Merge branch '1960-fix-install-tests' into 'master'

Resolve "fix install tests" Closes #1960 See merge request !1650

Merge branch '1960-fix-install-tests' into 'master'
Resolve "fix install tests" Closes #1960 See merge request !1650
dea7ea7e · Piotr Gawron · 0894927d · 7a131415 · dea7ea7e · dea7ea7e
Commit dea7ea7e authored 1 year ago by Piotr Gawron
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -464,73 +464,13 @@ build_debian_package:
    - export DEBEMAIL="piotr.gawron@uni.lu"
    - debian/create-debian-pkg.sh

-test_upgrade_debian_package:
-  image: debian:stretch
-  stage: test
-  only:
-    - tags
-# we need to run it in privileged mode due to: https://stackoverflow.com/questions/29683231/tomcat7-fail-to-start-inside-ubuntu-docker-container
-  tags:
-     - privileged
-  services:
-     - name: piotrgawron/debian-repo
-       alias: debian-repo
-  dependencies:
-     - build_debian_package
-  script:
-     - echo "deb http://archive.debian.org/debian stretch main" > /etc/apt/sources.list
-     - echo "deb-src http://archive.debian.org/debian stretch main" >> /etc/apt/sources.list
-     - echo "deb http://archive.debian.org/debian stretch-backports main" >> /etc/apt/sources.list
-     - echo "deb http://archive.debian.org/debian-security stretch/updates main" >> /etc/apt/sources.list
-     - echo "deb-src http://archive.debian.org/debian-security stretch/updates main" >> /etc/apt/sources.list
-     - apt-get update
-     - DEBIAN_FRONTEND=noninteractive apt-get install -y ssh software-properties-common dirmngr wget curl apt-transport-https postgresql
-     - service postgresql start
-     - debian_file=$(ls debian/*.deb)
-     - version=$(echo $debian_file| cut -f2 -d"_")
-     - echo "PUT $debian_file /docker/incoming" | sftp -o StrictHostKeyChecking=no user@debian-repo
-     - ssh root@debian-repo /usr/local/sbin/reprepro-import
-     - apt-add-repository "deb http://repo-r3lab.uni.lu/debian/ stable main"
-     - apt-key adv --no-tty --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 0xcb185f4e31872412
-     - echo debconf minerva/internal/skip-preseed boolean true | debconf-set-selections
-     - echo debconf minerva/dbconfig-install select true | debconf-set-selections
-     - echo debconf minerva/pgsql/app-pass select secret_password | debconf-set-selections
-     - echo debconf minerva/remote/host select localhost | debconf-set-selections
-     - echo debconf minerva/db/dbname select minerva_db | debconf-set-selections
-     - echo debconf minerva/db/app-user select minerva_user@localhost | debconf-set-selections
-     - apt-get update
-#hacky way of installing minerva on docker - by default rc-invoke is preventing services changes on docker
-     - mv /usr/sbin/policy-rc.d /usr/sbin/policy-rc.d.backup
-     - mv gitlab-ci-policy-rc.d /usr/sbin/policy-rc.d
-     - chmod 0755 /usr/sbin/policy-rc.d
-     - DEBIAN_FRONTEND=noninteractive apt-get install -y --allow-unauthenticated minerva
-
-#local repository with new version
-     - apt-add-repository "deb http://debian-repo/ unstable main"
-     - apt-get update --allow-unauthenticated
-     - apt-get dist-upgrade -y --allow-unauthenticated
-     - mv /usr/sbin/policy-rc.d.backup /usr/sbin/policy-rc.d
-     - service tomcat8 start
-#we need to wait a bit for tomcat start
-     - sleep 15
-     - wget http://localhost:8080/minerva/
-
-#test if we can login and get configuration using new version
-     - test 200 = $(curl -X POST -d "login=admin&password=admin" --write-out %{http_code} --silent --output /dev/null -c cookie.txt http://localhost:8080/minerva/api/doLogin)
-     - test 200 = $(curl --write-out %{http_code} --silent --output configuration.json --cookie cookie.txt http://localhost:8080/minerva/api/configuration/)
-     - test 1 = $(cat configuration.json| grep $version | wc -l)
-
 test_install_debian_package:
  image: debian:stretch
  stage: test
  only:
    - tags
-# we need to run it in privileged mode due to: https://stackoverflow.com/questions/29683231/tomcat7-fail-to-start-inside-ubuntu-docker-container
  tags:
     - privileged
-  services:
-     - name: piotrgawron/debian-repo
-       alias: debian-repo
  dependencies:
     - build_debian_package
  script:
@@ -543,23 +483,15 @@ test_install_debian_package:
     - DEBIAN_FRONTEND=noninteractive apt-get install -y ssh software-properties-common dirmngr wget curl postgresql
     - service postgresql start
     - debian_file=$(ls debian/*.deb)
-     - echo "PUT $debian_file /docker/incoming" | sftp -o StrictHostKeyChecking=no user@debian-repo
-     - ssh root@debian-repo /usr/local/sbin/reprepro-import
-     - apt-add-repository "deb http://debian-repo/ unstable main"
     - echo debconf minerva/internal/skip-preseed boolean true | debconf-set-selections
     - echo debconf minerva/dbconfig-install select true | debconf-set-selections
     - echo debconf minerva/pgsql/app-pass select secret_password | debconf-set-selections
     - echo debconf minerva/remote/host select localhost | debconf-set-selections
     - echo debconf minerva/db/dbname select minerva_db | debconf-set-selections
     - echo debconf minerva/db/app-user select minerva_user@localhost | debconf-set-selections
-     - apt-get update --allow-insecure-repositories
-#hacky way of installing minerva on docker - by default rc-invoke is preventing services changes on docker
-     - mv /usr/sbin/policy-rc.d /usr/sbin/policy-rc.d.backup
-     - mv gitlab-ci-policy-rc.d /usr/sbin/policy-rc.d
-     - chmod 0755 /usr/sbin/policy-rc.d
-     - DEBIAN_FRONTEND=noninteractive apt-get install -y --allow-unauthenticated minerva
-     - mv /usr/sbin/policy-rc.d.backup /usr/sbin/policy-rc.d 
-     - service tomcat8 start
+     - apt-get update
+     - DEBIAN_FRONTEND=noninteractive apt-get install -y ./$debian_file
+     - java -jar /usr/share/minerva/minerva.jar &
 #we need to wait a bit for tomcat start
     - sleep 15
     - wget http://localhost:8080/minerva/
@@ -587,9 +519,9 @@ test_deploy_with_db_without_superadmin_rights:
    - echo "database.password=test" >> /etc/minerva/db.properties
    - echo "CREATE DATABASE test;CREATE USER test WITH ENCRYPTED PASSWORD 'test';GRANT ALL PRIVILEGES ON DATABASE test TO test;" >tmp.sql
    - PGPASSWORD=$POSTGRES_PASSWORD psql -h postgres -U $POSTGRES_USER $POSTGRES_DB < tmp.sql
-    - FIX ME!!!!!!!!!
-    - mv minerva.war /usr/local/tomcat/webapps/minerva.war
-    - /usr/local/tomcat/bin/startup.sh
+    - mkdir -p /usr/share/minerva/data/
+    - mv minerva.jar /usr/share/minerva/
+    - java -jar /usr/share/minerva/minerva.jar
    - sleep 15
    - curl http://localhost:8080/minerva/
 #test if we can login and list projects

--- a/annotation/pom.xml
+++ b/annotation/pom.xml
@@ -76,18 +76,6 @@
 			<version>${annotation-api.version}</version>
 		</dependency>

-		<dependency>
-			<groupId>com.sun.xml.bind</groupId>
-			<artifactId>jaxb-impl</artifactId>
-			<version>${jaxb.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>com.sun.xml.bind</groupId>
-			<artifactId>jaxb-core</artifactId>
-			<version>${jaxb.version}</version>
-		</dependency>
-

 		<!-- XML parser -->
 		<dependency>

--- a/converter-SBGNML/pom.xml
+++ b/converter-SBGNML/pom.xml
@@ -48,19 +48,6 @@
 			<version>${xercesImp.version}</version>
 		</dependency>

-		<!-- Java xml serialization -->
-		<dependency>
-			<groupId>javax.xml.bind</groupId>
-			<artifactId>jaxb-api</artifactId>
-			<version>${jaxb.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>org.glassfish.jaxb</groupId>
-			<artifactId>jaxb-runtime</artifactId>
-			<version>${jaxb.version}</version>
-		</dependency>
-
 		<dependency>
 			<groupId>com.github.sbgn</groupId>
 			<artifactId>libsbgn</artifactId>
@@ -125,18 +112,6 @@
 			</exclusions>
 		</dependency>

-		<dependency>
-			<groupId>com.sun.xml.bind</groupId>
-			<artifactId>jaxb-impl</artifactId>
-			<version>${jaxb.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>com.sun.xml.bind</groupId>
-			<artifactId>jaxb-core</artifactId>
-			<version>${jaxb.version}</version>
-		</dependency>
-
 		<!-- Log4J2 -->
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
@@ -148,7 +123,8 @@
 			<artifactId>log4j-core</artifactId>
 			<version>${log4j2.version}</version>
 		</dependency>
-		<!-- Spring uses commons-logging, so: https://stackoverflow.com/a/41475146/1127920 -->
+		<!-- Spring uses commons-logging, so:
+		https://stackoverflow.com/a/41475146/1127920 -->
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-jcl</artifactId>

--- a/model/pom.xml
+++ b/model/pom.xml
@@ -22,9 +22,22 @@
 		<dependency>
 			<groupId>javax.xml.bind</groupId>
 			<artifactId>jaxb-api</artifactId>
-			<version>${jaxb.version}</version>
+			<version>${jaxb-api.version}</version>
 		</dependency>

+		<dependency>
+			<groupId>com.sun.xml.bind</groupId>
+			<artifactId>jaxb-impl</artifactId>
+			<version>${jaxb-impl.version}</version>
+		</dependency>
+
+		<dependency>
+			<groupId>com.sun.xml.bind</groupId>
+			<artifactId>jaxb-core</artifactId>
+			<version>${jaxb-core.version}</version>
+		</dependency>
+
+
 		<!-- Hibernate -->
 		<dependency>
 			<groupId>org.hibernate</groupId>

--- a/pom.xml
+++ b/pom.xml
@@ -22,7 +22,9 @@
 		<xalan.version>2.7.3</xalan.version>

 		<annotation-api.version>1.3.2</annotation-api.version>
-		<jaxb.version>2.3.0</jaxb.version>
+		<jaxb-api.version>2.3.1</jaxb-api.version>
+		<jaxb-core.version>2.3.0.1</jaxb-core.version>
+		<jaxb-impl.version>2.3.9</jaxb-impl.version>

 		<apache.httpcomponents.version>4.5.14</apache.httpcomponents.version>
 		<apache.httpcomponents-core.version>4.4.16</apache.httpcomponents-core.version>

--- a/service/pom.xml
+++ b/service/pom.xml
@@ -161,6 +161,10 @@
 			<version>${greenmail.version}</version>
 			<scope>test</scope>
 			<exclusions>
+				<exclusion>
+					<groupId>com.sun.activation</groupId>
+					<artifactId>jakarta.activation</artifactId>
+				</exclusion>
 				<exclusion>
 					<groupId>org.slf4j</groupId>
 					<artifactId>slf4j-api</artifactId>