feat: LockException (snakemake#1276)

Maarten-vd-Sande · johanneskoester · web-flow · commit f5e6fa68a686 · 2022-05-10T16:21:40.000+02:00
* add LockException

* add tests

* try older mamba

Co-authored-by: Johannes Köster &lt;johannes.koester@tu-dortmund.de&gt;
diff --git a/snakemake/exceptions.py b/snakemake/exceptions.py
@@ -530,3 +530,17 @@ def __init__(self, rule, targetfile):
 
 class CacheMissException(Exception):
     pass
+
+
+class LockException(WorkflowError):
+    def __init__(self):
+        super().__init__(
+            "Error: Directory cannot be locked. Please make "
+            "sure that no other Snakemake process is trying to create "
+            "the same files in the following directory:\n{}\n"
+            "If you are sure that no other "
+            "instances of snakemake are running on this directory, "
+            "the remaining lock was likely caused by a kill signal or "
+            "a power loss. It can be removed with "
+            "the --unlock argument.".format(os.getcwd())
+        )
diff --git a/snakemake/persistence.py b/snakemake/persistence.py
@@ -15,6 +15,7 @@
 from itertools import filterfalse, count
 from pathlib import Path
 
+import snakemake.exceptions
 from snakemake.logging import logger
 from snakemake.jobs import jobfiles
 from snakemake.utils import listfiles
@@ -167,7 +168,7 @@ def lock_warn_only(self):
 
     def lock(self):
         if self.locked:
-            raise IOError("Another snakemake process " "has locked this directory.")
+            raise snakemake.exceptions.LockException()
         self._lock(self.all_inputfiles(), "input")
         self._lock(self.all_outputfiles(), "output")
 
diff --git a/snakemake/workflow.py b/snakemake/workflow.py
@@ -798,20 +798,7 @@ def files(items):
         dag.update_checkpoint_dependencies()
         dag.check_dynamic()
 
-        try:
-            self.persistence.lock()
-        except IOError:
-            logger.error(
-                "Error: Directory cannot be locked. Please make "
-                "sure that no other Snakemake process is trying to create "
-                "the same files in the following directory:\n{}\n"
-                "If you are sure that no other "
-                "instances of snakemake are running on this directory, "
-                "the remaining lock was likely caused by a kill signal or "
-                "a power loss. It can be removed with "
-                "the --unlock argument.".format(os.getcwd())
-            )
-            return False
+        self.persistence.lock()
 
         if cleanup_shadow:
             self.persistence.cleanup_shadow()
diff --git a/tests/testapi.py b/tests/testapi.py
@@ -80,3 +80,17 @@ def test_dicts_in_config():
                 "test": {"this_dict": "shoult_not_either"},
             },
         )
+
+def test_lockexception():
+    from snakemake.persistence import Persistence
+    from snakemake.exceptions import LockException
+
+    persistence = Persistence()
+    persistence.all_inputfiles = lambda: ["A.txt"]
+    persistence.all_outputfiles = lambda: ["B.txt"]
+    persistence.lock()
+    try:
+        persistence.lock()
+    except LockException as e:
+        return True
+    assert False
