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In Sept 2011 Jeff Sale joined the cipres team as a new developer.  These are notes about what I 
had to do to configure a build and development environment for him on 8ball.sdsc.edu.  We use 
8ball to host our test instance of the application and I also use it to run my development 
instance. Some of the issues I ran into were making sure the ports used by our tomcat servers 
didn't conflict and that we weren't writing to any of the same files.

According to Paul Hoover it is possible to set up a development instance on one's mac, you 
just need to configure database.tempfileRoot to point to a local path.  It isn't however 
possible to deploy to windows and have a fully functional application because of our use of 
shell scripts. 

	* Jeff's login name is "jsale".

	* Jeff got an account on 8ball in the ngbw group, with login shell = /bin/bash.

	* I created /projects/cipres/jsale directory for Jeff since none of us have enough 
	space in our home directories.

Here's what we needed to do next:

	* Check out trunk versions of sdk, cipres-portal and documents directories from svn, to
	/projects/cipres/jsale.

	* Install tomcat 5.5.27 under /projects/cipres/jsale. Find free ports to run tomcat on and 
	configure tomcat's conf/server.xml file.  Jeff is using 6080.

	* Create an sdk_versions directory and set the env var SDK_VERSIONS to point to it.  
	Here are all the changes to Jeff's .bashrc, including SDK_VERSIONS:

		export SDK_VERSIONS=/projects/cipres/jsale/cipres/sdk_versions
		export PATH=$SDK_VERSIONS:$SDK_VERSIONS/current:$PATH

		export LD_LIBRARY_PATH=/usr/local/lib:${LD_LIBRARY_PATH}
		export PYTHONPATH=/fs/cipres/misc/python-gd/lib/python:/archive/science/ngbt/python/PyMySQL-0.4
		export CATALINA_HOME=/projects/cipres/jsale/apache-tomcat-5.5.27
		export SVNROOT=http://nladr-cvs.sdsc.edu/svn/CIPRES/cipresdev
		export SVN_EDITOR=/bin/vi
		export MAVEN_OPTS=-"Xms512M -Xmx512M"
		export JAVA_HOME=/usr/local/apps/java-1.5

		# Jeff is using my globus installation.
		export GLOBUS_LOCATION=/projects/cipres/terri/teragrid/globus
		export MYPROXY_SERVER=myproxy.teragrid.org
		export MYPROXY_SERVER_PORT=7514
		export GLOBUS_TCP_PORT_RANGE=50000,51000
		source $GLOBUS_LOCATION/etc/globus-user-env.sh

	* Create ~jsale/.m2/settings.xml and set permissions to 600 (ie. only owner can read it).
	Passwords are shown here as PASSWORD - need to be replaced with the real passwords.

		<settings>
			<servers>
				<server>
					<id>tomcat</id>
					<username>admin</username>
					<password>PASSWORD</password>
				</server>
				<!-- For adding jars to our maven repository -->
				<server>
					<id>maven-repository-production</id>
					<username>maven</username>
					<password>PASSWORD</password>
				</server>
			</servers>
			<activeProfiles>
				<activeProfile>always</activeProfile>
			</activeProfiles>
			<profiles>
				<!-- This is always active for sdsc builds -->
				<profile>
					<id>always</id>
					<properties>
						<eightball.username>bwbatch</eightball.username> 
						<eightball.password>PASSWORD</eightball.password> 
						<snooker.username>bwbatch</snooker.username> 
						<snooker.password>PASSWORD</snooker.password> 
						<db.ngbw.test.username>ngbw</db.ngbw.test.username>
						<db.ngbw.test.password>PASSWORD</db.ngbw.test.password>
						<db.ngbw.production.username>ngbw</db.ngbw.production.username>
						<db.ngbw.production.password>PASSWORD</db.ngbw.production.password>
						<teragrid.username>cipres</teragrid.username> 
						<teragrid.password>PASSWORD</teragrid.password> 
						<triton.username>cipres_test</triton.username>
						<triton.keyFile>${env.HOME}/.ssh/id_dsa</triton.keyFile>
					</properties>
				</profile>
			</profiles>
		</settings>

	* To submit serial jobs like clustalw to triton the developer must make sure he can ssh to 
	cipres_test@triton-login.sdsc.edu without being prompted for a password.  To make this work, 
	append the developer's .ssh/id_dsa.pub to cipres_test@triton-login.sdsc.edu/.ssh/authorized_keys.

	* Make sure the local maven repo is running on 8ball:
		maven repository on 8ball: http://8ball.sdsc.edu:9999/maven2/
		host: 8ball.sdsc.edu
		port: 9999
		login: maven
		password: cac...
		Apache installation: /users/u4/maven/apache_webserver
		To start/stop the server: apachectl [start | stop | restart]

	* I found that the sdk/properties/cipres-dev.properties had a number of settings that would 
	cause collisions between Jeff and my development instances.  I grouped these properties together 
	at the end of the file AND I moved cipres-dev.properties to cipres-dev.properties.template.  
	This way we will both need to copy the .template file to cipres-dev.properties and
	modify it before we can do a build.  

	I used to create certain files in /tmp.  Now, I instead have a ~/cipres_tmp directory, and 
	I configured the same for Jeff.  Jeff's properties are:

		grid.myproxyfile=/users/u2/jsale/cipres_tmp/x509_cipres
		disabled.resources.file=/users/u2/jsale/cipres_tmp/disabled_resources
		process_worker_logs=/users/u2/jsale/cipres_tmp
		portal.url=http://8ball.sdsc.edu:6080/portal2
		job.callback.url=http://8ball.sdsc.edu:6080/portal2/taskupdate.action

	* Once the application was built and deployed, I got an error getting a certificate when I tried to 
	submit a teragrid job.  To fix this I: 
		- moved Jeff's existing ~/.globus directory to ~/.globus_save and created a new 
		empty ~/.globus
		- reran the build so that ~/.globus would be populated with our files.
		- ran sdk/scripts/update_crl.sh to populate the ~/.globus/certificates
		  directory.

The development build process is usually just:
	cd cipres-portal
	sh tl.sh

But, the first time (and then again, if either tl.sh or cipres-dev.properties.template have changed) 
there are a few extra steps:

	[ put the build script, "tl.sh" where it's needed ]
	cd cipres-portal
	cp scripts/tl.sh .

	[ create cipres-dev.properties from the template ]
	cd ../sdk/properties
	cp cipres-dev.properties.template cipres-dev.properties
	[and then edit cipres-dev.properties as explained above]

	[ now you can do the build ]
	cd ../cipres-portal
	sh tl.sh

Log files are under $CATALINA_HOME/logs and ~/cipres_tmp.