Tetrad components now compile and archive using ant. Cleaning up dire…

…ctories.
LearnSphere · Oct 11, 2017 · e5ed8ac · e5ed8ac
1 parent 338fc42
commit e5ed8ac
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Showing 109 changed files with 282 additions and 1,391 deletions.
diff --git a/GraphEditor/build.xml b/GraphEditor/build.xml
@@ -7,17 +7,21 @@
     <property file="build.properties" />
     <property name="source" location="${basedir}/source" />
     <property name="build" location="${basedir}/build" />
+    <property name="program" location="${basedir}/program" />
     <property name="dist" location="${basedir}/dist" />
     <property name="lib" location="../CommonLibraries" />
     <property name="javadoc" location="${basedir}/javadoc" />
     <property name="tetrad.lib" location="../CustomLibraries/Tetrad" />
 
     <property name="version" value="1.0" />
 
+    <property name="javac8" location="/usr/java/jdk1.8.0_131/bin/javac" />
+
     <property name="component.id" value="GraphEditor" />
     <property name="component.version" value="v${version} 2015" />
 
     <property name="ToolTemplate.jar" value="${dist}/${component.id}-${version}.jar" />
+    <property name="TetradTemplate.jar" value="${dist}/${component.id}.jar" />
 
     <path id="lib.path">
         <fileset dir="${lib}">
@@ -36,6 +40,9 @@
             <fileset dir="${lib}">
                 <include name="*.jar" />
             </fileset>
+            <fileset dir="${tetrad.lib}">
+               <include name="*.jar" />
+           </fileset>
         </path>
         <manifestclasspath property="lib.list" jarfile="${ToolTemplate.jar}">
             <classpath refid="build-classpath" />
@@ -46,6 +53,17 @@
                 <attribute name="Class-Path" value="${lib.list}" />
             </manifest>
         </jar>
+
+        <!-- build component jar -->
+        <manifestclasspath property="tetrad.lib.list" jarfile="${TetradTemplate.jar}">
+            <classpath refid="build-classpath" />
+        </manifestclasspath>
+        <jar jarfile="${TetradTemplate.jar}" basedir="${build}" includes="**">
+            <manifest>
+                <attribute name="Main-Class" value="GraphEditor" />
+                <attribute name="Class-Path" value="${tetrad.lib.list}" />
+            </manifest>
+        </jar>
     </target>
 
     <path id="run.classpath">
@@ -64,9 +82,11 @@
 
     <target name="compile" depends="init" description="compile the source ">
         <!-- Compile the java code from ${source} into ${build} -->
-        <javac includeantruntime="false" srcdir="${source}" destdir="${build}" debug="on" fork="true">
+        <javac includeantruntime="false" srcdir="${source}" destdir="${build}" debug="on">
+            <classpath refid="lib.path" />
+        </javac>
+        <javac includeantruntime="false" srcdir="${program}" destdir="${build}" debug="on" fork="yes" executable="${javac8}">
             <classpath refid="lib.path" />
-			<compilerarg line="-nowarn" />
         </javac>
     </target>
 

diff --git a/GraphEditor/dist/TetradDataConversion-1.0.jar b/GraphEditor/dist/TetradDataConversion-1.0.jar
diff --git a/GraphEditor/makeJar.bat b/GraphEditor/makeJar.bat
diff --git a/GraphEditor/program/GraphEditor.class b/GraphEditor/program/GraphEditor.class
diff --git a/GraphEditor/program/GraphEditor.jar b/GraphEditor/program/GraphEditor.jar
diff --git a/GraphEditor/program/README.md b/GraphEditor/program/README.md
@@ -1,12 +1,10 @@
 You have to give run.sh permission to run on the linux server.  do this with:
-	"chmod +x run.sh"
+  "chmod ug+x run.sh"
 
 run.sh is used on linux machines and runOnWindows.bat is used for windows
 
 To run on a windows machine, change run.sh to runOnWindows.bat in the 
-	build.properties file.  You'll also need to change the path to java
-	and the path to other files inside of runOnWindows.bat.
-
-To remake the GraphEditor.jar, look at makeJar.bat in the parent directory.
-
+  build.properties file.  You'll also need to change the path to java
+  and the path to other files inside of runOnWindows.bat.
+
 -Peter
diff --git a/GraphEditor/program/manifest.txt b/GraphEditor/program/manifest.txt
diff --git a/GraphEditor/program/run.sh b/GraphEditor/program/run.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-"/usr/java/jdk1.8.0_131/jre/bin/java" -cp /datashop/workflow_components/GraphEditor/program/tetrad-gui-6.3.4-launch.jar -jar /datashop/workflow_components/GraphEditor/program/GraphEditor.jar $@
+"/usr/java/jdk1.8.0_131/jre/bin/java" -cp /datashop/workflow_components/CustomLibraries/tetrad-gui-6.3.4-launch.jar -jar /datashop/workflow_components/GraphEditor/dist/GraphEditor.jar $@
diff --git a/GraphEditor/program/runOnWindows.bat b/GraphEditor/program/runOnWindows.bat
@@ -2,4 +2,4 @@ FOR %%A IN (%*) DO (
      ECHO BATCH ARG: %%A
 )
 
-"C:/Program Files/Java/jdk1.8.0_91/bin/java.exe" -cp C:\Users\peter\Documents\CMURound2\WorkflowComponents\GraphEditor\program\tetrad-gui-6.3.4-launch.jar -jar C:\Users\peter\Documents\CMURound2\WorkflowComponents\GraphEditor\program\GraphEditor.jar %*
+"C:/Program Files/Java/jdk1.8.0_91/bin/java.exe" -cp C:\Users\peter\Documents\CMURound2\WorkflowComponents\CustomLibraries\tetrad-gui-6.3.4-launch.jar -jar C:\Users\peter\Documents\CMURound2\WorkflowComponents\GraphEditor\dist\GraphEditor.jar %*
diff --git a/GraphEditor/program/tetrad-gui-6.3.4-launch.jar b/GraphEditor/program/tetrad-gui-6.3.4-launch.jar
diff --git a/GraphEditor/test/resources/iq_brain_size.tetrad.txt b/GraphEditor/test/resources/iq_brain_size.tetrad.txt
diff --git a/RowOperations/build.xml b/RowOperations/build.xml
@@ -7,17 +7,21 @@
     <property file="build.properties" />
     <property name="source" location="${basedir}/source" />
     <property name="build" location="${basedir}/build" />
+    <property name="program" location="${basedir}/program" />
     <property name="dist" location="${basedir}/dist" />
     <property name="lib" location="../CommonLibraries" />
     <property name="javadoc" location="${basedir}/javadoc" />
     <property name="tetrad.lib" location="../CustomLibraries/Tetrad" />
 
     <property name="version" value="1.0" />
 
+    <property name="javac8" location="/usr/java/jdk1.8.0_131/bin/javac" />
+
     <property name="component.id" value="RowOperations" />
     <property name="component.version" value="v${version} 2015" />
 
     <property name="ToolTemplate.jar" value="${dist}/${component.id}-${version}.jar" />
+    <property name="TetradTemplate.jar" value="${dist}/${component.id}.jar" />
 
     <path id="lib.path">
         <fileset dir="${lib}">
@@ -36,6 +40,9 @@
             <fileset dir="${lib}">
                 <include name="*.jar" />
             </fileset>
+            <fileset dir="${tetrad.lib}">
+               <include name="*.jar" />
+           </fileset>
         </path>
         <manifestclasspath property="lib.list" jarfile="${ToolTemplate.jar}">
             <classpath refid="build-classpath" />
@@ -46,6 +53,17 @@
                 <attribute name="Class-Path" value="${lib.list}" />
             </manifest>
         </jar>
+
+        <!-- build component jar -->
+        <manifestclasspath property="tetrad.lib.list" jarfile="${TetradTemplate.jar}">
+            <classpath refid="build-classpath" />
+        </manifestclasspath>
+        <jar jarfile="${TetradTemplate.jar}" basedir="${build}" includes="**">
+            <manifest>
+                <attribute name="Main-Class" value="RowOperations" />
+                <attribute name="Class-Path" value="${tetrad.lib.list}" />
+            </manifest>
+        </jar>
     </target>
 
     <path id="run.classpath">
@@ -64,9 +82,11 @@
 
     <target name="compile" depends="init" description="compile the source ">
         <!-- Compile the java code from ${source} into ${build} -->
-        <javac includeantruntime="false" srcdir="${source}" destdir="${build}" debug="on" fork="true">
+        <javac includeantruntime="false" srcdir="${source}" destdir="${build}" debug="on">
+            <classpath refid="lib.path" />
+        </javac>
+        <javac includeantruntime="false" srcdir="${program}" destdir="${build}" debug="on" fork="yes" executable="${javac8}">
             <classpath refid="lib.path" />
-			<compilerarg line="-nowarn" />
         </javac>
     </target>
 

diff --git a/RowOperations/dist/TetradDataConversion-1.0.jar b/RowOperations/dist/TetradDataConversion-1.0.jar
diff --git a/RowOperations/makeJar.bat b/RowOperations/makeJar.bat
diff --git a/RowOperations/program/README.md b/RowOperations/program/README.md
@@ -1,12 +1,10 @@
 You have to give run.sh permission to run on the linux server.  do this with:
-	"chmod +x run.sh"
+  "chmod ug+x run.sh"
 
 run.sh is used on linux machines and runOnWindows.bat is used for windows
 
 To run on a windows machine, change run.sh to runOnWindows.bat in the 
-	build.properties file.  You'll also need to change the path to java
-	and the path to other files inside of runOnWindows.bat.
-
-To remake the RowOperations.jar, look at makeJar.bat in the parent directory.
-
+  build.properties file.  You'll also need to change the path to java
+  and the path to other files inside of runOnWindows.bat.
+
 -Peter
diff --git a/RowOperations/program/RowOperations.class b/RowOperations/program/RowOperations.class
diff --git a/RowOperations/program/RowOperations.jar b/RowOperations/program/RowOperations.jar
diff --git a/RowOperations/program/manifest.txt b/RowOperations/program/manifest.txt
diff --git a/RowOperations/program/run.sh b/RowOperations/program/run.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-"/usr/java/jdk1.8.0_131/jre/bin/java" -cp /datashop/workflow_components/RowOperations/program/tetrad-gui-6.3.4-launch.jar -jar /datashop/workflow_components/RowOperations/program/RowOperations.jar $@
+"/usr/java/jdk1.8.0_131/jre/bin/java" -cp /datashop/workflow_components/CustomLibraries/tetrad-gui-6.3.4-launch.jar -jar /datashop/workflow_components/RowOperations/dist/RowOperations.jar $@
diff --git a/RowOperations/program/runOnWindows.bat b/RowOperations/program/runOnWindows.bat
@@ -2,4 +2,4 @@ FOR %%A IN (%*) DO (
      ECHO BATCH ARG: %%A
 )
 
-"C:/Program Files/Java/jdk1.8.0_91/bin/java.exe" -cp C:\Users\peter\Documents\CMURound2\WorkflowComponents\RowOperations\program\tetrad-gui-6.3.4-launch.jar -jar C:\Users\peter\Documents\CMURound2\WorkflowComponents\RowOperations\program\RowOperations.jar %*
+"C:/Program Files/Java/jdk1.8.0_91/bin/java.exe" -cp C:\Users\peter\Documents\CMURound2\WorkflowComponents\CustomLibraries\tetrad-gui-6.3.4-launch.jar -jar C:\Users\peter\Documents\CMURound2\WorkflowComponents\RowOperations\dist\RowOperations.jar %*
diff --git a/RowOperations/program/tetrad-gui-6.3.4-launch.jar b/RowOperations/program/tetrad-gui-6.3.4-launch.jar
diff --git a/RowOperations/test/resources/iq_brain_size.tetrad.txt b/RowOperations/test/resources/iq_brain_size.tetrad.txt
diff --git a/TetradClassifier/build.xml b/TetradClassifier/build.xml
@@ -7,17 +7,21 @@
     <property file="build.properties" />
     <property name="source" location="${basedir}/source" />
     <property name="build" location="${basedir}/build" />
+    <property name="program" location="${basedir}/program" />
     <property name="dist" location="${basedir}/dist" />
     <property name="lib" location="../CommonLibraries" />
     <property name="javadoc" location="${basedir}/javadoc" />
     <property name="tetrad.lib" location="../CustomLibraries/Tetrad" />
 
     <property name="version" value="1.0" />
 
+    <property name="javac8" location="/usr/java/jdk1.8.0_131/bin/javac" />
+
     <property name="component.id" value="TetradClassifier" />
     <property name="component.version" value="v${version} 2015" />
 
     <property name="ToolTemplate.jar" value="${dist}/${component.id}-${version}.jar" />
+    <property name="TetradTemplate.jar" value="${dist}/${component.id}.jar" />
 
     <path id="lib.path">
         <fileset dir="${lib}">
@@ -36,6 +40,9 @@
             <fileset dir="${lib}">
                 <include name="*.jar" />
             </fileset>
+            <fileset dir="${tetrad.lib}">
+               <include name="*.jar" />
+           </fileset>
         </path>
         <manifestclasspath property="lib.list" jarfile="${ToolTemplate.jar}">
             <classpath refid="build-classpath" />
@@ -46,6 +53,17 @@
                 <attribute name="Class-Path" value="${lib.list}" />
             </manifest>
         </jar>
+
+        <!-- build component jar -->
+        <manifestclasspath property="tetrad.lib.list" jarfile="${TetradTemplate.jar}">
+            <classpath refid="build-classpath" />
+        </manifestclasspath>
+        <jar jarfile="${TetradTemplate.jar}" basedir="${build}" includes="**">
+            <manifest>
+                <attribute name="Main-Class" value="TetradClassifier" />
+                <attribute name="Class-Path" value="${tetrad.lib.list}" />
+            </manifest>
+        </jar>
     </target>
 
     <path id="run.classpath">
@@ -64,9 +82,11 @@
 
     <target name="compile" depends="init" description="compile the source ">
         <!-- Compile the java code from ${source} into ${build} -->
-        <javac includeantruntime="false" srcdir="${source}" destdir="${build}" debug="on" fork="true">
+        <javac includeantruntime="false" srcdir="${source}" destdir="${build}" debug="on">
+            <classpath refid="lib.path" />
+        </javac>
+        <javac includeantruntime="false" srcdir="${program}" destdir="${build}" debug="on" fork="yes" executable="${javac8}">
             <classpath refid="lib.path" />
-			<compilerarg line="-nowarn" />
         </javac>
     </target>
 

diff --git a/TetradClassifier/dist/TetradClassifier-1.0.jar b/TetradClassifier/dist/TetradClassifier-1.0.jar
diff --git a/TetradClassifier/makeJar.bat b/TetradClassifier/makeJar.bat
diff --git a/TetradClassifier/program/TetradClassifier.class b/TetradClassifier/program/TetradClassifier.class
diff --git a/TetradClassifier/program/TetradClassifier.jar b/TetradClassifier/program/TetradClassifier.jar
diff --git a/TetradClassifier/program/manifest.txt b/TetradClassifier/program/manifest.txt
diff --git a/TetradClassifier/program/run.sh b/TetradClassifier/program/run.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-"/usr/java/jdk1.8.0_131/jre/bin/java" -cp /datashop/workflow_components/TetradClassifier/program/tetrad-gui-6.3.4-launch.jar -jar /datashop/workflow_components/TetradClassifier/program/TetradClassifier.jar $@
+"/usr/java/jdk1.8.0_131/jre/bin/java" -cp /datashop/workflow_components/CustomLibraries/tetrad-gui-6.3.4-launch.jar -jar /datashop/workflow_components/TetradClassifier/dist/TetradClassifier.jar $@
diff --git a/TetradClassifier/program/runOnWindows.bat b/TetradClassifier/program/runOnWindows.bat
@@ -2,4 +2,4 @@ FOR %%A IN (%*) DO (
      ECHO BATCH ARG: %%A
 )
 
-"C:/Program Files/Java/jdk1.8.0_91/bin/java.exe" -cp C:\Users\peter\Documents\CMURound2\WorkflowComponents\TetradClassifier\program\tetrad-gui-6.3.4-launch.jar -jar C:\Users\peter\Documents\CMURound2\WorkflowComponents\TetradClassifier\program\TetradClassifier.jar %*
+"C:/Program Files/Java/jdk1.8.0_91/bin/java.exe" -cp C:\Users\peter\Documents\CMURound2\WorkflowComponents\CustomLibraries\tetrad-gui-6.3.4-launch.jar -jar C:\Users\peter\Documents\CMURound2\WorkflowComponents\TetradClassifier\dist\TetradClassifier.jar %*