fix(reingest): rewrite embedded absolute paths when copying execution outputs#736
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ESMValTool records absolute output paths in its diagnostic_provenance.yml
files. Reingest copies an execution's scratch tree to a new fragment with
shutil.copytree, which duplicates those paths verbatim, so
build_execution_result tried to relativise them against the new output
directory and raised ValueError ("not in the subpath of"), silently rolling
back every ESMValTool reingest.
Re-point the embedded paths from the original scratch directory to the new
one after copying so the result can be rebuilt.
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Replace the bespoke _rewrite_copied_paths helper with the existing climate_ref_core.output_files.rewrite_tree, which does the same content rewrite with longest-match-first ordering and the shared SANITISED_FILE_GLOBS set. Drops the now-redundant unit tests (rewrite_tree is covered in test_output_files.py); the end-to-end reingest regression test is retained.
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Description
ref executions reingestfailed for every ESMValTool diagnostic.Reingest creates a new execution and copies the original execution's scratch tree to the new fragment with
shutil.copytree, then re-runsbuild_execution_resultagainst it. ESMValTool records absolute output paths in itsdiagnostic_provenance.ymlfiles, andcopytreeduplicates those contents verbatim — so the copied provenance still pointed at the original execution's directory (.../<old_id>/executions/...).build_execution_resultthen tried to express those paths relative to the new output directory (.../<new_id>) and raised:The exception propagated to reingest's catch-all, which logged "Ingestion failed … Rolling back changes" and discarded the copy — so ESMValTool executions silently never reingested.
PMP/ILAMB were unaffected because they build their output lists by globbing the live output directory (always in-tree), whereas ESMValTool is the only provider that reads paths from a recorded artifact.
Fix
After
copytree, rewrite the copied text artifacts to use the new scratch dir. Binary artefacts are never touched and unchanged files are left alone.Checklist
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