Euler is an open source toolkit (mostly written in Python) for merging taxonomies (taxonomical organized datasets) and visualizing the results. See Euler Toolkit Wiki for more information.

We have all the EulerFO source code, EulerASP source code, and a bunch of use cases in this toolkit. EulerFO is a modified version of CleanTax which was firstly developed by Dave Thau. CleanTax/EulerFO are built upon Prover9/Mace4 reasoning software. EulerASP is a brand new taxonomy reasoning tool that Mingmin built from scratch. EulerASP is built based on popular ASP reasoners DLV and Potassco. This readme page is mainly focusing on the use of EulerASP.

Euler is designed for UNIX-like operating systems (Linux, Mac, etc). If you are running on Windows, you need to install a virtual machine to run Euler.

Before using Euler/X, you need to download it from this git repo. You can first check the installation of git.

$ git —-version

If you are a first-time user for git, please download and install it [http://git-scm.com/downloads/].

The latest version is v2.0. Download it from the release page.

To use the development version, which has the latest code, clone the master branch:

$ git clone -b master https://github.com/EulerProject/EulerX.git

Euler/X is written in Python, so it requires Python2.X or later installed in your computer.

$ python --version
Python 2.7.8

Installation of Python2 can be found at [https://www.python.org/downloads/].

Euler/X use either DLV or Clingo as underlining reasoner. Please install them and make sure they are in your PATH:

$ dlv --version
DLV [build BEN/Dec 17 2012   gcc 4.2.1 (Apple Inc. build 5666) (dot 3)]

usage: dlv {FRONTEND} {OPTIONS} [filename [filename [...]]]

Specify -help for more detailed usage information.


$ clingo -v
clingo version 5.2.0
Address model: 64-bit

libgringo version 5.2.0
Configuration: without Python, with Lua 5.3.4

libclasp version 3.3.0 (libpotassco version 1.0.0)
Configuration: WITH_THREADS=1
Copyright (C) Benjamin Kaufmann

License: The MIT License <https://opensource.org/licenses/MIT>

To install DLV, please use the version static no ODBC support from DLV download page. To install Clingo, please use the version 5.2.0. Note: You do not need to install all to use Euler/X, either DLV or Clingo will do the job.

All knowledge products generated by Euler/X use Graphviz for rendering visualizations, to check the installation of it:

$ dot -V
dot - graphviz version 2.36.0 (20140111.2315)

Installation of Graphviz can be found at [http://www.graphviz.org/].

The Euler/X command line interface 2.0 use python module docopt as the parser generator. Use pip to install it:

$ pip install docopt==0.6.1

Installation of pip can be found at [https://pip.pypa.io/en/latest/installing.html]. To get more about docopt, please check [http://docopt.org/].

Euler/X use python module yaml for representing graph and stylesheet files. Install it by pip:

$ pip install pyyaml

See other installation methods here.

Please run installCheck.sh and make sure the minimal dependency check passes before running this toolkit. Make sure all commands of running softwares before and main entry of source code (e.g. src-el/ of EulerASP) are in your PATH env. Note: Prover9/Mace4 is not necessary to install if you do not want to use EulerFO.

Use example abstract4

List all usage commands.

$ euler2 -h

Check the validity of input file, including “multiple roots per taxonomy”, “multiple parents per child”, “unmatched leaves (leaves that are not involved in any articulations)”.

$ euler2 check abstract4.txt

The main task for Euler/X, you can suggest the encoding method, the reasoning tool, options to switch on/off coverage and sibling disjointness, et al.

$ euler2 align abstract4.txt

TO show the input visualization of the last run (the same as the following show commands), need to do “euler2 align” first. The result will be in 0-Input/ folder.

$ euler2 show iv

The result will be in 4-PWs/ folder

$ euler2 show pw

The result will be in 5-Aggregates/ folder

$ euler2 show sv

Still under example/ directory (assuming src-el/ is in your PATH env, and gringo, claspD, dlv in your PATH env),

0. euler -h or euler --help wil give you the options that you have
1. euler -i example/abstract4.txt -e vr, you will get all the mir relations in the generated output file using binary encoding.
2. euler -i example/abstract4.txt -e vrpw, you will get all the possible worlds in the console using binary encoding.
3. euler -i example/abstract4.txt -e vrve, you will get all the valid euler regions in the console using binary encoding.
4. euler -i example/abstract4.txt -e mn, you will get all the mir relations in the generated output file using polynomial encoding.
5. euler -i example/abstract4.txt -e mnpw, you will get all the possible worlds in the console using polynomial encoding.
6. euler -i example/abstract4.txt -e mnve, you will get all the valid euler regions in the console using polynomial encoding.

Here are examples under example/ directory,

1. cd to example/ directory
2. run ./test.sh, you will find the output files in output/test/
3. ./runct.sh abstract, you will find the output files in output/abstract/
4. ./runct.sh abstract2, you will find the output files in output/abstract2/
5. ./runct.sh abstract3, you will find the output files in output/abstract3/
6. ./runct.sh abstract3b, you will find the output files in output/abstract3b/, it is the "Bertram" mode for abstract3.
7. ./runct.sh abstract2c, you will find the output files in output/abstract2c/, it is the test case with articulation confidence for abstract2.

If you have any question or comments, please contact Bertram Ludäscher at ludaesch@illinois.edu.