerticalMargin) - VerticalMargin + 1;
var doc = new SvgDocument()
{
Width = (float)(width),
Height = (float)(height),
FontSize = 10,
FontFamily = "Arial",
};
var defsElement = new SvgDefinitionList()
{
ID = "defsMap"
};
doc.Children.Add(defsElement);
defsElement.Children.Add(arrowMarker);
if (showTitle)
{
var text = new SvgText()
{
FontSize = 14,
FontWeight = SvgFontWeight.Bold,
Nodes = { new SvgContentNode()
{
Content = title
} },
TextAnchor = SvgTextAnchor.Middle,
X = new SvgUnitCollection()
{
0f
},
Y = new SvgUnitCollection()
{
0f
},
Dx = new SvgUnitCollection()
{
(float)width / 2f
},
Fill = new SvgColourServer(Color.Black),
};
text.Dy = new SvgUnitCollection()
{
2 * text.Bounds.Height
};
doc.Children.Add(text);
}
var keyEventNodes = DrawKeyEvents(
doc,
layers,
offsetX,
offsetY
);
var indirectKers = aopNetwork.GetIndirectKeyEventRelationships();
var cyclicKers = aopNetwork.FindFeedbackRelationships();
var kers = aopNetwork.KeyEventRelationships
.Except(indirectKers)
.Except(cyclicKers)
.ToList();
DrawKeyEventRelationships(doc, kers, keyEventNodes);
doc.FlushStyles(true);
doc.Write(fileName);
}
private static void createSvg(AopNetwork network, string fileName)
{
var visualizer = new AopNetworkGraphCreator();
visualizer.Create(network, Path.Combine(_outputPath, fileName));
}
/// <summary>
/// Identifies key-event relationships that can also be reached indirectly (and may be
/// non-adjecent).
/// </summary>
/// <param name="aopNetwork"></param>
/// <returns></returns>
public static ICollection <KeyEventRelationship> GetIndirectKeyEventRelationships(this AopNetwork aopNetwork)
{
var cyclicKers = aopNetwork.FindFeedbackRelationships();
var kers = aopNetwork.KeyEventRelationships.Except(cyclicKers);
var toNodesLookup = kers.ToLookup(r => r.ToNode, r => r.FromNode);
var fromNodesLookup = kers.ToLookup(r => r.FromNode, r => r);
var rootNodes = aopNetwork.KeyEvents.Where(r => !toNodesLookup.Contains(r)).ToList();
var indirectRelationships = new HashSet <KeyEventRelationship>();
foreach (var node in rootNodes)
{
_ = GetIndirectRelationshipsRecursive(node, fromNodesLookup, indirectRelationships);
}
return(indirectRelationships);
}
