Merge pull request galaxyproject#21276 from nilchia/fix_container

[25.0] Update the mulled.py script to check json output

Author: mvdbeek

lib/galaxy/tool_util/deps/container_classes.py

@@ -52,23 +52,28 @@
 from __future__ import print_function
 
 import json
-import re
 import subprocess
 import tarfile
 
 t = tarfile.TarFile("${cached_image_file}")
 meta_str = t.extractfile('repositories').read()
 meta = json.loads(meta_str)
-tag, tag_value = next(iter(meta.items()))
-rev, rev_value = next(iter(tag_value.items()))
+repository, tag_value = next(iter(meta.items()))
+tag, id = next(iter(tag_value.items()))
 cmd = "${images_cmd}"
-proc = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
+proc = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, text=True)
 stdo, stde = proc.communicate()
 found = False
 for line in stdo.split("\n"):
-    tmp = re.split(r'\s+', line)
-    if tmp[0] == tag and tmp[1] == rev and tmp[2] == rev_value:
-        found = True
+    line = line.strip()
+    if line:
+        try:
+            img = json.loads(line)
+            if img.get("Repository") == repository and img.get("Tag") == tag and img.get("ID") == id:
+                found = True
+                break
+        except (json.JSONDecodeError, ValueError):
+            pass
 if not found:
     print("Loading image")
     cmd = "cat ${cached_image_file} | ${load_cmd}"
@@ -502,7 +507,7 @@ def containerize_command(self, command: str) -> str:
 {run_command}"""
 
     def __cache_from_file_command(self, cached_image_file: str, docker_host_props: Dict[str, Any]) -> str:
-        images_cmd = docker_util.build_docker_images_command(truncate=False, **docker_host_props)
+        images_cmd = docker_util.build_docker_images_command(truncate=False, format="json", **docker_host_props)
         load_cmd = docker_util.build_docker_load_command(**docker_host_props)
 
         return string.Template(LOAD_CACHED_IMAGE_COMMAND_TEMPLATE).safe_substitute(

lib/galaxy/tool_util/deps/container_resolvers/mulled.py

@@ -1,5 +1,6 @@
 """This module describes the :class:`MulledContainerResolver` ContainerResolver plugin."""
 
+import json
 import logging
 import os
 import subprocess
@@ -188,13 +189,27 @@ def list_docker_cached_mulled_images(
     if resolution_cache is not None and cache_key in resolution_cache:
         images_and_versions = resolution_cache.get(cache_key)
     else:
-        command = build_docker_images_command(truncate=True, sudo=False, to_str=False)
+        command = build_docker_images_command(truncate=True, format="json", sudo=False, to_str=False)
         try:
-            images_and_versions = unicodify(subprocess.check_output(command)).strip().splitlines()
+            output = unicodify(subprocess.check_output(command)).strip()
         except subprocess.CalledProcessError:
             log.info("Call to `docker images` failed, configured container resolution may be broken")
             return []
-        images_and_versions = [":".join(line.split()[0:2]) for line in images_and_versions[1:]]
+
+        # Parse JSON output from docker images
+        images_and_versions = []
+        for line in output.splitlines():
+            if line.strip():
+                try:
+                    image_info = json.loads(line)
+                    repository = image_info.get("Repository", "")
+                    tag = image_info.get("Tag", "")
+                    if repository and tag:
+                        images_and_versions.append(f"{repository}:{tag}")
+                except json.JSONDecodeError:
+                    log.warning(f"Failed to parse docker image JSON: {line}")
+                    continue
+
         if resolution_cache is not None:
             resolution_cache[cache_key] = images_and_versions
 

lib/galaxy/tool_util/deps/docker_util.py

@@ -63,8 +63,12 @@ def build_docker_cache_command(image: str, **kwds) -> str:
     return cache_command
 
 
-def build_docker_images_command(truncate=True, **kwds) -> Union[str, List[str]]:
-    args = ["--no-trunc"] if not truncate else []
+def build_docker_images_command(truncate=True, format: Optional[str] = None, **kwds) -> Union[str, List[str]]:
+    args = []
+    if not truncate:
+        args.append("--no-trunc")
+    if format:
+        args.extend(["--format", format])
     return command_shell("images", args, **kwds)