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Sigma Knowledge Engineering Environment
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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. 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 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 = "5000" 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 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 ========================== create user theuser useradd theuser add password for theuser passwd theuser add to sudoers file usermod -aG sudo 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 echo "export PATH=$PATH:$JAVA_HOME/bin" >> .bashrc You may need to download Java and set your JAVA_HOME http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html . The following command line version may work wget --no-check-certificate --no-cookies --header "Cookie: oraclelicense=accept-securebackup-cookie" http://download.oracle.com/otn-pub/java/jdk/8u112-b15/jdk-8u112-linux-x64.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="$HOST_TYPE:"PS1 Linux Installation ================== mkdir workspace mkdir Programs cd Programs wget 'http://ftp.wayne.edu/apache/tomcat/tomcat-8/v8.5.23/bin/apache-tomcat-8.5.23.zip' wget 'http://wordnetcode.princeton.edu/3.0/WordNet-3.0.tar.gz' wget 'http://wwwlehre.dhbw-stuttgart.de/~sschulz/WORK/E_DOWNLOAD/V_2.0/E.tgz' tar -xvzf E.tgz unzip apache-tomcat-8.5.23.zip rm apache-tomcat-8.5.23.zip cd ~/Programs/apache-tomcat-8.5.23/bin chmod 777 * cd ~/workspace/ sudo apt-get install git git clone https://github.com/ontologyportal/sigmakee git clone https://github.com/ontologyportal/sumo cd ~ mkdir .sigmakee cd .sigmakee mkdir KBs cp -R ~/workspace/sumo/* KBs me="$(whoami)" cp ~/workspace/sigmakee/config.xml ~/.sigmakee/KBs sed -i "s/theuser/$me/g" KBs/config.xml cd ~/Programs gunzip WordNet-3.0.tar.gz tar -xvf WordNet-3.0.tar cp WordNet-3.0/dict/* ~/.sigmakee/KBs/WordNetMappings/ cd ~/Programs/E sudo apt-get install make sudo apt-get install gcc ./configure make make install cd ~ sudo apt-get install graphviz echo "export SIGMA_HOME=~/.sigmakee" >> .bashrc echo "export ONTOLOGYPORTAL_GIT=~/workspace" >> .bashrc echo "export CATALINA_OPTS=\"$CATALINA_OPTS -Xms500M -Xmx2500M\"" >> .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 -Xmx2500m -classpath ~/workspace/sigmakee/build/classes:/home/theuser/workspace/sigmakee/build/lib/* com.articulate.sigma.KB Start Tomcat with $CATALINA_HOME/bin/startup.sh Point your browser at http://localhost:8080/sigma/login.html Debugging - If login.html redirects you to init.jsp that means the system is still initializing. Wait a minute or two and try again. - If you are on mac and getting errors related to not finding jars when running com.articulate.sigma.KB, copy all jars from /home/theuser/workspace/sigmakee/build/lib/ to /Library/Java/Extensions Apple install notes =================== use "curl -o filename URL" if you don't have wget installed java will be installed in /usr/libexec/java_home get git from the xcode tools - "xcode-select --install" instead of .bashrc edit .bash_profile install Homebrew from http://brew.sh mkdir workspace mkdir Programs cd Programs curl -O 'http://www-us.apache.org/dist/tomcat/tomcat-8/v8.5.23/bin/apache-tomcat-8.5.23.zip' curl -O 'http://wordnetcode.princeton.edu/3.0/WordNet-3.0.tar.gz' curl -O 'http://wwwlehre.dhbw-stuttgart.de/~sschulz/WORK/E_DOWNLOAD/V_2.0/E.tgz' tar -xvzf E.tgz unzip apache-tomcat-8.5.23.zip rm apache-tomcat-8.5.23.zip cd ~/Programs/apache-tomcat-8.5.23/bin chmod 777 * cd ~/workspace/ sudo apt-get install git git clone https://github.com/ontologyportal/sigmakee git clone https://github.com/ontologyportal/sumo cd ~ mkdir .sigmakee cd .sigmakee mkdir KBs cp -R ~/workspace/sumo/* KBs me="$(whoami)" cp ~/workspace/sigmakee/config.xml ~/.sigmakee/KBs sed -i "s/theuser/$me/g" config.xml cd ~/Programs gunzip WordNet-3.0.tar.gz tar -xvf WordNet-3.0.tar cp WordNet-3.0/dict/* ~/.sigmakee/KBs/WordNetMappings/ cd ~/Programs/E brew install make brew install gcc ./configure make make install cd ~ brew install graphviz echo "export SIGMA_HOME=~/.sigmakee" >> .bash_profile echo "export ONTOLOGYPORTAL_GIT=~/workspace" >> .bash_profile echo "export CATALINA_OPTS=\"$CATALINA_OPTS -Xms500M -Xmx2500M\"" >> .bash_profile echo "export CATALINA_HOME=~/Programs/apache-tomcat-8.5.23" >> .bash_profile source .bash_profile cd ~/workspace/sigmakee brew install ant ant Follow the steps in section "Account Management" below to set up accounts To test run java -Xmx2500m -classpath ~/workspace/sigmakee/build/classes:~/workspace/sigmakee/build/lib/* com.articulate.sigma.KB Start Tomcat with $CATALINA_HOME/bin/startup.sh Point your browser at http://localhost:8080/sigma/login.html Debugging - If login.html redirects you to init.jsp that means the system is still initializing. Wait a minute or two and try again. - If you are on mac and getting errors related to not finding jars when running com.articulate.sigma.KB, copy all jars from ~/workspace/sigmakee/build/lib/ to /Library/Java/Extensions jUnit testing on the command line ================================= java -Xmx4g -classpath ~/workspace/sigmakee/build/classes:~/workspace/sigmakee/build/lib/* org.junit.runner.JUnitCore com.articulate.sigma.UnitTestSuite one test method at a time can be run with help from the SingleJUnitTestRunner class, for example java -Xmx4g -classpath /home/apease/workspace/sigmakee/build/classes: /home/apease/workspace/sigmakee/build/lib/* com.articulate.sigma.SingleJUnitTestRunner com.articulate.sigma.KbIntegrationTest#testIsChildOf3 RESTful Interface ================ see the SigmaRest project - https://github.com/ontologyportal/SigmaRest python Interface ================ Compile SigmaKEE then run with user@user-machine:~/workspace/sigmakee$ python Python 2.7.12 (default, Nov 19 2016, 06:48:10) [GCC 5.4.0 20160609] on linux2 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 ====================== 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. 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.