Merge pull request #1508 from phac-nml/update-springdoc-openapi-gradl…

…e-plugin

Update springdoc openapi gradle plugin

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "gradle"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/ci-test.yml

@@ -99,7 +99,7 @@ jobs:
       MYSQL_HOST: 127.0.0.1
 
     steps:
-      - uses: actions/checkout@v3 #Checkout the project from git
+      - uses: actions/checkout@v4 #Checkout the project from git
       - name: Get pnpm store directory
         id: pnpm-cache
         run: |
@@ -123,8 +123,6 @@ jobs:
           mysql password: ${{ env.MYSQL_PASSWORD }}
       - name: Setup Ruby
         uses: actions/setup-ruby@v1
-        with:
-          ruby-version: "2.7"
       - name: Set up JDK 11 # Installs java 11
         uses: actions/setup-java@v1
         with:
@@ -139,4 +137,4 @@ jobs:
             sleep 1
           done
       - name: Build Documentation Site
-        run: ./gradlew clean buildDocsSite -Dliquibase.update.database.schema=true -Dspring.datasource.url=jdbc:mysql://${{env.MYSQL_HOST}}:${{env.MYSQL_PORT}}/${{env.MYSQL_DATABASE}} -Dspring.datasource.dbcp2.max-wait=10000
+        run: ./gradlew clean buildDocsSite -Dliquibase.update.database.schema=true -Dspring.datasource.url=jdbc:mysql://${{env.MYSQL_HOST}}:${{env.MYSQL_PORT}}/${{env.MYSQL_DATABASE}} -Dspring.datasource.dbcp2.max-wait=10000

build.gradle.kts

@@ -205,7 +205,7 @@ dependencies {
     implementation(files("${projectDir}/lib/blend4j-0.2.1-2201df9.jar"))
 
     // Runtime dependencies
-    runtimeOnly("mysql:mysql-connector-java")
+    runtimeOnly("com.mysql:mysql-connector-j")
     providedRuntime("org.springframework.boot:spring-boot-starter-tomcat")
 
     // Testing dependencies
@@ -435,8 +435,14 @@ task<JavaExec>("toolsListExport") {
     args("${buildDir}/tools-list.yml")
 }
 
-tasks.named<BootRun>("bootRun") {
-    if (project.gradle.taskGraph.hasTask(":generateOpenApiDocs")) {
+task<Exec>("generateJWKKeyStore") {
+    workingDir(file("${projectDir}/src/main/resources"))
+    commandLine(listOf("keytool", "-genkeypair", "-alias", "JWK", "-keyalg", "RSA", "-noprompt", "-dname", "CN=irida.bioinformatics.corefacility.ca, OU=ID, O=IRIDA, L=IRIDA, S=IRIDA, C=CA", "-keystore", "jwk-key-store.jks", "-validity", "3650", "-storepass", "SECRET", "-keypass", "SECRET", "-storetype", "PKCS12"))
+    outputs.file(file("${projectDir}/src/main/resources/jwk-key-store.jks"))
+}
+
+openApi {
+    customBootRun {
         val defaultSystemProperties = mapOf(
             "spring.profiles.active" to "dev,swagger",
             "liquibase.update.database.schema" to "false",
@@ -445,17 +451,8 @@ tasks.named<BootRun>("bootRun") {
         )
         val providedSystemProperties = System.getProperties().mapKeys { it.key as String }
         val filteredProvidedSystemProperties = providedSystemProperties.filterKeys { it in defaultSystemProperties}
-        systemProperties(defaultSystemProperties + filteredProvidedSystemProperties)
+        systemProperties.set(defaultSystemProperties + filteredProvidedSystemProperties)
     }
-}
-
-task<Exec>("generateJWKKeyStore") {
-    workingDir(file("${projectDir}/src/main/resources"))
-    commandLine(listOf("keytool", "-genkeypair", "-alias", "JWK", "-keyalg", "RSA", "-noprompt", "-dname", "CN=irida.bioinformatics.corefacility.ca, OU=ID, O=IRIDA, L=IRIDA, S=IRIDA, C=CA", "-keystore", "jwk-key-store.jks", "-validity", "3650", "-storepass", "SECRET", "-keypass", "SECRET", "-storetype", "PKCS12"))
-    outputs.file(file("${projectDir}/src/main/resources/jwk-key-store.jks"))
-}
-
-openApi {
     outputDir.set(file("${projectDir}/doc/swagger-ui"))
     outputFileName.set("open-api.json")
     waitTimeInSeconds.set(60)

settings.gradle.kts

@@ -8,7 +8,7 @@ pluginManagement {
         id("io.spring.dependency-management") version "1.0.11.RELEASE"
         id("org.gradle.test-retry") version "1.4.0"
         id("org.springframework.boot") version "2.7.6"
-        id("org.springdoc.openapi-gradle-plugin") version "1.3.4"
+        id("org.springdoc.openapi-gradle-plugin") version "1.9.0"
     }
 }