Rename mutable to managed

README.md

@@ -11,8 +11,8 @@ An [Ansible][ansible] role for installing and managing [Galaxy][galaxyproject] s
 Requirements
 ------------
 
-This role has the same dependencies as the git module. In addition, [pip][pip] and [Python virtualenv][venv] are required. These can easily be installed via a pre-task in
-the same play as this role:
+This role has the same dependencies as the git module. In addition, [pip][pip] and [Python virtualenv][venv] are required.
+These can easily be installed via a pre-task in the same play as this role:
 
 ```yaml
 - hosts: galaxyservers
@@ -206,8 +206,8 @@ Several variables control which functions this role will perform (all default to
   well as set up a [virtualenv][virtualenv] from which it can be run.
 - `galaxy_manage_static_setup`: Manage "static" Galaxy configuration files - ones which are not modifiable by the Galaxy
   server itself. At a minimum, this is the primary Galaxy configuration file, `galaxy.ini`.
-- `galaxy_manage_mutable_setup`: Manage "mutable" Galaxy configuration files - ones which are modifiable by Galaxy (e.g.
-  as you install tools from the Galaxy Tool Shed).
+- `galaxy_manage_managed_setup`: Manage "managed" Galaxy configuration files - ones which are modifiable by Galaxy
+  (e.g. as you install tools from the Galaxy Tool Shed).
 - `galaxy_manage_database`: Upgrade the database schema as necessary, when new schema versions become available.
 - `galaxy_fetch_dependencies`: Fetch Galaxy dependent modules to the Galaxy virtualenv.
 - `galaxy_build_client`: Build the Galaxy client application (web UI).
@@ -225,7 +225,10 @@ Options for configuring Galaxy and controlling which version is installed.
 - `galaxy_config`: The contents of the Galaxy configuration file (`galaxy.ini` by default) are controlled by this
   variable. It is a hash of hashes (or dictionaries) that will be translated in to the configuration
   file. See the Example Playbooks below for usage.
-- `galaxy_config_files`: List of hashes (with `src` and `dest` keys) of files to copy from the control machine. For example, to set job destinations, you can use the `galaxy_config_dir` variable followed by the file name as the `dest`, e.g. `dest: "{{ galaxy_config_dir }}/job_conf.xml"`. Make sure to add the appropriate setup within `galaxy_config` for each file added here (so, if adding `job_conf.xml` make sure that `galaxy_config.galaxy.job_config_file` points to that file).
+- `galaxy_config_files`: List of hashes (with `src` and `dest` keys) of files to copy from the control machine. For example,
+  to set job destinations, you can use the `galaxy_config_dir` variable followed by the file name as the `dest`, e.g.
+  `dest: "{{ galaxy_config_dir }}/job_conf.xml"`. Make sure to add the appropriate setup within `galaxy_config` for each file
+  added here (so, if adding `job_conf.xml` make sure that `galaxy_config.galaxy.job_config_file` points to that file).
 - `galaxy_config_templates`: List of hashes (with `src` and `dest` keys) of templates to fill from the control machine.
 - `galaxy_local_tools`: List of local tool files or directories to copy from the control machine, relative to
   `galaxy_local_tools_src_dir` (default: `files/galaxy/tools` in the playbook).
@@ -257,9 +260,9 @@ Options for controlling where certain Galaxy components are placed on the filesy
   to use when creating the virtualenv. For Galaxy < 20.01, use python2.7 (if it is not the default), for Galaxy >=
   20.01, use `python3.5` or higher.
 - `galaxy_config_dir` (default: `<galaxy_server_dir>`): Directory that will be used for "static" configuration files.
-- `galaxy_mutable_config_dir` (default: `<galaxy_server_dir>`): Directory that will be used for "mutable" configuration
+- `galaxy_managed_config_dir` (default: `<galaxy_server_dir>`): Directory that will be used for "managed" configuration
   files, must be writable by the user running Galaxy.
-- `galaxy_mutable_data_dir` (default: `<galaxy_server_dir>/database`): Directory that will be used for "mutable" data
+- `galaxy_managed_data_dir` (default: `<galaxy_server_dir>/database`): Directory that will be used for "managed" data
   and caches, must be writable by the user running Galaxy.
 - `galaxy_config_file` (default: `<galaxy_config_dir>/galaxy.ini`): Galaxy's primary configuration file.
 
@@ -329,7 +332,7 @@ $ sh run.sh
 
 Install Galaxy as per the current production server best practices:
 
-- Galaxy code (clone) is "clean": no configs or mutable data live underneath the clone
+- Galaxy code (clone) is "clean": no configs or managed data live underneath the clone
 - Galaxy code and static configs are privilege separated: not owned/writeable by the user that runs Galaxy
 - Configuration files are not world-readable
 - PostgreSQL is used as the backing database

defaults/main.yml

@@ -12,7 +12,7 @@ galaxy_manage_paths: no
 galaxy_manage_clone: yes
 galaxy_manage_download: no
 galaxy_manage_static_setup: yes
-galaxy_manage_mutable_setup: yes
+galaxy_manage_managed_setup: yes
 galaxy_manage_database: yes
 galaxy_fetch_dependencies: yes
 galaxy_build_client: yes
@@ -84,8 +84,8 @@ galaxy_create_privsep_user: "{{ galaxy_create_user if __galaxy_privsep_user_name
 
 # Directories to create as the Galaxy user if galaxy_manage_paths is enabled
 galaxy_dirs:
-  - "{{ galaxy_mutable_data_dir }}"
-  - "{{ galaxy_mutable_config_dir }}"
+  - "{{ galaxy_managed_data_dir }}"
+  - "{{ galaxy_managed_config_dir }}"
   - "{{ galaxy_cache_dir }}"
   - "{{ galaxy_shed_tools_dir }}"
   - "{{ galaxy_tool_dependency_dir }}"
@@ -147,7 +147,7 @@ galaxy_tool_config_files:
 
 # The shed tool conf path is needed separate from the value of tool_conf for instantiation. The 'conf' version is a
 # legacy variable name and should not be used.
-galaxy_shed_tool_conf_file: "{{ galaxy_mutable_config_dir }}/shed_tool_conf.xml"
+galaxy_shed_tool_conf_file: "{{ galaxy_managed_config_dir }}/shed_tool_conf.xml"
 galaxy_shed_tool_config_file: "{{ galaxy_shed_tool_conf_file }}"
 
 # The Python `requirements.txt` file that should be used to install Galaxy dependent modules using pip
@@ -184,17 +184,17 @@ galaxy_app_config_default:
   openid_consumer_cache_path: "{{ galaxy_cache_dir }}/openid_consumer_cache"
   citation_cache_data_dir: "{{ galaxy_cache_dir }}/citations/data"
   citation_cache_lock_dir: "{{ galaxy_cache_dir }}/citations/locks"
-  new_file_path: "{{ galaxy_mutable_data_dir }}/tmp"
-  mulled_resolution_cache_data_dir: "{{ galaxy_mutable_data_dir }}/mulled/data"
-  mulled_resolution_cache_lock_dir: "{{ galaxy_mutable_data_dir }}/mulled/lock"
+  new_file_path: "{{ galaxy_managed_data_dir }}/tmp"
+  mulled_resolution_cache_data_dir: "{{ galaxy_managed_data_dir }}/mulled/data"
+  mulled_resolution_cache_lock_dir: "{{ galaxy_managed_data_dir }}/mulled/lock"
 
-  # Mutable config files
-  integrated_tool_panel_config: "{{ galaxy_mutable_config_dir }}/integrated_tool_panel.xml"
-  migrated_tools_config: "{{ galaxy_mutable_config_dir }}/migrated_tools_conf.xml"
-  shed_data_manager_config_file: "{{ galaxy_mutable_config_dir }}/shed_data_manager_conf.xml"
-  shed_tool_data_table_config: "{{ galaxy_mutable_config_dir }}/shed_tool_data_table_conf.xml"
+  # Managed config files
+  integrated_tool_panel_config: "{{ galaxy_managed_config_dir }}/integrated_tool_panel.xml"
+  migrated_tools_config: "{{ galaxy_managed_config_dir }}/migrated_tools_conf.xml"
+  shed_data_manager_config_file: "{{ galaxy_managed_config_dir }}/shed_data_manager_conf.xml"
+  shed_tool_data_table_config: "{{ galaxy_managed_config_dir }}/shed_tool_data_table_conf.xml"
 
-  # Directories that would often be stored outside the mutable data dir, these values are either from the layout or set by the user
+  # Directories that would often be stored outside the managed data dir, these values are either from the layout or set by the user
   file_path: "{{ galaxy_file_path }}"
   job_working_directory: "{{ galaxy_job_working_directory }}"
   tool_dependency_dir: "{{ galaxy_tool_dependency_dir }}"
@@ -210,13 +210,13 @@ galaxy_app_config_default:
 galaxy_config_default: "{{ {} | combine({galaxy_app_config_section: galaxy_app_config_default}) }}"
 galaxy_config_merged: "{{ galaxy_config_default | combine(galaxy_config | default({}), recursive=True) }}"
 
-# Automatically instantiate mutable config files from copies in role if they don't exist
-galaxy_mutable_config_files:
+# Automatically instantiate managed config files from copies in role if they don't exist
+galaxy_managed_config_files:
   - src: "shed_data_manager_conf.xml"
     dest: "{{ galaxy_config_merged[galaxy_app_config_section].shed_data_manager_config_file }}"
   - src: "shed_tool_data_table_conf.xml"
     dest: "{{ galaxy_config_merged[galaxy_app_config_section].shed_tool_data_table_config }}"
-galaxy_mutable_config_templates:
+galaxy_managed_config_templates:
   - src: "shed_tool_conf.xml.j2"
     dest: "{{ galaxy_config_merged[galaxy_app_config_section].migrated_tools_config }}"
   - src: "shed_tool_conf.xml.j2"
@@ -227,7 +227,7 @@ galaxy_config_instance_resource_url: "{{ galaxy_config_merged[galaxy_app_config_
 galaxy_errordocs_server_name: Galaxy
 galaxy_errordocs_prefix: /error
 
-# These are lists of hashes in the same format as galaxy_mutable_configs that can be used to cause extra files and
+# These are lists of hashes in the same format as galaxy_managed_configs that can be used to cause extra files and
 # templates to be installed on the managed host.
 galaxy_config_files: []
 galaxy_config_templates: []

tasks/_inc_galaxy_version.yml

@@ -1,7 +1,7 @@
 ---
 # Determine Galaxy version
 
-# Currently only used by mutable config setup but placed in an include because it'll probably be used by more
+# Currently only used by managed config setup but placed in an include because it'll probably be used by more
 
 - name: Collect Galaxy version file
   slurp:

tasks/layout.yml

@@ -12,8 +12,8 @@
     - galaxy_venv_dir
     - galaxy_server_dir
     - galaxy_config_dir
-    - galaxy_mutable_data_dir
-    - galaxy_mutable_config_dir
+    - galaxy_managed_data_dir
+    - galaxy_managed_config_dir
     - galaxy_shed_tools_dir
     - galaxy_cache_dir
     - galaxy_local_tools_dir

tasks/main.yml

@@ -56,11 +56,11 @@
   tags:
     - galaxy_fetch_dependencies
 
-- name: Include mutable config setup tasks
-  include_tasks: mutable_setup.yml
-  when: galaxy_manage_mutable_setup
+- name: Include managed config setup tasks
+  include_tasks: managed_setup.yml
+  when: galaxy_manage_managed_setup
   tags:
-    - galaxy_manage_mutable_setup
+    - galaxy_manage_managed_setup
 
 - name: Include database management tasks
   include_tasks: database.yml

tasks/mutable_setup.yml → tasks/managed_setup.yml

@@ -1,27 +1,27 @@
 ---
-# Instantiate mutable config files
+# Instantiate managed config files
 
-- name: Mutable config setup
+- name: Managed config setup
   block:
 
     - name: Ensure Galaxy version is set
       include_tasks: _inc_galaxy_version.yml
       when: __galaxy_major_version is undefined
 
     # force: no in the following 2 tasks will not overwrite existing configs
-    - name: Instantiate mutable configuration files
+    - name: Instantiate managed configuration files
       copy:
         src: "{{ item.src }}"
         dest: "{{ item.dest }}"
         force: no
-      with_items: "{{ galaxy_mutable_config_files }}"
+      with_items: "{{ galaxy_managed_config_files }}"
 
-    - name: Instantiate mutable configuration templates
+    - name: Instantiate managed configuration templates
       template:
         src: "{{ item.src }}"
         dest: "{{ item.dest }}"
         force: no
-      with_items: "{{ galaxy_mutable_config_templates }}"
+      with_items: "{{ galaxy_managed_config_templates }}"
 
   remote_user: "{{ galaxy_remote_users.galaxy | default(__galaxy_remote_user) }}"
   become: "{{ true if galaxy_become_users.galaxy is defined else __galaxy_become }}"

tests/test_playbook.yml

@@ -19,7 +19,7 @@
     galaxy_privsep_user: gxpriv
     galaxy_config:
       galaxy:
-        database_connection: sqlite:///{{ galaxy_mutable_data_dir }}/universe.sqlite
+        database_connection: sqlite:///{{ galaxy_managed_data_dir }}/universe.sqlite
     # needed because we've disabled facts
     ansible_user_uid: "{{ lookup('env', 'UID') }}"
     ansible_user_id: "{{ lookup('env', 'USER') }}"

vars/layout-custom.yml

@@ -4,15 +4,15 @@
 # - galaxy_server_dir
 # - galaxy_venv_dir
 # - galaxy_config_dir
-# - galaxy_mutable_data_dir
+# - galaxy_managed_data_dir
 
 # Layout defaults
-__galaxy_mutable_config_dir: "{{ galaxy_mutable_data_dir }}/config"
-__galaxy_cache_dir: "{{ galaxy_mutable_data_dir }}/cache"
+__galaxy_managed_config_dir: "{{ galaxy_managed_data_dir }}/config"
+__galaxy_cache_dir: "{{ galaxy_managed_data_dir }}/cache"
 __galaxy_local_tools_dir: null
-__galaxy_shed_tools_dir: "{{ galaxy_mutable_data_dir }}/shed_tools"
+__galaxy_shed_tools_dir: "{{ galaxy_managed_data_dir }}/shed_tools"
 
 # These correspond to galaxy config options
-__galaxy_tool_dependency_dir: "{{ galaxy_mutable_data_dir }}/dependencies"
-__galaxy_file_path: "{{ galaxy_mutable_data_dir }}/datasets"
-__galaxy_job_working_directory: "{{ galaxy_mutable_data_dir }}/jobs"
+__galaxy_tool_dependency_dir: "{{ galaxy_managed_data_dir }}/dependencies"
+__galaxy_file_path: "{{ galaxy_managed_data_dir }}/datasets"
+__galaxy_job_working_directory: "{{ galaxy_managed_data_dir }}/jobs"

vars/layout-legacy-improved.yml

@@ -3,13 +3,13 @@
 # Layout defaults
 __galaxy_venv_dir: "{{ galaxy_server_dir }}/.venv"
 __galaxy_config_dir: "{{ galaxy_server_dir }}/config"
-__galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
-__galaxy_mutable_config_dir: "{{ galaxy_server_dir }}/config"
-__galaxy_cache_dir: "{{ galaxy_mutable_data_dir }}"
+__galaxy_managed_data_dir: "{{ galaxy_server_dir }}/database"
+__galaxy_managed_config_dir: "{{ galaxy_server_dir }}/config"
+__galaxy_cache_dir: "{{ galaxy_managed_data_dir }}"
 __galaxy_local_tools_dir: null
-__galaxy_shed_tools_dir: "{{ galaxy_mutable_data_dir }}/shed_tools"
+__galaxy_shed_tools_dir: "{{ galaxy_managed_data_dir }}/shed_tools"
 
 # These correspond to galaxy config options
-__galaxy_tool_dependency_dir: "{{ galaxy_mutable_data_dir }}/dependencies"
-__galaxy_file_path: "{{ galaxy_mutable_data_dir }}/datasets"
-__galaxy_job_working_directory: "{{ galaxy_mutable_data_dir }}/jobs"
+__galaxy_tool_dependency_dir: "{{ galaxy_managed_data_dir }}/dependencies"
+__galaxy_file_path: "{{ galaxy_managed_data_dir }}/datasets"
+__galaxy_job_working_directory: "{{ galaxy_managed_data_dir }}/jobs"

vars/layout-legacy.yml

@@ -3,13 +3,13 @@
 # Layout defaults
 __galaxy_venv_dir: "{{ galaxy_server_dir }}/.venv"
 __galaxy_config_dir: "{{ galaxy_server_dir }}"
-__galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
-__galaxy_mutable_config_dir: "{{ galaxy_server_dir }}"
-__galaxy_cache_dir: "{{ galaxy_mutable_data_dir }}"
+__galaxy_managed_data_dir: "{{ galaxy_server_dir }}/database"
+__galaxy_managed_config_dir: "{{ galaxy_server_dir }}"
+__galaxy_cache_dir: "{{ galaxy_managed_data_dir }}"
 __galaxy_local_tools_dir: null
 __galaxy_shed_tools_dir: "{{ galaxy_server_dir }}/../shed_tools"
 
 # These correspond to galaxy config options
-__galaxy_tool_dependency_dir: "{{ galaxy_mutable_data_dir }}/dependencies"
-__galaxy_file_path: "{{ galaxy_mutable_data_dir }}/datasets"
-__galaxy_job_working_directory: "{{ galaxy_mutable_data_dir }}/jobs"
+__galaxy_tool_dependency_dir: "{{ galaxy_managed_data_dir }}/dependencies"
+__galaxy_file_path: "{{ galaxy_managed_data_dir }}/datasets"
+__galaxy_job_working_directory: "{{ galaxy_managed_data_dir }}/jobs"

vars/layout-opt.yml

@@ -4,13 +4,13 @@
 __galaxy_server_dir: "/opt/galaxy"
 __galaxy_venv_dir: "/var/opt/galaxy/venv"
 __galaxy_config_dir: "/etc/opt/galaxy"
-__galaxy_mutable_data_dir: "/var/opt/galaxy/data"
-__galaxy_mutable_config_dir: "{{ galaxy_mutable_data_dir }}/config"
-__galaxy_cache_dir: "{{ galaxy_mutable_data_dir }}/cache"
+__galaxy_managed_data_dir: "/var/opt/galaxy/data"
+__galaxy_managed_config_dir: "{{ galaxy_managed_data_dir }}/config"
+__galaxy_cache_dir: "{{ galaxy_managed_data_dir }}/cache"
 __galaxy_local_tools_dir: "/var/opt/galaxy/local_tools"
-__galaxy_shed_tools_dir: "{{ galaxy_mutable_data_dir }}/shed_tools"
+__galaxy_shed_tools_dir: "{{ galaxy_managed_data_dir }}/shed_tools"
 
 # These correspond to galaxy config options
-__galaxy_tool_dependency_dir: "{{ galaxy_mutable_data_dir }}/dependencies"
+__galaxy_tool_dependency_dir: "{{ galaxy_managed_data_dir }}/dependencies"
 __galaxy_file_path: "/srv/galaxy/datasets"
-__galaxy_job_working_directory: "{{ galaxy_mutable_data_dir }}/jobs"
+__galaxy_job_working_directory: "{{ galaxy_managed_data_dir }}/jobs"

vars/layout-root-dir.yml

@@ -4,13 +4,13 @@
 __galaxy_server_dir: "{{ galaxy_root }}/server"
 __galaxy_venv_dir: "{{ galaxy_root }}/venv"
 __galaxy_config_dir: "{{ galaxy_root }}/config"
-__galaxy_mutable_data_dir: "{{ galaxy_root }}/var"
-__galaxy_mutable_config_dir: "{{ galaxy_mutable_data_dir }}/config"
-__galaxy_cache_dir: "{{ galaxy_mutable_data_dir }}/cache"
+__galaxy_managed_data_dir: "{{ galaxy_root }}/var"
+__galaxy_managed_config_dir: "{{ galaxy_managed_data_dir }}/config"
+__galaxy_cache_dir: "{{ galaxy_managed_data_dir }}/cache"
 __galaxy_local_tools_dir: "{{ galaxy_root }}/local_tools"
-__galaxy_shed_tools_dir: "{{ galaxy_mutable_data_dir }}/shed_tools"
+__galaxy_shed_tools_dir: "{{ galaxy_managed_data_dir }}/shed_tools"
 
 # These correspond to galaxy config options
-__galaxy_tool_dependency_dir: "{{ galaxy_mutable_data_dir }}/dependencies"
+__galaxy_tool_dependency_dir: "{{ galaxy_managed_data_dir }}/dependencies"
 __galaxy_file_path: "{{ galaxy_root }}/datasets"
 __galaxy_job_working_directory: "{{ galaxy_root }}/jobs"