Merge pull request #144 from galaxyproject/lint

Lint all the things

README.md

@@ -71,6 +71,11 @@ If using `root-dir`:
 
 ### Optional variables ###
 
+The `galaxy_config_perms` option controls the permissions that Galaxy configuration files will be set to. This option
+has been added in version 0.9.18 of the role and the default value is `0640` (user read-write, group read-only, other
+users have no permissions). **In older versions, the role did not control the permissions of configuration files, so be
+aware that your configuration file permissions may change as of 0.9.18 and later.**
+
 **Layout control**
 
 - `galaxy_layout`: available layouts can be found in the [vars/][vars] subdirectory and possible values include:

defaults/main.yml

@@ -172,6 +172,9 @@ galaxy_config_file_template: "{{ galaxy_config_file_basename }}.j2"
 galaxy_config_file: "{{ galaxy_config_dir }}/{{ galaxy_config_file_basename }}"
 galaxy_app_config_section: "{{ 'galaxy' if galaxy_config_style in ('yaml', 'yml') else 'app:main' }}"
 
+# Galaxy configuration files will be written with these permissions (mode argument to Ansible copy/template module)
+galaxy_config_perms: 0640
+
 # The default Galaxy configuration, ensures that Galaxy can find all of the configs if galaxy_config_dir !=
 # galaxy_server_dir
 galaxy_paste_app_factory: "galaxy.web.buildapp:app_factory"

meta/main.yml

@@ -1,50 +1,39 @@
 ---
 galaxy_info:
+  namespace: galaxyproject
+  role_name: galaxy
   author: The Galaxy Project
   description: Install and manage a Galaxy (http://galaxyproject.org/) server.
   company: The Galaxy Project
   license: AFL v3.0
   min_ansible_version: 2.7
   github_branch: main
   platforms:
-  - name: EL
-    versions:
-    - all
-  - name: GenericUNIX
-    versions:
-    - all
-    - any
-  - name: Fedora
-    versions:
-    - all
-  - name: opensuse
-    versions:
-    - all
-  - name: Amazon
-    versions:
-    - all
-  - name: GenericBSD
-    versions:
-    - all
-    - any
-  - name: FreeBSD
-    versions:
-    - all
-  - name: Ubuntu
-    versions:
-    - all
-  - name: SLES
-    versions:
-    - all
-  - name: GenericLinux
-    versions:
-    - all
-    - any
-  - name: Debian
-    versions:
-    - all
+    - name: EL
+      versions:
+        - all
+    - name: GenericUNIX
+      versions:
+        - all
+        - any
+    - name: Fedora
+      versions:
+        - all
+    - name: Amazon
+      versions:
+        - all
+    - name: Ubuntu
+      versions:
+        - all
+    - name: GenericLinux
+      versions:
+        - all
+        - any
+    - name: Debian
+      versions:
+        - all
   galaxy_tags:
-  - system
-  - web
+    - system
+    - web
 dependencies: []
 allow_duplicates: yes

tasks/_inc_client_build_steps.yml

@@ -19,7 +19,7 @@
     success_msg: "Deconstructed client build is supported"
     fail_msg: "Deconstructed client build is not supported for Galaxy version {{ __galaxy_major_version }}, please set 'galaxy_client_make_target'"
 
-- name: Run gulp
+- name: Run gulp  # noqa no-changed-when
   command: yarn run gulp {{ item }}
   args:
     chdir: "{{ galaxy_server_dir }}/client"
@@ -29,7 +29,7 @@
     VIRTUAL_ENV: "{{ galaxy_venv_dir }}"
     NODE_ENV: "{{ galaxy_client_node_env }}"
 
-- name: Run webpack
+- name: Run webpack  # noqa no-changed-when
   command: "yarn run webpack{{ (galaxy_client_node_env == 'production') | ternary('-production', '') }}"
   args:
     chdir: "{{ galaxy_server_dir }}/client"
@@ -42,3 +42,4 @@
   copy:
     content: "{{ __galaxy_current_commit_id }}"
     dest: "{{ galaxy_static_dir }}/client_build_hash.txt"
+    mode: 0644

tasks/client.yml

@@ -7,6 +7,7 @@
       copy:
         content: "new-unbuilt"
         dest: "{{ galaxy_static_dir }}/client_build_hash.txt"
+        mode: 0644
         force: no
 
     - name: Get current client commit id
@@ -19,7 +20,7 @@
         path: "{{ galaxy_server_dir }}/.git"
       register: __galaxy_from_git
 
-    - name: Get current Galaxy commit id
+    - name: Get current Galaxy commit id  # noqa git-latest
       git:
         dest: "{{ galaxy_server_dir }}"
         repo: "{{ galaxy_repo }}"

tasks/download.yml

@@ -13,6 +13,7 @@
       file:
         path: "{{ galaxy_server_dir }}"
         state: directory
+        mode: 0755
 
     - name: Install current version of Galaxy
       unarchive:
@@ -26,6 +27,7 @@
       file:
         path: "{{ galaxy_server_dir }}/{{ galaxy_commit_id }}_receipt"
         state: touch
+        mode: 0644
       when: not download_receipt.stat.exists
 
     - name: Include virtualenv setup tasks

tasks/layout.yml

@@ -4,7 +4,7 @@
 - name: Include layout vars
   include_vars: "layout-{{ galaxy_layout | default('legacy') }}.yml"
 
-- name: Set any unset variables from layout defaults
+- name: Set any unset variables from layout defaults  # noqa var-naming
   set_fact:
     "{{ item }}": "{{ lookup('vars', '__' ~ item) }}"
   when: item not in vars
@@ -33,7 +33,7 @@
     - job_working_directory
     - shed_tool_config_file
 
-- name: Set any unset variables corresponding to Galaxy config options from galaxy_config or layout defaults
+- name: Set any unset variables corresponding to Galaxy config options from galaxy_config or layout defaults  # noqa var-naming
   set_fact:
     "{{ 'galaxy_' ~ item }}": "{{ ((galaxy_config | default({}))[galaxy_app_config_section] | default({}))[item] | default(lookup('vars', '__galaxy_' ~ item)) }}"
   when: "'galaxy_' ~ item not in vars"

tasks/mutable_setup.yml

@@ -14,13 +14,15 @@
         src: "{{ item.src }}"
         dest: "{{ item.dest }}"
         force: no
+        mode: "{{ galaxy_config_perms }}"
       with_items: "{{ galaxy_mutable_config_files }}"
 
     - name: Instantiate mutable configuration templates
       template:
         src: "{{ item.src }}"
         dest: "{{ item.dest }}"
         force: no
+        mode: "{{ galaxy_config_perms }}"
       with_items: "{{ galaxy_mutable_config_templates }}"
 
   remote_user: "{{ galaxy_remote_users.galaxy | default(__galaxy_remote_user) }}"

tasks/static_setup.yml

@@ -13,6 +13,7 @@
         src: "{{ item.src }}"
         dest: "{{ item.dest }}"
         backup: "{{ galaxy_backup_configfiles }}"
+        mode: "{{ galaxy_config_perms }}"
       with_items: "{{ galaxy_config_files }}"
       notify:
         - "{{ galaxy_restart_handler_name }}"
@@ -22,6 +23,7 @@
         src: "{{ item.src }}"
         dest: "{{ item.dest }}"
         backup: "{{ galaxy_backup_configfiles }}"
+        mode: "{{ galaxy_config_perms }}"
       with_items: "{{ galaxy_config_templates }}"
       notify:
         - "{{ galaxy_restart_handler_name }}"
@@ -30,13 +32,15 @@
       copy:
         src: "{{ galaxy_local_tools_src_dir }}/{{ item }}"
         dest: "{{ galaxy_local_tools_dir }}/{{ item }}"
+        mode: preserve
       with_items: "{{ galaxy_local_tools | default([]) }}"
       when: galaxy_local_tools is defined
 
     - name: Install local_tool_conf.xml
       template:
         src: local_tool_conf.xml.j2
         dest: "{{ galaxy_config_dir }}/local_tool_conf.xml"
+        mode: "{{ galaxy_config_perms }}"
       when: galaxy_local_tools is defined
 
     - name: Append local_tool_conf.xml to tool_config_file Galaxy config option
@@ -53,6 +57,7 @@
       file:
         path: "{{ galaxy_dynamic_job_rules_dir }}/{{ item | dirname }}"
         state: directory
+        mode: 0755
       loop_control:
         label: "{{ galaxy_dynamic_job_rules_dir }}/{{ item | dirname }}"
       with_items: "{{ galaxy_dynamic_job_rules }}"
@@ -61,13 +66,15 @@
       copy:
         src: "{{ galaxy_dynamic_job_rules_src_dir }}/{{ item }}"
         dest: "{{ galaxy_dynamic_job_rules_dir }}/{{ item }}"
+        mode: 0644
       with_items: "{{ galaxy_dynamic_job_rules }}"
       when: not item.endswith(".j2")
 
     - name: Install dynamic job rules (template)
       template:
         src: "{{ galaxy_dynamic_job_rules_src_dir }}/{{ item }}"
         dest: "{{ galaxy_dynamic_job_rules_dir }}/{{ item | regex_replace(regex) }}"
+        mode: 0644
       vars:
         regex: '\.j2$'
       with_items: "{{ galaxy_dynamic_job_rules }}"
@@ -78,6 +85,7 @@
         content: ""
         dest: "{{ galaxy_dynamic_job_rules_dir }}/{{ item | dirname }}/__init__.py"
         force: no
+        mode: 0644
       loop_control:
         label: "{{ galaxy_dynamic_job_rules_dir }}/{{ ((item | dirname) != '') | ternary ((item | dirname) ~ '/', '') }}__init__.py"
       with_items: "{{ galaxy_dynamic_job_rules }}"
@@ -117,6 +125,7 @@
         src: "{{ galaxy_config_file_template }}"
         dest: "{{ galaxy_config_file }}"
         backup: "{{ galaxy_backup_configfiles }}"
+        mode: "{{ galaxy_config_perms }}"
       notify:
         - "{{ galaxy_restart_handler_name }}"
 

tasks/virtualenv.yml

@@ -14,10 +14,10 @@
   environment:
     VIRTUAL_ENV: "{{ galaxy_venv_dir }}"
 
-- name: Ensure pip and setuptools are the latest release
+- name: Ensure pip is the desired release
   pip:
     name: pip
-    state: latest
+    state: "{{ galaxy_pip_version | default('latest') }}"
     extra_args: "{{ pip_extra_args | default('') }}"
     virtualenv: "{{ galaxy_venv_dir }}"
     virtualenv_command: "{{ galaxy_virtualenv_command | default(pip_virtualenv_command | default(omit)) }}"

tests/test_playbook.yml

@@ -18,6 +18,7 @@
     galaxy_root: /srv/galaxy
     galaxy_separate_privileges: yes
     galaxy_user: galaxy
+    galaxy_group: galaxy
     galaxy_privsep_user: gxpriv
     galaxy_config:
       galaxy: