Treat undetermined file stages as a soft error - #103
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Skip files whose pipeline stage cannot be determined, record them as file_discovery diagnostics, and continue building the Experiment Summary. Co-authored-by: max.karlsson <max.karlsson@pixelgen.com>
cli cannot pluralize a bullet that carries no quantity, which aborted the build with 'Cannot pluralize without a quantity'. Co-authored-by: max.karlsson <max.karlsson@pixelgen.com>
maxkarlsson
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September 4, 2026 15:54
Unknown-stage files were recorded as diagnostics but filtered out of the report data issues callout, so the Samples page showed nothing for them. Co-authored-by: max.karlsson <max.karlsson@pixelgen.com>
Aratz
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Looks good in principle 👍 Some R idioms are still a bit hard to digest for me, but it gets a little easier each time :)
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Description
Experiment Summary ingestion no longer aborts when a
.jsonor.pxlfile in the data folder has a pipeline stage that is not in the workflow vocabulary. Those files are skipped, a warning is emitted per file, and each path is recorded as afile_discoverydiagnostic. Recognised files continue to load as before.Standalone
get_file_paths()still errors by default. Passon_unknown_stage = "omit"to skip unknown files; Experiment Summary builds use that mode automatically.file_discoverydiagnostics are reported in both places diagnostics surface: the "Report data issues" callout on the Samples page, and the Diagnostics section under Run info. They do not add a warning marker to any individual sample, since an unrecognised file is not attributable to a sample.Type of change
How Has This Been Tested?
Unit tests cover:
get_file_paths()still errors on unknown stages by default, and omits them when requestedbuild_es_data()continues when extra unknown-stage files are present and recordsfile_discoverydiagnosticsfile_discoverydiagnostics appear in the Samples page callout and the diagnostics table without marking samplesR-CMD-check passes on ubuntu-latest, macos-latest, and windows-latest.
PR checklist: