Pivotal ID # 177040448: Store request as plain json

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

@@ -15,7 +15,6 @@ class FileSystemService(
         ftpLinksService.cleanFtpFolder(submission.relPath)
         val processedSubmission = filesService.persistSubmissionFiles(submission, mode)
         if (submission.released) ftpLinksService.createFtpFolder(submission.relPath)
-
         return processedSubmission
     }
 }

submission/persistence-mongo/src/main/kotlin/ac/uk/ebi/biostd/persistence/doc/integration/ExternalConfig.kt

@@ -10,6 +10,7 @@ import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
 import org.springframework.context.annotation.Bean
 import org.springframework.context.annotation.Configuration
 import org.springframework.context.annotation.Import
+import uk.ac.ebi.extended.serialization.service.ExtSerializationService
 
 @Configuration
 @Import(MongoDbServicesConfig::class)
@@ -19,6 +20,7 @@ class ExternalConfig {
     @Bean
     internal fun submissionRequestService(
         submissionDocDataRepository: SubmissionDocDataRepository,
+        serializationService: ExtSerializationService,
         submissionRequestDocDataRepository: SubmissionRequestDocDataRepository,
         submissionDraftDocDataRepository: SubmissionDraftDocDataRepository,
         systemService: FileSystemService
@@ -27,6 +29,7 @@ class ExternalConfig {
             submissionDocDataRepository,
             submissionRequestDocDataRepository,
             submissionDraftDocDataRepository,
+            serializationService,
             systemService
         )
     }

submission/persistence-mongo/src/main/kotlin/ac/uk/ebi/biostd/persistence/doc/integration/MongoDbServicesConfig.kt

@@ -1,15 +1,15 @@
 package ac.uk.ebi.biostd.persistence.doc.integration
 
-import ac.uk.ebi.biostd.persistence.common.service.StatsDataService
 import ac.uk.ebi.biostd.persistence.common.service.ProjectDataService
+import ac.uk.ebi.biostd.persistence.common.service.StatsDataService
 import ac.uk.ebi.biostd.persistence.common.service.SubmissionQueryService
 import ac.uk.ebi.biostd.persistence.doc.db.data.SubmissionDocDataRepository
 import ac.uk.ebi.biostd.persistence.doc.db.data.SubmissionDraftDocDataRepository
 import ac.uk.ebi.biostd.persistence.doc.db.data.SubmissionRequestDocDataRepository
 import ac.uk.ebi.biostd.persistence.doc.db.data.SubmissionStatsDataRepository
 import ac.uk.ebi.biostd.persistence.doc.mapping.to.ToExtSubmissionMapper
-import ac.uk.ebi.biostd.persistence.doc.service.StatsMongoDataService
 import ac.uk.ebi.biostd.persistence.doc.service.ProjectMongoDataService
+import ac.uk.ebi.biostd.persistence.doc.service.StatsMongoDataService
 import ac.uk.ebi.biostd.persistence.doc.service.SubmissionDraftMongoService
 import ac.uk.ebi.biostd.persistence.doc.service.SubmissionMongoMetaQueryService
 import ac.uk.ebi.biostd.persistence.doc.service.SubmissionMongoQueryService
@@ -27,10 +27,12 @@ class MongoDbServicesConfig {
     internal fun submissionQueryService(
         submissionDocDataRepository: SubmissionDocDataRepository,
         submissionRequestDocDataRepository: SubmissionRequestDocDataRepository,
+        serializationService: ExtSerializationService,
         toExtSubmissionMapper: ToExtSubmissionMapper
     ): SubmissionQueryService = SubmissionMongoQueryService(
         submissionDocDataRepository,
         submissionRequestDocDataRepository,
+        serializationService,
         toExtSubmissionMapper)
 
     @Bean

submission/persistence-mongo/src/main/kotlin/ac/uk/ebi/biostd/persistence/doc/model/SubmissionRequest.kt

@@ -1,5 +1,6 @@
 package ac.uk.ebi.biostd.persistence.doc.model
 
+import com.mongodb.DBObject
 import org.springframework.data.annotation.Id
 import org.springframework.data.mongodb.core.mapping.Document
 
@@ -9,5 +10,5 @@ data class SubmissionRequest(
     val id: String? = null,
     val accNo: String,
     val version: Int,
-    val submission: DocSubmission
+    val submission: DBObject
 )

submission/persistence-mongo/src/main/kotlin/ac/uk/ebi/biostd/persistence/doc/service/SubmissionMongoPersistenceService.kt

@@ -9,16 +9,19 @@ import ac.uk.ebi.biostd.persistence.doc.db.data.SubmissionRequestDocDataReposito
 import ac.uk.ebi.biostd.persistence.doc.mapping.from.toDocSubmission
 import ac.uk.ebi.biostd.persistence.doc.model.DocProcessingStatus.PROCESSED
 import ac.uk.ebi.biostd.persistence.doc.model.SubmissionRequest
+import com.mongodb.BasicDBObject
 import ebi.ac.uk.extended.model.ExtProcessingStatus.PROCESSING
 import ebi.ac.uk.extended.model.ExtProcessingStatus.REQUESTED
 import ebi.ac.uk.extended.model.ExtSubmission
 import ebi.ac.uk.extended.model.FileMode.MOVE
+import uk.ac.ebi.extended.serialization.service.ExtSerializationService
 import kotlin.math.absoluteValue
 
 internal class SubmissionMongoPersistenceService(
     private val subDataRepository: SubmissionDocDataRepository,
     private val submissionRequestDocDataRepository: SubmissionRequestDocDataRepository,
     private val draftDocDataRepository: SubmissionDraftDocDataRepository,
+    private val serializationService: ExtSerializationService,
     private val systemService: FileSystemService
 ) : SubmissionRequestService {
     override fun saveAndProcessSubmissionRequest(saveRequest: SaveSubmissionRequest): ExtSubmission {
@@ -29,9 +32,7 @@ internal class SubmissionMongoPersistenceService(
     override fun saveSubmissionRequest(saveRequest: SaveSubmissionRequest): ExtSubmission {
         val submission = saveRequest.submission
         val newVersion = submission.copy(version = getNextVersion(submission.accNo), status = REQUESTED)
-
         submissionRequestDocDataRepository.saveRequest(asRequest(newVersion))
-
         return newVersion
     }
 
@@ -43,7 +44,7 @@ internal class SubmissionMongoPersistenceService(
     private fun asRequest(submission: ExtSubmission) = SubmissionRequest(
         accNo = submission.accNo,
         version = submission.version,
-        submission = submission.toDocSubmission()
+        submission = BasicDBObject.parse(serializationService.serialize(submission))
     )
 
     override fun processSubmission(saveRequest: SaveSubmissionRequest): ExtSubmission {

submission/persistence-mongo/src/main/kotlin/ac/uk/ebi/biostd/persistence/doc/service/SubmissionMongoQueryService.kt

@@ -9,10 +9,12 @@ import ac.uk.ebi.biostd.persistence.doc.mapping.to.ToExtSubmissionMapper
 import ac.uk.ebi.biostd.persistence.doc.model.asBasicSubmission
 import ebi.ac.uk.extended.model.ExtSubmission
 import org.springframework.data.domain.Page
+import uk.ac.ebi.extended.serialization.service.ExtSerializationService
 
 internal class SubmissionMongoQueryService(
     private val submissionRepo: SubmissionDocDataRepository,
     private val requestRepository: SubmissionRequestDocDataRepository,
+    private val serializationService: ExtSerializationService,
     private val toExtSubmissionMapper: ToExtSubmissionMapper
 ) : SubmissionQueryService {
     override fun existByAccNo(accNo: String): Boolean = submissionRepo.existsByAccNo(accNo)
@@ -42,7 +44,7 @@ internal class SubmissionMongoQueryService(
     }
 
     override fun getRequest(accNo: String, version: Int): ExtSubmission {
-        val submission = requestRepository.getByAccNoAndVersion(accNo, version).submission
-        return toExtSubmissionMapper.toExtSubmission(submission)
+        val submission = requestRepository.getByAccNoAndVersion(accNo, version)
+        return serializationService.deserialize(submission.submission.toString())
     }
 }

submission/persistence-mongo/src/test/kotlin/ac/uk/ebi/biostd/persistence/doc/service/SubmissionMongoPersistenceServiceTest.kt

@@ -23,20 +23,27 @@ 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 uk.ac.ebi.extended.serialization.service.ExtSerializationService
 
 @ExtendWith(MockKExtension::class)
 class SubmissionMongoPersistenceServiceTest(
     @MockK private val systemService: FileSystemService,
     @MockK private val dataRepository: SubmissionDocDataRepository,
     @MockK private val draftRepository: SubmissionDraftDocDataRepository,
-    @MockK private val submissionRequestRepository: SubmissionRequestDocDataRepository
+    @MockK private val submissionRequestRepository: SubmissionRequestDocDataRepository,
+    @MockK private val serializationService: ExtSerializationService
 ) {
     private val submission = extSubmission()
     private val docSubmission = slot<DocSubmission>()
-    private val persistedSubmissionSlot = slot<ExtSubmission>()
+    private val submissionSlot = slot<ExtSubmission>()
     private val submissionRequestSlot = slot<SubmissionRequest>()
-    private val testInstance =
-        SubmissionMongoPersistenceService(dataRepository, submissionRequestRepository, draftRepository, systemService)
+
+    private val testInstance = SubmissionMongoPersistenceService(
+        dataRepository,
+        submissionRequestRepository,
+        draftRepository,
+        serializationService,
+        systemService)
 
     @AfterEach
     fun afterEach() = clearAllMocks()
@@ -45,7 +52,8 @@ class SubmissionMongoPersistenceServiceTest(
     fun beforeEach() {
         setUpDataRepository()
         setUpDraftRepository()
-        every { systemService.persistSubmissionFiles(capture(persistedSubmissionSlot), MOVE) } returns submission
+        every { serializationService.serialize(capture(submissionSlot)) } returns "{}"
+        every { systemService.persistSubmissionFiles(capture(submissionSlot), MOVE) } returns submission
         every { submissionRequestRepository.saveRequest(capture(submissionRequestSlot)) } answers { nothing }
     }
 
@@ -68,7 +76,7 @@ class SubmissionMongoPersistenceServiceTest(
     }
 
     private fun assertPersistedSubmission() {
-        val persistedSubmission = persistedSubmissionSlot.captured
+        val persistedSubmission = submissionSlot.captured
         assertThat(persistedSubmission.version).isEqualTo(2)
         assertThat(persistedSubmission.status).isEqualTo(REQUESTED)
         verify(exactly = 1) { systemService.persistSubmissionFiles(persistedSubmission, MOVE) }
@@ -97,8 +105,6 @@ class SubmissionMongoPersistenceServiceTest(
 
     private fun setUpDraftRepository() {
         every { draftRepository.deleteByUserIdAndKey(submission.owner, submission.accNo) } answers { nothing }
-        every {
-            draftRepository.deleteByUserIdAndKey(submission.submitter, submission.accNo)
-        } answers { nothing }
+        every { draftRepository.deleteByUserIdAndKey(submission.submitter, submission.accNo) } answers { nothing }
     }
 }