Add support of baseUrl

.github/workflows/create-release.yml

@@ -11,10 +11,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up JDK 11
+    - name: Set up JDK 17
       uses: actions/setup-java@v2
       with:
-        java-version: '11'
+        java-version: '17'
         distribution: 'adopt'
     - name: Build MIS
       run: mvn install

.github/workflows/maven-test.yml

@@ -12,10 +12,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up JDK 11
+    - name: Set up JDK 17
       uses: actions/setup-java@v2
       with:
-        java-version: '11'
+        java-version: '17'
         distribution: 'adopt'
     - name: Run JUnit Tests
       run: mvn install

aot-jar.properties

@@ -0,0 +1,40 @@
+# AOT configuration properties for jar packaging
+# Please review carefully the optimizations enabled below
+# Check https://micronaut-projects.github.io/micronaut-aot/latest/guide/ for more details
+
+# Caches environment property values: environment properties will be deemed immutable after application startup.
+cached.environment.enabled=true
+
+# Precomputes Micronaut configuration property keys from the current environment variables
+precompute.environment.properties.enabled=true
+
+# Converts YAML configuration files to Java configuration
+yaml.to.java.config.enabled=true
+
+# Scans for service types ahead-of-time, avoiding classpath scanning at startup
+serviceloading.jit.enabled=true
+
+# Scans reactive types at build time instead of runtime
+scan.reactive.types.enabled=true
+
+# Deduces the environment at build time instead of runtime
+deduce.environment.enabled=true
+
+# Checks of existence of some types at build time instead of runtime
+known.missing.types.enabled=true
+
+# Precomputes property sources at build time
+sealed.property.source.enabled=true
+
+# The list of service types to be scanned (comma separated)
+service.types=io.micronaut.context.env.PropertySourceLoader,io.micronaut.inject.BeanConfiguration,io.micronaut.inject.BeanDefinitionReference,io.micronaut.http.HttpRequestFactory,io.micronaut.http.HttpResponseFactory,io.micronaut.core.beans.BeanIntrospectionReference,io.micronaut.core.convert.TypeConverterRegistrar,io.micronaut.context.env.PropertyExpressionResolver
+
+# A list of types that the AOT analyzer needs to check for existence (comma separated)
+known.missing.types.list=io.reactivex.Observable,reactor.core.publisher.Flux,kotlinx.coroutines.flow.Flow,io.reactivex.rxjava3.core.Flowable,io.reactivex.rxjava3.core.Observable,io.reactivex.Single,reactor.core.publisher.Mono,io.reactivex.Maybe,io.reactivex.rxjava3.core.Single,io.reactivex.rxjava3.core.Maybe,io.reactivex.Completable,io.reactivex.rxjava3.core.Completable,io.methvin.watchservice.MacOSXListeningWatchService,io.micronaut.core.async.publisher.CompletableFuturePublisher,io.micronaut.core.async.publisher.Publishers.JustPublisher,io.micronaut.core.async.subscriber.Completable
+
+# It fetches remote Json Web Key Set at Build Time. https://micronaut-projects.github.io/micronaut-security/latest/guide/index.html#aotJwks
+micronaut.security.jwks.enabled=false
+
+# It fetches OpenID Connect metadata at Build time. https://micronaut-projects.github.io/micronaut-security/latest/guide/index.html#aotOpenidConfiguration
+micronaut.security.openid-configuration.enabled=false
+

pom.xml

@@ -8,10 +8,9 @@
 	<packaging>${packaging}</packaging>
 
 	<parent>
-		<relativePath>io.micronaut:micronaut-parent</relativePath>
-		<groupId>io.micronaut</groupId>
+		<groupId>io.micronaut.platform</groupId>
 		<artifactId>micronaut-parent</artifactId>
-		<version>3.9.1</version>
+		<version>4.1.6</version>
 	</parent>
 
 	<name>Cloudgene</name>
@@ -39,18 +38,21 @@
 
 	<properties>
 		<hadoop.version>2.6.0-cdh5.16.1</hadoop.version>
-		<node.version>v8.11.4</node.version>
+		<node.version>v10.4.0</node.version>
 		<npm.version>6.4.1</npm.version>
 		<webapp>${basedir}/src/main/html/webapp</webapp>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 		<packaging>jar</packaging>
-		<jdk.version>11</jdk.version>
-		<release.version>11</release.version>
-		<java.version>11</java.version>
-		<micronaut.version>3.3.4</micronaut.version>
+		<jdk.version>17</jdk.version>
+		<release.version>17</release.version>
+		<java.version>17</java.version>
+		<micronaut.version>4.1.6</micronaut.version>
+		<micronaut.runtime>netty</micronaut.runtime>
 		<exec.mainClass>cloudgene.mapred.server.Application</exec.mainClass>
 		<micronaut.runtime>netty</micronaut.runtime>
+		<micronaut.aot.enabled>false</micronaut.aot.enabled>
+
 	</properties>
 
 	<dependencyManagement>
@@ -156,11 +158,6 @@
 			<version>1.7</version>
 		</dependency>
 
-		<dependency>
-			<groupId>com.sun.mail</groupId>
-			<artifactId>javax.mail</artifactId>
-		</dependency>
-
 
 
 		<dependency>
@@ -214,16 +211,11 @@
 		<!-- Micronaut -->
 
 
-		<dependency>
-			<groupId>io.micronaut</groupId>
-			<artifactId>micronaut-inject</artifactId>
-			<scope>compile</scope>
-		</dependency>
-		<dependency>
-			<groupId>io.micronaut</groupId>
-			<artifactId>micronaut-validation</artifactId>
-			<scope>compile</scope>
-		</dependency>
+	    <dependency>
+		      <groupId>io.micronaut.validation</groupId>
+		      <artifactId>micronaut-validation</artifactId>
+		      <scope>compile</scope>
+	    </dependency>		
 		<dependency>
 			<groupId>org.junit.jupiter</groupId>
 			<artifactId>junit-jupiter-api</artifactId>
@@ -240,9 +232,9 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-		    <groupId>io.micronaut.test</groupId>
-		    <artifactId>micronaut-test-rest-assured</artifactId>
-		    <scope>test</scope>
+			<groupId>io.micronaut.test</groupId>
+			<artifactId>micronaut-test-rest-assured</artifactId>
+			<scope>test</scope>
 		</dependency>	
 		<dependency>
 			<groupId>io.micronaut</groupId>
@@ -259,11 +251,20 @@
 			<artifactId>micronaut-jackson-databind</artifactId>
 			<scope>compile</scope>
 		</dependency>
+		<dependency>
+			<groupId>io.micronaut.serde</groupId>
+			<artifactId>micronaut-serde-jackson</artifactId>
+			<scope>compile</scope>
+		</dependency>
 		<dependency>
 			<groupId>io.micronaut</groupId>
 			<artifactId>micronaut-runtime</artifactId>
 			<scope>compile</scope>
 		</dependency>
+		<dependency>
+			<groupId>io.micronaut</groupId>
+			<artifactId>micronaut-websocket</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>io.micronaut.security</groupId>
 			<artifactId>micronaut-security-jwt</artifactId>
@@ -296,13 +297,29 @@
 			<artifactId>netty-resolver-dns-native-macos</artifactId>
 			<scope>runtime</scope>
 		</dependency>
+		<dependency>
+			<groupId>org.yaml</groupId>
+			<artifactId>snakeyaml</artifactId>
+			<scope>runtime</scope>
+		</dependency>
 
 		<dependency>
 			<groupId>ch.qos.logback</groupId>
 			<artifactId>logback-classic</artifactId>
 			<scope>compile</scope>
 		</dependency>
 
+		<dependency>
+		    <groupId>io.micronaut.email</groupId>
+		    <artifactId>micronaut-email-javamail</artifactId>
+		</dependency>
+
+		<dependency>
+		    <groupId>org.eclipse.angus</groupId>
+		    <artifactId>angus-mail</artifactId>
+		    <scope>runtime</scope>
+		</dependency>
+
 	</dependencies>
 
 	<!-- **** Build **** -->
@@ -324,10 +341,24 @@
 		<plugins>
 
 			<plugin>
-				<groupId>io.micronaut.build</groupId>
-				<artifactId>micronaut-maven-plugin</artifactId>
-			</plugin>
-
+		        <groupId>io.micronaut.maven</groupId>
+		        <artifactId>micronaut-maven-plugin</artifactId>
+		          <configuration>
+		              <aotDependencies>
+		                  <dependency>
+		                      <groupId>io.micronaut.security</groupId>
+		                      <artifactId>micronaut-security-aot</artifactId>
+		                      <version>${micronaut.security.version}</version>
+		                  </dependency>
+		              </aotDependencies>
+		            <configFile>aot-${packaging}.properties</configFile>
+		          </configuration>
+		      </plugin>
+		      <plugin>
+		        <groupId>org.apache.maven.plugins</groupId>
+		        <artifactId>maven-enforcer-plugin</artifactId>
+		      </plugin>
+
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-compiler-plugin</artifactId>
@@ -337,43 +368,36 @@
 					<!-- Uncomment to enable incremental compilation -->
 					<!-- <useIncrementalCompilation>false</useIncrementalCompilation> -->
 
-					<annotationProcessorPaths
-						combine.children="append">
-						<path>
-							<groupId>io.micronaut</groupId>
-							<artifactId>micronaut-http-validation</artifactId>
-							<version>${micronaut.version}</version>
-						</path>
-						<path>
-							<groupId>io.micronaut.security</groupId>
-							<artifactId>micronaut-security-annotations</artifactId>
-							<version>${micronaut.security.version}</version>
-						</path>
-					</annotationProcessorPaths>
+			          <annotationProcessorPaths combine.children="append">
+			            <path>
+			              <groupId>io.micronaut</groupId>
+			              <artifactId>micronaut-http-validation</artifactId>
+			              <version>${micronaut.core.version}</version>
+			            </path>
+			            <path>
+			              <groupId>io.micronaut.security</groupId>
+			              <artifactId>micronaut-security-annotations</artifactId>
+			              <version>${micronaut.security.version}</version>
+			            </path>
+						  <path>
+							  <groupId>io.micronaut.serde</groupId>
+							  <artifactId>micronaut-serde-processor</artifactId>
+							  <version>${micronaut.serialization.version}</version>
+							  <exclusions>
+								  <exclusion>
+									  <groupId>io.micronaut</groupId>
+									  <artifactId>micronaut-inject</artifactId>
+								  </exclusion>
+							  </exclusions>
+					  </path>
+			          </annotationProcessorPaths>
 					<compilerArgs>
 						<arg>-Amicronaut.processing.group=cloudgene</arg>
 						<arg>-Amicronaut.processing.module=cloudgene</arg>
 					</compilerArgs>
 				</configuration>
 			</plugin>
 
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-surefire-plugin</artifactId>
-				<dependencies>
-					<dependency>
-						<groupId>org.junit.platform</groupId>
-						<artifactId>junit-platform-surefire-provider</artifactId>
-						<version>1.3.0</version>
-					</dependency>
-					<dependency>
-						<groupId>org.junit.jupiter</groupId>
-						<artifactId>junit-jupiter-engine</artifactId>
-						<version>5.7.2</version>
-					</dependency>
-				</dependencies>
-			</plugin>
-
 			<!-- Create webapp for production -->
 
 			<plugin>
@@ -467,28 +491,6 @@
 				</executions>
 			</plugin>
 
-			<!-- Code Coverage -->
-
-			<plugin>
-				<groupId>org.jacoco</groupId>
-				<artifactId>jacoco-maven-plugin</artifactId>
-				<version>0.8.5</version>
-				<executions>
-					<execution>
-						<goals>
-							<goal>prepare-agent</goal>
-						</goals>
-					</execution>
-					<execution>
-						<id>report</id>
-						<phase>test</phase>
-						<goals>
-							<goal>report</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
-
 		</plugins>
 	</build>
 

src/main/html/webapp/components/admin/dashboard/dashboard.js

@@ -22,7 +22,7 @@ export default Control.extend({
       }));
       $(element).fadeIn();
 
-      $.getJSON("/api/v2/admin/server/statistics", {
+      $.getJSON("api/v2/admin/server/statistics", {
         days: 1
       }, function(mydata) {
 
@@ -55,7 +55,7 @@ export default Control.extend({
 
     var days = $("#day_combo").val();
     var that = this;
-    $.getJSON("/api/v2/admin/server/statistics", {
+    $.getJSON("api/v2/admin/server/statistics", {
       days: days
     }, function(mydata) {
 

src/main/html/webapp/components/admin/settings/logs/logs.js

@@ -12,6 +12,6 @@ export default Control.extend({
     $(element).hide();
     $(element).html(template());
     $(element).fadeIn();
-    $("#log-cloudgene").load("/api/v2/admin/server/logs/cloudgene.log");
+    $("#log-cloudgene").load("api/v2/admin/server/logs/cloudgene.log");
   }
 });

src/main/html/webapp/components/core/job/detail/logs/logs.js

@@ -8,7 +8,7 @@ export default Control.extend({
 
   "init": function(element, options) {
 
-    $.get('/logs/' + options.job.attr('id'),function(data) {
+    $.get('logs/' + options.job.attr('id'),function(data) {
       $(element).html(template({
         content: data,
         job: options.job

src/main/html/webapp/components/core/job/submit/submit.stache

@@ -36,7 +36,7 @@
 <div class="container">
 
 
-<form id="parameters" class="form-horizontal" action="/api/v2/jobs/submit/{{application.id}}" method="POST" enctype="multipart/form-data" novalidate autocomplete="off">
+<form id="parameters" class="form-horizontal" action="api/v2/jobs/submit/{{application.id}}" method="POST" enctype="multipart/form-data" novalidate autocomplete="off">
 
 <div class="form-group row">
 	<label for="job-name" class="col-sm-2 col-form-label">Name</label>

src/main/html/webapp/components/core/user/activate/activate.stache

@@ -2,7 +2,7 @@
 <br>
 {{#data.success}}
     <div class="alert alert-success" id="success-message">
-    <b>Well done!</b> Your account is now active. <a href="/">Login now</a>.
+    <b>Well done!</b> Your account is now active. <a href="./">Login now</a>.
     <br>
     </div>
 {{else}}