def get_token_tree(self, token, depth_limit, cooccurrence_threshold):
# Basic strategy is to pull the entire tree, which can be memory
# intensive, and then to dfs_tree it to get the specific tree.
g = rebuild_graph(
self.repository.pull_graph(
GetTokenTreeQuery(token, depth_limit, cooccurrence_threshold)))
print(g.number_of_nodes())
print(g.number_of_edges())
if g.number_of_nodes() == 0:
warn("empty result tree")
return None
# At this stage the occurrence properties should have been migrated to
# in memory graph. However they won't appear on the tree export yet.
# So, migrate the strength attributes correctly.
g2 = transform(g)
root = get_node_by_attribute(g2, 'content', token)
g2.nodes[root]['strength'] = None
tree = dfs_tree_with_node_attributes(g2, root, depth_limit=depth_limit)
print("Number of nodes in tree", tree.number_of_nodes())
print("Number of edges in tree", tree.number_of_edges())
return networkx.tree_data(tree, root)
def export(self, root=None):
if self.graph_type is 'node_link':
graph_json = nx.node_link_data(self.graph)
elif self.graph_type is 'cytoscape':
graph_json = nx.cytoscape_data(self.graph)
elif self.graph_type is 'tree':
if nx.is_directed(self.graph):
graph_json = nx.tree_data(self.graph, root)
else:
print('Graph passed into export data is not directed')
return 0
return graph_json
def export_taxonomy_tree(self, root):
"""
Export the taxonomy tree in a JSON-able format. Should be interpretable
by d3-hierarchy, networkx, and the JavaScript TreeModel library.
Root is a string that specifies the 'content' property of a Taxon node
with in-degree zero. That is, root is a string that uniquely names the
'top' Taxon of a taxonomy. If the database contains two taxonomies
with a top-node with the same value for 'content', the behaviour is
undefined (i.e. this should never happen and is considered a corruption).
"""
result = self.repository.pull_graph(SlurpTaxonomiesQuery())
g = rebuild_graph(result)
root_id = find_root_by_content(g, root)
tree = dfs_tree_with_node_attributes(g, root_id, depth_limit=None)
return networkx.tree_data(tree, root_id)
def search_with_taxons(self, token, taxon_uris, depth_limit,
cooccurrence_threshold):
g = rebuild_graph(
self.repository.pull_graph(
GetTokenRootWithTaxonFilterQuery(token, taxon_uris,
depth_limit,
cooccurrence_threshold)))
# if the graph is empty then nothing was matched. re-add the root
# node
if is_null_graph(g):
g.add_node(0, content=token)
# now reconnect the graph
root = get_node_by_attribute(g, 'content', token)
for node in g.nodes:
g.nodes[node]['strength'] = 0
if node != root: g.add_edge(root, node)
g.nodes[root]['strength'] = None
return networkx.tree_data(g, root)
import json
import networkx as nx
G = nx.DiGraph()
G.add_nodes_from(range(8))
weights = {0: 4, 1: 7, 2: 8, 3: 4, 4: 5, 5: 6, 6: 1, 7: 2}
nx.set_node_attributes(G, weights, 'weight')
edges = [
(0, 1),
(0, 2),
(2, 4),
(4, 6),
(4, 7),
(1, 3),
(1, 5),
]
G.add_edges_from(edges)
# save in json
node_link_data = nx.tree_data(G, root=0)
with open('tree.json', 'w') as f:
json.dump(node_link_data, f, indent=4, sort_keys=True)
if __name__ == "__main__":
df = load_data()
df, child_counter = update_header(df)
graph, G = create_node_links(df, child_counter)
# print(graph)
file_object = open("graph.json", 'w')
json.dump(graph, file_object)
# print(G.nodes.data())
# T = dfs_tree(G, 1)
T = bfs_tree(G, 1)
# print(T.nodes.data())
for node in T.nodes.data():
nodule = G.nodes[node[0]]
index = int(node[0])
for attribute in nodule.keys():
T.nodes[node[0]][attribute] = nodule[attribute]
treeJSON = tree_data(T, 1)
print(treeJSON)
file_object = open("tree.json", 'w')
json.dump(treeJSON, file_object)
# f = open("graph.json", "r")
# print(f.read())
# G = nx.readwrite.json_graph.node_link_graph(graph)
# Skip to the next parent if it doesn't exist as a concrete row
# This can happen and it's not an error
if get_uri(source) not in g:
continue
for j in range(i + 1, len(category_sequence)):
possible_target = get_concat_id(category_sequence, j)
if get_uri(possible_target) in g:
g.add_edge(get_uri(source), get_uri(possible_target))
break
sources = [v for v, indegree in g.in_degree() if indegree == 0]
print("Possible roots:", sources)
ARTIFICIAL_ROOT = get_uri('00')
# artificially reparent to form a rooted tree
g.add_node(ARTIFICIAL_ROOT, content='Theme')
for source in sources:
g.add_edge(ARTIFICIAL_ROOT, source)
tree = dfs_tree_with_node_attributes(g, ARTIFICIAL_ROOT)
return tree
if __name__ == '__main__':
obj = SamuelsLoader()
print("Tree is", networkx.tree_data(obj.load(sys.argv[1]), '00'))
sentences = [
'keep a bar',
'keep a shop',
'keep the peace',
'keep the books'
]
backend = occubrow.backend.OccubrowBackend(Mock(), Mock())
g = networkx.DiGraph()
def consecutive_pairs(sequence):
for i in range(len(sequence) - 1):
yield sequence[i], sequence[i + 1]
for sentence in sentences:
tokens = backend.preprocess(sentence)
for token1, token2 in consecutive_pairs(tokens):
g.add_node(token1)
g.add_node(token2)
g.add_edge(token1, token2)
result = networkx.tree_data(g, 'keep')
pprint.pprint(result)
def narrow_graph_to_tree(
self, graph, chosen_source, depth_limit, coocurrence_threshold
):
g2 = dfs_tree_with_node_attributes(graph, chosen_source, depth_limit=depth_limit)
data = networkx.tree_data(g2, root=chosen_source)
return data
