test(backend): test /get-original-metadata locked during new submis…

…sions This is a follow-up to #2846
loculus-project · Sep 20, 2024 · 9deb1f6 · 9deb1f6
1 parent 266b7bf
commit 9deb1f6
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Showing 5 changed files with 46 additions and 11 deletions.
diff --git a/backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt b/backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt
@@ -352,7 +352,7 @@ open class SubmissionController(
     )
     @ApiResponse(
         responseCode = "423",
-        description = "Locked. The metadata is currently being processed.",
+        description = "Locked. New sequence entries are currently being uploaded.",
     )
     @GetMapping("/get-original-metadata", produces = [MediaType.APPLICATION_JSON_VALUE])
     fun getOriginalMetadata(
@@ -375,7 +375,7 @@ open class SubmissionController(
             headers.add(HttpHeaders.CONTENT_ENCODING, compression.compressionName)
         }
 
-        val stillProcessing = submissionDatabaseService.checkIfStillProcessingSubmittedData()
+        val stillProcessing = submitModel.checkIfStillProcessingSubmittedData()
         if (stillProcessing) {
             return ResponseEntity.status(HttpStatus.LOCKED).build()
         }

diff --git a/backend/src/main/kotlin/org/loculus/backend/model/SubmitModel.kt b/backend/src/main/kotlin/org/loculus/backend/model/SubmitModel.kt
@@ -17,11 +17,14 @@ import org.loculus.backend.controller.UnprocessableEntityException
 import org.loculus.backend.service.datauseterms.DataUseTermsPreconditionValidator
 import org.loculus.backend.service.groupmanagement.GroupManagementPreconditionValidator
 import org.loculus.backend.service.submission.CompressionAlgorithm
+import org.loculus.backend.service.submission.MetadataUploadAuxTable
+import org.loculus.backend.service.submission.SequenceUploadAuxTable
 import org.loculus.backend.service.submission.UploadDatabaseService
 import org.loculus.backend.utils.FastaReader
 import org.loculus.backend.utils.metadataEntryStreamAsSequence
 import org.loculus.backend.utils.revisionEntryStreamAsSequence
 import org.springframework.stereotype.Service
+import org.springframework.transaction.annotation.Transactional
 import org.springframework.web.multipart.MultipartFile
 import java.io.BufferedInputStream
 import java.io.File
@@ -313,4 +316,13 @@ class SubmitModel(
             throw UnprocessableEntityException(metadataNotPresentErrorText + sequenceNotPresentErrorText)
         }
     }
+
+    @Transactional(readOnly = true)
+    fun checkIfStillProcessingSubmittedData(): Boolean {
+        val metadataInAuxTable: Boolean =
+            MetadataUploadAuxTable.select(MetadataUploadAuxTable.submissionIdColumn).count() > 0
+        val sequencesInAuxTable: Boolean =
+            SequenceUploadAuxTable.select(SequenceUploadAuxTable.sequenceSubmissionIdColumn).count() > 0
+        return metadataInAuxTable || sequencesInAuxTable
+    }
 }
diff --git a/backend/src/main/kotlin/org/loculus/backend/service/submission/SubmissionDatabaseService.kt b/backend/src/main/kotlin/org/loculus/backend/service/submission/SubmissionDatabaseService.kt
@@ -950,14 +950,6 @@ open class SubmissionDatabaseService(
         )
     }
 
-    fun checkIfStillProcessingSubmittedData(): Boolean {
-        val metadataInAuxTable: Boolean =
-            MetadataUploadAuxTable.select(MetadataUploadAuxTable.submissionIdColumn).count() > 0
-        val sequencesInAuxTable: Boolean =
-            SequenceUploadAuxTable.select(SequenceUploadAuxTable.sequenceSubmissionIdColumn).count() > 0
-        return metadataInAuxTable || sequencesInAuxTable
-    }
-
     fun streamOriginalMetadata(
         authenticatedUser: AuthenticatedUser,
         organism: Organism,

diff --git a/backend/src/main/kotlin/org/loculus/backend/service/submission/UploadDatabaseService.kt b/backend/src/main/kotlin/org/loculus/backend/service/submission/UploadDatabaseService.kt
@@ -7,7 +7,6 @@ import org.jetbrains.exposed.sql.VarCharColumnType
 import org.jetbrains.exposed.sql.and
 import org.jetbrains.exposed.sql.batchInsert
 import org.jetbrains.exposed.sql.deleteWhere
-import org.jetbrains.exposed.sql.select
 import org.jetbrains.exposed.sql.selectAll
 import org.jetbrains.exposed.sql.statements.StatementType
 import org.jetbrains.exposed.sql.transactions.transaction

diff --git a/.../test/kotlin/org/loculus/backend/controller/submission/GetOriginalMetadataEndpointTest.kt b/.../test/kotlin/org/loculus/backend/controller/submission/GetOriginalMetadataEndpointTest.kt
@@ -2,13 +2,18 @@ package org.loculus.backend.controller.submission
 
 import com.fasterxml.jackson.module.kotlin.readValue
 import com.github.luben.zstd.ZstdInputStream
+import io.mockk.every
+import io.mockk.mockk
+import kotlinx.datetime.LocalDateTime
 import org.hamcrest.CoreMatchers.`is`
 import org.hamcrest.MatcherAssert.assertThat
 import org.hamcrest.Matchers.hasSize
 import org.hamcrest.Matchers.not
 import org.junit.jupiter.api.Test
 import org.loculus.backend.api.AccessionVersionOriginalMetadata
+import org.loculus.backend.api.Organism
 import org.loculus.backend.api.Status
+import org.loculus.backend.auth.AuthenticatedUser
 import org.loculus.backend.controller.DEFAULT_ORGANISM
 import org.loculus.backend.controller.EndpointTest
 import org.loculus.backend.controller.OTHER_ORGANISM
@@ -18,6 +23,8 @@ import org.loculus.backend.controller.groupmanagement.GroupManagementControllerC
 import org.loculus.backend.controller.groupmanagement.andGetGroupId
 import org.loculus.backend.controller.jacksonObjectMapper
 import org.loculus.backend.controller.submission.SubmitFiles.DefaultFiles
+import org.loculus.backend.service.submission.UploadDatabaseService
+import org.loculus.backend.utils.MetadataEntry
 import org.springframework.beans.factory.annotation.Autowired
 import org.springframework.http.HttpHeaders
 import org.springframework.http.MediaType
@@ -33,6 +40,7 @@ class GetOriginalMetadataEndpointTest(
     @Autowired val convenienceClient: SubmissionConvenienceClient,
     @Autowired val submissionControllerClient: SubmissionControllerClient,
     @Autowired val groupManagementClient: GroupManagementControllerClient,
+    @Autowired val uploadDatabaseService: UploadDatabaseService,
 ) {
     @Test
     fun `GIVEN invalid authorization token THEN returns 401 Unauthorized`() {
@@ -148,4 +156,28 @@ class GetOriginalMetadataEndpointTest(
         val responseAccessionVersions = responseBody.map { it.displayAccessionVersion() }.toSet()
         assertThat(responseAccessionVersions, `is`(expectedAccessionVersions))
     }
+
+    @Test
+    fun `GIVEN there are sequences currently being uploaded THEN returns locked`() {
+        val uploadId = "upload id"
+        val mockUser = mockk<AuthenticatedUser>()
+        every { mockUser.username }.returns("username")
+
+        uploadDatabaseService.batchInsertMetadataInAuxTable(
+            uploadId = uploadId,
+            authenticatedUser = mockUser,
+            groupId = 1,
+            submittedOrganism = Organism("organism"),
+            uploadedMetadataBatch = listOf(MetadataEntry("submission id", mapOf("key" to "value"))),
+            uploadedAt = LocalDateTime(2024, 1, 1, 1, 1, 1),
+        )
+
+        submissionControllerClient.getOriginalMetadata()
+            .andExpect(status().isLocked)
+
+        uploadDatabaseService.deleteUploadData(uploadId)
+
+        submissionControllerClient.getOriginalMetadata()
+            .andExpect(status().isOk)
+    }
 }