Merge pull request #1 from khaledk2/feedback

Feedback

README.md

@@ -15,30 +15,30 @@ OMERO-Server and OMERO-Web are required.
 Role Variables
 --------------
 
-- ms_user: 'omero-server': icroservice user, the defaults is omero-server
-ms_user: 'omero-server'
-- ms_folder: Microservice installation folder
-- ms_port: Microservice port 
-- databse_url: Omero Database URL
-- db_port:  Omero database server port
-- db_name: Omero database name
-- db_user_name: Omero database user name
-- db_pass: 'omero' :Omero database user password
-- log_evel: Log level, it can be info, debug or error
+- omero_ms_image_region_user: 'omero-server': icroservice user, the defaults is omero-server
+omero_ms_image_region_user: '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' :Omero database user password
+- omero_ms_image_region_log_level: Log level, it can be info, debug or error
 - omero_data_dir: Omero data folder
 - omero_script_repo_root: Omero scripts folder
-- worker_pool_size: No of Microservice workers, the default is double the number of processors which the machine has
+- omero_ms_image_region_ms_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:
 
 
     /opt/omero/web/OMERO.web/bin/omero config get omero.web.session_cookie_name
 
-- update_nginx: if false, it will not update the nginx config file
+- omero_ms_image_region_update_nginx: if false, it will not update the nginx config file
 
 Example Playbook
 ----------------
 
     - hosts: localhost
       roles:
         - role: ome.omero_ms_image_region
-          update_nginx: true
+          omero_ms_image_region_update_nginx: true

defaults/main.yml

@@ -2,31 +2,31 @@
 # defaults for omero_ms_image_region
 
 # Microservice user, the defaults is omero-server
-ms_user: 'omero-server'
+omero_ms_image_region_user: 'omero-server'
 
 # Microservice installation folder
-ms_folder: '/opt/omero/microservice'
+omero_ms_image_region_folder: '/opt/omero/microservice'
 
 # Microservice port
-ms_port: '8081'
+omero_ms_image_region_port: '8081'
 
 # Omero Database URL
-databse_url: '127.0.0.1'
+omero_ms_image_region_db_url: '127.0.0.1'
 
 # Omero database server port
-db_port: '5432'
+omero_ms_image_region_db_port: '5432'
 
 # Omero database name
-db_name: 'omero'
+omero_ms_image_region_db_name: 'omero'
 
 # Omero database user name
-db_user_name: 'omero'
+omero_ms_image_region_db_username: 'omero'
 
 # Omero database user password
-db_pass: 'omero'
+omero_ms_image_region_db_pass: 'omero'
 
 # Log level, it can be info, debug or error
-log_evel: 'debug'
+omero_ms_image_region_log_level: 'debug'
 
 # Omero data folder
 omero_data_dir: '/OMERO'
@@ -35,21 +35,25 @@ omero_data_dir: '/OMERO'
 omero_script_repo_root: '/opt/omero/server/OMERO.server/lib/scripts/'
 
 # No of Microservice workers, the default is double the number of processors which the machine has
-worker_pool_size: '10'
+omero_ms_image_region_ms_worker_pool_size: '10'
 
 # Omero Session id, 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
-session_id: 'sessionid'
+omero_ms_image_region_session_id: 'sessionid'
 
 # This role variable controls updating the nginx config file, omero-web.conf
 # if false, it will not update the file
-update_nginx: false
+omero_ms_image_region_update_nginx: false
 
 # Microservice download URL, you should updated with version which is compatable with your omero-server
 # The bio-format version for both the microservice and Omero-Server should be the same
 # Also, in case of using ngff data, the version of OMEZarrReader should be the same for both of Microsevice and Omero-Server
-download_URL: 'https://github.com/khaledk2/ice-archh-64/releases/download/new_tag/omero-ms-image-region-0.8.7.zip'
+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'
 
-omero_ms_sha256: f984bb78fa81d4fa603387df919d383485944a15a6a762f5c136cf35aefafeaa
+omero_ms_image_region_ms_sha256: f984bb78fa81d4fa603387df919d383485944a15a6a762f5c136cf35aefafeaa
 
-ms_name: "{{ download_URL | basename }}"
+omero_ms_image_region_ms_name: "{{ omero_ms_image_region_download_URL | basename }}"
+
+omero_ms_image_region_ms_redis_url: 'localhost'
+omero_ms_image_region_ms_redis_port: '6379'
+omero_ms_image_region_ms_redis_pass: ''

tasks/main.yml

@@ -1,60 +1,63 @@
 ---
 # tasks for omero_ms_image_region
 
-
 - name: Check that the ms conf exists
   become: true
   ansible.builtin.stat:
-     path: "{{ ms_folder }}/{{ ms_name }}"
+     path: "{{ omero_ms_image_region_folder }}/{{ omero_ms_image_region_ms_name }}"
   register: stat_result
 
-- name: display stats
-  debug:
-    var: stat_result.stat.exists
-
 - name: Use sha256 to calculate the checksum
   become: true
   ansible.builtin.stat:
-    path: "{{ ms_folder }}/{{ ms_name }}"
+    path: "{{ omero_ms_image_region_folder }}/{{ omero_ms_image_region_ms_name }}"
     checksum_algorithm: sha256
   register: stat_ssh256
 
-- name: display stats
-  debug:
-    var: stat_ssh256.stat.checksum
-
 - import_tasks: pre_tasks.yml
   when:
-   - stat_ssh256.stat.checksum is undefined or  omero_ms_sha256 !=  stat_ssh256.stat.checksum
+   - stat_ssh256.stat.checksum is undefined or omero_ms_image_region_ms_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:
+    omero_ms_image_region_ms_redis_uri:
+      "redis://:@{{ omero_ms_image_region_ms_redis_url }}:{{ omero_ms_image_region_ms_redis_port }}/0"
+  when: not omero_ms_image_region_ms_redis_pass
+
+- name: omero-ms-image-region | set redis uri in not protected mode
+  ansible.builtin.set_fact:
+    omero_ms_image_region_ms_redis_uri:
+      "redis://:{{ omero_ms_image_region_ms_redis_pass }}@{{ omero_ms_image_region_ms_redis_url }}:{{ omero_ms_image_region_ms_redis_port }}/0"
+  when: omero_ms_image_region_ms_redis_pass
+
 - name: omero-ms-image-region | copy config file
   become: true
-  become_user: "{{ ms_user }}"
+  become_user: "{{ omero_ms_image_region_user }}"
   ansible.builtin.template:
-    dest: "{{ ms_folder }}/omero-ms-image-region/conf/config.yaml"
+    dest: "{{ omero_ms_image_region_folder }}/omero-ms-image-region/conf/config.yaml"
     src: config.yaml.j2
 
 - name: omero-ms-image-region | copy log config file
   become: true
-  become_user: "{{ ms_user }}"
+  become_user: "{{ omero_ms_image_region_user }}"
   ansible.builtin.template:
-    dest: "{{ ms_folder }}/omero-ms-image-region/conf/logback.xml"
+    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: "{{ ms_user }}"
+  become_user: "{{ omero_ms_image_region_user }}"
   ansible.builtin.template:
-    dest: "{{ ms_folder }}/omero-ms-image-region/run.sh"
+    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: "{{ ms_user }}"
+  become_user: "{{ omero_ms_image_region_user }}"
   ansible.builtin.template:
-    dest: "{{ ms_folder }}/omero-ms-image-region/stop.sh"
+    dest: "{{ omero_ms_image_region_folder }}/omero-ms-image-region/stop.sh"
     src: stop.sh.j2
     mode: +x
 
@@ -71,7 +74,7 @@
 - name: omero-ms-image-region | selinux http_port_t for ms port
   become: true
   ansible.builtin.seport:
-    ports: "{{ ms_port }}"
+    ports: "{{ omero_ms_image_region_port }}"
     proto: tcp
     setype: http_port_t
     state: present
@@ -80,4 +83,4 @@
   when: ansible_facts.selinux.status == 'enabled'
 
 - import_tasks: update_nginx_config.yml
-  when: update_nginx
+  when: omero_ms_image_region_update_nginx

tasks/pre_tasks.yml

@@ -3,27 +3,27 @@
 - name: omero-ms-image-region | create ms folder
   become: true
   ansible.builtin.file:
-    path: "{{ ms_folder }}"
+    path: "{{ omero_ms_image_region_folder }}"
     state: directory
     mode: 0755
 
 - name: omero-ms-image-region | download omero-ms-image-region
   include_role:
       name: ome.deploy_archive
   vars:
-    deploy_archive_dest_dir: "{{ ms_folder }}"
-    deploy_archive_src_url: "{{ download_URL }}"
-    deploy_archive_sha256: "{{ omero_ms_sha256 }}"
-    deploy_archive_symlink: "{{ ms_folder }}/omero-ms-image-region"
+    deploy_archive_dest_dir: "{{ omero_ms_image_region_folder }}"
+    deploy_archive_src_url: "{{ omero_ms_image_region_download_URL }}"
+    deploy_archive_sha256: "{{ omero_ms_image_region_ms_sha256 }}"
+    deploy_archive_symlink: "{{ omero_ms_image_region_folder }}/omero-ms-image-region"
     deploy_archive_internal_root: >-
       omero-ms-image-region-0.8.7
 
 - name: omero-ms-image-region | chown to ms-user
   become: true
   ansible.builtin.file:
-    path: "{{ ms_folder }}"
-    owner: "{{ ms_user }}"
-    group: "{{ ms_user }}"
+    path: "{{ omero_ms_image_region_folder }}"
+    owner: "{{ omero_ms_image_region_user }}"
+    group: "{{ omero_ms_image_region_user }}"
     state: directory
     recurse: true
     mode: 0755

templates/config.yaml.j2

@@ -1,5 +1,5 @@
 # The port that the microservice will listen on
-port: {{ ms_port }}
+port: {{ omero_ms_image_region_port }}
 # Configuration for request parsing limits
 #  * https://vertx.io/docs/apidocs/io/vertx/core/http/HttpServerOptions.html#setMaxInitialLineLength-int-
 #  * https://vertx.io/docs/apidocs/io/vertx/core/http/HttpServerOptions.html#setMaxHeaderSize-int-
@@ -17,11 +17,11 @@ omero:
 # Copy of the OMERO server configuration which will be reused
 omero.server:
     omero.data.dir: "{{ omero_data_dir }}"
-    omero.db.host: "{{ databse_url }}"
-    omero.db.name: "{{ db_name }}"
-    omero.db.port: "{{ db_port }}"
-    omero.db.user: "{{ db_user_name }}"
-    omero.db.pass: "{{ db_pass }}"
+    omero.db.host: "{{ omero_ms_image_region_db_url }}"
+    omero.db.name: "{{ omero_ms_image_region_db_name }}"
+    omero.db.port: "{{ omero_ms_image_region_db_port }}"
+    omero.db.user: "{{ omero_ms_image_region_db_username }}"
+    omero.db.pass: "{{ omero_ms_image_region_db_pass }}"
     # OMERO_HOME/lib/scripts
     omero.script_repo_root: "{{ omero_script_repo_root }}"                              
     omero.pixeldata.max_tile_length: "2048"
@@ -34,11 +34,11 @@ omero.server:
     omero.client.viewer.interpolate_pixels: "true"
 # OMERO.web configuration
 omero.web:
-   session_cookie_name: "{{ session_id }}"
+   session_cookie_name: "{{ omero_ms_image_region_session_id }}"
 
 
 # Size of the worker pool (defaults to CPUs x 2)
-worker_pool_size: {{ worker_pool_size }}
+worker_pool_size: {{ omero_ms_image_region_ms_worker_pool_size }}
 #
 # Configuration for zipkin http tracing
 http-tracing:
@@ -63,10 +63,7 @@ session-store:
     # * https://jdbc.postgresql.org/documentation/80/connect.html
     # * https://github.com/lettuce-io/lettuce-core/wiki/Redis-URI-and-connection-details
     # uri: "jdbc:postgresql://localhost:5432/omero_database?user=omero&password=omero"
-    # For Redis in protected mode
-    uri: "redis://:@localhost:6379/0"
-    # For Redis in non-protected mode
-    # uri: "redis://:password@localhost:6379/0"
+    uri: "{{ omero_ms_image_region_ms_redis_uri }}"
 
 redis-cache:
     #uri: "redis://cf33da71-d81f-42e3-9932-71c82d52de32@localhost:6379/1"

templates/logback.xml.j2

@@ -18,11 +18,11 @@
     </encoder>
   </appender>
 
-  <logger name="com.glencoesoftware.omero.ms" level="{{ log_evel }}"/>
+  <logger name="com.glencoesoftware.omero.ms" level="{{ omero_ms_image_region_log_level }}"/>
   <logger name="loci" level="debug"/><!-- Bio-Formats -->
-  <logger name="loci.formats.Memoizer" level="{{ log_evel }}"/><!-- Bio-Formats memoizer -->
+  <logger name="loci.formats.Memoizer" level="{{ omero_ms_image_region_log_level }}"/><!-- Bio-Formats memoizer -->
 
-  <root level="{{ log_evel }}">
+  <root level="{{ omero_ms_image_region_log_level }}">
     <appender-ref ref="FILE" />
   </root>
 </configuration>

templates/omero-ms-image-region.service.j2

@@ -7,12 +7,11 @@ After=network.service
 USER=omero-server
 UMask=0002
 Type=simple
-WorkingDirectory={{ ms_folder }}/omero-ms-image-region
-ExecStart={{ ms_folder }}/omero-ms-image-region/run.sh
-ExecStop={{ ms_folder }}/omero-ms-image-region/stop.sh
+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
 Restart=always
 RestartSec=3
 
 [Install]
 WantedBy=multi-user.target
-

templates/omero-web.conf.j2

@@ -1,6 +1,6 @@
 
 upstream image_region_backend {
-    server 127.0.0.1:8081 fail_timeout=0 max_fails=0;
+    server 127.0.0.1:{{ omero_ms_image_region_port }} fail_timeout=0 max_fails=0;
 }
 
 {{ nginx_contents['content'] | b64decode | regex_replace('}$', '')  }}

templates/run.sh.j2

@@ -1,2 +1,2 @@
-#! /bin/bash
-sudo -u {{ ms_user }} JAVA_OPTS="-Dlogback.configurationFile=conf/logback.xml" bash bin/omero-ms-image-region
+#! /bin/bash
+sudo -u {{ omero_ms_image_region_user }} JAVA_OPTS="-Dlogback.configurationFile=conf/logback.xml" bash bin/omero-ms-image-region

templates/stop.sh.j2

@@ -1,2 +1,2 @@
-#! /bin/bash
-sudo kill -9 `ps aux | grep omero-ms-image-regio | awk '{print $2}'`
+#! /bin/bash
+sudo kill -9 `ps aux | grep omero-ms-image-region | awk '{print $2}'`