Here we just document the various pieces needed to run the BioScholar system within Tomcat on a Linux server.
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:
This is where all the
*.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.txtis for logging into ScienceDirect for full text of Elsevier articles.
owlare development directories designed to use with semantic web extensions to BioScholar.
webapp.propertiesare locations of executables for use of
bratfrom within the interface.
The format is as shown below:
/etc/my.cnf configuration file with the following:
max_allowed_packet = 10485760 innodb_log_file_size = 125242880
bmkeg.properties file must have a current login to the local MySQL system with sufficient permissions to add and delete 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).
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
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.