WiP: Branch with auto converted linkml model by yarikoptic · Pull Request #381 · dandi/dandi-schema

yarikoptic · 2026-03-10T19:46:27Z

NEVER TO BE MERGED

To preview and test results, actual changes should go to

Linkml conversion tooling #387

yarikoptic

initial review pointers

yarikoptic · 2026-03-10T20:31:38Z

+        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}$


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

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

Identifier = str

ORCID = str

RORID = str

DANDI = str

RRID = str

.

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.

yarikoptic · 2026-03-10T20:58:07Z

+    notes:
+    - 'pydantic2linkml: Unable to translate the logic contained in the wrap validation
+      function, <function _BaseUrl.__get_pydantic_core_schema__.<locals>.wrap_val
+      at 0x7f8c96c36f80>.'


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.

codecov · 2026-03-10T22:07:26Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.92%. Comparing base (4b89e4f) to head (bd38142).

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #381   +/-   ##
=======================================
  Coverage   97.92%   97.92%           
=======================================
  Files          18       18           
  Lines        2405     2405           
=======================================
  Hits         2355     2355           
  Misses         50       50

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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 ^^^

These prefixes are copied from https://github.com/dandi/schema/blob/master/releases/0.7.0/context.json

…_orig for now

…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>

for more information, see https://pre-commit.ci

candleindark · 2026-03-31T01:26:48Z

I reset the merge target to the master branch. Not doing so will cause whatever changes newly introduced in master to show up in the diff as well. However, github doesn't see to be working correctly to get the correct diff in files.

yarikoptic commented Mar 10, 2026

View reviewed changes

candleindark force-pushed the linkml-auto-converted branch from fa28737 to c78f9d3 Compare March 10, 2026 23:08

yarikoptic commented Mar 12, 2026

View reviewed changes

Comment thread dandischema/models.yaml

This was referenced Mar 12, 2026

Duplicate Publishable attributes in CommonModel + DOI in Dandiset as Optional #285

Closed

Migration to LinkML from Pydantic #382

Open

yarikoptic commented Mar 13, 2026

View reviewed changes

Comment thread pyproject.toml

yarikoptic added 2 commits March 13, 2026 17:01

[DATALAD RUNCMD] Auto-convert the model

21e7e9c

=== 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 ^^^

Now we will sanitize the converted model addresses

f109ff4

yarikoptic force-pushed the linkml-auto-converted branch from 28c5b44 to bd38142 Compare March 13, 2026 21:17

yarikoptic and others added 9 commits March 13, 2026 18:32

more sanitization

7580f80

More Sanitization applied

f130f4f

Reextracted model (now less clutter and with spaces)

0a8ef6b

feat: provide prefixes definition in the overlay file

63dd301

These prefixes are copied from https://github.com/dandi/schema/blob/master/releases/0.7.0/context.json

Added linkml: prefix and sorted all the entries

f8125d0

Provide default prefix to be custom dandi_default

7c5077a

Reextracted model (now with prefixes and deterministic order of notes)

3485245

rename original models into models_orig

bff037c

Adding models.py back to import from converted and some symbols from …

6bb4b52

…_orig for now

yarikoptic force-pushed the linkml-auto-converted branch from bd38142 to 6bb4b52 Compare March 13, 2026 22:33

candleindark and others added 3 commits March 15, 2026 22:40

Expand comment for linkml-auto-converted hatch env with usage instruc…

725e957

…tions Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

fix: correct default_prefix to dandi

a2324fa

There is no prefix defined as `dandi_default`. The intended default prefix is `dandi`

yarikoptic mentioned this pull request Mar 20, 2026

Linkml conversion tooling #387

Draft

11 tasks

yarikoptic and others added 2 commits March 20, 2026 18:12

'Merged' with linkml-conversion 0.12.1-55-g76a9d77 and 2 branches

7ab9964

[pre-commit.ci] auto fixes from pre-commit.com hooks

78d6899

for more information, see https://pre-commit.ci

yarikoptic changed the base branch from master to linkml-conversion March 20, 2026 22:22

yarikoptic and others added 2 commits March 20, 2026 18:29

'Merged' with linkml-conversion 0.12.1-57-ge2d124c and 2 branches

3938e26

'Merged' with linkml-conversion 0.12.1-59-gc0fbd02 and 2 branches

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candleindark force-pushed the linkml-conversion branch from c0fbd02 to 59b0587 Compare March 31, 2026 00:38

candleindark force-pushed the linkml-conversion branch from 59b0587 to c0fbd02 Compare March 31, 2026 00:59

'Merged' with linkml-conversion 0.12.1-59-gc0fbd02 and 2 branches

991790f

candleindark changed the base branch from linkml-conversion to master March 31, 2026 01:17

yarikoptic changed the base branch from master to linkml-conversion March 31, 2026 19:52

candleindark added 8 commits April 1, 2026 00:07

'Merged' with linkml-conversion 0.12.1-61-gb92119c and 2 branches

b4177a5

'Merged' with linkml-conversion 0.12.1-62-g043c3d6 and 2 branches

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'Merged' with linkml-conversion 0.12.1-63-g9209976 and 2 branches

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'Merged' with linkml-conversion 0.12.1-65-ge404946 and 2 branches

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'Merged' with linkml-conversion 0.12.1-67-g7dd492d and 2 branches

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'Merged' with linkml-conversion 0.12.1-69-g0a21040 and 2 branches

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'Merged' with linkml-conversion 0.12.1-69-g0a21040 and 2 branches

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'Merged' with linkml-conversion 0.12.1-69-g0a21040 and 2 branches

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candleindark force-pushed the linkml-auto-converted branch from 91300e9 to 06fcc9c Compare April 13, 2026 20:11

candleindark added 2 commits April 13, 2026 16:57

'Merged' with linkml-conversion 0.12.1-70-gaeae21f and 2 branches

a5f2818

'Merged' with linkml-conversion 0.12.1-70-gaeae21f and 2 branches

78ec4ff

candleindark mentioned this pull request Apr 14, 2026

Run validation of dandiset manifest using translated LinkML schema #397

Open

candleindark added 3 commits April 15, 2026 10:49

'Merged' with linkml-conversion 0.12.1-71-g2c38801 and 2 branches

bc36198

'Merged' with linkml-conversion 0.12.1-72-g7773f75 and 2 branches

68b5b82

'Merged' with linkml-conversion 0.12.1-78-g33dd458 and 2 branches

70b9ada

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WiP: Branch with auto converted linkml model#381

WiP: Branch with auto converted linkml model#381
yarikoptic wants to merge 32 commits intolinkml-conversionfrom
linkml-auto-converted

yarikoptic commented Mar 10, 2026 •

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NEVER TO BE MERGED

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yarikoptic commented Mar 10, 2026 •

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