pivotal-173792650: Replace base path for multiple absolute paths (#239)

* removed base path

client/bio-commandline/src/test/kotlin/ebi/ac/uk/paths/SubmissionFolderResolverTest.kt

@@ -1,31 +1,29 @@
 package ebi.ac.uk.paths
 
-import ebi.ac.uk.extended.model.ExtSubmission
-import io.mockk.every
-import io.mockk.impl.annotations.MockK
 import io.mockk.junit5.MockKExtension
 import org.assertj.core.api.Assertions.assertThat
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.extension.ExtendWith
 import java.nio.file.Paths
 
 @ExtendWith(MockKExtension::class)
-internal class SubmissionFolderResolverTest(@MockK val submission: ExtSubmission) {
-    private val testInstance = SubmissionFolderResolver(Paths.get("/tmp/nfs"))
+internal class SubmissionFolderResolverTest {
+    private val testInstance = SubmissionFolderResolver(
+        Paths.get("/tmp/nfs/submission"),
+        Paths.get("/tmp/nfs/submission/ftp")
+    )
 
     @Test
     fun getSubmissionFolder() {
         val submissionPath = "part1/part2"
-        every { submission.relPath } returns submissionPath
 
-        assertThat(testInstance.getSubmissionFolder(submission).toString())
+        assertThat(testInstance.getSubmissionFolder(submissionPath).toString())
             .isEqualTo("/tmp/nfs/submission/part1/part2")
     }
 
     @Test
     fun getSubFilePath() {
         val submissionPath = "part1/part2"
-        every { submission.relPath } returns submissionPath
 
         assertThat(testInstance.getSubFilePath(submissionPath, "/test-file.txt").toString())
             .isEqualTo("/tmp/nfs/submission/part1/part2/Files/test-file.txt")

commons/commons-bio/src/main/kotlin/ebi/ac/uk/paths/SubmissionFolderResolver.kt

@@ -1,25 +1,20 @@
 package ebi.ac.uk.paths
 
-import ebi.ac.uk.extended.model.ExtSubmission
 import java.nio.file.Path
 
 const val FILES_PATH = "Files"
-const val SUBMISSION_PATH = "submission"
-const val FTP_FOLDER = "submission/ftp"
 
-class SubmissionFolderResolver(private val basePath: Path) {
+class SubmissionFolderResolver(
+    private val submissionFolder: Path,
+    private val ftpFolder: Path
+) {
 
-    fun getSubmissionFtpFolder(submission: ExtSubmission): Path =
-        basePath.resolve(FTP_FOLDER).resolve(submission.relPath)
+    fun getSubmissionFtpFolder(submissionRelPath: String): Path = ftpFolder.resolve(submissionRelPath)
 
-    fun getSubmissionFolder(submission: ExtSubmission): Path =
-        basePath.resolve(SUBMISSION_PATH).resolve(submission.relPath)
-
-    fun getSubmissionFolder(submissionRelPath: String): Path =
-        basePath.resolve(SUBMISSION_PATH).resolve(submissionRelPath)
+    fun getSubmissionFolder(submissionRelPath: String): Path = submissionFolder.resolve(submissionRelPath)
 
     fun getSubFilePath(relPath: String, fileName: String): Path =
-        basePath.resolve(SUBMISSION_PATH).resolve(relPath).resolve(FILES_PATH).resolve(escapeFileName(fileName))
+        submissionFolder.resolve(relPath).resolve(FILES_PATH).resolve(escapeFileName(fileName))
 
     private fun escapeFileName(fileName: String) = fileName.removePrefix("/")
 }

commons/commons-bio/src/test/kotlin/ebi/ac/uk/model/paths/FolderResolverTest.kt

@@ -6,12 +6,21 @@ import org.junit.jupiter.api.Test
 import java.nio.file.Paths
 
 class FolderResolverTest {
-    private val testInstance = SubmissionFolderResolver(Paths.get("/nfs/biostudies"))
+    private val testInstance = SubmissionFolderResolver(
+        submissionFolder = Paths.get("/nfs/biostudies/submission"),
+        ftpFolder = Paths.get("/nfs/bisotudies/ftp"))
 
     @Test
     fun `get submission file path`() {
         assertThat(testInstance
             .getSubFilePath("ABCxxx123/ABC-123", "File1.txt"))
             .isEqualTo(Paths.get("/nfs/biostudies/submission/ABCxxx123/ABC-123/Files/File1.txt"))
     }
+
+    @Test
+    fun `get submission ftp path`() {
+        assertThat(testInstance
+            .getSubmissionFtpFolder("ABCxxx123/ABC-123"))
+            .isEqualTo(Paths.get("/nfs/bisotudies/ftp/ABCxxx123/ABC-123"))
+    }
 }

submission/persistence/src/main/kotlin/ac/uk/ebi/biostd/persistence/service/filesystem/FileSystemService.kt

@@ -8,8 +8,8 @@ class FileSystemService(
     private val ftpLinksService: FtpFilesService
 ) {
     fun persistSubmissionFiles(submission: ExtSubmission, mode: FileMode) {
-        ftpLinksService.cleanFtpFolder(submission)
+        ftpLinksService.cleanFtpFolder(submission.relPath)
         filesService.persistSubmissionFiles(submission, mode)
-        if (submission.released) ftpLinksService.createFtpFolder(submission)
+        if (submission.released) ftpLinksService.createFtpFolder(submission.relPath)
     }
 }

submission/persistence/src/main/kotlin/ac/uk/ebi/biostd/persistence/service/filesystem/FtpFilesService.kt

@@ -1,6 +1,5 @@
 package ac.uk.ebi.biostd.persistence.service.filesystem
 
-import ebi.ac.uk.extended.model.ExtSubmission
 import ebi.ac.uk.io.FileUtils
 import ebi.ac.uk.paths.SubmissionFolderResolver
 import java.io.File
@@ -11,19 +10,19 @@ private val ALL_READ: Set<PosixFilePermission> = PosixFilePermissions.fromString
 
 class FtpFilesService(private val folderResolver: SubmissionFolderResolver) {
 
-    fun createFtpFolder(submission: ExtSubmission) {
-        val submissionFolder = folderResolver.getSubmissionFolder(submission.relPath).toFile()
-        val ftpFolder = getFtpFolder(submission)
+    fun createFtpFolder(relPath: String) {
+        val submissionFolder = folderResolver.getSubmissionFolder(relPath).toFile()
+        val ftpFolder = getFtpFolder(relPath)
         FileUtils.createHardLink(submissionFolder, ftpFolder)
     }
 
-    private fun getFtpFolder(submission: ExtSubmission): File =
+    private fun getFtpFolder(relPath: String): File =
         FileUtils.getOrCreateFolder(
-            folderResolver.getSubmissionFtpFolder(submission),
+            folderResolver.getSubmissionFtpFolder(relPath),
             ALL_READ
         ).toFile()
 
-    fun cleanFtpFolder(submission: ExtSubmission) {
-        FileUtils.deleteFile(folderResolver.getSubmissionFtpFolder(submission).toFile())
+    fun cleanFtpFolder(relPath: String) {
+        FileUtils.deleteFile(folderResolver.getSubmissionFtpFolder(relPath).toFile())
     }
 }

submission/persistence/src/test/kotlin/ac/uk/ebi/biostd/persistence/service/filesystem/FilesServiceTest.kt

@@ -40,7 +40,10 @@ class FilesServiceTest(
     private lateinit var extSubmission: ExtSubmission
 
     private val testInstance =
-        FilesService(SubmissionFolderResolver(temporaryFolder.root.toPath()), mockSerializationService)
+        FilesService(SubmissionFolderResolver(
+            Paths.get("${temporaryFolder.root.toPath()}/submission"),
+            Paths.get("${temporaryFolder.root.toPath()}/ftp")
+        ), mockSerializationService)
 
     @BeforeEach
     fun beforeEach() {

submission/persistence/src/test/kotlin/ac/uk/ebi/biostd/persistence/service/filesystem/FtpFilesServiceTest.kt

@@ -1,6 +1,5 @@
 package ac.uk.ebi.biostd.persistence.service.filesystem
 
-import ebi.ac.uk.extended.model.ExtSubmission
 import ebi.ac.uk.io.ext.asFileList
 import ebi.ac.uk.io.ext.createDirectory
 import ebi.ac.uk.io.ext.createNewFile
@@ -9,59 +8,54 @@ import ebi.ac.uk.test.clean
 import ebi.ac.uk.util.collections.second
 import io.github.glytching.junit.extension.folder.TemporaryFolder
 import io.github.glytching.junit.extension.folder.TemporaryFolderExtension
-import io.mockk.every
-import io.mockk.impl.annotations.MockK
 import io.mockk.junit5.MockKExtension
 import org.assertj.core.api.Assertions.assertThat
-import org.junit.jupiter.api.BeforeAll
 import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.extension.ExtendWith
 import java.io.File
 
+private const val REL_PATH = "My/Path/To/Submission"
+
 @ExtendWith(TemporaryFolderExtension::class, MockKExtension::class)
 internal class FtpFilesServiceTest(
-    private val temporaryFolder: TemporaryFolder,
-    @MockK private val submission: ExtSubmission
+    private val temporaryFolder: TemporaryFolder
 ) {
 
     private lateinit var expectedDirectory: File
     private lateinit var expectedFile1: File
     private lateinit var expectedFile2: File
 
-    private val folderResolver = SubmissionFolderResolver(temporaryFolder.root.toPath())
+    private val folderResolver = SubmissionFolderResolver(
+        temporaryFolder.root.toPath().resolve("submission"),
+        temporaryFolder.root.toPath().resolve("ftp"))
     private val testInstance = FtpFilesService(folderResolver)
 
-    @BeforeAll
-    fun beforeAll() {
-        every { submission.relPath } returns "My/Path/To/Submission"
-    }
-
     @BeforeEach
     fun beforeEach() {
         temporaryFolder.clean()
 
-        val submissionFolder = folderResolver.getSubmissionFolder(submission).toFile().apply { mkdirs() }
+        val submissionFolder = folderResolver.getSubmissionFolder(REL_PATH).toFile().apply { mkdirs() }
         expectedDirectory = submissionFolder.createDirectory("my-directory")
         expectedFile1 = expectedDirectory.createNewFile("file.txt", "file-content")
         expectedFile2 = expectedDirectory.createNewFile("file-2.txt", "file-text")
     }
 
     @Test
     fun createFtpFolder() {
-        testInstance.createFtpFolder(submission)
+        testInstance.createFtpFolder(REL_PATH)
 
-        assertFolder(folderResolver.getSubmissionFolder(submission).toFile())
-        assertFolder(folderResolver.getSubmissionFtpFolder(submission).toFile())
+        assertFolder(folderResolver.getSubmissionFolder(REL_PATH).toFile())
+        assertFolder(folderResolver.getSubmissionFtpFolder(REL_PATH).toFile())
     }
 
     @Test
     fun cleanFtpFolder() {
-        testInstance.createFtpFolder(submission)
-        testInstance.cleanFtpFolder(submission)
+        testInstance.createFtpFolder(REL_PATH)
+        testInstance.cleanFtpFolder(REL_PATH)
 
-        assertFolder(folderResolver.getSubmissionFolder(submission).toFile())
-        assertThat(folderResolver.getSubmissionFtpFolder(submission).toFile()).doesNotExist()
+        assertFolder(folderResolver.getSubmissionFolder(REL_PATH).toFile())
+        assertThat(folderResolver.getSubmissionFtpFolder(REL_PATH).toFile()).doesNotExist()
     }
 
     private fun assertFolder(ftpFolder: File) {

submission/submission-security/src/main/kotlin/ebi/ac/uk/security/integration/SecurityProperties.kt

@@ -6,6 +6,7 @@ class SecurityProperties {
     lateinit var environment: String
     lateinit var filesDirPath: String
     lateinit var captchaKey: String
+    lateinit var magicFolderPath: String
 
     var checkCaptcha: Boolean = false
     var requireActivation: Boolean = false

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

@@ -13,7 +13,7 @@ import org.assertj.core.api.Assertions.assertThat
 import java.nio.file.Paths
 
 internal class AllInOneSubmissionHelper(
-    private val basePath: String,
+    private val submissionPath: String,
     private val submissionRepository: SubmissionRepository
 ) {
     internal fun assertSavedSubmission(accNo: String, method: ExtSubmissionMethod = ExtSubmissionMethod.PAGE_TAB) {
@@ -25,7 +25,7 @@ internal class AllInOneSubmissionHelper(
     }
 
     private fun assertSubmissionFiles(submission: ExtSubmission) {
-        val submissionFolderPath = "$basePath/submission/${submission.relPath}"
+        val submissionFolderPath = "$submissionPath/${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

@@ -7,15 +7,18 @@ import io.github.glytching.junit.extension.folder.TemporaryFolder
 import org.junit.jupiter.api.BeforeAll
 
 internal open class BaseIntegrationTest(private val tempFolder: TemporaryFolder) {
-    protected lateinit var basePath: String
+    protected lateinit var submissionPath: String
+    protected lateinit var ftpPath: String
 
     @BeforeAll
     fun init() {
         val dropbox = tempFolder.createDirectory("dropbox")
         val temp = tempFolder.createDirectory("tmp")
-        basePath = tempFolder.root.absolutePath
+        submissionPath = "${tempFolder.root.absolutePath}/submission"
+        ftpPath = "${tempFolder.root.absolutePath}/ftpPath"
 
-        System.setProperty("app.basepath", tempFolder.root.absolutePath)
+        System.setProperty("app.submissionPath", submissionPath)
+        System.setProperty("app.ftpPath", ftpPath)
         System.setProperty("app.tempDirPath", temp.absolutePath)
         System.setProperty("app.security.filesDirPath", dropbox.absolutePath)
     }

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/test/project/submit/ProjectSubmitTest.kt

@@ -30,7 +30,7 @@ import org.springframework.test.annotation.DirtiesContext
 import org.springframework.test.context.junit.jupiter.SpringExtension
 
 @ExtendWith(TemporaryFolderExtension::class)
-internal class ProjectSubmitTest(private val tempFolder: TemporaryFolder) : BaseIntegrationTest(tempFolder) {
+internal class ProjectSubmitTest(tempFolder: TemporaryFolder) : BaseIntegrationTest(tempFolder) {
     @Nested
     @Import(PersistenceConfig::class)
     @ExtendWith(SpringExtension::class)

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/test/submission/submit/AllInOneMultipartFileSubmissionTest.kt

@@ -45,7 +45,7 @@ internal class AllInOneMultipartFileSubmissionTest(
         @BeforeAll
         fun init() {
             webClient = getWebClient(serverPort, SuperUser)
-            allInOneSubmissionHelper = AllInOneSubmissionHelper(basePath, submissionRepository)
+            allInOneSubmissionHelper = AllInOneSubmissionHelper(submissionPath, submissionRepository)
         }
 
         @Test

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/test/submission/submit/AllInOneSubmissionTest.kt

@@ -40,7 +40,7 @@ internal class AllInOneSubmissionTest(private val tempFolder: TemporaryFolder) :
         @BeforeAll
         fun init() {
             webClient = getWebClient(serverPort, SuperUser)
-            allInOneSubmissionHelper = AllInOneSubmissionHelper(basePath, submissionRepository)
+            allInOneSubmissionHelper = AllInOneSubmissionHelper(submissionPath, submissionRepository)
         }
 
         @Test

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/test/submission/submit/FileListSubmissionTest.kt

@@ -161,7 +161,7 @@ internal class FileListSubmissionTest(private val tempFolder: TemporaryFolder) :
         private fun assertSubmissionFiles(accNo: String, testFile: String) {
             val fileListName = "FileList"
             val createdSubmission = submissionRepository.getActiveExtByAccNo(accNo)
-            val submissionFolderPath = "$basePath/submission/${createdSubmission.relPath}"
+            val submissionFolderPath = "$submissionPath/${createdSubmission.relPath}"
 
             assertThat(createdSubmission.section.fileList?.fileName).isEqualTo(fileListName)
             assertThat(createdSubmission.section.fileList).isEqualTo(

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/test/submission/submit/MultipartFileSubmissionApiTest.kt

@@ -255,7 +255,7 @@ internal class MultipartFileSubmissionApiTest(
         private fun assertSubmissionFiles(accNo: String, testFile: String) {
             val fileListName = "FileList"
             val createdSubmission = submissionRepository.getActiveExtByAccNo(accNo)
-            val submissionFolderPath = "$basePath/submission/${createdSubmission.relPath}"
+            val submissionFolderPath = "$submissionPath/${createdSubmission.relPath}"
 
             assertThat(createdSubmission.section.fileList?.fileName).isEqualTo(fileListName)
             assertThat(createdSubmission.section.fileList).isEqualTo(

submission/submission-webapp/src/itest/resources/application.yml

@@ -18,7 +18,8 @@ spring:
     port: 5672
 
 app:
-  basepath:
+  submissionPath:
+  ftpPath:
   tempDirPath:
   instanceBaseUrl: http://localhost:8080
   security:

submission/submission-webapp/src/main/kotlin/ac/uk/ebi/biostd/common/config/PersistenceConfig.kt

@@ -33,6 +33,7 @@ import org.springframework.context.annotation.Configuration
 import org.springframework.data.jpa.repository.config.EnableJpaRepositories
 import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate
 import uk.ac.ebi.stats.persistence.repositories.SubmissionStatsRepository
+import java.nio.file.Paths
 
 @Suppress("TooManyFunctions")
 @Configuration
@@ -65,7 +66,7 @@ class PersistenceConfig(
     ) = ToDbSubmissionMapper(tagsRepo, tagsRefRepo, userRepo)
 
     @Bean
-    fun toExtSubmissionMapper() = ToExtSubmissionMapper(applicationProperties.submissionsPath)
+    fun toExtSubmissionMapper() = ToExtSubmissionMapper(Paths.get(applicationProperties.submissionPath))
 
     @Bean
     fun submissionRepository(toExtSubmissionMapper: ToExtSubmissionMapper) =

submission/submission-webapp/src/main/kotlin/ac/uk/ebi/biostd/common/config/SubmitterConfig.kt

@@ -45,7 +45,9 @@ class SubmitterConfig {
     class FilesHandlerConfig(private val appProperties: ApplicationProperties) {
         @Bean
         @Lazy
-        fun folderResolver() = SubmissionFolderResolver(Paths.get(appProperties.basepath))
+        fun folderResolver() = SubmissionFolderResolver(
+            submissionFolder = Paths.get(appProperties.submissionPath),
+            ftpFolder = Paths.get(appProperties.ftpPath))
     }
 
     @Configuration

submission/submission-webapp/src/main/kotlin/ac/uk/ebi/biostd/common/property/ApplicationProperties.kt

@@ -1,22 +1,17 @@
 package ac.uk.ebi.biostd.common.property
 
 import ebi.ac.uk.notifications.integration.NotificationProperties
-import ebi.ac.uk.paths.SUBMISSION_PATH
 import ebi.ac.uk.security.integration.SecurityProperties
 import org.springframework.boot.context.properties.ConfigurationProperties
 import org.springframework.boot.context.properties.NestedConfigurationProperty
-import java.nio.file.Path
-import java.nio.file.Paths
 
 @ConfigurationProperties(prefix = "app")
 open class ApplicationProperties {
-    lateinit var basepath: String
     lateinit var tempDirPath: String
+    lateinit var submissionPath: String
+    lateinit var ftpPath: String
     lateinit var instanceBaseUrl: String
 
-    val submissionsPath: Path
-        get() = Paths.get(basepath).resolve(SUBMISSION_PATH)
-
     @NestedConfigurationProperty
     var security: SecurityProperties = SecurityProperties()
 

submission/submission-webapp/src/main/resources/application-local.yml

@@ -24,8 +24,9 @@ spring:
       max-request-size: 10240MB
 
 app:
-  basepath: # Absolute path to the folder to be used as storage
-  tempDirPath: # Absolute of the temp folder to store files
+  submissionPath:
+  ftpPath:
+  tempDirPath:
   instanceBaseUrl: http://localhost:8080
   security:
     captchaKey: # Captcha validation token. Not required for local environment