diff --git a/backend/src/main/kotlin/org/loculus/backend/config/Config.kt b/backend/src/main/kotlin/org/loculus/backend/config/Config.kt index adcb4a735..1e660a9f5 100644 --- 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, ) diff --git a/backend/src/test/resources/backend_config.json b/backend/src/test/resources/backend_config.json index 97101302b..694d37b20 100644 --- 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 index 1dbc81429..f1d14b5dc 100644 --- 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 index 6888c7558..795b2743c 100644 --- 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 index e8960f9ac..dafcb42ab 100644 --- 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: {{ $metadata := (include "loculus.patchMetadataSchema" . | fromYaml).metadata diff --git a/kubernetes/loculus/templates/lapis-silo-database-config.yaml b/kubernetes/loculus/templates/lapis-silo-database-config.yaml index e64edd416..181834f82 100644 --- a/kubernetes/loculus/templates/lapis-silo-database-config.yaml +++ b/kubernetes/loculus/templates/lapis-silo-database-config.yaml @@ -12,7 +12,7 @@ data: {{- with ($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 index 63e8c6179..4ea5a0442 100644 --- 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×tamp=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 index 13c631584..4ae0db9d3 100644 --- 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 index 54bfff48d..93e86b47f 100644 --- 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 index 445a0e3a7..85b477db6 100644 --- 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 index 6e37b169a..1f746d442 100644 --- 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 index f12f4a022..aad6e40cc 100644 --- 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',