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chore(lapis): rename remaining occurences of "SILO" to "RhyDB" - #1916
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October 14, 2026 08:59
fengelniederhammer
added this pull request to stack #1915
October 14, 2026 08:59
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🟡 Changes recommended
The contributor guide omits the renamed exception type and uses identifier casing inconsistent with the codebase.
2 open findings
What changed in this PR
Renames remaining SILO references to RhyDB across LAPIS code, tests, documentation, and CI.
Changes:
- Updates documentation, OpenAPI descriptions, logs, and test labels.
- Corrects documentation paths and CI step naming.
- Updates contributor guidance, with a few remaining consistency issues noted.
| File | Description |
|---|---|
.github/workflows/lapis.yml |
Renames the integration-test step. |
lapis-docs/README.md |
Updates example test-data paths. |
lapis/AGENTS.md |
Updates exception and test guidance. |
lapis/src/main/kotlin/org/genspectrum/lapis/controller/ControllerDescriptions.kt |
Updates query parsing API documentation. |
lapis/src/main/kotlin/org/genspectrum/lapis/controller/ExceptionHandler.kt |
Updates RhyDB exception log messages. |
lapis/src/main/kotlin/org/genspectrum/lapis/model/QueryParseModel.kt |
Updates data-version warning text. |
lapis/src/main/kotlin/org/genspectrum/lapis/model/RhyDbQueryModel.kt |
Updates ordering documentation. |
lapis/src/main/kotlin/org/genspectrum/lapis/model/mutationsOverTime/QueriesOverTimeModel.kt |
Updates RhyDB query documentation. |
lapis/src/main/kotlin/org/genspectrum/lapis/request/QueryParseRequest.kt |
Updates OpenAPI request descriptions. |
lapis/src/main/kotlin/org/genspectrum/lapis/request/ScalarFunction.kt |
Updates scalar-function documentation. |
lapis/src/main/kotlin/org/genspectrum/lapis/response/QueryParseResponse.kt |
Updates response schema documentation. |
lapis/src/main/resources/application.properties |
Updates the health configuration comment. |
lapis/src/test/kotlin/org/genspectrum/lapis/model/RhyDbFilterExpressionMapperTest.kt |
Updates parameterized-test labels. |
lapis/src/test/kotlin/org/genspectrum/lapis/rhydb/RhyDbQueryTest.kt |
Updates serialization-test labels. |
🧠 Review effort: Balanced
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taepper
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Oct 14, 2026
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Looks good. No strong opinion on copilot nits
fhennig
approved these changes
Oct 14, 2026
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resolves #1818
After this, there should be no mentions left of "SILO" (other than in the changelog).
PR Checklist
llms.txt.