Deploying the BioScholar System

Here we just document the various pieces needed to run the BioScholar system within Tomcat on a Linux server.

1. bmkeg.properties

You will need to place a bmkeg.properties file that you will need to refer to when you run Tomcat.

bmkeg.workingDirectory=/nfs/amber/burns/Projects/2_active/bigMechanisms/workingDirectory/wd
bmkeg.dbDriver=com.mysql.jdbc.Driver
bmkeg.dbUrl=dbName
bmkeg.dbUser=dbLogin
bmkeg.dbPassword=dbPassword

This refers to several pieces that we will elaborate on here:

1.1 workingDirectory

This is where all the *.pdf, *.xml and *.txt files go. Typically, a working directory will have the following substructure.

+ wd
  +=> pdfs
    +=> journal
      +=> year
        +=> vol
          +=> 12345.pdf
          +=> 12345.swf
          +=> 12345_pmc.xml
          +=> 12345.txt
  +=> lod
  +=> owl
  +=> elsevierKeyFile.txt
  +=> webapp.properties

• elsevierKeyFile.txt is for logging into ScienceDirect for full text of Elsevier articles.
• lod and owl are development directories designed to use with semantic web extensions to BioScholar.
• webapp.properties are locations of executables for use of swftools and brat from within the interface.

The format is as shown below:

swftools.bin.path=/usr/local/bin
bratData.bin.path=/path/to/brat/installation/brat/brat-v1.3_Crunchy_Frog/

1. MySQL installation

Update the /etc/my.cnf configuration file with the following:

max_allowed_packet = 10485760
innodb_log_file_size = 125242880

The bmkeg.properties file must have a current login to the local MySQL system with sufficient permissions to add and delete data.

1. VPDMf data

The BioScholar system uses the ‘View-Primitive-Data-Modeling framework’ as its basis This is a local system developed within the BMKEG (see https://github.com/BMKEG/vpdmfProject which permits a data archive to be easily installed into the underlying MySQL database (or saved from an existing database).

VPDMf Binary jar file: data/vpdmfCore-1.1.5-SNAPSHOT-jar-with-dependencies.jar (34MB)

Installing the database is then pretty easy using this command:

java -cp vpdmfCore-1.1.5-SNAPSHOT-jar-with-dependencies.jar
 	edu.isi.bmkeg.vpdmf.bin.BuildDatabaseFromVpdmfArchive
 	/path/to/vpdmf/archive.zip
	dbName
	dbLogin
	dbPassword

Dumping a VPDMf database to a zip file is also pretty easy with this command (you need to refer to a previous vpdmf archive to build the system):

java -cp vpdmfCore-1.1.5-SNAPSHOT-jar-with-dependencies.jar
 	edu.isi.bmkeg.vpdmf.bin.DumpDatabaseToVpdmfArchive
 	/path/to/old/vpdmf/archive.zip
	dbName
	dbLogin
	dbPassword
 	/path/to/new/vpdmf/archive.zip		

4. Running tomcat

In order to inform Tomcat where the working directory is, you need to set some environment variables.

export TOMCAT_HOME=/path/to/tomcat
export CATALINA_OPTS="-Dbmkeg.propertiesfile=/path/to/bmkeg.properties -Xmx1096M -Xms512M"

You will then need to build the BioScholar *.war file (and place it into the $TOMCAT_HOME/webapps directory). This is 111MB in size and so is a little too big for this site.

Then all you do is TOMCAT_HOME/bin/startup.sh to start up the system.