Populate per-asset dataStandard for BIDS, HED, NWB, and extensions#1811
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yarikoptic wants to merge 7 commits intomasterfrom
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Populate per-asset dataStandard for BIDS, HED, NWB, and extensions#1811yarikoptic wants to merge 7 commits intomasterfrom
yarikoptic wants to merge 7 commits intomasterfrom
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- BIDSDatasetDescriptionAsset.get_metadata(): always sets BIDS standard (with BIDSVersion), adds HED when HEDVersion present in JSON, warns on read failure - NWBAsset.get_metadata(): sets NWB standard - ZarrBIDSAsset.get_metadata(): sets OME/NGFF for .ome.zarr assets - Guard for older dandischema without dataStandard on BareAsset; RuntimeError if dandischema >= 0.12.2 lacks it - Register ai_generated pytest marker in tox.ini Requires dandischema with per-asset dataStandard support (0.12.2+). Works silently with older dandischema. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add get_nwb_extensions() to pynwb_utils that reads h5file["specifications"] to discover ndx-* namespaces and their versions (filtering out core/hdmf) - NWBAsset.get_metadata() populates StandardsType.extensions with ndx-* extensions found in the NWB file - BIDSDatasetDescriptionAsset.get_metadata() extracts HED library schemas from list-valued HEDVersion (e.g. ["8.2.0", "sc:1.0.0"]) into extensions - Add tests for both NWB extension extraction and HED library schema parsing Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…S_DATASTANDARD Single bool in bases.py guards all dataStandard/version/extensions features that ship together in dandischema >= 0.12.2, replacing scattered "field in Model.model_fields" checks. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Move json, h5py, get_nwb_extensions, and _SCHEMA_BAREASSET_HAS_DATASTANDARD imports to module top level in tests. Keep pynwb_utils import deferred in bases.py (heavy transitive deps: h5py/pynwb/hdmf/numpy) per existing convention. Add import guidance to CLAUDE.md. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
hed_standard does not exist in dandischema < 0.12.2, so gate the import on _SCHEMA_BAREASSET_HAS_DATASTANDARD (all new symbols ship together). HED detection is skipped when unavailable. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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| from dandi.bids_validator_deno import bids_validate | ||
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| from .bases import GenericAsset, LocalFileAsset, NWBAsset | ||
| from .bases import GenericAsset, LocalFileAsset, NWBAsset, _SCHEMA_BAREASSET_HAS_DATASTANDARD |
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Additional details and impacted files@@ Coverage Diff @@
## master #1811 +/- ##
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- Coverage 75.11% 74.79% -0.32%
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Files 84 84
Lines 11920 12079 +159
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+ Hits 8954 9035 +81
- Misses 2966 3044 +78
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Summary
dataStandardfield (new in dandischema) for all standards:dataset_description.jsonwithBIDSVersionHEDVersionindataset_description.json, including library schemas (e.g."sc:1.0.0") asextensionsh5file["specifications"]group.ome.zarrassets in BIDS datasets_SCHEMA_BAREASSET_HAS_DATASTANDARDinbases.py— single bool gates all new dandischema features (dataStandard, version, extensions), with RuntimeError if dandischema >= 0.12.2 unexpectedly lacks the fieldget_nwb_extensions()topynwb_utils.py— reads HDF5specificationsgroup, filters core namespaces, returns{name: latest_version}for each extensionDepends on: dandi/dandischema#XXXX
Test plan
TestBIDSDatasetDescriptionDataStandard— 5 tests covering BIDS always set, HED detected/absent, HED list form, HED library schemas as extensionstest_get_nwb_extensions— verifies ndx-* extraction with version sorting, core namespace filteringtest_get_nwb_extensions_no_specs— empty dict when no specifications groupPR in dandi-schema:
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