From 34e78205147e1fed90c3b28453d35eccb272c839 Mon Sep 17 00:00:00 2001
From: Lucio Lelii <lucio@Lucios-MacBook-Air.local>
Date: Fri, 22 Nov 2024 11:28:38 +0100
Subject: [PATCH] solved issue on upload Archive functionality

---
 CHANGELOG.md                                  |  2 +-
 pom.xml                                       |  8 +--
 .../handlers/items/ItemHandler.java           | 51 +++++++++----------
 .../storage/backend/impl/S3Backend.java       |  5 +-
 src/main/resources/init/NodeType.cnd          |  4 +-
 5 files changed, 32 insertions(+), 38 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 226f5f6..c461d91 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [v2.0.0]
+## [v2.0.0-SNAPSHOT]
 
  - ceph as default storage
  - vre folders can define specific bucket as backend
diff --git a/pom.xml b/pom.xml
index a5bc679..8aa2a2e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -10,7 +10,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.gcube.data.access</groupId>
 	<artifactId>storagehub</artifactId>
-	<version>2.0.0</version>
+	<version>2.0.0-SNAPSHOT</version>
 	<name>storagehub</name>
 	<scm>
 		<connection>
@@ -42,7 +42,7 @@
 			<dependency>
 				<groupId>org.gcube.distribution</groupId>
 				<artifactId>gcube-smartgears-bom</artifactId>
-				<version>4.0.0</version>
+				<version>4.0.1-SNAPSHOT</version>
 				<type>pom</type>
 				<scope>import</scope>
 			</dependency>
@@ -343,8 +343,8 @@
 			<artifactId>aws-java-sdk-s3</artifactId>
 			<version>1.12.763</version>
 		</dependency>
-		
-		<!-- https://mvnrepository.com/artifact/io.minio/minio 
+
+		<!-- https://mvnrepository.com/artifact/io.minio/minio
 		<dependency>
 			<groupId>io.minio</groupId>
 			<artifactId>minio</artifactId>
diff --git a/src/main/java/org/gcube/data/access/storagehub/handlers/items/ItemHandler.java b/src/main/java/org/gcube/data/access/storagehub/handlers/items/ItemHandler.java
index beef969..c605608 100644
--- a/src/main/java/org/gcube/data/access/storagehub/handlers/items/ItemHandler.java
+++ b/src/main/java/org/gcube/data/access/storagehub/handlers/items/ItemHandler.java
@@ -1,6 +1,7 @@
 package org.gcube.data.access.storagehub.handlers.items;
 
 import java.io.BufferedInputStream;
+import java.io.IOException;
 import java.io.InputStream;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -102,27 +103,15 @@ public class ItemHandler {
 		authChecker.checkWriteAuthorizationControl(ses, parameters.getUser(), destination.getIdentifier(), true);
 
 		try {
-			Node newNode = null;
-			switch (parameters.getMangedType()) {
-			case FILE:
-				newNode = create((FileCreationParameters) parameters, destination);
-				break;
-			case FOLDER:
-				newNode = create((FolderCreationParameters) parameters, destination);
-				break;
-			case ARCHIVE:
-				newNode = create((ArchiveStructureCreationParameter) parameters, destination);
-				break;
-			case URL:
-				newNode = create((URLCreationParameters) parameters, destination);
-				break;
-			case GCUBEITEM:
-				newNode = create((GCubeItemCreationParameters) parameters, destination);
-				break;
-			default:
-				throw new InvalidCallParameters("Item not supported");
-			}
-			log.debug("item with id {} correctly created", newNode.getIdentifier());
+			Node newNode = switch (parameters.getMangedType()) {
+                case FILE -> create((FileCreationParameters) parameters, destination);
+                case FOLDER -> create((FolderCreationParameters) parameters, destination);
+                case ARCHIVE -> create((ArchiveStructureCreationParameter) parameters, destination);
+                case URL -> create((URLCreationParameters) parameters, destination);
+                case GCUBEITEM -> create((GCubeItemCreationParameters) parameters, destination);
+                default -> throw new InvalidCallParameters("Item not supported");
+            };
+            log.debug("item with id {} correctly created", newNode.getIdentifier());
 			return newNode.getIdentifier();
 		} finally {
 			if (parameters.getSession().getWorkspace().getLockManager().isLocked(destination.getPath()))
@@ -174,7 +163,7 @@ public class ItemHandler {
 
 		ArchiveInputStream input = new ArchiveStreamFactory()
 				.createArchiveInputStream(new BufferedInputStream(params.getStream()));
-		
+
 		ArchiveEntry entry;
 		while ((entry = input.getNextEntry()) != null) {
 			String entirePath = entry.getName();
@@ -182,7 +171,7 @@ public class ItemHandler {
 			if (entry.isDirectory()) {
 				log.debug("creating directory with entire path {} ", entirePath);
 				createPath(entirePath, directoryNodeMap, parentDirectoryNode, params.getSession(), params.getUser());
-			} else {
+			} else
 				try {
 					String name = entirePath.replaceAll("([^/]*/)*(.*)", "$2");
 					String parentPath = entirePath.replaceAll("(([^/]*/)*)(.*)", "$1");
@@ -192,22 +181,27 @@ public class ItemHandler {
 					long fileSize = entry.getSize();
 					FormDataContentDisposition fileDetail = FormDataContentDisposition.name(name).size(fileSize)
 							.build();
+					//this code has been added for a bug on s3 client(v1) that closes the stream
+					InputStream notClosableIS = new BufferedInputStream(input) {
+						@Override
+						public void close() throws IOException { }
+					};
+
 					if (parentPath.isEmpty()) {
-						fileNode = createFileItemInternally(params.getSession(), parentDirectoryNode, input, name, "",
+						fileNode = createFileItemInternally(params.getSession(), parentDirectoryNode, notClosableIS, name, "",
 								fileDetail, params.getUser(), false);
 					} else {
 						Node parentNode = directoryNodeMap.get(parentPath);
 						if (parentNode == null)
 							parentNode = createPath(parentPath, directoryNodeMap, parentDirectoryNode,
 									params.getSession(), params.getUser());
-						fileNode = createFileItemInternally(params.getSession(), parentNode, input, name, "",
+						fileNode = createFileItemInternally(params.getSession(), parentNode, notClosableIS, name, "",
 								fileDetail, params.getUser(), false);
 					}
 					fileNodes.add(fileNode);
 				} catch (Throwable e) {
 					log.warn("error getting file {}", entry.getName(), e);
 				}
-			}
 		}
 
 		log.info("archive {} uploading finished ", params.getParentFolderName());
@@ -217,6 +211,8 @@ public class ItemHandler {
 		return parentDirectoryNode;
 	}
 
+
+
 	private Node createPath(String parentPath, Map<String, Node> directoryNodeMap, Node rootNode, Session ses,
 			String user) throws StorageHubException, RepositoryException {
 		String[] parentPathSplit = parentPath.split("/");
@@ -346,8 +342,7 @@ public class ItemHandler {
 			throws BackendGenericError {
 		log.trace("UPLOAD: filling content");
 		ContentHandler handler = getContentHandler(stream, storageBackend, name, fileDetails, relPath, login);
-		AbstractFileItem item = handler.buildItem(name, description, login);
-		return item;
+		return handler.buildItem(name, description, login);
 	}
 
 	private ContentHandler getContentHandler(InputStream stream, StorageBackend storageBackend, String name,
diff --git a/src/main/java/org/gcube/data/access/storagehub/storage/backend/impl/S3Backend.java b/src/main/java/org/gcube/data/access/storagehub/storage/backend/impl/S3Backend.java
index 5a0f4c6..6220f25 100644
--- a/src/main/java/org/gcube/data/access/storagehub/storage/backend/impl/S3Backend.java
+++ b/src/main/java/org/gcube/data/access/storagehub/storage/backend/impl/S3Backend.java
@@ -169,7 +169,7 @@ public class S3Backend extends StorageBackend{
 				fileSize = size;
 			else 
 				fileSize = client.getObjectMetadata(bucketName, storageId).getContentLength();
-			
+
 			IOUtils.drainInputStream(stream);
 			log.info("uploading file {} in {} seconds",name, (System.currentTimeMillis()-start)/1000);
 			return new MetaInfo(fileSize,storageId, null, getPayloadConfiguration());
@@ -183,8 +183,7 @@ public class S3Backend extends StorageBackend{
 	@Override
 	public InputStream download(String id) throws StorageIdNotFoundException{
 		try {
-			InputStream inputStream = client.getObject(bucketName, id).getObjectContent();
-			return inputStream;
+			return client.getObject(bucketName, id).getObjectContent();
 		}catch (Exception e) {
 			log.error("error downloading file form s3");
 			throw new RuntimeException("error downloading file from s3",e);
diff --git a/src/main/resources/init/NodeType.cnd b/src/main/resources/init/NodeType.cnd
index 8c89017..c70a55f 100644
--- a/src/main/resources/init/NodeType.cnd
+++ b/src/main/resources/init/NodeType.cnd
@@ -114,7 +114,7 @@
   = nthl:payloadBackend
   	mandatory autocreated  	
 
-  + *
+  + * (nthl:workspaceItem)
 
 [nthl:workspaceSharedItem] > nthl:workspaceItem, mix:shareable
   - hl:privilege (String)
@@ -212,7 +212,7 @@
 		
 [nthl:externalPdf] > nthl:workspaceLeafItem
 
-nthl:externalLink > nthl:workspaceItem
+[nthl:externalLink] > nthl:workspaceItem
       - hl:value