Lint (#36)

* Conform to ansible-lint
* Enable ansible-lint workflow

.ansible-lint

@@ -0,0 +1,9 @@
+---
+profile: production
+exclude_paths:
+  - docs
+  - .github
+  - molecule/
+skip_list:
+  - role-name
+  - var-naming

.github/workflows/ansible_lint.yml

@@ -0,0 +1,29 @@
+name: ansible-lint
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - '**/**.yaml'
+      - '**/**.yml'
+  pull_request:
+    branches:
+      - main
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
+    paths:
+      - '**/**.yaml'
+      - '**/**.yml'
+jobs:
+  build:
+    name: Ansible Lint # Naming the build is important to use it as a status check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Run ansible-lint
+        uses: ansible/ansible-lint@main
+        with:
+          args: "."

tasks/bootstrap.yml

@@ -1,16 +1,15 @@
 ---
 - name: Wait for galaxy server to come up
   ansible.builtin.uri:
-    url: "http://{{ _galaxy_local_address }}/api/version"
+    url: http://{{ _galaxy_local_address }}/api/version
   register: galaxy_service_live
-  until: "galaxy_service_live.status == 200"
+  until: galaxy_service_live.status == 200
   retries: 30
   delay: 10 # check every 10 seconds for a maximum of 5 minutes
 
 - name: Get user defined tools and workflows from a custom git repo
   when: _galaxy_custom_repo | length > 0
   block:
-
     - name: Clone the git repo
       ansible.builtin.git:
         repo: "{{ _galaxy_custom_repo }}"
@@ -23,29 +22,29 @@
       ansible.builtin.find:
         paths: "{{ _galaxy_custom_repo_clone_dest }}/{{ _galaxy_custom_repo_tool_location }}"
         file_type: file
-        patterns: ['*.yml', '*.yaml']
+        patterns: ["*.yml", "*.yaml"]
       register: _galaxy_custom_repo_tool_files
 
     - name: Set custom tool files array
-      set_fact:
+      ansible.builtin.set_fact:
         _galaxy_custom_tool_files: "{{ _galaxy_custom_repo_tool_files['files'] | map(attribute='path') | list | default([]) }}"
 
     - name: Find all workflows in repo
       ansible.builtin.find:
         paths: "{{ _galaxy_custom_repo_clone_dest }}/{{ _galaxy_custom_repo_workflow_location }}"
         file_type: file
-        patterns: ['*.ga']
+        patterns: ["*.ga"]
       register: _galaxy_custom_repo_workflow_files
 
     - name: Set custom workflow files array
-      set_fact:
+      ansible.builtin.set_fact:
         _galaxy_custom_workflow_files: "{{ _galaxy_custom_repo_workflow_files['files'] | map(attribute='path') | list | default([]) }}"
 
 - name: Install tools and workflows
   ansible.builtin.include_role:
     name: galaxyproject.galaxy-tools
   vars:
-    galaxy_tools_base_dir: "/home/{{ galaxy_user }}"
+    galaxy_tools_base_dir: /home/{{ galaxy_user }}
     galaxy_tools_api_key: "{{ _galaxy_config.galaxy.bootstrap_admin_api_key }}"
     galaxy_tools_create_bootstrap_user: true
     galaxy_tools_delete_bootstrap_user: true
@@ -54,6 +53,6 @@
     galaxy_tools_install_workflows: true
     galaxy_tools_galaxy_publish_workflows: true
     galaxy_tools_ignore_errors: false
-    galaxy_tools_galaxy_instance_url: "http://{{ _galaxy_local_address }}"
+    galaxy_tools_galaxy_instance_url: http://{{ _galaxy_local_address }}
     galaxy_tools_tool_list_files: "{{ (_galaxy_tool_files | default([])) + (_galaxy_custom_tool_files | default([])) }}"
     galaxy_tools_workflows: "{{ (_galaxy_workflow_files | default([])) + (_galaxy_custom_workflow_files | default([])) }}"

tasks/interactive_tools.yml

@@ -1,21 +1,22 @@
 ---
 - name: Add interactive tool proxy conf for nginx
   ansible.builtin.template:
-    src: "templates/nginx/galaxy-gie-proxy.j2"
-    dest: "/etc/nginx/conf.d/gie-server.conf"
+    src: templates/nginx/galaxy-gie-proxy.j2
+    dest: /etc/nginx/conf.d/gie-server.conf
     mode: "0640"
-    owner: "www-data"
-    group: "www-data"
+    owner: www-data
+    group: www-data
   notify: restart nginx
 
 - name: Remove comment to activate default interactive tools
   # match [\d\D\n] to match digits, non-digits, and newlines -- this is because .* does not match newlines in ansible.builtin.replace
   ansible.builtin.replace:
     path: "{{ galaxy_config_dir }}/tool_conf.xml"
-    regexp: '\s*<!--\s*\n.*(<section id="interactivetools" name="Interactive tools">[\d\D\n]*</section>)\n\s*-->'
-    replace: '\n  \1'
+    regexp: \s*<!--\s*\n.*(<section id="interactivetools" name="Interactive tools">[\d\D\n]*</section>)\n\s*-->
+    replace: \n  \1
 
 - name: Copy script to dynamically determine if a job should use Docker
   ansible.builtin.template:
     src: default_dispatch.py.j2
     dest: "{{ galaxy_server_dir }}/lib/galaxy/jobs/rules/{{ _galaxy_default_dispatcher }}.py"
+    mode: "0755"

tasks/nginx.yml

@@ -1,5 +1,4 @@
 ---
-
 - name: Add custom 502 page
   ansible.builtin.copy:
     src: nginx/error502.html

tasks/set_config.yml

@@ -17,17 +17,19 @@
 
 - name: Set admins from CO group
   ansible.builtin.set_fact:
-    _galaxy_admins: "{{ fact_co_groups[_galaxy_admin_co_group] | product(['@' + _galaxy_remote_user_maildomain]) | map('join') | list | join(',') | default('') }}"
+    _galaxy_admins: >-
+      {{ fact_co_groups[_galaxy_admin_co_group] | product(['@' + _galaxy_remote_user_maildomain]) |
+        map('join') | list | join(',') | default('') }}
   when: fact_co_groups[_galaxy_admin_co_group] is defined
 
 - name: Set admins to blank
   ansible.builtin.set_fact:
-    _galaxy_admins: ''
+    _galaxy_admins: ""
   when: fact_co_groups[_galaxy_admin_co_group] is not defined
 
 - name: Determine whether to bootstrap Galaxy
-  set_fact:
-    _galaxy_do_bootstrap:  "{{ _galaxy_bootstrap and _galaxy_tool_files | length + _galaxy_workflow_files | length + _galaxy_custom_repo | length  > 0}}"
+  ansible.builtin.set_fact:
+    _galaxy_do_bootstrap: "{{ _galaxy_bootstrap and _galaxy_tool_files | length + _galaxy_workflow_files | length + _galaxy_custom_repo | length > 0 }}"
 
 - name: Generate a bootstrap key
   when: _galaxy_do_bootstrap and not _molecule_idempotence

vars/galaxy_vars.yml

@@ -1,3 +1,4 @@
+---
 # Variables for the galaxyproject.galaxy role
 galaxy_config_style: yaml
 galaxy_layout: custom
@@ -6,8 +7,8 @@ galaxy_root: "{{ galaxy_server_dir }}" # workaround https://github.com/galaxypro
 galaxy_manage_systemd: false
 galaxy_venv_dir: "{{ _galaxy_root }}/venv"
 galaxy_config_dir: "{{ _galaxy_root }}/config"
-galaxy_mutable_data_dir: "{{ src_galaxy_storage_path | default(_galaxy_root+'/datadir', true) }}" # component variable src_galaxy_storage_path
-galaxy_commit_id: "release_{{ src_galaxy_version | default('23.2', true) }}" # component variable src_galaxy_version
+galaxy_mutable_data_dir: "{{ src_galaxy_storage_path | default(_galaxy_root + '/datadir', true) }}" # component variable src_galaxy_storage_path
+galaxy_commit_id: release_{{ src_galaxy_version | default('23.2', true) }} # component variable src_galaxy_version
 galaxy_separate_privileges: true
 galaxy_create_user: true
 galaxy_manage_paths: true
@@ -27,7 +28,7 @@ galaxy_config_templates:
     dest: "{{ galaxy_config_dir }}/pulsar_app.yml"
 postgresql_objects_users:
   - name: galaxy
-    password: null
+    password:
 postgresql_objects_databases:
   - name: galaxy
     owner: galaxy
@@ -39,7 +40,7 @@ galaxy_configuration:
     admin_users: "{{ _galaxy_admins }}"
     remote_user_maildomain: "{{ _galaxy_remote_user_maildomain }}"
     remote_user_secret: "{{ _galaxy_remote_user_secret }}"
-    database_connection: "postgresql:///galaxy?host=/var/run/postgresql"
+    database_connection: postgresql:///galaxy?host=/var/run/postgresql
     file_path: "{{ galaxy_mutable_data_dir }}/datasets"
     job_config_file: "{{ galaxy_config_dir }}/job_conf.yml"
     tool_config_file: "{{ galaxy_config_dir }}/tool_conf.xml"
@@ -62,7 +63,7 @@ galaxy_configuration:
       # Other options that will be passed to gunicorn
       # This permits setting of 'secure' headers like REMOTE_USER (and friends)
       # https://docs.gunicorn.org/en/stable/settings.html#forwarded-allow-ips
-      extra_args: '--forwarded-allow-ips="*"'
+      extra_args: --forwarded-allow-ips="*"
       # This lets Gunicorn start Galaxy completely before forking which is faster.
       # https://docs.gunicorn.org/en/stable/settings.html#preload-app
       preload: true

vars/interactive_tools_vars.yml

@@ -1,3 +1,4 @@
+---
 gie_proxy_dir: "{{ _galaxy_root }}/gie-proxy/proxy"
 gie_proxy_sessions_path: "{{ galaxy_mutable_data_dir }}/interactivetools_map.sqlite"
 gie_proxy_path_prefix: /interactivetool/ep

vars/internal_vars.yml

@@ -1,17 +1,18 @@
+---
 # Internal variables that are not user configurable
 
 # Is this a molecule run?
 _molecule_active: "{{ true if 'molecule-notest' in ansible_skip_tags else false }}"
 _molecule_idempotence: "{{ true if 'molecule-idempotence-notest' in ansible_skip_tags else false }}"
 
 # Authorisation and authentication
-_galaxy_remote_user_maildomain: "src.surf-hosted.nl"
+_galaxy_remote_user_maildomain: src.surf-hosted.nl
 _galaxy_custom_repo_clone_dest: /tmp/galaxy_load_on_deploy
 
 # if using a user-supplied git repo for installing tools, what subdirectory are the tools in?
-_galaxy_custom_repo_tool_location: 'tools' 
+_galaxy_custom_repo_tool_location: tools
 # if using a user-supplied git repo for installing workflows, what subdirectory are the workflows in?
-_galaxy_custom_repo_workflow_location: 'workflows'
+_galaxy_custom_repo_workflow_location: workflows
 
 # Paths to server dir
 _galaxy_root: /srv/galaxy

vars/nginx_vars.yml

@@ -1,34 +1,35 @@
+---
 galaxy_nginx_vhost_config:
   - name: galaxy
     location: /
     error_page: 502 /galaxy502.html
-    proxy_pass: "http://{{ _galaxy_local_address }}"
+    proxy_pass: http://{{ _galaxy_local_address }}
     auth: "{{ _molecule_active | ternary(omit, 'sram') }}"
     proxy_set_header:
       GX_SECRET: "{{ _galaxy_remote_user_secret | default(omit) }}"
   - name: api
     location: /api/
-    proxy_pass: "http://{{ _galaxy_local_address }}/api/"
+    proxy_pass: http://{{ _galaxy_local_address }}/api/
     auth: "{{ _galaxy_api_exposed | ternary('noauth', 'sram') }}"
   - name: static
     location: /static
     alias: "{{ galaxy_server_dir }}/static"
     auth: noauth
   - name: static_plugins
-    location: "~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$"
-    expires: '24'
+    location: ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$
+    expires: "24"
     alias: "{{ galaxy_server_dir }}/config/plugins/$plug_type/$vis_name/static/$static_file"
     auth: noauth
   - name: favicon
     location: /favicon.ico
     expires: 24h
     auth: noauth
   - name: interactive_tools
-    location: "~* ^/(interactivetool/.+)$"
-    proxy_redirect: 'off'
-    proxy_http_version: '1.1'
-    proxy_pass: "http://localhost:{{ gie_proxy_port }}"
+    location: ~* ^/(interactivetool/.+)$
+    proxy_redirect: "off"
+    proxy_http_version: "1.1"
+    proxy_pass: http://localhost:{{ gie_proxy_port }}
   - name: custom_502
     location: = /galaxy502.html
     root: "{{ _galaxy_error_502 | dirname }}"
-    internal: ''
+    internal: ""

vars/src_galaxy_vars.yml

@@ -1,6 +1,7 @@
+---
 # Variables derived from component parameters in ResearchCLoud
 
-_galaxy_bootstrap: "{{ _molecule_idempotence | ternary(false, src_galaxy_bootstrap | default(true, true) | bool ) }}"
+_galaxy_bootstrap: "{{ _molecule_idempotence | ternary(false, src_galaxy_bootstrap | default(true, true) | bool) }}"
 _galaxy_ibridges_enabled: "{{ src_ibridges | default(true, true) | bool }}"
 _galaxy_default_tool_files:
   - path: tools/ibridges.yml
@@ -13,10 +14,12 @@ _galaxy_api_exposed: "{{ src_galaxy_api_exposed | default(true, true) }}"
 _galaxy_use_interactive_tools: "{{ src_galaxy_interactive_tools | default(true, true) | bool }}"
 _galaxy_server_fqdn: "{{ workspace_fqdn | default('localhost', true) }}"
 _galaxy_jobs_default: "{{ src_galaxy_jobs_default | default('local', true) }}"
-_galaxy_enable_docker: "{{ _galaxy_use_interactive_tools or (_galaxy_jobs_default == 'docker' )  }}"
+_galaxy_enable_docker: "{{ _galaxy_use_interactive_tools or (_galaxy_jobs_default == 'docker') }}"
 
 # Build the final lists of tool and workflow installation files
-_galaxy_tool_files: "{{ src_galaxy_tool_files | default('', true) | split(',') | select() + _galaxy_default_tool_files_list }}"  # select() necessary because split on the default '' yields ['']
+
+# select() necessary because split on the default '' yields ['']
+_galaxy_tool_files: "{{ src_galaxy_tool_files | default('', true) | split(',') | select() + _galaxy_default_tool_files_list }}"
 _galaxy_workflow_files: "{{ src_galaxy_workflow_files | default('') | split(',') | select() }}"
 
 # Note that some component parameters are also used in galaxy_vars.yml: