Fix Vagrant Deployment

README.md

@@ -32,7 +32,7 @@ Note that you will need to set up the appropriate proxying *outside* the Web Lab
 
 ### Using Vagrant
 
-Version 2.2 of Vagrant is required for this. We recommend using the VirtualBox provider with it.
+Version 2.4 of Vagrant is required for this. We recommend using the VirtualBox provider with it.
 
 You may need to edit some options in the `Vagrantfile` depending on how you have configured your local variables.
 For instance, remove the `raw_arguments` if you're not encrypting any secrets.

Vagrantfile

@@ -9,25 +9,28 @@ Vagrant.configure("2") do |config|
     # Needs plugin vagrant-disksize: `vagrant plugin install vagrant-disksize`
     config.disksize.size = '40GB'
 
-    config.vm.network :forwarded_port, guest: 80, host: 8088    # Django front-end
-    config.vm.network :forwarded_port, guest: 8080, host: 8089  # Expt runner
+    # NOTE: This will enable public access to the opened ports.
+    config.vm.network "forwarded_port", guest: 80, host: 8088    # Django front-end
+    config.vm.network "forwarded_port", guest: 8080, host: 8089  # Experiment runner
+
+    # NOTE: This restricts access to the opened ports via 127.0.0.1 only.
+    # config.vm.network "forwarded_port", guest: 80, host: 8088, host_ip: "127.0.0.1"
+    # config.vm.network "forwarded_port", guest: 8080, host: 8089, host_ip: "127.0.0.1"
 
     # This needs to look real enough for git to set a default identity
     config.vm.hostname = "weblab.local"
 
+    # Provider-specific configuration for VirtualBox
     config.vm.provider "virtualbox" do |vb|
         vb.name = "WebLab18"
         vb.memory = "4096"
+        vb.cpus = "4"
     end
 
     # Install the Web Lab using Ansible
     config.vm.provision "ansible_local" do |ansible|
-        # Install a specific Ansible version with pip
+        ansible.compatibility_mode = "2.0"
         ansible.install = true
-        ansible.install_mode = "pip"
-        ansible.pip_install_cmd = "sudo apt-get install -y python-pip"
-        # The line above is because otherwise Vagrant tries to use pip3 and breaks because OS is Python 2
-        ansible.version = "2.8.0"
 
         ansible.playbook = "site.yml"
         ansible.inventory_path = "inventories/dev"
@@ -43,4 +46,3 @@ Vagrant.configure("2") do |config|
         ansible.verbose = true
     end
 end
-

patches/fc/pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "wheel", "numpy>=1,<2", "cython>=0,<3"]
+build-backend = "setuptools.build_meta"

roles/add_user/tasks/main.yml

@@ -1,13 +1,13 @@
 # Create a new user account, and record meta information
 
 - name: Create user's group
-  become: yes
+  become: true
   group:
     name: '{{ user_group }}'
     state: present
 
 - name: Create user
-  become: yes
+  become: true
   user:
     name: '{{ user_name }}'
     group: '{{ user_group }}'

roles/celery/meta/main.yml

@@ -10,7 +10,7 @@ dependencies:
   - role: prep_venv
     user: '{{ celery_user }}'
     virtualenv: '{{ celery_virtualenv }}'
-    virtualenv_python: python3.7
+    virtualenv_python: python3.6
   # Then we need the FC backend available for the celery user,
   # since our tasks import modules from it
   - role: fc-backend

roles/celery/tasks/main.yml

@@ -10,31 +10,31 @@
     - '{{ celery_dir }}'
     - '{{ celery_state_dir }}'
     - '{{ celery_log_dir }}'
-  become: yes
+  become: true
 
 - name: Celery | List celery state
-  become: yes
+  become: true
   find:
     paths: '{{ celery_state_dir }}'
     patterns: '*'
   register: celery_state_files
 
 - name: Celery | Checkout repository
-  become: yes
+  become: true
   become_user: '{{ celery_user }}'
   git:
-    clone: yes
+    clone: true
     dest: '{{ celery_checkout }}'
     repo: '{{ celery_git_repo }}'
     version: '{{ celery_git_branch }}'
-    update: yes
-    force: yes
+    update: true
+    force: true
   notify:
     - clean celery state
     - restart experiment runner
 
 - name: Celery | Install python packages
-  become: yes
+  become: true
   become_user: '{{ celery_user }}'
   pip:
     requirements: '{{ celery_checkout }}/requirements/base.txt'
@@ -46,7 +46,7 @@
     - restart experiment runner
 
 - name: Celery | FCWS configuration
-  become: yes  # Because the celery_user may not be in the nginx_group
+  become: true  # Because the celery_user may not be in the nginx_group
   template:
     src: '{{ item }}.j2'
     dest: '{{ celery_checkout }}/fcws/{{ item }}'
@@ -59,7 +59,7 @@
     - restart experiment runner
 
 - name: Install Celery service
-  become: yes
+  become: true
   block:
     - name: Celery | Systemd service definition
       template:
@@ -83,5 +83,5 @@
       # TODO: Make this an always-run notify of 'start celery' handler?
       service:
         name: '{{ celery_service_name }}'
-        enabled: yes
+        enabled: true
         state: started

roles/core/tasks/main.yml

@@ -1,7 +1,13 @@
 # Setup common to all hosts
 
+- name: Install ufw
+  apt:
+    name: ["ufw"]
+    state: present
+  become: true
+
 - name: Open SSH port in firewall
-  become: yes
+  become: true
   ufw:
     name: OpenSSH
     rule: allow

roles/django/meta/main.yml

@@ -3,13 +3,13 @@ dependencies:
   - role: add_user
     user_name: "{{ django_user }}"
     user_comment: Web Lab Django user account
-  - { role: geerlingguy.postgresql, become: yes }
+  - { role: geerlingguy.postgresql, become: true }
 
   # And we need a virtualenv
   - role: prep_venv
     user: '{{ django_user }}'
     virtualenv: '{{ django_virtualenv }}'
-    virtualenv_command: pyvenv
+    virtualenv_python: python3.6
 
   # Ensure node is new enough (and installed)
-  - { role: geerlingguy.nodejs, become: yes }
+  - { role: geerlingguy.nodejs, become: true }

roles/django/tasks/main.yml

@@ -3,7 +3,7 @@
 - name: Install postfix for Django email sending if needed
   import_role:
     name: postfix
-  become: yes
+  become: true
   when: email_smtp_host == 'localhost'
 
 - name: Ensure the Django dirs exist with correct permissions
@@ -17,10 +17,10 @@
     - '{{ django_data_path }}'
     - '{{ django_experiments_path }}'
     - '{{ django_datasets_path }}'
-  become: yes
+  become: true
 
 - name: Raise limit on max open files for Django
-  become: yes
+  become: true
   template:
     src: ulimit.j2
     dest: /etc/security/limits.d/weblab.conf
@@ -29,27 +29,32 @@
 # Install Django & dependencies
 
 - name: Install Django
-  become: yes
+  become: true
   become_user: "{{ django_user }}"
   become_method: sudo
   block:
     - name: Django | Checkout repository
       git:
-        clone: yes
+        clone: true
         dest: "{{ django_checkout }}"
         repo: "{{ django_git_repo }}"
         version: "{{ django_git_branch }}"
-        update: yes
-        force: yes
+        update: true
+        force: true
       notify:
         - restart uwsgi
 
-    - name: Django | Build psycopg2 from source
+    - name: Django | fix git-python dependency
+      lineinfile:
+        path: '{{ django_checkout }}/requirements/base.txt'
+        regexp: '^gitpython=='
+        line: gitpython==3.1.18
+
+    - name: Django |  Install psycopg2
       pip:
         name: psycopg2
-        version: 2.7.7
+        version: 2.8.6
         state: present
-        extra_args: '--no-binary psycopg2'
         virtualenv: '{{ django_virtualenv }}'
         virtualenv_command: pyvenv
       become_flags: "-H"
@@ -122,29 +127,29 @@
   command: npm install
   args:
     chdir: "{{ django_static_path }}"
-  become: yes
+  become: true
   become_user: "{{ django_user }}"
 
 - block:
     - name: gulp | Build static assets
       command: ./node_modules/gulp/bin/gulp.js
       args:
         chdir: "{{ django_static_path }}"
-      become: yes
+      become: true
       become_user: "{{ django_user }}"
   rescue:
     # Errors are often due to a node upgrade
     - name: gulp | Rebuild on npm/node version change
       command: npm rebuild
       args:
         chdir: "{{ django_static_path }}"
-      become: yes
+      become: true
       become_user: "{{ django_user }}"
     - name: gulp | Rebuild static assets
       command: ./node_modules/gulp/bin/gulp.js
       args:
         chdir: "{{ django_static_path }}"
-      become: yes
+      become: true
       become_user: "{{ django_user }}"
 
 - name: Django | Collect static files
@@ -153,7 +158,7 @@
     app_path: "{{ django_app_path }}"
     settings: config.settings.deployed
     virtualenv: '{{ django_virtualenv }}'
-  become: yes
+  become: true
   become_user: "{{ django_user }}"
 
 - name: Django | Copy ontology definition
@@ -174,4 +179,4 @@
     weekday: "*"
     job: systemctl restart uwsgi
     state: present
-  become: yes
+  become: true

roles/fc-backend/defaults/main.yml

@@ -7,7 +7,7 @@ fc_user: celery
 legacy_fc_virtualenv: "{{ user_meta[fc_user].home }}/python2_venv"
 
 # Chaste backend configuration
-chaste_repo: https://chaste.cs.ox.ac.uk/git/chaste.git
+chaste_repo: https://github.com/Chaste/Chaste.git
 fc_repo: https://chaste.cs.ox.ac.uk/svn/chaste/projects/FunctionalCuration
 chaste_root: "{{ user_meta[fc_user].home }}/eclipse/workspace/Chaste"
 fc_project_name: FunctionalCuration

roles/fc-backend/meta/main.yml

@@ -10,9 +10,9 @@ dependencies:
     user: '{{ fc_user }}'
     virtualenv: '{{ legacy_fc_virtualenv }}'
     virtualenv_python: python2
-    virtualenv_site_packages: yes
+    virtualenv_site_packages: true
   - role: prep_venv
     user: '{{ fc_user }}'
     virtualenv: '{{ weblab_fc_virtualenv }}'
-    virtualenv_python: python3.7
-    virtualenv_site_packages: no
+    virtualenv_python: python3.6
+    virtualenv_site_packages: false