Pivotal ID # 184191732: Prioritize Pagetab files processing (#673)

https://www.pivotaltracker.com/story/show/184191732
EBIBioStudies · Feb 1, 2023 · 4ac22f9 · 4ac22f9
1 parent 9e2c3d7
commit 4ac22f9
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Showing 2 changed files with 15 additions and 5 deletions.
diff --git a/...on/src/main/kotlin/uk/ac/ebi/extended/serialization/service/ExtSerializationServiceExt.kt b/...on/src/main/kotlin/uk/ac/ebi/extended/serialization/service/ExtSerializationServiceExt.kt
@@ -5,13 +5,18 @@ import ebi.ac.uk.extended.model.ExtSubmission
 import ebi.ac.uk.extended.model.allFileList
 import ebi.ac.uk.extended.model.allSectionsFiles
 
+/**
+ * Return a sequence with all file list of a submission. Pagetab files are retrieved first, followed by section files
+ * and file list files.
+ */
 fun ExtSerializationService.fileSequence(submission: ExtSubmission): Sequence<ExtFile> {
     return sequence {
-        for (fileList in submission.allFileList) {
-            fileList.file.inputStream().use { deserializeList(it).forEach { yield(it) } }
-            fileList.pageTabFiles.forEach { yield(it) }
-        }
-        submission.allSectionsFiles.forEach { yield(it) }
         submission.pageTabFiles.forEach { yield(it) }
+        submission.allFileList.forEach { fileList -> fileList.pageTabFiles.forEach { yield(it) } }
+
+        submission.allSectionsFiles.forEach { yield(it) }
+        submission.allFileList
+            .map { it.file }
+            .forEach { it.inputStream().use { stream -> deserializeList(stream).forEach { file -> yield(file) } } }
     }
 }
diff --git a/...src/main/kotlin/ac/uk/ebi/biostd/submission/submitter/request/SubmissionRequestIndexer.kt b/...src/main/kotlin/ac/uk/ebi/biostd/submission/submitter/request/SubmissionRequestIndexer.kt
@@ -15,6 +15,11 @@ class SubmissionRequestIndexer(
     private val requestService: SubmissionRequestPersistenceService,
     private val filesRequestService: SubmissionRequestFilesPersistenceService,
 ) {
+    /**
+     * Index submission request file by creating records for each one. Note that pagetab files are processed first,
+     * guarantee by @see uk.ac.ebi.extended.serialization.service.ExtSerializationService.fileSequence to reduce time
+     * submission main/core data is not available.
+     */
     fun indexRequest(accNo: String, version: Int) {
         val request = requestService.getPendingRequest(accNo, version)
         val sub = request.submission