From ed53b05f61aee216c1bf1aea933c9281d6050f8a Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Thu, 12 Aug 2021 16:50:18 -0400 Subject: [PATCH] Fix for empty docker_volumes/singularity_volumes in job config --- lib/galaxy/tool_util/deps/container_classes.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/lib/galaxy/tool_util/deps/container_classes.py b/lib/galaxy/tool_util/deps/container_classes.py index e9cc48803ec..29ec8bb7148 100644 --- a/lib/galaxy/tool_util/deps/container_classes.py +++ b/lib/galaxy/tool_util/deps/container_classes.py @@ -117,6 +117,10 @@ def preprocess_volumes(volumes_raw_str, container_type): ro for Singularity iff no subdirectories are rw (Singularity does not allow ro parent directories with rw subdirectories). + >>> preprocess_volumes(None, DOCKER_CONTAINER_TYPE) + [] + >>> preprocess_volumes("", DOCKER_CONTAINER_TYPE) + [] >>> preprocess_volumes("/a/b", DOCKER_CONTAINER_TYPE) ['/a/b:rw'] >>> preprocess_volumes("/a/b:ro,/a/b/c:rw", DOCKER_CONTAINER_TYPE) @@ -131,6 +135,9 @@ def preprocess_volumes(volumes_raw_str, container_type): ['/a/b', '/a/b/c'] """ + if not volumes_raw_str: + return [] + volumes_raw_strs = [v.strip() for v in volumes_raw_str.split(",")] volumes = [] rw_paths = []