feat(lapis): make the SILO info timeout configurable

[corneliusroemer]

callInfo() has had a hard-coded 100 ms request timeout since #1593, picked so that the health endpoint cannot block when SILO does not respond. That same budget governs /sample/info, so a SILO that is merely a little slow (takes longer than 100ms) rather than down makes LAPIS return a 500. Users would not mind at all waiting say 200ms.

Rather than making a new judgment on what the timeout should be (there's a tradeoff between how long health can take if unhealthy and how slow silo can be before lapis returns 500) I propose to make the timeout configurable. So nothing changes unless users override.

Loculus would use this override to avoid flakes when SILO is just a bit slow (related to loculus-project/loculus#7298)

There's a separate issue about why info is sometimes slow: #682 - if that's still the case then 100ms is definitely too short and the default should be raised.

Claude-Session: https://claude.ai/code/session_01PRvw1U8cSHWotT9kL5r8FC

[vercel]

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[Copilot]

🟡 Changes recommended

The new configurable timeout should be validated as positive to avoid runtime failures on misconfiguration, and the docs should clarify that it also impacts the SILO health check path.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Pull request overview

This PR makes the timeout used when LAPIS calls SILO’s /info endpoint configurable, keeping the existing 100ms behavior by default while allowing deployments to increase it to reduce flakiness when SILO is slow.

Changes:

• Inject a configurable silo.infoTimeout (default 100ms) into CachedSiloClient and use it for the SILO info request timeout.
• Document the new --silo.infoTimeout startup parameter in the maintainer docs.

File summaries

File	Description
lapis/src/main/kotlin/org/genspectrum/lapis/silo/SiloClient.kt	Replaces the hard-coded info request timeout with a configurable silo.infoTimeout value.
lapis-docs/src/content/docs/maintainer-docs/references/starting-silo-and-lapis.mdx	Adds documentation for the new --silo.infoTimeout parameter and its default.

Review details

Suppressed comments (1)

lapis/src/main/kotlin/org/genspectrum/lapis/silo/SiloClient.kt:100

• infoTimeout is now configurable, but HttpRequest.Builder.timeout(...) rejects non-positive durations (throws IllegalArgumentException). Without validation, a misconfiguration like 0ms or a negative value will crash the /info call path at runtime; it’s better to fail fast during bean construction with a clear message.

    @param:Value("\${silo.infoTimeout:100ms}") private val infoTimeout: Duration,
) {
    private val httpClient = HttpClient.newBuilder()
        // Create our own thread pool explicitly to not use the ForkJoinPool.commonPool()
        // Use fixed pool with unbounded queue to prevent RejectedExecutionExeceptions

• Files reviewed: 2/2 changed files
• Comments generated: 1
• Review effort level: Lite

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