Add validation of filepaths for non-BIDS NWB assets #1173
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Codecov ReportBase: 88.92% // Head: 89.16% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## master #1173 +/- ##
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+ Coverage 88.92% 89.16% +0.23%
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Files 76 76
Lines 9393 9506 +113
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+ Hits 8353 8476 +123
+ Misses 1040 1030 -10
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![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
| @@ -29,6 +29,7 @@ | |||
| from dandi.dandiapi import RemoteAsset, RemoteDandiset, RESTFullAPIClient | |||
| from dandi.metadata import get_default_metadata, nwb2asset | |||
| from dandi.misctypes import DUMMY_DIGEST, Digest, P | |||
| from dandi.organize import validate_organized_path | |||
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| @@ -537,6 +541,29 @@ | |||
| raise | |||
| # TODO: might reraise instead of making it into an error | |||
| return _pydantic_errors_to_validation_results([e], str(self.filepath)) | |||
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| from .bids import NWBBIDSAsset | |||
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dandi/organize.py
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| LABELREGEX = r"[^_*\\/<>:|\"'?%@;.]+" | ||
| ORGANIZED_FILENAME_REGEX = ( | ||
| rf"sub-{LABELREGEX}(_(ses|tis|slice|cell)-{LABELREGEX})*(_[a-z]+(\+[a-z]+)*)?\.nwb" |
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- let's make at least
_sesstrictly followingsub-if present - according to https://github.com/dandi/dandi-cli/blob/HEAD/dandi/organize.py#L45 is still missing
probeandobj.
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ideally there should be a single data structure describing entities etc we should have in the filename. In principle that potential_fields is the one but I guess can't be used here "as is", unless you enrich that structure with regexes for the values, in particular for extensions etc. Then this regex can be constructed programmatically and we would avoid duplication of this knowledge.
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@yarikoptic Can tis/slice/cell/probe/obj occur without a preceding ses, or is ses a prerequisite for them?
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according to potential_fields, ses is not mandatory, so other entities could occur without a preceding ses.
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ok, I dislike that we have duplication of specification ATM between organize and validate but ok -- let's RF it after. Meanwhlie filed #1174 which found while test driving, and seems to work: although messages are a bit cryptic I guess. |
Closes #1163.