berkeleybop / bbop-graph

General purpose (mathematical) graph library in JavaScript.

Generic repository, README, and scratch space for the Berkeley BOP.

bbop-graph's Issues

Error in graph.prototype.walker

Hello,

I think there is a bug function graph.prototype.walker. As it is, it only works if for a given node X, the function walking_fun returns an edge in which node X is the object, but not if node X is the subject. This gave a problem with get_descendent_subgraph or get_ancestor_subgraph, I don't remember which one of the two.

Need metadata information as part of format

There are new use cases where we may be running into incomplete graphs. In order to catch these up and down the stack, we'll be switching metadata into a key/value variable, which can be generally used.

In this case, we'll be looking at:

{
   "incomplete-p": bool, // true or "true"
   "complete-node-count": 40,
   "complete-edge-count": 40,
}

tagging @hdietze

Move documentation over from old repo

https://github.com/berkeleybop/bbop-js/wiki/Graph

I would just insert this into either the README.md or in a separate md file in the repo, multiple small wikis don't really do it for me but YMMV

We still need a computable description (JSON-Schema, protobuf, kwalify, or other)

Add remove_edge to model

Maybe remove_edge_clean as well?

Allow multiple preidcates for walker

It would be great if for walker functions instead of allowing a single predicate, multiple predicates would be allowed. A recent use-case for me was to find all children of a given GO term related through part_of or is_a relationships. To do that I had to filter out relationships in the json before parsing the graph, but it would be nice to be able to do this within the library, providing a list instead of a string for the in_pred aragument in functions like the one below:

bbop-graph/lib/graph.js

Lines 1091 to 1099 in 8837355

	graph.prototype.get_parent_edges = function(nb_id, in_pred){
	var anchor = this;
	var results = [];
	// Get all parents, or just parents from a specific relation.
	var preds_to_use = [];
	if( in_pred ){
	preds_to_use.push(in_pred);

Add remove_node to model

Maybe remove_node_clean as well?

Document how to programmatically visualize a bbop-graph

This is stale: http://wiki.geneontology.org/index.php/AmiGO_2_Manual:_Visualize_Freeform

This doesn't work visualize

Motivation: https://github.com/monarch-initiative/monarch-app/issues/1232#issuecomment-209572296