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Add support for detection and addition of ome/ngff "standard" into assets summary #252

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Add support for detection and addition of ome/ngff "standard" into assets summary #252

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b4d3e4e
Add support for detection and addition of ome/ngff "standard" into as…
yarikoptic Aug 30, 2024
d1cfea6
Use DOI for OME/NGFF
yarikoptic Sep 6, 2024
551faf7
Use OME-NGFF in favor over OME/NGFF
yarikoptic Sep 6, 2024
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13 changes: 9 additions & 4 deletions dandischema/metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -378,13 +378,18 @@
stats["tissuesample"].append(sample)

stats["dataStandard"] = stats.get("dataStandard", [])

def maybe_add_standard(standard: str) -> None:
if standard not in stats["dataStandard"]:
stats["dataStandard"].append(standard)

if "nwb" in assetmeta["encodingFormat"]:
if models.nwb_standard not in stats["dataStandard"]:
stats["dataStandard"].append(models.nwb_standard)
maybe_add_standard(models.nwb_standard)
# TODO: RF assumption that any .json implies BIDS
if set(Path(assetmeta["path"]).suffixes).intersection((".json", ".nii")):
if models.bids_standard not in stats["dataStandard"]:
stats["dataStandard"].append(models.bids_standard)
maybe_add_standard(models.bids_standard)

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if Path(assetmeta["path"]).suffixes == [".ome", ".zarr"]:
maybe_add_standard(models.ome_ngff_standard)

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# TODO?: move/bind such helpers as .from_metadata or alike within
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5 changes: 5 additions & 0 deletions dandischema/models.py
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Expand Up @@ -807,6 +807,11 @@ class StandardsType(BaseType):
identifier="RRID:SCR_016124",
).model_dump(mode="json", exclude_none=True)

ome_ngff_standard = StandardsType(
name="OME-NGFF Standard",
identifier="DOI:10.25504/FAIRsharing.9af712",
).model_dump(mode="json", exclude_none=True)


class ContactPoint(DandiBaseModel):
email: Optional[EmailStr] = Field(
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