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<!-- 
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  *   '$RCSfile$'
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  *     Purpose: web page describing the installation of Metacat
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  *   Copyright: 2000 Regents of the University of California and the
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  *               National Center for Ecological Analysis and Synthesis
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  *     Authors: Chad Berkley
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  *
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  *    '$Author: costa $'
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  *      '$Date: 2004-09-17 15:00:31 -0700 (Fri, 17 Sep 2004) $'
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  *  '$Revision: 2302 $'
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  *
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  *
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<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
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<html>
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<head>
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  <title>Metacat Installation Instructions</title>
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  <link rel="stylesheet" type="text/css" href="@docrooturl@default.css">
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</head>
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<body>
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<table class="tabledefault" width="100%">
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<tr><td rowspan="2"><img src="@docrooturl@images/KNBLogo.gif"></td>
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<td colspan="7">
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<div class="title">Metacat UNIX Installation Instructions</div>
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</td>
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</tr>
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<tr>
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  <td><a href="@server@/" class="toollink"> KNB Home </a></td>
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  <td><a href="@server@/data.html" class="toollink"> Data </a></td>
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  <td><a href="@server@/people.html" class="toollink"> People </a></td>
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  <td><a href="@server@/informatics" class="toollink"> Informatics </a></td>
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  <td><a href="@server@/biodiversity" class="toollink"> Biocomplexity </a></td>
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  <td><a href="@server@/education" class="toollink"> Education </a></td>
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  <td><a href="@server@/software" class="toollink"> Software </a></td>
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</tr>
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</table>
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<hr>
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<table class="tabledefault" width="100%">
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<td class="tablehead" colspan="2"><p class="emphasis">***Disclaimer***</p></td>
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<tr>
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<td>
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  <p class="emphasis">
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   These installation instructions are meant for a systems administrator/DBA
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   or someone who is an advanced computer user.  They are NOT meant for
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   the average computer user.  Please realize that by executing these
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   instructions, you may have to trouble shoot many advanced issues yourself.
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</td>
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</tr>
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</table>
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<table class="tabledefault" width="100%">
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<td class="tablehead" colspan="2"><p>Pre-Installation</p></td>
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<tr>
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<td>
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  <p class="header">Minimum Requirements</p> 
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  <p>
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   Installing Metacat requires a server running an SQL92 compliant database
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   (Oracle 8i recommended) with at least 128MB RAM, and a Pentium III class
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   processor or higher.  The amount of disk space required depends on the
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   size of your RDBMS tablespace (which should be at least 10 MB, 
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   however Metacat itself requires only about 1 MB of free space after 
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   installation.  These instructions assume a Linux environment but may
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   work on other UNIX type environments, however this has not been tested.
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  </p>
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  <p class = "header">Additional Required Software</p>
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  <p>
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   The server on which you wish to install Metacat must have the following
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   software installed and running correctly before attempting to install
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   Metacat.
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   <ul>
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     <li><a href="http://www.oracle.com">Oracle 8i</a> (or another SQL92
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         compliant RDBMS like Postgres)</li>
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     <li><a href="http://jakarta.apache.org/ant/index.html">Apache Jakarta-Ant</a>
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     </li>
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     <li><a href="http://jakarta.apache.org/tomcat/index.html">Apache Jakarta-Tomcat</a>
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       <p class="emphasis">Note: For a more robust web serving environment, 
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       Apache web server should
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       be installed along with Tomcat and the two should be integrated
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       as described on the Apache web site.</p>
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     </li>
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   </ul>
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  </p>
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</td>
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</tr>
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</table>
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<table class="tabledefault" width="100%">
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<td class="tablehead" colspan="2"><p>Aditional Software Setup</p></td>
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<tr>
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<td>
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  <p class="header">Java</p>
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  <p>You'll need a recent Java SDK; j2sdk1.4.2 or later is required.  We haven't 
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  tested with any of the 1.5.x versions yet, so probably best to stay with 1.4.x.
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  Make sure that JAVA_HOME environment variable is properly set and that both
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  java and javac are on your PATH.
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  </p>
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  <p class="header">Oracle 8i or Postgres</p>
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  <p><i>Oracle:</i><br>
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   The Oracle RDBMS must be installed and running as a daemon on the system.
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   In addition the JDBC listener must be enabled.  You can enable it by
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   logging in as your Oracle user and typing the following:
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   <pre>lsnrctl start</pre>
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   Your instance should have a table space of at least 5 MB (10 MB or higher 
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   recommended).  You should also have a username specific to Metacat
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   created and enabled.  This user must have most normal permissions 
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   including CREATE SESSION, CREATE TABLE, CREATE INDEX, CREATE TRIGGER, 
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   EXECUTE PROCEDURE, EXECUTE TYPE, etc.  If an action is unexplainably 
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   rejected by Metacat it is probably because the user permissions are not
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   correctly set.
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  </p>
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  <p><i>Postgres:</i><br>
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  Postgres can be easily installed on most linux distributions and on
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  Windows (using cygwin) and Mac OS X.  Using Fedora Core or RedHat Linux,
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  you can install the rpms for postgres and then run 
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  <code>/etc/init.d/postgresql start</code> in order to start the database.
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  This initializes the data files.  You need to do a bit of configuration
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  to create a database and set up a user account and allow internet access
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  via jdbc.  See the postgres documentation for this, but here is a quick 
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  start:
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  <ul>
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     <li>Switch to the "postgres" user account and edit "data/pg_hba.conf", adding the following line to the file:<br>
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     <code>host   metacat  metacat      127.0.0.1         255.255.255.255   password</code></li>
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     <li>Edit the "data/postgres.conf" file and uncomment and edit the line
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     starting with "tcpip_socket" so that it reads 
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     <code>tcpip_socket = true</code></li>
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     <li>Run <code>createdb metacat</code> to create a new database</li>
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     <li>Run <code>psql metacat</code> to log in using the postgres account and create a new "metacat" user account
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     <ul>
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        <li>In postgres, run <code>CREATE USER metacat WITH UNENCRYPTED PASSWORD 'apasswordyoulike';</code></li>
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        <li>This creates a new account called metacat on the database named metacat</li>
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        <li>Note: there are many ways to do this, so others such as using 
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        ENCRYPTED passwords will work fine.</li>
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     </ul>
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     </li>
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     <li>Exit the postgres account back to root and restart the postgres 
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     database with <code>/etc/init.d/postgresql restart</code></li>
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     <li>Test logging into the postgres db using the metacat account with 
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     the following command: 
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     <code>psql -U metacat -W -h localhost metacat</code></li>
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  </ul>
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  </p>
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  <p class="header">Ant</p>
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  <p>
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   Ant is a Java based build application similar to Make on UNIX systems.  
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   It takes in installation parameters from a file in the root installation
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   directory named "build.xml".  The Metacat CVS module contains a default
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   build.xml file that may require some modification upon installation.  Ant
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   should be installed on the system and the "ant" executable shell script 
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   should be available in the users path. We note that the current build is 
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   not working with Ant 1.6.x, so you'll need to use an earler version.  We have 
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   successfully used Ant 1.5.1, 1.5.2, and some earlier versions.
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  </p>
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  <p class="header">Tomcat</p>
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  <p>
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    Install Tomcat into the directory of your choice. The directory in which 
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    you install Tomcat itself will be referred to as the "$CATALINA_HOME".
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    We recommend that you install Tomcat version 4.0.  More details about 
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    Tomcat installation is available <a href=" http://jakarta.apache.org/tomcat/index.html">here</a>.
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  </p>
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 </td>
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</tr>
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</table>
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<table class="tabledefault" width="100%">
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<td class="tablehead" colspan="2"></td>
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<tr>
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<td>
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  <p>
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   Once all of the prerequisite software is installed as described above, 
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   the installation of Metacat can begin.  First you must have a current
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   version of the source distribution of Metacat.  You can get it two ways.
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   Authorized users can check it out of the NCEAS 
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   <a href="http://www.nceas.ucsb.edu/cgi-bin/cvsweb.cgi/xmltodb/">CVS</a>
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   system. You'll need both the "metacat" module and the "utilities" module to
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   be checked out in sibling directories. The command is as follows: 
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   <pre>mkdir knb-software</pre>
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   <pre>cd knb-software</pre>
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   <pre>cvs checkout -P metacat</pre>
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   <pre>cvs checkout -P utilities</pre>  
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   Or you can 
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   <a href="@server@/software/download.html">download</a> a gzipped tar file
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   from this site.
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  </p>
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  <p><h2>Edit <code>build.properties</code> File</h2></p>
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  <p>
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   Once you have either checked out or unzipped and untarred the source
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   distribution, you can begin the installation process.  Change into the 
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   metacat directory and edit the file called "<code>build.properties</code>".  You will need 
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   to change a number of configuration properties to match the setup on
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   your system.
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  </p>
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  <p>
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  The properties that you will likely need to change will include 
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  <code>tomcat</code>, <code>tomcatversion</code>, <code>webapps</code>, 
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  <code>context</code>, <code>server</code>, <code>httpserver</code>, 
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  <code>database</code>, <code>jdbc-connect</code>, <code>jdbc-base</code>, 
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  <code>user</code>, <code>password</code>, <code>datafilepath</code>, 
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  <code>inlinedatafilepath</code>, <code>cvsroot</code>, 
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  <code>cvsroot-alternate</code>, and <code>default-style</code>. 
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  Each is described in detail in the table below.
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  </p>
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  Properties you will likely need to change:
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  <br><br>
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  <table border="1">
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    <tr>
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      <td><b>Property</b></td>
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      <td><b>Description</b></td>
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      <td><b>Default value and examples of other values</b></td>
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    </tr>
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    <tr>
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      <td>tomcat</td>
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      <td>The tomcat property is the location in which tomcat is installed.</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>/usr/local/devtools/jakarta-tomcat</code>
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      <br><br>Example:&nbsp;&nbsp;
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          <code>C:/Tomcat4</code></td>
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    </tr>
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    <tr>
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      <td>tomcatversion</td>
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      <td>The tomcatversion property is the version of your Tomcat. You should 
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          put tomcat3 or tomcat4 here.</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>tomcat4</code>
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      <br><br>Example:&nbsp;&nbsp;
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          <code>tomcat3</code>
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      </td>
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    </tr>
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    <tr>
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      <td>webapps</td>
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      <td>The webapps property is the location in which your tomcat servlet 
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          contexts are installed. This is typically "TOMCAT_HOME/webapps",
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          where TOMCAT_HOME is the same value that you entered for the 'tomcat'
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          property above.
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      </td>
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      <td>Default:&nbsp;&nbsp;
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          <code>/var/www/org.ecoinformatics.knb</code>
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      <br><br>Example:&nbsp;&nbsp;
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          <code>C:/Tomcat4/webapps</code>
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      </td>
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    </tr>
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    <tr>
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      <td>context</td>
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      <td>The context property is the name of the servlet context in which you 
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          want Metacat to be installed. This will determine the installation 
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          directory for the servlet and many of the URLs that are used to access
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          the installed Metacat server.</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>knb</code>
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      <br><br>Example:&nbsp;&nbsp;
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          <code>mycontext</code>
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      </td>
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    </tr>
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    <tr>
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      <td>server</td>
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      <td>The server property is the secure HTTPS address on which Metacat is 
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          running (note that you should not include the 'http://' in the server 
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          property). The server setting should include the SSL port number 
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          appended to the end if Tomcat is running stand-alone (see example).</td>
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      <td>Default:&nbsp;&nbsp;
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         <code>knb.ecoinformatics.org</code>
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      <br><br>Example:&nbsp;&nbsp;
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         <code>somehost.university.edu:8443</code>
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      </td>
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    </tr>
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    <tr>
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      <td>httpserver</td>
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      <td>httpserver is the plain HTTP address on which Metacat is running 
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          (note that you should not include the 'http://' in the httpserver property).
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          The httpserver setting should include the HTTP plain port number 
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          appended to the end if Tomcat is running stand-alone (see example).</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>knb.ecoinformatics.org</code>
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      <br><br>Example:&nbsp;&nbsp;
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          <code>somehost.university.edu:8080</code>
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      </td>
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    </tr>
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    <tr>
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      <td>ldapUrl</td>
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      <td>URL to the LDAP server</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>ldap://ldap.ecoinformatics.org/dc=ecoinformatics,dc=org</code>
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      </td>
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    </tr>
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    <tr>
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      <td>database</td>
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      <td>Select the database to use for metadata storage.
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          Valid values are <code>oracle</code>, <code>postgresql</code>, or
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          <code>sqlserver</code>.
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      </td>
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      <td>Default:&nbsp;&nbsp;
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          <code>oracle</code>
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      <br><br>Other possible values:&nbsp;&nbsp;
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          <code>postgresql</code>&nbsp;&nbsp;
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          <code>sqlserver</code>
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      </td>
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    </tr>
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    <tr>
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      <td>jdbc-connect</td>
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      <td>The JDBC connection string used to connect to the database.</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>jdbc:oracle:thin:@metacat.nceas.ucsb.edu:1521:knb</code>
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      </td>
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    <tr>
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      <td>jdbc-base</td>
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      <td>The base directory for locating JDBC jar files (not needed for postgresql).</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>/usr/oracle/jdbc/lib</code>
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      <br><br>Example:&nbsp;&nbsp;
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          <code>C:/jdev10g/jdbc/lib</code><br>
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      </td>
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    </tr>
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    <tr>
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      <td>user</td>
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      <td>The database user name that you set up to use Metacat. For example, 
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          an Oracle username.</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>knb</code>
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      <br><br>Example:&nbsp;&nbsp;
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          <code>metacatdb</code>
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      </td>
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    </tr>
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    <tr>
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      <td>password</td>
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      <td>The database password that you set up to use Metacat.</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>yourPasswordHere</code>
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      <br><br>Example:&nbsp;&nbsp;
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          <code>metacat123</code>
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      </td>
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    </tr>
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    <tr>
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      <td>datafilepath</td>
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      <td>The datafilepath is the directory to store the data file.</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>/var/metacat/data</code>
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      <br><br>Example:&nbsp;&nbsp;
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          <code>C:/Tomcat4/data/knb/data</code>
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      </td>
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    </tr>
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    <tr>
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      <td>inlinedatafilepath</td>
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      <td>The inlinedatafilepath is the directory to store inline data.</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>/var/metacat/inline-data</code>
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      <br><br>Example:&nbsp;&nbsp;
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          <code>C:/Tomcat4/data/knb/inlinedata</code>
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      </td>
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    </tr>
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    <tr>
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      <td>cvsroot</td>
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      <td>CVS access to retrieve latest EML.</td>
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      <td>Default:&nbsp;&nbsp;
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          <code><pre>:ext:${env.USER}@cvs.ecoinformatics.org:/cvs</pre></code>
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          Example:&nbsp;&nbsp;
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          <code><pre>:ext:myaccount@cvs.ecoinformatics.org:/cvs</pre></code>
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      </td>
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    </tr>
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    <tr>
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      <td>cvsroot-alternate</td>
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      <td>CVS access to retrieve latest conversion styles.</td>
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      <td>Default:&nbsp;&nbsp;
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          <code><pre>:ext:${env.USER}@cvs.nceas.ucsb.edu:/cvs/pbi</pre></code>
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          Example:&nbsp;&nbsp;
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          <code><pre>:ext:myaccount@cvs.nceas.ucsb.edu:/cvs/pbi</pre></code>
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      </td>
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    </tr>
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    <tr>
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      <td>default-style</td>
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      <td>The default-style parameter defines the "style-set" that is to be used
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          by default when the qformat parameter is missing or set to "html"
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          during a query. It is set to "knb", which is one of the styles that 
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          ships with the default metacat distribution. Other possible settings
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          are shown in the examples to the right.</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>knb</code>
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      <br><br>Examples:&nbsp;&nbsp;
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          <pre><code>default   esa   knb2   nceas   nrs   obfs   specnet</code></pre>
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      </td>
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    </tr>
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  </table>
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  <br>
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  <p>
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   Note that the build file is preconfigured to install Metacat either using 
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   Oracle, PostgreSQL, or Microsoft SQL Server as a backend database.  
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   To change the database system, simply change the value of the 'database' 
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   property to be the name of the database target that you wish to use 
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   (either 'oracle', 'postgresql', or 'sqlserver').
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  </p>
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  Other properties in <code>build.properties</code> that you can (but generally need not) change:<br />
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  <br>
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  <table border="1">
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    <tr>
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      <td><b>Property</b></td>
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      <td><b>Description</b></td>
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      <td><b>Default value and examples of other values</b></td>
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    </tr>
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    <tr>
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      <td>inst.cgi.dir</td>
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      <td>Installation directory for registry CGI scripts</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>/var/www/cgi-knb</code>
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      </td>
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    </tr>
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    <tr>
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      <td>cgi-prefix</td>
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      <td>&nbsp;</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>http://knb.ecoinformatics.org/cgi-bin</code>
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      </td>
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    </tr>
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    <tr>
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      <td>knb-site-url</td>
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      <td>This is the URL to the web context root for the knb site. 
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          It is used for the qformat=knb skin only.</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>http://knb.ecoinformatics.org</code>
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      </td>
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    </tr>
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    <tr>
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      <td>forcereplicationwaitingtime</td>
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      <td>The waiting time before replication is forced to begin after
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          uploading a package. The default value should usually suffice.</td>
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      <td>Default:&nbsp;&nbsp;
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          <code>30000</code>
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          <code>&nbsp;</code>
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      </td>
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    </tr>
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  </table>
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  <p>
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  Metacat has a number of additional settable properties in file
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  <code>metacat/lib/metacat.properties</code>. Under most circumstances,
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  you will not need to modify this file because the properties of interest
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  to you can be controlled by editing <code>build.properties</code> as
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  described above. To learn more about Metacat's additional properties,
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  see <a href="./properties.html">Metacat Properties File</a>.
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  </p>
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  <p class="emphasis">
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   Note: When setting properties, DO NOT add a trailing slash [/] to the end of any paths that are specified.
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   Metacat will not function correctly if you do so.
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  </p>
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  <p class="header"><h2>SQL Scripts</h2></p>
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  <p>
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   You now need to set up the table structure in your database.  You can do
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   either do this using the ant build system, or by manually running the
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   scripts using a sql utility.
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  </p>
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  <p><b>WARNING: Do NOT run this on an existing metacat installation as it
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  will delete all of your data.  If you have an existing metacat installation,
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  see the instructions for "Upgrading" below.</b></p>
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  <p>To run the scripts using ant, type <code>ant installdb</code>.  This does 
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  not work for postgres, so you'll need to run the xmltables-postgres.sql script 
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  manually (see next paragraph).
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  </p>
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  <p>To run the scripts manually, change to the
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   metacat/build/src directory.  Then run you RDBMS's SQL utility.  In Oracle it is
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   SQLPlus.  This tutorial assumes an Oracle database so this example is for
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   SQLPlus.  Login as the oracle user that was set up for use with Metacat.
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   At the SQLPlus prompt type the following: <pre><b>@xmltables.sql;</b></pre>
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   For postgres, use a command like: 
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   <code>psql -U metacat -W -h localhost -f build/src/xmltables-postgres.sql metacat</code>
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  </p>
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  <p>Either way, 
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   you should see a bunch of output showing the creation of the Metacat table
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   space. The first time you run this script you will get several errors at the 
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   beginning saying that you cannot drop a table/index/trigger because it 
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   does not exist.  This is normal.  Any other errors besides this need to be
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   resolved before continuing. The script file name for PostgreSQL is 
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   xmltables-postgres.sql and for Microsoft SQL server is 
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   xmltables-sqlserver.sql.
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  </p>
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  <p>
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   If the script has run correctly you should be able to type 
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   <pre>describe xml_documents</pre> and it should tell you
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   <pre>
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    Name            Null?         Type
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    --------------  ------------  ---------------- 
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     DOCID          NOT NULL      VARCHAR2(250)
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     ROOTNODEID                   NUMBER(20)
485
     DOCNAME                      VARCHAR2(100)
486
     DOCTYPE                      VARCHAR2(100)
487
     DOCTITLE                     VARCHAR2(1000)
488
     USER_OWNER                   VARCHAR2(100)
489
     USER_UPDATED                 VARCHAR2(100)
490
     SERVER_LOCATION              NUMBER(20)
491
     REV                          NUMBER(10)
492
     DATE_CREATED                 DATE
493
     DATE_UPDATED                 DATE
494
     PUBLIC_ACCESS                NUMBER(1)
495
     UPDATED                      NUMBER(1)
496
   </pre>
497
  </p>
498
  <p class="header"><h2>Upgrading SQL Scripts</h2></p>
499
  <p>
500
    If you have an existing metacat installation, you should not run the install
501
    script because it will replace all of the older tables with new, empty 
502
    copies of the tables.  Thus you would lose your data!  Instead, you can 
503
    run some upgrade scripts that will change the table structure as needed for
504
    the new version.  If you are skipping versions, run each upgrade script
505
    for the intermediate versions as well.  Currently the upgrade scripts are:
506
   </p>
507
    <ul>
508
      <li>upgrade-db-to-1.2.sql</li>
509
      <li>upgrade-db-to-1.3.sql</li>
510
      <li>upgrade-db-to-1.4.sql</li>
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    </ul>
512
   <p>
513
    So, if you had an existing metacat 1.0 installation and you were upgrading 
514
    to 1.4, you would need to run all three scripts in sequence:
515
    upgrade-db-to-1.2.sql, upgrade-db-to-1.3.sql, and upgrade-db-to-1.4.sql. 
516
    However, if you were starting from a Metacat 1.3.x
517
    installation, you would only need to run the upgrade-db-to-1.4.sql script.
518
   </p>
519
  </p>
520
</td>
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</tr>
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</table>
523

    
524
<table class="tabledefault" width="100%">
525
<td class="tablehead" colspan="2"><p><h2>Compilation and Installation</h2></p></td>
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<tr>
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<td>
528
  <a name="protocol"></a>
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  <p>
530
   Ant allows compilation and installation to be done in one step.
531
   Change into the metacat directory and type: 
532
   <pre><b>ant geteml install</b></pre>
533
   or, if you are upgrading an existing installation, type:
534
   <pre><b>ant clean geteml upgrade</b></pre>
535
   <p>
536
   You should see a bunch of messages telling you the progress of compilation
537
   and installation.  When it is done you should see the message 
538
   BUILD SUCCESSFUL
539
   and you should be returned to a UNIX command prompt.  If you do not see
540
   the message BUILD SUCCESSFUL then there was an error that you need to 
541
   resolve.
542
   This may come up if you are logged in as a user that does not have write
543
   access to one or more of the directories that are listed in the build.xml
544
   file, or if any of the paths to files are not configured correctly in the
545
   "config" target.
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  </p>
547
  <p>Once metacat itself is installed, you should also register
548
  the Ecological Metadata Language (EML) DTDs and schemas. This process is done most
549
  easily by running:</p>
550
  <pre><b>ant dtdschemasql</b></pre> 
551
  <p>This command registers the DTDs' and schemas' location in the 
552
  metacat server.  Your database username and password have to be set correctly
553
  for this to work.
554
  </p>
555
  <p>
556
  Note: The 'data' directory in the installation directory must be writeable
557
  by whatever user is running Tomcat or you will not be able to upload data 
558
  files to the system.
559
  <h2>Restart Tomcat</h2>
560
  <p>
561
   Once you have successfully installed Metacat, there is one more step.  Tomcat
562
   (and Apache if you have Tomcat integrated with it) must be restarted.  To do
563
   this, login as the user that runs your tomcat server (often "tomcat"),
564
   go to $CATALINA_HOME/bin and type:
565
   <pre>
566
   ./shutdown.sh 
567
   ./startup.sh 
568
   </pre>
569
   In the Tomcat startup messages you should see something in log file like:
570
   <pre>
571
    MetacatServlet Initialize
572
    Context log path="/metadata" :Metacat: init
573
    MetacatServlet Initialize
574
   </pre>
575
   If you see that message Tomcat is successfully loading the Metacat servlet.
576
   Next, try to run your new servlet.  Go to a web browser and type:
577
   <pre>http://yourserver.yourdomain.com/yourcontext/</pre>
578
   You should substitute your context name for "yourcontext" in the url above.
579
   If everything is working correctly, you should see a query page followed
580
   by an empty result set.  Note that if you do not have Tomcat integrated with
581
   Apache you will probably have to type
582
   <pre>http://yourserver.yourdomain.com:8080/yourcontext/</pre>
583
  </p>
584
</td>
585
</tr>
586
</table>
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</body>
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