README.md

e3

Introduction

This repository is for the command line wrapper e3 of the EulerX toolkit. The EulerX toolkit developed by the EulerProject team allows to solve the taxonomy alignment problem ("tap") [1, 2]. Here we created a wrapper around the EulerX toolkit to achieve the following benefits.

Benefits

• Use of e3 as an interactive shell, or directly in scripts
• Use of modular commands with single responsiblities
• Ability to refine taxonomy alignment problems on-the-go
• Reduced exposure to certain expert options
• Reduced knowledge of the EulerX life-cycle
• Reduced exposure to EulerX generated output data
• Re-use of existing computation results in "projects"

Demo

Configuration

Tap naming and refinement on-the-go

Command-Manual

Miscellaneous Commands

Command	Description
exit	Exit e3.
help	Shows this help.
reset	Resets to factory settings.
clear	Clears the history and cache. Keeps the configuration and style settings.
show history	Shows the html rendered history.
clear history	Clears the history.
print config	Prints the configuration settings.
set config <parameter>=<value>	Sets the configuration <parameter> with <value>.
reset config	Resets the configuration to default.
print style	Prints the style settings.
set style <parameterPath>=<value>	Sets the style parameter with (e.g. aggregate/graphstyle/legend) with .
reset style	Resets the style to default.
git credentials <host> <username> "<password>"	Sets the <username> and <password> for the git <host>.
git pull <path>	Clones or pulls an e3_data workspace from the <path> at the configured git repository.
git push <path> <message>	Commits (with <message>) and pushes the e3_data workspace to the <path> at the configured git repository.
git state pull <path>	Clones or pulls the e3 state from the <path> at the configured git repository.
git state push <path> <message>	Commits (with <message> and pushes the e3 state to the <path> at the configured git repository.

Tap Commands

Command	Description
print tap [<tap>]	Prints the current tap, or the optionally provided <tap>
print taxonomies [<tap>]	Prints the taxonomies of the current tap, or the optionally provided <tap>.
print articulations [<tap>]	Prints the articulations of the current tap, or the optionally provided <tap>.
add taxonomy <taxonomyId> <taxonomyName> [<tap>]	Adds a taxonomy with <taxonomyId> and <taxonomyName> to the current tap, or the optionally provided <tap>.
remove taxonomy <taxonomyId> [<tap>]	Removes the taxonomy with <taxonomyId> and all referencing articulations from the current tap, or the optionally provided <tap>.
set taxonomy info <oldTaxonomyId> <newTaxonomyId> <newTaxonomyName> [<tap>]	Sets the <newTaxonomyid> and <newTaxonomyName> to the taxonomy with <oldTaxonomyId> of the current tap, or the optionally provided <tap>.
add concepts <taxonomyId> (<parentConcepts> <childConcept 1> ... <childConcept n>) [<tap>]	Adds set of <childConcept> to <parentConcept>, creating non-existing concept's as needed to the taxonomy with <taxonomyId> of the current tap, or the optionally provided <tap>.
remove concepts <recursive> <taxonomyId> (<parentConcepts> <childConcept 1> ... <childConcept n>) [<tap>]	Removes set of <childConcept> from <parentConcept> in the taxonomy with <taxonomyId> of the current tap, or the optionally provided <tap>.
rename concept <taxonomyId> <oldName> <newName> [<tap>]	Renames the concept in taxonomy with <taxonomyId> from <oldName> to <newName> for the current tap, or the optionally provided <tap>.
clear taxonomy <taxonomyId> [<tap>]	Clears the taxonomy with <taxonomyId> of the current tap, or the optionally provided <tap>.
add articulation <articulation> [<tap>]	Adds <articulation> to the current tap, or the optionally provided <tap>.
remove articulation <articulation_index|articulation> [<tap>]	Removes articulation with index <articulation_index> or string <articulation> from the current tap, or the optionally provided <tap>.
clear articulations [<tap>]	Clears the articulations of the current tap, or the optionally provided <tap>.
set sibling disjointness <true|false> [<tap>]	Sets the sibling disjointness for the current tap, or the optionally provided <tap>.
set coverage <true|false> [<tap>]	Sets the coverage for the current tap, or the optionally provided <tap>.
set regions <mnpw|mncb|mnve|vrpw|vrve> [<tap>]	Sets the regions for the current tap, or the optionally provided <tap>.
load tap <cleantax file>	Loads a tap from the <cleantax file>.
clear tap	Sets the empty tap as the current tap.
print names	Shows all stored names and their corresponding taps.
name tap <name> [<tap>]	Names the current tap, or the optionally provided <tap> as <name>.
use tap <tap>	Makes <tap> the current tap.

Euler Commands

Command	Description
graph tap [<tap>]	Creates a graph visualization of the current tap, or the optionally provided <tap>.
is consistent [<tap>]	Checks the consistency of the current tap, or the optionally provided <tap>.
is unique [<tap>]	Checks if there is a unique world for the current tap, or the optionally provided <tap>.
is ambiguous [<tap>]	Checks if there is more than 1 world for the current tap, or the optionally provided <tap>.
is true <articulation> [<tap>]	Checks if the articulation holds true for the current tap, or the optionally provided <tap>.
more than <count> worlds [<tap>]	Checks if there are more than <count> number of worlds in the current tap, or the optionally provided <tap>.
graph worlds [<maxWorlds>] [<tap>]	Creates graph visualizations of the worlds, if any exist, and if provided maximally <maxWorlds> for the current tap, or the optionally provided <tap>.
print worlds [<maxWorlds>] [<tap>]	Prints the worlds, if any exist, and if provided maximally <maxWorlds> for the current tap, or the optionally provided <tap>.
use world [<worldId>] [<tap>]	Replaces the articulations of the current tap or the optionally provided <tap> with all the articulations extracted from the given <worldId> or the unique world of the tap, if applicable and no <worldId> is given.
print minimal articulations [<tap>]	Prints minimal sets articulations for the unique world of the current tap, or the optionally provided <tap>.
use minimal articulations <minimal articulation set id> [<tap>]	Replaces the articulations of the current tap or the optionally provided <tap> with the articulations of the given <minimal articulation set id>.
print maximal articulations [<tap>]	Prints maximal sets of articulations for all worlds of the current tap, or the optionally provided <tap>.
use maximal articulations <maximal articulation set id> [<tap>]	Replaces the articulations of the current tap or the optionally provided <tap> with the articulations of the given <maximal articulation set id>.
graph ambiguity [<tap>]	Creates an ambiguity visualization of the current tap, or the optionally provided <tap>.
graph summary [<tap>]	Creates a summary visualization of the current tap, or the optionally provided <tap>.
graph four in one [<tap>]	Creates a four-in-one visualization of the current tap, or the optionally provided <tap>.
print minimal uniqueness [<tap>]	Prints the minimal subsets of articulations that create uniqueness for the current tap, or the optionally provided <tap>.
use minimal uniqueness <set id> [<tap>]	Replaces the articulations of the current tap or the optionally provided <tap> with the articulations of the given minimal uniqueness <set id>.
print minimal inconsistency [<tap>]	Prints the minimal subsets of articulations that create inconsistency for the current tap, or the optionally provided <tap>.
use minimal inconsistency <set id> [<tap>]	Replaces the articulations of the current tap or the optionally provided <tap> with the articulations of the given minimal inconsistency <set id>.
print maximal consistency [<tap>]	Prints the maximal subsets of articulations that create consistency for the current tap, or the optionally provided <tap>.
use maximal consistency <set id> [<tap>]	Replaces the articulations of the current tap or the optionally provided <tap> with the articulations of the given maximal consistency <set id>.
print maximal ambiguity [<tap>]	Prints the maximal subsets of articulations that create ambiguity for the current tap, or the optionally provided <tap>.
use maximal ambiguity <set id> [<tap>]	Replaces the articulations of the current tap or the optionally provided <tap> with the articulations of the given maximal ambiguity <set id>.
graph [<full|reduced>] inconsistency [<tap>]	Creates a graph visualization of the inconsistency, if any exists, for the current tap, or the optionally provided <tap>.
print fix [<tap>]	Prints a set of suggested fixes of the inconsistency, if any exists, for the current tap, or the optionally provided <tap>.
use fix <fix set id> [<tap>]	Uses the fix with <fix set id> to create a consistent input from the current tap, or the optionally provided <tap>.
create tap from worlds <tap_1> ... <tap_n>	Creates a tap with the unique worlds of <tap_1> ... <tap_n> as taxonomies.

Prerequisites

• Python 2.7.x
• Python modules:
  • autologging
  • pinject
  • pyyaml
  • networkx
  • gitpython
  • python-numpy
  • matplotlib
  • beautifulsoup4
  • html5lib
  • ruamel.yaml
• EulerX

Setup

• Setup preqrequistis
• Clone this repository
• Run e3
• If euler2 is not in your $PATH, do:
  • e3 > set config euler2Executable = <your_path_to_EulerX_src-el>/euler2

File organization

e3 workspace:

Directory	Description
$CWD/e3_data	e3 workspace files.
$CWD/e3_data/index.html	Command history as browsable HTML.
$CWD/e3_data/{tap}/index.html	{tap} as browsable HTML.
$CWD/e3_data/{tap}/input.txt	{tap} as cleantax file.
$CWD/e3_data/{tap}/{command}/config.txt	Configuration at the time of {command} execution on {tap}.
$CWD/e3_data/{tap}/{command}/*	Output files created by {command} execution on {tap}.

e3 state:

Directory	Description
$CWD/.e3	e3 state files
$CWD/.e3/config	stores the configuration settings
$CWD/.e3/current_tap	stores the current tap
$CWD/.e3/history	stores the command history
$CWD/.e3/names	stores the tap to name mappings
$CWD/.e3/style	stores style settings
$CWD/.e3/taps	stores taps and computed reasoning data