2024 November 2 - We're making some improvements to clean up the configuration and code of Sigma and its associated projects. For existing installations, some changes are needed to stay in sync. OpenJDK is now supported, eliminating the dependency on Oracle JDK. Tomcat 9 is now required. A new environment variable SIGMA_CP is now required in your .bashrc (or similar for non-Linux). Please let us know if you have any issues!
To upgrade to Tomcat 9 and add the SIGMA_CP:
cd ~
echo "export SIGMA_CP=$SIGMA_SRC/build/sigmakee.jar:$SIGMA_SRC/lib/*" >> .bashrc
cd Programs
rm -r apache-tomcat-8.5.23/
wget 'https://archive.apache.org/dist/tomcat/tomcat-9/v9.0.97/bin/apache-tomcat-9.0.97.zip'
unzip apache-tomcat-9.0.97.zip
rm apache-tomcat-9.0.97.zip
cd ~/Programs/apache-tomcat-9.0.97/bin
chmod 777 *
cd ../webapps
chmod 777 *update CATALINA_HOME in your ~/.bashrc file
CATALINA_HOME=~/Programs/apache-tomcat-9.0.97Recompile sigmakee
cd ~/workspace/sigmakee/
antSigma is an integrated development environment for logical theories that extend the Suggested Upper Merged Ontology (SUMO). There is a public installation with read-only functions enabled linked from http://www.ontologyportal.org
Warning 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. Tomcat V9 is required. Later versions of Tomcat are not yet
supported. 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. 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 There is a video on installing Sigma, as well as many others about related tools at https://www.youtube.com/playlist?list=PLpBQIgki3izeUmFD8c65INdmxRNjjxOzP
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-ceThen get the docker image and run it
Pull with
sudo docker pull apease/sigmakee:latestRun with
sudo docker run -it -d -p 8080:8080 --name trial04 apease/sigmakee:latestAccess from a browser with http://localhost:8080/sigma/login.html . Use admin for username and admin for password
Warning Vagrant build is not maintained. Original vagrant files can be found in attic
Please note that the Docker container version of Sigma is several years out of date. A native install of Sigma is recommended.
To build a new docker container follow these steps where $SIGMA_SRC is your sigmakee git repo path.
First, download Linux/x64 from https://download.java.net/java/GA/jdk23/3c5b90190c68498b986a97f276efd28a/37/GPL/openjdk-23_linux-x64_bin.tar.gz
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: 2417Make sure that throughout the commands below that you replace "theuser" with your desired user name
create user theuser
sudo useradd theuseradd password for theuser
sudo passwd theuseradd to sudoers file
sudo usermod -aG sudo theuserswitch over to the new user
su theuser
cd /home
sudo mkdir theuser
sudo chown theuser theuser
cd theusermake sure you're running bash (and answer /bin/bash)
chshInstall unzip
sudo apt-get install unzip
sudo apt-get updateInstall git
sudo apt-get install gitInstall ant
sudo apt-get install antInstall make
sudo apt-get install makeInstall cmake
sudo apt-get install cmakeInstall gcc
sudo apt-get install gccInstall graphViz
sudo apt-get install graphvizUpdate apt-get
sudo add-apt-repository universe
sudo apt-get updatemay need to create a .bashrc
touch .bashrchandy 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/jdk-23" >> .bashrcload the definitions into your environment
source .bashrcthen you can add the last one
echo "export PATH=$PATH:$JAVA_HOME/bin" >> .bashrc
source .bashrcmkdir /home/theuser/Programs
cd ProgramsInstall a Java Development Kit (JDK) from OpenJDK, at least version 21 or greater. Avoid JDK 17
The following command line version may work but you may need to update the name of the jdk zipfile
wget https://download.java.net/java/GA/jdk23/3c5b90190c68498b986a97f276efd28a/37/GPL/openjdk-23_linux-x64_bin.tar.gz
gunzip openjdk-23_linux-x64_bin.tar.gzCopy the download link into this command. Then you need two commands to install the new Java (check that the paths conform to the java version you downloaded) -
sudo update-alternatives --install "/usr/bin/java" "java" "/home/theuser/Programs/jdk-23/bin/java" 1
sudo update-alternatives --set java /home/theuser/Programs/jdk-23/bin/javaVerify that it's installed correctly with
java -versionYou should see something like -
openjdk version "23" 2024-09-17
OpenJDK Runtime Environment (build 23+37-2369)
OpenJDK 64-Bit Server VM (build 23+37-2369, mixed mode, sharing)Verify that you see the same Java version when you startup Apache Tomcat that you do when you run java -version . It's also a good idea to run javac -version to verify that you have installed the full JDK and not just te JRE.
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="$HOST_TYPE:"PS1or on Vagrant, something like
PS1=Vagrant:$PS1First, comply with System preparation on Linux above
Clone SigmaKEE
git clone https://github.com/ontologyportal/sigmakeeThen,
cd sigmakeeant installThe following steps are now legacy. The call to ant install above will perform\ these steps more efficiently.
cd ~
mkdir workspace
mkdir Programs
cd Programs
wget 'https://archive.apache.org/dist/tomcat/tomcat-9/v9.0.97/bin/apache-tomcat-9.0.97.zip'
wget 'https://wordnetcode.princeton.edu/3.0/WordNet-3.0.tar.gz'
wget 'https://wwwlehre.dhbw-stuttgart.de/~sschulz/WORK/E_DOWNLOAD/V_2.0/E.tgz'
tar -xvzf E.tgz
unzip apache-tomcat-9.0.97.zip
rm apache-tomcat-9.0.97.zip
cd ~/Programs/apache-tomcat-9.0.97/bin
chmod 777 *
cd ../webapps
chmod 777 *
cd ~/workspace/
git clone https://github.com/ontologyportal/sigmakee
git clone https://github.com/ontologyportal/sumo
git clone https://github.com/ontologyportal/TPTP-ANTLR
git clone https://github.com/ontologyportal/SigmaUtils
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
./configure
make
make install
cd ~
echo "export SIGMA_HOME=~/.sigmakee" >> .bashrc
echo "export ONTOLOGYPORTAL_GIT=~/workspace" >> .bashrc
echo "export SIGMA_SRC=$ONTOLOGYPORTAL_GIT/sigmakee" >> .bashrc
echo "export CATALINA_OPTS=\"$CATALINA_OPTS -Xmx10g -Xss1m\"" >> .bashrc
echo "export CATALINA_HOME=~/Programs/apache-tomcat-9.0.97" >> .bashrc
echo "export PATH=$CATALINA_HOME/bin:$PATH" >> .bashrc
echo "export SIGMA_CP=$SIGMA_SRC/build/sigmakee.jar:$SIGMA_SRC/lib/*" >> .bashrc
source .bashrc
cd ~/workspace/sigmakee
antEnd legacy Linux install
To test run
java -Xmx10g -Xss1m -cp $SIGMA_CP \
com.articulate.sigma.KB -c Object TransactionStart Tomcat with
$CATALINA_HOME/bin/startup.shor simply
startup.shsince $CATALINA_HOME/bin is on your PATH
Point your browser at http://localhost:8080/sigma/login.html Default credentials are: admin/admin
Debugging
If you want to use Vampire instead of or in addition to E, follow these instructions. Please note that the command:
ant installwill also install Vampire
You may need to install the Zlib library if you don't have it already installed
sudo apt-get install libz-devand also possibly
sudo apt-get install g++then execute the following:
cd $ONTOLOGYPORTAL_GIT
git clone https://github.com/vprover/vampire
cd vampire
make vampire_rel
mv vampire_rel_master* vampireYou'll then need to edit your config.xml file to point to the vampire executable. Add the line
<preference name="vampire" value="/home/theuser/workspace/vampire/vampire" />editing the path to conform to your system
If you want to use Vampire with options different from Avatar or the latest CASC strategy, for example, an older CASC strategy, you can set an environment variable, as in the assignment below, being sure to terminate with -t for the timeout
VAMPIRE_OPTS="--mode portfolio --avatar off -qa answer_literal --schedule casc_2019 --proof tptp -t"See INSTALL.MacOS
Open up CMD prompt
wsl –install
.bashrc already existed in home directory. Did not update path.
echo "alias dir='ls --color=auto --format=vertical -la'" >> .bashrc
Manually changed with "nano .bashrc" HISTSIZE=10000 and HISTFILESIZE=100000
mkdir /home/theuser/Programs
cd Programs
sudo apt-get install openjdk-23-jdk
(This step might not be necessary, I'd try without it first) echo "export JAVA_HOME=/usr/lib/jvm/java-23-openjdk-amd64/jre" >> .bashrcFollow Linux install instructions on:
https://github.com/ontologyportal/sigmakeeModify the following files, replace "theuser" with your username
me="$(whoami)"
sed -i "s/theuser/$me/g" ~/workspace/sigmakee/config.xml
sed -i "s/theuser/$me/g" ~/workspace/sigmakee/test/unit/java/resources/config_all.xml
sed -i "s/theuser/$me/g" ~/workspace/sigmakee/test/unit/java/resources/config_topAndMid.xml
sed -i "s/theuser/$me/g" ~/workspace/sigmakee/test/integration/java/resources/config_all.xml
sed -i "s/theuser/$me/g" ~/workspace/sigmakee/test/integration/java/resources/config_topAndMid.xml
sed -i "s/theuser/$me/g" ~/workspace/sigmakee/test/integration/java/resources/config_topOnly.xmlIf 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" />java -Xmx10g -Xss1m -cp $SIGMA_CP:\
$SIGMA_SRC/build/test/classes \
org.junit.runner.JUnitCore \
com.articulate.sigma.UnitTestSuiteone test method at a time can be run with help from the SingleJUnitTestRunner class, for example
java -Xmx10g -Xss1m -cp $SIGMA_CP:\
$SIGMA_SRC/build/test/classes \
com.articulate.sigma.SingleJUnitTestRunner \
com.articulate.sigma.KbIntegrationTest#testIsChildOf3You 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
see the SigmaRest project - https://github.com/ontologyportal/SigmaRest
make sure you have python3
python --versionmake sure you have pip or install with
sudo apt install python3-pipinstall the py4j module
pip3 install py4jCompile SigmaKEE then run with
java -Xmx10g -Xss1m -cp $SIGMA_CP com.articulate.sigma.KBmanager -pthen start python
user@user-machine:~/workspace/sigmakee$ 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
Create the account database with
java -Xmx4g -cp $SIGMA_CP com.articulate.sigma.PasswordService -cThen create the administrator account and password
java -Xmx4g -cp $SIGMA_CP com.articulate.sigma.PasswordService -aYou 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 lib/h2-2.3.232.jar -webAllowOthers -tcpAllowOthersand you'll need to change JDBCstring in PasswordService.java to your path instead of /home/apease and recompile
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/
Define a nbproject/private/private.properties file with these keys:
# private properties\ javaapis.dir=${user.home}/javaapis\ workspace=${javaapis.dir}/INSAFE
# The default installation space is: ~/workspace. However, it can be anywhere on\ # your system as long as you define the "workspace" key above.
catalina.home=${path.to.your.tomcat9}
private.resources.dir=nbproject/private/resources\ main.config=${private.resources.dir}/config.xml\ integration.config=${private.resources.dir}/config_topAndMid.xml\ unit.config=${private.resources.dir}/config_topOnly.xml
# The above properties allow you to keep and restore the various forms of\ # config.xml that get overwritten when running Unit Tests. Copy these files\ # to the respective "resources" directory complete with your personal system\ # paths replacing the "/home/theuser/" pseudos. config.xml is found in the\ # base directory and the other two are found in test/*/resources directories
# JavaMail properties\ user=${your.email.user.name}\ my.email=${user}@${your.email.domain}\ my.name=${your.name}
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.