README.md · Haozhe Xie/mitagger

Medical Image Tagger
=====================

The project is designed for Harvard Medical School. Users can put some tags for an medical image within the system.

[![Build Status](https://travis-ci.org/zjhzxhz/mitagger.png?branch=master)](https://travis-ci.org/zjhzxhz/mitagger)

----------

Installation Guide
---------

> **NOTE:**
> 
> - We're going to assume that you have installed Python 2.7 and MySQL 5.x on your computer.

#### Install Django

> **NOTE:**
> Python 2.7 required

1. Install `pip`
   
   For Unbuntu/Mint Users:
   ```
   apt-get install python-pip
   ```

Or you can get standalone [pip installer](http://www.pip-installer.org/en/latest/installing.html#using-the-installer).

2. Install Django using `pip`

For users who has installed `pip`
   
   ```
   pip install django==1.7.6
   ```
   Or you can install Django manually.

> **Tip:** Know more information on install Django at https://docs.djangoproject.com/en/1.6/intro/install/

#### Set up MITagger
1. Open `mitagger/settings.py`.
2. Edit your database configuration at line 59.

#### Set up Database
1. To connect MySQL in Python, we need install `mysql-python` first.
   You can install it using `pip`:

```
   pip install mysql-python
   ```
   
   > **Tip:** If you get error message like this: `EnvironmentError: mysql_config not found`. 
   
   > **Reference:** http://stackoverflow.com/questions/7475223/mysql-config-not-found-when-installing-mysqldb-python-interface

2. Create database named `mitagger` in MySQL.
3. Use following command to create tables in the database:
   
   ```
   cd /path/to/the/app
   python manage.py syncdb
   ```

#### Install Additional Package
1. Install libtiff to Convert tiff to jpg

For Ubuntu/Mint Users:
   ```
   apt-get install libtiff5 libtiff5-dev
   pip install --upgrade setuptools
   pip install --upgrade pip
   pip install numpy
   pip install -e svn+http://pylibtiff.googlecode.com/svn/trunk/
   ```
2. Install Wand to Convert tiff to jpg

For Ubuntu/Mint Users:
   ```
   apt-get install libmagickwand-dev
   pip install Wand
   ```

3. Install NLTK to process natural language

For Ubuntu/Mint Users:
   ```
   apt-get install libyaml-dev
   pip install nltk
   ```

4. Download NLTK Data
   
   ```
   python 
   >>> import nltk 
   >>> nltk.download() 
   # Press d to start downloading 
   >>> d 
   # Type all to download all packages 
   >>> all 
   ```

5. Install Elasticsearch

For Ubuntu/Mint Users:
   Elasticsearch is running on Java, if you don't have a JRE on your machine, please install one.
   
   For example, We use OpenJDK7:
   ```
   apt-get install openjdk-7-jre
   ```
   
   Download and install the Public Signing Key
   ```
   wget -qO - http://packages.elasticsearch.org/GPG-KEY-elasticsearch | sudo apt-key add -
   ```
   
   Add the following to your /etc/apt/sources.list to enable the repository
   ```
   deb http://packages.elasticsearch.org/elasticsearch/1.3/debian stable main
   ```
   
   Run apt-get update and the repository is ready for use. You can install it with :
   ```
   apt-get install elasticsearch
   ```

For RHEL/CentOS Users:
   Download and install the Public Signing Key
   ```
   rpm --import http://packages.elasticsearch.org/GPG-KEY-elasticsearch
   ```
   Add the following in your /etc/yum.repos.d/ directory in a file named (for example) elasticsearch.repo
   ```
   [elasticsearch-1.3]
   name=Elasticsearch repository for 1.3.x packages
   baseurl=http://packages.elasticsearch.org/elasticsearch/1.3/centos
   gpgcheck=1
   gpgkey=http://packages.elasticsearch.org/GPG-KEY-elasticsearch
   enabled=1
   ```
   
   And your repository is ready for use. You can install it with :
   ```
   yum install elasticsearch
   ```

Install Elasticsearch bind for python:
   ```
   pip install elasticsearch
   ```

#### Start Server
1. If you want to use this application on a production site, use Apache with mod_wsgi. 
   > **Tip**: Get more information at https://docs.djangoproject.com/en/1.6/howto/deployment/wsgi/modwsgi/

2. If you just want to experiment with this application, just use following command:
   
   ```
   python manage.py runserver
   ```
   If you will get following output,
   ```
   May 14, 2014 - 04:50:57
   Django version 1.6.4, using settings 'mitagger.settings'
   Starting development server at http://127.0.0.1:8000/
   Quit the server with CONTROL-C.
   ```
   The application is deployed successfully. And you can use the application by visit http://127.0.0.1:8000 in web browser.

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