From 8d64af2cb905fef95585055c7b69fd1c45d44108 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20K=C3=B6ster?= <johannes.koester@tu-dortmund.de>
Date: Thu, 3 Mar 2022 12:08:09 +0100
Subject: [PATCH] fix: more details on input and output exceptions (missing
 input, protected output, etc.) (#1453)

---
 snakemake/dag.py        |  4 ++--
 snakemake/exceptions.py | 47 ++++++++++++++++++-----------------------
 snakemake/jobs.py       |  2 +-
 3 files changed, 23 insertions(+), 30 deletions(-)

diff --git a/snakemake/dag.py b/snakemake/dag.py
index a1c066caf..a6e99ca9f 100755
--- a/snakemake/dag.py
+++ b/snakemake/dag.py
@@ -516,7 +516,7 @@ def check_and_touch_output(
             if (f.is_directory and not f.remote_object and not os.path.isdir(f)) or (
                 not f.remote_object and os.path.isdir(f) and not f.is_directory
             ):
-                raise ImproperOutputException(job.rule, [f])
+                raise ImproperOutputException(job, [f])
 
         # It is possible, due to archive expansion or cluster clock skew, that
         # the files appear older than the input.  But we know they must be new,
@@ -921,7 +921,7 @@ def update_(
 
         if missing_input:
             self.delete_job(job, recursive=False)  # delete job from tree
-            raise MissingInputException(job.rule, missing_input)
+            raise MissingInputException(job, missing_input)
 
         if skip_until_dynamic:
             self._dynamic.add(job)
diff --git a/snakemake/exceptions.py b/snakemake/exceptions.py
index c753d4556..e8752ce4d 100644
--- a/snakemake/exceptions.py
+++ b/snakemake/exceptions.py
@@ -245,18 +245,23 @@ def __init__(
 
 
 class IOException(RuleException):
-    def __init__(self, prefix, rule, files, include=None, lineno=None, snakefile=None):
-        message = (
-            "{} for rule {}:\n{}".format(prefix, rule, "\n".join(files))
-            if files
-            else ""
-        )
+    def __init__(self, prefix, job, files, include=None, lineno=None, snakefile=None):
+        from snakemake.logging import format_wildcards
+
+        msg = ""
+        if files:
+            msg = f"{prefix} for rule {job.rule}:"
+            if job.output:
+                msg += "\n" + f"    output: {', '.join(job.output)}"
+            if job.wildcards:
+                msg += "\n" + f"    wildcards: {format_wildcards(job.wildcards)}"
+            msg += "\n    affected files:\n        " + "\n        ".join(files)
         super().__init__(
-            message=message,
+            message=msg,
             include=include,
             lineno=lineno,
             snakefile=snakefile,
-            rule=rule,
+            rule=job.rule,
         )
 
 
@@ -277,8 +282,9 @@ def __init__(
 
 
 class MissingInputException(IOException):
-    def __init__(self, rule, files, include=None, lineno=None, snakefile=None):
+    def __init__(self, job, files, include=None, lineno=None, snakefile=None):
         msg = "Missing input files"
+
         if any(map(lambda f: f.startswith("~"), files)):
             msg += (
                 "(Using '~' in your paths is not allowed as such platform "
@@ -286,7 +292,7 @@ def __init__(self, rule, files, include=None, lineno=None, snakefile=None):
                 "try sticking to relative paths for everything inside the "
                 "working directory.)"
             )
-        super().__init__(msg, rule, files, include, lineno=lineno, snakefile=snakefile)
+        super().__init__(msg, job, files, include, lineno=lineno, snakefile=snakefile)
 
 
 class PeriodicWildcardError(RuleException):
@@ -294,10 +300,10 @@ class PeriodicWildcardError(RuleException):
 
 
 class ProtectedOutputException(IOException):
-    def __init__(self, rule, files, include=None, lineno=None, snakefile=None):
+    def __init__(self, job, files, include=None, lineno=None, snakefile=None):
         super().__init__(
             "Write-protected output files",
-            rule,
+            job,
             files,
             include,
             lineno=lineno,
@@ -306,24 +312,11 @@ def __init__(self, rule, files, include=None, lineno=None, snakefile=None):
 
 
 class ImproperOutputException(IOException):
-    def __init__(self, rule, files, include=None, lineno=None, snakefile=None):
+    def __init__(self, job, files, include=None, lineno=None, snakefile=None):
         super().__init__(
             "Outputs of incorrect type (directories when expecting files or vice versa). "
             "Output directories must be flagged with directory().",
-            rule,
-            files,
-            include,
-            lineno=lineno,
-            snakefile=snakefile,
-        )
-
-
-class UnexpectedOutputException(IOException):
-    def __init__(self, rule, files, include=None, lineno=None, snakefile=None):
-        super().__init__(
-            "Unexpectedly present output files "
-            "(accidentally created by other rule?)",
-            rule,
+            job,
             files,
             include,
             lineno=lineno,
diff --git a/snakemake/jobs.py b/snakemake/jobs.py
index 786a4301c..d8a36a7e6 100644
--- a/snakemake/jobs.py
+++ b/snakemake/jobs.py
@@ -703,7 +703,7 @@ def existing_output(self):
     def check_protected_output(self):
         protected = list(filter(lambda f: f.protected, self.expanded_output))
         if protected:
-            raise ProtectedOutputException(self.rule, protected)
+            raise ProtectedOutputException(self, protected)
 
     def remove_existing_output(self):
         """Clean up both dynamic and regular output before rules actually run"""