Introduction
============

Sigma is an integrated development environment for logical theories that
extend the Suggested Upper Merged Ontology.  There is a public installation
with read-only functions enabled linked from http://www.ontologyportal.org

The easiest install is with the Docker container system.  The next section below
describes how to do this.

Please read these notes thoroughly if you want to do a native install not
with a container.  Most installation issues result from not
carefully following the instructions.

You can follow the steps below to do a manual installation on linux or Mac. This
procedure assumes that you start from your home directory and are happy with
having directories created there. The sed command below attempts to modify
~/.sigmakee/KBs/config.xml to conform to your local paths.  If your paths
differ, then you may need to edit your config.xml manually. If you are running
tomcat on vagrant or another VM, you may need to change the port value from 8080.
If you are running on a server, rather than your localhost you'll need to set
the hostname parameter in your config.xml file. E will only work if your $TMPDIR
is set correctly.  No particular version of tomcat is required. If you load a
different version of tomcat, be sure to change $CATALINA_HOME and your paths to
conform to the version. If you use a different mirror or version you'll need to
change the wget commend below and Oracle Java appears to now have a key embedded
in their URL that will change every time. Change "theuser" below to your user name.

If your installation isn't working and you're getting funny "null"s in your paths
try opening permissions on your $SIGMA_HOME, $CATALINA_HOME and $SIGMA_SRC directories.

After installing, recommended reading is the Sigma manual
https://github.com/ontologyportal/sigmakee/blob/master/doc/manual/SigmaManual.pdf

Container-Based installation
==========================

First, install docker if you don't have it already

sudo apt-get update
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
sudo add-apt-repository \
   "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
   $(lsb_release -cs) \
   stable"
sudo apt-get update
sudo apt-get install docker-ce

Then get the docker image and run it

Pull with
sudo docker pull apease/sigmakee2018:latest

Run with
sudo docker run -it -d -p 8080:8080 --name trial04 apease/sigmakee2018:latest "./sigmastart.sh"

Access from a browser with http://localhost:8080/sigma/login.html . Use admin for username and admin for password


Vagrant Virtual Machine installation
==========================

If you want an additional level of system independence and security, you can also
run the docker image in a virtual machine.  For Vagrant you would do the following -

Install it if you haven't already -

sudo apt-get install vagrant

then get a virtual machine image -

vagrant box add ubuntu/xenial64
vagrant init ubuntu/xenial64

You'll need to add two commands to the Vagrantfile configuration

config.vm.network "forwarded_port", guest: 8080, host: 8888
config.vm.provider "virtualbox" do |vb|
  vb.memory = "9000"
end

Then execute the following

vagrant up
vagrant ssh

then

Access from a browser with http://localhost:8888/sigma/login.html . Use admin for username and admin for password


Build a New Docker Image
=========================

To build a new docker container follow these steps where $SIGMA_SRC is your sigmakee git repo path.
First, download jdk-8u171-linux-x64.rpm from http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
Note that if you don't download that exact version, you'll need to edit sigmastart.sh so that the filename
matches.  You'll also need to make changes to track the latest Tomcat, in the bashrc and Dockerfile

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
sudo add-apt-repository \
   "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
   $(lsb_release -cs) \
   stable"
sudo apt-get update
sudo apt-get install docker-ce
mkdir images
cd images
cp $SIGMA_SRC/docker/* .
sudo docker build -t sigmakee2018:latest .

to push the image to dockerhub

>:~/images$ sudo docker login
Login with your Docker ID to push and pull images from Docker Hub. If you don't have a Docker ID, head over to https://hub.docker.com to create one.
Username (apease):
Password:
Login Succeeded

>:~/images$ sudo docker ps
CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS                    NAMES
1f7d0cef7874        51a041125329        "./sigmastart.sh"   56 minutes ago      Up 56 minutes       0.0.0.0:4000->8080/tcp   trial11
>:~/images$ sudo docker tag 51a041125329 apease/sigmakee2018:latest
>:~/images$ sudo docker push apease/sigmakee2018:latest
The push refers to a repository [docker.io/apease/sigmakee2018]
ab5e94769be7: Pushed
1c15947f83dc: Pushed
c2007c9776df: Pushed
829ef5b0378d: Pushed
6fd852e99bda: Pushed
85c7d96adccb: Pushed
6b2f14c09222: Pushed
9a9a3d9cc4bc: Pushed
38c81b36edfb: Pushed
bcc97fbfc9e1: Pushed
latest: digest: sha256:xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx size: 2417


System preparation on Linux
==========================
Make sure that throughout the commands below that you replace "theuser" with your desired user name

create user theuser
  sudo useradd theuser

add password for theuser
  sudo passwd theuser

add to sudoers file
  sudo usermod -aG sudo theuser

switch over to the new user
  su theuser
  cd /home
  sudo mkdir theuser
  sudo chown theuser theuser
  cd theuser

install unzip
  sudo apt-get install unzip
  sudo apt-get update

may need to create a .bashrc
  touch .bashrc

handy to add stuff to .bashrc
  echo "alias dir='ls --color=auto --format=vertical -la'" >> .bashrc
  echo "export HISTSIZE=10000 HISTFILESIZE=100000" >> .bashrc
  echo "export JAVA_HOME=/home/theuser/Programs/jdk1.8.0_112" >> .bashrc

load the definitions into your environment

  source .bashrc

then you can add the last one

  echo "export PATH=$PATH:$JAVA_HOME/bin" >> .bashrc

  source .bashrc

You may need to download Java and set your
JAVA_HOME http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html .  First,

  mkdir /home/theuser/Programs
  cd Programs

The following command line version may work but you may need to update the name of the jdk zipfile

wget --no-check-certificate -c --header "Cookie: oraclelicense=accept-securebackup-cookie"
  https://download.oracle.com/otn-pub/java/jdk/14.0.1+7/664493ef4a6946b186ff29eb326336a2/jdk-14.0.1_linux-x64_bin.tar.gz
  gunzip jdk-14.0.1_linux-x64_bin.tar.gz

but you also may need to go to the web site, accept the license, then copy the download link
into this command

On AWS it helps to be reminded of which server you're on.  I use machine size as a reminder with

export HOST_TYPE=`curl http://169.254.169.254/latest/meta-data/instance-type`
PS1="$HOST_TYPE:"PS1

or on Vagrant, something like

PS1=Vagrant:$PS1


Linux Installation
==================

mkdir workspace
mkdir Programs
cd Programs
wget 'https://archive.apache.org/dist/tomcat/tomcat-8/v8.5.23/bin/apache-tomcat-8.5.23.zip'
wget 'http://wordnetcode.princeton.edu/3.0/WordNet-3.0.tar.gz'
wget 'http://wwwlehre.dhbw-stuttgart.de/~sschulz/WORK/E_DOWNLOAD/V_2.0/E.tgz'
tar -xvzf E.tgz
unzip apache-tomcat-8.5.23.zip
rm apache-tomcat-8.5.23.zip
cd ~/Programs/apache-tomcat-8.5.23/bin
chmod 777 *
cd ../webapps
chmod 777 *
cd ~/workspace/
sudo apt-get install git
git clone https://github.com/ontologyportal/sigmakee
git clone https://github.com/ontologyportal/sumo
cd ~
mkdir .sigmakee
cd .sigmakee
mkdir KBs
cp -R ~/workspace/sumo/* KBs
me="$(whoami)"
cp ~/workspace/sigmakee/config.xml ~/.sigmakee/KBs
sed -i "s/theuser/$me/g" KBs/config.xml
cd ~/Programs
gunzip WordNet-3.0.tar.gz
tar -xvf WordNet-3.0.tar
cp WordNet-3.0/dict/* ~/.sigmakee/KBs/WordNetMappings/
cd ~/Programs/E
sudo apt-get install make
sudo apt-get install gcc
./configure
make
make install
cd ~
sudo apt-get install graphviz
echo "export SIGMA_HOME=~/.sigmakee" >> .bashrc
echo "export SIGMA_SRC=~/workspace/sigmakee" >> .bashrc
echo "export ONTOLOGYPORTAL_GIT=~/workspace" >> .bashrc
echo "export CATALINA_OPTS=\"$CATALINA_OPTS -Xms500M -Xmx7g\"" >> .bashrc
echo "export CATALINA_HOME=~/Programs/apache-tomcat-8.5.23" >> .bashrc
source .bashrc
cd ~/workspace/sigmakee
sudo add-apt-repository universe
sudo apt-get update
sudo apt-get install ant
ant

Follow the steps in section "Account Management" below to set up accounts

To test run

  java  -Xmx7g -classpath /home/theuser/workspace/sigmakee/build/classes:/home/theuser/workspace/sigmakee/build/lib/*
    com.articulate.sigma.KB


Start Tomcat with
  $CATALINA_HOME/bin/startup.sh

Point your browser at http://localhost:8080/sigma/login.html


Debugging

- If login.html redirects you to init.jsp that means the system is still initializing. Wait a minute or two and try
again.
- If you are on mac and getting errors related to not finding jars when running com.articulate.sigma.KB, copy all jars
from /home/theuser/workspace/sigmakee/build/lib/ to /Library/Java/Extensions


Vampire
==================
If you want to use Vampire instead of or in addition to E, follow these instructions.
You may need to install the Zlib library if you don't have it already installed

 sudo apt-get install libz-dev

and also possibly

  sudo apt-get install g++

then execute the following:

  cd $ONTOLOGYPORTAL_GIT
  git clone https://github.com/vprover/vampire
  cd vampire
  make vampire_rel
  mv vampire_rel_master* vampire

You'll then need to edit your config.xml file to point to the vampire executable.  Add the line

  <preference name="vampire" value="/home/theuser/workspace/vampire/vampire" />

editing the path to conform to your system


MacOS install notes
===================

See INSTALL.MacOS


jEdit Integration (optional)
============================

If you install jEdit (see http://jedit.org) and configure Sigma properly, you can click on a source
file and line number for a statement in the Sigma Browse page and be taken to
the editor, open on that line.  By default, the edit feature will make use of your $ONTOLOGYPORTAL_GIT
environment variable, and try to open the file in that location in the "sumo" module. Recommended practice
is to edit .kif files in your local Git repository and then copy them to the .sigmakee/KBs directory. If
you wish to edit in a different location, either a different repository or a different directory altogether,
the you can set the editDir configuration variable in your config.xml file, for example

  <preference name="editDir" value="/home/user/workspace/myproject" />

If you wish to install jEdit so that there's no path to it, for example on a shared machine as a user-specific
program, you'll need to set a path in config.xml, for example

  <preference name="jedit" value="/home/user/jedit/jedit" />


jUnit testing on the command line
=================================

java  -Xmx4g -classpath
  ~/workspace/sigmakee/build/classes:~/workspace/sigmakee/build/lib/*
  org.junit.runner.JUnitCore com.articulate.sigma.UnitTestSuite

one test method at a time can be run with help from the SingleJUnitTestRunner class,
for example

java -Xmx4g -classpath /home/apease/workspace/sigmakee/build/classes:
  /home/apease/workspace/sigmakee/build/lib/* com.articulate.sigma.SingleJUnitTestRunner
  com.articulate.sigma.KbIntegrationTest#testIsChildOf3

You will have to edit the resources files that correspond to config.xml to conform to your
paths.  They are in test/integration/java/resources/config*.xml and test/unit/java/resources/config*.xml

RESTful Interface
================

see the SigmaRest project - https://github.com/ontologyportal/SigmaRest


python Interface
================

make sure you have python3

python --version

make sure you have pip or install with

sudo apt install python3-pip

install the py4j module

pip3 install py4j

Compile SigmaKEE then run with

java -Xmx7g -cp $SIGMA_SRC/build/classes:$SIGMA_SRC/build/lib/* com.articulate.sigma.KBmanager -p

then start python

user@user-machine:~/workspace/sigmakee$ python3
Python 3.8.2 (default, Jul 16 2020, 14:00:26)
[GCC 9.3.0] on linux

Type "help", "copyright", "credits" or "license" for more information.
>>> from py4j.java_gateway import JavaGateway
>>> gateway = JavaGateway()
>>> sigma_app = gateway.entry_point
>>> print(sigma_app.getTerms())

set([u'-1', u'-3', u'-6', u'-7235', u'.5', u'<=>', u'=>', u'AAA-Rating', u'AAM', u'AAV', u'ABPFn', u'ABTest', u'ACPowerSource', ...

Look at com.articulate.sigma.KBmanager.pythonServer() to expose the API of more classes
than just com.articulate.sigma.KB


Account Management
======================

Please note this is not working as of Apr, 2020.

Create the account database with

java -Xmx5G -cp $SIGMA_SRC/build/classes:$SIGMA_SRC/build/lib/* com.articulate.sigma.PasswordService -c

Then create the administrator account and password

java -Xmx5G -cp $SIGMA_SRC/build/classes:$SIGMA_SRC/build/lib/* com.articulate.sigma.PasswordService -a

You can use Sigma without being administrator, but you'll have limited use of its functionality.

You'll also need to set a few parameters in your config.xml file

  <preference name="dbUser" value="sa" />
  <preference name="loadFresh" value="false" />

To handle the account registration feature, you'll need to have an email account and supply the
password in the .bashrc file where your Sigma installation is runnning.  Gmail might be convenient
for this.  Change the password "my_pass" to your password on Gmail (or other service that you specify)

export SIGMA_EMAIL_PASS="my_pass"
export SIGMA_EMAIL_SERVER="smtp.gmail.com"

There are three types of user roles: "guest", "user" and "admin".  Guests are users who have not
registered.  They can access read-only functions that are not computationally expensive.
Registered users are granted access to computationally more expensive features.  Admin users
have access to all Sigma functions.  Currently, this control is hard coded into the JSP pages
that will check for user roles.  At some point in the future this may be changed to a more flexible
scheme of access rights driven from a file or database mapping roles to allowed functions.

You'll need to start the database server with

 java -jar h2-1.4.197.jar -webAllowOthers -tcpAllowOthers

and you'll need to change JDBCstring in PasswordService.java to your path instead of /home/apease
and recompile


Old Installation Notes
======================

Install via script from source on Linux or Mac OS with
bash <(curl -L https://raw.githubusercontent.com/ontologyportal/sigmakee/master/install.sh)

Note that you need to enter the entire statement above, including calling "bash".

Users should also see

https://sourceforge.net/p/sigmakee/wiki/required_data_files/
Mac instructions - https://sourceforge.net/p/sigmakee/wiki/Sigma%20Setup%20on%20Mac/ 
Ubuntu - https://sourceforge.net/p/sigmakee/wiki/Setting%20up%20Sigma%20on%20Ubuntu/

You can also install Sigma on a Vagrant virtual machine.  You'll need VirtualBox too
https://www.virtualbox.org/

> mkdir sigma_vagrant
> cd sigma_vagrant
> wget https://raw.githubusercontent.com/ontologyportal/sigmakee/master/Vagrantfile
> vagrant up
> vagrant ssh
> bash <(curl -L https://raw.githubusercontent.com/ontologyportal/sigmakee/master/install-vagrant.sh)

follow the prompts and Sigma will be running.  Then on the browser of your host machine, go to
http://localhost:9090/sigma/login.html

To run natural language interpretation from the command line in the virtual machine,
run the following additional steps

> cd ~
> mkdir Programs
> cd Programs
> cp /vagrant/Downloads/stanford-corenlp-full-2018-01-31.zip .
> unzip stanford-corenlp-full-2018-01-31.zip
> cd stanford-corenlp-full-2018-01-31
> export SIGMA_HOME="/home/vagrant/.sigmakee"
> jar -xf stanford-corenlp-3.9.0-models.jar
> cd ~/Programs/stanford-corenlp-full-2018-01-31
> java  -Xmx2500m -classpath  /home/vagrant/workspace/sigma/sigma/build/classes:/home/vagrant/workspace/sigma/sigma/build/lib/*  com.articulate.sigma.semRewrite.Interpreter -i


User Interface
=====================

There's not enough documentation on Sigma so I'm starting a bit here in preparation for a real
manual.

Sigma has a number of functions controlled through its JSP-based interface.  

AddConstituent.jsp - adds a constituent SUO-KIF file to a knowledge base.  Accessible only to
admin users.  It just responds to a command from another page and has no UI of its own.
Redirects back to KBs.jsp when done.

AllPictures.jsp - shows all the pictures linked to a term at once.  Accessible to all users.

ApproveUser.jsp - handles approving a new user.  Accessible only to admin users. Redirects
to KB.jsp once acknowledge.

AskTell.jsp - interface to the local theorem provers. Accessible only to admin users. This function
has not been well maintained and the interfaces to SystemOnTPTP and LEO-II may be out of date.

BrowseBody.jsp - shows terms, axioms, lexicon links, etc

BrowseExtra.jsp - includes Prelude.jsp and Postlude.jsp

BrowseHeader.jsp - primary ontology browser controls including term and word search, as well as
the menu for selecting natural language and formal language

Browse.jsp - top level browsing JSP that includes Prelude.jsp, BrowseHeader.jsp, BrowseBody.jsp
and Postlude.jsp.  Really just a shell for the included JSPs

CCheck.jsp - interface to KBmanager.initiateCCheck() that initiates consistency checking of a KB.
Handles selection of which theorem prover to use, and several parameters.  Includes Prelude.jsp
and Postlude.jsp

CELT.jsp - Obsolete.  Handles invocation of the Controlled English to Logic Translation system,
which is now superceded by the Semantic Rewriting approach in the sigmanlp project.

CreateUser.jsp - handles a request from a user to create an account.  Creates a guest account
and sends mail to the moderator for approval.  Has no UI.

Diag.jsp - Interface to run tests in Diagnostics.java.  Depends on Prelude.jsp and Postlude.jsp.
Accessible for "admin" and "user" but not unregistered guest users

EditFile.jsp - Obsolete

EditStmt.jsp - Obsolete

Graph.jsp - Create graphs of binary relationships as a graphical view and as indented text.
Relies on Prelude.jsp and Postlude.jsp

InferenceTestSuite.jsp - run a suite of inference tests with the prover and parameters selected.
Depends on Prelude.jsp and Postlude.jsp.  Accessible only for admin users.

init.jsp - A status page with periodic automatic refresh to catch requests to Sigma during the
process of initialization.

InstFiller.jsp - Page to allow simple editing of ground formulas.  Deprecated.  Accessible only
for admin users. Depends on Prelude.jsp and Postlude.jsp.

Intersect.jsp - Find appearances of two or more terms in the same axiom.  Depends on
Prelude.jsp and Postlude.jsp.

KBs.jsp - Main entry point for creating or selecting a knowledge base.  Some functions are
available for "admin" or "user" roles but not "guest". Depends on Prelude.jsp and Postlude.jsp.

login.html - login page for Sigma that handles existing accounts and new account registration.
Existing accounts are dispatched to login.jsp and registrations are dispatched to
Registration.jsp

login.jsp - handle the login process by using PasswordService.jsp to validate a login against
an H2 database of account info.  This page has no UI.

Manifest.jsp - UI for handling loading and saving KB constituents including saving in various
exportable formats, such as OWL. Depends on Prelude.jsp and Postlude.jsp. Most functionality
is limited to admin users.

Mapping.jsp - Use some simple string matching approaches to suggest equivalences between terms
in two files.  Depends on Prelude.jsp and Postlude.jsp. Access limited to admin users.

MiscUtilities.jsp - Depends on Prelude.jsp and Postlude.jsp. Most functionality
is limited to admin users. Little utilities to generate dot graph files and OWL versions of
the Open Multilingual Wordnet content.

ModeratorApproval.jsp - Functionality is limited to admin users. Dispatches to ApproveUser.jsp
when user clicks "ok".

OMW.jsp - Display results from the many languages in Open Multilingual Wordnet linked to
WordNet synsets. Depends on Prelude.jsp and Postlude.jsp.

OWL.jsp - Display all the axioms for a given term in OWL format, if expressible in that
language.

Postlude.jsp - Encapsulates footing information displayed on most pages.

Prelude.jsp - Encapsulates header information displayed on most pages.

ProcessFile.jsp - No UI. Called from MiscUtilities.jsp to generate KIF from other
formats. Calls DocGen.dataFileToKifFile() to do the real work. Depends on Prelude.jsp and
Postlude.jsp. Access limited to admin users.

Properties.jsp - An interface for setting many of Sigma's parameters.  Some of these are
also accessible from the browsing interface, such as the language for the natural
language paraphrases. Depends on Prelude.jsp and Postlude.jsp. Access limited to admin users.

Register.jsp - An interface to allow people to submit a request for registration and
priviledges beyond that of unregistered guest users.  Calls on CreateUser.jsp

Save.jsp - not used

SimpleBrowseBody.jsp - Analogue to BrowseBody.jsp but showing only simple axioms in a simple
and non-technical language

SimpleBrowseHeader.jsp - Analogue to BrowseHeader.jsp for simple axioms

SimpleBrowse.jsp - Analogue to Browse.jsp for simple axioms

SystemOnTPTP.jsp - Interface to the SystemOnTPTP system hosted as U. Miami that collects
dozens of theorem provers with a common programmatic interface.  This code has not been
maintained so use at your own risk. Depends on Prelude.jsp and Postlude.jsp. Access
limited to admin users.

TreeView.jsp - A simple tree view of the taxonomic structure of the ontology with collapsable
nodes.  Uses the SimpleBrowse.jsp code to display axioms for any node in the taxonomy.

WNDiag.jsp - Diagnostics for WordNet. Depends on Prelude.jsp and Postlude.jsp. Accessible
for "admin" and "user" but not unregistered guest users.

WordNet.jsp - show synsets and SUMO-WordNet mappings for a word. Depends on Prelude.jsp
and Postlude.jsp.

WordSenseFile.jsp - show word sense disambiguation and sentiment analysis results for a
file of text.  Calls WordNet.wn.sumoFileDisplay() for the real work. Depends on
Prelude.jsp and Postlude.jsp.

WordSense.jsp - show word sense disambiguation and sentiment analysis results for a
sentence.  Calls WordNet.wn.sumoSentenceDisplay() for the real work. Depends on
Prelude.jsp and Postlude.jsp.