Merge pull request #5 from khaledk2/new_ms_release

New ms release
ome · Sep 5, 2024 · 64540e9 · 64540e9
2 parents a007606 + 859aca8
commit 64540e9
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diff --git a/README.md b/README.md
@@ -1,10 +1,10 @@
 OMERO MS Image Region
 =====================
 
-[![Actions Status](https://github.com/ome/ansible-role-omero-server/workflows/Molecule/badge.svg)](https://github.com/ome/ansible-role-omero-server/actions)
-[![Ansible Role](https://img.shields.io/badge/ansible--galaxy-omero_ms_image_region-blue.svg)](https://galaxy.ansible.com/ui/standalone/roles/ome/omero_server/)
+[![Actions Status](https://github.com/ome/ansible-role-omero-ms-image-region/workflows/Molecule/badge.svg)](https://github.com/ome/ansible-role-omero-ms-image-region/actions)
+[![Ansible Role](https://img.shields.io/badge/ansible-galaxy-omero_ms_image_region-blue.svg)](https://galaxy.ansible.com/ui/standalone/roles/ome/omero_ms_image_region/)
 
-Installs and configures OMERO ms image region
+Installs and configures the OMERO microservice image region.
 
 Dependencies
 ------------
@@ -15,31 +15,31 @@ OMERO.server and OMERO.web are required.
 Role Variables
 --------------
 
-- omero_ms_image_region_user: Microservice user, the defaults is 'omero-server'
-- omero_ms_image_region_folder: Microservice installation folder
-- omero_ms_image_region_port: Microservice port 
-- omero_ms_image_region_db_url: OMERO database URL
-- omero_ms_image_region_db_port:  OMERO database server port
-- omero_ms_image_region_db_name: OMERO database name
-- omero_ms_image_region_db_username: OMERO database user name
-- omero_ms_image_region_db_pass: OMERO database user password
-- omero_ms_image_region_log_level: Logging level, allowed values: ``info``, ``debug``,  ``error``
-- omero_data_dir: OMERO data folder
-- omero_script_repo_root: OMERO scripts folder
-- omero_ms_image_region_worker_pool_size: No of Microservice workers, the default is double the number of processors which the machine has
-- session_id: OMERO Session id, if you do not know it, you may get it using this command:
-- omero_ms_image_region_max_active_channels: Max number of channels to allow per request default is 10
+- `omero_ms_image_region_user`: The microservice user, the default is `omero-server`
+- `omero_ms_image_region_folder`: The microservice installation folder
+- `omero_ms_image_region_port`: The microservice port 
+- `omero_ms_image_region_db_url`: The OMERO database URL
+- `omero_ms_image_region_db_port`:  The OMERO database server port
+- `omero_ms_image_region_db_name`: The OMERO database name
+- `omero_ms_image_region_db_username`: The OMERO database user name
+- `omero_ms_image_region_db_pass`: The OMERO database user password
+- `omero_ms_image_region_log_level`: The logging level, allowed values: ``info``, ``debug``,  ``error``
+- `omero_data_dir`: The OMERO data folder
+- `omero_script_repo_root`: The OMERO scripts folder
+- `omero_ms_image_region_worker_pool_size`: Number of microservice workers, the default is double the number of available processors
+- `session_id`: The OMERO session identifier, if you do not know it, you may get it using this command:
 
-    /opt/omero/web/OMERO.web/bin/omero config get omero.web.session_cookie_name
+      /opt/omero/web/OMERO.web/bin/omero config get omero.web.session_cookie_name
 
-- omero_ms_image_region_update_nginx: if false, it will not update the nginx config file
+- `omero_ms_image_region_max_active_channels`: The maximum number of channels to allow per request, the default is `10`
+- `omero_ms_image_region_update_nginx`: if set to `false`, it will not update the NGINX configuration file
+- `omero_ms_image_region_download_URL`: The download URL for the distributed microservice build (zip file)
+- `omero_ms_image_region_package_sha256`: The sha256 for the distributed microservice build
+- `java_version`: The Java version matching the server version. Supported versions are 11, 17 and 21
 
-- omero_ms_image_region_download_URL: The download URl for the distibuted ms build (zip file)
-- omero_ms_image_region_package_sha256: The sha256 for the distibuted ms build
-
-The ms build should be compatible with the installed OMERO.server, i.e.:
-- The bio-format version for the Microservice should match the Bio-Formats version of the OMERO.server
-- Also, in case of using ngff data, the version of OMEZarrReader should be the same for both of the Microsevice and the OMERO.server.
+The microservice build **must be compatible** with the installed OMERO.server:
+- The Bio-Formats version used in the microservice must match the Bio-Formats version of the OMERO.server.
+- Also, in the case of using NGFF data, the version of OMEZarrReader should be the same for both the Microsevice and the OMERO.server.
 
 Example Playbook
 ----------------
@@ -48,3 +48,33 @@ Example Playbook
       roles:
         - role: ome.omero_ms_image_region
           omero_ms_image_region_update_nginx: true
+
+Another example:
+----------------
+The following example is used to deploy in multiple nodes and configure the microservice download url and other roles variables. 
+For example, it can be used to deploy the microservice on the IDR omeroreadonly servers. The variable values inside the playbook should be modified for the IDR environment in which the microservice will be deployed.
+
+    - hosts: nodes
+      become: true
+
+      roles:
+        - role: ome.omero_ms_image_region
+          omero_ms_image_region_update_nginx: true
+          omero_ms_image_region_db_url: databse_url
+          omero_ms_image_region_db_name: database_name
+          omero_ms_image_region_db_username: database_username
+          omero_ms_image_region_db_pass: database_password
+          omero_data_dir: /data/OMERO
+          omero_ms_image_region_session_id: sessionid
+          # URL pointing to the micro service omero-ms-region-download
+          # It is important to have a version of the micro service using a version of Bio-Formats and OMEZarrReader that
+          # match the versions running on the server
+          omero_ms_image_region_download_URL: 'https://github.com/ome/omero-ms-image-region/releases/download/2024.07.15/omero-ms-image-region-0.10.0_b16.zip' 
+          # sha256 for the Latest build
+          omero_ms_image_region_package_sha256: 77bd3df2241c2beb439001fb00bfd8b207a06de63b8ee78c7170916d6dde963e
+
+
+Author Information
+------------------
+
+[email protected]
diff --git a/defaults/main.yml b/defaults/main.yml
@@ -44,11 +44,22 @@ omero_ms_image_region_session_id: 'sessionid'
 # Controls updating of the nginx config file (omero-web.conf). If False, the file does not get update
 omero_ms_image_region_update_nginx: false
 
-# Microservice download URL should be updated to match Bio-Formats versions of the Microservice and OMERO.server.
-#Also, the OMEZarrReader (if NGFF is used) versions of the Microservice and OMERO.server must match.
-omero_ms_image_region_download_URL: 'https://github.com/khaledk2/ice-archh-64/releases/download/new_tag/omero-ms-image-region-0.8.7.zip'
+java_version: 11
+
+all_omero_ms_image_region_download_URL:
+   11:
+     url: "https://github.com/ome/omero-ms-image-region/releases/download/2024.08.13/omero-ms-image-region-0.10.0_11.zip"
+     sha256: f45fb83cf55b4c87bb15b58a5c314ebd355d59cab9225d1bb598130d32fb86d9
+   17:
+     url: "https://github.com/ome/omero-ms-image-region/releases/download/2024.08.13/omero-ms-image-region-0.10.0_17.zip"
+     sha256: 694114e67dfe20f5d03803591e37e20e9835b3247d26bcc3534876711ec3a4a9
+   21:
+     url: "https://github.com/ome/omero-ms-image-region/releases/download/2024.08.13/omero-ms-image-region-0.10.0_21.zip"
+     sha256: 9f80c421ae6a746a8bf1199b65425e0616d539b26979a41220056d9e10bf7723
+
+omero_ms_image_region_download_URL: "{{ all_omero_ms_image_region_download_URL[java_version]['url'] }}"
+omero_ms_image_region_package_sha256: "{{ all_omero_ms_image_region_download_URL[java_version]['sha256'] }}"
 
-omero_ms_image_region_package_sha256: 9da1606fb1141b1044e0544451c92305710bca4c378febf003214b920ff510d2
 
 omero_ms_image_region_name: "{{ omero_ms_image_region_download_URL | basename }}"
 

diff --git a/handlers/main.yml b/handlers/main.yml
@@ -9,7 +9,7 @@
 - name: restart omero-ms-image-region service
   become: true
   ansible.builtin.service:
-    state: started
+    state: restarted
     daemon_reload: true
     name: omero-ms-image-region.service
 

diff --git a/molecule/resources/playbook.yml b/molecule/resources/playbook.yml
@@ -13,6 +13,9 @@
         password: omero
         databases: [ omero ]
 
+  - role: ome.java
+    java_versions: 11
+
   - role: ome.omero_server
     omero_server_release: 5.6.10
     postgresql_version: "14"

diff --git a/molecule/resources/requirements.yml b/molecule/resources/requirements.yml
@@ -2,3 +2,4 @@
 - src: ome.omero_server
 - src: ome.postgresql
 - src: ome.omero_web
+- src: ome.java
diff --git a/tasks/main.yml b/tasks/main.yml
@@ -17,7 +17,6 @@
 - import_tasks: pre_tasks.yml
   when:
    - stat_ssh256.stat.checksum is undefined or omero_ms_image_region_package_sha256 !=  stat_ssh256.stat.checksum
-   - not stat_result.stat.exists
 
 - name: omero-ms-image-region | set redis uri in protected mode
   ansible.builtin.set_fact:
@@ -33,35 +32,28 @@
 
 - name: omero-ms-image-region | copy config file
   become: true
-  become_user: "{{ omero_ms_image_region_user }}"
   ansible.builtin.template:
     dest: "{{ omero_ms_image_region_folder }}/omero-ms-image-region/conf/config.yaml"
     src: config.yaml.j2
+  notify:
+    - enable omero-ms-image-region service
+    - restart omero-ms-image-region service
 
 - name: omero-ms-image-region | copy log config file
   become: true
-  become_user: "{{ omero_ms_image_region_user }}"
   ansible.builtin.template:
     dest: "{{ omero_ms_image_region_folder }}/omero-ms-image-region/conf/logback.xml"
     src: logback.xml.j2
 
+
 - name: omero-ms-image-region | copy run.sh
   become: true
-  become_user: "{{ omero_ms_image_region_user }}"
   ansible.builtin.template:
     dest: "{{ omero_ms_image_region_folder }}/omero-ms-image-region/run.sh"
     src: run.sh.j2
     mode: +x
 
-- name: omero-ms-image-region | copy stop.sh
-  become: true
-  become_user: "{{ omero_ms_image_region_user }}"
-  ansible.builtin.template:
-    dest: "{{ omero_ms_image_region_folder }}/omero-ms-image-region/stop.sh"
-    src: stop.sh.j2
-    mode: +x
-
-- name: omero-ms-image-region | systemd service
+- name: omero-ms-image-region | copy systemd service
   become: true
   ansible.builtin.template:
     dest: /etc/systemd/system/omero-ms-image-region.service
@@ -73,6 +65,8 @@
 
 - name: omero-ms-image-region | selinux http_port_t for ms port
   become: true
+  ignore_errors: true
+
   ansible.builtin.seport:
     ports: "{{ omero_ms_image_region_port }}"
     proto: tcp

diff --git a/tasks/pre_tasks.yml b/tasks/pre_tasks.yml
@@ -1,4 +1,10 @@
 ---
+- name: omero-ms-image-region | delete ms folder if it exists
+  become: true
+  ansible.builtin.file:
+    path: "{{ omero_ms_image_region_folder }}"
+    state: absent
+  when: stat_result.stat.exists
 
 - name: omero-ms-image-region | create ms folder
   become: true
@@ -16,7 +22,7 @@
     deploy_archive_sha256: "{{ omero_ms_image_region_package_sha256 }}"
     deploy_archive_symlink: "{{ omero_ms_image_region_folder }}/omero-ms-image-region"
     deploy_archive_internal_root: >-
-      omero-ms-image-region-0.8.7
+        {{ omero_ms_image_region_name | splitext | first | replace(java_version,'') | replace('_','') }}
 
 - name: omero-ms-image-region | chown to ms-user
   become: true

diff --git a/templates/omero-ms-image-region.service.j2 b/templates/omero-ms-image-region.service.j2
@@ -4,12 +4,11 @@ Requires=redis.service
 After=network.service
 
 [Service]
-USER=omero-server
+User=omero-server
 UMask=0002
 Type=simple
 WorkingDirectory={{ omero_ms_image_region_folder }}/omero-ms-image-region
-ExecStart={{ omero_ms_image_region_folder }}/omero-ms-image-region/run.sh
-ExecStop={{ omero_ms_image_region_folder }}/omero-ms-image-region/stop.sh
+ExecStart=/bin/bash {{ omero_ms_image_region_folder }}/omero-ms-image-region/run.sh
 Restart=always
 RestartSec=3
 

diff --git a/templates/omero-web.conf.j2 b/templates/omero-web.conf.j2
@@ -1,7 +1,8 @@
+proxy_cache_path /tmp/cache levels=1:2 keys_zone=ms_cache:10m max_size={{ nginx_cache_max_size }} inactive={{ nginx_cache_inactive_time }} use_temp_path=off;
 
 upstream image_region_backend {
-    server 127.0.0.1:{{ omero_ms_image_region_port }} git push
-proxy_cache_path /tmp/cache levels=1:2 keys_zone=ms_cache:10m max_size={{ nginx_cache_max_size }} inactive={{ nginx_cache_inactive_time }} use_temp_path=off;
+    server 127.0.0.1:{{ omero_ms_image_region_port }} fail_timeout=0 max_fails=0;
+}
 
 {{ nginx_contents['content'] | b64decode | regex_replace('}$', '')  }}
 

diff --git a/templates/run.sh.j2 b/templates/run.sh.j2
@@ -1,2 +1,2 @@
 #! /bin/bash
-sudo -u {{ omero_ms_image_region_user }} JAVA_OPTS="-Dlogback.configurationFile=conf/logback.xml" bash bin/omero-ms-image-region
+JAVA_OPTS="-Dlogback.configurationFile=conf/logback.xml" bash bin/omero-ms-image-region
diff --git a/templates/stop.sh.j2 b/templates/stop.sh.j2