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Fix polymorphic URL artifact input validation - #67

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johnchase merged 2 commits into
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fix/url-polymorphic-input-validation
Oct 17, 2026
Merged

johnchase merged 2 commits into
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fix/url-polymorphic-input-validation

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@johnchase johnchase commented Oct 16, 2026 •

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URL-backed artifact inputs failed before execution when a pipeline declared a polymorphic type such as FeatureTable[Frequency¹ | PresenceAbsence² | RelativeFrequency³]. Remote staging passed that human-readable label to parse_type, which rejects the superscript type-variable annotations. Downloading the same artifact and supplying a local path avoided this extra parsing step.

Remove the redundant URL-only semantic type parser and subtype check. After downloading and archive validation, remote inputs enter the same artifact-loading and framework action-validation path as local inputs. The runtime change only deletes 11 lines; there is no new type checker or action-resolution refactor. Keep a staging regression for annotated display labels and a real taxa.filter_table regression comparing URL and local-file results, including framework rejection of wrong artifact types through both paths.

Validation:

  • Full CLI unit suite: 271 passed, 1 optional Docker cache test skipped. Targeted Ruff checks pass.
  • The integration script passes inside ghcr.io/cymis/qiime2-plugin-taxa:2026.7: URL and local inputs produce identical filtered tables, and a taxonomy artifact supplied as a table is rejected.
  • The original worker-file hotfix is installed on the AWS runner. This simplified revision has been tested in an isolated container there; the service has not been restarted for this revision. No package release is included.

@johnchase
johnchase merged commit ee85aa1 into dev Oct 17, 2026
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@johnchase
johnchase deleted the fix/url-polymorphic-input-validation branch October 17, 2026 00:43
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