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Commit 419f1d8b authored by Ossi Laine's avatar Ossi Laine
Browse files

Merge branch 'feat-dockerize-app' into 'master'

Feat dockerize app

See merge request tithei/pet-rating!10
parents c433a793 408856b7
...@@ -12,10 +12,12 @@ config.py ...@@ -12,10 +12,12 @@ config.py
*.pyc *.pyc
*.db *.db
/embody /embody
/app/static/lib
.env .env
/app/static/*.png /app/static/*.png
/app/static/embody_images /app/static/embody_images
.vscode/ .vscode/
documentation documentation
/deploy/dbdata/*
/deploy/log/nginx/access.log
/deploy/log/nginx/error.log
FROM python:3.7-slim
WORKDIR /srv/app
COPY requirements.txt /srv/app
RUN apt-get update && \
apt-get install -y \
build-essential \
make \
gcc \
pkg-config
#ython3-matplotlib
RUN pip install --upgrade pip -r requirements.txt
COPY app/. /srv/app/app
COPY run.py /srv/app
COPY config.py /srv/app
COPY messages.pot /srv/app
RUN mkdir logs
...@@ -2,11 +2,18 @@ ...@@ -2,11 +2,18 @@
### Prerequisites ### Prerequisites
Flask app with MariaDB Flask app with MySql/MariaDB
Check requirements.txt Check requirements.txt
### Installing ### Deployment
There are multiple deployment options, but one working solution is:
nginx + gunicorn (with gevent worker)
Working directory: /srv/rating
#### Installing prequisites
Install python packages with pip and preferably in virtual environment: Install python packages with pip and preferably in virtual environment:
``` ```
...@@ -19,13 +26,10 @@ Create user 'rating' and grant access to database 'rating_db'. ...@@ -19,13 +26,10 @@ Create user 'rating' and grant access to database 'rating_db'.
Create necessary tables by running the initialization script: Create necessary tables by running the initialization script:
``` ```
mysql -u rating -p -D rating_db < create_rating_db.sql mysql -u rating -p -D rating_db < db/create_rating_db.sql
``` ```
### Deployment #### Setting startup script
There are multiple deployment options, but one working solution is:
nginx + gunicorn (with gevent worker)
Create systemd startup script in '/etc/systemd/system/gunicorn.service' Create systemd startup script in '/etc/systemd/system/gunicorn.service'
...@@ -52,16 +56,37 @@ service gunicorn enable ...@@ -52,16 +56,37 @@ service gunicorn enable
service gunicorn start service gunicorn start
``` ```
### Logs #### Logs
Error logs are saved to application folder (/srv/rating/logs/) Error logs are saved to application folder (/srv/rating/logs/)
Optionally with journalctl: Optionally with journalctl:
journalctl -u gunicorn.service journalctl -u gunicorn.service
### Restart server after updates #### Restart server after updates
``` ```
service gunicorn restart service gunicorn restart
``` ```
### Deployment with docker
Install docker and docker-compose
Generate users and groups in deploy/config/mysql/data.sql
Password can be generated with generate_password.py -script
Go to deploy folder. Build containers and run them with:
```
docker-compose -f docker-compose.yml up -d --build
```
This will create persistent database 'rating_db' to deploy/dbdata with user 'rating'.
Application should be up and running in 'localhost'.
### Project contact details
- osmala@utu.fi
- timo.t.heikkila@utu.fi
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/*
Copyright (C) Federico Zivolo 2018
Distributed under the MIT License (license terms are at http://opensource.org/licenses/MIT).
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n;if(!q(e.instance.modifiers,'arrow','keepTogether'))return e;var i=o.element;if('string'==typeof i){if(i=e.instance.popper.querySelector(i),!i)return e;}else if(!e.instance.popper.contains(i))return console.warn('WARNING: `arrow.element` must be child of its popper element!'),e;var r=e.placement.split('-')[0],p=e.offsets,s=p.popper,d=p.reference,a=-1!==['left','right'].indexOf(r),l=a?'height':'width',f=a?'Top':'Left',m=f.toLowerCase(),h=a?'left':'top',c=a?'bottom':'right',u=S(i)[l];d[c]-u<s[m]&&(e.offsets.popper[m]-=s[m]-(d[c]-u)),d[m]+u>s[c]&&(e.offsets.popper[m]+=d[m]+u-s[c]),e.offsets.popper=g(e.offsets.popper);var b=d[m]+d[l]/2-u/2,y=t(e.instance.popper),w=parseFloat(y['margin'+f],10),E=parseFloat(y['border'+f+'Width'],10),v=b-e.offsets.popper[m]-w-E;return v=$(J(s[l]-u,v),0),e.arrowElement=i,e.offsets.arrow=(n={},ae(n,m,Q(v)),ae(n,h,''),n),e},element:'[x-arrow]'},flip:{order:600,enabled:!0,fn:function(e,t){if(W(e.instance.modifiers,'inner'))return e;if(e.flipped&&e.placement===e.originalPlacement)return e;var o=v(e.instance.popper,e.instance.reference,t.padding,t.boundariesElement,e.positionFixed),n=e.placement.split('-')[0],i=T(n),r=e.placement.split('-')[1]||'',p=[];switch(t.behavior){case he.FLIP:p=[n,i];break;case he.CLOCKWISE:p=z(n);break;case he.COUNTERCLOCKWISE:p=z(n,!0);break;default:p=t.behavior;}return p.forEach(function(s,d){if(n!==s||p.length===d+1)return e;n=e.placement.split('-')[0],i=T(n);var a=e.offsets.popper,l=e.offsets.reference,f=Z,m='left'===n&&f(a.right)>f(l.left)||'right'===n&&f(a.left)<f(l.right)||'top'===n&&f(a.bottom)>f(l.top)||'bottom'===n&&f(a.top)<f(l.bottom),h=f(a.left)<f(o.left),c=f(a.right)>f(o.right),g=f(a.top)<f(o.top),u=f(a.bottom)>f(o.bottom),b='left'===n&&h||'right'===n&&c||'top'===n&&g||'bottom'===n&&u,y=-1!==['top','bottom'].indexOf(n),w=!!t.flipVariations&&(y&&'start'===r&&h||y&&'end'===r&&c||!y&&'start'===r&&g||!y&&'end'===r&&u);(m||b||w)&&(e.flipped=!0,(m||b)&&(n=p[d+1]),w&&(r=G(r)),e.placement=n+(r?'-'+r:''),e.offsets.popper=le({},e.offsets.popper,C(e.instance.popper,e.offsets.reference,e.placement)),e=P(e.instance.modifiers,e,'flip'))}),e},behavior:'flip',padding:5,boundariesElement:'viewport'},inner:{order:700,enabled:!1,fn:function(e){var t=e.placement,o=t.split('-')[0],n=e.offsets,i=n.popper,r=n.reference,p=-1!==['left','right'].indexOf(o),s=-1===['top','left'].indexOf(o);return i[p?'left':'top']=r[o]-(s?i[p?'width':'height']:0),e.placement=T(t),e.offsets.popper=g(i),e}},hide:{order:800,enabled:!0,fn:function(e){if(!q(e.instance.modifiers,'hide','preventOverflow'))return e;var t=e.offsets.reference,o=D(e.instance.modifiers,function(e){return'preventOverflow'===e.name}).boundaries;if(t.bottom<o.top||t.left>o.right||t.top>o.bottom||t.right<o.left){if(!0===e.hide)return e;e.hide=!0,e.attributes['x-out-of-boundaries']=''}else{if(!1===e.hide)return e;e.hide=!1,e.attributes['x-out-of-boundaries']=!1}return e}},computeStyle:{order:850,enabled:!0,fn:function(e,t){var o=t.x,n=t.y,i=e.offsets.popper,r=D(e.instance.modifiers,function(e){return'applyStyle'===e.name}).gpuAcceleration;void 0!==r&&console.warn('WARNING: `gpuAcceleration` option moved to `computeStyle` modifier and will not be supported in future versions of Popper.js!');var s,d,a=void 0===r?t.gpuAcceleration:r,l=p(e.instance.popper),f=u(l),m={position:i.position},h={left:Z(i.left),top:Q(i.top),bottom:Q(i.bottom),right:Z(i.right)},c='bottom'===o?'top':'bottom',g='right'===n?'left':'right',b=B('transform');if(d='bottom'==c?-f.height+h.bottom:h.top,s='right'==g?-f.width+h.right:h.left,a&&b)m[b]='translate3d('+s+'px, '+d+'px, 0)',m[c]=0,m[g]=0,m.willChange='transform';else{var y='bottom'==c?-1:1,w='right'==g?-1:1;m[c]=d*y,m[g]=s*w,m.willChange=c+', '+g}var E={"x-placement":e.placement};return e.attributes=le({},E,e.attributes),e.styles=le({},m,e.styles),e.arrowStyles=le({},e.offsets.arrow,e.arrowStyles),e},gpuAcceleration:!0,x:'bottom',y:'right'},applyStyle:{order:900,enabled:!0,fn:function(e){return j(e.instance.popper,e.styles),K(e.instance.popper,e.attributes),e.arrowElement&&Object.keys(e.arrowStyles).length&&j(e.arrowElement,e.arrowStyles),e},onLoad:function(e,t,o,n,i){var r=L(i,t,e,o.positionFixed),p=O(o.placement,r,t,e,o.modifiers.flip.boundariesElement,o.modifiers.flip.padding);return t.setAttribute('x-placement',p),j(t,{position:o.positionFixed?'fixed':'absolute'}),o},gpuAcceleration:void 0}}},ce});
//# sourceMappingURL=popper.min.js.map
This diff is collapsed.
MYSQL_USER=rating
MYSQL_PASSWORD=rating_passwd
MYSQL_SERVER=db
MYSQL_DB=rating_db
/* password:password */
INSERT INTO user VALUES(1,'admin',NULL,'pbkdf2:sha256:50000$6Cc6Mjmo$3fe413a88db1bacfc4d617f7c1547bd1ea4cbd6c5d675a58e78332201f6befc6');
/* password:password */
INSERT INTO user VALUES(2,'editor',NULL,'pbkdf2:sha256:50000$Rq2WwVVi$12335e8d02fa3f25ffd11ba9f02fd1db7ca2964c5eaa13ca179a02ee3f19a656');
INSERT INTO research_group(id, name, tag, description) VALUES(1, 'Human Emotion Systems', 'emotion', 'Welcome to the Human Emotion Systems -laboratory`s Onni-net laboratory! The experiments that are currently underway are listed below - you can participate for as many experiments you want.');
INSERT INTO research_group(id, name, tag, description) VALUES(2, 'Turku Eye-tracking', 'eyelabs', 'Welcome to the Turku Eyelabs -laboratory`s Onni-net laboratory! The experiments that are currently underway are listed below - you can participate for as many experiments you want.');
INSERT INTO user_in_group VALUES (1,1, 'admin');
INSERT INTO user_in_group VALUES (2,1, 'editor');
[mysqld]
explicit_defaults_for_timestamp = 1
\ No newline at end of file
/*
SQL initialization script
Run: mysql -u rating -p -D rating_db < create_rating_db.sql
This will create user 'admin' with password 'password'.
*/
CREATE DATABASE IF NOT EXISTS rating_db;
USE rating_db;
GRANT ALL PRIVILEGES ON rating_db.* TO 'rating'@'%' WITH GRANT OPTION;
/* Drop all tables (cascade removes foreign keys also) */
DROP TABLE IF EXISTS background_question_answer;
DROP TABLE IF EXISTS background_question_option;
DROP TABLE IF EXISTS background_question;
DROP TABLE IF EXISTS forced_id;
DROP TABLE IF EXISTS user;
DROP TABLE IF EXISTS trial_randomization;
DROP TABLE IF EXISTS embody_answer;
DROP TABLE IF EXISTS embody_question;
DROP TABLE IF EXISTS answer;
DROP TABLE IF EXISTS answer_set;
DROP TABLE IF EXISTS question;
DROP TABLE IF EXISTS page;
DROP TABLE IF EXISTS experiment;
/* Experiment set */
CREATE TABLE experiment (
idexperiment INTEGER NOT NULL AUTO_INCREMENT,
name VARCHAR(120),
instruction TEXT,
directoryname VARCHAR(120),
language VARCHAR(120),
status VARCHAR(120),
randomization VARCHAR(120),
short_instruction TEXT,
single_sentence_instruction TEXT,
is_archived VARCHAR(120),
creator_name VARCHAR(120),
research_notification_filename VARCHAR(120),
creation_time DATETIME,
stimulus_size VARCHAR(120),
consent_text TEXT,
use_forced_id VARCHAR(120),
PRIMARY KEY (idexperiment)
);
/* Answer set holds session information about users experiment */
CREATE TABLE answer_set (
idanswer_set INTEGER NOT NULL AUTO_INCREMENT,
experiment_idexperiment INTEGER,
session VARCHAR(120),
agreement VARCHAR(120),
answer_counter INTEGER,
registration_time DATETIME,
last_answer_time DATETIME,
PRIMARY KEY (idanswer_set),
FOREIGN KEY(experiment_idexperiment) REFERENCES experiment (idexperiment)
);
/* Background questions are asked before the experiment begins */
CREATE TABLE background_question (
idbackground_question INTEGER NOT NULL AUTO_INCREMENT,
background_question VARCHAR(120),
experiment_idexperiment INTEGER,
PRIMARY KEY (idbackground_question)
);
CREATE TABLE background_question_option (
idbackground_question_option INTEGER NOT NULL AUTO_INCREMENT,
background_question_idbackground_question INTEGER,
`option` VARCHAR(120),
PRIMARY KEY (idbackground_question_option),
FOREIGN KEY(background_question_idbackground_question) REFERENCES background_question (idbackground_question)
);
CREATE TABLE background_question_answer (
idbackground_question_answer INTEGER NOT NULL AUTO_INCREMENT,
answer_set_idanswer_set INTEGER,
answer VARCHAR(120),
background_question_idbackground_question INTEGER,
PRIMARY KEY (idbackground_question_answer),
FOREIGN KEY(answer_set_idanswer_set) REFERENCES answer_set (idanswer_set),
FOREIGN KEY(background_question_idbackground_question) REFERENCES background_question (idbackground_question)
);
/* Randomize experiment page order */
CREATE TABLE trial_randomization (
idtrial_randomization INTEGER NOT NULL AUTO_INCREMENT,
page_idpage INTEGER,
randomized_idpage INTEGER,
answer_set_idanswer_set INTEGER,
experiment_idexperiment INTEGER,
PRIMARY KEY (idtrial_randomization)
);
CREATE TABLE user (
id INTEGER NOT NULL AUTO_INCREMENT,
username VARCHAR(64),
email VARCHAR(120),
password_hash VARCHAR(128),
PRIMARY KEY (id)
);
/* By using forced ID login subjects can only participate to a rating task by logging in with a pregenerated ID */
CREATE TABLE forced_id (
idforced_id INTEGER NOT NULL AUTO_INCREMENT,
experiment_idexperiment INTEGER,
pregenerated_id VARCHAR(120),
PRIMARY KEY (idforced_id),
FOREIGN KEY(experiment_idexperiment) REFERENCES experiment (idexperiment)
);
/* Information about stimulus type and content on a page */
CREATE TABLE page (
idpage INTEGER NOT NULL AUTO_INCREMENT,
experiment_idexperiment INTEGER,
type VARCHAR(120),
text VARCHAR(120),
media VARCHAR(120),
PRIMARY KEY (idpage),
FOREIGN KEY(experiment_idexperiment) REFERENCES experiment (idexperiment)
);
/* Slider question */
CREATE TABLE question (
idquestion INTEGER NOT NULL AUTO_INCREMENT,
experiment_idexperiment INTEGER,
question VARCHAR(120),
`left` VARCHAR(120),
`right` VARCHAR(120),
PRIMARY KEY (idquestion),
FOREIGN KEY(experiment_idexperiment) REFERENCES experiment (idexperiment)
);
/* Slider answer */
CREATE TABLE answer (
idanswer INTEGER NOT NULL AUTO_INCREMENT,
question_idquestion INTEGER,
answer_set_idanswer_set INTEGER,
answer VARCHAR(120),
page_idpage INTEGER,
PRIMARY KEY (idanswer),
FOREIGN KEY(answer_set_idanswer_set) REFERENCES answer_set (idanswer_set),
FOREIGN KEY(page_idpage) REFERENCES page (idpage),
FOREIGN KEY(question_idquestion) REFERENCES question (idquestion)
);
/* Create indexes for faster operations */
CREATE INDEX ix_experiment_consent_text ON experiment (consent_text(255));
CREATE INDEX ix_experiment_creation_time ON experiment (creation_time);
CREATE UNIQUE INDEX ix_experiment_directoryname ON experiment (directoryname);
CREATE INDEX ix_experiment_instruction ON experiment (instruction(255));
CREATE INDEX ix_experiment_name ON experiment (name);
CREATE INDEX ix_experiment_short_instruction ON experiment (short_instruction(255));
CREATE INDEX ix_experiment_single_sentence_instruction ON experiment (single_sentence_instruction(255));
CREATE UNIQUE INDEX ix_user_email ON user (email);
CREATE UNIQUE INDEX ix_user_username ON user (username);
CREATE INDEX ix_answer_set_last_answer_time ON answer_set (last_answer_time);
CREATE INDEX ix_answer_set_registration_time ON answer_set (registration_time);
CREATE INDEX ix_page_media ON page (media);
CREATE INDEX ix_page_text ON page (text);
CREATE INDEX ix_page_type ON page (type);
/* New fields for updating embody tool to onni.utu.fi */
/* Embody picture/question information */
CREATE TABLE embody_question (
idembody INTEGER NOT NULL AUTO_INCREMENT,
experiment_idexperiment INTEGER,
picture TEXT,
question TEXT,
PRIMARY KEY (idembody),
FOREIGN KEY(experiment_idexperiment) REFERENCES experiment (idexperiment)
);
/* Embody answer (coordinates). Answer is saved as a json object:
{x:[1,2,100,..], y:[3,4,101,..], r:[13,13,8,...]} */
CREATE TABLE embody_answer (
idanswer INTEGER NOT NULL AUTO_INCREMENT,
answer_set_idanswer_set INTEGER,
page_idpage INTEGER,
embody_question_idembody INTEGER DEFAULT 0,
coordinates TEXT,
PRIMARY KEY (idanswer),
FOREIGN KEY(answer_set_idanswer_set) REFERENCES answer_set (idanswer_set),
FOREIGN KEY(page_idpage) REFERENCES page (idpage) ,
FOREIGN KEY(embody_question_idembody) REFERENCES embody_question (idembody)
);
/* Set flag if embody tool is enabled -> this is not the most modular solution, but works for now */
ALTER TABLE experiment ADD COLUMN (embody_enabled BOOLEAN DEFAULT 0);
/* Set current answer type (embody/slider/etc..) so returning users are routed to correct question */
ALTER TABLE answer_set ADD COLUMN (answer_type VARCHAR(120));
ALTER TABLE experiment ADD COLUMN (group_id INTEGER), ADD FOREIGN KEY(group_id) REFERENCES research_group(id);
CREATE TABLE research_group (
id INTEGER NOT NULL AUTO_INCREMENT,
name TEXT,
tag TEXT,
description TEXT,
PRIMARY KEY (id)
);
CREATE TABLE user_in_group (
idgroup INTEGER,
iduser INTEGER,
role TEXT,
FOREIGN KEY(idgroup) REFERENCES research_group (id),
FOREIGN KEY(iduser) REFERENCES user (id)
);
upstream flask_app {
server gunicorn:8000 fail_timeout=5s max_fails=5;
}
server {
# NON-SSL
listen 80;
# SSL
#listen 443 ssl http2;
#listen [::]:443 ssl http2;
#ssl_certificate "/etc/nginx/tls/onni.utu.fi-rsa+chain.pem";
#ssl_certificate_key "/etc/nginx/tls/private/onni.utu.fi-rsa.key";
#ssl_protocols TLSv1.2;
#ssl_session_cache shared:SSL:1m;
#ssl_session_timeout 10m;
#ssl_ciphers HIGH:!aNULL:!MD5;
#ssl_prefer_server_ciphers on;
#server_name _;
client_max_body_size 0;
location / {
proxy_pass http://flask_app;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header Host $host;
proxy_redirect off;
proxy_read_timeout 30s;
}
location /create_embody {
#location /socket.io {
proxy_pass http://flask_app/socket.io;
proxy_http_version 1.1;
proxy_redirect off;
proxy_buffering off;
proxy_connect_timeout 1d;
proxy_send_timeout 1d;
proxy_read_timeout 1d;
proxy_set_header Host $host;
proxy_set_header X-Real-IP $remote_addr;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection "Upgrade";
}
error_page 404 /404.html;
location = /40x.html {
}
error_page 500 502 503 504 /50x.html;
location = /50x.html {
}
}
version: "3.3"
services:
nginx:
#image: nginx:latest
build: ./nginx
restart: always
ports:
- "80:80"
#- "443:443"
volumes:
#- ./tls:/etc/nginx/tls
#- ./config/nginx/rating.conf:/etc/nginx/conf.d/rating.conf
- ./log/nginx:/var/log/nginx
depends_on:
- gunicorn
gunicorn:
#image: rating_app:latest
build: ../.