def test_list_tables(self):
cogdb = Cog(config=config)
cogdb.create_namespace("test_ns")
cogdb.create_or_load_table("table1", "test_ns")
cogdb.create_or_load_table("table2", "test_ns")
cogdb.create_or_load_table("table3", "test_ns")
self.assertEquals(cogdb.list_tables(), ['table2', 'table3', 'table1'])
def test_list_tables(self):
cogdb = Cog()
cogdb.create_namespace("test_ns")
cogdb.create_table("table1", "test_ns")
cogdb.create_table("table2", "test_ns")
cogdb.create_table("table3", "test_ns")
self.assertEqual(set(cogdb.list_tables()), {'table2', 'table3', 'table1'})
cogdb.close()
class Graph:
"""
https://www.w3.org/TR/WD-rdf-syntax-971002/
https://github.com/cayleygraph/cayley/blob/master/docs/GizmoAPI.md
"""
def __init__(self, graph_name, cog_dir):
'''
:param graph_name:
:param cog_dir:
list of
'''
self.config = cfg
self.cog = Cog(db_path=cog_dir, config=cfg)
self.graph_name = graph_name
self.cog_dir = cog_dir
self.all_predicates = self.cog.list_tables()
self.last_visited_vertices = None
self.cog.create_namespace(self.graph_name)
#self.cog.create_or_load_table(self.config.GRAPH_NODE_SET_TABLE_NAME, self.graph_name)
def load_edgelist(self, edgelist_file_path, graph_name, predicate="none"):
self.cog.load_edgelist(edgelist_file_path, graph_name, predicate)
self.all_predicates = self.cog.list_tables()
def load_triples(self, graph_data_path, graph_name):
'''
Loads a list of triples
:param graph_data_path:
:param graph_name:
:return:
'''
self.cog.load_triples(graph_data_path, graph_name)
self.all_predicates = self.cog.list_tables()
def put(self, vertex1, predicate, vertex2):
#self.cog.create_or_load_table(predicate, self.graph_name)
self.cog.use_namespace(self.graph_name).use_table(predicate)
self.cog.put_node(vertex1, predicate, vertex2)
self.all_predicates = self.cog.list_tables()
return self
def list_predicate_tables(self, cog_dir, graph_name):
p = set(())
path = "/".join([cog_dir, graph_name])
if not os.path.exists(path): return p
files = [f for f in listdir(path) if isfile(join(path, f))]
for f in files:
p.add(f.split("-")[0])
return p
def v(self, vertex=None):
#TODO: need to check if node exists
if vertex:
self.last_visited_vertices = [Vertex(vertex)]
else:
self.last_visited_vertices = []
self.cog.use_namespace(self.graph_name).use_table(
self.config.GRAPH_NODE_SET_TABLE_NAME)
for r in self.cog.scanner():
self.last_visited_vertices.append(Vertex(r))
return self
def out(self, predicates=None):
'''
List of string predicates
:param predicates:
:return:
'''
if predicates:
assert type(predicates) == list
self.__hop("out", predicates)
return self
def inc(self, predicates=None):
self.__hop("in", predicates)
return self
def __hop(self, direction, predicates=None, tag=NOTAG):
self.cog.use_namespace(self.graph_name)
predicates = self.all_predicates if not predicates else predicates
#print "hopping from vertices: " + str(map(lambda x : x.id, self.last_visited_vertices))
#print "direction: " + str(direction) + " predicates: "+str(self.all_predicates)
traverse_vertex = []
for predicate in predicates:
for v in self.last_visited_vertices:
if direction == "out":
record = self.cog.use_table(predicate).get(out_nodes(v.id))
else:
record = self.cog.use_table(predicate).get(in_nodes(v.id))
#print "==? " + str(direction)+ " <> " + str(predicate) + " ::: " + str(v.id) + " ==> " + str(record)
if record:
for v_adjacent in ast.literal_eval(record[1][1]):
v_adjacent_obj = Vertex(v_adjacent)
v_adjacent_obj.tags.update(v.tags)
traverse_vertex.append(v_adjacent_obj)
self.last_visited_vertices = traverse_vertex
def tag(self, tag_name):
'''
Saves nodes with a tag name and returned in the result set.
Primarily used to capture nodes while navigating the graph.
:param tag_name:
:return:
'''
for v in self.last_visited_vertices:
v.tags[tag_name] = v.id
return self
def count(self):
return len(self.last_visited_vertices)
def all(self):
"""
returns all the nodes in the result.
https://github.com/cayleygraph/cayley/blob/master/docs/GizmoAPI.md
:return:
"""
result = []
for v in self.last_visited_vertices:
#print "all:: tag: " + v + " vertex:"+ str(self.last_visited_vertices[v])
item = {"id": v.id}
item.update(v.tags)
result.append(item)
return {"result": result}
class Graph:
"""
Creates a graph object.
"""
def __init__(self, graph_name, cog_home="cog_home", cog_path_prefix=None):
'''
:param graph_name:
:param cog_home: Home directory name, for most use cases use default.
:param cog_path_prefix: sets the root directory location for Cog db. Default: '/tmp' set in cog.Config. Change this to current directory when running in an IPython environment.
'''
self.config = cfg
self.config.COG_HOME = cog_home
if cog_path_prefix:
self.config.COG_PATH_PREFIX = cog_path_prefix
self.graph_name = graph_name
self.cache = {}
dictConfig(self.config.logging_config)
self.logger = logging.getLogger("torque")
self.logger.debug("Torque init on graph: " + graph_name + " predicates: ")
self.cog = Cog(self.cache)
self.cog.create_or_load_namespace(self.graph_name)
self.all_predicates = self.cog.list_tables()
self.views_dir = self.config.cog_views_dir()
if not os.path.exists(self.views_dir):
os.mkdir(self.views_dir)
self.logger.debug("predicates: " + str(self.all_predicates))
self.last_visited_vertices = None
def refresh(self):
self.cog.refresh_all()
def load_triples(self, graph_data_path, graph_name=None):
'''
Loads a list of triples
:param graph_data_path:
:param graph_name:
:return:
'''
graph_name = self.graph_name if graph_name is None else graph_name
self.cog.load_triples(graph_data_path, graph_name)
self.all_predicates = self.cog.list_tables()
return None
def load_csv(self, csv_path, id_column_name, graph_name=None):
"""
Loads CSV to a graph. One column must be designated as ID column.
:param csv_path:
:param id_column_name:
:param graph_name:
:return:
"""
if id_column_name is None:
raise Exception("id_column_name must not be None")
graph_name = self.graph_name if graph_name is None else graph_name
self.cog.load_csv(csv_path, id_column_name, graph_name)
self.all_predicates = self.cog.list_tables()
def close(self):
self.logger.info("closing graph: "+self.graph_name)
self.cog.close()
def put(self, vertex1, predicate, vertex2):
self.cog.use_namespace(self.graph_name).use_table(predicate)
self.cog.put_node(vertex1, predicate, vertex2)
self.all_predicates = self.cog.list_tables()
return self
def v(self, vertex=None, func=None):
if vertex is not None:
if isinstance(vertex, list):
self.last_visited_vertices = [Vertex(v) for v in vertex]
else:
self.last_visited_vertices = [Vertex(vertex)]
else:
self.last_visited_vertices = []
self.cog.use_namespace(self.graph_name).use_table(self.config.GRAPH_NODE_SET_TABLE_NAME)
for r in self.cog.scanner():
if func is not None and not func(r.key):
continue
self.last_visited_vertices.append(Vertex(r.key))
return self
def out(self, predicates=None, func=None):
'''
Traverse forward through edges.
:param predicates: A string or a List of strings.
:return:
'''
if func:
assert callable(func), "func must be a lambda. Example: func = lambda d: int(d) > 5"
assert not isinstance(predicates, list), "func cannot be used with a list of predicates"
if predicates is not None:
if not isinstance(predicates, list):
predicates = [predicates]
predicates = list(map(hash_predicate, predicates))
else:
predicates = self.all_predicates
self.logger.debug("OUT: predicates: "+str(predicates))
self.__hop("out", predicates=predicates, func=func)
return self
def inc(self, predicates=None, func=None):
'''
Traverse backward through edges.
:param predicates:
:return:
'''
if func:
assert callable(func), "func must be a lambda. Example: func = lambda d: int(d) > 5"
assert not isinstance(predicates, list), "func cannot be used with a list of predicates"
if predicates is not None:
if not isinstance(predicates, list):
predicates = [predicates]
predicates = list(map(hash_predicate, predicates))
else:
predicates = self.all_predicates
self.__hop("in", predicates, func=func)
return self
def __adjacent_vertices(self, vertex, predicates, direction='out'):
self.cog.use_namespace(self.graph_name)
adjacent_vertices = []
for predicate in predicates:
if direction == 'out':
out_record = self.cog.use_table(predicate).get(out_nodes(vertex.id))
if out_record is not None:
for v_adj in out_record.value:
adjacent_vertices.append(Vertex(v_adj).set_edge(predicate))
elif direction == 'in':
in_record = self.cog.use_table(predicate).get(in_nodes(vertex.id))
if not in_record is not None:
for v_adj in in_record.value:
adjacent_vertices.append(Vertex(v_adj).set_edge(predicate))
return adjacent_vertices
def has(self, predicates, vertex):
"""
Filters all outgoing edges from a vertex that matches a list of predicates.
:param predicates:
:param vertex:
:return:
"""
if predicates is not None:
if not isinstance(predicates, list):
predicates = [predicates]
predicates = list(map(hash_predicate, predicates))
has_vertices = []
for lv in self.last_visited_vertices:
adj_vertices = self.__adjacent_vertices(lv, predicates)
for av in adj_vertices:
if av.id == vertex:
has_vertices.append(lv)
self.last_visited_vertices = has_vertices
return self
def hasr(self, predicates, vertex):
"""
'Has' in reverse. Filters all incoming edges from a vertex that matches a list of predicates.
:param predicates:
:param vertex:
:return:
"""
if predicates is not None:
if not isinstance(predicates, list):
predicates = [predicates]
predicates = list(map(hash_predicate, predicates))
has_vertices = []
for lv in self.last_visited_vertices:
adj_vertices = self.__adjacent_vertices(lv, predicates, 'in')
# print(lv.id + " -> " + str([x.id for x in adj_vertices]))
for av in adj_vertices:
if av.id == vertex:
has_vertices.append(lv)
self.last_visited_vertices = has_vertices
return self
def scan(self, limit=10, scan_type='v'):
'''
Scans vertices or edges in a graph.
:param limit:
:param scan_type:
:return:
'''
assert type(scan_type) is str, "Scan type must be either 'v' for vertices or 'e' for edges."
if scan_type == 'e':
self.cog.use_namespace(self.graph_name).use_table(self.config.GRAPH_EDGE_SET_TABLE_NAME)
else:
self.cog.use_namespace(self.graph_name).use_table(self.config.GRAPH_NODE_SET_TABLE_NAME)
result = []
for i, r in enumerate(self.cog.scanner()):
if i < limit:
if scan_type == 'v':
v = Vertex(r.key)
else:
v = Vertex(r.value)
result.append({"id": v.id})
else:
break
return {"result": result}
def __hop(self, direction, predicates=None, tag=NOTAG, func=None):
self.logger.debug("__hop : direction: " + str(direction) + " predicates: " + str(predicates) + " graph name: "+self.graph_name)
self.cog.use_namespace(self.graph_name)
self.logger.debug("hopping from vertices: " + str(map(lambda x : x.id, self.last_visited_vertices)))
self.logger.debug("direction: " + str(direction) + " predicates: "+str(self.all_predicates))
traverse_vertex = []
for predicate in predicates:
self.logger.debug("__hop predicate: "+predicate + " of "+ str(predicates))
for v in self.last_visited_vertices:
if direction == "out":
record = self.cog.use_table(predicate).get(out_nodes(v.id))
else:
record = self.cog.use_table(predicate).get(in_nodes(v.id))
if record is not None:
for v_adjacent in record.value:
if func is not None and not func(v_adjacent):
continue
v_adjacent_obj = Vertex(v_adjacent).set_edge(predicate)
v_adjacent_obj.tags.update(v.tags)
traverse_vertex.append(v_adjacent_obj)
self.last_visited_vertices = traverse_vertex
def tag(self, tag_name):
'''
Saves vertices with a tag name. Used to capture vertices while traversing a graph.
:param tag_name:
:return:
'''
for v in self.last_visited_vertices:
v.tags[tag_name] = v.id
return self
def count(self):
return len(self.last_visited_vertices)
def all(self, options=None):
"""
Returns all the vertices that are resultant of the graph query. Options 'e' would include the edges that were traversed.
https://github.com/cayleygraph/cayley/blob/master/docs/GizmoAPI.md
:return:
"""
result = []
show_edge = True if options is not None and 'e' in options else False
for v in self.last_visited_vertices:
item = {"id": v.id}
if show_edge and v.edges:
item['edges'] = [self.cog.use_namespace(self.graph_name).use_table(self.config.GRAPH_EDGE_SET_TABLE_NAME).get(edge).value for edge in v.edges]
# item['edge'] = self.cog.use_namespace(self.graph_name).use_table(self.config.GRAPH_EDGE_SET_TABLE_NAME).get(item['edge']).value
item.update(v.tags)
result.append(item)
res = {"result": result}
return res
def view(self, view_name, js_src="https://cdnjs.cloudflare.com/ajax/libs/vis/4.21.0/vis.min.js"):
"""
Returns html view of the resulting graph from a query.
:return:
"""
assert view_name is not None, "a view name is required to create a view, it can be any string."
result = self.all()
view_html = script_part1 + graph_lib_src.format(js_src=js_src) + graph_template.format(plot_data_insert=json.dumps(result['result'])) + script_part2
view = self.views_dir+"/{view_name}.html".format(view_name=view_name)
view = View(view, view_html)
view.persist()
return view
def getv(self, view_name):
view = self.views_dir + "/{view_name}.html".format(view_name=view_name)
assert os.path.isfile(view), "view not found, create a view by calling .view()"
with open(view, 'r') as f:
view_html = f.read()
view = View(view, view_html)
return view
def lsv(self):
return [f.split(".")[0] for f in listdir(self.views_dir)]
def get_new_graph_instance(self):
return Graph(self.graph_name, self.config.COG_HOME, self.config.COG_PATH_PREFIX)