fix: keep every element when constructing controlled terms from a struct array

[ehennestad]

A multi-valued property linking to controlled instances kept only its first entry when read back. An AtlasAnnotation with laterality set to both left and right reloaded with left alone. This is the defect the previous PRs listed as a known gap against 30 types.

Cause

Deserializing such a property assigns a struct array of references to it:

annotation.laterality = struct('at_id', {".../laterality/left", ".../laterality/right"});

MATLAB converts that by calling the controlled term constructor with the whole array. initializeControlledTerm handles it correctly at first glance:

numInstances = numel(instanceSpec);
if numInstances > 1
    obj(numInstances) = feval(class(obj));   % grow to one element per struct
end

But initializeControlledTerm is a method on a handle class that returned nothing. Growing obj inside it expands only the local copy; the caller keeps the original scalar handle it passed in, which is element one. Everything after the first element was built, populated and then discarded when the method returned.

The for loop below the expansion did populate each element, which is why this looked correct on inspection — the values existed, they just never left the method.

Fix

initializeControlledTerm returns the object array, and the three constructors that call it take the returned value. That covers the current ControlledTerm and the v2 and v3 variants under +abstract/private/controlledTerms.

Effect

The round-trip suite goes from 261 to 288 of 292 types, and 30 entries come off ommtest.helper.knownRoundTripGap.

What is left

The four remaining failures have nothing to do with each other and are now listed individually rather than as a group:

• ParcellationTerminologyVersion and QuantitativeRelationAssessment fail during serialization, because a property holding an unresolved MixedTypeReference reaches openminds.internal.meta.fromInstance, and the meta type registry does not recognise it as a metadata type.
• ChemicalSubstance fails because one of its controlled instances is named (N-methyl-(11c))2-(4''-methylaminophenyl)-6-hydroxybenzothiazole. Looking that up from a bare reference runs the name through matlab.lang.makeValidName, which mangles it beyond matching, so it reloads as an empty term with a fresh blank node identifier.
• TermSuggestion fails because of the missing LINKED_PROPERTIES entry described in the controlled term deserialization PR.

Tests

Two cases in ControlledTermTest: one constructs the terms directly from a struct array, one goes through a property, which is the path deserialization actually takes. Both assert the element count and the identifiers, so a regression that silently drops entries is caught rather than a regression that merely changes a count.

🤖 Generated with Claude Code

[github-actions]

Test Results (R2022a)

750 tests  +2   748 ✅ +4   2m 31s ⏱️ -1s
 19 suites ±0     1 💤  - 2 
  1 files   ±0     1 ❌ ±0 

For more details on these failures, see this check.

Results for commit a5ac5dd. ± Comparison against base commit 68c97f7.

♻️ This comment has been updated with latest results.

[codecov]

Codecov Report

❌ Patch coverage is 33.33333% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.20%. Comparing base (68c97f7) to head (a5ac5dd).

Files with missing lines	Patch %	Lines
...stract/private/controlledTerms/v2/ControlledTerm.m	0.00%	1 Missing ⚠️
...stract/private/controlledTerms/v3/ControlledTerm.m	0.00%	1 Missing ⚠️

Additional details and impacted files

@@                       Coverage Diff                       @@
##           add-graph-traversal-visitor     #109      +/-   ##
===============================================================
+ Coverage                        79.17%   79.20%   +0.02%     
===============================================================
  Files                              419      419              
  Lines                             4077     4077              
===============================================================
+ Hits                              3228     3229       +1     
+ Misses                             849      848       -1     

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