Pivotal ID # 170971193: Prepare Model For Async Processing (#173)

* Pivotal ID # 170971193: Prepare Model For Async Processing

- added independent domain model object ext

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

@@ -10,7 +10,7 @@ private const val GROUP_URL = "/groups"
 private const val PROJECTS_URL = "/projects"
 
 class CommonOperationsClient(private val template: RestTemplate) : GeneralOperations {
-    override fun getGroups(): List<Group> = template.getForObject<Array<Group>>(GROUP_URL).orEmpty().toList()
+    override fun getGroups(): List<Group> = template.getForObject<Array<Group>>(GROUP_URL).toList()
 
-    override fun getProjects(): List<Project> = template.getForObject<Array<Project>>(PROJECTS_URL).orEmpty().toList()
+    override fun getProjects(): List<Project> = template.getForObject<Array<Project>>(PROJECTS_URL).toList()
 }

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

@@ -5,7 +5,6 @@ import ac.uk.ebi.biostd.client.integration.web.FilesOperations
 import ac.uk.ebi.biostd.client.integration.web.GeneralOperations
 import ac.uk.ebi.biostd.client.integration.web.GroupFilesOperations
 import ac.uk.ebi.biostd.client.integration.web.MultipartSubmissionOperations
-import ac.uk.ebi.biostd.client.integration.web.ProjectOperations
 import ac.uk.ebi.biostd.client.integration.web.SubmissionClient
 import ac.uk.ebi.biostd.client.integration.web.SubmissionOperations
 import ac.uk.ebi.biostd.integration.SerializationService
@@ -18,7 +17,6 @@ internal class SubmissionClientImpl(
     FilesOperations by UserFilesClient(template),
     GroupFilesOperations by GroupFilesClient(template),
     SubmissionOperations by SubmissionClient(template, serializationService),
-    ProjectOperations by ProjectClient(template, serializationService),
     MultipartSubmissionOperations by MultiPartSubmissionClient(template, serializationService),
     GeneralOperations by CommonOperationsClient(template),
     DraftSubmissionOperations by SubmissionDraftClient(template)

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

@@ -21,7 +21,6 @@ interface SubmissionClient :
     SubmissionOperations,
     FilesOperations,
     GroupFilesOperations,
-    ProjectOperations,
     MultipartSubmissionOperations,
     GeneralOperations,
     DraftSubmissionOperations
@@ -80,12 +79,6 @@ interface MultipartSubmissionOperations {
     ): ResponseEntity<Submission>
 }
 
-interface ProjectOperations {
-    fun submitProject(project: File): ResponseEntity<Submission>
-
-    fun attachSubmission(projectAccNo: String, submission: File, files: List<File>): ResponseEntity<Submission>
-}
-
 interface SecurityOperations {
     fun getAuthenticatedClient(user: String, password: String): BioWebClient
 

commons/commons-bio/src/main/kotlin/ebi/ac/uk/api/dto/SubmissionDto.kt

@@ -1,5 +1,6 @@
 package ebi.ac.uk.api.dto
 
+import ebi.ac.uk.model.SubmissionMethod
 import java.time.OffsetDateTime
 
 data class SubmissionDto(
@@ -8,5 +9,6 @@ data class SubmissionDto(
     val version: Int,
     val ctime: OffsetDateTime,
     val mtime: OffsetDateTime,
-    val rtime: OffsetDateTime?
+    val rtime: OffsetDateTime?,
+    val method: SubmissionMethod?
 )

commons/commons-bio/src/main/kotlin/ebi/ac/uk/model/AccNumber.kt

@@ -1,8 +1,10 @@
 package ebi.ac.uk.model
 
+import ebi.ac.uk.base.EMPTY
+
 /**
  * Represents an submission accession number which include a pattern an a numeric value.
  */
-class AccNumber(val prefix: String, val numericValue: Long) {
-    override fun toString() = "$prefix$numericValue"
+data class AccNumber(val prefix: String, val numericValue: Long? = null) {
+    override fun toString() = "$prefix${numericValue ?: EMPTY}"
 }

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

@@ -10,6 +10,9 @@ class SubmissionFolderResolver(private val basePath: Path) {
     fun getSubmissionFolder(submission: ExtendedSubmission): Path =
         basePath.resolve(SUBMISSION_PATH).resolve(submission.relPath)
 
+    fun getSubmissionFolder(submissionRelPath: String): Path =
+        basePath.resolve(SUBMISSION_PATH).resolve(submissionRelPath)
+
     fun getSubFilePath(relPath: String, fileName: String): Path =
         basePath.resolve(SUBMISSION_PATH).resolve(relPath).resolve(FILES_PATH).resolve(escapeFileName(fileName))
 

commons/commons-model-extended/src/main/kotlin/ebi/ac/uk/extended/mapping/serialization/from/ToExtAttribute.kt

@@ -4,9 +4,13 @@ import ebi.ac.uk.extended.model.ExtAttribute
 import ebi.ac.uk.extended.model.ExtAttributeDetail
 import ebi.ac.uk.model.Attribute
 import ebi.ac.uk.model.AttributeDetail
+import ebi.ac.uk.model.constants.SectionFields
 
 internal const val TO_EXT_ATTRIBUTE_EXTENSIONS = "ebi.ac.uk.extended.mapping.serialization.from.ToExtAttributeKt"
 
-fun Attribute.toExtAttribute() = ExtAttribute(name, value, reference, toDetails(nameAttrs), toDetails(valueAttrs))
+fun Attribute.toExtAttribute(): ExtAttribute {
+    val attrValue = if (name == SectionFields.FILE_LIST.value) value.substringBeforeLast(".") else value
+    return ExtAttribute(name, attrValue, reference, toDetails(nameAttrs), toDetails(valueAttrs))
+}
 
 private fun toDetails(details: List<AttributeDetail>) = details.map { ExtAttributeDetail(it.name, it.value) }

commons/commons-model-extended/src/main/kotlin/ebi/ac/uk/extended/mapping/serialization/from/ToExtFileList.kt

@@ -7,4 +7,7 @@ import ebi.ac.uk.model.FileList
 internal const val TO_EXT_LIBRARY_FILE_EXTENSIONS = "ebi.ac.uk.extended.mapping.serialization.from.ToExtFileListKt"
 
 fun FileList.toExtFileList(fileSource: FilesSource): ExtFileList =
-    ExtFileList(name, fileSource.getFile(name), referencedFiles.map { it.toExtFile(fileSource) })
+    ExtFileList(
+        name.substringBeforeLast("."),
+        fileSource.getFile(name),
+        referencedFiles.map { it.toExtFile(fileSource) })

commons/commons-model-extended/src/main/kotlin/ebi/ac/uk/extended/mapping/serialization/from/ToExtSection.kt

@@ -14,14 +14,5 @@ fun Section.toExtSection(source: FilesSource): ExtSection {
         attributes = attributes.map { it.toExtAttribute() },
         files = files.map { either -> either.bimap({ it.toExtFile(source) }, { it.toExtTable(source) }) },
         links = links.map { either -> either.bimap({ it.toExtLink() }, { it.toExtTable() }) },
-        sections = sections.map { either -> either.bimap({ it.toExtSubSection(source) }, { it.toExtTable(source) }) })
-}
-
-fun Section.toExtSubSection(source: FilesSource): ExtSection {
-    return ExtSection(
-        type = type,
-        accNo = accNo,
-        fileList = fileList?.toExtFileList(source),
-        attributes = attributes.map { it.toExtAttribute() }
-    )
+        sections = sections.map { either -> either.bimap({ it.toExtSection(source) }, { it.toExtTable(source) }) })
 }

commons/commons-model-extended/src/main/kotlin/ebi/ac/uk/extended/mapping/serialization/to/ToSection.kt

@@ -13,13 +13,5 @@ fun ExtSection.toSection(): Section {
         attributes = attributes.mapTo(mutableListOf()) { it.toAttribute() },
         files = files.mapTo(mutableListOf()) { either -> either.bimap({ it.toFile() }, { it.toTable() }) },
         links = links.mapTo(mutableListOf()) { either -> either.bimap({ it.toLink() }, { it.toTable() }) },
-        sections = sections.mapTo(mutableListOf()) { either -> either.bimap({ it.toSubSection() }, { it.toTable() }) })
-}
-
-fun ExtSection.toSubSection(): Section {
-    return Section(
-        type = type,
-        accNo = accNo,
-        fileList = fileList?.toFileList(),
-        attributes = attributes.mapTo(mutableListOf()) { it.toAttribute() })
+        sections = sections.mapTo(mutableListOf()) { either -> either.bimap({ it.toSection() }, { it.toTable() }) })
 }

commons/commons-model-extended/src/main/kotlin/ebi/ac/uk/extended/mapping/serialization/to/ToSubmission.kt

@@ -1,7 +1,9 @@
 package ebi.ac.uk.extended.mapping.serialization.to
 
 import ebi.ac.uk.extended.model.ExtSubmission
+import ebi.ac.uk.model.Attribute
 import ebi.ac.uk.model.Submission
+import ebi.ac.uk.model.constants.SubFields
 import ebi.ac.uk.model.extensions.creationTime
 import ebi.ac.uk.model.extensions.modificationTime
 import ebi.ac.uk.model.extensions.releaseTime
@@ -14,11 +16,20 @@ fun ExtSubmission.toSimpleSubmission(): Submission {
     return Submission(
         accNo = accNo,
         section = section.toSection(),
-        attributes = attributes.map { it.toAttribute() }.toMutableList(),
+        attributes = getSubmissionAttributes(),
         tags = tags.mapTo(mutableListOf()) { Pair(it.name, it.value) }
     )
 }
 
+private fun ExtSubmission.getSubmissionAttributes(): List<Attribute> {
+    val subAttrs = attributes.map { it.toAttribute() }.toMutableList()
+
+    return when (releaseTime) {
+        null -> subAttrs
+        else -> subAttrs.plus(Attribute(SubFields.RELEASE_DATE, releaseTime.toLocalDate()))
+    }
+}
+
 /**
  * Return a extended submission which contains submission secret information and internal information.
  */

commons/commons-model-extended/src/main/kotlin/ebi/ac/uk/extended/model/ExtSubmissionExtensions.kt

@@ -9,5 +9,5 @@ val ExtSubmission.allReferencedFiles
 val ExtSubmission.allFiles
     get(): List<ExtFile> = allSections.flatMap { it.allFiles }
 
-val ExtSubmission.allFileLists
+val ExtSubmission.allFileListSections
     get(): List<ExtFileList> = allSections.mapNotNull { it.fileList }

commons/commons-model-extended/src/main/kotlin/ebi/ac/uk/extended/model/ExtendedModel.kt

@@ -1,6 +1,7 @@
 package ebi.ac.uk.extended.model
 
 import arrow.core.Either
+import ebi.ac.uk.model.SubmissionMethod
 import ebi.ac.uk.model.constants.ProcessingStatus
 import java.io.File
 import java.time.OffsetDateTime
@@ -38,7 +39,9 @@ data class ExtSection(
 
 data class ExtSubmission(
     val accNo: String,
+    var version: Int,
     val title: String?,
+    val method: SubmissionMethod,
     val relPath: String,
     val rootPath: String?,
     val released: Boolean,

commons/commons-model-extended/src/test/kotlin/ebi/ac/uk/extended/mapping/serialization/from/ToExtSectionTest.kt

@@ -8,7 +8,6 @@ import ebi.ac.uk.extended.model.ExtFileList
 import ebi.ac.uk.extended.model.ExtFileTable
 import ebi.ac.uk.extended.model.ExtLink
 import ebi.ac.uk.extended.model.ExtLinkTable
-import ebi.ac.uk.extended.model.ExtSection
 import ebi.ac.uk.extended.model.ExtSectionTable
 import ebi.ac.uk.io.sources.FilesSource
 import ebi.ac.uk.model.Attribute
@@ -37,25 +36,24 @@ class ToExtSectionTest(
     @MockK val fileTable: FilesTable,
     @MockK val link: Link,
     @MockK val linkTable: LinksTable,
-    @MockK val subsection: Section,
     @MockK val sectionTable: SectionsTable,
     @MockK val extFileList: ExtFileList,
     @MockK val extAttribute: ExtAttribute,
     @MockK val extFile: ExtFile,
     @MockK val extFileTable: ExtFileTable,
     @MockK val extLink: ExtLink,
     @MockK val extLinkTable: ExtLinkTable,
-    @MockK val extSubsection: ExtSection,
     @MockK val extSectionTable: ExtSectionTable
 ) {
+    private val subSection = Section(type = "subtype", accNo = "accNo1")
     private val section = Section(
         type = "type",
         accNo = "accNo",
         fileList = fileList,
         attributes = listOf(attribute),
         files = mutableListOf(left(file), right(fileTable)),
         links = mutableListOf(left(link), right(linkTable)),
-        sections = mutableListOf(left(subsection), right(sectionTable))
+        sections = mutableListOf(left(subSection), right(sectionTable))
     )
 
     @Test
@@ -76,7 +74,6 @@ class ToExtSectionTest(
             every { linkTable.toExtTable() } returns extLinkTable
             every { sectionTable.toExtTable(fileSource) } returns extSectionTable
             every { fileList.toExtFileList(fileSource) } returns extFileList
-            every { subsection.toExtSubSection(fileSource) } returns extSubsection
 
             val sectionResult = section.toExtSection(fileSource)
             assertThat(sectionResult.accNo).isEqualTo(section.accNo)
@@ -87,8 +84,11 @@ class ToExtSectionTest(
             assertThat(sectionResult.files.second()).isEqualTo(right(extFileTable))
             assertThat(sectionResult.links.first()).isEqualTo(left(extLink))
             assertThat(sectionResult.links.second()).isEqualTo(right(extLinkTable))
-            assertThat(sectionResult.sections.first()).isEqualTo(left(extSubsection))
             assertThat(sectionResult.sections.second()).isEqualTo(right(extSectionTable))
+            sectionResult.sections.first().mapLeft {
+                assertThat(it.type).isEqualTo("subtype")
+                assertThat(it.accNo).isEqualTo("accNo1")
+            }
         }
     }
 }

commons/commons-model-extended/src/test/kotlin/ebi/ac/uk/extended/mapping/serialization/to/ToSectionTest.kt

@@ -16,7 +16,6 @@ import ebi.ac.uk.model.FileList
 import ebi.ac.uk.model.FilesTable
 import ebi.ac.uk.model.Link
 import ebi.ac.uk.model.LinksTable
-import ebi.ac.uk.model.Section
 import ebi.ac.uk.model.SectionsTable
 import ebi.ac.uk.util.collections.second
 import io.mockk.every
@@ -35,25 +34,24 @@ class ToSectionTest(
     @MockK val fileTable: FilesTable,
     @MockK val link: Link,
     @MockK val linkTable: LinksTable,
-    @MockK val subsection: Section,
     @MockK val sectionTable: SectionsTable,
     @MockK val extFileList: ExtFileList,
     @MockK val extAttribute: ExtAttribute,
     @MockK val extFile: ExtFile,
     @MockK val extFileTable: ExtFileTable,
     @MockK val extLink: ExtLink,
     @MockK val extLinkTable: ExtLinkTable,
-    @MockK val extSubsection: ExtSection,
     @MockK val extSectionTable: ExtSectionTable
 ) {
+    private val subSection = ExtSection(type = "subtype", accNo = "accNo1")
     private val section = ExtSection(
         type = "type",
         accNo = "accNo",
         fileList = extFileList,
         attributes = listOf(extAttribute),
         files = listOf(left(extFile), right(extFileTable)),
         links = listOf(left(extLink), right(extLinkTable)),
-        sections = listOf(left(extSubsection), right(extSectionTable))
+        sections = listOf(left(subSection), right(extSectionTable))
     )
 
     @Test
@@ -74,7 +72,6 @@ class ToSectionTest(
             every { extLinkTable.toTable() } returns linkTable
             every { extSectionTable.toTable() } returns sectionTable
             every { extFileList.toFileList() } returns fileList
-            every { extSubsection.toSubSection() } returns subsection
 
             val sectionResult = section.toSection()
             assertThat(sectionResult.accNo).isEqualTo(section.accNo)
@@ -85,8 +82,11 @@ class ToSectionTest(
             assertThat(sectionResult.files.second()).isEqualTo(right(fileTable))
             assertThat(sectionResult.links.first()).isEqualTo(left(link))
             assertThat(sectionResult.links.second()).isEqualTo(right(linkTable))
-            assertThat(sectionResult.sections.first()).isEqualTo(left(subsection))
             assertThat(sectionResult.sections.second()).isEqualTo(right(sectionTable))
+            sectionResult.sections.first().mapLeft {
+                assertThat(it.type).isEqualTo("subtype")
+                assertThat(it.accNo).isEqualTo("accNo1")
+            }
         }
     }
 }