Pivotal ID # 181807913: Add MD5 To Pagetab

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

@@ -72,7 +72,6 @@ internal class SubmissionClient(
         template.postForEntity<Void>("$SUBMISSIONS_URL/fileLists/validate", HttpEntity(body, headers))
     }
 
-
     private fun submitSingle(request: HttpEntity<String>, register: RegisterConfig): SubmissionResponse {
         return template
             .postForEntity<String>(buildUrl(register), request)

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

@@ -1,15 +1,23 @@
 package ebi.ac.uk.extended.mapping.to
 
+import ebi.ac.uk.extended.model.ExtAttribute
 import ebi.ac.uk.extended.model.ExtFile
 import ebi.ac.uk.extended.model.FireFile
 import ebi.ac.uk.extended.model.NfsFile
 import ebi.ac.uk.io.ext.size
+import ebi.ac.uk.model.Attribute
 import ebi.ac.uk.model.BioFile
+import ebi.ac.uk.model.constants.FileFields.MD5
 
 internal const val TO_FILE_EXTENSIONS = "ebi.ac.uk.extended.mapping.to.ToFileKt"
 
 fun ExtFile.toFile(): BioFile =
     when (this) {
-        is NfsFile -> BioFile(filePath, file.size(), type.value, attributes.mapTo(mutableListOf()) { it.toAttribute() })
-        is FireFile -> BioFile(filePath, size, type.value, attributes.mapTo(mutableListOf()) { it.toAttribute() })
+        is NfsFile -> BioFile(filePath, file.size(), type.value, generateAttributes(md5, attributes))
+        is FireFile -> BioFile(filePath, size, type.value, generateAttributes(md5, attributes))
     }
+
+private fun generateAttributes(
+    md5: String,
+    extAttrs: List<ExtAttribute>
+) = extAttrs.map { it.toAttribute() } + Attribute(MD5.value, md5)

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

@@ -8,6 +8,7 @@ import ebi.ac.uk.io.ext.md5
 import ebi.ac.uk.io.ext.size
 import ebi.ac.uk.model.Attribute
 import ebi.ac.uk.model.BioFile
+import ebi.ac.uk.model.constants.FileFields.MD5
 import ebi.ac.uk.test.createFile
 import io.github.glytching.junit.extension.folder.TemporaryFolder
 import io.github.glytching.junit.extension.folder.TemporaryFolderExtension
@@ -27,13 +28,15 @@ internal class ToFileTest(
     tempFolder: TemporaryFolder
 ) {
     private var file = tempFolder.createFile("myFile", "test content")
+    private val md5 = file.md5()
+    private val md5Attribute = Attribute(MD5.value, md5)
     private val extFile =
         NfsFile(
             "folder/myFile",
             "Files/folder/myFile",
             file,
             file.absolutePath,
-            file.md5(),
+            md5,
             file.size(),
             listOf(extAttribute)
         )
@@ -51,12 +54,12 @@ internal class ToFileTest(
 
     @Test
     fun `from fire file`() {
-        val fireFile = FireFile("folder/myFile", "Files/folder/myFile", "fireId", "md5", 12, FILE, listOf(extAttribute))
+        val fireFile = FireFile("folder/myFile", "Files/folder/myFile", "fireId", md5, 12, FILE, listOf(extAttribute))
         assertFile(fireFile.toFile())
     }
 
     private fun assertFile(file: BioFile) {
-        assertThat(file.attributes).containsExactly(attribute)
+        assertThat(file.attributes).containsExactly(attribute, md5Attribute)
         assertThat(file.size).isEqualTo(12L)
         assertThat(file.path).isEqualTo(extFile.filePath)
     }

commons/commons-serialization/src/test/kotlin/ac/uk/ebi/biostd/json/serialization/FileJsonSerializerTest.kt

@@ -15,7 +15,6 @@ import org.skyscreamer.jsonassert.JSONAssert
 import org.skyscreamer.jsonassert.JSONCompareMode
 
 class FileJsonSerializerTest {
-
     private val testInstance = createSerializer()
     val file = BioFile(
         path = "folder1/file.txt",

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/factory/AllInOneSubmissionTsv.kt

@@ -34,6 +34,7 @@ fun allInOneSubmissionTsv(accNo: String) = tsv {
 
     line("File", "DataFile1.txt")
     line("Description", "Data File 1")
+    line("md5", "D41D8CD98F00B204E9800998ECF8427E")
     line()
 
     line("Files", "Description", "Type")

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/factory/TsvSubmissionFactory.kt

@@ -54,39 +54,40 @@ fun assertAllInOneSubmissionTsv(tsv: String, accNo: String) {
     val expectedRootSectionFile = tsv {
         line("File", "DataFile1.txt")
         line("Description", "Data File 1")
+        line("md5", "D41D8CD98F00B204E9800998ECF8427E")
         line()
     }
-    assertTsvBlock(lines, 16, 18, expectedRootSectionFile)
+    assertTsvBlock(lines, 16, 19, expectedRootSectionFile)
 
     val expectedRootSectionFilesTable = tsv {
-        line("Files", "Description", "Type")
-        line("DataFile2.txt", "Data File 2", "Data")
-        line("Folder1/DataFile3.txt", "Data File 3", "Data")
-        line("Folder1/Folder2/DataFile4.txt", "Data File 4", "Data")
+        line("Files", "Description", "Type", "md5")
+        line("DataFile2.txt", "Data File 2", "Data", "D41D8CD98F00B204E9800998ECF8427E")
+        line("Folder1/DataFile3.txt", "Data File 3", "Data", "D41D8CD98F00B204E9800998ECF8427E")
+        line("Folder1/Folder2/DataFile4.txt", "Data File 4", "Data", "D41D8CD98F00B204E9800998ECF8427E")
         line()
     }
-    assertTsvBlock(lines, 19, 23, expectedRootSectionFilesTable)
+    assertTsvBlock(lines, 20, 24, expectedRootSectionFilesTable)
 
     val expectedSubsection = tsv {
         line("Stranded Total RNA-Seq", "SUBSECT-001", "SECT-001")
         line("File List", "sub-folder/file-list2.tsv")
         line()
     }
-    assertTsvBlock(lines, 24, 26, expectedSubsection)
+    assertTsvBlock(lines, 25, 27, expectedSubsection)
 
     val expectedSubsectionLinksTable = tsv {
         line("Links", "Type", "Assay type", "(TermId)", "[Ontology]")
         line("EGAD00001001282", "EGA", "RNA-Seq", "EFO_0002768", "EFO")
         line()
     }
-    assertTsvBlock(lines, 27, 29, expectedSubsectionLinksTable)
+    assertTsvBlock(lines, 28, 30, expectedSubsectionLinksTable)
 
     val expectedSubsectionsTable = tsv {
         line("Data[SECT-001]", "Title", "Description")
         line("DT-1", "Group 1 Transcription Data", "The data for zygotic transcription in mammals group 1")
         line()
     }
-    assertTsvBlock(lines, 30, 32, expectedSubsectionsTable)
+    assertTsvBlock(lines, 31, 33, expectedSubsectionsTable)
 }
 
 private fun assertTsvBlock(lines: List<String>, from: Int, to: Int, expected: Tsv) {

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/wiremock/FireMockDatabase.kt

@@ -77,7 +77,7 @@ class FireMockDatabase(
     fun findByMetadata(entries: List<MetadataEntry>): List<FireApiFile> =
         records.values.map { it.file }.filter { it.metadata?.containsAll(entries).orFalse() }
 
-    fun findByMd5(md5: String): FireApiFile? = records.values.map { it.file }.firstOrNull { it.objectMd5 == md5 }
+    fun findByMd5(md5: String): List<FireApiFile> = records.values.map { it.file }.filter { it.objectMd5 == md5 }
 
     fun findByPath(path: String): FireApiFile? = records.values.firstOrNull { it.path == path }?.file
 

submission/submission-webapp/src/itest/kotlin/ac/uk/ebi/biostd/itest/wiremock/handlers/QueryHandlers.kt

@@ -17,8 +17,9 @@ class Md5QueryHandler(
 
     override fun handle(rqt: Request): ResponseDefinition {
         val md5 = urlPattern.getGroup(rqt.url, 1)
-        val fireObject = fireDB.findByMd5(md5)
-        return ResponseDefinition.okForJson(fireObject)
+        val matches = fireDB.findByMd5(md5)
+
+        return ResponseDefinition.okForJson(matches)
     }
 }
 
@@ -31,6 +32,7 @@ class PathQueryHandler(
     override fun handle(rqt: Request): ResponseDefinition {
         val path = urlPattern.getGroup(rqt.url, 1)
         val fireObject = fireDB.findByPath(path)
+
         return if (fireObject == null) ResponseDefinition.notFound() else ResponseDefinition.okForJson(fireObject)
     }
 }
@@ -45,6 +47,7 @@ class QueryMetadataHandler(
     override fun handle(rqt: Request): ResponseDefinition {
         val keys = objectMapper.readValue<Map<String, String>>(rqt.body).map { MetadataEntry(it.key, it.value) }
         val matches = fireDB.findByMetadata(keys)
+
         return ResponseDefinition.okForJson(matches)
     }
 }