Merge pull request #154 from gdcc/jakarta

Jakarta EE 10 and Java 17
gdcc · Aug 21, 2023 · 9012317 · 9012317
2 parents d1a32e0 + 3d98566
commit 9012317
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diff --git a/README.md b/README.md
@@ -7,11 +7,26 @@ This server library is an implementation of the SWORD 2.0 standard defined [here
 The variant hosted in this repository is being used as the library of choice to implement the compliant interface
 for [Dataverse](https://dataverse.org). It also gets pushed to [Maven Central](https://mvnrepository.com/artifact/io.gdcc/sword2-server).
 
+## Important changes
+
+### Removed `multipart/related` support
+This library does no longer support [RFC2387 type uploads (multipart/related)](dx.doi.org/10.17487/RFC2387)!
+It will present users an error message, telling them to use Atom instead.
+
+Support for this type of uploads was broken for a long time and did not make it into SWORD v3.
+[It was tagged for removal for a SWORD v2.1 spec](http://www.mail-archive.com/sword-app-tech@lists.sourceforge.net/msg00327.html),
+which never happened.
+
+### Requires Jakarta EE 10+
+This library uses Jakarta EE Servlet API 6+ contained in Jakarta EE 10 or newer. Implementing applications should use
+these namespace-shifted libs, too. Your mileage may vary, depending on your application server's possibilities.
+
+### Requires Java 17
+This library requires Java 17.
+
 ## History of this library
 
 1. This library has been develop by @richard-jonnes and @bmckinney at https://github.com/swordapp/JavaServer2.0 first.
-2. As development has been staled, DANS-KNAW took as part of project EASY at https://github.com/DANS-KNAW/easy-sword2-lib
+2. As development has been stalled, DANS-KNAW took as part of project EASY at https://github.com/DANS-KNAW/easy-sword2-lib
 3. MyCoRe project forked and maintain their own version with interesting changes. https://github.com/MyCoRe-Org/easy-sword2-lib
-4. IQSS needed a fix in this library, so they currently have their own fork at https://github.com/IQSS/swordv2-java-server-library
-   This project aims to replace that fork and provide a version with updated dependencies. It has been replaced with
-   releases from this repo in the meantime.
+4. IQSS needed a fix in the original library and has switched from their own fork at https://github.com/IQSS/swordv2-java-server-library to this fork.
diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,8 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>io.gdcc</groupId>
     <artifactId>sword2-server</artifactId>
-    <version>1.2.3-SNAPSHOT</version>
+    <!--Leave -SNAPSHOT in the version. It will be removed by Maven Release Plugin: https://maven.apache.org/maven-release/maven-release-plugin/-->
+    <version>2.0.0-SNAPSHOT</version>
     <packaging>jar</packaging>
     <name>SWORD v2 Common Server Library (forked)</name>
     <description>
@@ -19,10 +20,11 @@
         <skipAnalysis>false</skipAnalysis>
         <!-- Key 2DFF887456235B4550B857DFBAFC446FC031F36B for Dataverse Bot <dataversebot@gdcc.io> expiring 2024-07-29 -->
         <gpg.keyname>0xC031F36B</gpg.keyname>
-        <jdk.version>11</jdk.version>
+        <jdk.version>17</jdk.version>
 
         <!-- Dependency versions -->
-        <servlet-api.version>4.0.4</servlet-api.version>
+        <servlet-api.version>6.0.0</servlet-api.version>
+        <jersey.version>3.0.4</jersey.version>
         <abdera.version>1.1.3</abdera.version>
         <fileupload.version>1.5</fileupload.version>
         <jena.version>4.9.0</jena.version>
@@ -480,6 +482,11 @@
             <version>${servlet-api.version}</version>
             <scope>provided</scope>
         </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.media</groupId>
+            <artifactId>jersey-media-multipart</artifactId>
+            <version>${jersey.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.apache.abdera</groupId>
             <artifactId>abdera-core</artifactId>
@@ -496,11 +503,6 @@
             <version>${abdera.version}</version>
             <scope>runtime</scope>
         </dependency>
-        <dependency>
-            <groupId>commons-fileupload</groupId>
-            <artifactId>commons-fileupload</artifactId>
-            <version>${fileupload.version}</version>
-        </dependency>
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-core</artifactId>

diff --git a/src/main/java/org/swordapp/server/CollectionAPI.java b/src/main/java/org/swordapp/server/CollectionAPI.java
@@ -7,9 +7,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.io.StringWriter;
 import java.nio.charset.StandardCharsets;
@@ -130,7 +130,7 @@ public void post(final HttpServletRequest req, final HttpServletResponse resp) t
 
             // do the different kinds of deposit details extraction
             if (isMultipart) {
-                this.addDepositPropertiesFromMultipart(deposit, req);
+                throw new SwordError(UriRegistry.ERROR_METHOD_NOT_ALLOWED, "This server does not support RFC2387 Multipart uploads, to be removed in SWORD v2.1");
             } else if (isEntryOnly) {
                 this.addDepositPropertiesFromEntry(deposit, req);
             } else if (isBinaryOnly) {

diff --git a/src/main/java/org/swordapp/server/ContainerAPI.java b/src/main/java/org/swordapp/server/ContainerAPI.java
@@ -6,9 +6,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.io.StringWriter;
 import java.text.SimpleDateFormat;
@@ -163,10 +163,7 @@ public void put(final HttpServletRequest req, final HttpServletResponse resp) th
             DepositReceipt receipt;
 
             if (isMultipart) {
-                this.addDepositPropertiesFromMultipart(deposit, req);
-
-                // defer to the implementation layer to update both the metadata and the media resource
-                receipt = this.cm.replaceMetadataAndMediaResource(iri, deposit, auth, this.config);
+                throw new SwordError(UriRegistry.ERROR_METHOD_NOT_ALLOWED, "This server does not support RFC2387 Multipart uploads, to be removed in SWORD v2.1");
             } else if (isEntryOnly) {
                 // check that we have the right content type
                 if (!(contentType.startsWith("application/atom+xml") || contentType.startsWith("application/atom+xml;type=entry"))) {
@@ -179,7 +176,7 @@ public void put(final HttpServletRequest req, final HttpServletResponse resp) th
                 receipt = this.cm.replaceMetadata(iri, deposit, auth, this.config);
             } else {
                 // some other sort of deposit which is not supported
-                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "PUT to Edit-IRI MUST be a multipart request or an Atom Entry");
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "PUT to Edit-IRI MUST be an Atom Entry");
             }
 
             // prepare and return the response

diff --git a/src/main/java/org/swordapp/server/ErrorDocument.java b/src/main/java/org/swordapp/server/ErrorDocument.java
@@ -3,7 +3,7 @@
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 import javax.xml.XMLConstants;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;

diff --git a/src/main/java/org/swordapp/server/MediaResourceAPI.java b/src/main/java/org/swordapp/server/MediaResourceAPI.java
@@ -6,9 +6,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -204,15 +204,10 @@ public void post(final HttpServletRequest req, final HttpServletResponse resp) t
 
         Deposit deposit = null;
         try {
-            // the first thing to do is determine what the deposit type is:
-            String contentType = this.getContentType(req);
-            boolean isMultipart = contentType.startsWith("multipart/related");
-            String uri = this.getFullUrl(req);
-
             deposit = new Deposit();
 
-            if (isMultipart) {
-                this.addDepositPropertiesFromMultipart(deposit, req);
+            if (this.getContentType(req).startsWith("multipart/related")) {
+                throw new SwordError(UriRegistry.ERROR_METHOD_NOT_ALLOWED, "This server does not support RFC2387 Multipart uploads, to be removed in SWORD v2.1");
             } else {
                 this.addDepositPropertiesFromBinary(deposit, req);
             }
@@ -222,7 +217,7 @@ public void post(final HttpServletRequest req, final HttpServletResponse resp) t
             deposit.setMetadataRelevant(metadataRelevant);
 
             // now send the deposit to the implementation for processing
-            DepositReceipt receipt = this.mrm.addResource(uri, deposit, auth, this.config);
+            DepositReceipt receipt = this.mrm.addResource(this.getFullUrl(req), deposit, auth, this.config);
 
             // prepare and return the response
             IRI location = receipt.getLocation();

diff --git a/src/main/java/org/swordapp/server/ServiceDocumentAPI.java b/src/main/java/org/swordapp/server/ServiceDocumentAPI.java
@@ -4,9 +4,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 
 public class ServiceDocumentAPI extends SwordAPIEndpoint {

diff --git a/src/main/java/org/swordapp/server/StatementAPI.java b/src/main/java/org/swordapp/server/StatementAPI.java
@@ -3,9 +3,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.io.StringWriter;
 import java.text.SimpleDateFormat;

diff --git a/src/main/java/org/swordapp/server/SwordAPIEndpoint.java b/src/main/java/org/swordapp/server/SwordAPIEndpoint.java
@@ -6,18 +6,14 @@
 import org.apache.abdera.model.Entry;
 import org.apache.abdera.parser.ParseException;
 import org.apache.abdera.parser.Parser;
-import org.apache.commons.fileupload.FileItem;
-import org.apache.commons.fileupload.FileItemFactory;
-import org.apache.commons.fileupload.FileUploadException;
-import org.apache.commons.fileupload.ParameterParser;
-import org.apache.commons.fileupload.disk.DiskFileItemFactory;
-import org.apache.commons.fileupload.servlet.ServletFileUpload;
+import org.glassfish.jersey.media.multipart.ContentDisposition;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
+
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
@@ -29,7 +25,6 @@
 import java.util.Base64;
 import java.util.Enumeration;
 import java.util.HashMap;
-import java.util.List;
 import java.util.Map;
 import java.util.UUID;
 
@@ -191,46 +186,6 @@ protected void storeAndCheckBinary(final Deposit deposit, final SwordConfigurati
 
         log.debug("Package temporarily stored as: " + filename);
     }
-
-    protected void addDepositPropertiesFromMultipart(final Deposit deposit, final HttpServletRequest req) throws ServletException, IOException, SwordError {
-        // Parse the request for files (using the fileupload commons library)
-        List<FileItem> items = this.getPartsFromRequest(req);
-        for (FileItem item : items) {
-            // find out which part we are looking at
-            String contentDisposition = item.getHeaders().getHeader("Content-Disposition");
-            String name = this.getContentDispositionValue(contentDisposition, "name");
-
-            if ("atom".equals(name)) {
-                parseEntryFromInputStream(deposit, item.getInputStream());
-            } else if ("payload".equals(name)) {
-                String md5 = item.getHeaders().getHeader("Content-MD5");
-                String packaging = item.getHeaders().getHeader("Packaging");
-                String filename = this.getContentDispositionValue(contentDisposition, "filename");
-                if (filename == null || "".equals(filename)) {
-                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Filename could not be extracted from Content-Disposition");
-                }
-                String ct = item.getContentType();
-                String mimeType = "application/octet-stream";
-                if (ct != null) {
-                    String[] bits = ct.split(";");
-                    mimeType = bits[0].trim();
-                }
-                InputStream mediaPart = item.getInputStream();
-
-                deposit.setFilename(filename);
-                deposit.setInputStream(mediaPart);
-                deposit.setMimeType(mimeType);
-                deposit.setMd5(md5);
-                deposit.setPackaging(packaging);
-            }
-        }
-
-        try {
-            this.storeAndCheckBinary(deposit, this.config);
-        } catch (SwordServerException e) {
-            throw new ServletException(e);
-        }
-    }
 
     protected void cleanup(final Deposit deposit) {
         if (deposit == null) {
@@ -309,9 +264,14 @@ protected void addDepositPropertiesFromBinary(final Deposit deposit, final HttpS
         InputStream file = req.getInputStream();
 
         // now let's interpret and deal with the headers that we have
-        String filename = this.getContentDispositionValue(contentDisposition, "filename");
-        if (filename == null || "".equals(filename)) {
-            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Filename could not be extracted from Content-Disposition");
+        String filename;
+        try {
+            filename = new ContentDisposition(contentDisposition).getFileName();
+            if ("".equals(filename)) {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Filename could not be extracted from Content-Disposition");
+            }
+        } catch (java.text.ParseException e) {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Filename could not be extracted from Content-Disposition: " + e.getMessage());
         }
 
         deposit.setFilename(filename);
@@ -366,35 +326,6 @@ protected void swordError(final HttpServletRequest req, final HttpServletRespons
         }
     }
 
-    protected String getContentDispositionValue(final String contentDisposition, final String key) {
-        if (contentDisposition == null || key == null) {
-            return null;
-        }
-
-        ParameterParser parameterParser = new ParameterParser();
-        char separator = ';';
-        Map<String, String> parameters = parameterParser.parse(contentDisposition, separator);
-        return parameters.get(key);
-    }
-
-    protected List<FileItem> getPartsFromRequest(final HttpServletRequest request) throws ServletException {
-        try {
-            // Create a factory for disk-based file items
-            FileItemFactory factory = new DiskFileItemFactory();
-
-            // Create a new file upload handler
-            ServletFileUpload upload = new ServletFileUpload(factory);
-            upload.setFileCountMax(config.getMaxUploadFiles());
-
-            // Parse the request
-            List<FileItem> items = upload.parseRequest(request);
-
-            return items;
-        } catch (FileUploadException e) {
-            throw new ServletException(e);
-        }
-    }
-
     protected Map<String, String> getAcceptHeaders(final HttpServletRequest req) {
         Map<String, String> acceptHeaders = new HashMap<String, String>();
         Enumeration headers = req.getHeaderNames();

diff --git a/src/main/java/org/swordapp/server/SwordConfiguration.java b/src/main/java/org/swordapp/server/SwordConfiguration.java
@@ -20,8 +20,6 @@ public interface SwordConfiguration {
     String getTempDirectory();
 
     int getMaxUploadSize();
-
-    int getMaxUploadFiles();
 
     String getAlternateUrl();
 

diff --git a/src/main/java/org/swordapp/server/SwordConfigurationDefault.java b/src/main/java/org/swordapp/server/SwordConfigurationDefault.java
@@ -40,12 +40,7 @@ public String getTempDirectory() {
     public int getMaxUploadSize() {
         return -1;
     }
-
-    @Override
-    public int getMaxUploadFiles() {
-        return -1;
-    }
-
+
     public String getAlternateUrl() {
         return null;
     }

diff --git a/src/main/java/org/swordapp/server/servlets/CollectionServletDefault.java b/src/main/java/org/swordapp/server/servlets/CollectionServletDefault.java
@@ -6,9 +6,9 @@
 import org.swordapp.server.CollectionDepositManager;
 import org.swordapp.server.CollectionListManager;
 
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 
 public class CollectionServletDefault extends SwordServlet {

diff --git a/src/main/java/org/swordapp/server/servlets/ContainerServletDefault.java b/src/main/java/org/swordapp/server/servlets/ContainerServletDefault.java
@@ -6,9 +6,9 @@
 import org.swordapp.server.ContainerManager;
 import org.swordapp.server.StatementManager;
 
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 
 public class ContainerServletDefault extends SwordServlet {