Rewrite resolved container image path via the compute environment#23129
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Rewrite resolved container image path via the compute environment#23129natefoo wants to merge 2 commits into
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When a job is dispatched to Pulsar with rewrite_parameters (i.e. a PulsarComputeEnvironment is in use), route the resolved container image path through the same ComputeEnvironment.unstructured_path_rewrite() that already rewrites unstructured tool parameters. This lets a destination `file_actions`/`file_action_config` `rewrite` rule remap the image to a compute-node path. Container resolution runs against the Galaxy-side filesystem (where e.g. /cvmfs exists), but singularity reads the image on the compute node, which may expose CVMFS at a different path (cvmfsexec mountrepo mode). Previously the image path was the only container path not routed through the compute environment (working directory and volumes already are), so it required a bespoke rewrite on the Pulsar server. It is now handled by the same mechanism as every other path. Unmatched unstructured paths resolve to a NoneAction, so this is a no-op unless a matching `rewrite` rule is configured; `rewrite` is a non-staging action, so the image is never uploaded. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
jmchilton
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Jul 17, 2026
| """ | ||
| if container is None or compute_environment is None: | ||
| return | ||
| rewritten_container_id = compute_environment.unstructured_path_rewrite(container.container_id) |
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This is not what that is for - we have a lot of structure here and we should leverage it. This should be a new action type I assume if we actually want to use the path rewriter actions. Also I assume we can do better at figuring out if container_id might be a path - is it possible to determine if we expect it to be.
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I need to test it, but does the latest look better?
Address review feedback on galaxyproject#23129: - Instead of routing the resolved container image through `unstructured_path_rewrite` (meant for tool-parameter/tool-data paths), add a first-class `ComputeEnvironment.container_path_rewrite()` backed by the new `container` path type in the Pulsar file action mapper. A destination `file_actions` rule with `path_types: container` remaps the image without sharing a namespace with unstructured tool-parameter rewrites. - Only attempt the rewrite when the container image identifier is actually a filesystem path. Add `Container.image_identifier_is_path` (False for docker/registry references; `os.path.isabs()` for Singularity/Apptainer, so `docker://`, `library://`, `shub://`, `oras://` and registry refs are excluded) and guard on it in the runner. Depends on a pulsar-galaxy-lib release providing the `container` path type. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Introduce a first-class `container` path type in the file action mapper so a resolved container image path (e.g. a Singularity/Apptainer image on CVMFS) can be rewritten for the compute node via a `file_actions` `rewrite` rule with `path_types: container`, rather than overloading the `unstructured` tool-parameter path type. Like `unstructured`, `container` is not an ACTION_DEFAULT_PATH_TYPE, so its default action is `none` (no-op) and it is never staged -- container images live on CVMFS or in a registry. `PathMapper.check_for_container_rewrite()` applies a matching `rewrite` action and is a no-op otherwise. Consumed by Galaxy's PulsarComputeEnvironment.container_path_rewrite (dependent Galaxy PR galaxyproject/galaxy#23129). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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When a job is dispatched to Pulsar with rewrite_parameters (i.e. a PulsarComputeEnvironment is in use), route the resolved container image path through the same ComputeEnvironment.unstructured_path_rewrite() that already rewrites unstructured tool parameters. This lets a destination
file_actions/file_action_configrewriterule remap the image to a compute-node path.Container resolution runs against the Galaxy-side filesystem (where e.g. /cvmfs exists), but singularity reads the image on the compute node, which may expose CVMFS at a different path (cvmfsexec mountrepo mode). Previously the image path was the only container path not routed through the compute environment (working directory and volumes already are), so it required a bespoke rewrite on the Pulsar server. It is now handled by the same mechanism as every other path.
Unmatched unstructured paths resolve to a NoneAction, so this is a no-op unless a matching
rewriterule is configured;rewriteis a non-staging action, so the image is never uploaded.Corresponding Pulsar PR: galaxyproject/pulsar#475
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