Merge branch 'master' into configure-dependabot-for-gh-actions

icatproject · Sep 8, 2023 · 006f3f2 · 006f3f2
2 parents e261538 + 5163b81
commit 006f3f2
Show file tree

Hide file tree

Showing 98 changed files with 900 additions and 751 deletions.
diff --git a/.github/workflows/ci-build.yml b/.github/workflows/ci-build.yml
@@ -8,29 +8,21 @@ on:
 
 jobs:
   build_and_tests:
-    runs-on: ubuntu-20.04
-    continue-on-error: ${{ matrix.experimental }}
+    runs-on: ubuntu-22.04
     strategy:
-      fail-fast: false
       matrix:
-        include:
-          - version: 8
-            experimental: false
-          - version: 11
-            experimental: true
+        java_version: [11, 17]
 
     steps:
-      # Setup Java & Python
+      # Setup Java
       - 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: Run apt-get update
+        run: sudo apt-get update
 
       - name: Cache local Maven repository
         uses: actions/cache@69d9d449aced6a2ede0bc19182fadc3a0a42d2b0 # v3.2.6
@@ -46,7 +38,7 @@ jobs:
         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/README.md b/README.md
@@ -4,6 +4,6 @@
 
 General installation instructions are at https://icatproject.org/installation/component
 
-Specific installation instructions are at https://repo.icatproject.org/site/icat/server/5.0.0/installation.html
+Specific installation instructions are at https://repo.icatproject.org/site/icat/server/6.0.0/installation.html
 
-All documentation on the icat.server may be found at https://repo.icatproject.org/site/icat/server/5.0.0
+All documentation on the icat.server may be found at https://repo.icatproject.org/site/icat/server/6.0.0
diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
 
 	<groupId>org.icatproject</groupId>
 	<artifactId>icat.server</artifactId>
-	<version>5.0.1-SNAPSHOT</version>
+	<version>6.0.1-SNAPSHOT</version>
 	<packaging>war</packaging>
 	<name>ICAT Server</name>
 	<description>A metadata catalogue to support Large Facility experimental data, 
@@ -71,16 +71,16 @@
 	<dependencies>
 
 		<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>
 			<groupId>org.icatproject</groupId>
 			<artifactId>icat.authentication</artifactId>
-			<version>4.6.0</version>
+			<version>5.0.0</version>
 		</dependency>
 
 		<dependency>
@@ -96,18 +96,18 @@
 			<scope>test</scope>
 		</dependency>
 
-
 		<dependency>
-			<groupId>org.glassfish</groupId>
-			<artifactId>jakarta.json</artifactId>
-			<version>1.1.5</version>
+			<groupId>com.sun.xml.ws</groupId>
+			<artifactId>jaxws-rt</artifactId>
+			<version>4.0.0</version>
 			<scope>test</scope>
 		</dependency>
 
 		<dependency>
-			<groupId>commons-fileupload</groupId>
-			<artifactId>commons-fileupload</artifactId>
-			<version>1.4</version>
+			<groupId>org.eclipse.parsson</groupId>
+			<artifactId>parsson</artifactId>
+			<version>1.1.0</version>
+			<scope>test</scope>
 		</dependency>
 
 		<dependency>
@@ -119,7 +119,7 @@
 		<dependency>
 			<groupId>org.icatproject</groupId>
 			<artifactId>icat.client</artifactId>
-			<version>5.0.0</version>
+			<version>6.0.0</version>
 			<scope>test</scope>
 		</dependency>
 
@@ -159,7 +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>
@@ -260,21 +260,16 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-war-plugin</artifactId>
-				<version>2.4</version>
-				<configuration>
-					<failOnMissingWebXml>false</failOnMissingWebXml>
-					<archiveClasses>false</archiveClasses>
-				</configuration>
+				<version>3.4.0</version>
 			</plugin>
 
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-compiler-plugin</artifactId>
-				<version>3.3</version>
+				<version>3.10.1</version>
 				<configuration>
 					<encoding>${project.build.sourceEncoding}</encoding>
-					<source>1.8</source>
-					<target>1.8</target>
+					<release>11</release>
 				</configuration>
 			</plugin>
 

diff --git a/src/main/config/setup.properties.example b/src/main/config/setup.properties.example
@@ -22,8 +22,7 @@ port           = 4848
 !db.logging     = FINE
 
 # MySQL
-db.driver      = com.mysql.jdbc.jdbc2.optional.MysqlDataSource
-!db.driver     = mysql-connector-java-5.1.30-bin.jar_com.mysql.jdbc.Driver_5_1
+db.driver      = com.mysql.cj.jdbc.MysqlDataSource
 db.url         = jdbc:mysql://localhost:3306/icat
 db.username    = icat
 db.password    = secret

diff --git a/src/main/java/org/icatproject/core/entity/Affiliation.java b/src/main/java/org/icatproject/core/entity/Affiliation.java
@@ -2,13 +2,13 @@
 
 import java.io.Serializable;
 
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
 
 @Comment("The home institute or other affiliation of a user in the context of a data publication")
 @SuppressWarnings("serial")

diff --git a/src/main/java/org/icatproject/core/entity/Application.java b/src/main/java/org/icatproject/core/entity/Application.java
@@ -4,15 +4,15 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
 
 @Comment("Some piece of software")
 @SuppressWarnings("serial")

diff --git a/src/main/java/org/icatproject/core/entity/DataCollection.java b/src/main/java/org/icatproject/core/entity/DataCollection.java
@@ -4,9 +4,9 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.persistence.CascadeType;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.OneToMany;
 
 @Comment("A set of Investigations, Datasets and Datafiles which can span Facilities. "
 		+ "Note that it has no constraint fields. "

diff --git a/src/main/java/org/icatproject/core/entity/DataCollectionDatafile.java b/src/main/java/org/icatproject/core/entity/DataCollectionDatafile.java
@@ -2,12 +2,12 @@
 
 import java.io.Serializable;
 
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
 
 @Comment("Represents a many-to-many relationship between a DataCollection and its Datafiles.")
 @SuppressWarnings("serial")

diff --git a/src/main/java/org/icatproject/core/entity/DataCollectionDataset.java b/src/main/java/org/icatproject/core/entity/DataCollectionDataset.java
@@ -2,12 +2,12 @@
 
 import java.io.Serializable;
 
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
 
 @Comment("Represents a many-to-many relationship between a DataCollection and its datasets.")
 @SuppressWarnings("serial")

diff --git a/src/main/java/org/icatproject/core/entity/DataCollectionInvestigation.java b/src/main/java/org/icatproject/core/entity/DataCollectionInvestigation.java
@@ -2,12 +2,12 @@
 
 import java.io.Serializable;
 
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
 
 @Comment("Represents a many-to-many relationship between a DataCollection and its Investigations.")
 @SuppressWarnings("serial")

diff --git a/src/main/java/org/icatproject/core/entity/DataCollectionParameter.java b/src/main/java/org/icatproject/core/entity/DataCollectionParameter.java
@@ -2,12 +2,12 @@
 
 import java.io.Serializable;
 
-import javax.persistence.Entity;
-import javax.persistence.EntityManager;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.Entity;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
 
 import org.icatproject.core.IcatException;
 import org.icatproject.core.manager.EntityBeanManager.PersistMode;

diff --git a/src/main/java/org/icatproject/core/entity/DataPublication.java b/src/main/java/org/icatproject/core/entity/DataPublication.java
@@ -5,17 +5,17 @@
 import java.util.Date;
 import java.util.List;
 
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.Table;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
+import jakarta.persistence.UniqueConstraint;
 
 @Comment("A curated data publication")
 @SuppressWarnings("serial")

diff --git a/src/main/java/org/icatproject/core/entity/DataPublicationDate.java b/src/main/java/org/icatproject/core/entity/DataPublicationDate.java
@@ -2,13 +2,13 @@
 
 import java.io.Serializable;
 
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
 
 @Comment("A date relevant for the publication")
 @SuppressWarnings("serial")

diff --git a/src/main/java/org/icatproject/core/entity/DataPublicationFunding.java b/src/main/java/org/icatproject/core/entity/DataPublicationFunding.java
@@ -2,12 +2,12 @@
 
 import java.io.Serializable;
 
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
 
 @Comment("Represents a many-to-many relationship between a data publication and a funding reference")
 @SuppressWarnings("serial")

diff --git a/src/main/java/org/icatproject/core/entity/DataPublicationType.java b/src/main/java/org/icatproject/core/entity/DataPublicationType.java
@@ -4,15 +4,15 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
 
 @Comment("A type of data publication, for example, whole investigation, user-selected datasets/files. "
 		+ "This is likely to be for facility internal purposes following their own classification "