Change MeaningsTable.target from a link to an object-reference attribute - #1525
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Update the bundled hdmf-common schema to 1.10.0, which stores MeaningsTable.target as an object-reference attribute (reftype: object, target_type: VectorData) rather than a link. This matches VectorIndex.target and DynamicTableRegion.table, which use object references to point at a co-located dataset within table machinery. Add MeaningsTableMap to read files written with the hdmf-common 1.9.0 MeaningsTable, which stored target as a link named "target". On read, the legacy link is removed from the builder before the generic mapping would otherwise match it as a VectorData column of the table, and the VectorData it points to is supplied to the target constructor argument. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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## dev #1525 +/- ##
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- Coverage 93.23% 93.22% -0.01%
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Files 41 41
Lines 10186 10204 +18
Branches 2104 2106 +2
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+ Hits 9497 9513 +16
- Misses 413 414 +1
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rly
marked this pull request as ready for review
July 6, 2026 23:00
oruebel
approved these changes
Jul 6, 2026
Point the submodule at 4508b8f on main, the squash-merge of hdmf-dev/hdmf-common-schema#97, now that the schema PR is merged. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…bject-reference # Conflicts: # CHANGELOG.md
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Motivation
Depends on hdmf-dev/hdmf-common-schema#97, which changes
MeaningsTable.targetfrom a link to an object-reference attribute (dtypewithreftype: object,target_type: VectorData) in hdmf-common 1.10.0. This matchesVectorIndex.targetandDynamicTableRegion.table, which use object references to point at a co-located dataset within table machinery.This PR updates the bundled schema submodule to the released schema commit and adds API support, including backwards-compatible reading of files written with the 1.9.0 link layout.
Changes
hdmf-common-schemasubmodule to the mergedmaincommit for Change MeaningsTable.target from a link to an object-reference attribute hdmf-common-schema#97 (schema 1.10.0).MeaningsTableMap(common/io/table.py) to read files written with the hdmf-common 1.9.0MeaningsTable, which storedtargetas a link named "target". On read, the legacy link is removed from the builder before the generic mapping would otherwise match it as aVectorDatacolumn of the table (which fails the equal-length check), and theVectorDatait points to is supplied to thetargetconstructor argument. New-format files are handled by the default object-reference mapping.MeaningsTabledocstrings ("linked" -> "referenced") to match the schema.TestMeaningsTableLegacyTargetLinkReadto cover reading a file in the 1.9.0 "target" link layout.There is no change to the read/write API:
mt.targetstill returns the targetVectorData. The change is limited to the on-disk representation.🤖 Generated with Claude Code