Java 17 jakarta 10 Payara 6.2023.12

.github/workflows/ci.yml

@@ -5,6 +5,7 @@ on:
     branches:
       - main
       - dev
+      - java17*
     tags:
       - "v*"
   pull_request:
@@ -59,7 +60,7 @@ jobs:
         uses: actions/setup-java@v4
         with:
           distribution: "temurin"
-          java-version: 11
+          java-version: 17
           cache: "maven"
 
       - name: Set up QEMU

.github/workflows/gh-pages.yml

@@ -46,7 +46,7 @@ jobs:
         uses: actions/setup-java@v4
         with:
           distribution: "temurin"
-          java-version: 11
+          java-version: 17
           cache: 'maven'
 
       - name: Maven package without tests

README.md

@@ -22,6 +22,8 @@ echo "CREATE USER \"colab_test\" WITH PASSWORD '1234';
 CREATE DATABASE \"colab_test\" OWNER \"colab_test\";" |  docker exec colab_postgres psql -U colab
 ```
 
+If you have problems with authorization to drop and create colab_test, you may set colab_test user as a superuser.
+
 ### Mail Hog
 create en email testing tool
 ```
@@ -38,8 +40,9 @@ docker run -d --restart always -p 27017:27017 --name colab_mongo mongo:4.4
 ## Compile
 
 ### Tools & version to use
-* java11 & maven
-* node
+* java 17
+* maven
+* node 20
 * yarn
 
 
@@ -49,13 +52,22 @@ Rebuild everything with :
 mvn clean install
 ```
 
+If you use more than one java version, you may need to specify the JAVA_HOME.
+```bash
+JAVA_HOME="<your-path-to-java-bin>" mvn clean install
+```
+Typically
+```bash
+JAVA_HOME="/Library/Java/JavaVirtualMachines/temurin-17.jdk/Contents/Home" mvn clean install
+```
+
 Rebuild everything but skip tests with :
 ```bash
 mvn -DskipTests clean install
 ```
 
 ### Maven Site
-PMD and other tools may fails the build. You may want to consult human-readable reports.
+We use tools like PMD, spotbugs and checkstyle to ensure that the code is clean and healthy. The build can fail if there are bad errors. You may want to consult human-readable reports.
 
 Regenerate maven site:
 ```bash
@@ -67,22 +79,7 @@ And open ./target/staging/index.html
 ## Run (development)
 
 ### Configuration file
-Copy `./colab-webapp/default_colab.properties` to `./colab-webapp/colab.properties` and edit the colab.
-Edit `./colab-webapp/colab.properties` to match
-```
-#
-# coLAB properties
-#######################
-
-## Database
-colab.database.user=colab
-colab.database.password=<YOUR_SECRET_PASSWORD>
-colab.database.name=colab
-
-colab.default.admin.username=
-colab.default.admin.email=
-colab.default.admin.password=
-```
+Copy `./colab-webapp/default_colab.properties` to `./colab-webapp/colab.properties` and fill the database information.
 
 The `./colab-webapp/colab.properties` is your own configuration file and will never be committed.
 So you can safely put secrets in it.
@@ -129,7 +126,7 @@ Such refactors are defined with the help of [LiquiBase](https://www.liquibase.or
 
 Writing those changeLogs may be painfull. Luckily, LiquiBase ships with handy tools ([dowload here](https://github.com/liquibase/liquibase/releases)) to ease writing changeLogs. We are especially interested in the `diffChangeLog` tool.
 
-This tool compute a changeLog between a database and a reference. In our case, the database is the live database, the reference is the test database. Here is an script which stores the diff changeLog in a XML file named after the current timestamp.
+This tool compute a changeLog between a database and a reference. In our case, the database is the live database, the reference is the test database. Here is an script that you can run to generate a diff changeLog in a XML file named after the current timestamp. If there is no difference, no file will be generated.
 
 ```sh
 #!/bin/bash
@@ -231,4 +228,13 @@ yarn start
 
 The webapp will be available on http://localhost:3004
 
+### YJS
+Can be run via docker (see [YJS Docker setup in the wiki](https://github.com/Heigvd/colab/wiki/CoLab-YJS#docker-setup))
+
+Or with 
+```bash
+cd colab-api/src/main/node/colab-yjs
+yarn start
+```
+
 When using webpack-dev-server, one could add `-DskipWebappYarn` to each maven command

build-tools/src/main/resources/colab/pmd/default-ruleset.xml

@@ -17,7 +17,7 @@ KIND, either express or implied.  See the License for the
 specific language governing permissions and limitations
 under the License.
 -->
-<ruleset name="Default Maven PMD Plugin Ruleset" xmlns="http://pmd.sourceforge.net/ruleset/2.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pmd.sourceforge.net/ruleset/2.0.0 https://pmd.sourceforge.io/ruleset_2_0_0.xsd">
+<ruleset name="Default Maven PMD Plugin Ruleset" xmlns="http://pmd.sourceforge.net/ruleset/2.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pmd.sourceforge.net/ruleset/2.0.0 http://pmd.sourceforge.net/ruleset_2_0_0.xsd">
 
     <description>
         The default ruleset used by the Maven PMD Plugin, when no other ruleset is specified.
@@ -32,21 +32,20 @@ under the License.
     <rule ref="category/java/bestpractices.xml/AvoidUsingHardCodedIP"/>
     <rule ref="category/java/bestpractices.xml/CheckResultSet"/>
     <rule ref="category/java/bestpractices.xml/MissingOverride"/>
-    <rule ref="category/java/bestpractices.xml/UnusedImports"/>
+    <rule ref="category/java/bestpractices.xml/PrimitiveWrapperInstantiation" />
     <rule ref="category/java/bestpractices.xml/UnusedFormalParameter"/>
     <rule ref="category/java/bestpractices.xml/UnusedLocalVariable"/>
     <rule ref="category/java/bestpractices.xml/UnusedPrivateField"/>
     <rule ref="category/java/bestpractices.xml/UnusedPrivateMethod"/>
     <rule ref="category/java/bestpractices.xml/UseCollectionIsEmpty"/>
     <rule ref="category/java/bestpractices.xml/SystemPrintln"/>
 
+    <rule ref="category/java/codestyle.xml/EmptyControlStatement" />
     <rule ref="category/java/codestyle.xml/AvoidDollarSigns"/>
     <rule ref="category/java/codestyle.xml/CommentDefaultAccessModifier"/>
     <rule ref="category/java/codestyle.xml/ControlStatementBraces"/>
-    <rule ref="category/java/codestyle.xml/DontImportJavaLang"/>
-    <rule ref="category/java/codestyle.xml/DuplicateImports"/>
     <rule ref="category/java/codestyle.xml/ExtendsObject"/>
-    <rule ref="category/java/codestyle.xml/FieldDeclarationsShouldBeAtStartOfClass" />
+    <!--<rule ref="category/java/codestyle.xml/FieldDeclarationsShouldBeAtStartOfClass" />-->
     <!--<rule ref="category/java/codestyle.xml/FieldNamingConventions" />-->
     <rule ref="category/java/codestyle.xml/ForLoopShouldBeWhileLoop"/>
     <rule ref="category/java/codestyle.xml/GenericsNaming" />
@@ -57,8 +56,11 @@ under the License.
     <rule ref="category/java/codestyle.xml/NoPackage" />
     <rule ref="category/java/codestyle.xml/TooManyStaticImports"/>
     <rule ref="category/java/codestyle.xml/UnnecessaryFullyQualifiedName"/>
+    <rule ref="category/java/codestyle.xml/UnnecessaryImport" />
     <rule ref="category/java/codestyle.xml/UnnecessaryModifier"/>
     <rule ref="category/java/codestyle.xml/UnnecessaryReturn"/>
+    <rule ref="category/java/codestyle.xml/UnnecessarySemicolon" />
+    <!--<rule ref="category/java/codestyle.xml/UselessParentheses" />-->
     <rule ref="category/java/codestyle.xml/UselessQualifiedThis"/>
     <rule ref="category/java/codestyle.xml/UseDiamondOperator" />
 
@@ -72,11 +74,11 @@ under the License.
     <rule ref="category/java/design.xml/ExceptionAsFlowControl" />
     <rule ref="category/java/design.xml/SimplifyConditional" />
     <rule ref="category/java/design.xml/SimplifiedTernary"/>
-    <rule ref="category/java/design.xml/UseObjectForClearerAPI" />
+    <!--<rule ref="category/java/design.xml/UseObjectForClearerAPI" />-->
     <rule ref="category/java/design.xml/UselessOverridingMethod"/>
     <rule ref="category/java/design.xml/UseUtilityClass" />
 
-    <rule ref="category/java/documentation.xml/CommentRequired" />
+    <!--<rule ref="category/java/documentation.xml/CommentRequired" />-->
     <rule ref="category/java/documentation.xml/UncommentedEmptyConstructor" />
     <rule ref="category/java/documentation.xml/UncommentedEmptyMethodBody" />
 
@@ -92,16 +94,6 @@ under the License.
     <rule ref="category/java/errorprone.xml/ClassCastExceptionWithToArray"/>
     <rule ref="category/java/errorprone.xml/DontUseFloatTypeForLoopIndices"/>
     <rule ref="category/java/errorprone.xml/EmptyCatchBlock"/>
-    <rule ref="category/java/errorprone.xml/EmptyFinallyBlock"/>
-    <rule ref="category/java/errorprone.xml/EmptyIfStmt"/>
-    <rule ref="category/java/errorprone.xml/EmptyInitializer"/>
-    <rule ref="category/java/errorprone.xml/EmptyStatementBlock"/>
-    <rule ref="category/java/errorprone.xml/EmptyStatementNotInLoop"/>
-    <rule ref="category/java/errorprone.xml/EmptySwitchStatements"/>
-    <rule ref="category/java/errorprone.xml/EmptySynchronizedBlock"/>
-    <rule ref="category/java/errorprone.xml/EmptyTryBlock"/>
-    <rule ref="category/java/errorprone.xml/EmptyWhileStmt"/>
-    <rule ref="category/java/errorprone.xml/ImportFromSamePackage"/>
     <rule ref="category/java/errorprone.xml/JumbledIncrementer"/>
     <rule ref="category/java/errorprone.xml/MisplacedNullCheck"/>
     <rule ref="category/java/errorprone.xml/OverrideBothEqualsAndHashcode"/>
@@ -116,19 +108,14 @@ under the License.
     <rule ref="category/java/multithreading.xml/DoubleCheckedLocking"/>
 
     <rule ref="category/java/performance.xml/AddEmptyString" />
-    <rule ref="category/java/performance.xml/AppendCharacterWithChar" />
+    <!--<rule ref="category/java/performance.xml/AppendCharacterWithChar" />-->
     <rule ref="category/java/performance.xml/AvoidFileStream" />
 
-    <rule ref="category/java/performance.xml/AvoidUsingShortType" />
     <rule ref="category/java/performance.xml/BigIntegerInstantiation"/>
-    <rule ref="category/java/performance.xml/BooleanInstantiation"/>
     <rule ref="category/java/performance.xml/ConsecutiveAppendsShouldReuse" />
-    <rule ref="category/java/performance.xml/ConsecutiveLiteralAppends" />
+    <!--<rule ref="category/java/performance.xml/ConsecutiveLiteralAppends" />-->
     <rule ref="category/java/performance.xml/InefficientEmptyStringCheck" />
     <rule ref="category/java/performance.xml/InefficientStringBuffering" />
-    <rule ref="category/java/performance.xml/IntegerInstantiation" />
-    <rule ref="category/java/performance.xml/LongInstantiation" />
-    <rule ref="category/java/performance.xml/SimplifyStartsWith" />
     <rule ref="category/java/performance.xml/TooFewBranchesForASwitchStatement" />
     <rule ref="category/java/performance.xml/UseArraysAsList" />
     <rule ref="category/java/performance.xml/UseIndexOfChar" />

client-generator-model/src/main/java/ch/colabproject/colab/generator/model/exceptions/HttpErrorMessage.java

@@ -7,7 +7,7 @@
 package ch.colabproject.colab.generator.model.exceptions;
 
 import ch.colabproject.colab.generator.model.annotations.ExtractJavaDoc;
-import javax.ws.rs.core.Response;
+import jakarta.ws.rs.core.Response;
 
 /**
  * Throw an error message.

client-generator-model/src/main/java/ch/colabproject/colab/generator/model/exceptions/HttpException.java

@@ -8,10 +8,10 @@
 
 import ch.colabproject.colab.generator.model.interfaces.WithJsonDiscriminator;
 import ch.colabproject.colab.generator.model.tools.PolymorphicDeserializer;
-import javax.ejb.ApplicationException;
-import javax.json.bind.annotation.JsonbTransient;
-import javax.json.bind.annotation.JsonbTypeDeserializer;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.ApplicationException;
+import jakarta.json.bind.annotation.JsonbTransient;
+import jakarta.json.bind.annotation.JsonbTypeDeserializer;
+import jakarta.ws.rs.core.Response;
 
 /**
  * run-time exception which may be sent back to client.

client-generator-model/src/main/java/ch/colabproject/colab/generator/model/interfaces/WithId.java

@@ -7,7 +7,7 @@
 package ch.colabproject.colab.generator.model.interfaces;
 
 import ch.colabproject.colab.generator.model.tools.PolymorphicDeserializer;
-import javax.json.bind.annotation.JsonbTypeDeserializer;
+import jakarta.json.bind.annotation.JsonbTypeDeserializer;
 
 /**
  * Simple interface which depict objects having a Long id

client-generator-model/src/main/java/ch/colabproject/colab/generator/model/interfaces/WithJsonDiscriminator.java

@@ -9,8 +9,8 @@
 import ch.colabproject.colab.generator.model.annotations.JsonClassName;
 import ch.colabproject.colab.generator.model.tools.PolymorphicDeserializer;
 import java.io.Serializable;
-import javax.json.bind.annotation.JsonbProperty;
-import javax.json.bind.annotation.JsonbTypeDeserializer;
+import jakarta.json.bind.annotation.JsonbProperty;
+import jakarta.json.bind.annotation.JsonbTypeDeserializer;
 
 /**
  * Represent an object which can be serialize to JSON. Implementing this interface force

client-generator-model/src/main/java/ch/colabproject/colab/generator/model/tools/ClassDoc.java

@@ -8,7 +8,7 @@
 
 import java.util.HashMap;
 import java.util.Map;
-import javax.json.bind.annotation.JsonbTransient;
+import jakarta.json.bind.annotation.JsonbTransient;
 
 /**
  * Represent javadoc of a class, with fields and methods javadocs.

client-generator-model/src/main/java/ch/colabproject/colab/generator/model/tools/DateSerDe.java

@@ -10,12 +10,12 @@
 import java.time.Instant;
 import java.time.OffsetDateTime;
 import java.time.ZoneId;
-import javax.json.bind.serializer.DeserializationContext;
-import javax.json.bind.serializer.JsonbDeserializer;
-import javax.json.bind.serializer.JsonbSerializer;
-import javax.json.bind.serializer.SerializationContext;
-import javax.json.stream.JsonGenerator;
-import javax.json.stream.JsonParser;
+import jakarta.json.bind.serializer.DeserializationContext;
+import jakarta.json.bind.serializer.JsonbDeserializer;
+import jakarta.json.bind.serializer.JsonbSerializer;
+import jakarta.json.bind.serializer.SerializationContext;
+import jakarta.json.stream.JsonGenerator;
+import jakarta.json.stream.JsonParser;
 
 /**
  * Date Serializer and Deserializer.

client-generator-model/src/main/java/ch/colabproject/colab/generator/model/tools/JavaDocExtractor.java

@@ -8,39 +8,36 @@
 
 
 import ch.colabproject.colab.generator.model.annotations.ExtractJavaDoc;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.Writer;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-import java.util.stream.Stream;
+import jakarta.enterprise.util.TypeLiteral;
+import jakarta.json.bind.Jsonb;
+import jakarta.persistence.Entity;
+import jakarta.ws.rs.Path;
+
 import javax.annotation.processing.AbstractProcessor;
 import javax.annotation.processing.RoundEnvironment;
 import javax.annotation.processing.SupportedAnnotationTypes;
 import javax.annotation.processing.SupportedSourceVersion;
-import javax.enterprise.util.TypeLiteral;
-import javax.json.bind.Jsonb;
 import javax.lang.model.SourceVersion;
-import javax.lang.model.element.Element;
-import javax.lang.model.element.ExecutableElement;
-import javax.lang.model.element.PackageElement;
-import javax.lang.model.element.TypeElement;
-import javax.lang.model.element.VariableElement;
-import javax.persistence.Entity;
+import javax.lang.model.element.*;
 import javax.tools.Diagnostic.Kind;
 import javax.tools.FileObject;
 import javax.tools.StandardLocation;
-import javax.ws.rs.Path;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.Writer;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Stream;
 
 /**
  * Annotations Processor to extract Javadoc of REST endpoints and JPA entities.
  *
  * @author maxence
  */
-@SupportedSourceVersion(SourceVersion.RELEASE_11)
-@SupportedAnnotationTypes({"javax.ws.rs.Path", "javax.persistence.Entity"})
+@SupportedSourceVersion(SourceVersion.RELEASE_17)
+@SupportedAnnotationTypes({"jakarta.ws.rs.Path", "jakarta.persistence.Entity"})
 public class JavaDocExtractor extends AbstractProcessor {
 
     /**

client-generator-model/src/main/java/ch/colabproject/colab/generator/model/tools/JsonbProvider.java

@@ -6,11 +6,11 @@
  */
 package ch.colabproject.colab.generator.model.tools;
 
-import javax.json.bind.Jsonb;
-import javax.json.bind.JsonbBuilder;
-import javax.json.bind.JsonbConfig;
-import javax.ws.rs.ext.ContextResolver;
-import javax.ws.rs.ext.Provider;
+import jakarta.json.bind.Jsonb;
+import jakarta.json.bind.JsonbBuilder;
+import jakarta.json.bind.JsonbConfig;
+import jakarta.ws.rs.ext.ContextResolver;
+import jakarta.ws.rs.ext.Provider;
 
 /**
  * convenient way to customize the JSON-B mapper

client-generator-model/src/main/java/ch/colabproject/colab/generator/model/tools/PolymorphicDeserializer.java

@@ -11,10 +11,10 @@
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Optional;
-import javax.json.JsonObject;
-import javax.json.bind.serializer.DeserializationContext;
-import javax.json.bind.serializer.JsonbDeserializer;
-import javax.json.stream.JsonParser;
+import jakarta.json.JsonObject;
+import jakarta.json.bind.serializer.DeserializationContext;
+import jakarta.json.bind.serializer.JsonbDeserializer;
+import jakarta.json.stream.JsonParser;
 import org.reflections.Reflections;
 
 /**
@@ -26,7 +26,7 @@
  * from other packages.
  * </p>
  * All WithJsonDiscriminator abstract implementation MUST register this deserializer with the
- * {@link javax.json.bind.annotation.JsonbTypeDeserializer  JsonbTypeDeserializer} annotation.
+ * {@link jakarta.json.bind.annotation.JsonbTypeDeserializer  JsonbTypeDeserializer} annotation.
  * <p>
  * Yasson/JSON-b polymorphic deserializer is a "vieux serpent de mer". Some inputs:
  * <ul>