new linter and tomcat bump and icons issue

Jenkinsfile

@@ -27,7 +27,7 @@ pipeline {
                         changeset "molgenis8/**"
                     }
                     steps {
-                        container('toolset') {
+                        container('creator-ee') {
                             dir('molgenis8') {
                                 script{
                                     sh 'ansible-lint --force-color roles/*/*/main.yml'
@@ -41,7 +41,7 @@ pipeline {
                         changeset "molgenis9/**"
                     }
                     steps {
-                        container('toolset') {
+                        container('creator-ee') {
                             dir('molgenis9') {
                                 script{
                                     sh 'ansible-lint --force-color roles/*/*/main.yml'
@@ -55,7 +55,7 @@ pipeline {
                         changeset "molgenis10/**"
                     }
                     steps {
-                        container('toolset') {
+                        container('creator-ee') {
                             dir('molgenis10') {
                                 script{
                                     sh 'ansible-lint --force-color roles/*/*/main.yml'
@@ -69,7 +69,7 @@ pipeline {
                         changeset "armadillo1/**"
                     }
                     steps {
-                        container('toolset') {
+                        container('creator-ee') {
                             dir('armadillo1') {
                                 script {
                                     sh 'ansible-lint --force-color roles/*/*/main.yml'
@@ -90,7 +90,7 @@ pipeline {
                         changeset "molgenis8/**"
                     }
                     steps {
-                        container('toolset') {
+                        container('creator-ee') {
                             dir('molgenis8') {
                                 script {
                                     sh 'ansible-lint --force-color roles/*/*/main.yml'
@@ -107,7 +107,7 @@ pipeline {
                         changeset "molgenis9/**"
                     }
                     steps {
-                        container('toolset') {
+                        container('creator-ee') {
                             dir('molgenis9') {
                                 script {
                                     sh 'ansible-lint --force-color roles/*/*/main.yml'
@@ -124,7 +124,7 @@ pipeline {
                         changeset "molgenis10/**"
                     }
                     steps {
-                        container('toolset') {
+                        container('creator-ee') {
                             dir('molgenis10') {
                                 script {
                                     sh 'ansible-lint --force-color roles/*/*/main.yml'
@@ -141,7 +141,7 @@ pipeline {
                         changeset "armadillo1/**"
                     }
                     steps {
-                        container('toolset') {
+                        container('creator-ee') {
                             dir('armadillo1') {
                                 script {
                                     sh 'ansible-lint --force-color roles/*/*/main.yml'

molgenis10/README.md

@@ -1,7 +1,7 @@
 # Ansible Collection - molgenis.molgenis10
 
 ## Migration from Molgenis9 (molgenis 9.1.y)
-Molgenis 10.x.y uses elasticsearch 7 
+Molgenis 10.x.y uses elasticsearch 7. See playbook_upgrade_from_9.yml below.
 
 
 

molgenis10/galaxy.yml

@@ -9,7 +9,7 @@ namespace: molgenis
 name: molgenis10
 
 # The version of the collection. Must be compatible with semantic versioning
-version: 10.0.5
+version: 10.0.6
 
 # The path to the Markdown (.md) readme file. This path is relative to the root of the collection
 readme: README.md

molgenis10/playbook.yml

@@ -31,6 +31,8 @@
         access_key: "{{ minio.access_key }}"
         secret_key: "{{ minio.secret_key }}"
     - role: tomcat
+      vars:
+        tomcat_version: 9.0.64
     - role: molgenis_user
     - role: molgenis_application
     - role: nginx

molgenis10/roles/minio/meta/main.yml

@@ -5,7 +5,7 @@ galaxy_info:
   description: Minio file storage, used to get data into the federated platform
   company: MOLGENIS
   license: LGPL
-  min_ansible_version: 1.2
+  min_ansible_version: 2.7.9
   platforms:
     - name: EL
       versions:

molgenis10/roles/nginx/README.md

@@ -1 +1 @@
-The nginx role creates a proxy that listens on port tcp/80 and forwards that traffic either to molgenis running tomcat (backend) or the remote unpkg.com server for the frontend components.
+The nginx role creates a proxy that listens on port tcp/80 and forwards that traffic either to molgenis running tomcat (backend) or the remote unpkg.com server for the frontend components. The molgenis-theme frontend needs to be proxy-passed from unpkg otherwise the icons within it will not load properly. So all frontends are redirected except the molgenis-theme that nginx needs to proxy pass. On Ubuntu 22.04 the new OpenSSL >= 3.0.0 will not work properly with old unkpg.com server, we have a workaround in place on a local mirror server unpkg.molgeniscloud.org.

molgenis10/roles/nginx/tasks/main.yml

@@ -26,6 +26,15 @@
     src: molgenis.j2
     dest: /etc/nginx/default.d/molgenis.conf
     mode: '0644'
+  when: not ( ansible_distribution == "Ubuntu" and ansible_distribution_major_version == '22' )
+  notify: "restart nginx"
+
+- name: Install special molgenis frontend config for OpenSSL 3.x servers
+  ansible.builtin.template:
+    src: molgenis_openssl3.j2
+    dest: /etc/nginx/default.d/molgenis.conf
+    mode: '0644'
+  when: ansible_distribution == "Ubuntu" and ansible_distribution_major_version == '22'
   notify: "restart nginx"
 
 - name: Register project from molgenis-server.properties

molgenis10/roles/nginx/templates/molgenis.j2

@@ -1,3 +1,5 @@
+# Only the theme is proxied, the rest is all retrieved from unpkg.com by clients browser
+
 location / {
     proxy_pass http://localhost:8080;
     client_max_body_size 0;
@@ -7,15 +9,26 @@ location / {
     proxy_http_version 1.1;
 }
 
+
+location /@molgenis-ui/molgenis-theme{
+    # This is required because of the theme css being dependant on a relative url to images: 'url("/img/icons-rtl.gif")' which will otherwise be resolved as 'url("https://unpkg.com/img/icons-rtl.gif")'
+
+    proxy_pass https://unpkg.com/@molgenis-ui/molgenis-theme;
+    {% for app in frontend.proxy0[frontend.version] -%}
+    rewrite ^/@molgenis-ui/{{- app.split('@')[0] }}/(.*) /@molgenis-ui/{{- app }}/$1;
+    {% endfor %}
+
+    # do not cache these redirects too long
+    expires 60m;
+}
+
 location /@molgenis-ui{
 
     {% for app in frontend.proxy[frontend.version] -%}
-    rewrite ^/@molgenis-ui/{{- app.split('@')[0] }}/(.*) https://unpkg.com/@molgenis-ui/{{- app }}/$1  redirect;
+    rewrite ^/@molgenis-ui/{{- app.split('@')[0] }}/(.*) https://unpkg.com/@molgenis-ui/{{- app }}/$1 redirect;
     {% endfor %}
     # extra special frontends below
 
-    # do not cache these redirects too long
-    expires 10m;
 }
 
 {% if frontend.proxy2[frontend.version] is defined -%}
@@ -25,7 +38,5 @@ location /@molgenis/ {
     rewrite ^/@molgenis/{{- app.split('@')[0] }}(/(.*))?$ https://unpkg.com/@molgenis/{{- app }}$1  redirect;
     {% endfor %}
 
-    # do not cache these redirects too long
-    expires 10m;
 }
 {% endif %}

molgenis10/roles/nginx/templates/molgenis_openssl3.j2

@@ -0,0 +1,44 @@
+# Special config for OpenSSL >= 3.0.0 servers
+# Nginx proxy passes to unpkg.com fail over https due to OpenSSl incompatibility
+# Only the theme is proxied, the rest is all retrieved from unpkg.com by clients browser
+
+location / {
+    proxy_pass http://localhost:8080;
+    client_max_body_size 0;
+    proxy_read_timeout 600s;
+    proxy_redirect http://localhost:8080/ $scheme://$host/;
+    proxy_set_header Host $host;
+    proxy_http_version 1.1;
+}
+
+location /@molgenis-ui/molgenis-theme{
+    # This is required because of the theme css being dependant on a relative url to images: 'url("/img/icons-rtl.gif")' which will otherwise be resolved as 'url("https://unpkg.com/img/icons-rtl.gif")'
+    # Needs to use our own theme/unpkg mirror
+
+    proxy_pass https://unpkg.molgeniscloud.org/@molgenis-ui/molgenis-theme;
+    {% for app in frontend.proxy0[frontend.version] -%}
+    rewrite ^/@molgenis-ui/{{- app.split('@')[0] }}/(.*) /@molgenis-ui/{{- app }}/$1;
+    {% endfor %}
+
+    # do not cache these redirects too long
+    expires 60m;
+}
+
+location /@molgenis-ui{
+
+    {% for app in frontend.proxy[frontend.version] -%}
+    rewrite ^/@molgenis-ui/{{- app.split('@')[0] }}/(.*) https://unpkg.com/@molgenis-ui/{{- app }}/$1 redirect;
+    {% endfor %}
+    # extra special frontends below
+
+}
+
+{% if frontend.proxy2[frontend.version] is defined -%}
+location /@molgenis/ {
+
+    {% for app in frontend.proxy2[frontend.version] -%}
+    rewrite ^/@molgenis/{{- app.split('@')[0] }}(/(.*))?$ https://unpkg.com/@molgenis/{{- app }}$1  redirect;
+    {% endfor %}
+
+}
+{% endif %}

molgenis10/roles/postgres_11/handlers/main.yml

@@ -1,14 +1,14 @@
 ---
 - name: restart postgresql service on Centos
-  service:
+  ansible.builtin.service:
     name: postgresql-11
     state: restarted
   listen: "restart postgresql"
   when:
     - ansible_distribution == 'CentOS'
 
 - name: restart postgresql service on Ubuntu
-  service:
+  ansible.builtin.service:
     name: postgresql
     state: restarted
   listen: "restart postgresql"

molgenis10/roles/swap/tasks/main.yml

@@ -1,6 +1,6 @@
 ---
 - name: set swap_file variable
-  set_fact:
+  ansible.builtin.set_fact:
     swap_file: /swapfile.swap
 
 - name: check if swap file exists

molgenis10/roles/tomcat/tasks/main.yml

@@ -14,12 +14,12 @@
 
 - name: Register if tomcat is already there
   ansible.builtin.stat:
-    path: /usr/share/apache-tomcat-9.0.59/
+    path: /usr/share/apache-tomcat-{{ tomcat_version }}/
   register: tomcat_already_there
 
 - name: Install Tomcat from source
-  unarchive:
-    src: "https://archive.apache.org/dist/tomcat/tomcat-9/v9.0.59/bin/apache-tomcat-9.0.59.tar.gz"
+  ansible.builtin.unarchive:
+    src: "https://archive.apache.org/dist/tomcat/tomcat-9/v{{ tomcat_version }}/bin/apache-tomcat-{{ tomcat_version }}.tar.gz"
     dest: "/usr/share/"
     owner: tomcat
     group: molgenis
@@ -28,13 +28,13 @@
 
 - name: Register if first install tomcat
   ansible.builtin.stat:
-    path: /usr/share/apache-tomcat-9.0.59/webapps/examples
+    path: /usr/share/apache-tomcat-{{ tomcat_version }}/webapps/examples
   register: tomcat_first_install
 
 - name: Delete default folders tomcat webapps directory
   ansible.builtin.file:
     state: absent
-    path: "/usr/share/apache-tomcat-9.0.59/webapps/{{ item }}"
+    path: "/usr/share/apache-tomcat-{{ tomcat_version }}/webapps/{{ item }}"
   with_items:
     - ROOT
     - docs
@@ -45,26 +45,26 @@
 
 - name: create softlink to tomcat logs
   ansible.builtin.file:
-    src: /usr/share/apache-tomcat-9.0.59/logs
+    src: /usr/share/apache-tomcat-{{ tomcat_version }}/logs
     dest: /var/log/tomcat
     state: link
 
 - name: create softlink to tomcat conf
   ansible.builtin.file:
-    src: /usr/share/apache-tomcat-9.0.59/conf
+    src: /usr/share/apache-tomcat-{{ tomcat_version }}/conf
     dest: /etc/tomcat
     state: link
 
 - name: create softlink to tomcat shortname
   ansible.builtin.file:
-    src: /usr/share/apache-tomcat-9.0.59
+    src: /usr/share/apache-tomcat-{{ tomcat_version }}
     dest: /usr/share/tomcat
     state: link
 
 - name: Install molgenis server.xml file for tomcat
   ansible.builtin.copy:
     src: server.xml
-    dest: /usr/share/apache-tomcat-9.0.59/conf/server.xml
+    dest: /usr/share/apache-tomcat-{{ tomcat_version }}/conf/server.xml
     mode: '0644'
 
 - name: Install systemctl services file for tomcat