Merge pull request #136 from terry-norbraten/master

2 bug fixes

.github/workflows/ant.yml

@@ -28,14 +28,12 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: 'ontologyportal/TPTP-ANTLR'
-#          repository: 'terry-norbraten/TPTP-ANTLR'
           path: TPTP-ANTLR
 
       - name: checkout SigmaUtils
         uses: actions/checkout@v4
         with:
           repository: 'ontologyportal/SigmaUtils'
-#          repository: 'terry-norbraten/SigmaUtils'
           path: SigmaUtils
 
       - name: checkout sumo
@@ -177,12 +175,12 @@ jobs:
         uses: docker/setup-buildx-action@v3
 
       - name: Download artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v4.1.7
         with:
           name: artifact
 
       - name: Download artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v4.1.7
         with:
           name: sigma-webapp
 

CONTRIBUTING.md

@@ -4,14 +4,14 @@ By participating in this project, you agree to abide by the [code of conduct](#c
 
 ## Issues
 
-One of the easiest ways to contribute is to solve an issue https://github.com/ontologyportal/sigmakee/issues 
+One of the easiest ways to contribute is to solve an issue https://github.com/ontologyportal/sigmakee/issues
 
 ## Additions
 
 * We use jUnit for testing.  When making any addition of functionality, please add some jUnit tests to
 show that it works and prevent regressions.
 * adhere to the Java style guide for Sigma - https://github.com/ontologyportal/sigmakee/blob/master/CodeFormat.pdf
-* if the functionality requires a GUI, add a .jsp interface copying and modifying and existing JSP in Sigma
+* if the functionality requires a GUI, add a .jsp interface copying and modifying an existing JSP in Sigma
 * if the functionality can be meaningfully executed on the command line, add
 to the main() for the class, following the style of an existing class like com.articulate.sigma.KB
 with its showHelp() method so it functions like a standard Unix command with a man page
@@ -36,39 +36,39 @@ in the README https://github.com/ontologyportal/sigmakee/blob/master/README.txt)
 
 ## Code of conduct
 
-In order to foster an inclusive, kind, harassment-free, and cooperative community, 
+In order to foster an inclusive, kind, harassment-free, and cooperative community,
 we enforce this code of conduct on our open source projects.
 
 ### Summary
 
-Harassment in code and discussion or violation of physical boundaries is completely 
-unacceptable anywhere in our project. Violators will be warned by the core team. 
-Repeat violations will result in being blocked or banned by the core team at or 
+Harassment in code and discussion or violation of physical boundaries is completely
+unacceptable anywhere in our project. Violators will be warned by the core team.
+Repeat violations will result in being blocked or banned by the core team at or
 before the 3rd violation.
 
 ### In detail
 
-Harassment includes offensive verbal comments related to gender identity, 
-gender expression, sexual orientation, disability, physical appearance, body size, 
-race, religion, sexual images, deliberate intimidation, stalking, sustained 
+Harassment includes offensive verbal comments related to gender identity,
+gender expression, sexual orientation, disability, physical appearance, body size,
+race, religion, sexual images, deliberate intimidation, stalking, sustained
 disruption, and unwelcome sexual attention.
 
 Individuals asked to stop any harassing behavior are expected to comply immediately.
 
 Maintainers are also subject to the anti-harassment policy.
 
-If anyone engages in harassing behavior, including maintainers, we may take 
-appropriate action, up to and including warning the offender, deletion of 
-comments, removal from the project’s codebase and communication systems, 
+If anyone engages in harassing behavior, including maintainers, we may take
+appropriate action, up to and including warning the offender, deletion of
+comments, removal from the project’s codebase and communication systems,
 and escalation to GitHub support.
 
-If you are being harassed, notice that someone else is being harassed, or 
+If you are being harassed, notice that someone else is being harassed, or
 have any other concerns, please contact us immediately
 
 We expect everyone to follow these rules anywhere in our project.
 
-Finally, don't forget that it is human to make mistakes! We all do. Let’s 
-work together to help each other, resolve issues, and learn from the mistakes 
+Finally, don't forget that it is human to make mistakes! We all do. Let’s
+work together to help each other, resolve issues, and learn from the mistakes
 that we will all inevitably make from time to time.
 
 ### Thanks

INSTALL.MacOS

@@ -1,7 +1,7 @@
 Running the SigmaKEE docker image on macOS
 ==========================================
 
-With homebrew:
+With Homebrew:
 brew install --cask docker <- will install the latest Docker Desktop for macOS
 
 then:
@@ -24,7 +24,7 @@ macOS install notes
   Homebrew.
 - java will be installed in /usr/libexec/java_home
 - get git from the xcode tools with "xcode-select --install”
-- instead of .bashrc edit .bash_profile
+- instead of ~/.bash_profile edit ~/.zshrc
 - install Homebrew from http://brew.sh and the packages:
 
 brew install make
@@ -33,14 +33,15 @@ brew install git
 brew install graphviz
 brew install ant
 
-Add the following lines in your .profile and make sure to have all
-these variables created before the next step, and replace /Users/user with your home directory:
+Add the following lines in your ~/.zshrc and make sure to have all
+these variables created before the next step, and replace
+/Users/user with your home directory:
 
   ## SUMO/SIGMAKEE
   export SIGMA_HOME=/Users/user/.sigmakee
   export ONTOLOGYPORTAL_GIT=/Users/user/workspace
   export SIGMA_SRC=$ONTOLOGYPORTAL_GIT/sigmakee
-  export CATALINA_OPTS="-Xmx10g"
+  export CATALINA_OPTS="-Xmx10g -Xss1m"
   export CATALINA_HOME=/Users/user/Programs/apache-tomcat-9.0.96
   export PATH=$CATALINA_HOME/bin:$PATH
   export SIGMA_CP=$SIGMA_SRC/build/sigmakee.jar:$SIGMA_SRC/lib/*
@@ -56,11 +57,11 @@ You will need at least Java 11+ to compile SigmaKee and to run Apache Tomcat.
 
   /usr/libexec/java_home --verbose
 
-# Find your JDK (arm64) path and copy it (choose the one with the /JavaVirtualMachines/ instead of /Internet Plug-Ins/)
+# Find your JDK (arm64 or x64) path and copy it (choose the one with the /JavaVirtualMachines/ instead of /Internet Plug-Ins/)
 
   export JAVA_HOME= 'path from before', then make sure "bin" is on our PATH
 
-  export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home
+  export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-23.jdk/Contents/Home
   export PATH=$JAVA_HOME/bin:$PATH
 
 cd ~
@@ -110,6 +111,9 @@ May have to precede the last command with "sudo"
 cp ~/workspace/sigmakee/config.xml ~/.sigmakee/KBs
 (SOS) edit the config.xml changing all `wrong paths` to the value of `$HOME` and adapting all variables)
 
+For Homebrew installations of GraphViz, change the path in config.xml for
+graphVizDir to: /usr/local/bin
+
 cd ~/workspace/sigmakee
 source ~/.zshrc or ~/.bash_profile
 ant

README.md

@@ -21,9 +21,10 @@ 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 $TMPDIR
-is set correctly.  Tomcat V9 or later is required. Be sure to change `$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.
+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.
@@ -163,7 +164,7 @@ handy to add stuff to .bashrc
 ```sh
 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-11.0.2" >> .bashrc
+echo "export JAVA_HOME=/home/theuser/Programs/jdk-23" >> .bashrc
 ```
 
 load the definitions into your environment
@@ -272,7 +273,7 @@ sudo apt-get install graphviz
 echo "export SIGMA_HOME=~/.sigmakee" >> .bashrc
 echo "export ONTOLOGYPORTAL_GIT=~/workspace" >> .bashrc
 echo "export SIGMA_SRC=$ONTOLOGYPORTAL_GIT/sigmakee" >> .bashrc
-echo "export CATALINA_OPTS=\"-Xmx10g\"" >> .bashrc
+echo "export CATALINA_OPTS=\"-Xmx10g -Xss1m\"" >> .bashrc
 echo "export CATALINA_HOME=~/Programs/apache-tomcat-9.0.96" >> .bashrc
 echo "export PATH=$CATALINA_HOME/bin:$PATH" >> .bashrc
 echo "export SIGMA_CP=$SIGMA_SRC/build/sigmakee.jar:$SIGMA_SRC/lib/*" >> .bashrc
@@ -368,7 +369,7 @@ Open up CMD prompt
     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-11-openjdk-amd64/jre" >> .bashrc
+    (This step might not be necessary, I'd try without it first) echo "export JAVA_HOME=/usr/lib/jvm/java-23-openjdk-amd64/jre" >> .bashrc
 ```
 
 Follow Linux install instructions on:
@@ -481,9 +482,6 @@ than just com.articulate.sigma.KB
 
 ## Account Management
 
-> **Warning**
-> Please note this is not working as of Apr, 2020.
-
 Create the account database with
 
 ```sh
@@ -493,7 +491,7 @@ java -Xmx4g -cp $SIGMA_CP com.articulate.sigma.PasswordService -c
 Then create the administrator account and password
 
 ```sh
-java -Xmx4g -Xss1m -cp $SIGMA_CP com.articulate.sigma.PasswordService -a
+java -Xmx4g -cp $SIGMA_CP com.articulate.sigma.PasswordService -a
 ```
 
 You can use Sigma without being administrator, but you'll have limited use of its functionality.

build.xml

@@ -89,7 +89,7 @@
     <property name="build.test.classes.dir" value="${build.home}/test/classes"/>
     <property name="dist.dir" value="dist"/>
     <property name="dist.jar" value="${dist.dir}/${app.name}.jar"/>
-    <property name="dist.javadoc.dir" value="${dist.dir}/doc/api"/>
+    <property name="dist.javadoc.dir" value="doc"/>
     <property name="web.dir" value="web"/>
     <property name="reports.dir" value="${build.home}/reports"/>
     <property name="unit.test.suite" value="com.articulate.sigma.UnitTestSuite"/>
@@ -242,6 +242,7 @@
             <lib dir="${basedir}/lib">
                 <exclude name="junit*"/>
                 <exclude name="hamcrest*"/>
+                <exclude name="tomcat-servlet-api*"/>
             </lib>
             <classes dir="${build.classes.dir}"/>
         </war>
@@ -364,8 +365,6 @@
     </target>
 
     <target name="api_doc" depends="init" description="Build the JavaDocs and place in ${build.javadoc}.">
-        <delete dir="${dist.javadoc.dir}"/>
-        <mkdir dir="${dist.javadoc.dir}"/>
         <javadoc sourcepath="${src.dir}" destdir="${dist.javadoc.dir}" author="true" version="true" use="true"
                  windowtitle="Sigma API Specification" splitindex="true" packagenames="com.articulate.sigma.*">
             <classpath path="${run.classpath}"/>

ivy.xml

@@ -20,6 +20,8 @@
         <dependency org="com.servlets" name="cos" rev="09May2002" transitive="false" conf="api->default"/>
         <dependency org="edu.stanford.nlp" name="stanford-corenlp" rev="4.5.4" transitive="false" conf="api->default"/>
         <dependency org="javax.mail" name="mail" rev="1.4" transitive="false" conf="api->default"/>
+        <!-- https://mvnrepository.com/artifact/org.apache.tomcat/tomcat-servlet-api -->
+        <dependency org="org.apache.tomcat" name="tomcat-servlet-api" rev="9.0.96" transitive="false" conf="api->default"/>
         <dependency org="net.sf.py4j" name="py4j" rev="0.10.6" transitive="false" conf="api->default"/>
         <dependency org="org.antlr" name="antlr4-runtime" rev="4.9.3" transitive="false" conf="api->default"/>
         <dependency org="org.apache.commons" name="commons-lang3" rev="3.12.0" transitive="false" conf="api->default"/>

nbproject/build.properties

@@ -30,6 +30,7 @@ file.reference.integration-java=test/integration/java
 file.reference.unit-java=test/unit/java
 includes=**
 jar.compress=false
+lib.dir=lib
 javac.classpath=\
     lib/commons-lang3-3.12.0.jar:\
     lib/cos-09May2002.jar:\
@@ -124,10 +125,10 @@ kbs_home=../sumo
 project.license=LICENSE
 
 # Various runtime arguments here
-run.args=
+run.args=-g Transitway subclass
 
 # Tomcat Manager properties
-catalina.ops=-Xmx10g
+catalina.ops=-Xmx10g -Xss1m
 catalina.base=${catalina.home}
 catalina.logs.dir=${catalina.base}/logs
 catalina.out=${catalina.logs.dir}/catalina.out

nbproject/ide-targets.xml

@@ -55,7 +55,12 @@
         <copy todir="${basedir}/lib" file="${sigma.utils.home}/sigmaUtils.jar"/>
         <!-- Create WEB-INF/lib/ and copy over the needed jar files. -->
         <copy todir="${build.home}/WEB-INF/lib" flatten="true">
-            <path refid="compile.classpath"/>
+            <fileset dir="${lib.dir}">
+                <include name="*.jar"/>
+                <exclude name="junit*"/>
+                <exclude name="hamcrest*"/>
+                <exclude name="tomcat-servlet-api*"/>
+            </fileset>
         </copy>
     </target>
 
@@ -550,6 +555,9 @@
                 <include name="*.tptp"/>
                 <include name="*.ser"/>
             </fileset>
+            <fileset dir="${sigma_home}/KBs/WordNetMappings">
+                <include name="*.ser"/>
+            </fileset>
         </delete>
         <delete>
             <fileset dir="${catalina.logs.dir}">

nbproject/project.xml

@@ -354,9 +354,9 @@ auxiliary.show.customizer.message=<message>
             </compilation-unit>
             <compilation-unit>
                 <package-root>src/java</package-root>
-                <classpath mode="compile">lib/commons-lang3-3.12.0.jar:lib/cos-09May2002.jar:lib/guava-19.0.jar:lib/h2-2.3.232.jar:lib/java-prolog-parser-2.0.2.jar:lib/json-simple-1.1.1.jar:lib/kryo-5.6.2.jar:lib/mail-1.4.jar:lib/py4j-0.10.6.jar:lib/sigmaUtils.jar:lib/stanford-corenlp-4.5.4.jar:lib/tptp.jar</classpath>
+                <classpath mode="compile">lib/commons-lang3-3.12.0.jar:lib/cos-09May2002.jar:lib/guava-19.0.jar:lib/h2-2.3.232.jar:lib/java-prolog-parser-2.0.2.jar:lib/json-simple-1.1.1.jar:lib/kryo-5.6.2.jar:lib/mail-1.4.jar:lib/py4j-0.10.6.jar:lib/sigmaUtils.jar:lib/stanford-corenlp-4.5.4.jar:lib/tomcat-servlet-api-9.0.96.jar:lib/tptp.jar</classpath>
                 <built-to>build/WEB-INF/classes</built-to>
-                <javadoc-built-to>dist/doc/api</javadoc-built-to>
+                <javadoc-built-to>doc</javadoc-built-to>
                 <source-level>11</source-level>
             </compilation-unit>
         </java-data>