Merge branch 'payara6'

icatproject · Aug 14, 2023 · 414f8f0 · 414f8f0
2 parents 189062e + 382d1d7
commit 414f8f0
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Showing 23 changed files with 145 additions and 147 deletions.
diff --git a/.github/workflows/ci-build.yml b/.github/workflows/ci-build.yml
@@ -8,25 +8,18 @@ on:
 
 jobs:
   build_and_tests:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
-      fail-fast: false
       matrix:
-        include:
-          - version: 8
+        java_version: [11, 17]
 
     steps:
       # Setup Java & Python
       - name: Setup Java
         uses: actions/setup-java@3f07048e3d294f56e9b90ac5ea2c6f74e9ad0f98 # v3.10.0
         with:
           distribution: 'temurin'
-          java-version: ${{ matrix.version }}
-      - name: Setup Python
-        uses: actions/setup-python@d27e3f3d7c64b4bbf8e4abfb9b63b83e846e0435 # v4.5.0
-        with:
-          python-version: "3.9.7"
-          architecture: x64
+          java-version: ${{ matrix.java_version }}
 
       - name: Cache local Maven repository
         uses: actions/cache@69d9d449aced6a2ede0bc19182fadc3a0a42d2b0 # v3.2.6
@@ -36,13 +29,16 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-maven-
 
+      - name: Run apt-get update
+        run: sudo apt-get update
+
       # ICAT Ansible clone and install dependencies
       - name: Checkout icat-ansible
         uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
         with:
           repository: icatproject-contrib/icat-ansible
           path: icat-ansible
-          ref: master
+          ref: payara6
       - name: Install Ansible
         run: pip install -r icat-ansible/requirements.txt
 

diff --git a/pom.xml b/pom.xml
@@ -72,7 +72,7 @@
 		<dependency>
 			<groupId>org.icatproject</groupId>
 			<artifactId>icat.client</artifactId>
-			<version>4.10.0</version>
+			<version>6.0.0</version>
 		</dependency>
 
 		<dependency>
@@ -102,9 +102,10 @@
 		</dependency>
 
 		<dependency>
-			<groupId>javax</groupId>
-			<artifactId>javaee-api</artifactId>
-			<version>7.0</version>
+			<groupId>jakarta.platform</groupId>
+			<artifactId>jakarta.jakartaee-api</artifactId>
+			<version>10.0.0</version>
+			<scope>provided</scope>
 		</dependency>
 
 		<dependency>
@@ -114,15 +115,16 @@
 		</dependency>
 
 		<dependency>
-			<groupId>commons-fileupload</groupId>
-			<artifactId>commons-fileupload</artifactId>
-			<version>1.5</version>
+			<groupId>com.sun.xml.ws</groupId>
+			<artifactId>jaxws-rt</artifactId>
+			<version>4.0.0</version>
+			<scope>test</scope>
 		</dependency>
 
 		<dependency>
-			<groupId>org.glassfish</groupId>
-			<artifactId>javax.json</artifactId>
-			<version>1.0.4</version>
+			<groupId>org.eclipse.parsson</groupId>
+			<artifactId>parsson</artifactId>
+			<version>1.1.0</version>
 			<scope>test</scope>
 		</dependency>
 
@@ -157,7 +159,7 @@
 			<plugin>
 				<groupId>com.qmino</groupId>
 				<artifactId>miredot-plugin</artifactId>
-				<version>1.6.2</version>
+				<version>2.4.1-Java11</version>
 				<executions>
 					<execution>
 						<id>miredot</id>
@@ -253,10 +255,9 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-compiler-plugin</artifactId>
-				<version>3.3</version>
+				<version>3.10.1</version>
 				<configuration>
-					<source>1.8</source>
-					<target>1.8</target>
+					<release>11</release>
 				</configuration>
 			</plugin>
 
@@ -308,7 +309,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-war-plugin</artifactId>
-				<version>3.0.0</version>
+				<version>3.4.0</version>
 			</plugin>
 
 			<plugin>

diff --git a/src/main/java/org/icatproject/ids/CORSResponseFilter.java b/src/main/java/org/icatproject/ids/CORSResponseFilter.java
@@ -2,11 +2,11 @@
 
 import java.io.IOException;
 
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.container.ContainerResponseContext;
-import javax.ws.rs.container.ContainerResponseFilter;
-import javax.ws.rs.core.MultivaluedMap;
-import javax.ws.rs.ext.Provider;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.container.ContainerResponseContext;
+import jakarta.ws.rs.container.ContainerResponseFilter;
+import jakarta.ws.rs.core.MultivaluedMap;
+import jakarta.ws.rs.ext.Provider;
 
 @Provider
 public class CORSResponseFilter implements ContainerResponseFilter {

diff --git a/src/main/java/org/icatproject/ids/DataSelection.java b/src/main/java/org/icatproject/ids/DataSelection.java
@@ -9,9 +9,9 @@
 import java.util.Map;
 import java.util.Set;
 
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonValue;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonValue;
 
 import org.icatproject.Datafile;
 import org.icatproject.Dataset;

diff --git a/src/main/java/org/icatproject/ids/FileChecker.java b/src/main/java/org/icatproject/ids/FileChecker.java
@@ -18,11 +18,11 @@
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 
-import javax.annotation.PostConstruct;
-import javax.annotation.PreDestroy;
-import javax.ejb.EJB;
-import javax.ejb.Singleton;
-import javax.ejb.Startup;
+import jakarta.annotation.PostConstruct;
+import jakarta.annotation.PreDestroy;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Singleton;
+import jakarta.ejb.Startup;
 
 import org.icatproject.Datafile;
 import org.icatproject.Dataset;

diff --git a/src/main/java/org/icatproject/ids/FiniteStateMachine.java b/src/main/java/org/icatproject/ids/FiniteStateMachine.java
@@ -20,13 +20,13 @@
 import java.util.UUID;
 import java.util.concurrent.ConcurrentHashMap;
 
-import javax.annotation.PostConstruct;
-import javax.annotation.PreDestroy;
-import javax.ejb.DependsOn;
-import javax.ejb.EJB;
-import javax.ejb.Singleton;
-import javax.json.Json;
-import javax.json.stream.JsonGenerator;
+import jakarta.annotation.PostConstruct;
+import jakarta.annotation.PreDestroy;
+import jakarta.ejb.DependsOn;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Singleton;
+import jakarta.json.Json;
+import jakarta.json.stream.JsonGenerator;
 
 import org.icatproject.Dataset;
 import org.icatproject.ids.LockManager.Lock;

diff --git a/src/main/java/org/icatproject/ids/ICATGetter.java b/src/main/java/org/icatproject/ids/ICATGetter.java
@@ -3,7 +3,7 @@
 import java.net.MalformedURLException;
 import java.net.URL;
 
-import javax.xml.ws.WebServiceException;
+import jakarta.xml.ws.WebServiceException;
 
 import org.icatproject.ICAT;
 import org.icatproject.ICATService;

diff --git a/src/main/java/org/icatproject/ids/IcatReader.java b/src/main/java/org/icatproject/ids/IcatReader.java
@@ -2,8 +2,8 @@
 
 import java.util.List;
 
-import javax.annotation.PostConstruct;
-import javax.ejb.Singleton;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.Singleton;
 
 import org.icatproject.EntityBaseBean;
 import org.icatproject.ICAT;

diff --git a/src/main/java/org/icatproject/ids/IdsBean.java b/src/main/java/org/icatproject/ids/IdsBean.java
@@ -40,17 +40,17 @@
 import java.util.zip.ZipException;
 import java.util.zip.ZipOutputStream;
 
-import javax.annotation.PostConstruct;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.json.Json;
-import javax.json.JsonNumber;
-import javax.json.JsonObject;
-import javax.json.JsonReader;
-import javax.json.JsonValue;
-import javax.json.stream.JsonGenerator;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.StreamingOutput;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.json.Json;
+import jakarta.json.JsonNumber;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonReader;
+import jakarta.json.JsonValue;
+import jakarta.json.stream.JsonGenerator;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.core.StreamingOutput;
 import javax.xml.datatype.DatatypeFactory;
 
 import org.icatproject.Datafile;

diff --git a/src/main/java/org/icatproject/ids/IdsService.java b/src/main/java/org/icatproject/ids/IdsService.java
@@ -3,35 +3,33 @@
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import javax.annotation.PostConstruct;
-import javax.annotation.PreDestroy;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.json.Json;
-import javax.json.stream.JsonGenerator;
-import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.FormParam;
-import javax.ws.rs.GET;
-import javax.ws.rs.HeaderParam;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Path;
-import javax.ws.rs.Produces;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
-
-import org.apache.commons.fileupload.FileItemIterator;
-import org.apache.commons.fileupload.FileItemStream;
-import org.apache.commons.fileupload.FileUploadException;
-import org.apache.commons.fileupload.servlet.ServletFileUpload;
-import org.apache.commons.fileupload.util.Streams;
+import jakarta.annotation.PostConstruct;
+import jakarta.annotation.PreDestroy;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.json.Json;
+import jakarta.json.stream.JsonGenerator;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.Part;
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.FormParam;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.HeaderParam;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
+
 import org.icatproject.ids.exceptions.BadRequestException;
 import org.icatproject.ids.exceptions.DataNotOnlineException;
 import org.icatproject.ids.exceptions.InsufficientPrivilegesException;
@@ -652,11 +650,7 @@ public Response put(@Context HttpServletRequest request, InputStream body,
 	@Produces(MediaType.APPLICATION_JSON)
 	public Response putAsPost(@Context HttpServletRequest request) throws BadRequestException, NotFoundException,
 			InternalException, InsufficientPrivilegesException, NotImplementedException, DataNotOnlineException {
-		if (!ServletFileUpload.isMultipartContent(request)) {
-			throw new BadRequestException("Multipart content expected");
-		}
 		try {
-			ServletFileUpload upload = new ServletFileUpload();
 			String sessionId = null;
 			String name = null;
 			String datafileFormatId = null;
@@ -670,13 +664,11 @@ public Response putAsPost(@Context HttpServletRequest request) throws BadRequest
 			boolean padding = false;
 
 			// Parse the request
-			FileItemIterator iter = upload.getItemIterator(request);
-			while (iter.hasNext()) {
-				FileItemStream item = iter.next();
-				String fieldName = item.getFieldName();
-				InputStream stream = item.openStream();
-				if (item.isFormField()) {
-					String value = Streams.asString(stream);
+			for (Part part : request.getParts()) {
+				String fieldName = part.getName();
+				InputStream stream = part.getInputStream();
+				if (part.getSubmittedFileName() == null) {
+					String value = new String(stream.readAllBytes(), StandardCharsets.UTF_8);
 					if (fieldName.equals("sessionId")) {
 						sessionId = value;
 					} else if (fieldName.equals("name")) {
@@ -702,15 +694,17 @@ public Response putAsPost(@Context HttpServletRequest request) throws BadRequest
 					}
 				} else {
 					if (name == null) {
-						name = item.getName();
+						name = part.getSubmittedFileName();
 					}
 					result = idsBean.put(stream, sessionId, name, datafileFormatId, datasetId, description, doi,
 							datafileCreateTime, datafileModTime, wrap, padding, request.getRemoteAddr());
 				}
 			}
 			return result;
-		} catch (IOException | FileUploadException e) {
+		} catch (IOException e) {
 			throw new InternalException(e.getClass() + " " + e.getMessage());
+		} catch (ServletException e) {
+			throw new BadRequestException("Multipart content expected");
 		}
 	}
 

diff --git a/src/main/java/org/icatproject/ids/LockManager.java b/src/main/java/org/icatproject/ids/LockManager.java
@@ -5,8 +5,8 @@
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.Map;
-import javax.annotation.PostConstruct;
-import javax.ejb.Singleton;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.Singleton;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

diff --git a/src/main/java/org/icatproject/ids/PropertyHandler.java b/src/main/java/org/icatproject/ids/PropertyHandler.java
@@ -14,8 +14,8 @@
 import java.util.Properties;
 import java.util.Set;
 
-import javax.json.Json;
-import javax.json.JsonReader;
+import jakarta.json.Json;
+import jakarta.json.JsonReader;
 
 import org.icatproject.ICAT;
 import org.icatproject.IcatException_Exception;

diff --git a/src/main/java/org/icatproject/ids/Tidier.java b/src/main/java/org/icatproject/ids/Tidier.java
@@ -12,11 +12,11 @@
 import java.util.Timer;
 import java.util.TimerTask;
 
-import javax.annotation.PostConstruct;
-import javax.annotation.PreDestroy;
-import javax.ejb.EJB;
-import javax.ejb.Singleton;
-import javax.ejb.Startup;
+import jakarta.annotation.PostConstruct;
+import jakarta.annotation.PreDestroy;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Singleton;
+import jakarta.ejb.Startup;
 
 import org.icatproject.Datafile;
 import org.icatproject.Dataset;