Install: IWBase Domain Node

1. Install Tomcat on your computer, if you don't have it yet. Download and install Tomcat from jakarta.apache.org. We are going to use $TOMCAT to refer to the root directory where Tomcat is installed. The PML Browser may work with other servlet container or J2EE application server although we have tested it for Tomcat version 5.0 only.

2. Add owl to Tomcat default MIME type mappings.
   • Edit Tomcat configuration file web.xml located at $TOMCAT/conf
   • Search for a "<mime-mapping>" element.
   • You are probably at the top of a list of mime mappings. Thus, add the following lines to this list of mappings (for example, you may add the owl mapping below to top of the list):
   
   
   <mime-mapping>
       <extension>owl</extension>
       <mime-type>text/xml</mime-type>
   </mime-mapping>
   
   
   • Save Tomcat web.xml configuration file

   
   

3. An IW configuration file (iw.xml) is needed to setup the IWBase node. If your system has other IW applications installed, it may already have an iw.xml file and you can skip to step 5. Otherwise, you will need to follow the steps below:
   • Create a directory in your filesystem for storing your IW configurations. This is going to be your system's $IW_HOME directory. It can be located anywhere in your filesystem (for example, $IW_HOME can be created as $TOMCAT/iw).
   • Within $IW_HOME, create another directory named "conf".
   • download a copy of the [IW configuration file] and place it in $IW_HOME/conf.

   
   

4. Define $IW_HOME as a global JNDI resource in your Tomcat configuration file.
   • Edit Tomcat configuration file server.xml located at $TOMCAT/conf
   • Search for the <GlobalNamingResources> element in the file
   • Somewhere within the element (after <GlobalNamingResources> and before </GlobalNamingResources>), add the following line replacing (your IW_HOME) by the actual value of $IW_HOME:
     (Please use the absolute address of $IW_HOME)
   
   
   <Environment name="iwhome" type="java.lang.String" value="(your IW_HOME)" override="true"/>
   
   
   • Do not save the file yet.

   
   

5. Define a JNDI IWRegistrar context with a datasource. Associate $IW_HOME with the context.
   • Edit Tomcat configuration file server.xml that is located at $TOMCAT/conf (if it is not open yet)
   • Search for the "localhost" Host element (you may search for the string "<Host name="localhost"".
   • For Tomcat 5.0.* and early version, add the following lines within the host element:
   
   <Context path="/iwregistrar" docBase="iwregistrar"
       debug="5" reloadable="true" crossContext="true">
       <ResourceLink name="iwhome" global="iwhome" type="java.lang.String"/>
       <Resource name="jdbc/IWBase" reloadable="true" auth="Container"
          type="javax.sql.DataSource" description="" />
       <ResourceParams name="jdbc/IWBase">
          <parameter>
           <name>factory</name>
           <value>org.apache.commons.dbcp.BasicDataSourceFactory</value>
          </parameter>
          <parameter>
           <name>maxActive</name>
           <value>100</value>
          </parameter>
          <parameter>
           <name>maxIdle</name>
           <value>30</value>
          </parameter>
          <parameter>
           <name>maxWait</name>
           <value>10000</value>
          </parameter>
          <parameter>
           <name>removeAbandoned</name>
           <value>true</value>
          </parameter>
          <parameter>
           <name>removeAbandonedTimeout</name>
           <value>60</value>
          </parameter>
          <parameter>
           <name>username</name>
           <value>dbuname</value>
          </parameter>
          <parameter>
           <name>password</name>
           <value>dbuPWD</value>
          </parameter>
          <parameter>
           <name>driverClassName</name>
           <value>com.mysql.jdbc.Driver</value>
          </parameter>
          <parameter>
           <name>url</name>
           <value>jdbc:mysql://host.Stanford.EDU/dbname?autoReconnect=true</value>
          </parameter>
     </ResourceParams>
   </Context>
   
   For Tomcat 5.5.* and later version, add the following lines withing the host element:
   

           <Context path="/iwregistrar" docBase="iwregistrar"
   	  debug="5" reloadable="true" crossContext="true" >
            
             <ResourceLink name="iwhome" global="iwhome" type="java.lang.String" />
   
             <Resource name="jdbc/IWBase" reloadable="true" auth="Container"
                 type="javax.sql.DataSource" description=""
                 maxActive="100" maxWait="10000" maxIdle="30" 
                 username=dbuname password=dbuPWD 
                 driverClassName="com.mysql.jdbc.Driver"
                 url="jdbc:mysql://host.domain/dbname?autoreconnect=true" >
             </Resource>
   
           </Context>
          

   Please note that this intallation instruction assumes that the war file in step 12 is going to be named "iwregistrar.war". If not, you may need to change the context above accordingly.
   • More information regarding context datasources is available at jakarta.apache.org
   • Save the configuration file

   
   

6. Install MySQL on your computer, if you don't have it yet. Download and install MySQL from http://www.mysql.com. The IWBase node may work with other relational database management system although we have tested it for MySQL only.

7. Make sure you have the JDBC driver for your database. For MySQL, you can download Connector/J from http://www.mysql.com/products/connector/j/, and install it in $TOMCAT/common/lib directory.

8. Create a database for IW, lets say, named iwbase.
• Log into MySQL as root by typing "mysql at the prompt of your operating system.
• Once logged into mysql, type the following:
  

  "create database iwbase;"
  

  (Please do not forget to use semi-colon to finish commands in the mysql shell)

9. Define a database user account for IW to use, lest say, named iwuser.
   • This user account needs to have access to IW's databases and tables from host that Tomcat runs. Still logged as root in mysql, type the following:
     

     "grant all on iwbase.* to 'iwuser'@'(hostname)' identified by '(password)';
     

     (Please make sure that hostname corresponds to Tomcat's host machine)

10. Create IW tables in MySQL.
    • Download corresponding [IW domain node database schema].
    • Log into MySQL as iwuser: mysql -user=iwuser -p and then reply to the prompt asking for iwuser's password
    • Set iwbase as the current database by typing "\u iwbase;"
    • Execute the IW database schema file by typing the following:
      

      "\. IWBaseSchema.sql"
      

      (In the command above, we assume that IWBaseSchema.sql was saved with its original name and placed on the same directory from where you are calling mysql)

11. Create Tomcat users for IWBase maintenance.
    
    Some but not necessarily all IWBase Teams need to perform IWBase maintenance work such as entry adding and updating. For instance, your organization may have a team named ONTO-TEAM responsible for the development of some ontologies. Members of ONTO-TEAM, however, are not responsible for maintaining ontology entries in IWBase. Thus, ONTO-TEAM just needs to be registered in IWBase in order to be assigned as an IWBase Source for ontologies.

    Now, suppose that members of METADATA-TEAM are responsible for the maintenance of ontology entries in IWBase. Thus, a Tomcat user named METADATA-TEAM must be defined in order to authenticate METADATA-TEAM. In fact, one Tomcat user must be defined for each team performing maintenance work and IWsupervisor and IWontuser roles must be granted to these Tomcat users.

    Within $TOMCAT/conf/tomcat-users.xml, create Tomcat users and assign IWsupervisor and IWontuser roles to them. For example, to register METADATA-TEAM as a Tomcat user, add the following line:
    

    <user name="METADATA-TEAM" password="passwd" roles="IWontuser, IWsupervisor" />

    If you are familiar with Tomcat's "admin" application, feel free to use it to create roles and users.

12. Install JDBC driver properly. If you use Tomcat and MySQL combo, put the mysql connector jar file in Tomcat's common/lib directory.

13. Deploy the IWBase Domain Node software.
    • Download the [IW base domain node WAR file]
    • place the war file on $TOMCAT/webapps

14. If you deploy the registry as a Web application under a servlet engine, e.g. Tomcat, rather than a document tree under a Web server, make sure you have WEB-INF directory and web.xml file placed properly.

15. Restart Tomcat
    • If Tomcat is running, use $TOMCAT/bin/shutdown.sh to shut it down
    • If you are upgrading the IWBase Node software, we suggest a complete deletion of the following directories:
      • $TOMCAT/webapps/iwregistrar
      • $TOMCAT/work/Catalina/localhost/iwregistrar
    • Use $TOMCAT/bin/startup.sh to startup Tomcat

    
    

16. Initialize the first Team in the IWBase Domain Node
    • Log in selecting the Login link on the initial screen and using the login names and password specified on step 11.
    • Select options Team > Add.
    • When registering the first team, enter the Tomcat user ID as Short name exactly as it appears as in $TOMCAT/conf/tomcat-users.xml.
    • Enter a Full name for the team. The full name is not relevant for login purposes. An optional URL can also be specified for the team.
    • Click the Add buttom to insert the new team.

    The above steps will create the root team for the node.
    
    

17. The IWBase Node should be functional.