chore(silo, lapis, website): update lapis to v0.8.0, silo to v0.11.0

[anna-parker]

resolves #2679

Now in the case of multi-segmented organisms we do not download empty sequences as a long Ns string when we download all aligned sequences of a specific segment, but instead just download the sequences for entries where this segment exists - a much needed improvement!!

Update to LAPIS v0.7.0: https://github.com/GenSpectrum/LAPIS/releases/tag/v0.7.0 and then https://github.com/GenSpectrum/LAPIS/releases/tag/v0.8.0 which adds escaping in advanced queries, this update includes a breaking change where LAPIS treats NULL differently than the empty string.

We have used these fields interchangeably we need to update our calls: Exact filters for field=null should be modified to field.isNull=true. Null values in an array can still be sent too LAPIS in POST requests but not in GET requests e.g. country=[Australia, null], instead they should be converted into an advanced query: "advancedQuery": "IsNull(field) OR field='Australia'". As downloads use GET requests this PR adds a new function to convert values with NULL into advanced queries.

How do I get the SHAs?

I run

$ docker pull ghcr.io/genspectrum/lapis:0.8.0 
0.8.0: Pulling from genspectrum/lapis
afe150872799: Pull complete 
65d5c9ef4c7e: Pull complete 
b998a17eab92: Pull complete 
810318c22279: Pull complete 
d4d14ce49924: Download complete 
Digest: sha256:4da71d94aceb36b7ea5963aa2e7b0566567c6423fe7fdd39448e69aebda2a8bb
Status: Downloaded newer image 

PR Checklist

• All necessary documentation has been adapted.
• The implemented feature is covered by appropriate, automated tests.
• Any manual testing that has been done is documented (i.e. what exactly was tested?)
  I added O'Conner to the URL: https://update-lapis-silo.loculus.org/ebola-sudan/search?visibility_authors=true&geoLocCountry=Canada&geoLocCountry=O%27Conner&geoLocCountry=_null_
  and then checked that the download (POST) request to LAPIS works and returns results: https://lapis-update-lapis-silo.loculus.org/ebola-sudan/sample/details?downloadAsFile=true&downloadFileBasename=ebola-sudan_metadata_2026-03-20T1042&dataUseTerms=OPEN&dataFormat=tsv&fields=accessionVersion%2CsampleCollectionDate%2CgeoLocCountry%2Cauthors%2CsubmissionId%2CgroupName%2CdataUseTerms%2CdataUseTermsUrl%2CauthorAffiliations%2CearliestReleaseDate&versionStatus=LATEST_VERSION&isRevocation=false&advancedQuery=isNull%28geoLocCountry%29+OR+geoLocCountry%3D%27Canada%27+OR+geoLocCountry%3D%27O%5C%27Conner%27

🚀 Preview: https://update-lapis-silo.loculus.org

[claude]

Claude finished @anna-parker's task in 2m 21s —— View job

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Code Review

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The overall approach is correct — using NULL_QUERY_VALUE as a sentinel in toUrlSearchParams() and converting it at the GET request boundary in modifyParamsForLapisGetRequest is clean and well-structured. The removal of the unused lapisSilo image from values.yaml is the right cleanup.

One bug found (left as an inline comment on DownloadUrlGenerator.ts:112): values inside the advanced query clause are currently unquoted. Any value containing spaces (e.g. country = "United States") would produce country=United States, which LAPIS will likely reject or misparse. The fix is to wrap values in single quotes: `${name}='${v}'`.

Everything else looks good — the isNull param for single-null fields, the advancedQuery merging logic for multiple fields, and the test coverage are all solid.

[chaoran-chen]

This looks good to me, thanks very much!