Rename instanceName -> organismName (#2012)

* instanceName -> organismName * Update kubernetes/loculus/templates/lapis-silo-database-config.yaml Co-authored-by: Fabian Engelniederhammer <[email protected]> --------- Co-authored-by: Fabian Engelniederhammer <[email protected]>
loculus-project · May 22, 2024 · e2ab8e4 · e2ab8e4
1 parent 29c73d9
commit e2ab8e4
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Showing 12 changed files with 18 additions and 18 deletions.
diff --git a/backend/src/main/kotlin/org/loculus/backend/config/Config.kt b/backend/src/main/kotlin/org/loculus/backend/config/Config.kt
@@ -25,7 +25,7 @@ data class InstanceConfig(
 )
 
 data class Schema(
-    val instanceName: String,
+    val organismName: String,
     val metadata: List<Metadata>,
 )
 

diff --git a/backend/src/test/resources/backend_config.json b/backend/src/test/resources/backend_config.json
@@ -21,7 +21,7 @@
                 ]
             },
             "schema": {
-                "instanceName": "Test",
+                "organismName": "Test",
                 "metadata": [
                     {
                         "name": "date",
@@ -103,7 +103,7 @@
                 ]
             },
             "schema": {
-                "instanceName": "Test",
+                "organismName": "Test",
                 "metadata": [
                     {
                         "name": "date",

diff --git a/backend/src/test/resources/backend_config_single_segment.json b/backend/src/test/resources/backend_config_single_segment.json
@@ -21,7 +21,7 @@
                 ]
             },
             "schema": {
-                "instanceName": "Test",
+                "organismName": "Test",
                 "metadata": [
                     {
                         "name": "date",

diff --git a/docs/src/content/docs/guides/getting-started.md b/docs/src/content/docs/guides/getting-started.md
@@ -74,7 +74,7 @@ organisms:
   ebolavirus-sudan:
     schema:
       image: "https://cdn.britannica.com/01/179201-050-FED1B381/filamentous-ebolavirus-particles-scanning-electron-micrograph-cell.jpg?w=400&h=300&c=crop"
-      instanceName: "Ebolavirus Sudan"
+      organismName: "Ebolavirus Sudan"
       metadata:
         - name: date
           type: date

diff --git a/kubernetes/loculus/templates/_common-metadata.tpl b/kubernetes/loculus/templates/_common-metadata.tpl
@@ -97,7 +97,7 @@ organisms:
   {{ $key }}:
     schema:
       {{- with ($instance.schema | include "loculus.patchMetadataSchema" | fromYaml) }}
-      instanceName: {{ quote .instanceName }}
+      organismName: {{ quote .organismName }}
       loadSequencesAutomatically: {{ .loadSequencesAutomatically | default false }}
       {{ if .image }}
       image: {{ .image }}
@@ -167,7 +167,7 @@ organisms:
   {{ $key }}:
     schema:
       {{- with $instance.schema }}
-      instanceName: {{ quote .instanceName }}
+      organismName: {{ quote .organismName }}
       metadata:
         {{ $metadata := (include "loculus.patchMetadataSchema" .
           | fromYaml).metadata

diff --git a/kubernetes/loculus/templates/lapis-silo-database-config.yaml b/kubernetes/loculus/templates/lapis-silo-database-config.yaml
@@ -12,7 +12,7 @@ data:
   {{- with ($instance.schema | include "loculus.patchMetadataSchema" | fromYaml) }}
   database_config.yaml: |
     schema:
-      instanceName: {{ .instanceName }}
+      instanceName: {{ .organismName }}
       opennessLevel: OPEN
       metadata:
       {{- range (concat $commonMetadata .metadata) }}

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -22,7 +22,7 @@ logo:
 defaultOrganismConfig: &defaultOrganismConfig
   schema: &schema
     loadSequencesAutomatically: true
-    instanceName: "Ebola Zaire"
+    organismName: "Ebola Zaire"
     image: "https://cdn.britannica.com/01/179201-050-FED1B381/filamentous-ebolavirus-particles-scanning-electron-micrograph-cell.jpg?w=400&h=300&c=crop"
     ### Field list
     ## General fields
@@ -910,7 +910,7 @@ defaultOrganisms:
     <<: *defaultOrganismConfig
     schema:
       <<: *schema
-      instanceName: "Ebola Sudan"
+      organismName: "Ebola Sudan"
       image: "https://www.nih.gov/sites/default/files/styles/featured_media_breakpoint-medium/public/news-events/news-releases/2023/niaid-03.jpg?itok=m4wFNGkn&timestamp=1675437186"
     preprocessing:
     - <<: *preprocessing
@@ -949,7 +949,7 @@ defaultOrganisms:
     <<: *defaultOrganismConfig
     schema:
       <<: *schema
-      instanceName: "Mpox Virus"
+      organismName: "Mpox Virus"
       image: "https://cdn.who.int/media/images/default-source/health-topics/monkeypox/12763.tmb-1200v.jpg?sfvrsn=cd044fbd_37"
       metadataAdd:
         - name: clade
@@ -1013,7 +1013,7 @@ defaultOrganisms:
     <<: *defaultOrganismConfig
     schema:
       <<: *schema
-      instanceName: "West Nile Virus"
+      organismName: "West Nile Virus"
       image: "https://upload.wikimedia.org/wikipedia/commons/thumb/1/1e/West_Nile_Virus_Image.jpg/256px-West_Nile_Virus_Image.jpg?20200815184100"
       metadataAdd:
         - name: lineage
@@ -1078,7 +1078,7 @@ defaultOrganisms:
   dummy-organism:
     schema:
       image: "https://www.un.org/sites/un2.un.org/files/field/image/1583952355.1997.jpg"
-      instanceName: "Test Dummy Organism"
+      organismName: "Test Dummy Organism"
       metadata:
         - name: date
           type: date

diff --git a/website/src/components/SequenceDetailsPage/getTableData.spec.ts b/website/src/components/SequenceDetailsPage/getTableData.spec.ts
@@ -9,7 +9,7 @@ import type { Schema } from '../../types/config.ts';
 import type { MutationProportionCount } from '../../types/lapis.ts';
 
 const schema: Schema = {
-    instanceName: 'instance name',
+    organismName: 'instance name',
     metadata: [
         { name: 'metadataField1', type: 'string', header: 'testHeader1' },
         { name: 'metadataField2', type: 'string' },

diff --git a/website/src/config.ts b/website/src/config.ts
@@ -33,7 +33,7 @@ export type Organism = {
 export function getConfiguredOrganisms() {
     return Object.entries(getWebsiteConfig().organisms).map(([key, instance]) => ({
         key,
-        displayName: instance.schema.instanceName,
+        displayName: instance.schema.organismName,
         image: instance.schema.image,
         description: instance.schema.description,
     }));

diff --git a/website/src/pages/api_documentation/index.astro b/website/src/pages/api_documentation/index.astro
@@ -9,7 +9,7 @@ const organismKeys = Object.keys(websiteConfig.organisms);
 
 const organismToDisplayName = Object.fromEntries(
     organismKeys.map((organism) => {
-        return [organism, websiteConfig.organisms[organism].schema.instanceName];
+        return [organism, websiteConfig.organisms[organism].schema.organismName];
     }),
 );
 

diff --git a/website/src/types/config.ts b/website/src/types/config.ts
@@ -83,7 +83,7 @@ export type MutationFilter = {
 };
 
 const schema = z.object({
-    instanceName: z.string(),
+    organismName: z.string(),
     image: z.string().optional(),
     description: z.string().optional(),
     metadata: z.array(metadata),

diff --git a/website/tests/playwrightSetup.ts b/website/tests/playwrightSetup.ts
@@ -37,7 +37,7 @@ export default async function globalSetupForPlaywright() {
         lapisUrl,
         {
             metadata: [],
-            instanceName: 'Test',
+            organismName: 'Test',
             primaryKey: 'doesNotMatter',
             defaultOrderBy: 'neitherDoesThis',
             defaultOrder: 'ascending',