merge: #210 from dev

.gitignore

@@ -26,3 +26,5 @@ dist/
 api/phenome10k.egg-info/
 
 docker/local.env
+
+logs/

ansible/group_vars/all/main.yml

@@ -79,8 +79,9 @@ flower_broker_api: http://{{ p10k_db_user }}:{{ p10k_db_password|urlencode() }}@
 # p10k: flask
 cache_redis_url: redis://{{ redis_host }}:6379/1
 flask_secret_key: G}<Ci&XWqSqA/mF7ZCWI7JJ.:QuuZF
-gunicorn_binary: '{{ venv_bin }}/gunicorn'
-gunicorn_port: 8000
+uwsgi_binary: "{{ venv_bin }}/uwsgi"
+uwsgi_ini: "{{ p10k_home }}/uswgi.ini"
+uwsgi_port: 8000
 p10k_admin_email: [email protected]
 p10k_admin_password: pass
 password_salt: 7mrUh6kF*&PEh2gUTmHc

ansible/playbook.yml

@@ -25,7 +25,7 @@
     - monit/monit
   vars:
     monit_services:
-      - gunicorn
+      - uwsgi
       - systems
       - 50gb-root-partition
 

ansible/roles/monit/monit/defaults/main.yml

@@ -14,12 +14,12 @@ monit_eventqueue:
 # Active - try and restart services
 monit_monitoring_mode: active
 monit_services_conf:
-  gunicorn:
+  uwsgi:
     check_type: process
-    check_id: gunicorn
+    check_id: uwsgi
     id_type: matching
-    start: /bin/systemctl restart gunicorn
-    stop: /bin/systemctl stop gunicorn
+    start: /bin/systemctl restart uwsgi
+    stop: /bin/systemctl stop uwsgi
     group: web
     tests:
       - condition: cpu > 60% for 20 cycles

ansible/roles/nginx/templates/phenome10k.org.conf.j2

@@ -1,5 +1,5 @@
 upstream phenome10k {
-{% for server in app_servers %}  server {{ server }}:{{ gunicorn_port }};{% endfor %}
+{% for server in app_servers %}  server {{ server }}:{{ uwsgi_port }};{% endfor %}
 }
 
 server {

ansible/roles/nginx/templates/phenome10k.org.ssl.conf.j2

@@ -1,5 +1,5 @@
 upstream phenome10k {
-{% for server in app_servers %}  server {{ server }}:{{ gunicorn_port }};{% endfor %}
+{% for server in app_servers %}  server {{ server }}:{{ uwsgi_port }};{% endfor %}
 }
 
 server {

ansible/roles/phenome-10k/handlers/main.yml

@@ -17,9 +17,9 @@
   become: true
   become_user: phenome10k
 
-- name: restart gunicorn
+- name: restart uwsgi
   service:
-    name: gunicorn
+    name: uwsgi
     state: restarted
   become: true
 

ansible/roles/phenome-10k/tasks/app-flask.yml

@@ -55,17 +55,26 @@
   become_user: phenome10k
   run_once: true
 
-- name: Create the gunicorn service
+- name: Copy uwsgi.ini config
   template:
-    src: gunicorn.service.j2
-    dest: /etc/systemd/system/gunicorn.service
+    src: uwsgi.ini.j2
+    dest: '{{ uwsgi_ini }}'
+  become: true
+  become_user: phenome10k
+  notify:
+    - restart uwsgi
+
+- name: Create the uwsgi service
+  template:
+    src: uwsgi.service.j2
+    dest: /etc/systemd/system/uwsgi.service
   become: true
   notify:
-    - restart gunicorn
+    - restart uwsgi
 
-- name: Enable gunicorn service
+- name: Enable uwsgi service
   systemd:
-    name: gunicorn.service
+    name: uwsgi.service
     state: started
     enabled: y
   become: true

ansible/roles/phenome-10k/tasks/main.yml

@@ -17,7 +17,7 @@
   when: not skip_git_checkout
   notify:
     - rebuild front end
-    - restart gunicorn
+    - restart uwsgi
     - restart node
   tags:
     - flask
@@ -55,7 +55,7 @@
   become: true
   become_user: phenome10k
   notify:
-    - restart gunicorn
+    - restart uwsgi
 
 - name: Create log directory
   file:

ansible/roles/phenome-10k/templates/uwsgi.ini.j2

@@ -0,0 +1,14 @@
+[uwsgi]
+http = 0.0.0.0:{{ uwsgi_port }}
+wsgi-file = api/wsgi.py
+callable = app
+wsgi-disable-file-wrapper = true
+master = true
+processes = 3
+threads = 3
+buffer-size = 65535
+stats = 127.0.0.1:9191
+log-5xx = true
+
+req-logger = file:/var/log/phenome10k/u_access.log
+logger = file:/var/log/phenome10k/u_error.log

ansible/roles/phenome-10k/templates/gunicorn.service.j2 → ansible/roles/phenome-10k/templates/uwsgi.service.j2

@@ -3,7 +3,7 @@ Description=phenome10k service
 
 [Service]
 Type=simple
-ExecStart={{ gunicorn_binary }} --error-logfile /var/log/phenome10k/error.log --access-logfile /var/log/phenome10k/access.log -b 0.0.0.0:{{ gunicorn_port }} -w 9 --timeout 120 api.wsgi:app
+ExecStart={{ uwsgi_binary }} --ini {{ uwsgi_ini }}
 Restart=on-abort
 WorkingDirectory={{ p10k_src_dir }}
 User={{ p10k_linux_user }}

api/phenome10k/config.py

@@ -24,7 +24,7 @@ class Config(object):
     MAIL_PORT = os.environ.get('MAIL_PORT', 25)
     MAIL_USERNAME = os.environ.get('MAIL_USERNAME')
     MAIL_PASSWORD = os.environ.get('MAIL_PASSWORD')
-    ADMIN_EMAIL = os.environ.get('ADMIN_EMAIL') or '[email protected]'
+    ADMIN_EMAIL = os.environ.get('ADMIN_EMAIL') or '[email protected]'
     LOG_FILE = os.environ.get('LOG_FILE') or 'logs/phenome10k.log'
     LOG_LEVEL = os.environ.get('LOG_LEVEL', 'WARNING')
     SERVER_NAME = os.environ.get('SERVER_NAME') or None

api/phenome10k/routes/__init__.py

@@ -15,6 +15,7 @@ def init_routes(app):
         query.bp,
     ]
 
+    app.url_map.strict_slashes = False
     app.url_map.converters['scan'] = ScanConverter
     app.url_map.converters['publication'] = PublicationConverter
     app.url_map.converters['file'] = FileConverter

api/phenome10k/routes/_utils.py

@@ -161,6 +161,8 @@ def search(self, **kwargs):
                 for c in self._columns.values():
                     try:
                         v = c.type.python_type(r.q)
+                        if type(v) is bool:
+                            continue
                         or_filters.append(c == v)
                     except:
                         continue

api/phenome10k/routes/publications.py

@@ -123,7 +123,7 @@ def manage(page=1):
     return render_vue(data, title='Manage Publications')
 
 
-@bp.route('/<publication:pub_object>/')
+@bp.route('/<publication:pub_object>')
 def view(pub_object):
     if not pub_object.published and not (
         current_user.is_authenticated and current_user.can_edit(pub_object)

api/pyproject.toml

@@ -6,7 +6,7 @@ requires-python = ">=3.8"
 license = { text = "GPL-3.0-or-later" }
 authors = [
     { name = "Paul Kiddle" },
-    { name = "Ginger Butcher", email = "[email protected]" }
+    { name = "Ginger Burns", email = "[email protected]" }
 ]
 keywords = []
 classifiers = [

api/requirements.txt

@@ -11,13 +11,13 @@ Flask==2.0.3
 flask-caching==2.3.0
 flask-hcaptcha==0.6.0
 Flask-Mail==0.9.1
+Flask-Marshmallow==0.14.0
 Flask-Migrate==3.1.0
 flask-security-too==5.0.1
 Flask-SQLAlchemy==2.5.1
 Flask-WTF==1.0.1
-Flask-Marshmallow==0.14.0
 flower==1.2.0
-gunicorn==20.1.0
+pyuwsgi==2.0.26
 importlib-metadata==4.11.3
 marshmallow-sqlalchemy==0.28.0
 numpy==1.22.3