Merge remote-tracking branch 'origin/master' into issues/4633-cwl-pip…

…efish-compatibility

contrib/slurm-test/slurm_test.sh

@@ -16,7 +16,7 @@ docker exec ${LEADER} sudo apt install python3-pip -y
 docker exec ${LEADER} pip3 install "git+https://github.com/DataBiosphere/toil.git@${GIT_COMMIT}"
 docker exec ${LEADER} sinfo -N -l
 # Test 1: A really basic workflow to check Slurm is working correctly
-docker exec ${LEADER} python3 /home/admin/toil_workflow.py file:my-job-store --batchSystem slurm --disableCaching --retryCount 0
+docker exec ${LEADER} python3 /home/admin/toil_workflow.py file:my-job-store --batchSystem slurm --disableCaching --retryCount 0 --batchLogsDir ./nonexistent/paths
 docker cp ${LEADER}:/home/admin/output.txt output_Docker.txt
 # Test 2: Make sure that "sort" workflow runs under slurm
 docker exec ${LEADER} python3 /home/admin/sort.py file:my-job-store --batchSystem slurm --disableCaching --retryCount 0

src/toil/batchSystems/abstractBatchSystem.py

@@ -37,6 +37,7 @@
 from toil.deferred import DeferredFunctionManager
 from toil.fileStores.abstractFileStore import AbstractFileStore
 from toil.job import JobDescription, ParsedRequirement, Requirer
+from toil.lib.memoize import memoize
 from toil.resource import Resource
 
 logger = logging.getLogger(__name__)
@@ -392,6 +393,7 @@ def set_message_bus(self, message_bus: MessageBus) -> None:
         # We do in fact send messages to the message bus.
         self._outbox = message_bus.outbox()
 
+    @memoize
     def get_batch_logs_dir(self) -> str:
         """
         Get the directory where the backing batch system should save its logs.
@@ -404,6 +406,9 @@ def get_batch_logs_dir(self) -> str:
         """
         if self.config.batch_logs_dir:
             # Use what is specified
+            if not os.path.isdir(self.config.batch_logs_dir):
+                # But if it doesn't exist, make it exist
+                os.makedirs(self.config.batch_logs_dir, exist_ok=True)
             return self.config.batch_logs_dir
         # And if nothing is specified use the workDir.
         return Toil.getToilWorkDir(self.config.workDir)