Bug fix for binding JS_PIPELINE_PATH differences between run and pipelines #164
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…ipelines` commands
…his allows us to search for cached images without necessarily looking for the digest
…pretting $JS_PIPELINE_PATH and replace this with the context value since JS_PIPELINE_PATH isn't in the env until runtime
PedalheadPHX
approved these changes
Nov 3, 2023
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This fixes the handling of JS_PIPELINE_PATH within the slurm_singularity backend, namely due to the fact that
jetstream rundoes not setJS_PIPELINE_PATHat runtime unless--pipelineis defined. The slurm_singularity backend was assuming that this value was always populated and would attempt to bind it by default within singularity.Now, we check to see if
JS_PIPELINE_PATHis in the environment and handle the export accordingly. Additionally, this PR adds in some bash variable expansion as well as replacingJS_PIPELINE_PATHwith__pipeline__.pathwhen necessary (within functions such asmd5). Variable expansion is viaos.path.expandvars(), and sinceJS_PIPELINE_PATHdoesn't exist in the environment until runtime, we pass the pipeline context to themd5function.Finally, this also has adjustments for finding containers/images that are already in the cache dir. We previously only found images if the
digestwas defined for the task. Technicallydigestis an optional, but recommended directive. So now we search the cache dir within the job submission before attempting to pull externally. Theoretically, we should always find the image in the cache, but it's possible the cache has been cleaned since the start of the project and we want to avoid failures in these cases if possible.