Rename instances to organisms and more (#1209)

This PR makes two changes: it renames instances in helm Values to organisms, in line with our nomenclature. This was a backlog item. it renames the organisms in the default Values.yaml to defaultOrganisms. It only uses this if organisms is unset. Without this, if we make a new instance and set organisms appropriately, the dummy-organism, etc., gets added in too. It would be nice to do this with helm templates but I couldn't make that work.
loculus-project · Mar 1, 2024 · ed8e4eb · ed8e4eb
1 parent c051147
commit ed8e4eb
Show file tree

Hide file tree

Showing 23 changed files with 33 additions and 33 deletions.
diff --git a/backend/src/main/kotlin/org/loculus/backend/api/Organism.kt b/backend/src/main/kotlin/org/loculus/backend/api/Organism.kt
@@ -26,7 +26,7 @@ annotation class ValidOrganism(
 
 class OrganismValidator(private val backendConfig: BackendConfig) : ConstraintValidator<ValidOrganism, Organism> {
     override fun isValid(value: Organism, context: ConstraintValidatorContext): Boolean {
-        val keys = backendConfig.instances.keys
+        val keys = backendConfig.organisms.keys
         if (keys.contains(value.name)) {
             return true
         }

diff --git a/backend/src/main/kotlin/org/loculus/backend/config/Config.kt b/backend/src/main/kotlin/org/loculus/backend/config/Config.kt
@@ -5,11 +5,11 @@ import org.apache.commons.lang3.StringUtils.lowerCase
 import org.loculus.backend.api.Organism
 
 data class BackendConfig(
-    val instances: Map<String, InstanceConfig>,
+    val organisms: Map<String, InstanceConfig>,
     val accessionPrefix: String,
 ) {
-    fun getInstanceConfig(organism: Organism) = instances[organism.name] ?: throw IllegalArgumentException(
-        "Organism: ${organism.name} not found in backend config. Available organisms: ${instances.keys}",
+    fun getInstanceConfig(organism: Organism) = organisms[organism.name] ?: throw IllegalArgumentException(
+        "Organism: ${organism.name} not found in backend config. Available organisms: ${organisms.keys}",
     )
 }
 

diff --git a/backend/src/main/kotlin/org/loculus/backend/config/OpenApi.kt b/backend/src/main/kotlin/org/loculus/backend/config/OpenApi.kt
@@ -19,7 +19,7 @@ fun buildOpenApiSchema(backendConfig: BackendConfig): OpenAPI {
                     Schema<String>()
                         .type("string")
                         .description("valid names of organisms that this $PROJECT_NAME instance supports")
-                        ._enum(backendConfig.instances.keys.toList()),
+                        ._enum(backendConfig.organisms.keys.toList()),
                 )
                 .addSecuritySchemes(
                     "bearerAuth",

diff --git a/...src/main/kotlin/org/loculus/backend/service/submission/ProcessedSequenceEntryValidator.kt b/...src/main/kotlin/org/loculus/backend/service/submission/ProcessedSequenceEntryValidator.kt
@@ -78,7 +78,7 @@ enum class NucleotideSymbols(override val symbol: Char) : Symbol {
 @Component
 class ProcessedSequenceEntryValidatorFactory(private val backendConfig: BackendConfig) {
     fun create(organism: Organism): ProcessedSequenceEntryValidator {
-        val instanceConfig = backendConfig.instances[organism.name]!!
+        val instanceConfig = backendConfig.organisms[organism.name]!!
         return ProcessedSequenceEntryValidator(instanceConfig.schema, instanceConfig.referenceGenomes)
     }
 }

diff --git a/backend/src/test/kotlin/org/loculus/backend/service/CompressionServiceTest.kt b/backend/src/test/kotlin/org/loculus/backend/service/CompressionServiceTest.kt
@@ -25,7 +25,7 @@ class CompressionServiceTest(
             mapOf("test" to "test"),
             mapOf(segmentName to input),
         )
-        val organism = Organism(backendConfig.instances.keys.first())
+        val organism = Organism(backendConfig.organisms.keys.first())
         val compressed = compressor.compressSequencesInOriginalData(testData, organism)
         val decompressed = compressor.decompressSequencesInOriginalData(compressed, organism)
 

diff --git a/...end/src/test/kotlin/org/loculus/backend/service/GenerateAccessionFromNumberServiceTest.kt b/...end/src/test/kotlin/org/loculus/backend/service/GenerateAccessionFromNumberServiceTest.kt
@@ -11,7 +11,7 @@ const val PREFIX = "LOC_"
 
 class GenerateAccessionFromNumberServiceTest {
     private val accessionFromNumberService = GenerateAccessionFromNumberService(
-        BackendConfig(accessionPrefix = PREFIX, instances = emptyMap()),
+        BackendConfig(accessionPrefix = PREFIX, organisms = emptyMap()),
     )
 
     @Test

diff --git a/.../src/test/kotlin/org/loculus/backend/service/submission/EmptyProcessedDataProviderTest.kt b/.../src/test/kotlin/org/loculus/backend/service/submission/EmptyProcessedDataProviderTest.kt
@@ -25,7 +25,7 @@ class EmptyProcessedDataProviderTest {
     private val underTest = EmptyProcessedDataProvider(
         BackendConfig(
             accessionPrefix = "LOC_",
-            instances = mapOf(
+            organisms = mapOf(
                 DEFAULT_ORGANISM to InstanceConfig(
                     schema = Schema(
                         FIRST_NUCLEOTIDE_SEQUENCE,

diff --git a/backend/src/test/resources/backend_config.json b/backend/src/test/resources/backend_config.json
@@ -1,6 +1,6 @@
 {
     "accessionPrefix": "LOC_",
-    "instances": {
+    "organisms": {
         "dummyOrganism": {
             "referenceGenomes": {
                 "nucleotideSequences": [

diff --git a/backend/src/test/resources/backend_config_single_segment.json b/backend/src/test/resources/backend_config_single_segment.json
@@ -1,6 +1,6 @@
 {
     "accessionPrefix" : "LOC_",
-    "instances": {
+    "organisms": {
         "dummyOrganism": {
             "referenceGenomes": {
                 "nucleotideSequences": [

diff --git a/kubernetes/loculus/templates/_common-metadata.tpl b/kubernetes/loculus/templates/_common-metadata.tpl
@@ -34,8 +34,8 @@ name: {{ $.Values.name }}
 logo: {{ $.Values.logo | toYaml | nindent 6 }}
 accessionPrefix: {{ $.Values.accessionPrefix }}
 {{- $commonMetadata := (include "loculus.commonMetadata" . | fromYaml).fields }}
-instances:
-  {{- range $key, $instance := $.Values.instances }}
+organisms:
+  {{- range $key, $instance := (.Values.organisms | default .Values.defaultOrganisms) }}
   {{ $key }}:
 
     schema:
@@ -80,8 +80,8 @@ fields:
 {{- define "loculus.generateBackendConfig" }}
 accessionPrefix: {{$.Values.accessionPrefix}}
 name: {{ $.Values.name }}
-instances:
-  {{- range $key, $instance := $.Values.instances }}
+organisms:
+  {{- range $key, $instance := (.Values.organisms | default .Values.defaultOrganisms) }}
   {{ $key }}:
     schema:
       {{- with $instance.schema }}

diff --git a/kubernetes/loculus/templates/_lapis-urls.tpl b/kubernetes/loculus/templates/_lapis-urls.tpl
@@ -1,14 +1,14 @@
 {{/* generates internal LAPIS urls from given config object */}}
 {{ define "loculus.generateInternalLapisUrls" }}
-  {{ range $key, $_ := $.Values.instances }}
+  {{ range $key, $_ := (.Values.organisms | default .Values.defaultOrganisms) }}
     "{{ $key }}": "{{ if not $.Values.disableWebsite }}http://{{ template "loculus.lapisServiceName" $key }}:8080{{ else -}}http://localhost:8080/{{ $key }}{{ end }}"
   {{ end }}
 {{ end }}
 
 {{/* generates external LAPIS urls from { config, host } */}}
 {{ define "loculus.generateExternalLapisUrls"}}
 {{ $host := .host }}
-{{ range $key, $_ := .config.instances }}
+{{ range $key, $_ := (.config.organisms | default .config.defaultOrganisms) }}
 "{{ $key -}}": "{{ $host }}/{{ $key }}"
 {{ end }}
 {{ end }}

diff --git a/kubernetes/loculus/templates/lapis-ingress.yaml b/kubernetes/loculus/templates/lapis-ingress.yaml
@@ -5,13 +5,13 @@ kind: Ingress
 metadata:
   name: lapis-ingress
   annotations:
-    traefik.ingress.kubernetes.io/router.middlewares: "{{- $first := true }}{{- range $key, $_ := $.Values.instances }}{{ if $first }}{{ $first = false }}{{ else }},{{ end }}{{ $.Release.Namespace }}-strip-{{ $key }}-prefix@kubernetescrd{{- end }}"
+    traefik.ingress.kubernetes.io/router.middlewares: "{{- $first := true }}{{- range $key, $_ := (.Values.organisms | default .Values.defaultOrganisms) }}{{ if $first }}{{ $first = false }}{{ else }},{{ end }}{{ $.Release.Namespace }}-strip-{{ $key }}-prefix@kubernetescrd{{- end }}"
 spec:
   rules:
   - host: {{ if eq $.Values.environment "server" }}{{ $lapisHost }}{{ end }}
     http:
       paths:
-      {{- range $key, $_ := $.Values.instances }}
+      {{- range $key, $_ := (.Values.organisms | default .Values.defaultOrganisms) }}
       - path: /{{ $key }}/
         pathType: Prefix
         backend:
@@ -30,7 +30,7 @@ spec:
   {{- end }}
 
 
-{{- range $key, $_ := $.Values.instances }}
+{{- range $key, $_ := (.Values.organisms | default .Values.defaultOrganisms) }}
 ---
 apiVersion: traefik.containo.us/v1alpha1
 kind: Middleware

diff --git a/kubernetes/loculus/templates/lapis-service.yaml b/kubernetes/loculus/templates/lapis-service.yaml
@@ -1,4 +1,4 @@
-{{- range $key, $_ := $.Values.instances }}
+{{- range $key, $_ := (.Values.organisms | default .Values.defaultOrganisms) }}
 ---
 apiVersion: v1
 kind: Service

diff --git a/kubernetes/loculus/templates/lapis-silo-database-config.yaml b/kubernetes/loculus/templates/lapis-silo-database-config.yaml
@@ -1,7 +1,7 @@
 {{- $commonMetadata := (include "loculus.commonMetadata" . | fromYaml).fields }}
 {{- $importScriptLines := .Files.Lines "silo_import_job.sh" }}
 
-{{- range $key, $instance := $.Values.instances }}
+{{- range $key, $instance := (.Values.organisms | default .Values.defaultOrganisms) }}
 ---
 apiVersion: v1
 kind: ConfigMap

diff --git a/kubernetes/loculus/templates/lapis-silo-deployment.yaml b/kubernetes/loculus/templates/lapis-silo-deployment.yaml
@@ -1,5 +1,5 @@
 {{- $dockerTag := include "loculus.dockerTag" $.Values }}
-{{- range $key, $_ := $.Values.instances }}
+{{- range $key, $_ := (.Values.organisms | default .Values.defaultOrganisms) }}
 ---
 apiVersion: apps/v1
 kind: Deployment

diff --git a/kubernetes/loculus/templates/lapis-silo-import-cronjob.yaml b/kubernetes/loculus/templates/lapis-silo-import-cronjob.yaml
@@ -2,7 +2,7 @@
 {{- $keycloakTokenUrl := "http://loculus-keycloak-service:8083/realms/loculusRealm/protocol/openid-connect/token" }}
 
 
-{{- range $key, $_ := $.Values.instances }}
+{{- range $key, $_ := (.Values.organisms | default .Values.defaultOrganisms) }}
 ---
 apiVersion: batch/v1
 kind: CronJob

diff --git a/kubernetes/loculus/templates/lapis-silo-input-data-cache.yaml b/kubernetes/loculus/templates/lapis-silo-input-data-cache.yaml
@@ -1,4 +1,4 @@
-{{- range $key, $_ := $.Values.instances }}
+{{- range $key, $_ := (.Values.organisms | default .Values.defaultOrganisms) }}
 ---
 apiVersion: v1
 kind: PersistentVolumeClaim

diff --git a/kubernetes/loculus/templates/lapis-silo-shared-data.yaml b/kubernetes/loculus/templates/lapis-silo-shared-data.yaml
@@ -1,4 +1,4 @@
-{{- range $key, $_ := $.Values.instances }}
+{{- range $key, $_ := (.Values.organisms | default .Values.defaultOrganisms) }}
 ---
 apiVersion: v1
 kind: PersistentVolumeClaim

diff --git a/kubernetes/loculus/templates/loculus-preprocessing-config.yaml b/kubernetes/loculus/templates/loculus-preprocessing-config.yaml
@@ -1,4 +1,4 @@
-{{- range $key, $values := .Values.instances }}
+{{- range $key, $values := (.Values.organisms | default .Values.defaultOrganisms) }}
 {{- if $values.preprocessing.configFile }}
 ---
 apiVersion: v1

diff --git a/kubernetes/loculus/templates/loculus-preprocessing-deployment.yaml b/kubernetes/loculus/templates/loculus-preprocessing-deployment.yaml
@@ -8,7 +8,7 @@
     "http://loculus-keycloak-service:8083"
 }}
 {{- if not .Values.disablePreprocessing }}
-{{- range $key, $value := .Values.instances }}
+{{- range $key, $value := (.Values.organisms | default .Values.defaultOrganisms) }}
 ---
 apiVersion: apps/v1
 kind: Deployment

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -9,7 +9,7 @@ logo:
   url: "/favicon.svg"
   width: 100
   height: 100
-instances:
+defaultOrganisms:
   dummy-organism:
     schema:
       image: "https://www.un.org/sites/un2.un.org/files/field/image/1583952355.1997.jpg"

diff --git a/website/src/config.ts b/website/src/config.ts
@@ -31,7 +31,7 @@ export type Organism = {
 };
 
 export function getConfiguredOrganisms() {
-    return Object.entries(getWebsiteConfig().instances).map(([key, instance]) => ({
+    return Object.entries(getWebsiteConfig().organisms).map(([key, instance]) => ({
         key,
         displayName: instance.schema.instanceName,
         image: instance.schema.image,
@@ -41,10 +41,10 @@ export function getConfiguredOrganisms() {
 
 function getConfig(organism: string): InstanceConfig {
     const websiteConfig = getWebsiteConfig();
-    if (!(organism in websiteConfig.instances)) {
+    if (!(organism in websiteConfig.organisms)) {
         throw new Error(`No configuration for organism ${organism}`);
     }
-    return websiteConfig.instances[organism];
+    return websiteConfig.organisms[organism];
 }
 
 export function getSchema(organism: string): Schema {

diff --git a/website/src/types/config.ts b/website/src/types/config.ts
@@ -50,7 +50,7 @@ const logoConfig = z.object({
 });
 
 export const websiteConfig = z.object({
-    instances: z.record(instanceConfig),
+    organisms: z.record(instanceConfig),
     name: z.string(),
     logo: logoConfig,
 });