PyGMQL

API for calling interactively the GMQL Engine from Python

Documentation

The doucumentation can be found at the following link: http://pygmql.readthedocs.io

Examples

In the examples folder are available the Notebooks and the scripts to reproduce the analysis presented in the manuscript.

Docker image

If you want to run some of the examples provided in the example folder you can directly install the PyGMQL docker image.

docker pull gecopolimi/pygmql

You can run the docker instance using the following command:

docker run --rm \
           --name pygmql_instance \
           -p <port>:8888 \
           gecopolimi/pygmql

where you can set <port> to any free port number on your machine. This will start a Jupyter Lab server which will run at the address

https://localhost:<port>

Inside the docker you will find the example folder containing both notebooks and scripts.

Get in touch

You can ask questions or provide some feedback through our Gitter channel.

Requirements

The library requires the following:

• Python 3.4+
• The latest version of JAVA installed
• The JAVA_HOME variable set to the Java installation folder (example: C:\Program Files\Java\jdk1.8.0_161 or ~/jdk1.8.0_161)

Installation

From github

First of all download this repository in a choosen location:

git clone https://github.com/DEIB-GECO/PyGMQL.git

Than go inside the library folder and install the package as follows:

cd PyGMQL
pip install -e .

From PyPi

pip install gmql

Setup

Use Anaconda

We suggest to manage your python distribution through Anaconda. The latest version of can be downloaded from https://www.continuum.io/downloads.

Once your Anaconda distribution is installed, let's create a brand new environment:

conda create --name pygmql python=3

Check if JAVA is installed

Check that the JAVA_HOME enviroment variable is correctly set to the latest JAVA distribution.

echo $JAVA_HOME

If the variable is not set (the previous command does not show nothing), you may need to install JAVA (https://www.java.com/it/download/) and then set JAVA_HOME like the following:

On linux:

echo export "JAVA_HOME=/path/to/java" >> ~/.bash_profile
source ~/.bash_profile

On Mac:

echo export "JAVA_HOME=\$(/usr/libexec/java_home)" >> ~/.bash_profile
source ~/.bash_profile

On Windows:

1. Right click My Computer and select Properties.
2. On the Advanced tab, select Environment Variables, and then edit JAVA_HOME to point to where the JDK software is located, for example, C:\Program Files\Java\jdk1.6.0_02.

Use it in Jupyter Notebooks

We strongly suggest to use the library with the support of a Jupyter Notebook for the best graphical rendering of the data structures. It may be necessary to manually install the Jupyter kernel:

source activate pygmql
python -m ipykernel install --user --name pygmql --display-name "Python (pygmql)"

Keep the code updated

This is a constantly evolving project. Therefore the library will be constantly added with new features. Therefore we suggest to update your local copy periodically:

cd PyGMQL
git pull