Merge pull request #13925 from bernt-matthias/fix-mulled-respect-cond…

…a-channels fix two bugs in mulled container building
galaxyproject · May 19, 2022 · f12ee5c · f12ee5c
2 parents e65f1a8 + 92edf4f
commit f12ee5c
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Showing 3 changed files with 8 additions and 5 deletions.
diff --git a/lib/galaxy/tool_util/deps/conda_util.py b/lib/galaxy/tool_util/deps/conda_util.py
@@ -529,7 +529,7 @@ def best_search_result(
         hits = sorted(hits, key=lambda hit: hit["build_number"], reverse=True)
         hits = sorted(hits, key=lambda hit: packaging.version.parse(hit["version"]), reverse=True)
     except commands.CommandLineException as e:
-        log.error("Could not execute: '%s'\n%s", e.command, e)
+        log.error(f"Could not execute: '{e.command}'\n{e}")
         hits = []
 
     if len(hits) == 0:

diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build.py b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
@@ -246,14 +246,14 @@ def mull_targets(
             bind_path = channel[7:]
             binds.append(f"{bind_path}:{bind_path}")
 
-    channels = ",".join(channels)
+    channels_str = ",".join(channels)
     target_str = ",".join(map(conda_build_target_str, targets))
     bind_str = ",".join(binds)
     involucro_args = [
         "-f",
         f"{DIRNAME}/invfile.lua",
         "-set",
-        f"CHANNELS={channels}",
+        f"CHANNELS={channels_str}",
         "-set",
         f"TARGETS={target_str}",
         "-set",

diff --git a/lib/galaxy/tool_util/deps/mulled/util.py b/lib/galaxy/tool_util/deps/mulled/util.py
@@ -332,8 +332,11 @@ def v2_image_name(targets, image_build=None, name_override=None):
 
 def get_file_from_recipe_url(url):
     """Downloads file at url and returns tarball"""
-    r = requests.get(url, timeout=MULLED_SOCKET_TIMEOUT)
-    return tarfile.open(mode="r:bz2", fileobj=BytesIO(r.content))
+    if url.startswith("file://"):
+        return tarfile.open(mode="r:bz2", name=url[7:])
+    else:
+        r = requests.get(url, timeout=MULLED_SOCKET_TIMEOUT)
+        return tarfile.open(mode="r:bz2", fileobj=BytesIO(r.content))
 
 
 def split_container_name(name):