WiP: Branch with auto converted linkml model#381
WiP: Branch with auto converted linkml model#381yarikoptic wants to merge 18 commits intolinkml-conversionfrom
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initial review pointers
| name: identifier | ||
| range: string | ||
| required: true | ||
| pattern: ^(?:urn:uuid:)?[0-9a-fA-F]{8}-?[0-9a-fA-F]{4}-?4[0-9a-fA-F]{3}-?[89abAB][0-9a-fA-F]{3}-?[0-9a-fA-F]{12}$ |
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per discussion with @candleindark and claude -- it seems we should be able to use types here. Here is an example excerpt from https://claude.ai/share/66fe0f31-8cf1-40e6-b9fd-47c6719f2006
types:
ORCID:
uri: xsd:string
base: str
pattern: "^https://orcid\\.org/\\d{4}-\\d{4}-\\d{4}-\\d{3}[0-9X]$"
description: An ORCID identifier
ISSN:
uri: xsd:string
base: str
pattern: "^\\d{4}-\\d{3}[0-9X]$"
description: An ISSN identifier
UUID:
uri: xsd:string
base: str
pattern: "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"
description: A UUID
slots:
contributor_id:
range: ORCID
publication_id:
range: ISSN
asset_id:
range: UUID
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The definitions in dandischema.models doesn't define those types with patterns information attached. Those types are actually defines as alias of str
dandi-schema/dandischema/models.py
Lines 714 to 718 in 1deb319
Because of that, I don't think these type definitions should be part of the result of auto translation but added manually something to add to the result of the auto translation.
dandischema/models.yaml
Outdated
| notes: | ||
| - 'pydantic2linkml: Unable to translate the logic contained in the wrap validation | ||
| function, <function _BaseUrl.__get_pydantic_core_schema__.<locals>.wrap_val | ||
| at 0x7f8c96c36f80>.' |
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this is for List[AnyHttpUrl] and @candleindark says that there is custom validator attached. May be we could just provide custom type for validation here.
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## master #381 +/- ##
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Coverage 97.92% 97.92%
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Lines 2405 2405
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=== Do not change lines below ===
{
"chain": [],
"cmd": "hatch run linkml-auto-converted:2linkml",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
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These prefixes are copied from https://github.com/dandi/schema/blob/master/releases/0.7.0/context.json
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…tions Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
There is no prefix defined as `dandi_default`. The intended default prefix is `dandi`
… models.yaml The previous BRE pattern used `\+` (GNU sed extension) which silently fails on macOS BSD sed. Switch to `-E` (extended regex) with POSIX character class `[^[:space:]]` instead of `\S` (also unsupported by BSD sed), making the normalization work on both macOS and Linux. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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