From fef1a14b8eefd121beff1b8bdffcbb1f60e0ad58 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 27 Oct 2020 14:36:01 +0000 Subject: [PATCH 1/2] Update import --- lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py b/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py index 682c6755830..a5fd21bf284 100644 --- a/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py +++ b/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py @@ -15,9 +15,9 @@ from .mulled_build import ( add_build_arguments, add_single_image_arguments, args_to_mull_targets_kwds, - build_target, mull_targets, ) +from .util import build_target def main(argv=None): From 2030ddbe5d0da007a5574175f0780e1712b8c275 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 27 Oct 2020 14:38:44 +0000 Subject: [PATCH 2/2] Make package names lowercase for mulled dependency resolving Fix `planemo test --biocontainers --no_dependency_resolution --no_conda_auto_init ~/tools-devteam/tools/sicer/` where the requirement ```xml SICER ``` was not being resolved by `CachedMulledDockerContainerResolver` since commit f0a55a399cf96cd8c11e3ab8a0d283e9df852088 , while on 20.05 is correctly resolved to `quay.io/biocontainers/sicer:1.1--4` . --- lib/galaxy/tool_util/deps/mulled/util.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/tool_util/deps/mulled/util.py b/lib/galaxy/tool_util/deps/mulled/util.py index cc3d3acf650..f50355282cc 100644 --- a/lib/galaxy/tool_util/deps/mulled/util.py +++ b/lib/galaxy/tool_util/deps/mulled/util.py @@ -83,7 +83,7 @@ def mulled_tags_for(namespace, image, tag_prefix=None, resolution_cache=None): # Following check is pretty expensive against biocontainers... don't even bother doing it # if can't cache the response. if not _namespace_has_repo_name(namespace, image, resolution_cache): - log.debug("skipping mulled_tags_for [%s] no repository" % image) + log.info("skipping mulled_tags_for [%s] no repository" % image) return [] cache_key = "galaxy.tool_util.deps.container_resolvers.mulled.util:tag_cache" @@ -158,7 +158,8 @@ def build_target(package_name, version=None, build=None, tag=None): assert build is None version, build = split_tag(tag) - return Target(package_name, version, build, package_name) + # conda package and quay image names are lowercase + return Target(package_name.lower(), version, build, package_name) def conda_build_target_str(target):