Merge pull request #71 from RaulKite/master

Rapid Annotator Installation Guide With docker compose

Dockerfile

@@ -0,0 +1,28 @@
+## Dockerfile for RapidAnnotator 2.0
+## Raúl Sánchez <[email protected]>
+
+FROM ubuntu:18.04
+
+LABEL maintainer="Raúl Sánchez <[email protected]>"
+LABEL version="0.1"
+
+# Install dependencies
+WORKDIR /var/www/rapidannotator
+
+COPY . /var/www/rapidannotator
+COPY docker_files/rapidannotator_httpd.conf /etc/apache2/conf-enabled/rapidannotator.conf
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update  && apt-get install -y apache2 python3-pip libapache2-mod-wsgi-py3 default-libmysqlclient-dev vim net-tools default-mysql-client \
+                    && pip3 install --upgrade pip && pip3 install numpy && pip3 install -r requirements.txt 
+RUN cp docker_files/wsgi_template_docker.py wsgi.py \
+    && cp docker_files/config_template_docker.py rapidannotator/config.py && mkdir /videos && chmod 777 /videos && sed -i '1 i\Listen 8000' /etc/apache2/ports.conf
+
+
+VOLUME [ "/videos" ]
+
+EXPOSE 8000
+
+# Docker start apache2 in foreground
+CMD ["apachectl", "-D", "FOREGROUND"]

README.md

@@ -27,6 +27,7 @@ Red Hen’s Rapid Annotator provides a platform to users to annotate large chunk
 ## Installation and User Guide
 Please refer the following links to install the Rapid Annotator-2.0 .
 * For installation guide refer [here](https://github.com/RedHenLab/RapidAnnotator-2.0/blob/master/docs/installation_guide.md).
+* For Docker installation guide refer [here](https://github.com/RedHenLab/RapidAnnotator-2.0/blob/master/docs/installation_guide_docker.md).
 * For user guide refer [here](https://github.com/RedHenLab/RapidAnnotator-2.0/blob/master/docs/user_guide.md).
 
 ## Contributers from Google Summer of Code

docker-compose.yaml

@@ -0,0 +1,23 @@
+# Docker compose for RapidAnnotator
+# Raúl Sánchez <[email protected]>
+
+version: '3'
+
+services:
+  rapidannotator:
+    build: .
+    hostname: labyrinth01.inf.um.es
+    ports:
+      # external 80 port mapped to internal 8000 port
+      - "8888:8000"
+    depends_on:
+      - db
+
+  db:
+    image: mysql:8.0
+    environment:
+      MYSQL_ROOT_PASSWORD: root
+      MYSQL_DATABASE: rapidannotator
+      MYSQL_USER: rapidannotator
+      MYSQL_PASSWORD: rapidannotator
+

docker_files/config_template_docker.py

@@ -0,0 +1,34 @@
+# All variables should be uppercase
+# For sending Mails to the users TESTING should be False in DevlopmentConfig Class
+# UPLOAD_FOLDER path must be raw string
+
+class BaseConfig(object):
+    DEBUG = False
+    TESTING = False
+    SQLALCHEMY_ECHO = False
+    SQLALCHEMY_DATABASE_URI = 'mysql://rapidannotator:rapidannotator@db/rapidannotator'
+    SECRET_KEY = "sldjfhals13 2hhdwflkjdhfa"
+    SECURITY_PASSWORD_SALT = "SOME SECURITY SALT like abcdefre"
+    WTF_CSRF_ENABLED = True
+    CSRF_ENABLED = True
+    UPLOAD_FOLDER = r'/videos'
+    SQLALCHEMY_TRACK_MODIFICATIONS = False
+
+    # mail settings
+    MAIL_SERVER = 'smtp.xxx.xxx'
+    MAIL_PORT = 465
+    MAIL_USE_TLS = False
+    MAIL_USE_SSL = True
+
+    # gmail authentication
+    MAIL_USERNAME = "[email protected]"
+    MAIL_PASSWORD = "xxxxxxxx"
+
+    # mail accounts
+    MAIL_DEFAULT_SENDER = "[email protected]"
+
+class DevelopmentConfig(BaseConfig):
+    DEBUG = True
+    TESTING = False
+    SQLALCHEMY_ECHO = True
+    LOGIN_DISABLED = False

docker_files/rapidannotator_httpd.conf

@@ -0,0 +1,11 @@
+<VirtualHost *:8000>
+
+    WSGIScriptAlias / /var/www/rapidannotator/wsgi.py
+
+    <Directory /var/www/rapidannotator>
+
+      Require all granted
+
+    </Directory>
+
+</VirtualHost>

docker_files/wsgi_template_docker.py

@@ -0,0 +1,9 @@
+''' Delete the lines 2, 3 and 4 if you are not using virtualenv else uncomment it'''
+# activate_this = '[Path_to_virtual_environment]/bin/activate_this.py'
+# with open(activate_this) as file_:
+#    exec(file_.read(), dict(__file__=activate_this))
+
+import sys
+sys.path.insert(0, '/var/www/rapidannotator')
+
+from rapidannotator import app as application

docs/installation_guide_docker.md

@@ -0,0 +1,28 @@
+# Rapid Annotator Installation Guide With docker compose
+
+## Clone the repository
+
+```
+git clone https://github.com/RedHenLab/RapidAnnotator-2.0.git
+
+```
+
+## Edit config file
+
+Edit the file `docker_files/config_template_docker.py` to configure mail settings and key
+
+
+## Build and run the container
+
+```
+docker-compose build
+docker-compose up
+```
+
+Connect to http://localhost:8888
+
+> **Warning**
+> Use this installation method only for testing pourposes
+> It isn't fully secured. No SSL/TLS certificates. 
+> Database Access user/password in docker-compose.yaml file
+