chore: update to LAPIS 0.3.4, SILO 0.2.22 (#2934)

* chore(kubernetes): update to SILO 0.2.22

# Changelog

## [0.2.22](GenSpectrum/LAPIS-SILO@v0.2.21...v0.2.22) (2024-10-01)

### Bug Fixes

* correctly escape quotes in field names ([#595](GenSpectrum/LAPIS-SILO#595)) ([7e7b448](GenSpectrum/LAPIS-SILO@7e7b448))

## [0.2.21](GenSpectrum/LAPIS-SILO@v0.2.20...v0.2.21) (2024-09-20)

### Bug Fixes

* **preprocessing:** resolves spurious OOM crashes when handling large datasets ([6e4eae2](GenSpectrum/LAPIS-SILO@6e4eae2))

## [0.2.20](GenSpectrum/LAPIS-SILO@v0.2.19...v0.2.20) (2024-09-17)

### Features

* make duckdb memory limit configurable via preprocessing config ([c112eb1](GenSpectrum/LAPIS-SILO@c112eb1))

## [0.2.19](GenSpectrum/LAPIS-SILO@v0.2.18...v0.2.19) (2024-09-12)

### Bug Fixes

* preprocessing: validate that either a ndjson or tsv file was given as input ([#564](GenSpectrum/LAPIS-SILO#564)) ([7bf2ef7](GenSpectrum/LAPIS-SILO@7bf2ef7))

## [0.2.18](GenSpectrum/LAPIS-SILO@v0.2.17...v0.2.18) (2024-09-12)

### Features

* do not abort on assertment failures ([4e5f598](GenSpectrum/LAPIS-SILO@4e5f598))
* panic: add `ASSERT`, `UNREACHABLE`, `UNIMPLEMENTED`, safer env var ([867d08f](GenSpectrum/LAPIS-SILO@867d08f))
* update duckdb version ([577c1b2](GenSpectrum/LAPIS-SILO@577c1b2))

### Bug Fixes

* duplicate key in sample.ndjson ([c9b5232](GenSpectrum/LAPIS-SILO@c9b5232))
* increase duckdb memory limit to 80GB ([20131bb](GenSpectrum/LAPIS-SILO@20131bb))
* order of randomized tests changed ([d29b2f2](GenSpectrum/LAPIS-SILO@d29b2f2))

* chore(kubernetes): update to LAPIS 0.3.4

# Changelog

## [0.3.4](GenSpectrum/LAPIS@v0.3.3...v0.3.4) (2024-10-02)

### Features

* **lapis:** order CSV/TSV columns of aggregated/details data as specified in the request fields or as in the database config ([6cf8704](GenSpectrum/LAPIS@6cf8704)), closes [#910](GenSpectrum/LAPIS#910)

### Bug Fixes

* **lapis-docs:** fix link on landing page ([d4137b3](GenSpectrum/LAPIS@d4137b3))

## [0.3.3](GenSpectrum/LAPIS@v0.3.2...v0.3.3) (2024-09-25)

### Features

* **lapis:** abort on startup when silo url has invalid syntax ([373d662](GenSpectrum/LAPIS@373d662)), closes [#939](GenSpectrum/LAPIS#939)

### Bug Fixes

* **lapis-docs:** Sequence file naming scheme uses indexes now not names ([1e7cd60](GenSpectrum/LAPIS@1e7cd60))

## [0.3.2](GenSpectrum/LAPIS@v0.3.1...v0.3.2) (2024-09-10)

### Features

* **lapis:** add healthcheck to Docker containers ([0944990](GenSpectrum/LAPIS@0944990)), closes [#813](GenSpectrum/LAPIS#813)
* **lapis:** add instance name to landing page json ([6c5f81b](GenSpectrum/LAPIS@6c5f81b))

* refactor(kubernetes): reorder Loculus internal metadata to group related fields

kubernetes/loculus/templates/_common-metadata.tpl

@@ -14,6 +14,10 @@
 {{/* Get common metadata fields */}}
 {{- define "loculus.commonMetadata" }}
 fields:
+  - name: accessionVersion
+    type: string
+    notSearchable: true
+    hideOnSequenceDetailsPage: true
   - name: accession
     type: string
     notSearchable: true
@@ -26,10 +30,6 @@ fields:
     displayName: Submission ID
     type: string
     header: Submission details
-  - name: accessionVersion
-    type: string
-    notSearchable: true
-    hideOnSequenceDetailsPage: true
   - name: isRevocation
     type: boolean
     notSearchable: true
@@ -91,14 +91,6 @@ fields:
     displayName: Data use terms restricted until
     hideOnSequenceDetailsPage: true
     header: Data use terms
-  - name: versionStatus
-    type: string
-    notSearchable: true
-    hideOnSequenceDetailsPage: true
-  - name: versionComment
-    type: string
-    displayName: Version comment
-    header: Submission details
   {{- if $.Values.dataUseTermsUrls }}
   - name: dataUseTermsUrl
     displayName: Data use terms URL
@@ -109,6 +101,14 @@ fields:
       type: link
       url: "__value__"
   {{- end}}
+  - name: versionStatus
+    type: string
+    notSearchable: true
+    hideOnSequenceDetailsPage: true
+  - name: versionComment
+    type: string
+    displayName: Version comment
+    header: Submission details
 {{- end}}
 
 {{/* Patches schema by adding to it and overwriting overlapping fields by the value in metadataAdd*/}}

kubernetes/loculus/values.yaml

@@ -1442,8 +1442,8 @@ insecureCookies: false
 bannerMessage: "This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly."
 additionalHeadHTML: '<script defer data-domain="loculus.org" src="https://plausible.io/js/script.js"></script>'
 images:
-  lapisSilo: "ghcr.io/genspectrum/lapis-silo:0.2.17"
-  lapis: "ghcr.io/genspectrum/lapis:0.3.1"
+  lapisSilo: "ghcr.io/genspectrum/lapis-silo:0.2.22"
+  lapis: "ghcr.io/genspectrum/lapis:0.3.4"
 secrets:
   smtp-password:
     type: raw