From 00dd225b81678a0c26c28d2940eba1e41ce91c41 Mon Sep 17 00:00:00 2001
From: Jim Balhoff <jim@balhoff.org>
Date: Fri, 22 Oct 2021 11:14:31 -0400
Subject: [PATCH 1/3] Check for cycles in basic.owl using souffle.

---
 src/ontology/uberon.Makefile |  6 ++++++
 src/scripts/cycles.dl        | 25 +++++++++++++++++++++++++
 2 files changed, 31 insertions(+)
 create mode 100644 src/scripts/cycles.dl

diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile
index 9ad050b316..205e94ae9c 100644
--- a/src/ontology/uberon.Makefile
+++ b/src/ontology/uberon.Makefile
@@ -976,6 +976,12 @@ $(REPORTDIR)/basic-allcycles: basic.owl
 
 test: $(REPORTDIR)/basic-allcycles
 
+tmp/basic.facts: basic.owl
+	riot -q --output=n-triples $< | sed 's/ /\t/' | sed 's/ /\t/' | sed 's/ \.$$//' >$@
+
+tmp/basic-cycles.tsv: tmp/basic.facts
+	souffle -F tmp -D tmp ../scripts/cycles.dl && mv tmp/cycle.csv $@
+
 #%-synclash: %.obo
 #	blip-findall -u query_obo -i $< "same_label_as(X,Y,A,B,C),X@<Y,class_refcount(X,XC),class_refcount(Y,YC)" -select "same_label_as(X,Y,A,B,C,XC,YC)" -label > $@
 # TODO @matentzn - like mondo, make sure that there are no label/exact syn clashes, use ROBOT
diff --git a/src/scripts/cycles.dl b/src/scripts/cycles.dl
new file mode 100644
index 0000000000..9f2085a837
--- /dev/null
+++ b/src/scripts/cycles.dl
@@ -0,0 +1,25 @@
+#define RDF_TYPE "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type>"
+#define RDFS_SUBCLASS_OF "<http://www.w3.org/2000/01/rdf-schema#subClassOf>"
+#define OWL_RESTRICTION "<http://www.w3.org/2002/07/owl#Restriction>"
+#define OWL_ON_PROPERTY "<http://www.w3.org/2002/07/owl#onProperty>"
+#define OWL_SOME_VALUES_FROM "<http://www.w3.org/2002/07/owl#someValuesFrom>"
+
+.decl basic(s: symbol, p: symbol, o: symbol)
+.decl relation(s: symbol, p: symbol, o: symbol)
+.decl reachable(s: symbol, o: symbol)
+.decl cycle(s: symbol)
+
+relation(s, p, o) :-
+    basic(s, RDFS_SUBCLASS_OF, restr),
+    basic(restr, OWL_ON_PROPERTY, p),
+    basic(restr, OWL_SOME_VALUES_FROM, o),
+    basic(restr, RDF_TYPE, OWL_RESTRICTION),
+    match("<.+>", o).
+
+reachable(s, o) :- relation(s, _, o).
+reachable(s, o) :- relation(s, _, c), reachable(c, o).
+
+cycle(s) :- reachable(s, s).
+
+.input basic
+.output cycle

From 5145cafd3be95c5cd4bb203c54944688598467ea Mon Sep 17 00:00:00 2001
From: Jim Balhoff <jim@balhoff.org>
Date: Fri, 22 Oct 2021 12:06:42 -0400
Subject: [PATCH 2/3] Add is_a relations.

---
 src/scripts/cycles.dl | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/scripts/cycles.dl b/src/scripts/cycles.dl
index 9f2085a837..475e8b0858 100644
--- a/src/scripts/cycles.dl
+++ b/src/scripts/cycles.dl
@@ -14,8 +14,11 @@ relation(s, p, o) :-
     basic(restr, OWL_ON_PROPERTY, p),
     basic(restr, OWL_SOME_VALUES_FROM, o),
     basic(restr, RDF_TYPE, OWL_RESTRICTION),
+    match("<.+>", s),
     match("<.+>", o).
 
+relation(s, RDFS_SUBCLASS_OF, o) :- basic(s, RDFS_SUBCLASS_OF, o), match("<.+>", s), match("<.+>", o).
+
 reachable(s, o) :- relation(s, _, o).
 reachable(s, o) :- relation(s, _, c), reachable(c, o).
 

From 41d6d80a2b640a52ca2abeb950c48664d4e0283d Mon Sep 17 00:00:00 2001
From: Jim Balhoff <jim@balhoff.org>
Date: Thu, 9 Dec 2021 10:26:21 -0500
Subject: [PATCH 3/3] Improve cycle detector to report paths.

---
 src/scripts/cycles.dl | 28 +++++++++++++++++++++++-----
 1 file changed, 23 insertions(+), 5 deletions(-)

diff --git a/src/scripts/cycles.dl b/src/scripts/cycles.dl
index 475e8b0858..f1a6a1cfc3 100644
--- a/src/scripts/cycles.dl
+++ b/src/scripts/cycles.dl
@@ -4,10 +4,22 @@
 #define OWL_ON_PROPERTY "<http://www.w3.org/2002/07/owl#onProperty>"
 #define OWL_SOME_VALUES_FROM "<http://www.w3.org/2002/07/owl#someValuesFrom>"
 
+.type List = [
+    head : PathSegment,
+    tail : List
+]
+
+.type PathSegment = [
+    property: symbol,
+    filler: symbol
+]
+
 .decl basic(s: symbol, p: symbol, o: symbol)
 .decl relation(s: symbol, p: symbol, o: symbol)
-.decl reachable(s: symbol, o: symbol)
-.decl cycle(s: symbol)
+.decl reachable_via_path(s: symbol, o: symbol, reverse_path: List)
+.decl cycle_path(s: symbol, reverse_path: List)
+.decl cycle_path_text_builder(s: symbol, text_path: symbol, remaining: List)
+.decl cycle(text_path: symbol)
 
 relation(s, p, o) :-
     basic(s, RDFS_SUBCLASS_OF, restr),
@@ -19,10 +31,16 @@ relation(s, p, o) :-
 
 relation(s, RDFS_SUBCLASS_OF, o) :- basic(s, RDFS_SUBCLASS_OF, o), match("<.+>", s), match("<.+>", o).
 
-reachable(s, o) :- relation(s, _, o).
-reachable(s, o) :- relation(s, _, c), reachable(c, o).
+reachable_via_path(s, o, [[p, o], nil]) :- relation(s, p, o).
+reachable_via_path(s, o, [[p, o], path]) :- reachable_via_path(s, c, path), relation(c, p, o), s != c, s != o.
+
+cycle_path(s, path) :- reachable_via_path(s, s, path).
+cycle_path(s, [[p, s], path]) :- reachable_via_path(s, c, path), relation(c, p, s), s != c.
+
+cycle_path_text_builder(s, cat(" --[", p, "]--> ", o), remaining) :- cycle_path(s, [[p, o], remaining]).
+cycle_path_text_builder(s, cat(" --[", p, "]--> ", o, current), remaining) :- cycle_path_text_builder(s, current, [[p, o], remaining]).
 
-cycle(s) :- reachable(s, s).
+cycle(cat(s, current)) :- cycle_path_text_builder(s, current, nil).
 
 .input basic
 .output cycle