Output GraphML - Githubissues

thortiede commented 5 years ago

Write out networks in GraphML format.

thortiede commented 5 years ago

Basic GraphML Writing Functionality implemented. Open Issues:

Hard coded <graph id="G" edgedefault="undirected"> What should the graph id be set to? By default edges are undirected. Make that dynamically changeable. What are the implications for the rest of the GraphML?
// TODO: If graph is undirected: Be sure that the edges we add are unique also in the way that // N1 -e1-> N2 is the same as N2 -e1-> N1 As the comment from the code suggests, edges of same type in opposite direction must not be added when graph is undirected, but must be added if it is directed

thortiede commented 5 years ago

How would / could we create a graphml directly from a query result, i.e. not through the nodeEdgeList? Is this possible? Is this more performant?
When more annotations need to be added, the mechanism for them need to be generalised. This probably needs a rewrite of the whole thing..

thortiede commented 3 years ago

This has been fixed in the refactoring process. The directed/undirected attribute is taken from the user request and the graphml is created from the FlatEdges directly.

thortiede / sbml4j

Output GraphML #44