From 75242d11c067997b418261df2c32de33d0a2cdb0 Mon Sep 17 00:00:00 2001
From: Chaoran Chen <mail@chaoran-chen.de>
Date: Fri, 29 Mar 2024 18:03:38 +0100
Subject: [PATCH] feat(backend): add URLs to the data use terms to SILO (#1515)

---
 .../kotlin/org/loculus/backend/config/Config.kt |  6 ++++++
 .../loculus/backend/model/ReleasedDataModel.kt  | 17 +++++++++++++++--
 .../GenerateAccessionFromNumberServiceTest.kt   |  2 +-
 .../EmptyProcessedDataProviderTest.kt           |  1 +
 .../loculus/templates/_common-metadata.tpl      |  7 +++++++
 kubernetes/loculus/values.yaml                  |  3 +++
 6 files changed, 33 insertions(+), 3 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
index 0c7aca74eb..04e4c72571 100644
--- a/backend/src/main/kotlin/org/loculus/backend/config/Config.kt
+++ b/backend/src/main/kotlin/org/loculus/backend/config/Config.kt
@@ -7,12 +7,18 @@ import org.loculus.backend.api.Organism
 data class BackendConfig(
     val organisms: Map<String, InstanceConfig>,
     val accessionPrefix: String,
+    val dataUseTermsUrls: DataUseTermsUrls?,
 ) {
     fun getInstanceConfig(organism: Organism) = organisms[organism.name] ?: throw IllegalArgumentException(
         "Organism: ${organism.name} not found in backend config. Available organisms: ${organisms.keys}",
     )
 }
 
+data class DataUseTermsUrls(
+    val open: String,
+    val restricted: String,
+)
+
 data class InstanceConfig(
     val schema: Schema,
     val referenceGenomes: ReferenceGenome,
diff --git a/backend/src/main/kotlin/org/loculus/backend/model/ReleasedDataModel.kt b/backend/src/main/kotlin/org/loculus/backend/model/ReleasedDataModel.kt
index df05913508..89fa1f38a5 100644
--- a/backend/src/main/kotlin/org/loculus/backend/model/ReleasedDataModel.kt
+++ b/backend/src/main/kotlin/org/loculus/backend/model/ReleasedDataModel.kt
@@ -14,6 +14,7 @@ import org.loculus.backend.api.GeneticSequence
 import org.loculus.backend.api.Organism
 import org.loculus.backend.api.ProcessedData
 import org.loculus.backend.api.SiloVersionStatus
+import org.loculus.backend.config.BackendConfig
 import org.loculus.backend.service.submission.RawProcessedData
 import org.loculus.backend.service.submission.SubmissionDatabaseService
 import org.loculus.backend.utils.Accession
@@ -24,7 +25,10 @@ import org.springframework.transaction.annotation.Transactional
 private val log = KotlinLogging.logger { }
 
 @Service
-class ReleasedDataModel(private val submissionDatabaseService: SubmissionDatabaseService) {
+class ReleasedDataModel(
+    private val submissionDatabaseService: SubmissionDatabaseService,
+    private val backendConfig: BackendConfig,
+) {
     @Transactional(readOnly = true)
     fun getReleasedData(organism: Organism): Sequence<ProcessedData<GeneticSequence>> {
         log.info { "fetching released submissions" }
@@ -45,7 +49,7 @@ class ReleasedDataModel(private val submissionDatabaseService: SubmissionDatabas
 
         val currentDataUseTermsType = computeDataUseTerm(rawProcessedData)
 
-        val metadata = rawProcessedData.processedData.metadata +
+        var metadata = rawProcessedData.processedData.metadata +
             ("accession" to TextNode(rawProcessedData.accession)) +
             ("version" to LongNode(rawProcessedData.version)) +
             (HEADER_TO_CONNECT_METADATA_AND_SEQUENCES to TextNode(rawProcessedData.submissionId)) +
@@ -58,6 +62,15 @@ class ReleasedDataModel(private val submissionDatabaseService: SubmissionDatabas
             ("versionStatus" to TextNode(siloVersionStatus.name)) +
             ("dataUseTerms" to TextNode(currentDataUseTermsType.name))
 
+        if (backendConfig.dataUseTermsUrls != null) {
+            val url = if (rawProcessedData.dataUseTerms == DataUseTerms.Open) {
+                backendConfig.dataUseTermsUrls.open
+            } else {
+                backendConfig.dataUseTermsUrls.restricted
+            }
+            metadata += ("dataUseTermsUrl" to TextNode(url))
+        }
+
         return ProcessedData(
             metadata = metadata,
             unalignedNucleotideSequences = rawProcessedData.processedData.unalignedNucleotideSequences,
diff --git a/backend/src/test/kotlin/org/loculus/backend/service/GenerateAccessionFromNumberServiceTest.kt b/backend/src/test/kotlin/org/loculus/backend/service/GenerateAccessionFromNumberServiceTest.kt
index 865895ea5b..ad3b53fa80 100644
--- a/backend/src/test/kotlin/org/loculus/backend/service/GenerateAccessionFromNumberServiceTest.kt
+++ b/backend/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, organisms = emptyMap()),
+        BackendConfig(accessionPrefix = PREFIX, organisms = emptyMap(), dataUseTermsUrls = null),
     )
 
     @Test
diff --git a/backend/src/test/kotlin/org/loculus/backend/service/submission/EmptyProcessedDataProviderTest.kt b/backend/src/test/kotlin/org/loculus/backend/service/submission/EmptyProcessedDataProviderTest.kt
index f462af8dba..96a0dea239 100644
--- a/backend/src/test/kotlin/org/loculus/backend/service/submission/EmptyProcessedDataProviderTest.kt
+++ b/backend/src/test/kotlin/org/loculus/backend/service/submission/EmptyProcessedDataProviderTest.kt
@@ -46,6 +46,7 @@ class EmptyProcessedDataProviderTest {
                     ),
                 ),
             ),
+            dataUseTermsUrls = null,
         ),
     )
 
diff --git a/kubernetes/loculus/templates/_common-metadata.tpl b/kubernetes/loculus/templates/_common-metadata.tpl
index b47367a29e..bd51d8ec95 100644
--- a/kubernetes/loculus/templates/_common-metadata.tpl
+++ b/kubernetes/loculus/templates/_common-metadata.tpl
@@ -32,6 +32,11 @@ fields:
   - name: versionStatus
     type: string
     notSearchable: true
+  {{- if $.Values.dataUseTermsUrls }}
+  - name: dataUseTermsUrl
+    type: string
+    notSearchable: true
+  {{- end}}
 {{- end}}
 
 {{/* Generate website config from passed config object */}}
@@ -97,6 +102,8 @@ fields:
 {{- define "loculus.generateBackendConfig" }}
 accessionPrefix: {{$.Values.accessionPrefix}}
 name: {{ $.Values.name }}
+dataUseTermsUrls:
+  {{$.Values.dataUseTermsUrls | toYaml | nindent 2}}
 organisms:
   {{- range $key, $instance := (.Values.organisms | default .Values.defaultOrganisms) }}
   {{ $key }}:
diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
index 1eda8cb649..6a57f61e0f 100644
--- a/kubernetes/loculus/values.yaml
+++ b/kubernetes/loculus/values.yaml
@@ -15,6 +15,9 @@ disablePreprocessing: false
 disableIngest: false
 siloImportLimitSeconds: 3600
 accessionPrefix: "LOC_"
+dataUseTermsUrls:
+  open: https://#TODO-MVP/open
+  restricted: https://#TODO-MVP/restricted
 name: "Loculus"
 logo:
   url: "/favicon.svg"