Merge pull request #132 from galaxyproject/systemd

Add systemd, github actions support

.github/workflows/ci.yml

@@ -0,0 +1,30 @@
+name: Test the role
+
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-syntax-for-github-actions#example-using-a-list-of-events
+on: [pull_request]
+
+jobs:
+  setup:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 1
+
+      - name: Install dependencies
+        run: |
+            sudo apt-get install git python3 python3-virtualenv
+            pip3 install 'ansible<2.10'
+            printf '[defaults]\nroles_path = ../\ninterpreter_python = /usr/bin/python3' > ansible.cfg
+
+      - name: Run Test
+        run: |
+            export ANSIBLE_STDOUT_CALLBACK=yaml
+            ansible-playbook -i "localhost, " -c local tests/test_playbook.yml
+            systemctl status galaxy || true
+            journalctl -u galaxy
+            sleep 10
+            systemctl status galaxy
+            journalctl -u galaxy
+            sleep 10
+            curl http://127.0.0.1:8080/api/version

defaults/main.yml

@@ -19,6 +19,9 @@ galaxy_fetch_dependencies: yes
 galaxy_build_client: yes
 galaxy_manage_errordocs: no
 galaxy_backup_configfiles: yes
+galaxy_manage_systemd: no # For Galaxy
+galaxy_manage_systemd_reports: no # For Reports
+
 
 # Control whether to output verbose task diffs (e.g. when performing a git update) when running Ansible with --diff.
 # Only suppresses diff on tasks that are likely to be verbose, not all tasks
@@ -274,3 +277,17 @@ galaxy_client_build_steps:
     - stageLibs
     - plugins
 
+
+# systemd options
+galaxy_restart_handler_name: "{{ 'galaxy mule restart' if (galaxy_systemd.mode == 'mule' and galaxy_manage_systemd) else 'default restart galaxy handler' }}"
+galaxy_systemd:
+  env: "" #Any extra env vars
+  mode: mule
+  memory_limit:
+    mule: 16
+    reports: 5
+    #workflow: 5
+    #zergpool: 8
+    #zergling: 16
+    #handler: 5
+  stats: 4001 # Port for stats to listen on.

handlers/main.yml

@@ -13,3 +13,17 @@
     subject: "Galaxy instance {{ galaxy_instance_hostname | default( inventory_hostname ) }} is at commit {{ galaxy_commit_id }}"
     body: " "
   when: galaxy_admin_email_to is defined
+
+- name: daemon reload
+  systemd:
+    daemon_reload: yes
+
+- name: galaxy mule start
+  systemd:
+      name: galaxy.service
+      state: started
+
+- name: galaxy mule restart
+  systemd:
+      name: galaxy.service
+      state: restarted

tasks/clone.yml

@@ -15,7 +15,7 @@
       diff: "{{ galaxy_diff_mode_verbose }}"
       register: __galaxy_git_update_result
       notify:
-        - "{{ galaxy_restart_handler_name | default('default restart galaxy handler') }}"
+        - "{{ galaxy_restart_handler_name }}"
         - email administrator with commit id
 
     - name: Report Galaxy version change

tasks/main.yml

@@ -120,3 +120,30 @@
   when: galaxy_manage_errordocs
   tags:
     - galaxy_manage_errordocs
+
+#- name: Include systemd unit setup tasks (Zerg Mode)
+  #include_tasks:
+    #file: systemd-zerg.yml
+    #apply:
+      #tags: galaxy_manage_systemd
+  #when: galaxy_manage_systemd and galaxy_systemd.mode == "zerg"
+  #tags:
+    #- galaxy_manage_systemd
+
+- name: Include systemd unit setup tasks (Mules)
+  include_tasks:
+    file: systemd-mule.yml
+    apply:
+      tags: galaxy_manage_systemd
+  when: galaxy_manage_systemd and galaxy_systemd.mode == "mule"
+  tags:
+    - galaxy_manage_systemd
+
+- name: Include systemd unit setup tasks (Reports)
+  include_tasks:
+    file: systemd-reports.yml
+    apply:
+      tags: galaxy_manage_systemd_reports
+  when: galaxy_manage_systemd_reports
+  tags:
+    - galaxy_manage_systemd_reports

tasks/static_setup.yml

@@ -15,7 +15,7 @@
         backup: "{{ galaxy_backup_configfiles }}"
       with_items: "{{ galaxy_config_files }}"
       notify:
-        - "{{ galaxy_restart_handler_name | default('default restart galaxy handler') }}"
+        - "{{ galaxy_restart_handler_name }}"
 
     - name: Install additional Galaxy config files (template)
       template:
@@ -24,7 +24,7 @@
         backup: "{{ galaxy_backup_configfiles }}"
       with_items: "{{ galaxy_config_templates }}"
       notify:
-        - "{{ galaxy_restart_handler_name | default('default restart galaxy handler') }}"
+        - "{{ galaxy_restart_handler_name }}"
 
     - name: Install local tools
       copy:
@@ -78,7 +78,7 @@
         dest: "{{ galaxy_config_file }}"
         backup: "{{ galaxy_backup_configfiles }}"
       notify:
-        - "{{ galaxy_restart_handler_name | default('default restart galaxy handler') }}"
+        - "{{ galaxy_restart_handler_name }}"
 
   remote_user: "{{ galaxy_remote_users.privsep | default(__galaxy_remote_user) }}"
   become: "{{ true if galaxy_become_users.privsep is defined else __galaxy_become }}"

tasks/systemd-mule.yml

@@ -0,0 +1,24 @@
+---
+
+- name: Manage Paths
+  block:
+
+    - name: Deploy Galaxy Unit
+      template:
+        owner: root
+        group: root
+        mode: 0644
+        src: systemd/galaxy.service.j2
+        dest: /etc/systemd/system/galaxy.service
+      notify:
+        - daemon reload
+        - galaxy mule restart
+
+    - name: Enable Galaxy Unit
+      systemd:
+        name: galaxy.service
+        enabled: yes
+
+  remote_user: "{{ galaxy_remote_users.root | default(__galaxy_remote_user) }}"
+  become: "{{ true if galaxy_become_users.root is defined else __galaxy_become }}"
+  become_user: "{{ galaxy_become_users.root | default(__galaxy_become_user) }}"

tasks/systemd-reports.yml

@@ -0,0 +1,23 @@
+---
+
+- name: Manage Paths
+  block:
+
+    - name: Deploy Galaxy Reports unit
+      template:
+        owner: root
+        group: root
+        mode: 0644
+        src: systemd/galaxy-reports.service.j2
+        dest: /etc/systemd/system/galaxy-reports.service
+      notify: daemon reload
+
+    - name: Enable reports and ensure it is running
+      systemd:
+        name: galaxy-reports.service
+        enabled: yes
+        state: started
+
+  remote_user: "{{ galaxy_remote_users.root | default(__galaxy_remote_user) }}"
+  become: "{{ true if galaxy_become_users.root is defined else __galaxy_become }}"
+  become_user: "{{ galaxy_become_users.root | default(__galaxy_become_user) }}"

templates/systemd/galaxy-reports.service.j2

@@ -0,0 +1,23 @@
+[Unit]
+Description=Galaxy Reports
+After=network.target
+After=time-sync.target
+
+[Service]
+UMask=022
+Type=simple
+User={{ __galaxy_user_name }}
+Group={{ __galaxy_user_group }}
+WorkingDirectory={{ galaxy_server_dir }}
+TimeoutStartSec=10
+ExecStart={{ galaxy_venv_dir }}/bin/uwsgi {{ '--yaml' if galaxy_config_style in ('yaml', 'yml') else '--ini' }} {{ galaxy_reports_path }} --stats 127.0.0.1:4030
+Environment=HOME={{ galaxy_root }} VIRTUAL_ENV={{ galaxy_venv_dir }} PATH={{ galaxy_venv_dir }}/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin DOCUTILSCONFIG= PYTHONPATH={{ galaxy_dynamic_job_rules_dir }} {{ galaxy_systemd.env }}
+MemoryLimit={{ galaxy_systemd.memory_limit.reports }}G
+Restart=always
+
+MemoryAccounting=yes
+CPUAccounting=yes
+BlockIOAccounting=yes
+
+[Install]
+WantedBy=multi-user.target

templates/systemd/galaxy.service.j2

@@ -0,0 +1,24 @@
+[Unit]
+Description=Galaxy
+After=network.target
+After=time-sync.target
+
+[Service]
+UMask=022
+Type=simple
+User={{ __galaxy_user_name }}
+Group={{ __galaxy_user_group }}
+WorkingDirectory={{ galaxy_server_dir }}
+TimeoutStartSec=10
+ExecStart={{ galaxy_venv_dir }}/bin/uwsgi {{ '--yaml' if galaxy_config_style in ('yaml', 'yml') else '--ini' }} {{ galaxy_config_file }} {% if galaxy_systemd.stats %}--stats 127.0.0.1:{{ galaxy_systemd.stats }}{% endif %}
+
+Environment=HOME={{ galaxy_root }} VIRTUAL_ENV={{ galaxy_venv_dir }} PATH={{ galaxy_venv_dir }}/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin DOCUTILSCONFIG= PYTHONPATH={{ galaxy_dynamic_job_rules_dir }} {{ galaxy_systemd.env }}
+MemoryLimit={{ galaxy_systemd.memory_limit.mule }}G
+Restart=always
+
+MemoryAccounting=yes
+CPUAccounting=yes
+BlockIOAccounting=yes
+
+[Install]
+WantedBy=multi-user.target

tests/test_playbook.yml

@@ -2,16 +2,17 @@
 # Travis CI test playbook
 
 - hosts: localhost
-  gather_facts: False
   connection: local
-  remote_user: travis
+  become: true
+  remote_user: runner
   vars:
-    galaxy_commit_id: release_19.09
+    galaxy_commit_id: release_21.01
     galaxy_create_user: yes
     galaxy_manage_paths: yes
     galaxy_manage_clone: yes
     galaxy_manage_download: no
     galaxy_manage_existing: no
+    galaxy_manage_systemd: yes
     galaxy_config_style: yaml
     galaxy_layout: root-dir
     galaxy_root: /srv/galaxy
@@ -26,5 +27,6 @@
     ansible_user_id: "{{ lookup('env', 'USER') }}"
     ansible_env:
       PATH: "{{ lookup('env', 'PATH') }}"
+    pip_virtualenv_command: /usr/bin/python3 -m virtualenv
   roles:
     - role: ansible-galaxy