fix path errors (#424)

* fix path errors

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix Nonetype

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: megosato

app/referee/tasks.py

@@ -1,4 +1,5 @@
 import logging
+import os
 import tempfile
 from pathlib import Path
 
@@ -82,13 +83,19 @@ def cache_containers(submission_run, delayed_conditional):
         stdout=f"Container details: {container.uri}\n{container.container_type}\n"
     )
 
+    if container.local_save_path:
+        save_dir = container.local_save_path.parent.absolute()
+        if not save_dir.exists():
+            os.makedirs(container.local_save_path.parent.absolute())
+
     pull_code, stdout, stderr = ever_given.wrapper.pull_container(
         container.uri,
         container.container_type,
         settings.CONTAINER_ENGINE,
         container.local_save_path,
         aws_login_func,
     )
+
     if stderr:
         submission_run.append(stderr="Error message when pulling container:\n")
         submission_run.append(stderr=stderr)

ever_given/ever_given/engines/singularity_engine.py

@@ -112,14 +112,18 @@ def pull_container(cls, container_uri, container_type, save_path=None, aws_login
         cls.validate_common_arguments(container_type, aws_login_func)
 
         uri = cls.make_uri(container_uri, container_type)
+
         if save_path:   
             pull_cmd = ["singularity", "pull", "-F", save_path, uri]
         else:
             pull_cmd = ["singularity", "pull", "-F", uri]
+
         ended_proc = subprocess.run(pull_cmd, capture_output=True)
+
         code = ended_proc.returncode
         stdout = ended_proc.stdout.decode("utf-8")
         stderr = ended_proc.stderr.decode("utf-8")
+
         return code == 0, stdout, stderr