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Prefix HSSS result IDs with Variant_ instead of NGS_SNP. - #310

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jbrestel merged 4 commits into
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dnaseq-merge-experiments
Aug 13, 2026
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Prefix HSSS result IDs with Variant_ instead of NGS_SNP.#310
jbrestel merged 4 commits into
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dnaseq-merge-experiments

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@jbrestel jbrestel commented Aug 8, 2026

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Makes the HSSS plugins emit VariationRecordClass source_ids, by changing the ApiCommon
cohort default for the result-ID prefix:

-highspeedsnpsearchconfig_idPrefix: NGS_SNP.
+highspeedsnpsearchconfig_idPrefix: Variant_

Paired with the separator fix in ApiCommonWebService #20, this produces IDs of the form
Variant_<sequence>_<location> — which is what the record class has always actually held,
and what ApiCommonModel #212 renames the record to match.

Merge with ApiCommonModel #212 and ApiCommonWebService #20. The prefix, the
separator, and the record-class naming are one change spread across three repos; any two
of the three without the third leaves the HSSS searches emitting IDs the record class
won't resolve.

Scope of the cohort default

This is an ApiCommon cohort default, so it applies to every project in the cohort, not
just PlasmoDB. That is safe because no project has a live snp or chip search — those
imports are commented out in the shared apiCommonModel.xml. The chip default
(highspeedchipsnpsearchconfig_idPrefix: 'NULL') is left alone: that path is equally dead
but out of scope here.

The release note was pulled from this PR

This PR previously carried a news.xml entry for the corrected density and dN/dS
statistics. It has been reverted (965009fdd reverts a039aeee9) because its date
attribute was an unresolvable placeholder — the news page would have rendered TBD - set to the release date literally, and inventing a date was not an option.

The drafted text is preserved in this branch's history and can be recovered with
git show a039aeee9 when the release date is known. It should return as its own PR at
that point. Nothing about the statistics themselves changed; only the announcement is
deferred.


Related PRs

The variants work spans four repos. These four merge togetherApiCommonModel's record rename is a contract the other three depend on by name:

Coupling worth knowing when sequencing the merges: #1841's customization is resolved by recordClass.fullName, so without #212 it matches nothing and the override silently stops applying — no error, just the default heading back. #310's prefix and #20's separator together produce the ids #212's record class resolves; any two without the third leaves HSSS emitting ids the record class rejects.

Related but independent, cherry-picked onto mastermerge before the four above:

The release note originally in #310 has been deferred (reverted in 965009fdd) because its date attribute was an unresolvable placeholder. Recover the drafted text with git show a039aeee9 in ApiCommonWebsite and re-PR it once the release date is known.

jbrestel and others added 4 commits August 5, 2026 13:06
Paired with the separator fix in ApiCommonWebService, this makes the HSSS
plugins emit VariationRecordClass source_ids. This is an ApiCommon cohort
default and so applies to every project in the cohort, which is safe because
no project has a live snp or chip search -- those imports are commented out
in the shared apiCommonModel.xml.

The chip default (highspeedchipsnpsearchconfig_idPrefix: 'NULL') is left
alone; the chip path is equally dead but out of scope.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Both values change for every gene, so saved strategies filtering on either
will return different results. Also notes the three columns relabelled to
match what they actually contain.

The date attribute is left as a placeholder - it must be set to the release
date before this ships.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
@jbrestel jbrestel changed the title News: corrected density and dN/dS in the sample-set SNV search Prefix HSSS result IDs with Variant_ instead of NGS_SNP. Aug 10, 2026
@jbrestel
jbrestel merged commit 5e6d115 into master Aug 13, 2026
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@jbrestel
jbrestel deleted the dnaseq-merge-experiments branch August 13, 2026 17:12
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