fix(backend, deployment): fix seqsets so they can be configured to wo…

…rk in production (#2476) * towards production seqsets * adapt kotlin code * Update backend/src/main/kotlin/org/loculus/backend/service/crossref/CrossRefService.kt Co-authored-by: Chaoran Chen <mail@chaoran-chen.de> * update * add quote --------- Co-authored-by: Chaoran Chen <mail@chaoran-chen.de>
loculus-project · Aug 21, 2024 · dadd17b · dadd17b
1 parent 0ad25fe
commit dadd17b
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Showing 7 changed files with 25 additions and 19 deletions.
diff --git a/.github/workflows/backend-tests.yml b/.github/workflows/backend-tests.yml
@@ -17,8 +17,8 @@ jobs:
     timeout-minutes: 15
     env:
       CROSSREF_USERNAME: ${{ secrets.CROSSREF_USERNAME }}
-      CROSSREF_TEST_PASSWORD: ${{ secrets.CROSSREF_TEST_PASSWORD }}
-      CROSSREF_TEST_ENDPOINT: ${{ secrets.CROSSREF_TEST_ENDPOINT }}
+      CROSSREF_PASSWORD: ${{ secrets.CROSSREF_PASSWORD }}
+      CROSSREF_ENDPOINT: ${{ secrets.CROSSREF_ENDPOINT }}
       CROSSREF_DOI_PREFIX: ${{ secrets.CROSSREF_DOI_PREFIX }}
     steps:
       - name: Login to Docker Hub

diff --git a/backend/src/main/kotlin/org/loculus/backend/api/SeqSetCitations.kt b/backend/src/main/kotlin/org/loculus/backend/api/SeqSetCitations.kt
@@ -83,6 +83,5 @@ data class AuthorProfile(
 )
 
 object SeqSetCitationsConstants {
-    const val DOI_PREFIX = "placeholder"
     const val DOI_WEEKLY_RATE_LIMIT = 7
 }
diff --git a/backend/src/main/kotlin/org/loculus/backend/service/crossref/CrossRefService.kt b/backend/src/main/kotlin/org/loculus/backend/service/crossref/CrossRefService.kt
@@ -20,13 +20,19 @@ import java.util.UUID
 private val log = KotlinLogging.logger { }
 
 @ConfigurationProperties(prefix = "crossref")
-data class CrossRefServiceProperties(val endpoint: String?, val username: String?, val password: String?)
+data class CrossRefServiceProperties(
+    val endpoint: String?,
+    val username: String?,
+    val password: String?,
+    val doiPrefix: String?,
+)
 
 @Service
 class CrossRefService(private val crossRefServiceProperties: CrossRefServiceProperties) {
     val isActive = crossRefServiceProperties.endpoint != null &&
         crossRefServiceProperties.username != null &&
-        crossRefServiceProperties.password != null
+        crossRefServiceProperties.password != null &&
+        crossRefServiceProperties.doiPrefix != null
     val dateTimeFormatterMM = DateTimeFormatter.ofPattern("MM")
     val dateTimeFormatterdd = DateTimeFormatter.ofPattern("dd")
     val dateTimeFormatteryyyy = DateTimeFormatter.ofPattern("yyyy")

diff --git a/...main/kotlin/org/loculus/backend/service/seqsetcitations/SeqSetCitationsDatabaseService.kt b/...main/kotlin/org/loculus/backend/service/seqsetcitations/SeqSetCitationsDatabaseService.kt
@@ -32,6 +32,7 @@ import org.loculus.backend.auth.AuthenticatedUser
 import org.loculus.backend.config.BackendConfig
 import org.loculus.backend.controller.NotFoundException
 import org.loculus.backend.controller.UnprocessableEntityException
+import org.loculus.backend.service.crossref.CrossRefServiceProperties
 import org.loculus.backend.service.submission.AccessionPreconditionValidator
 import org.loculus.backend.utils.getNextSequenceNumber
 import org.springframework.stereotype.Service
@@ -47,6 +48,7 @@ private val log = KotlinLogging.logger { }
 class SeqSetCitationsDatabaseService(
     private val accessionPreconditionValidator: AccessionPreconditionValidator,
     private val backendConfig: BackendConfig,
+    private val crossRefServiceProperties: CrossRefServiceProperties,
     pool: DataSource,
 ) {
     init {
@@ -333,7 +335,8 @@ class SeqSetCitationsDatabaseService(
 
         validateCreateSeqSetDOI(username, seqSetId, version)
 
-        val seqSetDOI = "${SeqSetCitationsConstants.DOI_PREFIX}/$seqSetId.$version"
+        val doiPrefix = crossRefServiceProperties.doiPrefix ?: "no-prefix-configured"
+        val seqSetDOI = "$doiPrefix/$seqSetId.$version"
 
         SeqSetsTable.update(
             {

diff --git a/backend/src/test/resources/application.properties b/backend/src/test/resources/application.properties
@@ -4,6 +4,7 @@ loculus.config.path=src/test/resources/backend_config.json
 crossref.endpoint=dummy
 crossref.username=dummy
 crossref.password=dummy
+crossref.doi-prefix=placeholder
 
 keycloak.user=dummy
 keycloak.password=dummy

diff --git a/kubernetes/loculus/templates/loculus-backend.yaml b/kubernetes/loculus/templates/loculus-backend.yaml
@@ -46,9 +46,9 @@ spec:
             - containerPort: 8079
           args:
             - "--crossref.doi-prefix=$(CROSSREF_DOI_PREFIX)"
-            - "--crossref.endpoint=$(CROSSREF_TEST_ENDPOINT)"
+            - "--crossref.endpoint=$(CROSSREF_ENDPOINT)"
             - "--crossref.username=$(CROSSREF_USERNAME)"
-            - "--crossref.password=$(CROSSREF_TEST_PASSWORD)"
+            - "--crossref.password=$(CROSSREF_PASSWORD)"
             - "--keycloak.password=$(BACKEND_KEYCLOAK_PASSWORD)"
             - "--keycloak.realm=loculus"
             - "--keycloak.client=backend-client"
@@ -71,16 +71,15 @@ spec:
                secretKeyRef:
                  name: crossref
                  key: username
-            - name: CROSSREF_TEST_PASSWORD
+            - name: CROSSREF_PASSWORD
               valueFrom:
                secretKeyRef:
                  name: crossref
-                 key: testPassword
-            - name: CROSSREF_LIVE_PASSWORD
-              valueFrom:
-               secretKeyRef:
-                 name: crossref
-                 key: livePassword
+                 key: password
+            - name: CROSSREF_DOI_PREFIX
+              value: {{$.Values.crossRef.DOIPrefix | quote }}
+            - name: CROSSREF_ENDPOINT
+              value: {{$.Values.crossRef.endpoint | quote  }}
            {{- end }}
             - name: BACKEND_KEYCLOAK_PASSWORD
               valueFrom:

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -1,8 +1,7 @@
 environment: server
 crossRef:
   DOIPrefix: "10.62599"
-  testEndpoint: "https://test.crossref.org"
-  liveEndpoint: "https://doi.crossref.org"
+  endpoint: "https://test.crossref.org"
 disableWebsite: false
 disableBackend: false
 disablePreprocessing: false
@@ -1482,8 +1481,7 @@ secrets:
     type: raw
     data:
       username: "dummy"
-      testPassword: "dummy"
-      livePassword: "dummy"
+      password: "dummy"
   service-accounts:
     type: autogen
     data: