Promote to PROD (#313)

Features: * Pivotal ID # 174054535: Disable superUser in request * Pivotal ID # 174076301: Update pmc api (#248) * Pivotal ID # 172817960: Resubmit Notfication (#255) * Pivotal ID # 169837866: Async File Processing (#256) * Pivotal ID # 172671360: Warn Users About Upcoming Releases (#268) * Pivotal ID # 173783625: Partial Updates Timestamp (#269) * Pivotal ID # 174922363: Add support for previous submission files source * Pivotal ID # 173908844: Add ext file fields attributes (#260) * Pivotal ID # 173817309: FIRE Client (#272) * Pivotal ID # 174746920: Include status fetching submissions (#275) * Pivotal ID # 171026062: Submission files MD5 Generation (#274) * Pivotal ID # 175266840: Manual Set AccNo Sequence (#287) * Pivotal ID # 175101522: File Path Field (#294) * Pivotal:ID # 175839554 : include user tag as part of extended submission tags (#296) * Pivotal ID # 175825508: Store submission request - async processing Bug Fixes: * Pivotal ID # 173457302: RelPath Calculation (#244) * Pivotal ID # 173750220: Author TSV Serialization (#245) * pivotal ID # 174127719: Transaction lock (#250) * Pivotal ID # 171230259: Draft creation time outs for big submissions (#251) * Pivotal ID # 174275642: Submission loading strategy (#254) * Pivotal ID # 174316468: Project Refresh AccNo Template Validation (#257) * Pivotal ID # 173919045: Restrict Execute Permissions On HTTP Uploaded Files (#265) * Pivotal ID # 174621725: Wrong Notifications UI URL (#266) * Pivotal ID # 174697743: Delete draft missing transaction * Pivotal ID # 174801815: Permissions For Deleted Submissions (#270) * Pivotal ID # 171026062: FTP Hard Links (#276) * Pivotal ID # 175357899: Re-submit a submission with rooPath (#279) * Pivotal ID # 175359447: Async Concurrent Processing Submission (#281) * Pivotal ID # 175780531: Ext Submission Submitter Validation (#300) * Pivotal ID # 175632448: Regular User Resubmission (#306) * Pivotal ID # 176052254: JSON Submission Attributes Validation (#310) * Pivotal ID # 176052264: Inner Folder Mapping (#311) Chore Tasks: * Pivotal ID # 174275207: Test Using The Persistence Layer (#262) * Pivotal ID # 174947046: ExtSubmission list api (#273) * Pivotal ID # 174274579: User eager groups (#280) * Pivotal ID # 175632448: Extra persistence layer interfaces to avoid dependencies on SQL classes (#283) * Pivotal ID # 175163839: Submission Operations Refactor (#297) * Pivotal ID # 175926073: Simplify accNoService (#298) * Pivotal ID # 175163839: Stats Refactor (#299)
EBIBioStudies · Dec 10, 2020 · 31cbec5 · 31cbec5
1 parent ac70156
commit 31cbec5
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Showing 13 changed files with 68 additions and 14 deletions.
diff --git a/...ion/src/main/kotlin/uk/ac/ebi/extended/serialization/deserializers/ExtFileDeserializer.kt b/...ion/src/main/kotlin/uk/ac/ebi/extended/serialization/deserializers/ExtFileDeserializer.kt
@@ -9,7 +9,7 @@ import com.fasterxml.jackson.databind.node.TextNode
 import ebi.ac.uk.extended.model.ExtFile
 import uk.ac.ebi.extended.serialization.constants.ExtSerializationFields.ATTRIBUTES
 import uk.ac.ebi.extended.serialization.constants.ExtSerializationFields.FILE
-import uk.ac.ebi.extended.serialization.constants.ExtSerializationFields.FILE_NAME
+import uk.ac.ebi.extended.serialization.constants.ExtSerializationFields.FILE_PATH
 import uk.ac.ebi.serialization.extensions.convertList
 import uk.ac.ebi.serialization.extensions.findNode
 import uk.ac.ebi.serialization.extensions.getNode
@@ -27,8 +27,7 @@ class ExtFileDeserializer : JsonDeserializer<ExtFile>() {
 
         return ExtFile(
             file = file,
-            fileName = node.getNode<TextNode>(FILE_NAME).textValue(),
-            attributes = mapper.convertList(node.findNode(ATTRIBUTES))
-        )
+            fileName = node.getNode<TextNode>(FILE_PATH).textValue(),
+            attributes = mapper.convertList(node.findNode(ATTRIBUTES)))
     }
 }
diff --git a/...st/kotlin/uk/ac/ebi/extended/serialization/deserializers/EitherExtTypeDeserializerTest.kt b/...st/kotlin/uk/ac/ebi/extended/serialization/deserializers/EitherExtTypeDeserializerTest.kt
@@ -62,6 +62,7 @@ class EitherExtTypeDeserializerTest(private val tempFolder: TemporaryFolder) {
         val json = jsonObj {
             "file" to file.absolutePath
             "fileName" to "test-file.txt"
+            "path" to "test-file.txt"
             "extType" to "file"
         }.toString()
 
@@ -80,6 +81,7 @@ class EitherExtTypeDeserializerTest(private val tempFolder: TemporaryFolder) {
             "files" to jsonArray(jsonObj {
                 "file" to file.absolutePath
                 "fileName" to "test-file-table.txt"
+                "path" to "test-file-table.txt"
                 "extType" to "file"
             })
             "extType" to "filesTable"

diff --git a/...src/test/kotlin/uk/ac/ebi/extended/serialization/deserializers/ExtFileDeserializerTest.kt b/...src/test/kotlin/uk/ac/ebi/extended/serialization/deserializers/ExtFileDeserializerTest.kt
@@ -23,6 +23,7 @@ class ExtFileDeserializerTest(private val tempFolder: TemporaryFolder) {
         val json = jsonObj {
             "file" to file.absolutePath
             "fileName" to "test-file.txt"
+            "path" to "test-file.txt"
             "attributes" to jsonArray(jsonObj {
                 "name" to "Type"
                 "value" to "Data"
@@ -38,6 +39,28 @@ class ExtFileDeserializerTest(private val tempFolder: TemporaryFolder) {
         assertThat(extFile.attributes.first().value).isEqualTo("Data")
     }
 
+    @Test
+    fun `deserialize with inner path`() {
+        val file = tempFolder.createFile("test-file.txt")
+        val json = jsonObj {
+            "file" to file.absolutePath
+            "fileName" to "test-file.txt"
+            "path" to "a/b/test-file.txt"
+            "attributes" to jsonArray(jsonObj {
+                "name" to "Type"
+                "value" to "Data"
+            })
+            "extType" to "file"
+        }.toString()
+
+        val extFile = testInstance.deserialize<ExtFile>(json)
+        assertThat(extFile.file).isEqualTo(file)
+        assertThat(extFile.fileName).isEqualTo("a/b/test-file.txt")
+        assertThat(extFile.attributes).hasSize(1)
+        assertThat(extFile.attributes.first().name).isEqualTo("Type")
+        assertThat(extFile.attributes.first().value).isEqualTo("Data")
+    }
+
     @Test
     fun `invalid file`() {
         val json = jsonObj {

diff --git a/...st/kotlin/uk/ac/ebi/extended/serialization/deserializers/ExtFilesTableDeserializerTest.kt b/...st/kotlin/uk/ac/ebi/extended/serialization/deserializers/ExtFilesTableDeserializerTest.kt
@@ -22,6 +22,7 @@ class ExtFilesTableDeserializerTest(private val tempFolder: TemporaryFolder) {
             "files" to jsonArray(jsonObj {
                 "file" to file.absolutePath
                 "fileName" to "test-file.txt"
+                "path" to "test-file.txt"
                 "attributes" to jsonArray(jsonObj {
                     "name" to "Type"
                     "value" to "Data"

diff --git a/.../test/kotlin/uk/ac/ebi/extended/serialization/deserializers/ExtSectionDeserializerTest.kt b/.../test/kotlin/uk/ac/ebi/extended/serialization/deserializers/ExtSectionDeserializerTest.kt
@@ -45,8 +45,10 @@ class ExtSectionDeserializerTest(private val tempFolder: TemporaryFolder) {
             "type" to "Study"
             "fileList" to jsonObj {
                 "fileName" to "file-list.json"
+                "path" to "file-list.json"
                 "files" to jsonArray(jsonObj {
                     "fileName" to "ref-file.txt"
+                    "path" to "ref-file.txt"
                     "file" to referencedFile.absolutePath
                     "extType" to "file"
                 })
@@ -68,12 +70,14 @@ class ExtSectionDeserializerTest(private val tempFolder: TemporaryFolder) {
             })
 
             "files" to jsonArray(jsonObj {
-                "fileName" to "section-file.txt"
+                "fileName" to "section-file-inner-folders.txt"
+                "path" to "a/b/section-file-inner-folders.txt"
                 "file" to sectionFile.absolutePath
                 "extType" to "file"
             }, jsonObj {
                 "files" to jsonArray(jsonObj {
                     "fileName" to "section-file-table.txt"
+                    "path" to "section-file-table.txt"
                     "file" to sectionFilesTable.absolutePath
                     "extType" to "file"
                 })
@@ -131,7 +135,7 @@ class ExtSectionDeserializerTest(private val tempFolder: TemporaryFolder) {
         assertThat(extFile.isLeft()).isTrue()
         extFile.ifLeft {
             assertThat(it.file).isEqualTo(sectionFile)
-            assertThat(it.fileName).isEqualTo("section-file.txt")
+            assertThat(it.fileName).isEqualTo("a/b/section-file-inner-folders.txt")
         }
 
         val extFilesTable = extFiles.second()

diff --git a/...commons-serialization-util/src/main/kotlin/uk/ac/ebi/serialization/extensions/JsonNode.kt b/...commons-serialization-util/src/main/kotlin/uk/ac/ebi/serialization/extensions/JsonNode.kt
@@ -20,7 +20,7 @@ inline fun <reified T : JsonNode?> JsonNode.ensureType(node: JsonNode, property:
     require(node is T) {
         val type = node::class.java.simpleName
         val expectedType = T::class.java.simpleName
-        "Expecting node: '$this', property: '$property' to be of type '$expectedType' but '$type' find instead"
+        "Expecting node: '$this', property: '$property' to be of type '$expectedType' but '$type' was found instead"
     }
 
     return node

diff --git a/...zation/src/main/kotlin/ac/uk/ebi/biostd/json/deserialization/AttributeJsonDeserializer.kt b/...zation/src/main/kotlin/ac/uk/ebi/biostd/json/deserialization/AttributeJsonDeserializer.kt
@@ -5,6 +5,7 @@ import ac.uk.ebi.biostd.common.NAME_ATTRIBUTES
 import ac.uk.ebi.biostd.common.REFERENCE
 import ac.uk.ebi.biostd.common.VALUE
 import ac.uk.ebi.biostd.common.VAL_ATTRIBUTES
+import ac.uk.ebi.biostd.json.exception.NoAttributeValueException
 import com.fasterxml.jackson.core.JsonParser
 import com.fasterxml.jackson.databind.DeserializationContext
 import com.fasterxml.jackson.databind.JsonNode
@@ -20,10 +21,13 @@ internal class AttributeJsonDeserializer : StdDeserializer<Attribute>(Attribute:
     override fun deserialize(jp: JsonParser, ctxt: DeserializationContext): Attribute {
         val mapper = jp.codec as ObjectMapper
         val node: JsonNode = mapper.readTree(jp)
+        val name = node.getNode<TextNode>(NAME).textValue()
+        val value = node.getNode<TextNode>(VALUE).textValue()
+        require(value.isNotBlank()) { throw NoAttributeValueException(name) }
 
         return Attribute(
-            name = node.getNode<TextNode>(NAME).textValue(),
-            value = node.getNode<TextNode>(VALUE).textValue(),
+            name = name,
+            value = value,
             reference = node.get(REFERENCE)?.asBoolean().orFalse(),
             valueAttrs = mapper.convertList(node.get(VAL_ATTRIBUTES)),
             nameAttrs = mapper.convertList(node.get(NAME_ATTRIBUTES)))

diff --git a/...erialization/src/main/kotlin/ac/uk/ebi/biostd/json/exception/NoAttributeValueException.kt b/...erialization/src/main/kotlin/ac/uk/ebi/biostd/json/exception/NoAttributeValueException.kt
@@ -0,0 +1,3 @@
+package ac.uk.ebi.biostd.json.exception
+
+class NoAttributeValueException(name: String) : RuntimeException("The value for the attribute '$name' can't be empty")
diff --git a/...zation/src/test/kotlin/ac/uk/ebi/biostd/json/deserialization/AttributeDeserializerTest.kt b/...zation/src/test/kotlin/ac/uk/ebi/biostd/json/deserialization/AttributeDeserializerTest.kt
@@ -1,6 +1,7 @@
 package ac.uk.ebi.biostd.json.deserialization
 
 import ac.uk.ebi.biostd.json.JsonSerializer
+import ac.uk.ebi.biostd.json.exception.NoAttributeValueException
 import ebi.ac.uk.dsl.json.jsonArray
 import ebi.ac.uk.dsl.json.jsonObj
 import ebi.ac.uk.model.Attribute
@@ -14,21 +15,33 @@ class AttributeDeserializerTest {
     private val testInstance = JsonSerializer.mapper
 
     @Test
-    fun `deserialize no value`() {
+    fun `deserialize empty`() {
         val exception = assertThrows<IllegalStateException> { testInstance.deserialize<Attribute>("{}") }
 
         assertThat(exception.message).isEqualTo("Expecting to find property with 'name' in node '{}'")
     }
 
+    @Test
+    fun `deserialize no value`() {
+        val exception = assertThrows<NoAttributeValueException> { testInstance.deserialize<Attribute>("""{
+            |"name": "attr name",
+            |"value": ""
+            |}""".trimMargin()) }
+
+        assertThat(exception.message).isEqualTo("The value for the attribute 'attr name' can't be empty")
+    }
+
     @Test
     fun `deserialize with wrong type`() {
         val invalidJson = jsonObj {
             "name" to jsonArray(1, 2, 3)
         }.toString()
 
+        val node = "{\"name\":[1,2,3]}"
         val exception = assertThrows<IllegalArgumentException> { testInstance.deserialize<Attribute>(invalidJson) }
+
         assertThat(exception.message).isEqualTo(
-            "Expecting node: '{\"name\":[1,2,3]}', property: 'name' to be of type 'TextNode' but 'ArrayNode' find instead")
+            "Expecting node: '$node', property: 'name' to be of type 'TextNode' but 'ArrayNode' was found instead")
     }
 
     @Test

diff --git a/...rialization/src/test/kotlin/ac/uk/ebi/biostd/json/deserialization/FileDeserializerTest.kt b/...rialization/src/test/kotlin/ac/uk/ebi/biostd/json/deserialization/FileDeserializerTest.kt
@@ -26,9 +26,10 @@ class FileDeserializerTest {
             "path" to jsonArray(1, 2, 3)
         }.toString()
 
+        val node = "{\"path\":[1,2,3]}"
         val exception = assertThrows<IllegalArgumentException> { testInstance.deserialize<File>(invalidJson) }
         assertThat(exception.message).isEqualTo(
-            "Expecting node: '{\"path\":[1,2,3]}', property: 'path' to be of type 'TextNode' but 'ArrayNode' find instead")
+            "Expecting node: '$node', property: 'path' to be of type 'TextNode' but 'ArrayNode' was found instead")
     }
 
     @Test

diff --git a/...rialization/src/test/kotlin/ac/uk/ebi/biostd/json/deserialization/LinkDeserializerTest.kt b/...rialization/src/test/kotlin/ac/uk/ebi/biostd/json/deserialization/LinkDeserializerTest.kt
@@ -26,9 +26,10 @@ class LinkDeserializerTest {
             "url" to jsonArray(1, 2, 3)
         }.toString()
 
+        val node = "{\"url\":[1,2,3]}"
         val exception = assertThrows<IllegalArgumentException> { testInstance.deserialize<Link>(invalidJson) }
         assertThat(exception.message).isEqualTo(
-            "Expecting node: '{\"url\":[1,2,3]}', property: 'url' to be of type 'TextNode' but 'ArrayNode' find instead")
+            "Expecting node: '$node', property: 'url' to be of type 'TextNode' but 'ArrayNode' was found instead")
     }
 
     @Test

diff --git a/...lization/src/test/kotlin/ac/uk/ebi/biostd/json/deserialization/SectionDeserializerTest.kt b/...lization/src/test/kotlin/ac/uk/ebi/biostd/json/deserialization/SectionDeserializerTest.kt
@@ -19,9 +19,10 @@ class SectionDeserializerTest {
             "accno" to jsonArray(1, 2, 3)
         }.toString()
 
+        val node = "{\"accno\":[1,2,3]}"
         val exception = assertThrows<IllegalArgumentException> { testInstance.deserialize<Section>(invalidJson) }
         assertThat(exception.message).isEqualTo(
-            "Expecting node: '{\"accno\":[1,2,3]}', property: 'accno' to be of type 'TextNode' but 'ArrayNode' find instead")
+            "Expecting node: '$node', property: 'accno' to be of type 'TextNode' but 'ArrayNode' was found instead")
     }
 
     @Test

diff --git a/...on/persistence-sql/src/main/kotlin/ac/uk/ebi/biostd/persistence/model/DbSubmissionStat.kt b/...on/persistence-sql/src/main/kotlin/ac/uk/ebi/biostd/persistence/model/DbSubmissionStat.kt
@@ -3,6 +3,7 @@ package ac.uk.ebi.biostd.persistence.model
 import ac.uk.ebi.biostd.persistence.common.model.SubmissionStat
 import ac.uk.ebi.biostd.persistence.common.model.SubmissionStatType
 import ac.uk.ebi.biostd.persistence.common.model.SubmissionStatType.VIEWS
+import com.fasterxml.jackson.annotation.JsonIgnore
 import javax.persistence.Column
 import javax.persistence.Entity
 import javax.persistence.EnumType
@@ -26,6 +27,7 @@ class DbSubmissionStat(
 ) : SubmissionStat {
     @Id
     @GeneratedValue
+    @JsonIgnore
     var id: Long = 0L
 
     constructor() : this("", -1, VIEWS)
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		package ac.uk.ebi.biostd.json.exception

		class NoAttributeValueException(name: String) : RuntimeException("The value for the attribute '$name' can't be empty")