Add concept DOI model, dates field, IsVersionOf relations, DANDI identifier#401
Add concept DOI model, dates field, IsVersionOf relations, DANDI identifier#401satra wants to merge 8 commits into
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@yarikoptic - you can review this and we will likely want to release this before the PRs (to archive) will be merged for doi process (coming soon). |
yarikoptic
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This is an alternative (if merged, should close)
hence invited @asmacdo to review since we might have some memories on that effort back in his mind.
It is not clear to me on the value for the type in the otherIdentifiers and why not to use already reserved one based on identifiers.org URL type?
- remove uv.lock
- annotate AI produced tests with a dedicated mark (I am yet to get juice to review and potentially ask to condense or parametrize(
Tests for Phase 0 tasks T001-T004: - T001: Optional doi field on Dandiset model for concept DOIs - T002: dates field in to_datacite() output (dateType: Issued) - T003: IsVersionOf/HasVersion concept DOI relation support - T004: DANDI identifier in alternateIdentifiers 6 tests fail (expected), 3 pass (existing behavior). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…I ID Phase 0 implementation for DataCite DOI improvements: T001: Add optional `doi` field to Dandiset model for concept DOI support, with DANDI_CONCEPT_DOI_PATTERN using dynamic Config.doi_prefix (preserves vendorization). T002: Add `dates` field to to_datacite() output mapping datePublished to DataCite dateType "Issued". This brings recommended field coverage from 4/6 to 5/6 (83%). T003: Add `concept_doi` parameter to to_datacite(). When provided, emits an IsVersionOf relatedIdentifier pointing to the concept DOI. Backward compatible (defaults to None). T004: Add DANDI identifier (e.g., DANDI:000485) to DataCite alternateIdentifiers with type "DANDI". All changes are backward compatible. Existing callers of to_datacite() continue to work without modification. 9 new tests + 1 updated existing test. 105 passed, 0 failures. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
for more information, see https://pre-commit.ci
- Remove unused PublishedDandiset import from test_doi_improvements.py - Apply black formatting to all changed files - Fixes CI lint and pre-commit checks Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
The alternateIdentifierType for the DANDI identifier should come from the instance config (e.g., "DANDI", "EMBER-DANDI") rather than being hardcoded to "DANDI". This ensures multi-instance compatibility. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…add AI marker Per @yarikoptic review: - Remove the instance-name typed alternateIdentifier entry — the identifiers.org URL already contains the DANDI identifier, making the extra entry redundant - Remove uv.lock from the PR - Add note that tests are AI-generated (Claude Code, TDD methodology) - Remove T004 test (alternateIdentifier test) since the feature was removed per review 104 tests pass, 0 failures. Lint clean. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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…DOI test - Delete uv.lock (cc07c42 commit message claimed removal but file remained tracked); add to .gitignore. Resolves yarikoptic's open thread. - Bump DANDI_SCHEMA_VERSION 0.7.0 → 0.7.1: optional doi field on Dandiset and DataCite output shape change (added dates, removed instance-name alternateIdentifier) is a schema change. Downstream validators caching by version will pick up the new optional field. - Add parametrized test_dandiset_doi_rejects_malformed: 5 cases covering the new DANDI_CONCEPT_DOI_PATTERN — closes Codecov gap on models.py:1710. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Update — addressing review (commit 2077205):
@yarikoptic @asmacdo — ready for re-review. |
The bump in 2077205 broke dandi-cli's downstream snapshot tests (test_update_dandiset_from_doi) that hardcode the schema version in fixture data. The bump was speculative — adding an *optional* field to a pydantic model with pattern= validation is backwards-compatible: existing data without the field still validates, new data is validated against the regex, and the DataCite output shape change is purely on the emit side and doesn't touch model validation. When a future change requires a real semantic break, that PR should bump the version and update downstream fixtures together.
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test_doi_improvenents.py wont make sense after the merge. Instead I think it makes more sense to incorporate this into test_datacite, or split into a more expressive file name.
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| attributes["publicationYear"] = str(meta.datePublished.year) | ||
| # T002: Add dates field with Issued dateType |
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If this is done with spec-kit, it might be worth reviewing the spec itself.
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+1 -- we would need the "sources"! ;)
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| title="Concept DOI", | ||
| description="A version-independent DOI for the Dandiset as a whole.", | ||
| pattern=DANDI_CONCEPT_DOI_PATTERN, |
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@candleindark I believe this would be one more case where subclass would overload the constraint, and thus we would have difficulty expressing in linkml right?
I feel that in such cases we just need to define slot without any constraint and in specific class uses of the slots define their specific constraints thus making it all work without warning... can we do that?
NB this is just a note/question to @candleindark , not request to change anything here
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@candleindark I believe this would be one more case where subclass would overload the constraint, and thus we would have difficulty expressing in linkml right?
Yes, but not exactly right here though this will cause it. With this, we will have difficult of translating the doi slot_usage entry in PublishedDandiset. This is because LinkML has monotonic behavior per https://linkml.io/linkml/schemas/advanced.html#unions-as-ranges, and pattern is a constraint metadata slot in LinkML to which the monotonic behavior applies to. (However, we can actually do it currently because of a bug, but I wouldn't count on it.)
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I feel that in such cases we just need to define slot without any constraint and in specific class uses of the slots define their specific constraints thus making it all work without warning... can we do that?
No. In the schema level slot definitions in our LinkML schema of dandischema, a definitions already contains just the minimum maximum set of properties shared by all uses of the slot. The problem originates from inheritance. Since PublishedDandiset inherits from Dandiset. The doi slot in PublishedDandiset has all the properties of the doi slot in Dandiset, and overriding the value of pattern in the doi slot in PublishedDandiset is not possible per the monotonic behavior.
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NB this is just a note/question to @candleindark , not request to change anything here
I agree. This is problem adding to a category that we already have. I will just have to find a way to solve the problem category not any particular problem.
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The
doislot inPublishedDandisethas all the properties of thedoislot inDandiset, and overriding the value ofpatternin thedoislot inPublishedDandisetis not possible per the monotonic behavior.
that's what I am saying -- it will not override but only add it where actually used, i.e. not defined in the slot definition but only in the classes which would use that slot.
anyways -- remind where the issue on this is, we could continue there
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that's what I am saying -- it will not override but only add it where actually used, i.e. not defined in the
slotdefinition but only in the classes which would use that slot.
I don't think that will work conceptually. Where a slot is defined doesn't change the slot inheritance behavior in LinkML. A more detailed post is in the issue you are looking for #389 (comment).
However, overriding still works in practice because of the bug.
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IIRC, settting the instance name is one possible strategy for "safe testing" against a real datacite instance, ie instead of DANDI, we might use DANDI_TEST_2026_05_07
So if we set up some e2e test where real findable DOIs get created, they would be namespaced and not interfere with future tests.
Summary
doifield toDandisetmodel for concept DOI support (version-independent DOI per dandiset), withDANDI_CONCEPT_DOI_PATTERNusing dynamicConfig.doi_prefixto preserve vendorizationdatesfield toto_datacite()output mappingdatePublishedto DataCitedateType: "Issued", bringing recommended field coverage from 4/6 to 5/6 (83%)concept_doiparameter toto_datacite()that emits anIsVersionOfrelatedIdentifierwhen provided (backward compatible, defaults toNone)DANDI:000485) to DataCitealternateIdentifierswith type"DANDI"All changes are backward compatible. Existing callers of
to_datacite()continue to work without modification.Related issues: dandi/dandi-archive#1319, #259, #292
Test plan
test_doi_improvements.pycovering all 4 changestest_datacite_publishexpected output for new fieldsDANDI_DOI_PREFIX=10.80507 DANDI_INSTANCE_NAME=DANDI DANDI_INSTANCE_IDENTIFIER="RRID:SCR_017571"🤖 Generated with Claude Code