def all_shortest_paths(self, src_sid=None, dst_sid=None):
nv = GraphData()
if src_sid is None and dst_sid is None:
raise Exception('src_sid or dst_sid must be set')
elif src_sid is None and dst_sid is not None:
dst = self.__resolve_sid_to_id(dst_sid)
if dst is None:
raise Exception('SID not found!')
total = self.dbsession.query(func.count(
EdgeLookup.id)).filter_by(ad_id=self.domain_id).filter(
EdgeLookup.oid != self.domain_sid + '-513').scalar()
q = self.dbsession.query(
EdgeLookup.id).filter_by(ad_id=self.domain_id).filter(
EdgeLookup.oid != self.domain_sid + '-513')
for nodeid in tqdm(windowed_query(q, EdgeLookup.id, 1000),
desc='running',
total=total):
for path in all_shortest_paths(self.graph, nodeid[0], dst):
print(path)
self.__result_path_add(nv, path)
elif src_sid is not None and dst_sid is not None:
print(1)
print(src_sid)
print(dst_sid)
src = self.__resolve_sid_to_id(src_sid)
if src is None:
raise Exception('SID not found!')
dst = self.__resolve_sid_to_id(dst_sid)
if dst is None:
raise Exception('SID not found!')
print(src)
print(dst)
for path in all_shortest_paths(self.graph, src, dst):
print(path)
self.__result_path_add(nv, path)
return nv
def statistics_experiments(sentence_graphs):
sentence_graph = sentence_graphs[0]
print("sentence_graph graph: %s" % str(sentence_graph.get_graph()))
shortest_paths = dict()
for vertex_1 in sentence_graph.get_vertices():
for vertex_2 in sentence_graph.get_vertices():
if vertex_1 == vertex_2:
continue
all_shortest_paths_iterator = topology.all_shortest_paths(
sentence_graph.get_graph(), vertex_1, vertex_2)
#print("Iterating on path from %s to %s" % (sentence_graph.get_word_pos_tuple(vertex_1), sentence_graph.get_word_pos_tuple(vertex_2)))
#print("all_shortest_paths_iterator: %s" % str(all_shortest_paths_iterator))
saved_shortest_paths = []
for shortest_path in all_shortest_paths_iterator:
#print("shortest_path: %s" % str(shortest_path))
shortest_path_length = 0
for shortest_path_vertex_index in shortest_path:
#print("word_pos_tuple: %s" % str(sentence_graph.get_word_pos_tuple_by_index(shortest_path_vertex_index)))
shortest_path_length += 1
if shortest_path_length <= MAX_PATH_LENGTH:
saved_shortest_paths.append(shortest_path.copy())
if len(saved_shortest_paths) > 0:
shortest_paths[(vertex_1, vertex_2)] = saved_shortest_paths
print("\n\n\n=========================\n\n\n")
for vertex_tuple, saved_shortest_paths in shortest_paths.items():
vertex_1 = vertex_tuple[0]
vertex_2 = vertex_tuple[1]
print("Iterating on paths from %s to %s" %
(sentence_graph.get_word_pos_tuple(vertex_1),
sentence_graph.get_word_pos_tuple(vertex_2)))
for saved_shortest_path in saved_shortest_paths:
print("Path: %s" % str(saved_shortest_path))
for shortest_path_vertex_index in saved_shortest_path:
print("word_pos_tuple: %s" % str(
sentence_graph.get_word_pos_tuple_by_index(
shortest_path_vertex_index)))
"""
def run(
input_file: KGTKFiles,
path_file: KGTKFiles,
output_file: KGTKFiles,
statistics_only: bool,
undirected: bool,
max_hops: int,
source_column_name: typing.Optional[str],
target_column_name: typing.Optional[str],
shortest_path: bool,
errors_to_stdout: bool,
errors_to_stderr: bool,
show_options: bool,
verbose: bool,
very_verbose: bool,
**kwargs, # Whatever KgtkFileOptions and KgtkValueOptions want.
):
# import modules locally
from pathlib import Path
import sys
from graph_tool.all import find_vertex
from graph_tool.topology import all_paths
from graph_tool.topology import all_shortest_paths
from kgtk.gt.gt_load import load_graph_from_kgtk
from kgtk.io.kgtkreader import KgtkReader, KgtkReaderOptions
from kgtk.io.kgtkwriter import KgtkWriter
from kgtk.value.kgtkvalueoptions import KgtkValueOptions
from kgtk.exceptions import KGTKException
try:
# Select where to send error messages, defaulting to stderr.
error_file: typing.TextIO = sys.stdout if errors_to_stdout else sys.stderr
# Build the option structures.
input_reader_options: KgtkReaderOptions = KgtkReaderOptions.from_dict(
kwargs, who="input", fallback=True)
path_reader_options: KgtkReaderOptions = KgtkReaderOptions.from_dict(
kwargs, who="path", fallback=True)
value_options: KgtkValueOptions = KgtkValueOptions.from_dict(kwargs)
input_kgtk_file: Path = KGTKArgumentParser.get_input_file(input_file)
path_kgtk_file: Path = KGTKArgumentParser.get_input_file(path_file)
output_kgtk_file: Path = KGTKArgumentParser.get_output_file(
output_file)
id_col = 'name'
if verbose:
print("Reading the path file: %s" % str(path_kgtk_file),
file=error_file,
flush=True)
pairs = []
pkr: KgtkReader = KgtkReader.open(
path_kgtk_file,
error_file=error_file,
options=path_reader_options,
value_options=value_options,
verbose=verbose,
very_verbose=very_verbose,
)
path_source_idx: int = pkr.get_node1_column_index(source_column_name)
if path_source_idx < 0:
print("Missing node1 (source) column name in the path file.",
file=error_file,
flush=True)
path_target_idx: int = pkr.get_node2_column_index(target_column_name)
if path_target_idx < 0:
print("Missing node1 (target) column name in the path file.",
file=error_file,
flush=True)
if path_source_idx < 0 or path_target_idx < 0:
pkr.close()
raise KGTKException("Exiting due to missing columns.")
paths_read: int = 0
path_row: typing.List[str]
for path_row in pkr:
paths_read += 1
if len(path_row) != pkr.column_count:
raise KGTKException(
"Exiting because line %d in the path file (%s) is the wrong length: %d columns expected, %d were read."
% (paths_read, str(path_kgtk_file), pkr.column_count,
len(path_row)))
src: str = path_row[path_source_idx]
tgt: str = path_row[path_target_idx]
pairs.append((src, tgt))
pkr.close()
if verbose:
print("%d path rows read" % paths_read,
file=error_file,
flush=True)
if len(pairs) == 0:
print("No path pairs found, the output will be empty.",
file=error_file,
flush=True)
elif verbose:
print("%d path pairs found" % len(pairs),
file=error_file,
flush=True)
if verbose:
print("Reading the input file: %s" % str(input_kgtk_file),
file=error_file,
flush=True)
kr: KgtkReader = KgtkReader.open(
input_kgtk_file,
error_file=error_file,
options=input_reader_options,
value_options=value_options,
verbose=verbose,
very_verbose=very_verbose,
)
sub_index: int = kr.get_node1_column_index()
if sub_index < 0:
print("Missing node1 (subject) column.",
file=error_file,
flush=True)
pred_index: int = kr.get_label_column_index()
if pred_index < 0:
print("Missing label (predicate) column.",
file=error_file,
flush=True)
obj_index: int = kr.get_node2_column_index()
if obj_index < 0:
print("Missing node2 (object) column", file=error_file, flush=True)
id_index: int = kr.get_id_column_index()
if id_index < 0:
print("Missing id column", file=error_file, flush=True)
if sub_index < 0 or pred_index < 0 or obj_index < 0 or id_index < 0:
kr.close()
raise KGTKException("Exiting due to missing columns.")
predicate: str = kr.column_names[pred_index]
id_col_name: str = kr.column_names[id_index]
G = load_graph_from_kgtk(kr,
directed=not undirected,
ecols=(sub_index, obj_index),
verbose=verbose,
out=error_file)
output_columns: typing.List[str] = ['node1', 'label', 'node2', 'id']
kw: KgtkWriter = KgtkWriter.open(output_columns,
output_kgtk_file,
mode=KgtkWriter.Mode.EDGE,
require_all_columns=True,
prohibit_extra_columns=True,
fill_missing_columns=False,
verbose=verbose,
very_verbose=very_verbose)
id_count = 0
if not statistics_only:
for e in G.edges():
sid, oid = e
lbl = G.ep[predicate][e]
kw.write([
G.vp[id_col][sid], lbl, G.vp[id_col][oid],
'{}-{}-{}'.format(G.vp[id_col][sid], lbl, id_count)
])
id_count += 1
if verbose:
print("%d edges found." % id_count,
file=error_file,
flush=True)
id_count = 0
path_id = 0
for pair in pairs:
source_node, target_node = pair
source_ids = find_vertex(G,
prop=G.properties[('v', id_col)],
match=source_node)
target_ids = find_vertex(G,
prop=G.properties[('v', id_col)],
match=target_node)
if len(source_ids) == 1 and len(target_ids) == 1:
source_id = source_ids[0]
target_id = target_ids[0]
if shortest_path:
_all_paths = all_shortest_paths(G,
source_id,
target_id,
edges=True)
else:
_all_paths = all_paths(G,
source_id,
target_id,
cutoff=max_hops,
edges=True)
for path in _all_paths:
for edge_num, an_edge in enumerate(path):
edge_id = G.properties[('e', 'id')][an_edge]
node1: str = 'p%d' % path_id
kw.write([
node1,
str(edge_num), edge_id,
'{}-{}-{}'.format(node1, edge_num, id_count)
])
id_count += 1
path_id += 1
if verbose:
print("%d paths contining %d edges found." % (path_id, id_count),
file=error_file,
flush=True)
kw.close()
kr.close()
except Exception as e:
raise KGTKException('Error: ' + str(e))
def get_optimal_action(self, v_curr, v_goal):
paths = list(topology.all_shortest_paths(self.graph, v_curr, v_goal))
return paths[0][1]
def all_shortest_paths(g,
source,
target,
directed=None,
weights=None,
combine_weights="mean"):
'''
Yields all shortest paths from `source` to `target`.
The algorithms returns an empty generator if there is no path between the
nodes.
Parameters
----------
g : :class:`~nngt.Graph`
Graph to analyze.
source : int
Node from which the paths starts.
target : int, optional (default: all nodes)
Node where the paths ends.
directed : bool, optional (default: ``g.is_directed()``)
Whether the edges should be considered as directed or not
(automatically set to False if `g` is undirected).
weights : str or array, optional (default: binary)
Whether to use weighted edges to compute the distances. By default,
all edges are considered to have distance 1.
combine_weights : str, optional (default: 'mean')
How to combine the weights of reciprocal edges if the graph is directed
but `directed` is set to False. It can be:
* "sum": the sum of the edge attribute values will be used for the new
edge.
* "mean": the mean of the edge attribute values will be used for the
new edge.
* "min": the minimum of the edge attribute values will be used for the
new edge.
* "max": the maximum of the edge attribute values will be used for the
new edge.
Returns
-------
all_paths : generator
Generator yielding paths as lists of ints.
References
----------
.. [gt-sd] :gtdoc:`topology.all_shortest_paths`
'''
# source == target case
if source == target:
return ([source] for _ in range(1))
# not trivial cases
g, graph, w = _get_gt_graph(g,
directed,
weights,
combine_weights,
return_all=True)
w = _get_gt_weights(g, w)
all_paths = gtt.all_shortest_paths(graph, source, target, weights=w)
return ([int(v) for v in path] for path in all_paths)