Merge remote-tracking branch 'origin/master'

ontologyportal · Jan 19, 2025 · a77ce07 · a77ce07
2 parents abf9830 + aacb545
commit a77ce07
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diff --git a/.github/workflows/ant.yml b/.github/workflows/ant.yml
@@ -60,10 +60,10 @@ jobs:
           sed -i "s|/home/theuser/workspace/sumo|$ONTOLOGYPORTAL_GIT/sumo|g" $SIGMA_HOME/KBs/config.xml
           sed -i "s|/home/theuser/E/bin/e_ltb_runner|/usr/local/bin/e_ltb_runner|g" $SIGMA_HOME/KBs/config.xml
 
-      - name: Set up JDK 11 for x64
+      - name: Set up JDK 21 for x64
         uses: actions/setup-java@v4
         with:
-          java-version: '11'
+          java-version: '21'
           distribution: 'temurin'
 
       - name: Build with Ant

diff --git a/INSTALL.MacOS b/INSTALL.MacOS
@@ -49,7 +49,7 @@ these variables created before the next step, and replace
 
 Next, execute step-by-step the commands below (tested on MacOS 10.14.5 to Sonoma 14.5):
 
-You will need at least Java 11+ (avoid JDK 17) to compile SigmaKEE and to run
+You will need at least Java 21+ (avoid JDK 17) to compile SigmaKEE and to run
 Apache Tomcat.
 
 ! For ARM processors download it from here: https://jdk.java.net/archive/
@@ -66,7 +66,7 @@ Apache Tomcat.
   export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-23.jdk/Contents/Home
   export PATH=$JAVA_HOME/bin:$PATH
 
-Install (ensure the above preparation have been performed)
+Install (ensure the above preparations have been performed)
 > ant install
 
 *** Legacy install steps now taken care of by the above command "ant install"

diff --git a/README.md b/README.md
@@ -236,6 +236,17 @@ echo "export HISTSIZE=10000 HISTFILESIZE=100000" >> .bashrc
 echo "export JAVA_HOME=/home/theuser/Programs/jdk-23" >> .bashrc
 ```
 
+mandtory additions to .bashrc
+```sh
+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
+```
+
 load the definitions into your environment
 ```sh
 source .bashrc
@@ -303,9 +314,18 @@ PS1=Vagrant:$PS1
 
 First, comply with System preparation on Linux above
 
-Clone SigmaKEE
+Clone SigmaKEE. First, ensure the below exports are contained in your ~/.bashrc.
+If not, then perform the exports before cloning SigmaKEE.
 ```sh
 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
 mkdir workspace
 cd workspace
 git clone https://github.com/ontologyportal/sigmakee
@@ -458,7 +478,7 @@ See INSTALL.MacOS
 Open up CMD prompt
 
 ```
-    wsl –install
+    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

diff --git a/build.xml b/build.xml
@@ -115,7 +115,7 @@
     <property name="tomcat.version" value="9.0.97"/>
 
     <!-- Define the sigma user spaces -->
-    <property name="workspace.dir" value="${git.home}/workspace"/>
+    <property name="workspace.dir" value="${user.home}/workspace"/>
     <property name="programs.dir" value="${user.home}/Programs"/>
 
     <condition property="isUnixNotMac">
@@ -140,10 +140,19 @@
     </path>
 
     <target name="init" depends="init-ivy">
-        <available property="jdk11+" classname="java.net.http.HttpClient"/>
-        <fail message="Unsupported JDK version: ${ant.java.version}. Please use JDK version 11 or greater, but avoid JDK 17."
-              unless="jdk11+">
+        <condition property="jdk21+">
+            <javaversion atleast="21"/>
+        </condition>
+        <fail message="Unsupported JDK version: ${ant.java.version}. Please use a Java Development Kit (JDK) version 21 or greater."
+              unless="jdk21+">
         </fail>
+        <condition property="nojdk">
+            <contains string="${java.home}" substring="jdk"/>
+        </condition>
+        <fail message="Please install a Java Development Kit (JDK) version 21 or greater."
+              unless="nojdk">
+        </fail>
+
         <echo message="Welcome to the ${product.Name} v${product.Version}"/>
         <echo message="Specification Vendor:     ${spec.vendor}"/>
         <echo message=""/>
@@ -156,6 +165,7 @@
         <echo message="classpath:                ${env.SIGMA_CP}"/>
         <echo message="Java Version via Ant:     ${ant.java.version}"/>
         <echo message="Java Version System Prop: ${java.version}"/>
+        <echo message="JDK HOME:     is set to:  ${java.home}"/>
 
         <tstamp>
             <format property="TODAY_US" pattern="EEE, d MMM yyyy HHmm Z" locale="en,US"/>
@@ -359,9 +369,15 @@
     <!-- At this point we will assume you have already complied with the
          README.md under the heading "System preparation on Linux." This task
          will take over from the heading "Linux Installation."  -->
-    <target name="install" depends="init" description="Installs WordNetMappings and SUMO to ${sigma.home}/KBs">
+    <target name="install" depends="init" description="Appends .*hrc files, clones Sigma tools, installs WordNetMappings and SUMO to ${sigma.home}/KBs and builds the E and Vampire Theorem provers">
         <mkdir dir="${workspace.dir}"/>
+        <chmod dir="${workspace.dir}" perm="777" includeemptydirs="true">
+            <include name="**/*"/>
+        </chmod>
         <mkdir dir="${programs.dir}"/>
+        <chmod dir="${programs.dir}" perm="777" includeemptydirs="true">
+            <include name="**/*"/>
+        </chmod>
 
         <!-- Install Tomcat -->
         <antcall target="install.tomcat"/>
@@ -370,7 +386,7 @@
         <antcall target="retrieve.wordnet"/>
 
         <!-- Retrieve E prover -->
-        <antcall tareget="retrieve.E"/>
+        <antcall target="retrieve.E"/>
 
         <!-- Clone the sigma tools -->
         <antcall target="clone.sumo"/>
@@ -388,10 +404,6 @@
         <antcall target="clone.z3"/>
         <antcall target="build.z3"/>
         <antcall target="build.vampire"/>
-
-        <!-- Configure ~/.bashrc ~/.zshrc -->
-        <antcall target="append.bashrc"/>
-        <antcall target="append.zshrc"/>
     </target>
 
     <target name="retrieve.wordnet">
@@ -408,6 +420,9 @@
 
     <target name="copy.to.sigma.home">
         <mkdir dir="${user.home}/.${app.name}"/>
+        <chmod dir="${user.home}/.${app.name}" perm="777" includeemptydirs="true">
+            <include name="**/*"/>
+        </chmod>
         <mkdir dir="${user.home}/.${app.name}/KBs"/>
         <copy todir="${user.home}/.${app.name}/KBs">
             <fileset dir="${kbs.home}"/>
@@ -422,7 +437,8 @@
     </target>
 
     <target name="clone.sumo">
-        <git command="clone">
+        <mkdir dir="${workspace.dir}/sumo"/>
+        <git command="clone" dir="${workspace.dir}/sumo">
             <args>
                 <arg value="--progress"/>
                 <arg value="--verbose"/>
@@ -432,7 +448,8 @@
         </git>
     </target>
     <target name="clone.tptpantlr">
-        <git command="clone">
+        <mkdir dir="${workspace.dir}/TPTP-ANTLR"/>
+        <git command="clone" dir="${workspace.dir}/TPTP-ANTLR">
             <args>
                 <arg value="--progress"/>
                 <arg value="--verbose"/>
@@ -442,7 +459,8 @@
         </git>
     </target>
     <target name="clone.sigmautils">
-        <git command="clone">
+        <mkdir dir="${workspace.dir}/SigmaUtils"/>
+        <git command="clone" dir="${workspace.dir}/SigmaUtils">
             <args>
                 <arg value="--progress"/>
                 <arg value="--verbose"/>
@@ -470,6 +488,14 @@
             </args>
         </git>
     </target>
+    <target name="update.sigmakee">
+        <git command="pull" dir="${user.dir}">
+            <args>
+                <arg value="--progress"/>
+                <arg value="--verbose"/>
+            </args>
+        </git>
+    </target>
 
     <!-- git macro utils setup from: https://tonyyan.wordpress.com/2017/03/10/integrate-git-into-ant-targets/-->
     <macrodef name="git">
@@ -529,30 +555,36 @@
         </exec>
     </target>
 
+    <!-- If Vampire fails to build on Hamming, here is a alternate source of the binary -->
+    <target name="alternate.vampire">
+        <get src="https://github.com/vprover/vampire/releases/download/v4.9casc2024/vampire" dest="${programs.dir}/vampire/build" tryGzipEncoding="true"/>
+        <chmod dir="${programs.dir}/${programs.dir}/vampire/build" perm="ugo+rx" includes="vampire"/>
+    </target>
+
     <target name="append.bashrc" if="isUnixNotMac">
         <echo file="${user.home}/.bashrc" append="true">
-
 # For SIGMA
 export SIGMA_HOME=${user.home}/.${app.name}
 export ONTOLOGYPORTAL_GIT=${workspace.dir}
 export SIGMA_SRC=$ONTOLOGYPORTAL_GIT/${app.name}
 export CATALINA_OPTS="$CATALINA_OPTS ${run.jvmargs}"
 export CATALINA_HOME=${programs.dir}/apache-tomcat-${tomcat.version}
 export PATH=$CATALINA_HOME/bin:$PATH
-export SIGMA_CP=$SIGMA_SRC/build/${app.name}.jar:$SIGMA_SRC/lib/*</echo>
+export SIGMA_CP=$SIGMA_SRC/build/${app.name}.jar:$SIGMA_SRC/lib/*
+</echo>
     </target>
 
     <target name="append.zshrc" unless="isUnixNotMac">
         <echo file="${user.home}/.zshrc" append="true">
-
 # For SIGMA
 export SIGMA_HOME=${user.home}/.${app.name}
 export ONTOLOGYPORTAL_GIT=${workspace.dir}
 export SIGMA_SRC=$ONTOLOGYPORTAL_GIT/${app.name}
 export CATALINA_OPTS="$CATALINA_OPTS ${run.jvmargs}"
 export CATALINA_HOME=${programs.dir}/apache-tomcat-${tomcat.version}
 export PATH=$CATALINA_HOME/bin:$PATH
-export SIGMA_CP=$SIGMA_SRC/build/${app.name}.jar:$SIGMA_SRC/lib/*</echo>
+export SIGMA_CP=$SIGMA_SRC/build/${app.name}.jar:$SIGMA_SRC/lib/*
+</echo>
     </target>
 
     <target name="api_doc" depends="init" description="Build the JavaDocs and place in ${dist.javadoc.dir}.">

diff --git a/config.xml b/config.xml
@@ -25,7 +25,7 @@
   <preference name="sumokbname" value="SUMO" />
   <preference name="systemsDir" value="/home/theuser" />
   <preference name="termFormats" value="no" />
-  <preference name="testOutputDir" value="/var/tomcat/apache-tomcat-9.0.96/webapps/sigma/tests" />
+  <preference name="testOutputDir" value="/var/tomcat/apache-tomcat-9.0.97/webapps/sigma/tests" />
   <preference name="TPTPDisplay" value="no" />
   <preference name="tptpHomeDir" value="/home/theuser" />
   <preference name="TPTP" value="yes" />

diff --git a/docker/sigma-ci/Dockerfile b/docker/sigma-ci/Dockerfile
@@ -1,39 +1,39 @@
-FROM tomcat:9.0.96-jdk11-temurin-jammy AS builder
+FROM tomcat:9.0.97-jdk21-temurin-jammy AS builder
 
 # Followed instructions from: https://github.com/vprover/vampire/wiki/Source-Build-for-Users
-# for buildling latest vampire w/ latest Z3
+# for buildling latest vampire w/ latest z3
 
 RUN apt update; \
     apt-get install -y --no-install-recommends \
             build-essential \
             cmake \
             git \
             python3 \
-    ; \
+    ;\
     wget 'http://wwwlehre.dhbw-stuttgart.de/~sschulz/WORK/E_DOWNLOAD/V_2.6/E.tgz' &&\
-    tar xf E.tgz ; \
-    cd E ; \
+    tar xf E.tgz ;\
+    cd E ;\
     ./configure && make ;\
     cd .. ;\
-    wget 'https://wordnetcode.princeton.edu/3.0/WordNet-3.0.tar.gz' ; \
-    tar xf WordNet-3.0.tar.gz ; \
-    git clone https://github.com/vprover/vampire ; \
-    cd vampire ; \
-    git submodule update --init ; \
-    mkdir build ; \
-    mkdir z3/build && cd z3/build ; \
-    cmake .. -DZ3_SINGLE_THREADED=1 -DCMAKE_BUILD_TYPE=Release ; \
-    make -j`nproc` ; \
-    cd ../../build ; \
-    cmake .. ; \
-    make -j`nproc` ; \
-    cd .. ; \
-    cp build/vampire vampire ; \
+    wget 'https://wordnetcode.princeton.edu/3.0/WordNet-3.0.tar.gz' ;\
+    tar xf WordNet-3.0.tar.gz ;\
+    git clone https://github.com/vprover/vampire ;\
+    cd vampire ;\
+    git submodule update --init ;\
+    mkdir build ;\
+    mkdir z3/build && cd z3/build ;\
+    cmake .. -DZ3_SINGLE_THREADED=1 -DCMAKE_BUILD_TYPE=Release ;\
+    make -j`nproc` ;\
+    cd ../../build ;\
+    cmake .. ;\
+    make -j`nproc` ;\
+    cd .. ;\
+    cp build/vampire vampire ;\
     ./checks/sanity vampire
 
 #################################################
 # runtime image.
-FROM tomcat:9.0.96-jdk11-temurin-jammy AS runtime
+FROM tomcat:9.0.97-jdk21-temurin-jammy AS runtime
 
 COPY --from=builder \
     /usr/local/tomcat/E/PROVER/e_ltb_runner /usr/local/bin/e_ltb_runner
@@ -44,6 +44,9 @@ COPY --from=builder \
 COPY --from=builder \
     /usr/local/tomcat/vampire/vampire /usr/local/bin/vampire
 
+COPY --from=builder \
+    /usr/local/tomcat/vampire/z3/build/libz3.* /usr/local/bin/
+
 RUN apt update; \
     apt-get install -y --no-install-recommends \
             ant \

diff --git a/docker/sigmakee/Dockerfile b/docker/sigmakee/Dockerfile
@@ -3,7 +3,7 @@ FROM $IMAGE_ACCOUNT/sigma-ci:latest AS builder
 
 #################################################
 # runtime image.
-FROM tomcat:9.0.96-jdk11-temurin-jammy AS runtime
+FROM tomcat:9.0.97-jdk21-temurin-jammy AS runtime
 
 RUN apt update; \
     apt-get install -y --no-install-recommends \
@@ -18,6 +18,9 @@ COPY --from=builder \
 COPY --from=builder \
     /usr/local/bin/vampire /usr/local/bin/vampire
 
+COPY --from=builder \
+    /usr/local/bin/libz3.* /usr/local/bin/
+
 COPY ./sigmakee-runtime /root/sigmakee-runtime/
 
 COPY ./sigmakee/build/WEB-INF/lib/*.jar /root/sigmakee/

diff --git a/docker/sigmakee2023/Dockerfile b/docker/sigmakee2023/Dockerfile
@@ -34,7 +34,7 @@ RUN cd /root \
     && echo "export SIGMA_SRC=/root/workspace/sigmakee" >> .bashrc \
     && echo "export ONTOLOGYPORTAL_GIT=/root/workspace" >> .bashrc \
     && echo 'export CATALINA_OPTS="$CATALINA_OPTS -Xmx10g -Xss1m"' >> .bashrc \
-    && echo "export CATALINA_HOME=/root/Programs/apache-tomcat-9.0.96" >> .bashrc \
+    && echo "export CATALINA_HOME=/root/Programs/apache-tomcat-9.0.97" >> .bashrc \
     && source .bashrc
 
 # Setup Vampire

diff --git a/docker/sumo-ci/Dockerfile b/docker/sumo-ci/Dockerfile
@@ -3,7 +3,7 @@ FROM $IMAGE_ACCOUNT/sigma-ci:latest AS builder
 
 #################################################
 # runtime image.
-FROM tomcat:9.0.96-jdk11-temurin-jammy AS runtime
+FROM tomcat:9.0.97-jdk21-temurin-jammy AS runtime
 
 RUN apt update; \
     apt-get install -y --no-install-recommends \
@@ -18,6 +18,9 @@ COPY --from=builder \
 COPY --from=builder \
     /usr/local/bin/vampire /usr/local/bin/vampire
 
+COPY --from=builder \
+    /usr/local/bin/libz3.* /usr/local/bin/
+
 COPY ./sigmakee-runtime /root/sigmakee-runtime/
 
 COPY ./sigmakee/build/WEB-INF/lib/*.jar /root/sigmakee/

diff --git a/nbproject/ide-targets.xml b/nbproject/ide-targets.xml
@@ -556,6 +556,7 @@
             <fileset dir="${sigma_home}/KBs">
                 <include name="*.tptp"/>
                 <include name="*.ser"/>
+                <include name="vamp-out.txt"/>
             </fileset>
             <fileset dir="${sigma_home}/KBs/WordNetMappings">
                 <include name="*.ser"/>

diff --git a/nbproject/project.xml b/nbproject/project.xml
@@ -272,7 +272,7 @@ auxiliary.show.customizer.message=<message>
             </ide-actions>
             <export>
                 <type>folder</type>
-                <location>build/test/classes</location>
+                <location>build/WEB-INF/classes</location>
                 <script>${ant.script}</script>
                 <build-target>dist</build-target>
             </export>