Remove a lot of cruft, switch to yaml-style task params, and update for

Ansible 2.2 compatibility

defaults/main.yml

@@ -4,7 +4,6 @@
 # Controls which tasks are included, in case you need to perform different
 # options on different hosts or server directories.
 galaxy_manage_clone: yes
-galaxy_vcs: hg
 galaxy_force_checkout: no
 # Download the Galaxy instead cloning, for throw away boxes (e.g. Docker)
 galaxy_manage_download: no
@@ -13,22 +12,16 @@ galaxy_manage_mutable_setup: yes
 galaxy_manage_database: yes
 galaxy_fetch_dependencies: yes
 
-# Set a version of pip to install
-galaxy_pip_version: 8.1.2
-
-# legacy
-galaxy_fetch_eggs: yes
-
-# Where to clone Galaxy from
-galaxy_repo: https://bitbucket.org/galaxy/galaxy-dist
-galaxy_git_repo: https://github.com/galaxyproject/galaxy.git
+# Where to clone Galaxy from. Backwards compatibility with galaxy_git_repo
+galaxy_repo: "{{ galaxy_git_repo | default('https://github.com/galaxyproject/galaxy.git') }}"
 
 # This can be a tag (as shown here) but doing so will cause the revision check
-# task to always report "changed"
-galaxy_changeset_id: stable
+# task to always report "changed". Backwards compatibility with
+# galaxy_changeset_id.
+galaxy_commit_id: "{{ galaxy_changeset_id | default('master') }}"
 
 # Download URL (if used)
-galaxy_download_url: "{{ galaxy_repo }}/get/{{ galaxy_changeset_id }}.tar.gz"
+galaxy_download_url: "{{ galaxy_repo }}/get/{{ galaxy_commit_id }}.tar.gz"
 
 # This will automatically be used by run.sh
 galaxy_venv_dir: "{{ galaxy_server_dir }}/.venv"

files/makepyc.py

@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 
-import sys
 import compileall
+import sys
 
-from os import walk, unlink
-from os.path import join, splitext, exists
+from os import unlink, walk
+from os.path import exists, join, splitext
 
 
 assert sys.argv[1], "usage: makepyc /path/to/lib"

handlers/main.yml

@@ -3,10 +3,13 @@
 
 # TODO: Magical restarters depending on how you're running Galaxy.
 - name: restart galaxy
-  debug: msg="RESTARTER NOT IMPLEMENTED - Please restart Galaxy manually"
+  debug:
+    msg: "RESTARTER NOT IMPLEMENTED - Please restart Galaxy manually"
 
-- name: email administrator with changeset id
-  mail: from="{{ galaxy_admin_email_from | default( 'root' ) }}" to="{{ galaxy_admin_email_to }}"
-        subject="Galaxy instance {{ galaxy_instance_hostname | default( inventory_hostname ) }} is at changeset {{ galaxy_changeset_id }}"
-        body=" "
+- name: email administrator with commit id
+  mail:
+    from: "{{ galaxy_admin_email_from | default( 'root' ) }}"
+    to: "{{ galaxy_admin_email_to }}"
+    subject: "Galaxy instance {{ galaxy_instance_hostname | default( inventory_hostname ) }} is at commit {{ galaxy_commit_id }}"
+    body: " "
   when: galaxy_admin_email_to is defined

tasks/clone.yml

@@ -2,39 +2,34 @@
 # Manage Galaxy clone
 
 - name: Check for Galaxy
-  stat: path={{ galaxy_server_dir }}/lib/galaxy
-  register: lib_galaxy
-
-- name: Get current Galaxy changeset (hg)
-  command: "{{ hg_executable | default('hg') }} parents --template '{node}' chdir={{ galaxy_server_dir }}"
-  register: current_changeset_id
-  changed_when: False
-  when: lib_galaxy.stat.exists and galaxy_vcs == 'hg'
-
-- name: Get current Galaxy commit id (git)
-  command: "{{ git_executable | default('git') }} rev-parse HEAD chdir={{ galaxy_server_dir }}"
-  register: current_changeset_id
-  changed_when: False
-  when: lib_galaxy.stat.exists and galaxy_vcs == 'git'
-
-- name: Report current Galaxy changeset
-  debug: msg="Current changeset of {{ galaxy_server_dir }} {{ current_changeset_id.stdout | default(-1) }} does not match playbook version {{ galaxy_changeset_id }}"  #"
+  stat:
+    path: "{{ galaxy_server_dir }}/lib/galaxy"
+  register: galaxy_stat_out
+
+- name: Get current Galaxy commit id
+  command: "{{ git_executable | default('git') }} rev-parse HEAD"
+  args:
+      chdir: "{{ galaxy_server_dir }}"
+  register: current_commit_id
+  changed_when: no
+  when: galaxy_stat_out.stat.exists
+
+- name: Report current Galaxy commit id
+  debug:
+    msg: "Current version of {{ galaxy_server_dir }} {{ current_commit_id.stdout | default(-1) }} does not match playbook version {{ galaxy_commit_id }}"
   changed_when: True
-  when: lib_galaxy.stat.exists and (current_changeset_id.stdout | default(-1) != galaxy_changeset_id)
-
-- name: Update Galaxy to correct changeset (hg)
-  hg: dest={{ galaxy_server_dir }} force={{ galaxy_force_checkout }} purge=no repo={{ galaxy_repo }} revision={{ galaxy_changeset_id }} executable={{ hg_executable | default(omit) }}
-  when: galaxy_vcs == 'hg'
-  notify:
-    - restart galaxy
-    - email administrator with changeset id
-
-- name: Update Galaxy to correct changeset (git)
-  git: dest={{ galaxy_server_dir }} force={{ galaxy_force_checkout }} repo={{ galaxy_git_repo }} version={{ galaxy_changeset_id }} executable={{ git_executable | default(omit) }}
-  when: galaxy_vcs == 'git'
+  when: galaxy_stat_out.stat.exists and (current_commit_id.stdout | default(-1) != galaxy_commit_id)
+
+- name: Update Galaxy to correct ref (git)
+  git:
+    dest: "{{ galaxy_server_dir }}"
+    force: "{{ galaxy_force_checkout }}"
+    repo: "{{ galaxy_repo }}"
+    version: "{{ galaxy_commit_id }}"
+    executable: "{{ git_executable | default(omit) }}"
   notify:
     - restart galaxy
-    - email administrator with changeset id
+    - email administrator with commit id
 
 - include: virtualenv.yml
 

tasks/database.yml

@@ -2,28 +2,28 @@
 # Manage Galaxy Database
 
 - name: Get current Galaxy DB version
-  command: "{{ galaxy_venv_dir }}/bin/python {{ galaxy_server_dir }}/scripts/manage_db.py -c {{ galaxy_config_file }} db_version chdir={{ galaxy_server_dir }}"
-  environment:
-    GALAXY_EGGS_PATH: "{{ galaxy_eggs_path | default(galaxy_server_dir ~ '/eggs') }}"
+  command: "{{ galaxy_venv_dir }}/bin/python {{ galaxy_server_dir }}/scripts/manage_db.py -c {{ galaxy_config_file }} db_version"
+  args:
+    chdir: "{{ galaxy_server_dir }}"
   register: current_db_version
-  changed_when: False
+  changed_when: no
   failed_when: current_db_version.rc != 0 and 'migrate.exceptions.DatabaseNotControlledError' not in current_db_version.stderr
 
 - name: Get maximum Galaxy DB version
-  command: "{{ galaxy_venv_dir }}/bin/python {{ galaxy_server_dir }}/scripts/manage_db.py -c {{ galaxy_config_file }} version chdir={{ galaxy_server_dir }}"
-  environment:
-    GALAXY_EGGS_PATH: "{{ galaxy_eggs_path | default(galaxy_server_dir ~ '/eggs') }}"
+  command: "{{ galaxy_venv_dir }}/bin/python {{ galaxy_server_dir }}/scripts/manage_db.py -c {{ galaxy_config_file }} version"
+  args:
+    chdir: "{{ galaxy_server_dir }}"
   register: max_db_version
-  changed_when: False
+  changed_when: no
 
 - name: Create Galaxy DB
-  command: "{{ galaxy_venv_dir }}/bin/python {{ galaxy_server_dir }}/scripts/create_db.py -c {{ galaxy_config_file }} chdir={{ galaxy_server_dir }}"
-  environment:
-    GALAXY_EGGS_PATH: "{{ galaxy_eggs_path | default(galaxy_server_dir ~ '/eggs') }}"
+  command: "{{ galaxy_venv_dir }}/bin/python {{ galaxy_server_dir }}/scripts/create_db.py -c {{ galaxy_config_file }}"
+  args:
+    chdir: "{{ galaxy_server_dir }}"
   when: "'migrate.exceptions.DatabaseNotControlledError' in current_db_version.stderr"
 
 - name: Upgrade Galaxy DB
-  command: "{{ galaxy_venv_dir }}/bin/python {{ galaxy_server_dir }}/scripts/manage_db.py -c {{ galaxy_config_file }} upgrade chdir={{ galaxy_server_dir }}"
-  environment:
-    GALAXY_EGGS_PATH: "{{ galaxy_eggs_path | default(galaxy_server_dir ~ '/eggs') }}"
+  command: "{{ galaxy_venv_dir }}/bin/python {{ galaxy_server_dir }}/scripts/manage_db.py -c {{ galaxy_config_file }} upgrade"
+  args:
+    chdir: "{{ galaxy_server_dir }}"
   when: current_db_version.stdout != max_db_version.stdout and 'migrate.exceptions.DatabaseNotControlledError' not in current_db_version.stderr

tasks/dependencies.yml

@@ -1,33 +1,9 @@
 ---
-# Manage Galaxy Eggs
+# Manage Galaxy framework dependencies
 
-- name: Check if Galaxy uses eggs or wheels
-  stat:
-    path: "{{ galaxy_requirements_file }}"
-  register: requirements_txt
-
-- name: Fetch Galaxy eggs
-  command: "{{ galaxy_venv_dir }}/bin/python {{ galaxy_server_dir }}/scripts/fetch_eggs.py -c {{ galaxy_config_file }} chdir={{ galaxy_server_dir }}"
-  environment:
-    GALAXY_EGGS_PATH: "{{ galaxy_eggs_path | default(galaxy_server_dir ~ '/eggs') }}"
-    PYTHONPATH: null
-  when: not requirements_txt.stat.exists
-  register: fetch_eggs_result
-  changed_when: (fetch_eggs_result.rc == 0) and (fetch_eggs_result.stdout != "")
-
-# virtualenv_command is still required if `virtualenv` isn't on $PATH, even if
-# the venv already exists.
-- name: Install Galaxy pip
-  pip:
-    name: pip
-    version: "{{ galaxy_pip_version }}"
-    virtualenv: "{{ galaxy_venv_dir }}"
-    virtualenv_command: "{{ pip_virtualenv_command | default( 'virtualenv' ) }}"
-  environment:
-    PYTHONPATH: null
-    VIRTUAL_ENV: "{{ galaxy_venv_dir }}"
-  when: requirements_txt.stat.exists
+- include: virtualenv.yml
 
+# virtualenv_command is still required if `virtualenv` isn't on $PATH, even if the venv already exists.
 - name: Install Galaxy base dependencies
   pip:
     requirements: "{{ galaxy_requirements_file }}"
@@ -37,13 +13,11 @@
   environment:
     PYTHONPATH: null
     VIRTUAL_ENV: "{{ galaxy_venv_dir }}"
-  when: requirements_txt.stat.exists
 
 - name: Collect Galaxy conditional dependency requirement strings
   command: "{{ galaxy_venv_dir }}/bin/python -c \"import galaxy.dependencies; print '\\n'.join(galaxy.dependencies.optional('{{ galaxy_config_file }}'))\""
   environment:
     PYTHONPATH: "{{ galaxy_server_dir }}/lib"
-  when: requirements_txt.stat.exists
   register: conditional_dependencies
 
 - name: Install Galaxy conditional dependencies
@@ -56,4 +30,3 @@
   environment:
     PYTHONPATH: null
     VIRTUAL_ENV: "{{ galaxy_venv_dir }}"
-  when: requirements_txt.stat.exists

tasks/download.yml

@@ -1,9 +1,10 @@
 - name: Check for Galaxy download receipt
-  stat: path={{ galaxy_server_dir }}/{{ galaxy_changeset_id }}_receipt
+  stat:
+    path: "{{ galaxy_server_dir }}/{{ galaxy_commit_id }}_receipt"
   register: download_receipt
 
 - name: Replace current version of Galaxy
-  shell: "rm -rf '{{ galaxy_server_dir }}' && mkdir '{{ galaxy_server_dir }}' && wget -q -O - {{ galaxy_download_url }} | tar xzf - --strip-components=1 -C {{ galaxy_server_dir }} && touch '{{ galaxy_server_dir }}/{{ galaxy_changeset_id }}_receipt'"
+  shell: "rm -rf '{{ galaxy_server_dir }}' && mkdir '{{ galaxy_server_dir }}' && wget -q -O - {{ galaxy_download_url }} | tar xzf - --strip-components=1 -C {{ galaxy_server_dir }} && touch '{{ galaxy_server_dir }}/{{ galaxy_commit_id }}_receipt'"
   when: not download_receipt.stat.exists
 
 - include: virtualenv.yml

tasks/main.yml

@@ -20,7 +20,7 @@
    - galaxy_config_files
 
 - include: dependencies.yml
-  when: galaxy_fetch_dependencies and galaxy_fetch_eggs
+  when: galaxy_fetch_dependencies
 
 - include: mutable_setup.yml
   when: galaxy_manage_mutable_setup

tasks/mutable_setup.yml

@@ -2,11 +2,15 @@
 # Instantiate mutable config files
 
 - name: Create mutable configuration file directories
-  file: state=directory path={{ item }}
+  file:
+    path: "{{ item }}"
+    state: directory
   with_items:
     - "{{ galaxy_mutable_config_dir }}"
     - "{{ galaxy_tool_dependency_dir }}"
 
 - name: Instantiate mutable configuration files
-  command: cp {{ item.src }} {{ item.dest }} creates={{ item.dest }}
+  command: cp {{ item.src }} {{ item.dest }}
+  args:
+    creates: "{{ item.dest }}"
   with_items: "{{ galaxy_mutable_configs }}"

tasks/static_setup.yml

@@ -2,20 +2,31 @@
 # Manage static Galaxy configuration files
 
 - name: Create Galaxy config dirs
-  file: state=directory path={{ item }}
+  file:
+    path: "{{ item }}"
+    state: directory
   with_items:
     - "{{ galaxy_config_dir }}"
     - "{{ galaxy_shed_tools_dir }}"
 
 - name: Install additional Galaxy config files (static)
-  copy: src={{ item.src }} dest={{ item.dest }} backup=yes
+  copy:
+    src: "{{ item.src }}"
+    dest: "{{ item.dest }}"
+    backup: yes
   with_items: "{{ galaxy_config_files }}"
 
 - name: Install additional Galaxy config files (template)
-  template: src={{ item.src }} dest={{ item.dest }} backup=yes
+  template:
+    src: "{{ item.src }}"
+    dest: "{{ item.dest }}"
+    backup: yes
   with_items: "{{ galaxy_config_templates }}"
 
 - name: Create Galaxy configuration file
-  template: src=galaxy.ini.j2 dest={{ galaxy_config_file }} backup=yes
+  template:
+    src: "galaxy.ini.j2"
+    dest: "{{ galaxy_config_file }}"
+    backup: yes
   notify:
     - restart galaxy

tasks/virtualenv.yml

@@ -1,3 +1,23 @@
+---
+
+# Having pip installed on $PYTHONPATH can break upgrading it, so we install
+# once with $PYTHONPATH set (in case it's needed for virtualenv) and then once
+# the venv is created we upgrade pip with $PYTHONPATH unset
 
 - name: Create Galaxy virtualenv
-  pip: name=pip virtualenv={{ galaxy_venv_dir }} virtualenv_command="{{ pip_virtualenv_command | default( 'virtualenv' ) }}"
+  pip:
+    name: pip
+    virtualenv: "{{ galaxy_venv_dir }}"
+    virtualenv_command: "{{ pip_virtualenv_command | default('virtualenv') }}"
+  environment:
+    VIRTUAL_ENV: "{{ galaxy_venv_dir }}"
+
+- name: Ensure pip is the latest release
+  pip:
+    name: pip
+    state: latest
+    virtualenv: "{{ galaxy_venv_dir }}"
+    virtualenv_command: "{{ pip_virtualenv_command | default('virtualenv') }}"
+  environment:
+    PYTHONPATH: null
+    VIRTUAL_ENV: "{{ galaxy_venv_dir }}"