Pivotal ID # 185900074: Accept Requests With Large Directories Times …

…Out (#759)

https://www.pivotaltracker.com/story/show/185900074

Avoid directories calculation at the moment of generating pagetab

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

@@ -8,9 +8,15 @@ import ebi.ac.uk.model.BioFile
 
 internal const val TO_FILE_EXTENSIONS = "ebi.ac.uk.extended.mapping.to.ToFileKt"
 
+/**
+ * The file size for inner directories is not calculated in order to avoid timing out requests for submissions that
+ * include big sized directories. @see https://www.pivotaltracker.com/story/show/185900074
+ */
 fun ExtFile.toFile(): BioFile {
     return when (this) {
-        is NfsFile -> BioFile(filePath, file.size(), type.value, attributes.map { it.toAttribute() })
+        is NfsFile ->
+            BioFile(filePath, file.size(calculateDirectories = false), type.value, attributes.map { it.toAttribute() })
+
         is FireFile -> BioFile(filePath, size, type.value, attributes.map { it.toAttribute() })
     }
 }

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

@@ -8,4 +8,5 @@ import ebi.ac.uk.model.LinksTable
 internal const val TO_TABLE_EXTENSIONS = "ebi.ac.uk.extended.mapping.to.ToTableKt"
 
 fun ExtFileTable.toTable(): FilesTable = FilesTable(files.map { file -> file.toFile() })
+
 fun ExtLinkTable.toTable(): LinksTable = LinksTable(links.map { link -> link.toLink() })

submission/persistence-filesystem/src/test/kotlin/ac/uk/ebi/biostd/persistence/filesystem/pagetab/PageTabUtilTest.kt

@@ -0,0 +1,58 @@
+package ac.uk.ebi.biostd.persistence.filesystem.pagetab
+
+import ac.uk.ebi.biostd.integration.SerializationService
+import ac.uk.ebi.biostd.integration.SubFormat.Companion.JSON_PRETTY
+import ac.uk.ebi.biostd.integration.SubFormat.Companion.TSV
+import ac.uk.ebi.biostd.integration.SubFormat.Companion.XML
+import ebi.ac.uk.extended.mapping.to.ToFileListMapper
+import ebi.ac.uk.extended.mapping.to.ToSubmissionMapper
+import ebi.ac.uk.extended.model.ExtSubmission
+import ebi.ac.uk.io.RW_R__R__
+import ebi.ac.uk.model.Submission
+import io.github.glytching.junit.extension.folder.TemporaryFolder
+import io.github.glytching.junit.extension.folder.TemporaryFolderExtension
+import io.mockk.coEvery
+import io.mockk.coVerify
+import io.mockk.every
+import io.mockk.impl.annotations.MockK
+import io.mockk.junit5.MockKExtension
+import kotlinx.coroutines.test.runTest
+import org.assertj.core.api.Assertions.assertThat
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.extension.ExtendWith
+import java.io.File
+import java.nio.file.Files
+
+@ExtendWith(MockKExtension::class, TemporaryFolderExtension::class)
+class PageTabUtilTest(
+    private val tempFolder: TemporaryFolder,
+    @MockK private val serializationService: SerializationService,
+    @MockK private val toSubmissionMapper: ToSubmissionMapper,
+    @MockK private val fileListMapper: ToFileListMapper,
+    @MockK private val extSubmission: ExtSubmission,
+    @MockK private val submission: Submission,
+) {
+    private val testInstance = PageTabUtil(serializationService, toSubmissionMapper, fileListMapper)
+
+    @Test
+    fun `generate submission pagetab`() = runTest {
+        every { extSubmission.released } returns true
+        every { extSubmission.accNo } returns "S-BSST1"
+        every { serializationService.serializeSubmission(submission, TSV) } returns "tsv-sub"
+        every { serializationService.serializeSubmission(submission, XML) } returns "xml-sub"
+        every { serializationService.serializeSubmission(submission, JSON_PRETTY) } returns "json-sub"
+        coEvery { toSubmissionMapper.toSimpleSubmission(extSubmission) } returns submission
+
+        val pageTabFiles = testInstance.generateSubPageTab(extSubmission, tempFolder.root)
+        coVerify(exactly = 1) { toSubmissionMapper.toSimpleSubmission(extSubmission) }
+        assertPageTabFile(pageTabFiles.tsv, "tsv-sub")
+        assertPageTabFile(pageTabFiles.xml, "xml-sub")
+        assertPageTabFile(pageTabFiles.json, "json-sub")
+    }
+
+    private fun assertPageTabFile(file: File, content: String) {
+        assertThat(file.exists()).isTrue()
+        assertThat(file.readText()).isEqualTo(content)
+        assertThat(Files.getPosixFilePermissions(file.toPath())).isEqualTo(RW_R__R__)
+    }
+}

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

@@ -196,13 +196,4 @@ private fun fileList2() = jsonArray(
             }
         )
     },
-    {
-        "path" to "Folder1"
-        "attributes" to jsonArray(
-            {
-                "name" to "Type"
-                "value" to "referenced directory"
-            }
-        )
-    },
 )

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

@@ -67,5 +67,4 @@ private fun fileList() = tsv {
 private fun fileList2() = tsv {
     line("Files", "Type")
     line("DataFile7.txt", "referenced")
-    line("Folder1", "referenced directory")
 }

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

@@ -206,13 +206,4 @@ private fun fileList2() = xml("table") {
             }
         }
     }
-    "file" {
-        "path" { -"Folder1" }
-        "attributes" {
-            "attribute" {
-                "name" { -"Type" }
-                "value" { -"referenced directory" }
-            }
-        }
-    }
 }

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

@@ -52,17 +52,6 @@ internal val expectedAllInOneJsonInnerFileList = jsonArray(
         )
         "type" to "file"
     },
-    {
-        "path" to "Folder1"
-        "size" to 27
-        "attributes" to jsonArray(
-            {
-                "name" to "Type"
-                "value" to "referenced directory"
-            }
-        )
-        "type" to "directory"
-    },
 )
 
 fun assertAllInOneSubmissionJson(json: String, accNo: String) {

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

@@ -105,6 +105,5 @@ internal val expectedAllInOneTsvFileList = tsv {
 internal val expectedAllInOneTsvInnerFileList = tsv {
     line("Files", "Type")
     line("DataFile7.txt", "referenced")
-    line("Folder1", "referenced directory")
     line()
 }

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

@@ -51,17 +51,6 @@ internal val expectedAllInOneXmlInnerFileList = xml("table") {
             }
         }
     }
-    "file" {
-        attribute("size", 27)
-        "path" { -"Folder1" }
-        "type" { -"directory" }
-        "attributes" {
-            "attribute" {
-                "name" { -"Type" }
-                "value" { -"referenced directory" }
-            }
-        }
-    }
 }
 
 fun assertAllInOneSubmissionXml(xml: String, accNo: String) {