Complete the AUMCdb dataset registration - #305
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Prerequisite for the per-dataset registration PRs (#305 AUMCdb, #306 EHRShot, #307 HIRID, #308 INSPIRE, #309 NWICU, #310 SICdb, #311 eICU). Most of those datasets' upstream extractors don't ship a publicly installable demo, and the existing registry validation requires every dataset to declare a build_demo command. Switches the convention to: a dataset has a demo iff its commands declare build_demo. Absence is the signal — no separate metadata field. - `test_all_datasets_have_commands` now requires `build_full` (which every dataset still needs) and allows missing `build_demo`. - `tests/conftest.py` drops datasets without `build_demo` from the integration test matrix, so a per-dataset CI lane for one collects zero parametrized tests and passes cleanly rather than trying to build data the dataset can't produce. - `src/MEDS_DEV/datasets/__main__.py` raises a clear error when called with `demo=True` against a dataset that doesn't declare a build_demo command (instead of the previous KeyError). No dataset.yaml files change here — those changes ship with the sister per-dataset PRs that depend on this one. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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meds-transform version pin
rvandewater
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@prockenschaub Can you check the predicates in case you know more? |
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Summary
AUMCdb (Amsterdam UMCdb — ICU dataset) was previously registered only as a stub:
predicates.yaml+README.md, nodataset.yaml, no requirements, no refs. This PR completes the registration.Files added/modified:
dataset.yaml— metadata +build_fullcommand shelling out toMEDS_extract-AUMCdb. Nobuild_demo(the upstream extractor doesn't ship a demo recipe; Makebuild_demooptional, skip demo-less datasets in tests #312 makes the key optional and ensures integration tests skip it).predicates.yaml— replaced with the full ICU predicate set from the upstream contribution (mojibake�mol/lfixed toµmol/lalong the way).requirements.txt— pinsAUMCdb-MEDS==0.0.2.refs.bib— Thoral et al., 2021.tasks/mortality/in_icu/first_24h.yaml— adds AUMCdb tosupported_datasets. AUMCdb definesicu_admission/icu_discharge, so the task wires up.Depends on #312
#312 makes
build_demooptional in the registry and skips datasets that don't declare it from the integration test matrix. Targeted atfeat/dataset-demo-availabilityfor now; once #312 merges, this PR retargets todev.Open items not fixed here
Left for follow-ups so this PR's scope stays focused on AUMCdb itself:
# Todo: convert to mg/dLmarkers — value thresholds are in the source's native units rather than mg/dL. Worth tracking but not blocking registration.MEDS_cohort_dirvsMEDS_output_dirarg name — dev's MIMIC-IV usesMEDS_output_dir; this PR usesMEDS_cohort_dir(matching the contributor's branch and the AUMCdb-MEDS API). Whether one is stale upstream is a separate question.Test plan
build_demooptional, skip demo-less datasets in tests #312.build_demo).Supersedes / refs
AUMCdb-MEDS.🤖 Generated with Claude Code