Merge pull request nf-core#2576 from MatthiasZepper/Download_Docker_p…

…refix

Download: Add docker prefix for absolute container URIs as well.

CHANGELOG.md

@@ -12,7 +12,8 @@
 
 ### Download
 
-- Bugfix for AttributeError: 'ContainerError' object has no attribute 'absoluteURI' ([#2543](https://github.com/nf-core/tools/pull/2543)).
+- Add `docker://` prefix for absolute container URIs as well ([#2576](https://github.com/nf-core/tools/pull/2576)).
+- Bugfix for AttributeError: `ContainerError` object has no attribute `absoluteURI` ([#2543](https://github.com/nf-core/tools/pull/2543)).
 
 ### Linting
 

nf_core/download.py

@@ -1247,7 +1247,7 @@ def singularity_pull_image(self, container, out_path, cache_path, library, progr
         # Thus, if an explicit registry is specified, the provided -l value is ignored.
         container_parts = container.split("/")
         if len(container_parts) > 2:
-            address = container
+            address = f"docker://{container}"
             absolute_URI = True
         else:
             address = f"docker://{library}/{container.replace('docker://', '')}"

tests/test_download.py

@@ -264,6 +264,11 @@ def test_singularity_pull_image_singularity_installed(self, tmp_dir, mock_rich_p
                 "hello-world", f"{tmp_dir}/hello-world.sif", None, "docker.io", mock_rich_progress
             )
 
+        # Test successful pull with absolute URI (use tiny 3.5MB test container from the "Kogia" project: https://github.com/bschiffthaler/kogia)
+        download_obj.singularity_pull_image(
+            "docker.io/bschiffthaler/sed", f"{tmp_dir}/sed.sif", None, "docker.io", mock_rich_progress
+        )
+
         # try to pull from non-existing registry (Name change hello-world_new.sif is needed, otherwise ImageExists is raised before attempting to pull.)
         with pytest.raises(ContainerError.RegistryNotFound):
             download_obj.singularity_pull_image(
@@ -290,6 +295,16 @@ def test_singularity_pull_image_singularity_installed(self, tmp_dir, mock_rich_p
                 "a-container", f"{tmp_dir}/acontainer.sif", None, "ghcr.io", mock_rich_progress
             )
 
+        # test Image not found for absolute URI.
+        with pytest.raises(ContainerError.ImageNotFound):
+            download_obj.singularity_pull_image(
+                "docker.io/bschiffthaler/nothingtopullhere",
+                f"{tmp_dir}/nothingtopullhere.sif",
+                None,
+                "docker.io",
+                mock_rich_progress,
+            )
+
         # Traffic from Github Actions to GitHub's Container Registry is unlimited, so no harm should be done here.
         with pytest.raises(ContainerError.InvalidTag):
             download_obj.singularity_pull_image(