Pivotal ID # 172671360: Warn users about upcoming public release

submission/notifications/src/main/resources/templates/release-notification.txt

@@ -1,6 +1,6 @@
 Dear ${USERNAME},
 
-Your submission accession number ${ACC_NO} - "${TITLE}" will be made public on ${RELEASE_DATE}.
+Your submission with accession number ${ACC_NO} - "${TITLE}" will be made public on ${RELEASE_DATE}.
 
 If you want to keep your submission private after this date or make it public earlier, please log in to the BioStudies Submission Tool at ${UI_URL}/submissions/submissions and change the release date.
 

submission/notifications/src/main/resources/templates/successful-submission.txt

@@ -1,6 +1,6 @@
 Dear ${USERNAME},
 
-Thank you for submitting your data to BioStudies. Your submission "${TITLE}" has been assigned BioStudies accession number ${ACC_NO}.
+Thank you for submitting your data to BioStudies. Your submission "${TITLE}" has been assigned the BioStudies accession number ${ACC_NO}.
 
 You will be able to see it at ${UI_URL}/studies/${ACC_NO} in the next 24 hours. ${RELEASE_MESSAGE}
 

submission/persistence-common-api/src/main/kotlin/ac/uk/ebi/biostd/persistence/common/service/SubmissionOperations.kt

@@ -26,7 +26,7 @@ interface SubmissionQueryService {
 
     fun expireSubmission(accNo: String)
 
-    fun getExtendedSubmissions(filter: SubmissionFilter, offset: Long, limit: Int): Page<ExtSubmission>
+    fun getExtendedSubmissions(filter: SubmissionFilter, offset: Long, limit: Int): Page<Result<ExtSubmission>>
 
     fun getSubmissionsByUser(userId: Long, filter: SubmissionFilter): List<BasicSubmission>
 

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

@@ -29,9 +29,11 @@ internal class SubmissionMongoQueryService(
         submissionRepo.saveAll(actives)
     }
 
-    override fun getExtendedSubmissions(filter: SubmissionFilter, offset: Long, limit: Int): Page<ExtSubmission> {
-        TODO("Not yet implemented")
-    }
+    override fun getExtendedSubmissions(
+        filter: SubmissionFilter,
+        offset: Long,
+        limit: Int
+    ): Page<Result<ExtSubmission>> = TODO("Not yet implemented")
 
     override fun getSubmissionsByUser(userId: Long, filter: SubmissionFilter): List<BasicSubmission> {
         TODO("Not yet implemented")

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

@@ -57,13 +57,17 @@ internal open class SubmissionRepository(
     }
 
     @Transactional(readOnly = true)
-    override fun getExtendedSubmissions(filter: SubmissionFilter, offset: Long, limit: Int): Page<ExtSubmission> {
+    override fun getExtendedSubmissions(
+        filter: SubmissionFilter,
+        offset: Long,
+        limit: Int
+    ): Page<Result<ExtSubmission>> {
         val filterSpecs = SubmissionFilterSpecification(filter)
         val pageable = OffsetPageRequest(offset, limit, Sort.by(defaultOrder))
 
         return submissionRepository
             .findAll(filterSpecs.specification, pageable, EntityGraphs.named(SIMPLE_GRAPH))
-            .map { getExtByAccNoAndVersion(it.accNo, it.version) }
+            .map { runCatching { getExtByAccNoAndVersion(it.accNo, it.version) } }
     }
 
     override fun getSubmissionsByUser(userId: Long, filter: SubmissionFilter): List<BasicSubmission> {

submission/submission-webapp/src/main/kotlin/ac/uk/ebi/biostd/submission/domain/service/ExtSubmissionService.kt

@@ -8,7 +8,11 @@ import ac.uk.ebi.biostd.submission.web.model.ExtPageRequest
 import ebi.ac.uk.extended.model.ExtSubmission
 import ebi.ac.uk.extended.model.FileMode.COPY
 import ebi.ac.uk.security.integration.components.IUserPrivilegesService
+import mu.KotlinLogging
 import org.springframework.data.domain.Page
+import org.springframework.data.domain.PageImpl
+
+private val logger = KotlinLogging.logger {}
 
 class ExtSubmissionService(
     private val persistenceService: SubmissionRequestService,
@@ -25,7 +29,14 @@ class ExtSubmissionService(
     fun getExtendedSubmissions(request: ExtPageRequest): Page<ExtSubmission> {
         val filter = SubmissionFilter(
             rTimeFrom = request.fromRTime, rTimeTo = request.toRTime, released = request.released)
-        return submissionRepository.getExtendedSubmissions(filter, request.offset, request.limit)
+
+        val page = submissionRepository
+            .getExtendedSubmissions(filter, request.offset, request.limit)
+            .onEach { it.onFailure { logger.error { it.message ?: it.localizedMessage } } }
+            .map { it.getOrNull() }
+        val submissions = page.content.filterNotNull()
+
+        return PageImpl(submissions, page.pageable, submissions.size.toLong())
     }
 
     private fun validateUser(user: String) = require(userPrivilegesService.canSubmitExtended(user)) {

submission/submission-webapp/src/main/kotlin/ac/uk/ebi/biostd/submission/web/resources/SubmissionResource.kt

@@ -26,7 +26,6 @@ import org.springframework.web.bind.annotation.RestController
 class SubmissionResource(
     private val submissionsWebHandler: SubmissionsWebHandler
 ) {
-
     @GetMapping
     @ApiOperation("Get the basic data for the submissions that matches the given filter")
     @ApiImplicitParams(value = [

submission/submission-webapp/src/test/kotlin/ac/uk/ebi/biostd/submission/domain/service/ExtSubmissionServiceTest.kt

@@ -4,6 +4,7 @@ import ac.uk.ebi.biostd.persistence.common.request.SaveSubmissionRequest
 import ac.uk.ebi.biostd.persistence.common.request.SubmissionFilter
 import ac.uk.ebi.biostd.persistence.common.service.SubmissionQueryService
 import ac.uk.ebi.biostd.persistence.common.service.SubmissionRequestService
+import ac.uk.ebi.biostd.persistence.exception.ExtSubmissionMappingException
 import ac.uk.ebi.biostd.submission.web.model.ExtPageRequest
 import ebi.ac.uk.extended.model.ExtSubmission
 import ebi.ac.uk.extended.model.FileMode.COPY
@@ -20,7 +21,8 @@ import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.assertThrows
 import org.junit.jupiter.api.extension.ExtendWith
-import org.springframework.data.domain.Page
+import org.springframework.data.domain.PageImpl
+import org.springframework.data.domain.Pageable
 
 @ExtendWith(MockKExtension::class)
 class ExtSubmissionServiceTest(
@@ -48,7 +50,7 @@ class ExtSubmissionServiceTest(
     }
 
     @Test
-    fun `filtering extended submissions`(@MockK page: Page<ExtSubmission>) {
+    fun `filtering extended submissions`(@MockK extSubmission: ExtSubmission) {
         val filter = slot<SubmissionFilter>()
         val request = ExtPageRequest(
             fromRTime = "2019-09-21T15:00:00Z",
@@ -57,8 +59,19 @@ class ExtSubmissionServiceTest(
             offset = 1,
             limit = 2)
 
+        val pageable = Pageable.unpaged()
+        val result1 = Result.success(extSubmission)
+        val result2 = Result.failure<ExtSubmission>(ExtSubmissionMappingException("S-TEST123", "error"))
+        val results = mutableListOf(result1, result2)
+        val page = PageImpl(results, pageable, 2L)
+
         every { submissionRepository.getExtendedSubmissions(capture(filter), 1, 2) } returns page
-        testInstance.getExtendedSubmissions(request)
+
+        val result = testInstance.getExtendedSubmissions(request)
+        assertThat(result.content).hasSize(1)
+        assertThat(result.content.first()).isEqualTo(extSubmission)
+        assertThat(result.pageable).isEqualTo(pageable)
+        assertThat(result.totalElements).isEqualTo(1L)
 
         val submissionFilter = filter.captured
         assertThat(submissionFilter.released).isTrue()