Setting up Ptolemy II using Maven

Note that building Ptolemy II with Maven requires an Internet connection. The mvn compile step will download modules from the net.

These notes are based on Tristan King's work, see his July 21, 2008 ptolemy-hackers post: updates on ptII maven and actor.io work.

Setting up Maven

Download Maven from http://maven.apache.org/download.html

Install

Download Ptolemy II and set the $PTII environment variable.
example:

	  cd /path/to/working/directory/
          git clone --depth=50 --branch=master --single-branch https://github.com/icyphy/ptII
	  export PTII=/path/to/working/directory/ptII

Optional: Delete $PTII/vendors
example:
```
	  rm -r $PTII/vendors
	
```
Make sure that when in $PTII, $PTII==pwd:
```
          bash-3.2$ cd $PTII
          bash-3.2$ echo $PTII
          /Users/cxh/ptII
          bash-3.2$ pwd
          /Users/cxh/ptII
	
```
If the current working directory is a symbolic link to the actual directory where $PTII is located, then be sure to change either $PTII or the current working directory so they both match.
Set MAVEN_OPTS to configure maven to use large amounts of memory
example:
```
	  export MAVEN_OPTS="-Xms512m -Xmx512m -XX:PermSize=48m"
	
```
Configure Ptolemy II to Exclude the Eclipse plugi:
```
          ./configure --without-eclipse
	
```
FIXME: $PTII/pom.xml needs to be extended to include support for Eclipse, see below

Tell Maven about the jar files necessary to compile:

	  mvn install:install-file -DgroupId=caltrop -DartifactId=ptCal -Dversion=ptII -Dpackaging=jar -Dfile=$PTII/lib/ptCal.jar
	  mvn install:install-file -DgroupId=chic -DartifactId=chic -Dversion=ptII -Dpackaging=jar -Dfile=$PTII/lib/chic.jar
	  mvn install:install-file -DgroupId=jacl -DartifactId=jacl -Dversion=ptII -Dpackaging=jar -Dfile=$PTII/lib/ptjacl.jar
	  mvn install:install-file -DgroupId=javajoystick -DartifactId=joystick -Dversion=0.7 -Dpackaging=jar -Dfile=$PTII/vendors/misc/joystick/Joystick.jar 
	  mvn install:install-file -DgroupId=jna -DartifactId=jna -Dversion=4.0.0-variadic -Dpackaging=jar -Dfile=$PTII/lib/jna.jar 
	  mvn install:install-file -DgroupId=jxta -DartifactId=jxtasecurity -Dversion=1.0 -Dpackaging=jar -Dfile=$PTII/vendors/sun/jxta/jxtasecurity.jar
	  mvn install:install-file -DgroupId=kieler -DartifactId=kieler -Dversion=ptII -Dpackaging=jar -Dfile=$PTII/lib/kieler.jar
	  mvn install:install-file -DgroupId=mapss -DartifactId=mapss -Dversion=ptII -Dpackaging=jar -Dfile=$PTII/lib/mapss.jar
	  mvn install:install-file -DgroupId=org.eclipse.jetty -DartifactId=jetty-all -Dversion=8.1.5-v20120716 -Dpackaging=jar -Dfile=$PTII/lib/jetty-all-8.1.5-v20120716.jar
	  mvn install:install-file -DgroupId=PDFRenderer -DartifactId=PDFRenderer -Dversion=ptII -Dpackaging=jar -Dfile=$PTII/lib/PDFRenderer.jar
	  mvn install:install-file -DgroupId=javax.servlet -DartifactId=servlet-api -Dversion=3.0.1 -Dpackaging=jar -Dfile=$PTII/lib/javax.servlet-api-3.0.1.jar 
	  mvn install:install-file -DgroupId=soot -DartifactId=sootclasses -Dversion=ptII -Dpackaging=jar -Dfile=$PTII/lib/sootclasses.jar
	  mvn install:install-file -DgroupId=jivesoftware -DartifactId=smack -Dversion=3.0.4 -Dpackaging=jar -Dfile=$PTII/lib/smack.jar
	  mvn install:install-file -DgroupId=org.mobicents.slee.resource.smack -DartifactId=smackx -Dversion=3.0.4 -Dpackaging=jar -Dfile=$PTII/lib/smackx.jar
	  mvn install:install-file -DgroupId=protobuf -DartifactId=protobuf -Dversion=ptII -Dpackaging=jar -Dfile=$PTII/lib/protobuf-java-2.4.1.jar 
	  mvn install:install-file -DgroupId=g4ltl -DartifactId=g4ltl -Dversion=ptII -Dpackaging=jar -Dfile=$PTII/lib/g4ltl.jar
	  mvn install:install-file -DgroupId=oscP5 -DartifactId=oscP5 -Dversion=ptII -Dpackaging=jar -Dfile=$PTII/lib/oscP5.jar

$PTII/pdb uses db and dbxml, which are basically GPL'd. If you want use ptdb, download db and dbxml from http://www.oracle.com/technology/software/products/berkeley-db/xml/index.html and place them in $PTII/vendors/oracle/, then run:

	  mvn install:install-file -DgroupId=dbxml -DartifactId=db -Dversion=ptII -Dpackaging=jar -Dfile=$PTII/vendors/oracle/db.jar
	  mvn install:install-file -DgroupId=dbxml -DartifactId=dbxml -Dversion=ptII -Dpackaging=jar -Dfile=$PTII/vendors/oracle/dbxml.jar

Run vergil! This can be done in a few different ways:

Run vergil using maven.
example:
```
	      cd /path/to/ptII-maven/
	      mvn compile
	      mvn exec:exec
	    
```
Note that mvn exec:exec requires net access. To run offline, run: mvn -o exec:exec

Build a ptolemy II jar and run vergil from run-vergil.sh.
run-vergil.sh would look like:

	      #!/bin/bash
	      .java -classpath $PTII/target/ptII-7.1.devel-SNAPSHOT.jar:~/.m2/repository/caltrop/ptCal/unknown/ptCal-unknown.jar:~/.m2/repository/net/jini/jini-core/2.1/jini-core-2.1.jar:~/.m2/repository/antlr/antlr/2.7.6/antlr-2.7.6.jar:~/.m2/repository/javax/jms/jms/1.1/jms-1.1.jar:~/.m2/repository/jdom/jdom/1.0/jdom-1.0.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.15/jre/../lib/tools.jar:~/.m2/repository/chic/chic/unknown/chic-unknown.jar:~/.m2/repository/jxta/jxtasecurity/1.0/jxtasecurity-1.0.jar:~/.m2/repository/jxta/jxta/1.0/jxta-1.0.jar:~/.m2/repository/log4j/log4j/1.2.15/log4j-1.2.15.jar:~/.m2/repository/javax/activation/activation/1.1/activation-1.1.jar:~/.m2/repository/net/jini/jini-ext/2.1/jini-ext-2.1.jar:~/.m2/repository/jython/jython/svn/jython-svn.jar:~/.m2/repository/java3d/j3d-core/1.3.1/j3d-core-1.3.1.jar:~/.m2/repository/jacl/jacl/ptII/jacl-ptII.jar:~/.m2/repository/colt/colt/1.0.3/colt-1.0.3.jar:~/.m2/repository/org/beanshell/bsh/2.0b4/bsh-2.0b4.jar:~/.m2/repository/javajoystick/joystick/0.7/joystick-0.7.jar:~/.m2/repository/mapss/mapss/unknown/mapss-unknown.jar:~/.m2/repository/javax/mail/mail/1.4/mail-1.4.jar:~/.m2/repository/com/sun/jmx/jmxri/1.2.1/jmxri-1.2.1.jar:~/.m2/repository/java3d/vecmath/1.3.1/vecmath-1.3.1.jar:~/.m2/repository/javax/media/jai_core/1.1.2_01/jai_core-1.1.2_01.jar:~/.m2/repository/soot/sootclasses/ptII/sootclasses-ptII.jar:~/.m2/repository/com/sun/jdmk/jmxtools/1.2.1/jmxtools-1.2.1.jar
	      ptolemy.vergil.VergilApplication

example:

  
	      # run these two steps only once
	      cd /path/to/ptII-maven/	
	      mvn package
	      # then
	      /path/to/run-vergil.sh

Note that the version numbers are hardwired into the path, which is why this file is not checked in. Another issue is that this command build a jar file, which slows down the build/test cycle.

maven compile fails

Below are various issues that occurred during the build.

What about "make maven"?

mk/ptcommon.mk includes a rule that will create a ptII/src directory. The current ptII/pom.xml file does not use this directory, so there is no need to run make maven

Problem: you need to be on line to compile
[INFO] artifact org.apache.maven.plugins:maven-resources-plugin: checking for updates from central [WARNING] repository metadata for: 'artifact org.apache.maven.plugins:maven-resources-plugin' could not be retrieved from repository: central due to an error: Error transferring file [INFO] Repository 'central' will be blacklisted

This can happen if there is no network connection when

mvn
	  compile

is run.
Solution:
Remove ~/.m2/repository/org/apache/maven/plugins/maven-resources-plugin or just remove all of ~/.m2.

Problem: antlr not found
Missing: ---------- 1) antlr:antlr:jar:2.9.9 Try downloading the file manually from the project website. Then, install it using the command: mvn install:install-file -DgroupId=antlr -DartifactId=antlr \ -Dversion=2.9.9 -Dpackaging=jar -Dfile=/path/to/file Path to dependency: 1) edu.berkeley.eecs.ptolemy:ptII:jar:7.1.devel-SNAPSHOT 2) antlr:antlr:jar:2.9.9

Solution:

mvn install:install-file -DgroupId=antlr -DartifactId=antlr -Dversion=svn -Dpackaging=jar -Dfile=$PTII/ptolemy/actor/ptalon/antlr/antlr.jar

Then rerun mvn compile

Problem: antlr still not found

Solution: Edit pom.xml and change the antlr version number from 2.9.9 to 2.7.7

Problem: ptalon
[INFO] The grammar '/Users/cxh/Documents/workspace/ptII/src/main/antlr/ptolemy/actor/ptalon/parser.g' doesnt exist.

Solution: copy the files

	  cd $PTII
	  mkdir -p src/main/antlr/ptolemy/actor/ptalon
	  cp $PTII/ptolemy/actor/ptalon/*.g src/main/antlr/ptolemy/actor/ptalon

However, it turned out that none of the files were being copied because $PTII was a symbolic link. See below.

Problem: can't start
Exception in thread "main" java.lang.NoClassDefFoundError: ptolemy/vergil/VergilApplication

It turns out that the java files were not copied to the right location. $PTII/target/ptII-7.1.devel-SNAPSHOT.jar only contained the antlr classes. The problem was that the toplevel directory where make maven was run was a symbolic link to the actual $PTII directory. The fix was to make sure that in $PTII, $PTII==pwd:

	  bash-3.2$ cd $PTII
	  bash-3.2$ echo $PTII
	  /Users/cxh/ptII
	  bash-3.2$ pwd
	  /Users/cxh/ptII

and then to run


	  make maven
	  mvn compile

Problem: compilation fails
/Users/cxh/Documents/workspace/ptII/src/main/java/ptolemy/moml/jxta/JXTALibrary.java:[44,27] package net.jxta.credential does not exist

Solution:
Edit $PTII/pom.xml and uncomment the jxta section

Problem: compilation fails on Eclipse files /Users/cxh/Documents/workspace/ptII/src/main/java/ptolemy/backtrack/eclipse/ast/transform/PackageRule.java:[36,32] package org.eclipse.jdt.core.dom does not exist

Proposed Solution: We use the Maven Eclipse Plugin

	    mvn -Declipse.workspace=/Applications/eclipse eclipse:add-maven-repo
	    mvn -DeclipseDir=/Applications/eclipse eclipse:to-maven

However, the problem is telling Maven where to find the Eclipse jars. One idea would be to add dependencies for each jar via configure. However, our workaround is to just not copy the Eclipse plugin files to $PTII/src by running ./configure --without-eclipse.

"mvn package" fails because of backtracking /Users/cxh/ptII/ptolemy/backtrack/eclipse/plugin/editor/PtolemyEditor.java:[52,35] cannot find symbol

Solution: disable test-compile:

	    <properties>
	      <!-- skip test-compile when doing "maven package" -->
	      <maven.test.skip>true</maven.test.skip>
	    </properties>

Maven and Web Start

Install
```
	  mvn install webstart:jnlp
	
```

has no matching file, why? Check the logs

When running maven webstart:jnlp, I get

	  Embedded error: artifact org.ptolemy:ptII:jar:7.2.devel has no matching file, why? Check the logs...

See "3.5.3. Maven Coordinates" of the maven manual, which describes the naming for artifacts. It turns out that the jnlp rule needed to have:

	  <artifactItems>
	  <artifactItem>
	  <groupId>org.ptolemy</groupId>
	  <artifactId>ptII-7.2.devel.jar</artifactId>
	  <version>7.2.devel</version>
	  <type>jar</type>                            
	  </artifactItem>
	  </artifactItems>

Maven and OSGI

Bundle Plugin for Maven

Maven Notes

Why does make maven copy the .java files? This means that we have yet another copy of the code and that changes to the master .java files are not propagated?
Having resources separate from the sources makes no sense for a componetized architecture. Every time a package is moved, the resources need to be moved. The resources should be in the jar that uses the resources.
Don't run "mvn clean" it will remove $PTII!
The $PTII/pom.xml file lists dev.archer.edu.au as the repository, this should probably be changed.
What if not all optional components are available? Should there be a configure stage?
Can we automatically generate run-vergil.sh? That file has version numbers hard coded in.
What about the Eclipse jar files for backtracking?