Merge pull request #1092 from GenSpectrum/main

chore: update prod from main

Author: fengelniederhammer

.github/workflows/backend.yml

@@ -22,7 +22,7 @@ jobs:
           distribution: 'adopt'
 
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v5
+        uses: gradle/actions/setup-gradle@v6
 
       - name: Execute Tests
         run: ./gradlew test

.github/workflows/e2e.yml

@@ -37,14 +37,14 @@ jobs:
       run: echo "branchTag=${TAG##*:}" >> $GITHUB_OUTPUT
 
     - name: Wait for website Docker image
-      uses: lewagon/wait-on-check-action@v1.5.0
+      uses: lewagon/wait-on-check-action@v1.6.0
       with:
         ref: ${{ github.sha }}
         check-name: Build Website Docker Image
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         wait-interval: 10
     - name: Wait for backend Docker image
-      uses: lewagon/wait-on-check-action@v1.5.0
+      uses: lewagon/wait-on-check-action@v1.6.0
       with:
         ref: ${{ github.sha }}
         check-name: Build Backend Docker Image
@@ -65,7 +65,7 @@ jobs:
       if: github.ref != 'refs/heads/main'
       run: npm run e2e:chromium
 
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ !cancelled() }}
       with:
         name: playwright-report

backend/README.md

@@ -12,14 +12,40 @@ You have to provide config information to the backend:
 * Dashboards configuration, e.g. the LAPIS instances of the organisms.
   We have profiles available that only need to be activated via `spring.profiles.active`.
 * Database connection configuration: values need to be passed via [external properties](https://docs.spring.io/spring-boot/reference/features/external-config.html).
-  For local development, we have a `local-db` profile available. 
+  For local development, we have a `local-db` profile available.
   You can also check that for required properties.
 
+### Start local database
+
+Start the local PostgreSQL database using Docker Compose (from the repo root):
+
+```bash
+docker compose up -d database
+```
+
+Stop the database:
+
+```bash
+docker compose down database
+```
+
+Stop and remove data volumes:
+
+```bash
+docker compose down -v database
+```
+
+### Run the backend
+
 To run the backend locally, you can use the following command:
 ```bash
 ./gradlew bootRun --args='--spring.profiles.active=local-db,dashboards-prod'
 ```
 
+The backend will be available at:
+- Base URL: `http://localhost:8080`
+- Swagger UI: `http://localhost:8080/swagger-ui/index.html`
+
 Run tests:
 
 ```bash

backend/build.gradle.kts

@@ -39,8 +39,8 @@ dependencies {
         exclude(group = "org.mockito")
     }
     testImplementation("com.ninja-squad:springmockk:4.0.2")
-    testImplementation("org.testcontainers:testcontainers:2.0.3")
-    testImplementation("org.testcontainers:testcontainers-postgresql:2.0.3")
+    testImplementation("org.testcontainers:testcontainers:2.0.4")
+    testImplementation("org.testcontainers:testcontainers-postgresql:2.0.4")
     testImplementation("org.mock-server:mockserver-netty:5.15.0")
     testImplementation("org.mock-server:mockserver-spring-test-listener:5.15.0")
 

backend/gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-9.4.0-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.4.1-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

backend/gradlew

@@ -0,0 +1,81 @@
+package org.genspectrum.dashboardsbackend.api
+
+import io.swagger.v3.oas.annotations.media.Schema
+
+@Schema(
+    description = "A collection of variants",
+    example = """
+{
+    "id": 1,
+    "name": "My Collection",
+    "ownedBy": "user123",
+    "organism": "covid",
+    "description": "A collection of interesting variants",
+    "variants": []
+}
+""",
+)
+data class Collection(
+    val id: Long,
+    val name: String,
+    val ownedBy: String,
+    val organism: String,
+    val description: String?,
+    val variants: List<Variant>,
+)
+
+@Schema(
+    description = "Request to create a collection",
+    example = """
+{
+    "name": "My Collection",
+    "organism": "covid",
+    "description": "A collection of interesting variants",
+    "variants": [
+        {
+            "type": "query",
+            "name": "BA.2 in USA",
+            "description": "BA.2 lineage cases in USA",
+            "countQuery": "country='USA' & lineage='BA.2'",
+            "coverageQuery": "country='USA'"
+        }
+    ]
+}
+""",
+)
+data class CollectionRequest(
+    val name: String,
+    val organism: String,
+    val description: String? = null,
+    val variants: List<VariantRequest>,
+)
+
+@Schema(
+    description = "Request to update a collection",
+    example = """
+{
+    "name": "Updated Collection Name",
+    "description": "Updated description",
+    "variants": [
+        {
+            "type": "query",
+            "id": 1,
+            "name": "BA.2 in USA",
+            "description": "BA.2 lineage cases in USA",
+            "countQuery": "country='USA' & lineage='BA.2'",
+            "coverageQuery": "country='USA'"
+        },
+        {
+            "type": "query",
+            "name": "New Variant Without ID",
+            "countQuery": "country='Germany'"
+        }
+    ]
+}
+""",
+)
+data class CollectionUpdate(
+    val name: String? = null,
+    val description: String? = null,
+    val variants: List<VariantUpdate>? = null,
+)

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/api/Collection.kt

@@ -0,0 +1,47 @@
+package org.genspectrum.dashboardsbackend.api
+
+import com.fasterxml.jackson.annotation.JsonAnyGetter
+import com.fasterxml.jackson.annotation.JsonAnySetter
+import com.fasterxml.jackson.annotation.JsonInclude
+
+/**
+ * A JSON object with mutation lists (keys: aminoAcidMutations, nucleotideMutations, ...)
+ * as well as arbitrary extra properties (e.g. lineage filters) as top-level fields.
+ * In a validation step, the extra properties are validated to make sure only valid
+ * fields are used.
+ */
+@JsonInclude(JsonInclude.Include.NON_NULL)
+class FilterObject {
+    var aminoAcidMutations: List<String>? = null
+    var nucleotideMutations: List<String>? = null
+    var aminoAcidInsertions: List<String>? = null
+    var nucleotideInsertions: List<String>? = null
+
+    private val filters: MutableMap<String, String> = mutableMapOf()
+
+    @JsonAnyGetter
+    fun getFilters(): Map<String, String> = filters
+
+    @JsonAnySetter
+    fun set(key: String, value: String) {
+        filters[key] = value
+    }
+
+    override fun equals(other: Any?): Boolean {
+        if (this === other) return true
+        if (other !is FilterObject) return false
+        return aminoAcidMutations == other.aminoAcidMutations &&
+            nucleotideMutations == other.nucleotideMutations &&
+            aminoAcidInsertions == other.aminoAcidInsertions &&
+            nucleotideInsertions == other.nucleotideInsertions &&
+            filters == other.filters
+    }
+
+    override fun hashCode(): Int = arrayOf(
+        aminoAcidMutations,
+        nucleotideMutations,
+        aminoAcidInsertions,
+        nucleotideInsertions,
+        filters,
+    ).contentHashCode()
+}