From cb9f469369ee6f3c2751db2b2a1a393fe493156b Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Mon, 8 Jan 2024 10:34:58 +0100
Subject: [PATCH] Fix definition source propagation

---
 src/pyobo/obographs.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/pyobo/obographs.py b/src/pyobo/obographs.py
index 6e4db361..681b5a68 100644
--- a/src/pyobo/obographs.py
+++ b/src/pyobo/obographs.py
@@ -19,7 +19,7 @@
 from bioontologies.robot import ParseResults
 
 from pyobo.struct import Obo, Reference, Term
-from pyobo.struct.typedef import is_a
+from pyobo.struct.typedef import definition_source, is_a
 
 __all__ = [
     "graph_from_obo",
@@ -61,12 +61,12 @@ def _rewire(r: Reference) -> curies.Reference:
 
 
 def _get_class_node(term: Term) -> Node:
-    if not term.definition:
-        definition = None
-    else:
+    if term.definition or term.provenance:
         definition = Definition.from_parsed(
             value=term.definition, references=[_rewire(p) for p in term.provenance]
         )
+    else:
+        definition = None
 
     if term.xrefs:
         if not term.xref_types:
@@ -126,3 +126,11 @@ def _iter_edges(term: Term) -> Iterable[Edge]:
                 _rewire(typedef.reference),
                 _rewire(target),
             )
+
+    for provenance_reference in term.provenance:
+        yield Edge.from_parsed(
+            _rewire(term.reference),
+            _rewire(definition_source.reference),
+            _rewire(provenance_reference),
+        )
+    # TODO also look through xrefs and seealso to get provenance xrefs?