From 7f54c391f2821655ed168bcdafad6d07b96fcec7 Mon Sep 17 00:00:00 2001
From: dkuzminov <dmitry.kuzminov@gmail.com>
Date: Mon, 23 Aug 2021 06:38:35 -0400
Subject: [PATCH] fix: AmbiguousRuleException bug caused by weak ordering of
 rules (#1124)
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Link to the issue: https://github.com/snakemake/snakemake/issues/1106

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
---
 snakemake/dag.py | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/snakemake/dag.py b/snakemake/dag.py
index 6035aad68..44e4081d0 100755
--- a/snakemake/dag.py
+++ b/snakemake/dag.py
@@ -731,9 +731,8 @@ def update(
             visited = set()
         if known_producers is None:
             known_producers = dict()
-        producer = None
+        producers = []
         exceptions = list()
-        jobs = sorted(jobs, reverse=not self.ignore_ambiguity)
         cycles = list()
 
         for job in jobs:
@@ -756,12 +755,7 @@ def update(
                 )
                 # TODO this might fail if a rule discarded here is needed
                 # elsewhere
-                if producer:
-                    if job < producer or self.ignore_ambiguity:
-                        break
-                    elif producer is not None:
-                        raise AmbiguousRuleException(file, job, producer)
-                producer = job
+                producers.append(job)
             except (
                 MissingInputException,
                 CyclicGraphException,
@@ -783,7 +777,7 @@ def update(
                     if file
                     else "",
                 )
-        if producer is None:
+        if not producers:
             if cycles:
                 job = cycles[0]
                 raise CyclicGraphException(job.rule, file, rule=job.rule)
@@ -791,21 +785,27 @@ def update(
                 raise WorkflowError(*exceptions)
             elif len(exceptions) == 1:
                 raise exceptions[0]
-        else:
-            logger.dag_debug(dict(status="selected", job=producer))
-            logger.dag_debug(
-                dict(
-                    file=file,
-                    msg="Producer found, hence exceptions are ignored.",
-                    exception=WorkflowError(*exceptions),
-                )
-            )
 
         n = len(self.dependencies)
         if progress and n % 1000 == 0 and n and self._progress != n:
             logger.info("Processed {} potential jobs.".format(n))
             self._progress = n
 
+        producers.sort(reverse=True)
+        producer = producers[0]
+        ambiguities = list(
+            filter(lambda x: not x < producer and not producer < x, producers[1:])
+        )
+        if ambiguities and not self.ignore_ambiguity:
+            raise AmbiguousRuleException(file, producer, ambiguities[0])
+        logger.dag_debug(dict(status="selected", job=producer))
+        logger.dag_debug(
+            dict(
+                file=file,
+                msg="Producer found, hence exceptions are ignored.",
+                exception=WorkflowError(*exceptions),
+            )
+        )
         return producer
 
     def update_(