Pivotal ID # 181937926: Avoid restarting ITests containers

client/bio-commandline/src/test/kotlin/uk/ac/ebi/biostd/client/cli/services/SubmissionServiceTest.kt

@@ -21,8 +21,6 @@ import org.junit.jupiter.api.AfterEach
 import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.extension.ExtendWith
-import org.junit.jupiter.params.ParameterizedTest
-import org.junit.jupiter.params.provider.EnumSource
 import uk.ac.ebi.biostd.client.cli.dto.DeletionRequest
 import uk.ac.ebi.biostd.client.cli.dto.SubmissionRequest
 import uk.ac.ebi.biostd.client.cli.dto.ValidateFileListRequest
@@ -37,9 +35,8 @@ internal class SubmissionServiceTest {
     @BeforeEach
     fun beforeEach() = mockkObject(SecurityWebClient)
 
-    @ParameterizedTest
-    @EnumSource(FileMode::class)
-    fun submit(fileMode: FileMode) {
+    @Test
+    fun submit() {
         val slot = slot<FileMode>()
         every { create(SERVER).getAuthenticatedClient(USER, PASSWORD, ON_BEHALF) } returns bioWebClient
         every {
@@ -55,8 +52,7 @@ internal class SubmissionServiceTest {
         }
     }
 
-    @ParameterizedTest
-    @EnumSource(FileMode::class)
+    @Test
     fun `submit async`() {
         val slot = slot<FileMode>()
         every { create(SERVER).getAuthenticatedClient(USER, PASSWORD, ON_BEHALF) } returns bioWebClient

client/bio-webclient/src/main/kotlin/ac/uk/ebi/biostd/client/api/SubmissionClient.kt

@@ -72,7 +72,6 @@ internal class SubmissionClient(
         template.postForEntity<Void>("$SUBMISSIONS_URL/fileLists/validate", HttpEntity(body, headers))
     }
 
-
     private fun submitSingle(request: HttpEntity<String>, register: RegisterConfig): SubmissionResponse {
         return template
             .postForEntity<String>(buildUrl(register), request)

commons/commons-util/src/main/kotlin/ebi/ac/uk/io/ext/FileExtensions.kt

@@ -1,8 +1,11 @@
+@file:Suppress("TooManyFunctions")
+
 package ebi.ac.uk.io.ext
 
 import ebi.ac.uk.io.FileUtils
 import java.io.File
 import java.io.FileOutputStream
+import java.nio.charset.Charset
 import java.nio.file.Files
 import java.util.zip.GZIPOutputStream
 
@@ -39,3 +42,28 @@ fun File.resolveMany(vararg keys: String): File {
 fun File.gZipTo(target: File) {
     FileOutputStream(target).use { GZIPOutputStream(it).bufferedWriter().use { writer -> writer.write(readText()) } }
 }
+
+/**
+ * Creates a file with the given content in the temporary folder.
+ */
+fun File.createFile(fileName: String, content: String, charset: Charset = Charsets.UTF_8): File {
+    val file = createNewFile(fileName)
+    file.writeText(content, charset)
+    return file
+}
+
+/**
+ * Creates a file with the given content in the temporary folder.
+ */
+fun File.createFile(fileName: String): File {
+    return createNewFile(fileName)
+}
+
+/**
+ * Creates a file with the given name or replaces it if already exist.
+ */
+fun File.createOrReplaceFile(fileName: String): File {
+    val file = resolve(fileName)
+    if (file.exists()) file.delete()
+    return createNewFile(fileName)
+}

gradle.properties

@@ -1,2 +1,2 @@
 org.gradle.parallel=false
-org.gradle.jvmargs=-Xmx2g
+org.gradle.jvmargs=-Xmx4g

submission/persistence-sql/src/main/kotlin/ac/uk/ebi/biostd/persistence/repositories/Repositories.kt

@@ -61,6 +61,7 @@ interface UserGroupDataRepository : JpaRepository<DbUserGroup, Long> {
 }
 
 interface AccessPermissionRepository : JpaRepository<DbAccessPermission, Long> {
+    fun findAllByUserEmail(email: String): List<DbAccessPermission>
     fun findAllByUserEmailAndAccessType(email: String, accessType: AccessType): List<DbAccessPermission>
     fun existsByUserEmailAndAccessTypeAndAccessTagName(user: String, type: AccessType, accessTag: String): Boolean
 }

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/assertions/AllInOneSubmissionHelper.kt

@@ -7,11 +7,11 @@ import ac.uk.ebi.biostd.itest.factory.assertAllInOneSubmissionXml
 import ac.uk.ebi.biostd.persistence.common.service.SubmissionQueryService
 import arrow.core.Either
 import ebi.ac.uk.extended.mapping.to.ToSubmissionMapper
-import ebi.ac.uk.extended.model.FireFile
-import ebi.ac.uk.extended.model.NfsFile
 import ebi.ac.uk.extended.model.ExtProcessingStatus
 import ebi.ac.uk.extended.model.ExtSubmission
 import ebi.ac.uk.extended.model.ExtSubmissionMethod
+import ebi.ac.uk.extended.model.FireFile
+import ebi.ac.uk.extended.model.NfsFile
 import ebi.ac.uk.extended.model.createNfsFile
 import ebi.ac.uk.io.ext.md5
 import ebi.ac.uk.io.ext.size
@@ -22,7 +22,7 @@ import java.io.File
 import java.nio.file.Paths
 
 internal class AllInOneSubmissionHelper(
-    private val submissionPath: String,
+    private val submissionPath: File,
     private val submissionRepository: SubmissionQueryService,
     private val toSubmissionMapper: ToSubmissionMapper
 ) {
@@ -40,7 +40,7 @@ internal class AllInOneSubmissionHelper(
     }
 
     private fun assertSubmissionFiles(submission: ExtSubmission) {
-        val submissionFolderPath = "$submissionPath/${submission.relPath}"
+        val submissionFolderPath = submissionPath.resolve(submission.relPath)
         val accNo = submission.accNo
 
         assertAllInOneSubmissionXml(getSubFileContent("$submissionFolderPath/$accNo.xml"), accNo)

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/common/BaseIntegrationTest.kt

@@ -24,10 +24,10 @@ import uk.ac.ebi.fire.client.api.FIRE_OBJECTS_URL
 import java.nio.file.Paths
 import java.time.Duration.ofSeconds
 
-private const val CHARACTER_SET = "utf8mb4"
-private const val COLLATION = "utf8mb4_unicode_ci"
-private const val FIRE_USERNAME = "fireUsername"
-private const val FIRE_PASSWORD = "firePassword"
+const val CHARACTER_SET = "utf8mb4"
+const val COLLATION = "utf8mb4_unicode_ci"
+const val FIRE_USERNAME = "fireUsername"
+const val FIRE_PASSWORD = "firePassword"
 
 internal open class BaseIntegrationTest(private val tempFolder: TemporaryFolder) {
     private val mongoContainer: MongoDBContainer = MongoDBContainer(DockerImageName.parse(MONGO_VERSION))
@@ -126,4 +126,4 @@ internal open class BaseIntegrationTest(private val tempFolder: TemporaryFolder)
     }
 }
 
-internal class SpecificMySQLContainer(image: String) : MySQLContainer<SpecificMySQLContainer>(image)
+class SpecificMySQLContainer(image: String) : MySQLContainer<SpecificMySQLContainer>(image)

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/common/SecurityTestService.kt

@@ -15,7 +15,7 @@ class SecurityTestService(
     private val groupService: IGroupService
 ) {
 
-    fun registerUser(testUser: TestUser): SecurityUser {
+    private fun registerUser(testUser: TestUser): SecurityUser {
         val user = securityService.registerUser(testUser.asRegisterRequest())
         if (testUser.superUser) {
             val dbUser = userDataRepository.getByEmail(user.email)
@@ -26,6 +26,10 @@ class SecurityTestService(
         return user
     }
 
+    fun ensureRegisterUser(testUser: TestUser) {
+        if (userDataRepository.existsByEmail(testUser.email).not()) registerUser(testUser)
+    }
+
     fun createTestGroup(): DbUserGroup {
         return groupService.createGroup(TestGroup.testGroupName, TestGroup.testGroupDescription)
     }

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/entities/SuperUser.kt

@@ -1,7 +1,5 @@
 package ac.uk.ebi.biostd.itest.entities
 
-import ebi.ac.uk.api.security.RegisterRequest
-
 /**
  * Represents a bio studies super user.
  */
@@ -10,6 +8,4 @@ object SuperUser : TestUser {
     override val email = "biostudies-mgmt@ebi.ac.uk"
     override val password = "12345"
     override val superUser = true
-
-    override fun asRegisterRequest() = RegisterRequest(username, email, password)
 }

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/entities/TestUser.kt

@@ -8,5 +8,5 @@ interface TestUser {
     val password: String
     val superUser: Boolean
 
-    fun asRegisterRequest(): RegisterRequest
+    fun asRegisterRequest(): RegisterRequest = RegisterRequest(username, email, password)
 }

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/factory/AllInOne.kt

@@ -1,8 +1,7 @@
 package ac.uk.ebi.biostd.itest.factory
 
 import ebi.ac.uk.base.EMPTY
-import ebi.ac.uk.test.createOrReplaceFile
-import io.github.glytching.junit.extension.folder.TemporaryFolder
+import ebi.ac.uk.io.ext.createOrReplaceFile
 import java.io.File
 
 data class SubmissionSpec(
@@ -14,7 +13,7 @@ data class SubmissionSpec(
 
 data class SubmissionFile(val file: File, val folder: String = EMPTY)
 
-fun submissionsFiles(tempFolder: TemporaryFolder): List<SubmissionFile> = listOf(
+fun submissionsFiles(tempFolder: File): List<SubmissionFile> = listOf(
     SubmissionFile(tempFolder.createOrReplaceFile("DataFile1.txt")),
     SubmissionFile(tempFolder.createOrReplaceFile("DataFile2.txt")),
     SubmissionFile(tempFolder.createOrReplaceFile("DataFile3.txt"), "Folder1"),

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/factory/AllInOneSubmissionJson.kt

@@ -2,10 +2,10 @@ package ac.uk.ebi.biostd.itest.factory
 
 import ebi.ac.uk.dsl.json.jsonArray
 import ebi.ac.uk.dsl.json.jsonObj
-import ebi.ac.uk.test.createFile
-import io.github.glytching.junit.extension.folder.TemporaryFolder
+import ebi.ac.uk.io.ext.createFile
+import java.io.File
 
-fun submissionSpecJson(tempFolder: TemporaryFolder, accNo: String): SubmissionSpec = SubmissionSpec(
+fun submissionSpecJson(tempFolder: File, accNo: String): SubmissionSpec = SubmissionSpec(
     submission = tempFolder.createFile("submission.json", allInOneSubmissionJson(accNo).toString()),
     fileList = tempFolder.createFile("file-list.json", fileList().toString()),
     files = submissionsFiles(tempFolder),

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/factory/AllInOneSubmissionTsv.kt

@@ -2,10 +2,10 @@ package ac.uk.ebi.biostd.itest.factory
 
 import ebi.ac.uk.dsl.tsv.line
 import ebi.ac.uk.dsl.tsv.tsv
-import ebi.ac.uk.test.createFile
-import io.github.glytching.junit.extension.folder.TemporaryFolder
+import ebi.ac.uk.io.ext.createFile
+import java.io.File
 
-fun submissionSpecTsv(tempFolder: TemporaryFolder, accNo: String): SubmissionSpec = SubmissionSpec(
+fun submissionSpecTsv(tempFolder: File, accNo: String): SubmissionSpec = SubmissionSpec(
     submission = tempFolder.createFile("submission.tsv", allInOneSubmissionTsv(accNo).toString()),
     fileList = tempFolder.createFile("file-list.tsv", fileList().toString()),
     files = submissionsFiles(tempFolder),

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/factory/AllInOneSubmissionXml.kt

@@ -1,10 +1,10 @@
 package ac.uk.ebi.biostd.itest.factory
 
-import ebi.ac.uk.test.createFile
-import io.github.glytching.junit.extension.folder.TemporaryFolder
+import ebi.ac.uk.io.ext.createFile
 import org.redundent.kotlin.xml.xml
+import java.io.File
 
-fun submissionSpecXml(tempFolder: TemporaryFolder, accNo: String): SubmissionSpec = SubmissionSpec(
+fun submissionSpecXml(tempFolder: File, accNo: String): SubmissionSpec = SubmissionSpec(
     submission = tempFolder.createFile("submission.xml", allInOneSubmissionXml(accNo).toString()),
     fileList = tempFolder.createFile("file-list.xml", fileList().toString()),
     files = submissionsFiles(tempFolder),

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/itest/ITestListener.kt

@@ -0,0 +1,119 @@
+package ac.uk.ebi.biostd.itest.itest
+
+import ac.uk.ebi.biostd.itest.common.CHARACTER_SET
+import ac.uk.ebi.biostd.itest.common.COLLATION
+import ac.uk.ebi.biostd.itest.common.FIRE_PASSWORD
+import ac.uk.ebi.biostd.itest.common.FIRE_USERNAME
+import ac.uk.ebi.biostd.itest.common.SpecificMySQLContainer
+import ac.uk.ebi.biostd.itest.wiremock.TestWireMockTransformer
+import ac.uk.ebi.biostd.itest.wiremock.TestWireMockTransformer.Companion.newTransformer
+import com.github.tomakehurst.wiremock.WireMockServer
+import com.github.tomakehurst.wiremock.client.WireMock
+import com.github.tomakehurst.wiremock.client.WireMock.post
+import com.github.tomakehurst.wiremock.core.WireMockConfiguration
+import ebi.ac.uk.db.MINIMUM_RUNNING_TIME
+import ebi.ac.uk.db.MONGO_VERSION
+import ebi.ac.uk.db.MYSQL_VERSION
+import org.junit.platform.launcher.TestExecutionListener
+import org.junit.platform.launcher.TestPlan
+import org.testcontainers.containers.MongoDBContainer
+import org.testcontainers.containers.startupcheck.MinimumDurationRunningStartupCheckStrategy
+import org.testcontainers.utility.DockerImageName.parse
+import uk.ac.ebi.fire.client.api.FIRE_OBJECTS_URL
+import java.io.File
+import java.nio.file.Files
+import java.time.Duration.ofSeconds
+
+class ITestListener : TestExecutionListener {
+
+    override fun testPlanExecutionStarted(testPlan: TestPlan) {
+        mongoSetup()
+        mySqlSetup()
+        fireSetup()
+        appPropertiesSetup()
+    }
+
+    override fun testPlanExecutionFinished(testPlan: TestPlan) {
+        mongoContainer.stop()
+        mysqlContainer.stop()
+        fireApiMock.stop()
+    }
+
+    private fun mongoSetup() {
+        mongoContainer.start()
+        System.setProperty("spring.data.mongodb.uri", mongoContainer.getReplicaSetUrl("biostudies-test"))
+        System.setProperty("spring.data.mongodb.database", "biostudies-test")
+    }
+
+    private fun mySqlSetup() {
+        mysqlContainer.start()
+        System.setProperty("spring.datasource.url", mysqlContainer.jdbcUrl)
+        System.setProperty("spring.datasource.username", mysqlContainer.username)
+        System.setProperty("spring.datasource.password", mysqlContainer.password)
+    }
+
+    private fun fireSetup() {
+        fireApiMock.stubFor(
+            post(WireMock.urlMatching(FIRE_OBJECTS_URL))
+                .withBasicAuth(FIRE_USERNAME, FIRE_PASSWORD)
+                .willReturn(WireMock.aResponse().withTransformers(TestWireMockTransformer.name))
+        )
+        fireApiMock.start()
+
+        System.setProperty("app.fire.host", fireApiMock.baseUrl())
+        System.setProperty("app.fire.username", FIRE_USERNAME)
+        System.setProperty("app.fire.password", FIRE_PASSWORD)
+    }
+
+    private fun appPropertiesSetup() {
+        System.setProperty("app.submissionPath", submissionPath.absolutePath)
+        System.setProperty("app.ftpPath", ftpPath.absolutePath)
+        System.setProperty("app.fireTempDirPath", fireTempFolder.absolutePath)
+        System.setProperty("app.tempDirPath", tempDirPath.absolutePath)
+        System.setProperty("app.requestFilesPath", requestFilesPath.absolutePath)
+        System.setProperty("app.security.filesDirPath", dropboxPath.absolutePath)
+        System.setProperty("app.security.magicDirPath", magicDirPath.absolutePath)
+        System.setProperty("app.persistence.enableFire", "${System.getProperty("enableFire").toBoolean()}")
+    }
+
+    companion object {
+        private val testAppFolder = Files.createTempDirectory("test-app-folder").toFile()
+
+        internal val submissionPath = testAppFolder.createDirectory("submission")
+        internal val firePath = testAppFolder.createDirectory("fire-db")
+        internal val fireTempFolder = testAppFolder.createDirectory("fire-temp")
+        internal val ftpPath = testAppFolder.createDirectory("ftpPath")
+        internal val tempDirPath = testAppFolder.createDirectory("tempDirPath")
+        internal val tempFolder = testAppFolder.createDirectory("testTempDir")
+        internal val requestFilesPath = testAppFolder.createDirectory("requestFilesPath")
+        internal val magicDirPath = testAppFolder.createDirectory("magic")
+        internal val dropboxPath = testAppFolder.createDirectory("dropbox")
+
+        private val mongoContainer = createMongoContainer(MONGO_VERSION)
+        private val mysqlContainer = createMysqlContainer(MYSQL_VERSION, "Schema.sql")
+        private val fireApiMock = createFireApiMock(submissionPath, ftpPath, firePath)
+
+        val enableFire get() = System.getProperty("enableFire").toBoolean()
+
+        private fun createMongoContainer(version: String): MongoDBContainer =
+            MongoDBContainer(parse(version))
+                .withStartupCheckStrategy(MinimumDurationRunningStartupCheckStrategy(ofSeconds(MINIMUM_RUNNING_TIME)))
+
+        private fun createMysqlContainer(version: String, schema: String): SpecificMySQLContainer =
+            SpecificMySQLContainer(version)
+                .withCommand("mysqld --character-set-server=$CHARACTER_SET --collation-server=$COLLATION")
+                .withInitScript(schema)
+                .withStartupCheckStrategy(MinimumDurationRunningStartupCheckStrategy(ofSeconds(MINIMUM_RUNNING_TIME)))
+
+        private fun createFireApiMock(submissionDir: File, ftpDir: File, fireDir: File): WireMockServer {
+            val wireMockTransformer = newTransformer(submissionDir.toPath(), ftpDir.toPath(), fireDir.toPath())
+            return WireMockServer(WireMockConfiguration().dynamicPort().extensions(wireMockTransformer))
+        }
+
+        private fun File.createDirectory(path: String): File {
+            val file = resolve(path)
+            file.mkdir()
+            return file
+        }
+    }
+}

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/itest/TestFunctions.kt

@@ -0,0 +1,10 @@
+package ac.uk.ebi.biostd.itest.itest
+
+import ac.uk.ebi.biostd.client.integration.web.BioWebClient
+import ac.uk.ebi.biostd.client.integration.web.SecurityWebClient
+import ac.uk.ebi.biostd.itest.entities.TestUser
+
+fun getWebClient(serverPort: Int, user: TestUser): BioWebClient {
+    val securityClient = SecurityWebClient.create("http://localhost:$serverPort")
+    return securityClient.getAuthenticatedClient(user.email, user.password)
+}