kappa-dev/regraph

Tool for building graph-based hierarchical knowledge representation systems

regraph's Issues

Support for networkx 2.2

Networkx 2.2 and 1.11 are syntactically not compatible. I'm using the newer version and the ReGraph examples won't work. For instance

import networkx as nx
from regraph.primitives import add_nodes_from
G = nx.Graph()
add_nodes_from(G, [1, (2, {"a": 1}), 3])

gives

 File "test_graph_rewrite.py", line 23, in test_basics
    add_nodes_from(G, [1, (2, {"a": 1}), 3])
  File "regraph/primitives.py", line 79, in add_nodes_from
    add_node(graph, n)
  File "regraph/primitives.py", line 51, in add_node
    graph.node[node_id] = new_attrs
TypeError: 'NodeView' object does not support item assignment

The reason is that in the newer veresion of networkx graph.node gives a NodeView object. The errors can be fixed by downgrading to networkx 1.11 (e.g., by usingpip install regraph --upgrade) but that breaks the rest of my codebase. Moving on to the current networkx version would be really great!

Bug with updated data

When we update the data's node in python script, that doesn't replace the previous value but add the new one.

Accessing loop variable outside of loop

ReGraph/regraph/utils.py

Line 963 in 43e362d

value_set.add(v)

When the following try fails

try:
     for v in values:
         value_set.add(v)
except TypeError:
     value_set.add(v)

the exception causes an exception because the parameter 'v' is not assigned outside of the for-loop.

UnboundLocalError: local variable 'v' referenced before assignment

Errors in unit tests

Unit tests contain 3 errors: AttributeError: 'set' object has no attribute 'num_set'

ERROR: test_partial_typing.TestPartialTyping.test_apply_rule

   Traceback (most recent call last):
    /home/eugenia/anaconda3/lib/python3.5/site-packages/nose/case.py line 198 in runTest
      self.test(*self.arg)
    tests/test_partial_typing.py line 322 in test_apply_rule
      assert(new_h != self.hierarchy)
    regraph/hierarchy.py line 388 in __eq__
      if not equal(g1, g2):
    regraph/primitives.py line 1122 in equal
      if graph1.node[node] != graph2.node[node]:
    regraph/atset.py line 65 in __eq__
      return self.issubset(other) and other.issubset(self)
    regraph/atset.py line 56 in issubset
      return self.num_set.issubset(other.num_set) and\
   AttributeError: 'str' object has no attribute 'num_set'

ERROR: test_rules.TestRule.test_remove_edge_attrs

   Traceback (most recent call last):
    /home/eugenia/anaconda3/lib/python3.5/site-packages/nose/case.py line 198 in runTest
      self.test(*self.arg)
    tests/test_rules.py line 219 in test_remove_edge_attrs
      assert(rule.p.edge['b']['c'] == t1)
    regraph/atset.py line 65 in __eq__
      return self.issubset(other) and other.issubset(self)
    regraph/atset.py line 56 in issubset
      return self.num_set.issubset(other.num_set) and\
   AttributeError: 'set' object has no attribute 'num_set'

ERROR: test_rules.TestRule.test_update_edge_attrs

   Traceback (most recent call last):
    /home/eugenia/anaconda3/lib/python3.5/site-packages/nose/case.py line 198 in runTest
      self.test(*self.arg)
    tests/test_rules.py line 235 in test_update_edge_attrs
      assert(rule.rhs.edge['y']['z'] == test_dict)
    regraph/atset.py line 65 in __eq__
      return self.issubset(other) and other.issubset(self)
    regraph/atset.py line 56 in issubset
      return self.num_set.issubset(other.num_set) and\
   AttributeError: 'set' object has no attribute 'num_set'

Add not immediate lhs and rhs typing

• - Not immediate lhs typing helps to define more abstract typing of a pattern to match (to loosen the constraints)
• - Not immediate rhs typing allows to force propagation 'downwards'

Recurring error in unit tests

ERROR: test_primitives.TestPrimitives.test_set_edge

Traceback (most recent call last):
/home/eugenia/anaconda3/lib/python3.5/site-packages/nose/case.py line 198 in runTest
self.test(*self.arg)
tests/test_primitives.py line 241 in test_set_edge
set_edge(g, '6', '7', {'a': 'b'})
regraph/primitives.py line 422 in set_edge
"Edge %s->%s does not exist" % (str(source), str(target)))
GraphError: Edge 6->7 does not exist

Typing of a rule (+ changes in the typing of a rewritten graph)

How do we type a rule?
Before we had: all the typings (of both LHS and RHS) of a rule were total (could they be partial? if some of the nodes in the lhs are not typed at all: do we match any node in G? -> then how do we type the result of this rewriting?)

Creating NXGraph from existing Networkx graph

The NXGraph constructor has the incoming_graph_data=None that is never used, it seems that constructing a new NXGraph from the existing networkx graph is currently not supported.

Not compatible with latest version of Neo4j driver

There has been a backwards incompatible change to the Neo4j drivers which changed the package structure. As a result, installing and then importing regraph fails.

>>> import regraph
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/benbc/src/opensafely-core/databuilder/.venv/lib/python3.9/site-packages/regraph/__init__.py", line 6, in <module>
    from regraph.backends.neo4j.graphs import Neo4jGraph
  File "/home/benbc/src/opensafely-core/databuilder/.venv/lib/python3.9/site-packages/regraph/backends/neo4j/__init__.py", line 3, in <module>
    from regraph.backends.neo4j.graphs import Neo4jGraph
  File "/home/benbc/src/opensafely-core/databuilder/.venv/lib/python3.9/site-packages/regraph/backends/neo4j/graphs.py", line 10, in <module>
    from neo4j.v1 import GraphDatabase
ModuleNotFoundError: No module named 'neo4j.v1'

The fix needed is to pin the neo4j-driver dependency in setup.py to < 4.0.0.

As a workaround you can provide this dependency yourself alongside the dependency on regraph so that the latest version of neo4j-driver doesn't get installed.

(This project doesn't look like it's maintained, so I'm mostly putting this here as documentation so that other people can find the workaround.)