refactor(lapis): add abstract SaneQL serialization layer

[fengelniederhammer]

resolves #1754

Adds a reusable representation of SaneQL syntax in the code as an intermediate layer between the SILO expression object tree and the SaneQL string.

PR Checklist

• All necessary documentation has been adapted.
• All necessary changes are explained in the llms.txt.
• The implemented feature is covered by an appropriate test.

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Project	Deployment	Actions	Updated (UTC)
lapis	Ready	Preview, Comment	Jul 7, 2026 8:02am

[Copilot]

Pull request overview

Refactors the LAPIS Kotlin SILO query serialization path by introducing a small SaneQL AST as an intermediate representation, separating “what to render” (mapping from SiloQuery/SiloFilterExpression/SiloAction) from “how to render” (quoting/escaping/precedence in one place). This aligns with issue #1754 and keeps the SILO client callsite behavior the same while making serialization more testable.

Changes:

• Added a reusable SaneQL AST (SaneQlAst) with a single render() responsibility and dedicated unit tests.
• Moved serialization logic into SiloQuery.toSaneQl(), SiloFilterExpression.toSaneQl(), and SiloAction.toSaneQlSteps() (mapping to AST, then render).
• Removed the monolithic SiloQuerySaneQlSerializer and updated call sites/tests to use toSaneQl().

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
lapis/src/test/kotlin/org/genspectrum/lapis/silo/SiloQueryToSaneQlTest.kt	Updates serialization tests to use query.toSaneQl() and renames the test class accordingly.
lapis/src/test/kotlin/org/genspectrum/lapis/silo/SaneQlAstTest.kt	Adds focused unit tests validating AST rendering (escaping, precedence, steps/pipeline).
lapis/src/main/kotlin/org/genspectrum/lapis/silo/SiloQuerySaneQlSerializer.kt	Removes the old monolithic serializer implementation.
lapis/src/main/kotlin/org/genspectrum/lapis/silo/SiloQuery.kt	Introduces toSaneQl() and adds AST-mapping methods for actions and filter expressions.
lapis/src/main/kotlin/org/genspectrum/lapis/silo/SiloClient.kt	Switches SILO request construction to use query.toSaneQl().
lapis/src/main/kotlin/org/genspectrum/lapis/silo/SaneQlAst.kt	Adds the SaneQL AST types and centralized rendering logic (escaping/precedence/formatting).

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[Copilot]

Pull request overview

Copilot reviewed 6 out of 6 changed files in this pull request and generated no new comments.