Index: docs/user/index.html
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-<!DOCTYPE html PUBliC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>KNB Software: Metacat</title>
-  <link rel="stylesheet" type="text/css" href="./default.css">
-</head>
-
-<body>
-
-<table class="tabledefault" width="100%">
-<tr>
-  <td rowspan="2"><img src="./images/KNBLogo.gif"></td>
-  <td colspan="7"><div class="title">Metacat: data and metadata catalog</div></td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
-<p>&nbsp;</p>
-<table class="tabledefault" width="100%">
-<tr>
-  <td class="tablehead" colspan="2"><p class="label">Metacat: a flexible 
-      metadata catalog and data repository</p></td>
-</tr>
-<tr>
-  <td>
-  <p><a href="/software/download.html">Download Metacat</a></p>
-  <h3>Documentation and Installation Instructions</h3>
-  <ul>
-    <li><a
-    href="/software/dist/MetacatAdministratorGuide.pdf">Metacat
-    Administrator's Guide</a></li>
-  </ul>
-  <img src="images/metacat-logo.png" alt="Metacat" style="float: right;
-  height: 100px"/> 
-  <p>Metacat is a flexible, open source metadata catalog and data repository 
-  that targets scientific data, particularly from ecology and environmental
-  science.  Metacat accepts 
-     <a href="http://www.w3.org/TR/REC-xml" target="offline">XML</a> as a 
-     common syntax for representing the large number of metadata content
-     standards that are relevant to ecology and other sciences.  Thus, Metacat 
-     is a generic XML database that allows storage, query, and retrieval of 
-     arbitrary XML documents without prior knowledge of the XML schema.
-  </p>
-  <p>
-    Metacat is being used extensively <a href="/community.jsp">throughout the 
-    world</a> to manage environmental data. It is a key infrastructure
-    component for the <a href="http://data.nceas.ucsb.edu">NCEAS data catalog</a>, the <a href="http://knb.ecoinformatics.org/">Knowledge Network
-    for Biocomplexity (KNB)</a> data catalog, and for the <a href="http://dataone.org">DataONE</a> system, <a href="/community.jsp">among others</a>.</p>
-  </td>
-</tr>
-<tr><td>&nbsp;</td></tr>
-
-</table>
-
-<iframe width="500" height="350" frameborder="0" scrolling="no"
-marginheight="0" marginwidth="0"
-src="http://maps.google.com/maps/ms?ie=UTF8&amp;hl=en&amp;msa=0&amp;msid=111257081347673397900.00000111e7923f163c54e&amp;ll=10.487812,-8.4375&amp;spn=152.923473,351.5625&amp;z=1&amp;output=embed"></iframe><br
-/><small>View <a
-href="http://maps.google.com/maps/ms?ie=UTF8&amp;hl=en&amp;msa=0&amp;msid=111257081347673397900.00000111e7923f163c54e&amp;ll=10.487812,-8.4375&amp;spn=152.923473,351.5625&amp;z=1&amp;source=embed"
-style="color:#0000FF;text-align:left">Metacat deployments</a> in a larger
-map</small>
-
-<p class="contact">
-Web Contact: <a href="mailto:jones@nceas.ucsb.edu">jones@nceas.ucsb.edu</A>
-</p>
-</body>
-</html>

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Index: docs/user/replication.html
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-<!--
-  * replication.html
-  *
-  *      Authors: Chad Berkley
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2001 January 23
-  *      Version: 
-  *    File Info: '$ '
-  * 
-  * 
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat Replication</TITLE>
-<link rel="stylesheet" type="text/css" href="./common.css">
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Replication</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./packages.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./datafiles.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  
-  <div class="header1">Table of Contents</div>
-  <div class="toc1"><a href="#Intro">Metacat Replication</a></div>
-    <div class="toc2"><a href="#Overview">Overview</a></div>
-    <div class="toc2"><a href="#DatabasedInfo">Databased Information</a></div>
-    <div class="toc2"><a href="#Example">Example</a></div>
-      <div class="toc3"><a href="#gamma">What happens with gamma?</a></div>
-      <div class="toc3"><a href="#alpha">What happens with alpha?</a></div>
-      <div class="toc3"><a href="#lamda">What happens with lamda?</a></div>
-  <div class="toc1"><a href="#ControlPanel">The Replication Control Panel</a></div>
-  <div class="toc1"><a href="#Certificates">Certificates</a></div>
-    <div class="toc2"><a href="#GenerateCertificates">Generate Certificates on both the replication client and server.</a></div> 
-      <div class="toc3"><a href="#GenerateCertTomcat">Generate Certificate for Tomcat standalone (no Apache)</a></div>
-      <div class="toc3"><a href="#GenerateCertApache">Generate Certificate for Apache/Tomcat</a></div>
-    <div class="toc2"><a href="#RegisterPartner">Register the partner machines certificate</a></div> 
-  
-  <a name="Intro"></a><div class="header1">Metacat Replication</div>
-  <a name="Overview"></a><div class="header2">Overview</div>
-  <p>Metacat has built-in replication to allow different Metacat servers to 
-  share data between themselves. Metacat not only replicates XML documents but 
-  also data files. </p>
-  
-  <p>Metacat's hub feature allows it to replicate not only it's own server's original
-  documents, but also those that were replicated from other servers.  This functionality
-  allows for a more complex chaining replication structure.</p>
-  
-  <p>The replication scheme that Metacat uses is both push and pull.  There are 
-  several triggers that can start a replication mechanism: </p>
-  <ul class="list1">
-    <li><b>Delta-T monitoring</b> - at a set time interval a server checks each of the
-    other servers in its list for updated documents</li>
-    <li><b>INSERT trigger</b> - Whenever a document is inserted, the server notifies
-    the remote hosts in its list that it has a new file available.</li>
-    <li><b>UPDATE trigger</b> - Whenever a document is updated, the server notifies
-    each server in its list of the update.</li>
-    <li><b>File locking</b> - When a local user tries to alter a document on a local 
-    server that belongs to a remote server, the local server must first
-    obtain a lock on that file.  Once the lock is obtained, the file can 
-    be updated, then it is force replicated out to each server in the list.
-    The lock ensures that the remote copy is up to date and that an older
-    file does not overwrite a newer one.  Only a documents home server
-    can give a lock for that file to be altered.</li>
-  </ul>
-  
-  <a name="DatabasedInfo"></a><div class="header2">Databased Information</div>
-  <p>Each server contains a list of servers to which it can replicate.  One-way
-  replication is enabled by the 'replicate' and 'datareplicate' flags in the 
-  list.  The server list may look like the following.</p>
-  <table border="1">
-    <tr>
-      <td><b>serverid</b></td>
-      <td><b>server</b></td>
-      <td><b>last_checked</b></td>
-      <td><b>replicate</b></td>
-      <td><b>datareplicate</b></td>
-      <td><b>hub</b></td>
-    </tr>
-    <tr>
-      <td>1</td>
-      <td>localhost</td>
-      <td>null</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-    </tr>
-    <tr>
-      <td>2</td>
-      <td>alpha.nceas.ucsb.edu:8080/berkley/servlet/replication</td>
-      <td>2001-01-22 14:52:12.1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-    </tr>
-    <tr>
-      <td>3</td>
-      <td>dev.nceas.ucsb.edu/Metacat/servlet/replication</td>
-      <td>2001-01-23 9:10:02.5</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-    </tr>
-  </table>
-  
-  <br>
-  The server list is kept in a table in the database called xml_replication.
-  Localhost must always be the first entry in the table and have a serverid of 1.
-  The database fields are:
-  <ul class="list1">
-  <li><b>serverid</b> - a unique ID that is generated by the database when a new field is added.</li>
-  <li><b>server</b> - this field always points to the partner server's replication servlet,
-  hence the "servlet/replication" on the end of both of the sample servers.  Note
-  that any port numbers (if your servlet engine is not running on port 80) must
-  also be included. </li>
-  <li><b>last_checked</b> - a system generated values that holds the last time that a check was 
-  made to see if replication needed to be performed.<li>
-  <li><b>replicate</b> - flag that is set to 1 if you want this server to replicate XML 
-  metadata documents TO the remote host.  Note that if this flag is set to 0, datareplicate
-  and hub fields have no meaning.</li>
-  <li><b>datareplicate</b> - flag that is set to 1 if you want this server to copy data 
-  files to the remote host.  Note that this field has no meaning if replicate is not set to 1.</li>
-  If this server is a hub to the remote host, the hub flag should be set to.
-  <li><b>hub</b> - if this flag is set to true, this server will not only replicate it's own
-  original documents, it will also replicate documents that were replicated to it.  Thus it 
-  acts as a replication hub to one or more other Metacat servers.</li>
-  </ul>
-  
-  <a name="Example"></a><div class="header2">Example</div>
-  Here we show an example setup of three replication servers.  We will discuss each.<br><br>
-  
-  First, note that in order for replication to occur, both partner servers must have 
-  each other in their respective tables or replication will not take place.  Also, 
-  certificates must be set up correctly on both servers in order for replication to 
-  work.  See the <a href="#Certificates">certificates</a> section below.<br><br>
-
-  <table border="1">
-    <tr>
-      <td>host</td>
-      <td>replication table</td>
-    </tr>
-    <tr>
-     <td>gamma.nceas.ucsb.edu</td>
-     <td>
-      <table border="2">
-        <tr>
-          <td><b>server</b></td>
-          <td><b>last_checked</b></td>
-          <td><b>replicate</b></td>
-          <td><b>datareplicate</b></td>
-          <td><b>hub</b></td>
-        </tr>
-        <tr>
-          <td>localhost</td>
-          <td>null</td>
-          <td>0</td>
-          <td>0</td>
-          <td>0</td>
-        </tr>
-        <tr>
-          <td>alpha.nceas.ucsb.edu:8080/berkley/servlet/replication&nbsp;&nbsp;&nbsp;</td>
-          <td>2001-01-22 14:52:12.1</td>
-          <td>0</td>
-          <td>0</td>
-          <td>0</td>
-        </tr>
-        <tr>
-          <td>lamda.nceas.ucsb.edu/Metacat/servlet/replication</td>
-          <td>2001-01-23 9:10:02.5</td>
-          <td>1</td>
-          <td>1</td>
-          <td>0</td>
-        </tr>
-      </table>
-     </td>
-    </tr>
-    <tr>
-      <td>alpha.nceas.ucsb.edu</td>
-      <td>
-        <table border="2">
-          <tr>
-            <td><b>server</b></td>
-            <td><b>last_checked</b></td>
-            <td><b>replicate</b></td>
-            <td><b>datareplicate</b></td>
-            <td><b>hub</b></td>
-          </tr>
-          <tr>
-            <td>localhost</td>
-            <td>null</td>
-            <td>0</td>
-            <td>0</td>
-            <td>0</td>
-          </tr>
-          <tr>
-            <td>gamma.nceas.ucsb.edu:8080/berkley/servlet/replication</td>
-            <td>2001-01-21 11:33:12.7</td>
-            <td>0</td>
-            <td>1</td>
-            <td>0</td>
-          </tr>
-          <tr>
-            <td>lamda.nceas.ucsb.edu/Metacat/servlet/replication</td>
-            <td>2001-01-23 10:22:02.5</td>
-            <td>1</td>
-            <td>0</td>
-            <td>0</td>
-          </tr>
-        </table>
-      </td>
-    </tr>
-    <tr>
-      <td>lamda.nceas.ucsb.edu</td>
-      <td>
-        <table border="2">
-          <tr>
-            <td><b>server</b></td>
-            <td><b>last_checked</b></td>
-            <td><b>replicate</b></td>
-            <td><b>datareplicate</b></td>
-            <td><b>hub</b></td>
-          </tr>
-          <tr>
-            <td>localhost</td>
-            <td>null</td>
-            <td>0</td>
-            <td>0</td>
-            <td>0</td>
-          </tr>
-          <tr>
-            <td>gamma.nceas.ucsb.edu:8080/berkley/servlet/replication</td>
-            <td>2001-01-21 11:33:12.7</td>
-            <td>0</td>
-            <td>0</td>
-            <td>0</td>
-          </tr>
-          <tr>
-            <td>alpha.nceas.ucsb.edu:8080/Metacat/servlet/replication</td>
-            <td>2001-01-22 12:15:32.5</td>
-            <td>1</td>
-            <td>1</td>
-            <td>1</td>
-          </tr>
-        </table>
-      </td>
-    </tr>
-  </table>
-  
-  <a name="gamma"></a><div class="header3">What happens with gamma?</div>
-  <ul class="list1">
-  <li>The localhost entry is required internally for replication to work on 
-      gamma.  As long as we see it there, we can safely disregard it.</li>
-  <li>We see the entry for the alpha machine has all zeros in replicate, 
-      datareplicate and hub columns.  This means that gamma is configured to
-      accept replication information from alpha.  (As we will see in a moment,
-      alpha is not actually correctly configured to send data to gamma.)</li>
-  <li>We see that the entry for the lamda machine has ones in the replicate
-      and data replicate columns and a zero in the hub column.  This tells us
-      that gamma will replicate it's original documents to lamda, assuming that
-      lambda is configured to accept replication from gamma (we will see that it
-      is).  However, because the hub value is zero, any documents that replicate 
-      to gamma will not be further replicated to lamda.</li>
-  </ul>
-   
-  <a name="alpha"></a><div class="header3">What happens with alpha?</div>
-  <ul class="list1">
-  <li>The localhost entry is required internally for replication to work on 
-      alpha.  As long as we see it there, we can safely disregard it.</li>
-  <li>We see that the entry for gamma has a zero in the replicate column.  
-      This means that all other entries are meaningless and can be disregarded.
-      Even though there is a one in the datareplicate column on alpha and gamma 
-      is configured to accept replication from alpha, no replicationwill happen 
-      from alpha to gamma.</li>
-  <li>We see that the entry for lamda is a one in the replicate column and zeros
-      in the datareplicate and hub columns.  Assuming lamda is configured to 
-      accept replication from alpha, alpha will replicate metadata only to lamda 
-      (and indeed, we will see that lambda is set up to accept replication from 
-      alpha). </li>
-  </ul>
-      
-  <a name="lamda"></a><div class="header3">What happens with lamda?</div>
-  <ul class="list1">
-  <li>The localhost entry is required internally for replication to work on 
-      lamda.  As long as we see it there, we can safely disregard it.</li>
-  <li>We see that the entry for gamma has all zeros in replicate, datareplicate
-      and hub, so lamba is set up to accept replication from gamma.  As we have
-      already seen, gamma is correctly configured to replicate metadata and data
-      to lambda.  We should see data and metadata replication from gamma to lamda.
-  <li>We see that the entry for alpha has ones in the replicate datareplicate and 
-      hub columns.  There's a lot going on here:
-    <ul class="list2">
-    <li>First, lamda will replicate original metadata and data to alpha if 
-        alpha is configured to accept replication from lamda.  Because alpha 
-        has an entry for lambda, lamba will be allowed to replicate to alpha. </li>
-    <li>Second, because the alpha entry has a one in the hub column, lambda 
-        will not only replicate it's original data, it will also replicate 
-        data that was replicated to it.  Remember that gamma was configured 
-        to replicate to lamda.  So any data or metadata that gamma sends to 
-        lambda will get further replicated to alpha.</li>
-    <li>Finally, the alpha entry in the table allows the alpha server to 
-        replicate to lambda.  Since the alpha server is set up to replicate
-        metadata only, we would expect any original metadata on alpha to 
-        wind up on lambda.</li>
-    </ul>
-  </ul>
-
-<a name="ControlPanel"></a><div class="header1">The Replication Control Panel:</div>      
-  There is an html control panel for controling replication.  After
-  installing Metacat, you can access it by calling replControl.html.  For instance, if you 
-  setup a Metacat application context called 'knb' you would probably type :
-  
-  <div class="code">http://server.domain.com/knb/style/skins/dev/replControl.html</div>  
-  
-  The control panel is an easy interface for adding/removing/altering servers and 
-  starting the delta-T handler.  It will also allow you to 'force replicate' your 
-  server list.  This is useful if you want to initialize the state of one Metacat 
-  server from an existing state of another (i.e. copy all of the data from an existing
-  server).</p>
-  
-  <a name="Certificates"></a><div class="header1">Certificates:</div>
-  You will need to generate security certificates on both the replication client 
-  and server.  The certificates will be exchanged so that each machine understands
-  that the other has access for replication.<br><br>
-  The following are the steps to generate and exchange certificates on systems
-  running Tomcat 5 and java 1.5.  Note that if Tomcat is running in conjunction with
-  Apache, the process is somewhat different than if it is running standalone.
-
-  <a name="GenerateCertificates"></a><div class="header2">Generate Certificates on both the replication client and server.</div>  
-
-  <a name="GenerateCertTomcat"></a><div class="header3">Generate Certificate for Tomcat standalone (no Apache)</div>
-  <ul class="list1">
-  <li>Generate keys in java default key store - this will create a secure key and put it
-    into the binary certificates file located at $JAVA_HOME/lib/security/cacerts</li> 
-    <ul class="list2">
-    <li>Run the command: 
-   	  <div class="code">keytool -genkey -alias &lt;aliasname&gt; -keyalg RSA -validity 800 -keystore $JAVA_HOME/lib/security/cacerts</div>
-     where &lt;aliasname&gt; is a unique name that you choose for this cert.  Something like "&lt;hostname-tomcat&gt"
-     might be appropriate, where &lt;hostname-tomcat&gt is the name of this host.</li>
-    </ul>
-  </li>
-  <li>
-    Password - keytool will ask for a password.  If this is a pre-existing keystore, you will need
-    to know its password to modify it.  If you are creating a new keystore, the password you enter
-    will become the keystore password.
-  </li>
-  <li>Sample values when creating certificate</li>
-    <ul class="list2">
-    <li>What is your first and last name? <b>myserver.nceas.ucsb.edu </b>
-        (note: use the host name without port number)<li>
-    <li>What is the name of your organizional unit? <b>NCEAS</b></li>
-    <li>What is the name of your organizional unit? <b>UCSB</b></li>
-    <li>What is the name of your City or Locality? <b>Santa Barbara</b></li>
-    <li>What is the name of your State or Province? <b>California</b> 
-        (note: this is spelled in full)<li>
-    <li>What is the two-letter country code for this unit? <b>US</b></li>
-    </ul>
-  <li>Generate certificate - this will pull the certificate you created from the cacerts file
-      and put it into a local file</li>
-    <ul class="list2">
-    <li>Run the command:
-      <div class="code">keytool -export -alias &lt;aliasname&gt; -file &lt;outputfile&gt;.cert -keystore $JAVA_HOME/lib/security/cacerts</div>
-      where &lt;aliasname&gt; is the same name you used when you created the certificate.  </li>
-    <li>A file named &lt;outputfile&gt;.cert will be created in the same directory where you run the keytool 
-      command.  You can name the output file anything you like, but keep in mind that it will get sent to the 
-      partner machine used for replication.  The filename should have have enough meaning that someone who sees 
-      it on that machine can have some idea where it came from.  Again, something like "&lt;hostname&gt;-tomcat.cert"
-      will suffice.</li>   
-    </ul>
-  </li>
-  <li>Enable SSL in Tomcat 
-    <ul class="list2">
-    <li>Edit the Tomcat server file at $TOMCAT_HOME/conf/server.xml</li>
-    <li>
-      uncomment the section that starts with "&lt;Connector port="8443" ... (Note: Databased Informationcomments start with
-      &lt;!-- and end with --&gt;).
-    </li>
-  	<li>add two attribute to that section that read:
-  	  <div class="code">keystoreFile="&lt;JAVA_HOME&gt;/lib/security/cacerts"</div>
-  	  <div class="code">keystorePass="&lt;keystore_password&gt;"</div>
-  	  where &lt;JAVA_HOME&gt; should be the actual java path and &lt;keystore_password&gt; should be the 
-  	  password you used when you created the keystore.
-  	</li>
-  	</ul>
-  </li>
-  </ul>  
-    
-  <a name="GenerateCertApache"></a><div class="header3">Generate Certificate for Apache/Tomcat</div>
-  <ul class="list1">
-  <li>Generate keys using openssl
-    <ul class="list2">
-    <li>Run the command: 
-   	  <div class="code">   openssl req -new -out REQ.pem -keyout &lt;hostname&gt;-apache.key</div>
-    </li>
-    </ul>
-  </li>
-  <li>Sample values when creating certificate</li>
-    <ul class="list2">
-    <li>Enter PEM pass phrase: (note: I use the first part of the host name)
-    <li>Country Name (2 letter code) [AU]: <b>US</b></li>
-    <li>State or Province Name (full name) [Some-State]: <b>California</b> 
-        (note: this is spelled in full)</li>
-    <li>Locality Name (eg, city) []: <b>Santa Barbara</b></li>
-    <li>Organization Name (eg, company) [Internet Widgits Pty Ltd]: <b>UCSB</b></li>
-    <li>Organizational Unit Name (eg, section) []: <b>NCEAS</b></li>
-    <li>Common Name (eg, YOUR name) []: <b>myserver.mydomain.edu</b>
-        (note: use the host name without port number)</li>
-    <li>Email Address []:  <b>administrator@mydomain.edu</b></li>
-    <li>A challenge password []: (note: leave blank)</li>
-    <li>An optional company name []: (note: leave blank)</li>
-    </ul>
-  </li>    
-  <li>Generate certificate - this will create a local file with your certificate</li>
-    <ul class="list2">
-    <li>Run the command:
-      <div class="code">openssl req -x509 -days 800 -in REQ.pem -key &lt;hostname&gt;-apache.key -out &lt;hostname&gt;-apache.crt</div>
-      where &lt;hostname&gt; is the same name you used when you created the certificate.  </li>
-    <li>A file named &lt;hostname&gt;-apache.crt will be created in the same directory where you run the keytool 
-      command.  You can name the output file anything you like, but keep in mind that it will get sent to the 
-      partner machine used for replication.  The filename should have have enough meaning that someone who sees 
-      it on that machine can have some idea where it came from.  Again, something like "&lt;hostname&gt;-apache.crt"
-      will suffice.</li>   
-    </ul>
-  </li>   
-  <li>Enter the certificate into apache security configuration - you need to register the certificate
-      in the local Apache instance.  Note that the security files may be in a different place depending
-      on how you installed apache.</li>
-    <ul class="list2">
-    <li>Copy the certificate and key file to the apache ssl directories and enable ssl.</li>
-    <li>For Ubuntu/Debian based systems:
-      <ul class="list3">
-      <li>sudo cp &lt;hostname&gt;-apache.crt /etc/ssl/certs</li>
-      <li>sudo cp &lt;hostname&gt;-apache.key /etc/ssl/private</li>
-      <li>As root edit /etc/apache2/sites-available/default.  In the VirtualHost section
-          after the DocumentRoot line, add:<br>
-          SSLEngine on<br>
-          SSLOptions +FakeBasicAuth +ExportCertData +CompatEnvVars +StrictRequire<br>
-          SSLCertificateFile /etc/ssl/certs/server.crt<br>
-          SSLCertificateKeyFile /etc/ssl/private/server.key<br>
-      </li>
-      </ul>
-    </li>  
-    </ul>  
-    <ul class="list2">
-    <li>For other systems:
-      <ul class="list3">
-      <li>sudo cp &lt;hostname&gt;-apache.crt $APACHE_HOME/conf/ssl.crt</li>
-      <li>sudo cp &lt;hostname&gt;-apache.key $APACHE_HOME/conf/ssl.key</li> 
-      <li> ADD STEPS TO ENABLE SSL ON NON_DEBIAN SYSTEMS HERE</li>
-      </ul>
-    </li>  
-    </ul>    	  	        
-  <li>scp &lt;hostname&gt;-apache.crt to the replication partner machine.</li>
-  </ul>  
-  
-  <a name="RegisterPartner"></a><div class="header2">Register the partner machines certificate.</div>   
-  At this point, you have created a certificate for each replication server and 
-  scp-ed them across to each other.  Now you need to import the remote server's
-  certificate on the local machine.  Perform the following steps for each 
-  replication server.
-  <ul class="list1">
-  <li>Import the remote certificate by running:
-    <div class="code">keytool -import -alias &lt;remotehostalias&gt; -file &lt;remotehostfilename&gt;.crt -keystore $JAVA_HOME/jre/lib/security/cacerts</div>
-    where the &lt;remotehostfilename&gt; is the certificate file you created on the remote machine and
-    copied to this machine.  The &lt;remotehostalias&gt; is the name the certificate will use in
-    the keystore.  It should be something that identifies the remote host.  
-  </li>
-  <li>Restart Apache and Tomcat on both replication machines</li>
-  </ul>
-
-  <a href="./packages.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./datafiles.html">Next</a>
-  </ul>
-  
-
-</BODY>
-</HTML>

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Index: docs/user/pagedreturn.html
===================================================================
--- docs/user/pagedreturn.html	(revision 5315)
+++ docs/user/pagedreturn.html	(nonexistent)
@@ -1,86 +0,0 @@
-<!--
-  *      Authors: Chad Berkley
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2007 November 5
-  *      Version: 
-  *    File Info: '$Id$'
-  * 
-  * 
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Paged Query Returns</p></td>
-      <td class="tablehead" colspan="2" align="right">
-          <a href="./spatial_option.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-          <a href="./sitemaps.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  
-  <p>Metacat allows results sets to be broken up into "pages" to aid in the loading
-  of large result sets and to make the result sets more readable to users.  This is
-  facilitated by the addition of two variables to the parameter list.  Pagesize
-  indicates how many results should be returned for a given page.  Pagestart
-  indicates which page you are currently viewing.  These parameters can be
-  passed to Metacat when a query is submited.  </p>
-  
-  <p>When a paged query is performed, the resultset of that query contains
-  four extra fields.  Pagestart and pagesize are contained in the xml resultset
-  along with nextpage and previouspage.  This allows the xslt tranformation to
-  include navigational links in the rendered resultset.  Here's an example 
-  xml resultset.</p>
-  
-  <pre>
-    &lt;resultset&gt;
-      &lt;pagestart&gt;1&lt;/pagestart&gt;
-      &lt;pagesize&gt;10&lt;/pagesize&gt;
-      &lt;nextpage&gt;2&lt;/nextpage&gt;
-      &lt;previouspage&gt;0&lt;/previouspage&gt;
-      &lt;query&gt;
-      ...
-      &lt;/query&gt;
-      &lt;document&gt;...&lt;/document&gt;
-      &lt;document&gt;...&lt;/document&gt;
-    &lt;/resultset&gt;
-  </pre>
-  
-  <p>In the case of the resultset, pagestart will always indicate the page you
-  are currently viewing.</p>
-  
-  <p>Here's an example of the rendered result.</p>
-  
-  <img src="images/pagedquery.jpg"/>
-  
-  <p>The links to the previous and next pages look like this.</p>
-  
-  <pre>
-   &lt;a href="metacat?action=query&amp;operator=INTERSECT&amp;enableediting=false&amp;anyfield=actor&amp;qformat=kepler&amp;pagestart=0&amp;pagesize=10"&gt;Previous Page&lt;/a&gt;
-   &lt;a href="metacat?action=query&amp;operator=INTERSECT&amp;enableediting=false&amp;anyfield=actor&amp;qformat=kepler&amp;pagestart=2&amp;pagesize=10"&gt;Next Page&lt;/a&gt;
-  </pre>
-  
-  <p>The important bits of these links are the incremented pagestart parameters.  
-  The rendered page is on page 1 so the previous page is 0 and the next
-  page is 2.  By sequencing through the pages, the user can see the
-  entire resultset.  </p>
-  
-  <p>The Kepler skin in lib/style/skins/kepler is a good example of how to
-  render the resultset with paged query returns.  The XSLT uses the four extra 
-  fields in the resultset to render the next and previous links.  This could
-  also be used within a non-web application.
-  </p>
-  
-  <br>
-  <a href="./spatial_option.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./sitemaps.html">Next</a>
-  
-
-</BODY>
-</HTML>

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Index: docs/user/metacatload.html
===================================================================
--- docs/user/metacatload.html	(revision 5315)
+++ docs/user/metacatload.html	(nonexistent)
@@ -1,121 +0,0 @@
-<!--
-  * metacatload.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Document Loading</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./clientapi.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./metacatquery.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <P>Metacat provides functionality for inserting, updating, and deleting
-  XML documents in the database. Inserted or updated documents are read, checked 
-  for validity, decomposed into nodes and inserted into the db. Document validity 
-  is checked if a valid DTD is provided.
-  <P> <img alt="architecture diagram  of write action" src="metadatawrite.gif">
-  <P> <b>Operations</b>
-  <ul>
-    <li>INSERT - A new XML document is inserted into the DB with given unique
-    docid. The client must specify the docid.</li>
-    <li>UPDATE - A document is provided to update a document that already
-    has a valid docid.  The original document is archived, then overwritten.</li>
-    <li>DELETE - Document is archived, and pointer in xml_documents is moved
-    to xml_revisions, efectively deleting the document from public view but
-    preserving the revision for the revision history.</li>
-  </ul>
-  
-  <p>Insertions, updates and deletes are passed to Metacat as servlet parameters.
-  The following is an example of a web form that can perform these tasks.</p>
-  
-  <pre>
-    &lt;html&gt;
-    &lt;head&gt;
-    &lt;title&gt;MetaCat&lt;/title&gt;
-    &lt;link rel="stylesheet" type="text/css" href="metacat/style/rowcol.css"&gt;
-    &lt;/head&gt;
-    &lt;body class="emlbody"&gt;
-    &lt;b&gt;MetaCat XML Loader&lt;/b&gt;
-    &lt;p&gt;
-    Upload, Change, or Delete an XML document using this form.
-    &lt;/p&gt;
-    &lt;form action="http://dev.nceas.ucsb.edu/metacat/servlet/metacat" method="POST"&gt;
-      &lt;strong&gt;1. Choose an action: &lt;/strong&gt;
-      &lt;input type="radio" name="action" value="insert" checked&gt; Insert
-      &lt;input type="radio" name="action" value="update"&gt; Update
-      &lt;input type="radio" name="action" value="delete"&gt; Delete
-      &lt;input type="submit" value="Process Action"&gt;
-      &lt;br /&gt;
-      &lt;strong&gt;2. Provide a Document ID &lt;/strong&gt;
-      &lt;input type="text" name="docid"&gt; (optional for Insert)
-      &nbsp;&nbsp;&nbsp;&lt;input type="checkbox" name="public" value="yes" checked&gt;&lt;strong&gt;Public Document&lt;/strong&gt;
-      &lt;br /&gt;
-      &lt;strong&gt;3. Provide XML text &lt;/strong&gt; (not needed for Delete)
-      &lt;textarea name="doctext" cols="65" rows="15"&gt;&lt;/textarea&gt;
-      &lt;strong&gt;4. Provide DTD text for upload &lt;/strong&gt; (optional; not needed for Delete)
-      &lt;textarea name="dtdtext" cols="65" rows="15"&gt;&lt;/textarea&gt;
-    &lt;/form&gt;
-    &lt;/body&gt;
-    &lt;/html&gt;
-  </pre>
-  
-  <p>Once inserted into the database, the document looks like the following:</p>
-  
-  <PRE><b>SQL> select * from xml_nodes where docid='NCEAS:1'</b> <br>
-NODEID NODEINDEX NODETYPE   NODENAME        NODEDATA               PARENTNODEID ROOTNODEID DOCID  
------- --------- ---------- --------------- ---------------------- ------------ ---------- -------
-     1           DOCUMENT   eml-dataset                                                  1 NCEAS:1
-     2         1 ELEMENT    eml-dataset                                       1          1 NCEAS:1
-     3         1 TEXT                                                         2          1 NCEAS:1
-
-
-     4         2 ELEMENT    meta_file_id                                      2          1 NCEAS:1
-     5         1 TEXT                       NCEAS:1                           4          1 NCEAS:1
-     6         3 TEXT                                                         2          1 NCEAS:1
-
-
-     7         4 ELEMENT    dataset_id                                        2          1 NCEAS:1
-     8         1 TEXT                       Dist.ssd01                        7          1 NCEAS:1
-     9         5 TEXT                                                         2          1 NCEAS:1
-
-
-    10         6 ELEMENT    title                                             2          1 NCEAS:1
-    11         1 TEXT                       Insights on community            10          1 NCEAS:1
-                                            dynamics
-
-    12         7 TEXT                                                         2          1 NCEAS:1
-
-
-    13         8 ELEMENT    originator                                        2          1 NCEAS:1
-    14         1 ATTRIBUTE  description     Names and addresses of           13          1 NCEAS:1
-                                            principal investigator
-  </PRE>
-  
-  <p>If you follow the parentnodeid pointers you can recontruct this document.
-  The <a href="./metacatdb.html">Metacat Database</a> section provides more details
-  on the storage of XML documents.</p>
-
-  <br>
-  <a href="./clientapi.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./metacatquery.html">Next</a>
-  
-</BODY>
-</HTML>
-

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Index: docs/user/metacatquery.html
===================================================================
--- docs/user/metacatquery.html	(revision 5315)
+++ docs/user/metacatquery.html	(nonexistent)
@@ -1,152 +0,0 @@
-<!--
-  * metacatquery.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Queries and Results</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./metacatload.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./metacatread.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <P>The Metacat Server provides 
-  an interface for searching of metadata stored in the Metacat database.
-  <P> <img alt="architecture diagram of a Metacat query" src="metadataquery.gif">
-  <br><br><b>Steps to perform a query in Metacat</b>
-  <ol>
-    <li>A pathquery document is created from the search criteria provided through
-    the servlet parameters.</li>  
-    <li>This pathquery document is sent to DBQuery where it 
-    is processed and translated into SQL statements.</li>
-    <li>The SQL statements are executed against the database and the resultsets
-    are translated into an xml document of doctype "resultset".</li>
-    <li>The resultset document is either returned directly to the client as XML
-    or is transformed through XSLT and returned as HTML.</li>
-  </ol>
-  
-  <b>The Pathquery Document</b>
-  <pre>
-   &lt;pathquery version="1.0"&gt;
-      &lt;meta_file_id&gt;unspecified&lt;/meta_file_id&gt;
-      &lt;querytitle&gt;unspecified&lt;/querytitle&gt;
-      &lt;returnfield&gt;dataset/title&lt;/returnfield&gt;
-      &lt;returnfield&gt;keyword&lt;/returnfield&gt;
-      &lt;returnfield&gt;originator/individualName/surName&lt;/returnfield&gt;
-      &lt;returndoctype&gt;eml://ecoinformatics.org/eml-2.0.1&lt;/returndoctype&gt;
-      &lt;returndoctype&gt;eml://ecoinformatics.org/eml-2.0.0&lt;/returndoctype&gt;
-      &lt;querygroup operator="UNION"&gt;
-        &lt;queryterm casesensitive="false" searchmode="contains"&gt;
-          &lt;value&gt;Plant&lt;/value&gt;
-          &lt;pathexpr&gt;dataset/title&lt;/pathexpr&gt;
-        &lt;/queryterm&gt;
-        &lt;queryterm casesensitive="false" searchmode="contains"&gt;
-          &lt;value&gt;plant&lt;/value&gt;
-          &lt;pathexpr&gt;keyword&lt;/pathexpr&gt;
-        &lt;/queryterm&gt;
-      &lt;/querygroup&gt;
-  &lt;/pathquery&gt;
-  </pre>
-  
-  <p>The pathquery document was designed to be flexible enough to query specific
-  fields of any XML document.  It also allows the client to specify which fields
-  from a returned document are returned in the initial resultset.  Each
-  &lt;returnfield&gt; parameter specifies a field which the DB will return
-  for any query hit.  The returndoctype fields allows the client to limit the 
-  type of documents to be returned.  If no returndoctype element , all document types are returned.
-  A &lt;querygroup&gt; creates an AND or an OR statement of the &lt;queryterm&gt;s
-  in the group.  The operator can be UNION or INTERSECT.  A &lt;queryterm&gt;
-  defines the actual field against which the query is being performed.  The value
-  of the queryterm that we are quering for is encased in &lt;value&gt; tags.
-  The &lt;pathexpr&gt; tag specifies an exact path to which you want to restrict
-  the search.  A &lt;pathexpr&gt; tag which contains the keyword returndoc is 
-  a special case which is discussed in <a href="./packages.html">Packages and 
-  Relations</a>.</p><br>
-  
-  <b>The Resultset Document</b><br>
-  
-  <p>When the pathquery document is submitted and processed, Metacat returns
-  another XML document called a resultset document.<p>
-  
-  <pre>
-      &lt;resultset&gt;
-        &lt;query&gt;
-          &lt;pathquery version="1.0"&gt;
-            &lt;meta_file_id&gt;unspecified&lt;/meta_file_id&gt;
-            &lt;querytitle&gt;unspecified&lt;/querytitle&gt;
-            &lt;returnfield&gt;dataset/title&lt;/returnfield&gt;
-            &lt;returnfield&gt;keyword&lt;/returnfield&gt;
-            &lt;returnfield&gt;originator/individualName/surName&lt;/returnfield&gt;
-            &lt;returndoctype&gt;eml://ecoinformatics.org/eml-2.0.1&lt;/returndoctype&gt;
-            &lt;returndoctype&gt;eml://ecoinformatics.org/eml-2.0.0&lt;/returndoctype&gt;
-            &lt;querygroup operator="UNION"&gt;
-                  &lt;queryterm casesensitive="false" searchmode="contains"&gt;
-                      &lt;value&gt;Datos&lt;/value&gt;
-                      &lt;pathexpr&gt;dataset/title&lt;/pathexpr&gt;
-                  &lt;/queryterm&gt;
-                  &lt;queryterm casesensitive="false" searchmode="contains"&gt;
-                     &lt;value&gt;plant&lt;/value&gt;
-                     &lt;pathexpr&gt;keyword&lt;/pathexpr&gt;
-                  &lt;/queryterm&gt;
-           &lt;/querygroup&gt;
-         &lt;/pathquery&gt;
-        &lt;/query&gt;  
-      
-        &lt;document&gt;
-          &lt;docid&gt;nceas.44.1&lt;/docid&gt;
-          &lt;docname&gt;resource&lt;/docname&gt;
-          &lt;doctype&gt;eml://ecoinformatics.org/eml-2.0.1&lt;/doctype&gt;
-          &lt;createdate&gt;2001-01-12 16:12:06.0&lt;/createdate&gt;
-          &lt;updatedate&gt;2001-01-12 16:12:06.0&lt;/updatedate&gt;
-          &lt;param name="dataset/title"&gt;Datos Meteorologicos&lt;/param&gt;
-          &lt;param name="keyword"&gt;intertidal&lt;/param&gt;
-          &lt;param name="originator/individualName/surName"&gt;Smith&lt;/param&gt;
-        &lt;/document&gt;  
-        
-        &lt;document&gt;
-          &lt;docid&gt;nceas.42.1&lt;/docid&gt;
-          &lt;docname&gt;resource&lt;/docname&gt;
-          &lt;doctype&gt;eml://ecoinformatics.org/eml-2.0.1&lt;/doctype&gt;
-          &lt;createdate&gt;2001-01-12 16:11:31.0&lt;/createdate&gt;
-          &lt;updatedate&gt;2001-01-12 16:11:31.0&lt;/updatedate&gt;
-          &lt;param name="dataset/title"&gt;Ocean Surface Temperature&lt;/param&gt;
-          &lt;param name="keyword"&gt;Plant&lt;/param&gt;
-          &lt;param name="originator/individualName/surName"&gt;Henry&lt;/param&gt;   
-       &lt;/document&gt;
-      .....  
-      &lt;/resultset&gt;
-    
-  </pre>
-  <p>The first element in the resultset is &lt;query&gt;.  Its content is just 
-  the pathquery document.  The resultset always returns 
-  the pathquery document that created it in the &lt;query&gt; tag.  The next
-  major tag is &lt;document&gt;.  Each XML document returned by the query
-  is represented by a &lt;document&gt; tag.  The default document information returned
-  is docid, docname, doctype, doctitle, createdate and  
-  updatedate.  The param tags are present if the document found contained
-  the returnfield chosen in the pathquery document.  The name attribute of the
-  param tag is the full path to the node specified by the returnfield. <p>
-  
-  <br>
-  <a href="./metacatload.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./metacatread.html">Next</a>
-
-</BODY>
-</HTML>
-

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===================================================================
--- docs/user/packages.html	(revision 5315)
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@@ -1,243 +0,0 @@
-<!--
-  * packages.html
-  *
-  *      Authors: Chad Berkley
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2001 January 23
-  *      Version: 
-  *    File Info: '$ '
-  * 
-  * 
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Packages and Relationships</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./metacatapi.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./replication.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <p>Metacat allows a user to create a virtual link between XML documents within
-  the system.  These links are called <i>Relationships</i> and are defined by triples
-  in <i>eml-dataset</i>, <i>eml-literature</i> or <i>eml-software</i> files.  A relationship can be defined between two
-  XML or <a href="./datafiles.html">non-XML</a> files. 
-  The following is an example of an eml-dataset-2.0 file holding triples at the end:</p>
-  
-  <pre>
-&lt;?xml version="1.0"?&gt;
-&lt;!DOCTYPE dataset PUBLIC "-//NCEAS//eml-dataset-2.0//EN" "eml-dataset-2.0.dtd"&gt;
-&lt;dataset&gt;
-  &lt;identifier system="null"&gt;berkley.5.3&lt;/identifier&gt;
-  &lt;shortName&gt;allsp&lt;/shortName&gt;
-  &lt;title&gt;MARINE sampling data collected between spring 1992 and fall 1996&lt;/title&gt;
-  &lt;originator&gt;
-    &lt;individualName&gt;
-      &lt;salutation&gt;Dr.&lt;/salutation&gt;
-      &lt;givenName&gt;Peter&lt;/givenName&gt;
-      &lt;surName&gt;Raimondi&lt;/surName&gt;
-    &lt;/individualName&gt;
-    &lt;organizationName&gt;UCSC&lt;/organizationName&gt;
-    &lt;positionName&gt; &lt;/positionName&gt;
-    &lt;address&gt;
-      &lt;deliveryPoint&gt;Biology Dept.&lt;/deliveryPoint&gt;
-      &lt;deliveryPoint&gt;A309 Earth and Marine Science Building&lt;/deliveryPoint&gt;
-      &lt;city&gt;Santa Cruz&lt;/city&gt;
-      &lt;administrativeArea&gt;CA&lt;/administrativeArea&gt;
-      &lt;postalCode&gt;95060&lt;/postalCode&gt;
-      &lt;country&gt;USA&lt;/country&gt;
-    &lt;/address&gt;
-    &lt;phone phonetype="voice"&gt;831-459-1234 x5674&lt;/phone&gt;
-    &lt;electronicMailAddress&gt;raimondi@biology.ucsc.edu&lt;/electronicMailAddress&gt;
-    &lt;onlineLink&gt; &lt;/onlineLink&gt;
-    &lt;role&gt;Originator&lt;/role&gt;
-  &lt;/originator&gt;
-  &lt;pubdate&gt; &lt;/pubdate&gt;
-  &lt;pubplace&gt; &lt;/pubplace&gt;
-  &lt;series&gt; &lt;/series&gt;
-  &lt;abstract&gt;
-    &lt;paragraph&gt; &lt;/paragraph&gt;
-  &lt;/abstract&gt;
-  &lt;keywordSet&gt;
-    &lt;keyword keywordType="null"&gt;intertidal&lt;/keyword&gt;
-    &lt;keyword keywordType="null"&gt;santa barbara&lt;/keyword&gt;
-    &lt;keyword keywordType="null"&gt;photoplot&lt;/keyword&gt;
-    &lt;keyword keywordType="null"&gt;quadrat&lt;/keyword&gt;
-    &lt;keywordThesaurus&gt; &lt;/keywordThesaurus&gt;
-  &lt;/keywordSet&gt;
-  &lt;additionalInfo&gt;
-    &lt;paragraph&gt; &lt;/paragraph&gt;
-  &lt;/additionalInfo&gt; <font color="red">
-  &lt;triple&gt;
-    &lt;subject&gt;berkley.6.1&lt;/subject&gt;
-    &lt;relationship&gt;isRelatedTo&lt;/relationship&gt;
-    &lt;object&gt;berkley.5.3&lt;/object&gt;
-  &lt;/triple&gt;
-  &lt;triple&gt;
-    &lt;subject&gt;berkley.7.1&lt;/subject&gt;
-    &lt;relationship&gt;isRelatedTo&lt;/relationship&gt;
-    &lt;object&gt;berkley.6.1&lt;/object&gt;
-  &lt;/triple&gt;
-  &lt;triple&gt;
-    &lt;subject&gt;berkley.8.1&lt;/subject&gt;
-    &lt;relationship&gt;isRelatedTo&lt;/relationship&gt;
-    &lt;object&gt;berkley.5.3&lt;/object&gt;
-  &lt;/triple&gt;
-  &lt;triple&gt;
-    &lt;subject&gt;berkley.8.1&lt;/subject&gt;
-    &lt;relationship&gt;isRelatedTo&lt;/relationship&gt;
-    &lt;object&gt;berkley.6.1&lt;/object&gt;
-  &lt;/triple&gt;
-  &lt;triple&gt;
-    &lt;subject&gt;berkley.8.1&lt;/subject&gt;
-    &lt;relationship&gt;isRelatedTo&lt;/relationship&gt;
-    &lt;object&gt;berkley.7.1&lt;/object&gt;
-  &lt;/triple&gt;
-  &lt;triple&gt;
-    &lt;subject&gt;berkley.14.1&lt;/subject&gt;
-    &lt;relationship&gt;isRelatedTo&lt;/relationship&gt;
-    &lt;object&gt;berkley.6.1&lt;/object&gt;
-  &lt;/triple&gt; </font>
-  &lt;temporalCoverage&gt; 1992 to 1996&lt;/temporalCoverage&gt;
-  &lt;geographicCoverage&gt; &lt;/geographicCoverage&gt;
-  &lt;taxonomicCoverage&gt; &lt;/taxonomicCoverage&gt;
-&lt;/dataset&gt;
-  </pre>
-  
-  <b>Description of the Package File</b>
-  <p>Note that the doctype of this document is an unregistered NCEAS specific
-  DTD (-//NCEAS//eml-dataset-2.0//EN).  The package doctype is an application 
-  property of Metacat.  Setting this property (and others) is described in 
-  <a href="./properties.html">Setting Metacat Properties</a>.  The package file
-  contains <i>n</i> triples.  Each triple has a subject, relationship,
-  and an object.  This grouping can be read as follows:  &lt;subject&gt; has
-  &lt;relationship&gt; to &lt;object&gt;.  Each triple is a logical link
-  between the subject and object with the relationship being a description of that
-  link.</p>
-  <b>The Utility of Relations</b>
-  <p>Relations become useful because many XML data schemas are broken up into 
-  multiple DTDs.  Thus, there may be many different XML files that are all 
-  related to each other yet are stored seperately within the system.  Also, 
-  since we, here at NCEAS, are developing Metacat for use as a metadata 
-  repository for ecological data, we need some way of linking our metadata 
-  to the datafiles that they describe.  Packages are the way we do this.</p>
-  <b>Post Processed Relations</b>
-  <p>The package file is inserted into Metacat as any other file is.  Its doctype
-  is checked against the packagedoctype property in the <a href="properties.html">
-  Metacat.properties file</a>.  If it is of that type, the file is sent
-  to a postprocessor to be analyzed and inserted into the xml_relation table.  
-  The table looks like the following:</p>
-  
-  <table border="1">
-    <tr>
-      <td>relationid</td><td>docid</td><td>packagetype</td>
-      <td>subject</td><td>subjectdoctype</td>
-      <td>relationship</td><td>object</td><td>objectdoctype</td>
-    </tr>
-    <tr>
-      <td>1</td>
-      <td>berkley.5</td>
-      <td>-//NCEAS//eml-dataset-2.0//EN</td>
-      <td>berkley.6.1</td>
-      <td>null</td>
-      <td>isRelatedTo</td>
-      <td>berkley.5.3</td>
-      <td>null</td>
-    </tr>
-    <tr>
-      <td>2</td>
-      <td>berkley.5</td>
-      <td>-//NCEAS//eml-dataset-2.0//EN</td>
-      <td>berkley.7.1</td>
-      <td>null</td>
-      <td>isRelatedTo</td>
-      <td>berkley.6.1</td>
-      <td>null</td>
-    </tr>
-    <tr>
-      <td>3</td>
-      <td>berkley.5</td>
-      <td>-//NCEAS//eml-dataset-2.0//EN</td>
-      <td>berkley.8.1</td>
-      <td>null</td>
-      <td>isRelatedTo</td>
-      <td>berkley.5.3</td>
-      <td>null</td>
-    </tr>
-    <tr>
-      <td>4</td>
-      <td>berkley.5</td>
-      <td>-//NCEAS//eml-dataset-2.0//EN</td>
-      <td>berkley.8.1</td>
-      <td>null</td>
-      <td>isRelatedTo</td>
-      <td>berkley.6.1</td>
-      <td>null</td>
-    </tr>
-    <tr>
-      <td>5</td>
-      <td>berkley.5</td>
-      <td>-//NCEAS//eml-dataset-2.0//EN</td>
-      <td>berkley.8.1</td>
-      <td>null</td>
-      <td>isRelatedTo</td>
-      <td>berkley.7.1</td>
-      <td>null</td>
-    </tr>
-    <tr>
-      <td>6</td>
-      <td>berkley.5</td>
-      <td>-//NCEAS//eml-dataset-2.0//EN</td>
-      <td>berkley.14.1</td>
-      <td>null</td>
-      <td>isRelatedTo</td>
-      <td>berkley.6.1</td>
-      <td>null</td>
-    </tr>
-  </table>
-  
-  <p>Once, the system has processed the package file and inserted the relations
-  into the xml_relation table, the files relations are always returned to with it
-  in the <a href="./metacatquery.html">resultset</a> of a query.</p>
-
-  <b>Package Views (formerly known as 'backtracking')</b>
-  <p>Package View is a feature that was intentionally left out of the 
-  <a href="./Metacatquery.html">Queries and Results</a> section.  Package views 
-  involves sending a doctype (called a returndoctype) along with a query request.  
-  When there is a hit from that query, the system will check the doctype of the 
-  hit document against the returndoctype.  If the doctypes do not match, 
-  the system checks the xml_relation table to see if that document has been packed
-  by document of that doctype. If such package document exists, it
-  is returned instead of the one which was originally hit.  If no such
-  package document exists, then the document which was originally hit is returned.  
-  This allows a display system (such as a web browser) to try to display a 
-  certain type of document.</p>
-  <p>For example:  Take our package file from above.  Say we do a query for 
-  "intertidal" which returns the document berkley.6 of type -//NCEAS//eml-entity-2.0//EN.
-  However, we have set returndoctype equal to "-//NCEAS//eml-dataset-2.0//EN".
-  When berkley.6 is hit, the system will check its package documents to see if 
-  it is of type -//NCEAS//eml-dataset-2.0//EN.  Since it is, 
-  (relationid 1, 2 and 4) document berkley.5 is returned instead of berkley.6.
-  <p>From a client the returndoctype is a servlet parameter.
-  A URL with a returndoctype would look something like: </p>
-  <pre>http://server.domain.com/Metacat?action=query&amp;anyfield=%&amp;qformat=html&amp;returndoctype=-//NCEAS//eml-dataset-2.0//EN</pre>
-  <p>The system then inserts the returndoctype parameter value into a pathquery
-  document as illustrated in <a href="./metacatquery.html">Queries and Results</a>.
-  </p>
-  
-  
-  <br>
-  <a href="./metacatapi.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./replication.html">Next</a>
-  
-
-</BODY>
-</HTML>

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Index: docs/user/metacat-apache-config.html
===================================================================
--- docs/user/metacat-apache-config.html	(revision 5315)
+++ docs/user/metacat-apache-config.html	(nonexistent)
@@ -1,212 +0,0 @@
-<!-- 
-  *   '$RCSfile$'
-  *     Purpose: web page describing the installation of Metacat
-  *   Copyright: 2008 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *     Authors: Chad Berkley
-  *
-  *    '$Author: daigle $'
-  *    '$Date: 2008-11-24 11:57:40 -0800 (Mon, 24 Nov 2008) $'
-  *    '$Revision: 4621 $'
-  *
-  *
-  -->
-  
-<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>Metacat Apache Configuration</title>
-  <link rel="stylesheet" type="text/css" href="./common.css">
-  <link rel="stylesheet" type="text/css" href="./default.css">
-</head>
-
-<body>
-
-<table class="tabledefault" width="100%">
-<tr><td rowspan="2"><img src="./images/KNBLogo.gif"></td>
-<td colspan="7">
-<div class="title">Metacat Apache Configuration</div>
-</td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
-<div class="header1">Table of Contents</div>
-  <div class="toc">
-    <div class="toc1"><a href="#Intro">Introduction</a></div>
-    <div class="toc1"><a href="#UbuntuConfig">Unbuntu/Debian Configuration</a></div>
-      <div class="toc2"><a href="#ModJK">Set Up Mod JK</a></div>
-      <div class="toc2"><a href="#SetUpKnb">Set Up Metacat Site</a></div>
-      <div class="toc2"><a href="#LsidConfig">LSID Service Configuration</a></div>
-      <div class="toc2"><a href="#UbuntuReloadApache">Reload Apache</a></div>
-    <div class="toc1"><a href="#OtherConfig">Other O/S Configuration</a></div>
-  </div> 
-
-<a name="Intro"></a><div class="header1">Introduction</div>
-  <p>If you are going to run Tomcat behind the Apache web server, you have some additional
-  setup to perform.  One of the reasons for recommending the Ubuntu Linux O/S is its 
-  ease of setup.  This becomes abundantly clear when configuring Apache.  We will
-  address Ubuntu/Debian configurations separately from all other configurations.</p>
-  
-<a name="UbuntuConfig"></a><div class="header1">Unbuntu/Debian Configuration</div>  
-   <p>If you are installing on an Ubuntu/Debian system, and you installed Apache using 
-   apt-get, the Metacat code will have helper files that can be dropped into directories 
-   to configure Apache.  Depending on whether you are installing from binary distribution 
-   or source, these helper files will be in one of two locations:
-   
-   <ul>
-   <li>Installing From Binary Distribution - the helper files will be located in the 
-   directory where you extracted the distribution.</li>
-   <li>Installing From Source - regardless if it's a source distribution or source that 
-   you checked out from the SVN repository, the helper files will be located in:
-     <div class="code">&lt;metacat_code_dir&gt;/src/scripts</div></li>
-   </ul>
-   <p>We will refer to the directory with the helper scripts as &lt;metacat_helper_dir&gt;</p>
-   <p>We will refer to the directory where Apache is installed as &lt;apache_install_dir&gt;</p>
-   
-   <a name="ModJK"></a><div class="header2">Set Up Mod JK</div>
-	<p>Apache uses a module called Mod JK to talk to Tomcat applications.  If you haven't done so 
-	already, you can install it by typing:</p>	
-	  <div class="code">sudo apt-get install libapache2-mod-jk</div>
-	<p>The helper files that configure the interface between Apache and Tomcat are jk.conf and workers.properties.
-	To install these files:</p>
-      <div class="code">sudo cp &lt;metacat_helper_dir&gt;/jk.conf &lt;apache_install_dir&gt;/mods-available/</div>
-      <div class="code">sudo cp &lt;metacat_helper_dir&gt;/workers.properties &lt;apache_install_dir&gt;</div>
-    <p>Disabling and re-enabling the Apache Mod JK module will pick up the new changes:</p>
-      <div class="code">sudo a2dismod jk</div>
-      <div class="code">sudo a2enmod jk</div>
-    
-   <a name="SetUpKnb"></a><div class="header2">Set Up Metacat Site</div>   
-    <p>Next, Apache needs to know about the Metacat site.  The helper file named "knb" has rules that
-    tell Apache which traffic to route to Metacat.  Set up the knb (Metacat) site by dropping the 
-    knb file into the sites-available directory and running the a2ensite to enable the site:</p>
-      <div class="code">sudo cp &lt;metacat_helper_dir&gt;/knb &lt;apache_install_dir&gt;/sites-available</div>
-      <div class="code">sudo a2ensite knb</div>
-      
-    <a name="LsidConfig"></a><div class="header2">LSID Service Configuration</div>   
-    <p>If you want to run an optional LSID server along with the Metacat server, set up and enable the authority service site 
-      configurations by typing:</p>
-      <div class="code">sudo cp &lt;metacat_helper_dir&gt;/authority &lt;apache_install_dir&gt;/sites-available</div>
-      <div class="code">sudo a2ensite authority</div>
-      
-    <a name="UbuntuReloadApache"></a><div class="header2">Reload Apache</div>
-    <p>Reload apache to bring in changes by typing:</p>
-      <div class="code">sudo /etc/init.d/apache2 force-reload</div>
-  
-<a name="OtherConfig"></a><div class="header1">Other O/S Configuration</div>
-  <p>If you are running on an O/S other than Ubuntu/Debian or you installed the
-  Apache source or binary, you will need to manually edit the Apache configuration
-  file.</p> 
-     
-  <p>We will refer to the directory where Apache is installed as &lt;apache_install_dir&gt;</p>
-  
-  <p>Edit:</p>
-    <div class="code">&lt;apache_install_dir&gt;/conf/httpd.conf</div>
-   
-  <a name="ModJkLog"></a><div class="header2">Mod JK Log Configuration</div>
-    <p> You should configure the log location and level for Mod JK.  If you do not
-    already have a section like this, you should add it.</p>  
-    
-    <div class="code">
-    &lt;IfModule mod_jk.c&gt;<br>
-       &nbsp;&nbsp;JkLogFile "/var/log/tomcat/mod_jk.log"<br>
-       &nbsp;&nbsp;JkLogLevel info<br>
-    &lt;/IfModule&gt;
-    </div>
-    
-    <p>You can set the log location to any place you like</p>
-
-  <a name="VirtualHost"></a><div class="header2">Virtual Host Configuration</div>  
-  <p>The following section configures apache to talk to route traffic to the Metacat
-  application.</p>
-    <div class="code">
-    &lt;VirtualHost XXX.XXX.XXX.XXX:80&gt;<br>
-      &nbsp;&nbsp;DocumentRoot /var/www<br>
-      &nbsp;&nbsp;ServerName dev.nceas.ucsb.edu<br>
-      &nbsp;&nbsp;ErrorLog /var/log/httpd/error_log<br>
-      &nbsp;&nbsp;CustomLog /var/log/httpd/access_log common<br>
-    <br>
-      &nbsp;&nbsp;ScriptAlias /cgi-bin/ "/var/www/cgi-knb/"<br>
-      &nbsp;&nbsp;&lt;Directory /var/www/cgi-knb/&gt;<br>
-        &nbsp;&nbsp;&nbsp;&nbsp;AllowOverride None<br>
-        &nbsp;&nbsp;&nbsp;&nbsp;Options ExecCGI<br>
-        &nbsp;&nbsp;&nbsp;&nbsp;Order allow,deny<br>
-        &nbsp;&nbsp;&nbsp;&nbsp;Allow from all<br>
-      &nbsp;&nbsp;&lt;/Directory&gt;<br>
-    <br>
-      &nbsp;&nbsp;ScriptAlias /knb/cgi-bin/ "/var/www/webapps/knb/cgi-bin/"<br>
-      &nbsp;&nbsp;&lt;Directory "/var/www/webapps/knb/cgi-bin/"&gt;<br>
-        &nbsp;&nbsp;&nbsp;&nbsp;AllowOverride None<br>
-        &nbsp;&nbsp;&nbsp;&nbsp;Options ExecCGI<br>
-        &nbsp;&nbsp;&nbsp;&nbsp;Order allow,deny<br>
-        &nbsp;&nbsp;&nbsp;&nbsp;Allow from all<br>
-      &nbsp;&nbsp;&lt;/Directory&gt;<br>
-    <br>
-      &nbsp;&nbsp;JkMount /knb ajp13<br>
-      &nbsp;&nbsp;JkMount /knb/* ajp13<br>
-      &nbsp;&nbsp;JkMount /knb/metacat ajp13<br>
-      &nbsp;&nbsp;JkUnMount /knb/cgi-bin/* ajp13<br>
-      &nbsp;&nbsp;JkMount /*.jsp ajp13<br>
-      &nbsp;&nbsp;JkMount /metacat ajp13<br>
-      &nbsp;&nbsp;JkMount /metacat/* ajp13<br>
-    &lt;/VirtualHost&gt;<br>
-    </div>
-    
-    <p>Some notes:</p>
-    <ul>
-    <li>ServerName - should be set to the dns name where you will serve Metacat.</li>
-    <li> ScriptAlias /knb/cgi-bin/ - this directive and the following Directory section
-    should both point to the cgi-bin directory inside your Metacat installation.</li>
-    </ul>
-    
-
-  <a name="WorkersProperties"></a><div class="header2">workers.properties file</div> 
-   <p>You will need to drop a file named "workers.proerpties" file into your Apache 
-   configuration directory, and edit the file to make sure all properties are correct.
-   Metacat provides a base workers.properties file for you to use.  Depending on 
-   whether you are installing from binary distribution or source, the workers.properties
-   files will be in one of two locations:
-   
-   <ul>
-   <li>Installing From Binary Distribution - the file will be located in the 
-   directory where you extracted the distribution.</li>
-   <li>Installing From Source - regardless if it's a source distribution or source that 
-   you checked out from the SVN repository, the file will be located in:
-     <div class="code">&lt;metacat_code_dir&gt;/src/scripts/workers.properties</div></li>
-   </ul>   
-   
-   <p>Copy the workers.properties file into:</p>
-     &lt;apache_install_dir&gt;/conf/
-     
-   <p>Edit the workers.properties file and make sure the following properties are
-   set correctly:</p>
-   <ul>
-   <li>workers.tomcat_home - should be set to the Tomcat install directory on your system.</li>
-   <li>workers.java_home  - should be set to the Java install directory on your system.</li>
-   </ul> 
-   
-  <a name="LsidConfig"></a><div class="header2">LSID Service Configuration</div>   
-    <p>If you want to run an optional LSID server along with the Metacat server, add the following lines to the
-    VirtualHost section you configured above:</p>
-      <div class="code">
-        &nbsp;&nbsp;JkMount /authority ajp13<br>
-        &nbsp;&nbsp;JkMount /authority/* ajp13<br>
-      </div>
-      
-    <a name="UbuntuReloadApache"></a><div class="header2">Reload Apache</div>
-    <p>Restart apache to bring in changes by typing:</p>
-      <div class="code">sudo /etc/init.d/apache2 restart</div>
-      
-    <br>    
-</body>
-</html>

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-*
\ No newline at end of property
Index: docs/user/metacat-source-build.html
===================================================================
--- docs/user/metacat-source-build.html	(revision 5315)
+++ docs/user/metacat-source-build.html	(nonexistent)
@@ -1,159 +0,0 @@
-<!-- 
-  *   '$RCSfile$'
-  *     Purpose: web page describing the installation of Metacat
-  *   Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *     Authors: Chad Berkley
-  *
-  *    '$Author: daigle $'
-  *    '$Date: 2008-11-24 11:57:40 -0800 (Mon, 24 Nov 2008) $'
-  *    '$Revision: 4621 $'
-  *
-  *
-  -->
-  
-<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>Metacat Source Download and Build Instructions</title>
-  <link rel="stylesheet" type="text/css" href="./common.css">
-  <link rel="stylesheet" type="text/css" href="./default.css">
-</head>
-
-<body>
-
-<table class="tabledefault" width="100%">
-<tr><td rowspan="2"><img src="./images/KNBLogo.gif"></td>
-<td colspan="7">
-<div class="title">Metacat Source Download and Build Instructions</div>
-</td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
-<div class="header1">Table of Contents</div>
-  <div class="toc">
-    <div class="toc1"><a href="#Intro">Introduction</a></div>
-    <div class="toc1"><a href="#GetSource">Get Metacat Source</a></div>
-      <div class="toc2"><a href="#SourceDistribution">Source Distribution</a></div> 
-      <div class="toc2"><a href="#SVN">SVN Checkout</a></div>
-    <div class="toc1"><a href="#BuildFromSource">Build From Source</a></div>
-      <div class="toc2"><a href="#PrepareBuild">Prepare Build</a></div>
-      <div class="toc2"><a href="#DoAntBuild">Do Ant Build</a></div>
-  </div> 
-
-<a name="Intro"></a><div class="header1">Introduction</div>
-  <p>Metacat source can be downloaded either by getting and extracting the 
-  source distribution, or by checking out the code from the repository.</p>
-  
-  <p>Reasons for choosing one versus the other might be:</p>
-  <ul>
-  <li>Source Distribution - this is a faster download since the code is compressed.  You
-  might choose this if you want a stable versioned release, but you prefer to have
-  all of your applications built on the server where it will run.  (Although it shouldn't
-  matter where a java application is built.)</li>
-  <li>SVN Checkout - there are several reasons for choosing a checked out version of 
-  the code.  One is that you may want to build from the head of the code to pick up
-  new changes that are not yet in a versioned build.  Conversely, you may want to build
-  off of an older tag, to avoid an issue that was introduced in a build.  Lastly, you 
-  may want to develop and submit code to the Metacat repository</li>
-  </ul>
-  
-  <p>You will also need Apache Ant to do the build.  If you have not already 
-  installed Ant and you are running Ubuntu/Debian, you can get it by typing:</p>
-    <div class="code">sudo apt-get install ant</div>
-  
-  <p>Otherwise, you can get ant from
-  <a href="http://ant.apache.org/">The Apache Ant homepage</a></p>
-  
-  <p>If you are checking out Metacat code from the SVN repository, you will need both 
-  Subversion (SVN) and CVS clients installed and configured on your system.  Both are needed
-  because, while Metacat has been migrated to SVN, some of its supporting libraries (eml, 
-  utilities and seek) have not yet been migrated.  Eventually, SVN will be the only versioning 
-  client you will need.  You will need to make sure you have the appropriate accounts on these 
-  systems.  You won't have to worry about SVN or CVS if you are installing from a Metacat
-  source distribution.  These have all the required dependencies built in.</p>
-  
-  <p>If you have not already installed Subversion and you are running Ubuntu/Debian, you can 
-  get it by typing:</p>
-    <div class="code">sudo apt-get install subversion</div>
-    
-  <p>Otherwise, you can get if from <a href="http://subversion.tigris.org">The Subversion homepage</a></p>
-  
-  <p>If you have not already installed CVS and you are running Ubuntu/Debian, you can 
-  get it by typing:</p>
-    <div class="code">sudo apt-get install cvs</div>
-    
-  <p>Otherwise, you can get it from <a href="http://ximbiot.com/cvs/wiki/">The Ximbiot CVS homepage</a></p>
- 
-
-<a name="GetSource"></a><div class="header1">Get Metacat Source</div>
-
-  <a name="SourceDistribution"></a><div class="header2">Source Distribution</div>  
-    <p>To get the Metacat source distribution, browse to the 
-      <a href="http://knb.ecoinformatics.org/software/download.html">KNB Software Download Page</a>.
-      In the Metacat section, for Linux based systems, select the link that looks like:</p>
-	  <div class="code">metacat-src-X.X.X.tar.gz</div>
-	  <p>for Windows systems, select the link that looks like:</p>
-	  <div class="code">metacat-src-X.X.X.zip</div>
-    <p>where X.X.X is the latest version of Metacat.  Choose to save the file locally in the directory 
-    where your source should live.</p>
-    <p>Extract the Metacat package files on Linux systems by typing:
-      <div class="code">tar -xvzf metacat-src-X.X.X.tar.gz</div>
-    <p>or, on Windows, use your system unzip utility to extract the zip file.</p>
-    <p>Rename the metacat-X.X.X directory to metacat.</p>
- 
-  <a name="SVN"></a><div class="header2">SVN Checkout</div> 
-    <p>To check out the code from SVN, go to the directory where you would like the code 
-    to live and type:</p>
-      <div class="code">svn co https://code.ecoinformatics.org/code/metacat/tags/METACAT_&lt;rev&gt; metacat</div>
-    <p>Where &lt;rev&gt; is the version of the code you want to check out (like 1_9). </p>
-    
-    <p>If you are trying to check out the head, type:</p>
-      <div class="code">svn co https://code.ecoinformatics.org/code/metacat/trunk metacat</div>
-      
-    <p>You should see a list of files as they check out.</p>
-    
-  <a name="BuildFromSource"></a><div class="header1">Build From Source</div>
-     <p>You should now have the Metacat source in a directory named "metacat" in your
-     code directory (We will refer to the metacat source directory as &lt;metacat_src_dir&gt;.
-     
-  <a name="PrepareBuild"></a><div class="header2">Prepare Build</div>   
-    <p>Edit the file at:</p>
-      <div class="code">&lt;metacat_src_dir&gt;/build.properties</div> 
-    <p>Make sure that the "build.tomcat.dir" property is set to your tomcat installation
-    directory.  For instance:</p>
-      <div class="code">build.tomcat.dir=/usr/local/tomcat</div>
-    <p>Metacat will use some of the native Tomcat libraries during the build.</p>
-    
-    <p>If your cvs user is something other than the user your are logged in as, you
-    will need to change the ${env.USER} part of the cvsroot property to be your cvs 
-    user.  For instance:</p>
-      <div class="code">cvsroot=:ext:cvs-user@cvs.ecoinformatics.org:/cvs</div>
-    <p> where your cvs user name is "cvs-user"</p> 
-    
-  <a name="DoAntBuild"></a><div class="header2">Do Ant Build</div>   
-    <p>In the &lt;metacat_src_dir&gt;, run: </p>
-      <div class="code">ant clean build-metacat</div>
-      
-    <p>You will see the individual modules get built.  You will be prompted
-    for your cvs password several times.  You should see a "BUILD SUCCESSFUL"
-    message at the end.</p>
-    
-    <p>You should see a new file named:</p>
-      <div class="code">&lt;metacat_src_dir&gt;/dist/knb.war</div>
-      
-  <br>
-    
-</body>
-</html>

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Index: docs/user/metacattour.html
===================================================================
--- docs/user/metacattour.html	(revision 5315)
+++ docs/user/metacattour.html	(nonexistent)
@@ -1,100 +0,0 @@
-<!DOCTYPE html PUBliC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>KNB Software: Metacat: Metacat Tour Home</title>
-  <link rel="stylesheet" type="text/css" href="./default.css">
-</head>
-
-<body>
-
-<table class="tabledefault" width="100%">
-<tr>
-  <td rowspan="2"><img src="./images/KNBLogo.gif"></td>
-  <td colspan="7"><div class="title">Metacat Tour Home</div></td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
-<p>&nbsp;</p>
-<table class="tabledefault" width="100%">
-<tr>
-  <td class="tablehead" colspan="2"><p class="label">Background Information</p>
-  </td>
-</tr>
-<tr>
-  <td>
-   <ul>
-      <li> <a href="./xmldoc.html">XML documents</a></li>
-      <li> <a href="./xmltree.html">XML tree</a></li>
-      <li> <a href="./domapi.html">DOM API</a></li>
-    </ul>
-  </td>
-</tr>
-
-<tr>
-  <td class="tablehead" colspan="2"><p class="label">Basic Functionality</p></td>
-</tr>
-<tr>
-  <td>
-    <ul>
-      <li> <a href="./metacat.html">Metacat Server</a></li>
-      <li> <a href="./metacatdb.html">Metacat Database</a></li>
-      <li> <a href="./metacatdom.html">Metacat Document Object Model (DOM)</a></li>
-      <li> <a href="./clientapi.html">Metacat Client Programming Interface</a></li>
-      <li> <a href="./metacatload.html">Writing XML</a></li>
-      <li> <a href="./metacatquery.html">Searching the Database</a></li>
-      <li> <a href="./metacatread.html">Reading data from Metacat</a></li>
-      <li> <a href="./metacatgetlog.html">Event Log Reporting</a></li>
-    </ul>
-  </td>
-</tr>
-
-<tr>
-  <td class="tablehead" colspan="2"><p class="label">Advanced Functionality</p></td>
-</tr>
-<tr>
-  <td>
-    <ul>
-      <li> <a href="./saxparser.html">Document parsing</a></li>
-      <li> <a href="./xmlindex.html">XML Indexing</a></li>
-      <li> <a href="./acontrol.html">Access Control</a></li>
-      <li> <a href="./ldap.html">LDAP for Authentication</a></li>
-      <li> <a href="./metacatout.html">Metacat Output</a></li>
-      <li> <a href="./metacatapi.html">Metacat Interface</a></li>
-      <li> <a href="./packages.html">Packages and Relationships</a></li>
-      <li> <a href="./replication.html">Replication</a></li>
-      <li> <a href="./datafiles.html">Non-XML Data Files</a></li>
-      <li> <a href="./properties.html">Metacat Properties File</a></li>
-      <li> <a href="./harvester.html">Metacat Harvester</a></li>
-      <li> <a href="./lsid_authority.html">LSID Support</a></li>
-      <li> <a href="./spatial_option.html">Metacat Spatial Option</a></li>
-      <li> <a href="./pagedreturn.html">Paged Query Results</a></li>
-      <li> <a href="./sitemaps.html">Search Engine Sitemaps</a></li>
-    </ul>
-  </td>
-</tr>
-
-<tr>
-  <td class="tablehead" colspan="2"><p class="label">Future Functionality</p></td>
-</tr>
-<tr>
-  <td>
-    <ul>
-      <li> <a href="./unimplem.html">Unimplemented features</a></li>
-    </ul>
-  </td>
-</tr>
-
-</table>
-</body>
-</html>
\ No newline at end of file

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Index: docs/user/run-db-scripts.html
===================================================================
--- docs/user/run-db-scripts.html	(revision 5315)
+++ docs/user/run-db-scripts.html	(nonexistent)
@@ -1,65 +0,0 @@
-<!-- 
-  *   '$RCSfile$'
-  *     Purpose: web page describing how to manually run database scripts
-  *   Copyright: 2008 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *     Authors: Michael Daigle
-  *
-  *    '$Author: daigle $'
-  *    '$Date: 2008-11-19 16:48:24 -0800 (Wed, 19 Nov 2008) $'
-  *    '$Revision: 4597 $'
-  *
-  *
-  -->
-  
-<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>How to Manually Run Database Scripts</title>
-  <link rel="stylesheet" type="text/css" href="./common.css">
-  <link rel="stylesheet" type="text/css" href="./default.css">
-</head>
-
-<body>
-
-<table class="tabledefault" width="100%">
-<tr><td rowspan="2"><img src="./images/KNBLogo.gif"></td>
-<td colspan="7">
-<div class="title">How to Manually Run Database Scripts</div>
-</td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
-<div class="header1">Table of Contents</div>
-<div class="toc">
-  <div class="toc1"><a href="#Overview">Overview</a></div> 
-  <div class="toc1"><a href="#Postgres">PostgreSQL</a></div>
-    <div class="toc2"><a href="#Linux">Linux</a></div> 
-</div> 
-
-<a name="Overview"></a><div class="header1">Overview</div>
-   <p>Sometimes it will be necessary to run a database script 
-    manually.  The following sections describe how.</p>
-    
-<a name="Postgres"></a><div class="header1">PostgreSQL</div>
-  <a name="Linux"></a><div class="header2">Linux</div>
-    <p>At the command line, you can run:</p>
-      <div class="code">psql -U metacat -W -h localhost metacat &lt; &lt;script-name&gt;</div>
-    <p>where &lt;script-name&gt; is the name of the script you want 
-    to run.  This assumes that your database and username are metacat.  
-    You should adjust accordingly for different user or database names.</p>
-    
-      
-  </body>
-</html>
\ No newline at end of file

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===================================================================
--- docs/user/metacat-configure.html	(revision 5315)
+++ docs/user/metacat-configure.html	(nonexistent)
@@ -1,411 +0,0 @@
-<!-- 
-  *   '$RCSfile$'
-  *     Purpose: web page describing the installation of Metacat
-  *   Copyright: 2008 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *     Authors: Chad Berkley
-  *
-  *    '$Author$'
-  *    '$Date$'
-  *    '$Revision$'
-  *
-  *
-  -->
-  
-<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>Metacat Configuration Instructions</title>
-  <link rel="stylesheet" type="text/css" href="./common.css">
-  <link rel="stylesheet" type="text/css" href="./default.css">
-</head>
-
-<body>
-
-<table class="tabledefault" width="100%">
-<tr><td rowspan="2"><img src="./images/KNBLogo.gif"></td>
-<td colspan="7">
-<div class="title">Metacat Configuration</div>
-</td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
-<div class="header1">Table of Contents</div>
-<div class="toc">
-  <div class="toc1"><a href="#Overview">Overview</a></div>
-      <div class="toc2"><a href="#MetacatConfiguration">Metacat Configuration</a></div> 
-      <div class="toc2"><a href="#ConfigurationRules">Configuration Rules</a></div>
-  <div class="toc1"><a href="#authConfig">Authentication Configuration</a></div>
-      <div class="toc2"><a href="#AuthOverview">Authentication Overview</a></div> 
-      <div class="toc2"><a href="#GetToAuthConfig">Getting to the Authentication Configuration</a></div> 
-      <div class="toc2"><a href="#ConfigAuthNoAuth">Changing Authentication Configuration Without Authentication</a></div>
-  <div class="toc1"><a href="#AdminLogin">Admin Log In</a></div>
-    <div class="toc2"><a href="#AdminLoginOverview">Admin Log In</a></div>
-    <div class="toc2"><a href="#LoggingIn">Logging In</a></div>
-  <div class="toc1"><a href="#MainConfig">Main Configuration Page</a></div>
-    <div class="toc2"><a href="#MainConfigOverview">Main Configuration Overview</a></div>
-  <div class="toc1"><a href="#GlobalConfig">Global Properties Configuration</a></div>
-    <div class="toc2"><a href="#GlobalConfigOverview">Global Properties Overview</a></div>
-    <div class="toc2"><a href="#AutoDetection">Property Auto-Detection</a></div>
-    <div class="toc2"><a href="#GlobalConfigBackup">Global Property Backup</a></div>  
-  <div class="toc1"><a href="#SkinsConfig">Skins Configuration</a></div>  
-    <div class="toc2"><a href="#SkinsConfigOverview">Skins Overview</a></div>
-    <div class="toc2"><a href="#ChoosingDefaultSkin">Choosing a Default Skin</a></div>
-    <div class="toc2"><a href="#ConfigOnlineRegistry">Configuring Online Registry</a></div>
-  <div class="toc1"><a href="#DatabaseConfig">Database Configuration</a></div>
-    <div class="toc2"><a href="#DatabaseConfigOverview">Database Configuration Overview</a></div>
-    <div class="toc2"><a href="#DatabaseNewInstall">New Database Installation</a></div>
-    <div class="toc2"><a href="#DatabaseUpgrade">Database Upgrade</a></div>
-  <div class="toc1"><a href="#GeoserverConfig">Geoserver Configuration</a></div>
-    <div class="toc2"><a href="#GeoserverUpdatePassword">Geoserver Password Update</a></div>
-    <div class="toc2"><a href="#GeoserverManualUpdate">Geoserver Manual Update</a></div>  
-  <div class="toc1"><a href="#CompleteConfig">Complete the Metacat Configuration</a></div>
-</div> 
-
-<a name="Overview"></a><div class="header1">Overview</div>
-<a name="MetacatConfiguration"></a><div class="header2">Metacat Configuration</div>
-  <p>As of version 1.9.0, Metacat configuration is done internally by the application.  When
-  Metacat (Tomcat) is started, it will check to see if it is configured.  If not, you will be 
-  automatically sent to the configuration pages. </p>
-  
-  <p>If the installation is new, or the previous version is before 1.9.0, you will 
-  need to pay close attention to the configuration values.  If you have upgraded 
-  Metacat, and the previous version is 1.9.0 or later, Metacat will pull existing 
-  values from a backup location.  You should still verify that the values are
-  correct.</p>
-  
-  <p>Get to Metacat on your server by entering into the browser:</p>
-  <div class="code">http://&lt;your_context_url&gt;</div>
-  <p>Where &lt;your_context_url&gt is the url where Metacat will be served followed
-  by the name of the war file(application context) that you installed.  For instance, 
-  the KNB production Metacat url is:</p>
-  <div class="code">http://knb.ecoinformatics.org/knb</div>
-  
-  <p>You can always go to the configuration screen from within Metacat by typing:
-  <div class="code">&lt;your_context_url&gt;/admin</div>
-  
-<a name="ConfigurationRules"></a><div class="header2">Configuration Rules</div>   
-  <p>The system will follow these rules in order to determine the order
-  that the configuration will occur:</p>
-  
-  <ul>
-    <li>
-      Always prompt the user for the backup directories with the  
-      <a HREF="#BackupConfig">Backup Configuration Section</a>.  
-      You will need to have backup directories configured in order 
-      to continue with configuration.
-    </li>
-    <li>
-      Is Authentication Configured? If not, show 
-      <a HREF="#AuthConfig">Authentication Configuration Section</a>.  
-      You will need to have authorizaiton configured in order to define administrative accounts
-      and authenticate as one of these users.
-    </li>
-    <li>
-      Are you logged in as an administrative user?  If not, show 
-      <a HREF="#AdminLogin">Administrator Login Page</a>.
-      You can only configure Metacat as an administrator.
-    </li>
-    <li>
-      Are main properties, skins or database unconfigured?  If so, show 
-      <a HREF="#MainConfig">Main Configuration Page</a>
-      Note that you will not be able to select the database configuration utility 
-      until main properties have been configured.
-    </li>  
-    <li>
-      Are all sections configured?  If so, show 
-      <a HREF="#MainConfig">Main Configuration Page</a> which
-      include instructions for going to Metacat server (or restarting Metacat if you 
-      are reconfiguring a running server).
-    </li> 
-  </ul>
-  
-  <p> See the following sections for descriptions of how each of these work.  For more
-  information on each field, click on the blue question mark icon to the right.</p>
-
-<a name="BackupConfig"></a><div class="header1">Backup Configuration</div>
-  <a name="BackupOverview"></a><div class="header2">Backup Overview</div>
-  <p>Metacat backs up all configured values to a directory outside the application
-  installation directories.  This is so that we can preserve the configuration even
-  after you upgrade Metacat (and the application directories get removed).</p>
-  
-  <p>Since a new installation/upgrade won't know where this external directory is, it will
-  go through a discovery algorithm to give a best guess and pre-populate this value on the 
-  Backup Directory Configuration screen (see fig 1).  The algorithm is:
-  
-  <ul>
-  <li>Look for a saved backup location file in the user home dir - Is there a file named 
-    &lt;user_home&gt;/.metacat/backup-location for the user that started tomcat? if so, does 
-    it contain a single line which is a readable directory?  This directory was the backup 
-    directory used during a previous install.  Return that directory.</li>
-  <li>Look for an existing hidden (.metacat) directory in a default system directory.  Get 
-   the default base directory for the OS.  (See application.windowsBackupBaseDir and 
-   application.linuxBackupBaseDir in metacat.properties.)  If a directory called 
-   &lt;base_dir&gt;/metacat/.metacat exists, return &lt;base_dir&gt;/metacat.</li>
-  <li> Look for an existing hidden (.metacat) directory in the user directory. If a directory 
-    called &lt;user_home&gt;/.metacat exists for the user that started tomcat, return &lt;user_home&gt;.</li>
-  <li> Is the &lt;base_dir&gt; writable by the user that started tomcat?  If so, return &lt;base_dir&gt;</li>
-  <li> Does the &lt;user_home&gt; exist?  If so, return &lt;user_home&gt;</li>
-  <li> Otherwise, return null </li>
-  </ul>
-  <img class="screenshot" src="./images/backup-config.png"/>
-  <div class="fig-text"> fig 1 </div>  
-
-  <a name="ConfigBackup"></a><div class="header2">Configure Backup</div>
-  <p>If the pre-populated value is incorrect, you should change it to the correct
-  directory</p> 
-
-<a name="AuthConfig"></a><div class="header1">Authentication Configuration</div>
-  <a name="AuthOverview"></a><div class="header2">Authentication Overview</div>
-  <p>Metacat uses LDAP as it's primary authentication mechanism, but you can define
-  your own mechanism by creating a java class that implements 
-  AuthInterface. The configuration values needed are Authentication Class, Authentication URL, 
-  Authentication Secure URL and Metacat Administrators.  You need 
-  to verify that the the Authentication URL and Authentication Secure URL are correct (fig 2).  
-  <span class="emphasis">You need to make sure that your user 
-  account is entered into the Metacat Administrators field.  You will not be allowed
-  to continue with configuration if this is missing.</span>
-
-  <img class="screenshot" src="./images/auth-config.png"/>
-  <div class="fig-text"> fig 2 </div>
-
-<a name="GetToAdminConfig"></a><div class="header2">Getting to the Authentication Configuration</div>
-  <p>You will automatically be sent to the Authentication Configuration page if this is a new
-  installation or upgrade.</p>
-  
-  <p>You can also get to the Administrative configuration from a running Metacat by typing:</p>
-  <div class="code">&lt;your_context_url&gt;/admin</div>
-  <p>You will be required to log in as an administrator and restart Metacat once you
-  make changes.</p>
-  
-  <a name="ConfigAuthNoAuth"></a><div class="header2">Changing Authentication Configuration Without Authentication</div>
-  <p>There is one exception to the log in rule.  That is when you need to change or add 
-  authentication information, but you can't authenticate using the existing setup.  For example:</p>
-  
-  <ul>
-    <li>The existing Metacat administrator is no longer available</li>
-    <li>You forgot the administrator password.</li>
-    <li>The configured authentication urls are unavailable and you need to configure new ones.</li>  
-  </ul>
-  
-  <p>In this case, you will need to edit the Metacat configuration file by hand and
-  make the changes.  This insures that only a person who has access to the Metacat
-  server and the configuration files on that server will be able to change the
-  administrator accounts</p>
-
-  <p>Stop Tomcat and edit the Metacat properties file at:</p>
-  <div class="code">&lt;webapp_dir&gt;/&lt;context_dir&gt;/WEB-INF/metacat.properties</div>
-  <p>where &lt;webapp_dir&gt; is the place that Tomcat looks for applications and 
-  &lt;context_dir&gt; is the name of the Metacat application (usually knb).  Change the 
-  following properties appropriately:</p>
-  
-  <ul>
-    <li>auth.administrators - a colon separated list of administrators</li>
-    <li>auth.url - the authenication server url</li>
-    <li>auth.surl - the authentication secure server url</li>  
-  </ul>
-  
-  <p>Save the metacat.properties file and start Tomcat.</p>
-  
-<a name="AdminLogin"></a><div class="header1">Admin Log In</div>
-<a name="AdminLoginOverview"></a><div class="header2">Admin Log In Overview</div>
-  <p>Once authentication has been configured, you will be required to login as an 
-  administrative user if you haven't already.  You will be taken to 
-  the administrator login screen (fig 2).  You can also get to the login
-  screen by choosing the "log in as different user" link at the bottom of
-  any configuration screen.</p>
-  
-  <img class="screenshot" src="./images/admin-login.png"/>
-  <div class="fig-text"> fig 3 </div>
-
-<a name="LoggingIn"></a><div class="header2">Logging In</div>
-<p>You need to log in with an account that was configured as an administrative
-user in the authentication configuration section.  If you did not set up the correct user 
-there, you will need to go through the 
-<a href="#ConfigAuthNoAuth">Changing Authentication Configuration Without Authentication</a>
-instructions to set up the user.</p>
-
-<p>Enter your user name.  This is one of the Metacat administrators that you 
-entered in authenticationuthentication configuration.  Enter your password and
-hit the "Login" button.  You should successfully log in.</p>
-
-<a name="MainConfig"></a><div class="header1">Main Configuration Page</div>
-<a name="MainConfigOverview"></a><div class="header2">Main Configuration Overview</div>
-  <p>The main configuration screen acts as a gateway into individual configuration
-  sections (fig 4).  You should see that the authentication is already configured.</p>  
-  
-  <p>Each section is listed with a status to the left which can be one of:</p>
-  <ul>
-    <li><font color="red">[unconfigured]</font> - the section has yet to be configured</li>
-    <li><font color="green">[configured]</font> - the section has been configured</li>
-    <li>
-      <font color="green">[bypassed]</font> - this is currently only used for Geoserver 
-      configuration.  The administrator can choose not to configure the Geoserver user/password.
-      In essence, the bypass status acts like the configured status.
-    </li>  
-  </ul>
-  
-  <p>To the right of each section is an option which can be one of:
-  <ul>
-    <li>Configure Now - click on this link to configure that section</li>
-    <li>Reconfigure Now - the section was already configured, but you can choose to reconfigure it.</li>
-    <li>
-      Configure Global Properties First - this section has a dependency on the global
-      properties section.  Once global properties is configured, the option to configure
-      this section should become available.
-    </li>  
-    <li>Version: X.X.X - this is used for the Database Installation/Upgrade section.  The system
-      detects the database schema version.  If that version is the same as the application version,
-      that version will be displayed (i.e. 1.9.0) and no further database configuration is
-      required.
-    </li>
-  </ul>
-  
-  <p>All sections must be in a configured or bypassed state in order to run Metacat.</p>
-  
-  <img class="screenshot" src="./images/main-config.png"/>
-  <div class="fig-text"> fig 4 </div>
-  
-<a name="GlobalConfig"></a><div class="header1">Global Properties Configuration</div>
-<a name="GlobalConfigOverview"></a><div class="header2">Global Properties Overview</div>
-  <p>Metacat global properties are the bulk of the core properties needed to run Metacat 
-  (fig 5).  For detailed instructions on setting these properties, refer to the blue 
-  question mark icon to the right of each property.  Be sure that each of these are set
-  appropriately.</p>
-  
-  <img class="screenshot" src="./images/global-config.png"/>
-  <div class="fig-text"> fig 5 </div>
-
-<a name="AutoDetection"></a><div class="header2">Property Auto-Detection</div> 
-   <p>The first time you install Metacat, the system will attempt to auto-detect
-   some values.  These are:</p>
-   
-  <ul>
-    <li>Metacat Context - Name of the context under which Metacat will run. This is the name 
-        of the Metacat war file that was deployed (minus the .war extension).</li>
-    <li>Server Name - The DNS name of the server where Metacat will be available, not including
-        port numbers or the http:// header.</li>
-    <li>HTTP Port - The non-secure port where Metacat will be available. </li>  
-    <li>HTTP SSL Port - The secure port where Metacat will be available.</li>
-    <li>Deploy Location - The directory where the application is deployed.</li>
-  </ul>
-  
-  <p>You should be extra careful that these were detected correctly.</p>
-  
-<a name="GlobalConfigBackup"></a><div class="header2">Global Property Backup</div>
-  <p>When you save global properties, they are saved in a backup file that is 
-  located in the following directory on linux:</p>
-  <div class="code">/var/metacat/.metacat</div>
-  and on windows:
-  <div class="code">C:\Program Files\metacat\.metacat</div>
-  <p>When you update Metacat, the system will look for these backed up properties
-  so you won't have to re-enter all the information from previous installs.</p>
-  
-<a name="SkinsConfig"></a><div class="header1">Skins Configuration</div>
-<a name="SkinsConfigOverview"></a><div class="header2">Skins Overview</div>
-  <p>Metacat allows for a customized look and feel for the Metacat front end and for the 
-  online data registry services.  There are two major functions provided by the
-  skins configuration.  The first is to choose which skin will be the default.  The
-  second will be to configure the look and feel of the online data registry pages.  For
-  more information on the online data registry option, refer to the 
-  <a href="./registry_installation.html">Metacat Registry Installation</a> documentation.</p>
-  
-  <p>Note that if you are not using the online registry, and you don't have a custom skin,
-  you can just save the default skins configuration and move on to the next configuration
-  section.</p>
-  
-<a name="ChoosingDefaultSkin"></a><div class="header2">Choosing a Default Skin</div> 
-  <p>There are several skins available to choose from in Metacat (fig 6).  If you have a 
-  skin that has been developed specifically for your instance of Metacat, you should
-  select the checkbox next to that skin.  When you do, the form will open up with 
-  several options for that skin (fig 6).  choose the 'Make "skin_name" default" radio selection.
-  You should see "(default)" appear next to that skin name.  Save the configuration
-  and that skin will be the one that appears when users visit your Metacat site.  Note
-  that if you do not have a custom skin, you should leave your skin as the "default" skin.</p>
-  
-  <img class="screenshot" src="./images/skins-config.png"/>
-  <div class="fig-text"> fig 6 </div>  
-
-<a name="ConfigOnlineRegistry"></a><div class="header2">Configuring Online Registry</div> 
-  <p>The online registry code provides a web interface for entering data into Metacat.  The
-  screens are somewhat configurable as far as which fields show up and which are required.
-  You should select each for which you want to activate the registry and then select the
-  appropriate fields for that skin.</p> 
-   
-  <img class="screenshot" src="./images/skins-config-2.png"/>
-  <div class="fig-text"> fig 7 </div>  
-  
-<a name="DatabaseConfig"></a><div class="header1">Database Configuration</div>
-<a name="DatabaseConfigOverview"></a><div class="header2">Database Configuration Overview</div>
-  <p>Metacat will detect the schema version of your database, and upgrade it if necessary.  Once the
-  global Metacat properties have been configured, the Database Installation/Upgrade link 
-  will become active on the main Metacat configuration page (see fig 4).</p>
-
-<a name="DatabaseNewInstall"></a><div class="header2">New Database Installation</div>
-  <p>If this is a installation of Metacat, the database install/upgrade utility will
-  inform you of this (fig 8).  It will list the sql scripts that will get run in order
-  to create a database schema for the version of Metacat that you are installing.  If
-  there is any question as to whether the database is new, you should choose to cancel.
-  When you choose to continue, the server will run the scripts you saw earlier.</p>
-  <img class="screenshot" src="./images/database-config.png"/>
-  <div class="fig-text"> fig 8 </div> 
- 
-<a name="DatabaseUpgrade"></a><div class="header2">Database Upgrade</div> 
-  <p>If this is an upgrade of Metacat, the database install/upgrade utility will
-  inform you of the current version of the database (fig 9).  It will list the sql scripts 
-  that will get run in order to update the database schema to the upgraded version of 
-  Metacat.  If there is any question as to whether the detected database schema version is 
-  correct, you should choose to cancel. When you choose to continue, the server will run 
-  the scripts you saw earlier.</p>
-  <img class="screenshot" src="./images/database-config-2.png"/>
-  <div class="fig-text"> fig 9 </div> 
- 
-<a name="GeoserverConfig"></a><div class="header1">Geoserver Configuration</div>
-<a name="GeoserverOverview"></a><div class="header2">Geoserver Configuration Overview</div> 
-  <p>Metacat comes bundled with a Web Mapping Service called Geoserver which 
-  converts spatial data into web-deliverable map images.  For more information, see the
-  <a href="./spatial_option.html">Metacat Spatial Option documentation</a>.  Geoserver 
-  installs with a default admin username and password.  You should change these so that
-  only local administrators can make changes to Geoserver.</p>
-<a name="GeoserverUpdatePassword"></a><div class="header2">Geoserver Password Update</div>
-  <p>When you choose the Geoserver Configuration link on the main configuratio page, you
-  will go to a page that will prompt you for a user name and password (fig 10).  When you 
-  enter a user name and password, the metacat server will contact the embedded Geoserver
-  server and change the login credentails.</p>
-  <p>You also have the option of choosing "bypass".  This will leave Geoserver configured
-  with the default user name and password.  The main configuration screen will show the 
-  bypassed status.  The system will interpret the bypassed status the same as the configured
-  status.</p>
-  
-  <img class="screenshot" src="./images/geoserver-config.png"/>
-  <div class="fig-text"> fig 10 </div> 
-  
-<a name="GeoserverManualUpdate"></a><div class="header2">Geoserver Manual Update</div>
-  <p>You also have the option of changeing the Geoserver username and password by logging
-  in directly to the Geoserver.  For more information on changing the credentials directly,
-  refer to the <a href="./geoserver-manual-configure.html">Geoserver Password Change documentation</a>.
-  Note that once you change the credentails manually, you will not be able to use the 
-  Metacat admin tool to change it again (until a new Metacat Upgrade or installation).
-<a name="CompleteConfig"></a><div class="header1">Complete the Metacat Configuration</div>  
-  At this point, all the sections of the main configuration should be in a configured or
-  bypassed state (fig 11).  If you are configuring because of a Metacat install or upgrade,
-  you will have the option to click on the "go to metacat" link and you should get taken
-  directly to the running version of Metacat.  Note that this may take some time depending
-  on the amount of data in your database, since Metacat goes through an indexing process
-  at start-up time.</p>
-  
-  <p>If you are reconfiguring an already running version of Metacat, you will not have the
-  option to go directly back to Metacat.  You will need to restart the server (Tomcat).</p>
-  <img class="screenshot" src="./images/main-config-2.png"/>
-  <div class="fig-text"> fig 11 </div> 
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@@ -1,137 +0,0 @@
-<!-- 
-  *   '$RCSfile$'
-  *     Purpose: web page describing the installation of Metacat
-  *   Copyright: 2008 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *     Authors: Chad Berkley
-  *
-  *    '$Author: daigle $'
-  *    '$Date: 2008-11-19 16:48:24 -0800 (Wed, 19 Nov 2008) $'
-  *    '$Revision: 4597 $'
-  *
-  *
-  -->
-  
-<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>Metacat Configuration Instructions</title>
-  <link rel="stylesheet" type="text/css" href="./common.css">
-  <link rel="stylesheet" type="text/css" href="./default.css">
-</head>
-
-<body>
-
-<table class="tabledefault" width="100%">
-<tr><td rowspan="2"><img src="./images/KNBLogo.gif"></td>
-<td colspan="7">
-<div class="title">Metacat Configuration</div>
-</td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
-<div class="header1">Table of Contents</div>
-<div class="toc">
-  <div class="toc1"><a href="#BuildIssues">Build Issues</a></div>
-    <div class="toc2"><a href="#HttpServletExceptions">Ant BUILD FAILED : Multiple HttpServlet Exceptions</a></div> 
-  <div class="toc1"><a href="#InstallationIssues">Installation Issues</a></div>
-  <div class="toc1"><a href="#StartupIssues">Startup Issues</a></div>
-    <div class="toc2"><a href="#Jdk14Logger">Metacat doesn't start and Jdk14Logger exception</a></div> 
-  <div class="toc1"><a href="#ConfigurationIssues">Configuration Issues</a></div>
-   <div class="toc2"><a href="#DbUpdateIssue">Database Update Fails (not a connectivity issue)</a></div>
-  <div class="toc1"><a href="#GeneralApplicationIssues">General Application Issues</a></div>
-    <div class="toc2"><a href="#MapDisplayIssue">Maps will not display</a></div>
-  <div class="toc1"><a href="#UnitTestingIssues">Unit Testing Issues</a></div>
-    <div class="toc2"><a href="#503ServiceTemporarilyUnavailable">Mutliple Tests Fail : 503 Service Temporarily Unavailable</a></div>
-</div> 
-
-<a name="BuildIssues"></a><div class="header1">Build Issues</div>
-  <a name="HttpServletExceptions"></a><div class="header2">Ant BUILD FAILED : Multiple HttpSevlet Exceptions</div>
-    <p>During an Ant build of Metacat, you will see many HttpServletRequest, HttpServletResponse and
-    other errors.  The compiler will complain that it cannot find a symbol, for example:</p>
-      <div class="code">
-      [javac] /home/daigle/workspace/metacat/build/src/edu/ucsb/nceas/metacat/MetaCatServlet.java:506: cannot find symbol<br>
-      [javac] symbol  : class HttpServletResponse<br>
-      [javac] location: class edu.ucsb.nceas.metacat.MetaCatServlet<br>
-      [javac] &nbsp;&nbsp;&nbsp;&nbsp;HttpServletResponse response) throws ServletException, IOException {<br>
-      [javac] &nbsp;&nbsp;&nbsp;&nbsp;^<br>
-      </div>
-      
-    <p>This is usually caused by the build not being able to find native Tomcat libraries. edit your
-    build.properties file in  
-      
-<a name="InstallationIssues"></a><div class="header1">Installation Issues</div>
- 
-<a name="StartupIssues"></a><div class="header1">Startup Issues</div> 
-	<a name="Jdk14Logger"></a><div class="header2">Metacat doesn't start and Jdk14Logger exception</div>
-	<p>The symptoms are that the metacat service will not show up at all, even though Tomcat 
-      is serving, and the following error shows up in the tomcat log (catalina.log):</p>
-      
-      <div class="code">org.apache.commons.logging.LogConfigurationException: User-specified log
-      class 'org.apache.commons.logging.impl.Jdk14Logger' cannot be found or is
-      not useable </div>
-      
-      <p>This message typically occurs in the tomcat log (catalina.log) 
-      when Tomcat has been installed on an Ubuntu/Debian system using apt-get install.  
-      And the application is started using:
-        
-        <div class="code">/etc/init.d/tomcat5.5 start</div>  
-        
-      <p>The problem is that the standard startup scripts reference the 
-      common java service, jsvc.  Metacat will not run under jsvc.  The solutions are:
-      <ul>
-      <li>Download the <a href="http://knb.ecoinformatics.org/software/download.html">Metacat binary install package</a>
-       and replace your /etc/init.d/tomcat5.5 startup script with the one provided in the
-       package.</li>
-      <li>Run Tomcat from the Tomcat binary directory: <tomcat_home>/bin/startup.sh and 
-      <tomcat_home>/bin/shutdown.sh</li>
-      </ul>
-      </p>
-<a name="ConfigurationIssues"></a><div class="header1">Configuration Issues</div>
-  <a name="DbUpdateIssue"></a><div class="header2">Database Update Fails (not a connectivity issue)</div>
-    <p>There are a number of reasons why the database update utility might fail during 
-    configuration.  You will need to determine if the error returned indicates a connectivity issue
-    or some issue with the database schema/data.  If it is the latter, the first step in 
-    troubleshooting the issue is to run the db scripts manually and analyze the output.</p> 
-    
-    <p>The configuration utility will report which scripts it tried to run.  To 
-    run these scripts, refer to 
-    <a href="../user/run-db-scripts.html">how to run database scripts</a></p>
-    
-    <p>If the answer is not obvious, further troubleshooting may require a database 
-    administrator.</p>
-    
-<a name="GeneralApplicationIssues"></a><div class="header1">General Application Issues</div> 
-  <a name="MapDisplayIssue"></a><div class="header2">Maps will not display</div>
-    <p>There are two known reasons why maps might not display in a web browser.</p> 
-    <ul>
-    <li>Sarfari Browser - the safari browser is not supported by the map libraries.  You will
-        need to switch to a different browser.</li>
-    <li>Firefox Browser with the Firebug plugin - Firebug is a plugin that allows a developer
-        to easily view and troubleshoot web page layouts.  Unfortunately, this plugin can
-        keep the maps from displaying.  There is no plan by the third party map display
-        developers to address this issue.  You will need to disable Firebug in your 
-        browser.</li>
-    </ul>
-    
-<a name="UnitTestingIssues"></a><div class="header1">Unit Testing Issues</div>
-  <a name="503ServiceTemporarilyUnavailable"></a><div class="header2">Mutliple Tests Fail : 503 Service Temporarily Unavailable</div>
-    <p>When running "ant test", multiple tests fail.  The output files have the error: </p>
-      <div class="code">503 Service Temporarily Unavailable</div>
-    <p>This typically means your Metacat server is not running.</p>
-    
-    <br>
-    
-  </body>
-</html>
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@@ -1,70 +0,0 @@
-<!--
-  * datafiles.html
-  *
-  *      Authors: Chad Berkley
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2001 January 23
-  *      Version: 
-  *    File Info: '$ '
-  * 
-  * 
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Non-XML Data Files</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./replication.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./properties.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  
-  <p>Metacat has the capability of proxying a connection to a data file 
-  server.  This capability is provided through an abstract class called
-  DataFileUploadInterface.  Currently, there is a data file server implemented
-  for this interface that can store non-XML data files on the local UNIX
-  file system.  Theoretically, any file storage system could be proxied
-  through this interface.</p>
-  <P> <img alt="architecture diagram of the Metacat Data File Upload process" 
-           src="dataload.gif">  </p>
-
-  <b>Reasoning</b>
-  <p>Since Metacat has been designed as a metadata storage system for 
-  ecological data, there was a concern that data and metadata files were being
-  stored seperately and that users would find it impractical to have to use
-  two different systems to get their data and metadata.  This system also allows
-  users to specify <a href="./acontrol.html">access control</a> restraints on their
-  data files the same way that they are specified on the xml metadata files.</p>
-
-  <b>Data Download (GET)</b>
-  <p>Metacat Server can retrieve data files that are stored on Metacat
-     file system or in any other file system on Internet. <br>
-     Metacat stores data files in a directory under the servlet context.
-     It writes information about these data files in xml_documents just like
-     about any XML file. <br>
-     An example of HTTP request for download of data file on Metacat is shown below: </p>
-  <pre><i>http://server.domain.com/metacat?action=read&amp;docid=nceas.55</i></pre>
-  <p>An example of HTTP request for download of data file on Internet is shown below:</p>
-  <pre><i>http://server.domain.com/metacat?action=read&amp;docid=http://otherserver.domain.com/filename</i></pre>
-  <p>Note in <i>docid=http://otherserver.domain.com/filename</i> HTTP protocol is used,
-     i.e. currently for file download HTTP protocol is only supported.</p>
-
-  <p><b>Data Upload (PUT)</b></p>
-  <p>
-  The insertion and update process for a data file is the same as the 
-  insertion process for an <a href="metacatload.html">XML file</a>.
-  </p>
-  
-  <br>
-  <a href="./replication.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./properties.html">Next</a>
-</BODY>
-</HTML>

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Index: docs/user/xmldoc.html
===================================================================
--- docs/user/xmldoc.html	(revision 5315)
+++ docs/user/xmldoc.html	(nonexistent)
@@ -1,42 +0,0 @@
-<!--
-  * xmldoc.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">XML</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./metacattour.html">Home</a> | 
-        <a href="./xmltree.html">Next</a
-      </td>
-    </tr>
-  </table>
-  <P> 
-   XML (Extensible Markup Language) is a flexible way to create common 
-   information formats and share both the format and the data on the 
-   World Wide Web, intranets, and elsewhere (source: www.whatis.com). An XML
-   Document is defined by a Document Type Definition (DTD) which specifies
-   the structure of the document.  The following is an example of an XML
-   document.
-  <P> <img alt="sample XML document" src="xmldoc.gif">
-  <br>
-  <a href="./metacattour.html">Home</a> | 
-  <a href="./xmltree.html">Next</a>
-</BODY>
-</HTML>
-

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===================================================================
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Index: docs/user/common.css
===================================================================
--- docs/user/common.css	(revision 5315)
+++ docs/user/common.css	(nonexistent)
@@ -1,109 +0,0 @@
- /*
-  *   '$RCSfile$'
-  *     Purpose: Common style sheet for KNB project documentation pages 
-  *              Using this stylesheet rather than placing styles directly in 
-  *              the KNB web documents allows us to globally change the 
-  *              formatting styles of the entire site in one easy place.
-  *   Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *     Authors: Matt Jones
-  *
-  *    '$Author: daigle $'
-  *      '$Date: 2008-11-04 11:34:57 -0800 (Tue, 04 Nov 2008) $'
-  *  '$Revision: 4506 $'
-  *
-  * This program is free software; you can redistribute it and/or modify
-  * it under the terms of the GNU General Public License as published by
-  * the Free Software Foundation; either version 2 of the License, or
-  * (at your option) any later version.
-  *
-  * This program is distributed in the hope that it will be useful,
-  * but WITHOUT ANY WARRANTY; without even the implied warranty of
-  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  * GNU General Public License for more details.
-  *
-  * You should have received a copy of the GNU General Public License
-  * along with this program; if not, write to the Free Software
-  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-  */
-  
-  /***************************************************************
-   Please note that even though this css file is located in the user 
-   documents directory, it is used by html in other directories (most
-   notibly the ../dev directory).  We only keep this doc here because 
-   user documentation deploys to the top level on the knb server. 
-   *******************************************************************/
-.header1 {
-	background: #ccccff;
-    vertical-align: baseline;
-    color: black;
-    font-size: 1.25em;
-    font-weight: bold;
-    margin-left: 0.25em;
-    margin-right: 0.25em;
-    margin-top: 1em; 
-    padding-left: .5em;
-}
-.header2 {
-	font-size: 1.25em;
-	font-weight: bold;
-	margin-left: 0.25em;
-	margin-top: .5em;
-}
-.header3 {
-/*	font-size: 1em; */
-	font-weight: bold;
-	margin-left: 0.25em;
-	margin-top: .5em;
-}
-.list1 {
-	margin-top: .5em;
-	list-style-type: circle;
-	margin-left: -1em;
-}
-.list2 {
-	list-style-type: disc;
-	margin-left: -1em;
-}
-.list3 {
-	list-style-type: square;
-	margin-left: -1em;
-}
-.code {
-	font-family: courier;
-	margin-left: 1.5em;
-	margin-top: .5em;
-	margin-bottom: .5em;
-}
-.toc {
-	margin-top: 10px;
-}
-.toc1 {
-	font-size: 1em;
-	font-weight: bold; 
-	margin-left: 20px;
-}
-.toc2 {
-	font-size: 1em;
-/*	font-weight: bold; */
-	margin-left: 40px;
-}
-.toc3 {
-	font-size: 1em;
-/*	font-weight: bold; */
-	margin-left: 60px;
-}
-.indent {
-	margin-left: 1em;
-}
-img.screenshot {
-	display: block;
-	margin-top: 10px;
-	margin-left: auto;
-	margin-right: auto; 
-}
-.fig-text {
-	margin-top: 10px;
-	width: 100%;
-	text-align: center;
-}
\ No newline at end of file

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Index: docs/user/saxparser.html
===================================================================
--- docs/user/saxparser.html	(revision 5315)
+++ docs/user/saxparser.html	(nonexistent)
@@ -1,76 +0,0 @@
-<!--
-  * saxparser.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">XML Parsing with SAX</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./metacatgetlog.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./xmlindex.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <P>SAX, the <i>Simple API for XML</i>, is 
-  a standard interface for event-based XML parsing. The SAX API provides implemented 
-  interfaces for many different XML parsers. Metacat requires a SAX2 
-  API/Java1.2 with any SAX2-compatible XML parser.
-  <P>To avoid tying Metacat to any specific SAX parser, XMLReaderFactory is used
-  as the SAX interface to Metacat for easy plugability of parsers. The SAX parser
-  used must be set in the <a href="./properties.html">Metacat Properties</a> file.</p>
-  <p>The following is an example of instatiating a parser for Metacat.</p>
-  <PRE>
-  XMLReader parser = null;
-  // Set up the SAX document handlers for parsing
-  try {
-      ContentHandler chandler   = new DBSAXHandler(conn, action, docid, user);
-      EntityResolver dbresolver = new DBEntityResolver(conn, (DBSAXHandler)chandler);
-      DTDHandler dtdhandler     = new DBDTDHandler(conn);
-
-      // Get an instance of the parser
-      // Get the class name of SAX driver from some XML parser like:
-      // org.apache.xerces.parsers.SAXParser
-      <span class="emphasis">String parserName = util.getOption("xml.saxparser");</span>
-      // Given a class name, this method attempts to load and instantiate the class as an XML reader
-      <span class="emphasis">parser = XMLReaderFactory.createXMLReader(parserName);</span>
-
-      // Turn off validation
-      parser.setFeature("http://xml.org/sax/features/validation", false);
-      
-      parser.setProperty("http://xml.org/sax/properties/declaration-handler", chandler);
-      parser.setProperty("http://xml.org/sax/properties/lexical-handler", chandler);
-
-      // Set Handlers in the parser to receive XML parsing events
-      parser.setContentHandler((ContentHandler)chandler);
-      parser.setEntityResolver((EntityResolver)dbresolver);
-      parser.setDTDHandler((DTDHandler)dtdhandler);
-      parser.setErrorHandler((ErrorHandler)chandler);
-
-  } catch (SAXException saxe) {
-      throw saxe;
-  }
-
-  </PRE>
-  
-  <br>
-  <a href="./metacatgetlog.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./xmlindex.html">Next</a>
-  
-</BODY>
-</HTML>
-

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Index: docs/user/os_specific/install_metacat_windows.html
===================================================================
--- docs/user/os_specific/install_metacat_windows.html	(revision 5315)
+++ docs/user/os_specific/install_metacat_windows.html	(nonexistent)
@@ -1,129 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>Metacat Install - Windows XP</title>
-  <link rel="stylesheet" type="text/css" href="./../default.css">
-</head>
-
-<body>
-
-<table class="tabledefault" width="100%">
-<tr><td rowspan="2"><img src="./../images/KNBLogo.gif"></td>
-<td colspan="7">
-<div class="title">Metacat Install - Windows XP</div>
-</td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
-<table class="tabledefault" width="100%">
-<td class="tablehead" colspan="2"><p class="emphasis">Building Metacat from cvs on Windows XP</p></td>
-<tr>
-<td>
-<p>
-Matthew Perry<br />
-10/24/2006
-</p>
-  <p class="emphasis">
-Note: This is not intended to be a complete, step-by-step tutorial but rather a general overview of the process along with some specific "gotchas" that I encountered along the way.
-  </p>
-</td>
-</tr>
-</table>
-
-<h2>Download and Install via the standard windows installers</h2>
-<p>
-  Postgresql 8.1
-  Java 1.5 JDK
-  TortiseCVS 
-</p>
-
-<h2>Tomcat</h2>
-<p>
-Download Tomacat5.5 windows installer and install to C:\tomcat5 (or another directory w/out spaces)
-</p>
-
-<h2>Ant</h2>
-<p>
-Download ant 1.6.5-bin and extract to C:\ant
-</p>
-
-<h2>Environment variables</h2>
-<pre>
-Set environment variables (ctl panel > System > Advanced > Environment Variables). 
- ANT_HOME => C:\ant
- JAVA_HOME => C:\Program_Files\jdk1.5.0_09
- PATH => { THE EXISTING PATH };C:\Program_Files\jdk1.5.0_09\bin;C:\ant\bin;C:\Program Files\TortoiseCVS
- CVS_RSH => C:\Program Files\TortoiseCVS\TortoisePlink
-</pre>
-
-<h2>Database</h2>
-<pre>
-Use pgadmin to 
-* Create a new user named 'metacat'
-* Create a new database named 'metacat', owned by user 'metacat',  with UTF8 Encoding
-</pre>
-
-<h2>Checkout metacat</h2>
-<pre>
-Download the cvs version of metacat
-    cd c:\worskpace
-    cvs -d:ext:{ USER }@cvs.ecoinformatics.org:/cvs co metacat
-    cvs -d:ext:{ USER }@cvs.ecoinformatics.org:/cvs co utilities
-    cd metacat
-</pre>
-
-<h2>Edit build.properties</h2>
-<pre>
-Adjust build.properties
-  # Tomcat Properties
-  tomcat=C:/tomcat5
-  deploy.dir=C:/tomcat5/webapps
-
-  # Server Properties
-  config.hostname=localhost
-  config.port=8080
-
-  # Metacat database user and password and location of file stores
-  user=metacat
-  password=metacatpass
-  datafilepath=C:/workspace/metacat-data
-  inlinedatafilepath=C:/workspace/metacat-inline-data
-
-  # give username for CVS access to retrieve latest EML
-  cvsroot=:ext:perry@cvs.ecoinformatics.org:/cvs
-</pre>
-
-<h2>Run</h2>
-<pre> 
-  ant clean install 
-</pre>
-
-<h2>Create tables</h2>
-<pre>
-  "C:\Program Files\PostgreSQL\8.1\bin\psql.exe" -U metacat -W -h localhost -f build/src/xmltables-postgres.sql metacat
-</pre>
-
-<h2>Register schemas with metacat db</h2>
-<pre>
-  ant register-schemas
-</pre>
-
-<p>
-If all went well, you should be able to point your browser to http://localhost:8080/knb and see the default metacat skin
-</p>
-
-
-
-</body>
-</html>

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Index: docs/user/os_specific/install_metacat_mac.txt
===================================================================
--- docs/user/os_specific/install_metacat_mac.txt	(revision 5315)
+++ docs/user/os_specific/install_metacat_mac.txt	(nonexistent)
@@ -1,70 +0,0 @@
-Notes for Installing Metacat on Mac OSX
-Author: Matthew Perry
-Date: 11/9/2006
-
-
-Download apache and untar to /Users/nceas/Apps
-
-sudo mkdir /Users/nceas/Apps/postgres
-sudo chown -R nceas /Users/nceas/Apps/postgres
-mkdir ~/src
-
-Download & install Fink
-
-sudo  /sw/bin/fink install readline
-sudo  /sw/bin/fink install cvs
-
-Download postgres8.1.5 src and untar in ~/src
-
-cd ~/src/postgresql-8.1.5
-./configure --prefix=/Users/nceas/Apps/postgres
-make
-make install
-cd /Users/nceas/Apps/postgres
-mkdir data
-bin/initdb -D data
-bin/pg_ctl -D data -l logfile start
-bin/createdb metacat
-bin/psql -d metacat
-sql>   create user metacat with unencrypted password 'metapass';
-sql> /q
-
-Add to data/pg_hba.conf
-host metacat metacat 127.0.0.1 255.255.255.255 password
-
-bin/pg_ctl -D data -l logfile restart
-psql -U metacat -W -h localhost metacat
-
-
-cd ~/src
-export CVS_RSH="/usr/bin/ssh"
-cvs -d:ext:perry@cvs.ecoinformatics.org:/cvs co metacat
-cvs -d:ext:perry@cvs.ecoinformatics.org:/cvs co utilities
-
-
-Edit build.properties as needed
-cd metacat
-mkdir /Users/nceas/Apps/metacat
-sudo touch /Users/nceas/Apps/apache-tomcat-5.5.20/webapps/knb.war
-sudo chown nceas /Users/nceas/Apps/apache-tomcat-5.5.20/webapps/knb.war
-ant clean install
-
-Enter your cvs password a few times
-/Users/nceas/Apps/postgres/bin/psql -U metacat -W -h localhost -f build/src/xmltables-postgres.sql
-ant register-schemas
-
-Restart tomcat
-
-point your browser to http://localhost:8080/knb/ and you should be in business
-
-After restarting, you'll need to fire off the following commands in order to start up postgres/tomcat again.
-
-# Starup
-/Users/nceas/Apps/postgres/bin/pg_ctl -D /Users/nceas/Apps/postgres/data/ -l /Users/nceas/Apps/postgres/logfile -m fast start
-/Users/nceas/Apps/apache-tomcat-5.5.20/bin/startup.sh
-
-# Shutdown
-/Users/nceas/Apps/apache-tomcat-5.5.20/bin/shutdown.sh
-/Users/nceas/Apps/postgres/bin/pg_ctl -D /Users/nceas/Apps/postgres/data/ -l /Users/nceas/Apps/postgres/logfile -m fast stop
-
-You can create two shell scripts with the preceeding commands; start_metacat.sh and stop_metacat.sh

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Index: docs/user/os_specific/install_metacat_ubuntu.txt
===================================================================
--- docs/user/os_specific/install_metacat_ubuntu.txt	(revision 5315)
+++ docs/user/os_specific/install_metacat_ubuntu.txt	(nonexistent)
@@ -1,80 +0,0 @@
-Installing Metacat on Ubuntu
-
-Assumes you have the base ubuntu distribution set up already.
-
-* Add the extra repositories to your apt sources list. 
-    sudo gedit /etc/apt/sources.list
-    # add universe and multiverse to the following lines
-       deb http://us.archive.ubuntu.com/ubuntu/ dapper main restricted universe multiverse
-       deb-src http://us.archive.ubuntu.com/ubuntu/ dapper main restricted universe multiverse
-    sudo apt-get update
-
-* Install the ubuntu package dependencies
-    sudo apt-get install tomcat5-webapps postgresql-server-dev-8.1 postgresql-8.1 sun-java5-jdk \
-                         apache2 cvs 
-
-* Tell the ubuntu system to use the java jdk 
-    sudo update-java-alternatives -s java-1.5.0-sun
-
-    sudo vi /etc/default/tomcat5
-      JAVA_HOME=/usr/lib/jvm/java-1.5.0-sun
-      .......
-      CATALINA_OPTS="-Djava.awt.headless=true -Djava.util.prefs.syncInterval=2000000 -Xmx512M -server"
-      ....
-      TOMCAT_SECURITY=no
-
-    sudo /etc/init.d/tomcat5 restart
-
-* Download metacat from CVS and set up utilites     
-    
-    mkdir ~/workspace; cd ~/workspace
-    cvs -d:ext:perry@cvs.ecoinformatics.org:/cvs co metacat
-    cvs -d:ext:perry@cvs.ecoinformatics.org:/cvs co utilities
-    cd utilities
-    ant clean jar
-    cd ../metacat
-
-* prep postgres
-
-    # Setting up the postgres metacat db
-    sudo vi /etc/postgresql/8.1/main/pg_hba.conf
-    # add 
-      host metacat metacat 127.0.0.1 255.255.255.255 password
-    sudo su postgres
-    createdb metacat
-    psql -d metacat
-      create user metacat with unencrypted password 'metacatpass';
-      \q
-    exit
-
-    #restart postgres
-    sudo /etc/init.d/postgresql-8.1 restart
- 
-    # TEST
-    psql -U metacat -W -h localhost metacat
-
-* Build
-   sudo touch /var/lib/tomcat5/webapps/knb.war
-   sudo chown perry /var/lib/tomcat5/webapps/knb.war
-   cd ~/workspace/metacat
-   cp build.properties default.build.properties
-   # Edit build.properties 
-   vi lib/metacat.properties
-
-   #change
-     onlySecureLDAPConnection=false
-   # TODO set up the certificate *********
-
-   ant clean install
-   # may need to give cvs password a few times on the first build
-
-* Postgres configuration
-   psql -U metacat -W -h localhost -f build/src/xmltables-postgres.sql metacat
-   ant register-schemas
-
-* apache / tomcat integration
-    #the instructions at http://www.ubuntuforums.org/showthread.php?t=219985 cover this pretty well
-    #remember to add the 'knb' servlet context
- 
-* Make sure metacat_data and metacat_inline_data folders are readable/writable by tomcat user
-

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Index: docs/user/os_specific/install_metacat_mac.html
===================================================================
--- docs/user/os_specific/install_metacat_mac.html	(revision 5315)
+++ docs/user/os_specific/install_metacat_mac.html	(nonexistent)
@@ -1,204 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>Metacat Install - Mac OS X</title>
-  <link rel="stylesheet" type="text/css" href="./../default.css">
-</head>
-
-<body>
-
-<table class="tabledefault" width="100%">
-<tr><td rowspan="2"><img src="./../images/KNBLogo.gif"></td>
-<td colspan="7">
-<div class="title">Metacat Install - Mac OS X</div>
-</td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
-<table class="tabledefault" width="100%">
-<td class="tablehead" colspan="2"><p class="emphasis">Installing Metacat on Mac OSX (10.4.10)</p></td>
-<tr>
-<td>
-<p>
-Author: Matthew Perry<br />
-Date: 11/9/2006<br />
-Updated: 11/04/07 Derik Barseghian<br />
-</p>
-
-  <p class="emphasis">
-	This is a terse cheatsheet for installing metacat with postgres on os X. Please see the <a href="../metacat-install.html">general instructions</a> for the full details.
-  </p>
-</td>
-</tr>
-</table>
-
-<table class="tabledefault" width="100%">
-<td class="tablehead" colspan="2"><p class="emphasis">Pre-Requirements</p></td>
-<tr>
-<td>
-</td>
-</tr>
-</table>
-
-<h2>Install ant, postgres, tomcat using macports</h2>
-<p>Alternatively, download and install ant, postgres and tomcat from source or using fink.</p>
-<p>
-install <a href="http://www.macports.org/">macports</a>. 
-</p>
-
-<p>
-launch a terminal
-</p>
-
-<pre>
-sudo port -d sync
-sudo port search ant
-sudo port install ant
-sudo port search postgres
-sudo port install postgresql82
-sudo port search tomcat
-sudo port install tomcat5
-</pre>
-
-<table class="tabledefault" width="100%">
-<td class="tablehead" colspan="2"><p class="emphasis">Metacat Install</p></td>
-<tr>
-<td>
-</td>
-</tr>
-</table>
-
-<h2>Setup Postgres Database</h2>
-<pre>
-cd /opt/local/lib/postgresql82/
-sudo mkdir data
-chown -R yourusername.yourusername data
-cd data
-../bin/initdb -D data
-../bin/pg_ctl -D data -l logfile start
-../bin/createdb metacat
-../bin/psql -d metacat
-metacat=> create user metacat with unencrypted password 'metacat';
-metacat=> \q
-</pre>
-
-<p>
-test password:
-</p>
-<pre>
-	../bin/psql -U metacat -W -h localhost metacat
-	Password for user metacat:
-	metacat=> \q
-
-cd /opt/local/share/java/tomcat5
-sudo mkdir -p data/metacat/data
-sudo mkdir -p data/metacat/inlinedata
-chown -R yourusername.yourusername data
-
-</pre>
-
-<p>
-Add to data/pg_hba.conf:
-</p>
-<pre>
-	host metacat metacat 127.0.0.1 255.255.255.255 password
-
-bin/pg_ctl -D data -l logfile restart
-psql -U metacat -W -h localhost metacat
-</pre>
-
-
-<h2>Checkout Metacat</h2>
-<pre>
-mkdir ~/cvs_src/
-cd ~/cvs_src
-export CVS_RSH="/usr/bin/ssh"
-cvs -d:ext:your_cvs_name@cvs.ecoinformatics.org:/cvs co metacat
-cvs -d:ext:your_cvs_name@cvs.ecoinformatics.org:/cvs co utilities
-</pre>
-
-<h2>Edit build.properties as needed</h2>
-
-<pre>
-tomcat=/opt/local/share/java/tomcat5
-deploy.dir=/opt/local/share/java/tomcat5/webapps/
-config.hostname=localhost
-config.port=8080
-config.port.https=8443
-
-datafilepath=/opt/local/share/java/tomcat5/data/metacat/data
-inlinedatafilepath=/opt/local/share/java/tomcat5/data/metacat/inlinedata
-</pre>
-
-<p>
-if your mac username is different from your cvs name, hardcode hack:
-</p>
-<pre>
-	cvsroot=:ext:yourcvsname@cvs.ecoinformatics.org:/cvs
-
-log.dir=/opt/local/share/java/tomcat5/logs
-metacat.dir=/Users/yourname/nceas/metacat
-</pre>
-
-<h2>Install Metacat</h2>
-<pre>
-cd metacat
-sudo ant install
-</pre>
-
-<p>
-Enter your cvs password a few times...
-</p>
-
-<pre>
-psql82 -U metacat -W -h localhost -f build/src/xmltables-postgres.sql metacat
-ant register-schemas
-</pre>
-
-<p>Restart tomcat</p>
-<pre>
-sudo /opt/local/share/java/tomcat5/bin/shutdown.sh
-sudo /opt/local/share/java/tomcat5/bin/startup.sh
-</pre>
-
-<p>
-Point your browser to http://localhost:8080/knb/ and you should be in business.
-</p>
-
-<p>
-After restarting, you'll need to fire off the following commands in order to start up postgres/tomcat again:
-</p>
-<p>
-Startup
-</p>
-<pre>
-/Users/nceas/Apps/postgres/bin/pg_ctl -D /Users/nceas/Apps/postgres/data/ -l /Users/nceas/Apps/postgres/logfile -m fast start
-/Users/nceas/Apps/apache-tomcat-5.5.20/bin/startup.sh
-</pre>
-
-<p>
-Shutdown
-</p>
-<pre>
-/Users/nceas/Apps/apache-tomcat-5.5.20/bin/shutdown.sh
-/Users/nceas/Apps/postgres/bin/pg_ctl -D /Users/nceas/Apps/postgres/data/ -l /Users/nceas/Apps/postgres/logfile -m fast stop
-</pre>
-
-<p>
-You can create two shell scripts with the preceeding commands; start_metacat.sh and stop_metacat.sh
-</p>
-
-
-</body>
-</html>

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Index: docs/user/os_specific/install_metacat_ubuntu.html
===================================================================
--- docs/user/os_specific/install_metacat_ubuntu.html	(revision 5315)
+++ docs/user/os_specific/install_metacat_ubuntu.html	(nonexistent)
@@ -1,140 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>Metacat Install - Ubuntu</title>
-  <link rel="stylesheet" type="text/css" href="./../default.css">
-</head>
-
-<body>
-
-<table class="tabledefault" width="100%">
-<tr><td rowspan="2"><img src="./../images/KNBLogo.gif"></td>
-<td colspan="7">
-<div class="title">Metacat Install - Ubuntu</div>
-</td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
-<table class="tabledefault" width="100%">
-<td class="tablehead" colspan="2"><p class="emphasis">Installing Metacat on Ubuntu</p></td>
-<tr>
-<td>
-  <p class="emphasis">
-Assumes you have the base ubuntu distribution set up already.
-  </p>
-</td>
-</tr>
-</table>
-
-<h2>Repositories</h2>
-<pre>
-* Add the extra repositories to your apt sources list. 
-    sudo gedit /etc/apt/sources.list
-    # add universe and multiverse to the following lines
-       deb http://us.archive.ubuntu.com/ubuntu/ dapper main restricted universe multiverse
-       deb-src http://us.archive.ubuntu.com/ubuntu/ dapper main restricted universe multiverse
-    sudo apt-get update
-</pre>
-
-<h2>Ubuntu Package Dependencies</h2>
-<pre>
-* Install the ubuntu package dependencies
-    sudo apt-get install tomcat5-webapps postgresql-server-dev-8.1 postgresql-8.1 sun-java5-jdk \
-                         apache2 cvs 
-</pre>
-
-<h2>java jdk</h2>
-<pre>
-* Tell the ubuntu system to use the java jdk 
-    sudo update-java-alternatives -s java-1.5.0-sun
-
-    sudo vi /etc/default/tomcat5
-      JAVA_HOME=/usr/lib/jvm/java-1.5.0-sun
-      .......
-      CATALINA_OPTS="-Djava.awt.headless=true -Djava.util.prefs.syncInterval=2000000 -Xmx512M -server"
-      ....
-      TOMCAT_SECURITY=no
-
-    sudo /etc/init.d/tomcat5 restart
-</pre>
-
-<h2>Checkout Metacat</h2>
-<pre>
-* Download metacat from CVS and set up utilites     
-    
-    mkdir ~/workspace; cd ~/workspace
-    cvs -d:ext:perry@cvs.ecoinformatics.org:/cvs co metacat
-    cvs -d:ext:perry@cvs.ecoinformatics.org:/cvs co utilities
-    cd utilities
-    ant clean jar
-    cd ../metacat
-</pre>
-
-<h2>prep postgres</h2>
-
-<pre>
-    # Setting up the postgres metacat db
-    sudo vi /etc/postgresql/8.1/main/pg_hba.conf
-    # add 
-      host metacat metacat 127.0.0.1 255.255.255.255 password
-    sudo su postgres
-    createdb metacat
-    psql -d metacat
-      create user metacat with unencrypted password 'metacatpass';
-      \q
-    exit
-</pre>
-
-<h2>restart postgres</h2>
-<pre>
-    sudo /etc/init.d/postgresql-8.1 restart
- 
-    # TEST
-    psql -U metacat -W -h localhost metacat
-</pre>
-
-<h2>Build</h2>
-<pre>
-   sudo touch /var/lib/tomcat5/webapps/knb.war
-   sudo chown perry /var/lib/tomcat5/webapps/knb.war
-   cd ~/workspace/metacat
-   cp build.properties default.build.properties
-   # Edit build.properties 
-   vi lib/metacat.properties
-
-   #change
-     onlySecureLDAPConnection=false
-   # TODO set up the certificate *********
-
-   ant clean install
-   # may need to give cvs password a few times on the first build
-</pre>
-
-<h2>Postgres configuration</h2>
-<pre>
-   psql -U metacat -W -h localhost -f build/src/xmltables-postgres.sql metacat
-   ant register-schemas
-</pre>
-
-<h2>apache / tomcat integration</h2>
-<pre>
-    #the instructions at <a href="http://www.ubuntuforums.org/showthread.php?t=219985">http://www.ubuntuforums.org/showthread.php?t=219985</a> cover this pretty well
-    #remember to add the 'knb' servlet context
- 
-* Make sure metacat_data and metacat_inline_data folders are readable/writable by tomcat user
-</pre>
-
-
-</body>
-</html>

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Index: docs/user/os_specific/install_metacat_windows.txt
===================================================================
--- docs/user/os_specific/install_metacat_windows.txt	(revision 5315)
+++ docs/user/os_specific/install_metacat_windows.txt	(nonexistent)
@@ -1,65 +0,0 @@
-Building Metacat from cvs on Windows XP
-Matthew Perry
-10/24/2006
-
-Note: This is not intended to be a complete, step-by-step tutorial but rather a general overview of the process along with some specific "gotchas" that I encountered along the way.
-
-===============
-
-Download and Install via the standard windows installers:
-  Postgresql 8.1
-  Java 1.5 JDK
-  TortiseCVS 
-
-Download Tomacat5.5 windows installer and install to C:\tomcat5 (or another directory w/out spaces)
-
-Download ant 1.6.5-bin and extract to C:\ant
-
-Set environment variables (ctl panel > System > Advanced > Environment Variables). 
- ANT_HOME => C:\ant
- JAVA_HOME => C:\Program_Files\jdk1.5.0_09
- PATH => { THE EXISTING PATH };C:\Program_Files\jdk1.5.0_09\bin;C:\ant\bin;C:\Program Files\TortoiseCVS
- CVS_RSH => C:\Program Files\TortoiseCVS\TortoisePlink
-
-Use pgadmin to 
-* Create a new user named 'metacat'
-* Create a new database named 'metacat', owned by user 'metacat',  with UTF8 Encoding
-
-Download the cvs version of metacat
-    cd c:\worskpace
-    cvs -d:ext:{ USER }@cvs.ecoinformatics.org:/cvs co metacat
-    cvs -d:ext:{ USER }@cvs.ecoinformatics.org:/cvs co utilities
-    cd metacat
-
-Adjust build.properties
-  # Tomcat Properties
-  tomcat=C:/tomcat5
-  deploy.dir=C:/tomcat5/webapps
-
-  # Server Properties
-  config.hostname=localhost
-  config.port=8080
-
-  # Metacat database user and password and location of file stores
-  user=metacat
-  password=metacatpass
-  datafilepath=C:/workspace/metacat-data
-  inlinedatafilepath=C:/workspace/metacat-inline-data
-
-  # give username for CVS access to retrieve latest EML
-  cvsroot=:ext:perry@cvs.ecoinformatics.org:/cvs
-
-Run 
-  ant clean install 
-
-Create tables
-  "C:\Program Files\PostgreSQL\8.1\bin\psql.exe" -U metacat -W -h localhost -f build/src/xmltables-postgres.sql metacat
-
-Register schemas with metacat db
-  ant register-schemas
-
-If all went well, you should be able to point your browser to http://localhost:8080/knb and see the default metacat skin
-
-
-
-

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Index: docs/user/lsid_authority.html
===================================================================
--- docs/user/lsid_authority.html	(revision 5315)
+++ docs/user/lsid_authority.html	(nonexistent)
@@ -1,76 +0,0 @@
-<!--
-  * datafiles.html
-  *
-  *      Authors: Chad Berkley
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2001 January 23
-  *      Version: 
-  *    File Info: '$ '
-  * 
-  * 
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">LSID Support</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./harvester.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./spatial_option.html">Next</a> 
-      </td>
-    </tr>
-  </table>
-    </p>
-<p><u>What is an LSID:</u></p>
-<p>LSID's were designed to be a globally-recognized short identifiers for a complex
-  entities that are both computer and human readable.</p>
-<p>&nbsp;</p>
-<p><u>Why LSID's are in Metacat:</u></p>
-<p>We chose to incorporate LSID's in metacat so as to support a globally accepted
-  standard for identifying biological entities instead of using a proprietary
-  scheme.
-  By doing this we have exposed data and metadata stored in Metacat through 
-  a variety of LSID clients. Additionally, the LSID support in Metacat has
-  been implemented as a series Simple Object Access Protocol (SOAP) interfaces
-  with the intent of providing an easily modifiable system.</p>
-<p>&nbsp;</p>
-<p><u>What you get with Metacat's LSID Support:</u></p>
-<p>By enabling the Metacat LSID support you will be able to use the LSID clients
-  and notation to query Metacat for data and metadata. An example of an LSID
-  client is the <a href="http://lsid.sourceforge.net/">LSID Launchpad</a>. Furthermore,
-  one can use the LSID notation directly in the Metacat http query to access
-  data and metadata within a Metacat.
-  For example, a document (tao.12039.1) stored in a Metacat available at: http://qtz.homelinux.com:9999
-  can be accessed by the following http Metacat queries:</p>
-<br>
-
-<pre>http://qtz.homelinux.com:9999/authority/data?lsid=urn:lsid:sulphur.ecoinformatics.org:tao:12039:1</pre>
-<pre>http://qtz.homelinux.com:9999/authority/metadata?lsid=urn:lsid:sulphur.ecoinformatics.org:tao:12039:1</pre>
-<br>
-
-<p>The first query returns the data associated with that document and the second
-  query returns the metadata. Notice that the periods in the Metacat document
-  ID have been replaced with colons. Also notice the host urn attribute
-  (urn:lsid:sulphur.ecoinformatics.org), this host needs to be set as a SRV record
-  as DNS entry on the DNS server for ecoinformatics.org. To use LSID support
-  in Metacat the Metacat administrator does need to have access to the DNS server
-  for the domain hosting the Metacat so that he/she can modify the SRV record(s).
-  The Metacat build.proprties LSID attributes for the above example are: </p>
-<pre>authority.context=authority</pre>
-<pre>config.lsidauthority=sulphur.ecoinformatics.org</pre>
-<p>** the SRV record for sulphur.ecoinformatics.org points to qtz.homelinux.com
-  on port 9999</p>
-
-  <p><br>
-    <a href="./harvester.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-    <a href="./spatial_option.html">Next</a>    </p>
-  <p><br>
-</BODY>
-
-</HTML>

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Index: docs/user/KNB-LDAP-system-small.gif
===================================================================
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Index: docs/user/geoserver-manual-configure.html
===================================================================
--- docs/user/geoserver-manual-configure.html	(revision 5315)
+++ docs/user/geoserver-manual-configure.html	(nonexistent)
@@ -1,61 +0,0 @@
-<!-- 
-  *   '$RCSfile$'
-  *     Purpose: web page describing the installation of geoserver
-  *   Copyright: 2008 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *     Authors: Chad Berkley
-  *
-  *    '$Author: daigle $'
-  *    '$Date: 2008-07-06 21:25:34 -0700 (Sun, 06 Jul 2008) $'
-  *    '$Revision: 4080 $'
-  *
-  *
-  -->
-  
-<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>Geoserver Configuration Instructions</title>
-  <link rel="stylesheet" type="text/css" href="./default.css">
-</head>
-
-<body>
-<table class="tabledefault" width="100%">
-	<tr>
-		<td rowspan="2"><img src="./images/KNBLogo.gif"></td>
-		<td colspan="7">
-			<div class="title">Metacat Configuration</div>
-		</td>
-	</tr>
-	<tr>
-		<td><a href="/" class="toollink"> KNB Home </a></td>
-		<td><a href="/data.html" class="toollink"> Data </a></td>
-		<td><a href="/people.html" class="toollink"> People </a></td>
-		<td><a href="/informatics" class="toollink"> Informatics </a></td>
-		<td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-		<td><a href="/education" class="toollink"> Education </a></td>
-		<td><a href="/software" class="toollink"> Software </a></td>
-	</tr>
-</table>
-<hr>
-
-	<br>
-	<h3>Configuring Geoserver</h3>
-	<p>Metacat ships with <a href="http://docs.codehaus.org/display/GEOS/Home">Geoserver</a> to handle the spatial functionality.
-		Regardless of whether you plan on using the spatial functionality you should,
-		for security purposes, configure geoserver initially so that it doesn't use
-		the default password.<br><br>
-		
-		To configure geoserver with a new admin password:
-		<ol>
-			<li> Go to
-				<a href="../../geoserver.jsp" target="_blank"> Geoserver admin page </a>. </li>
-			<li> Login using the default username and password ( <em>admin</em> / <em>geoserver</em> ) </li>
-			<li> Then go to
-				<a href="../../config/loginEdit.do" target="_blank">Password Change Page </a> and  enter a new user and password then submit. </li>
-			<li> In the upper-left, click <em>Apply</em> then <em>Save</em> to save your new password.
-       </ol>
-	</p>
-</body>
-

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--- docs/user/metacatout.html	(revision 5315)
+++ docs/user/metacatout.html	(nonexistent)
@@ -1,53 +0,0 @@
-<!--
-  * Metacatout.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Output Transformations</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./ldap.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./metacatapi.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <p>Metacat uses XML for data exchange between the client application and 
-  the server.</p>
-  
-  <p>XSLT is used for transformations for visual presentation (e.g. XML->HTML). 
-  It can also be used to tranlate between different types of heterogeneous XML documents 
-  which are symantically similar.</p>
-  
-  <img src="xmltransform.gif">
-  
-  <p>Metacat can be set on the fly to either transform or not transform a resultset
-  from XML.  This is achieved by setting the 'qformat' servlet parameter to the name
-  of a <a href="metacatread.html">style-set</a> or to 'html'
-  or 'xml'.  When qformat is set to html, Metacat will transform the resultset based 
-  on the default style-set configured in the 
-  <a href="./properties.html">Metacat Properties</a> file.  This style-set
-  defines the rules for how to translate the XML tags into HTML tags.  
-  </p>
-  
-  <br>
-  <a href="./ldap.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./metacatapi.html">Next</a>
-  
-</BODY>
-</HTML>
-

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-<!--
-  * spatial_option.html
-  *
-  *      Authors: Matthew Perry
-  *    Copyright: 2006 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis,
-  *               and the University of New Mexico.
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2006 December 29
-  *      Version: 
-  *    File Info: '$ '
-  * 
-  * 
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat Spatial Option</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-<style>
- h5 { margin-left: 12px; }
-</style>
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2">
-        <p class="label">Metacat Spatial Option</p>
-      </td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./lsid_authority.html">Back</a> | 
-        <a href="./metacattour.html">Home</a> | 
-        <a href="./pagedreturn.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <h4>Introduction</h4>
-The Metacat spatial option enables you to query and visualize the geographic coverage of metacat documents. 
-This document is intended to provide a high-level overview of the Metacat spatial functionality. It is primarily a resource for users and developers who want to understand the architecture before digging into the code to extend the existing functionality.
-<P>
-Although the spatial option is included with a Metacat installation (beginning with
-Metacat version 1.7.0), it is an extention to Metacat's functionality
-that may be used optionally.
-</P>
-  <h4>Outline</h4>
- <ul>
-   <li> <a href="#definitions">Defintion of Terms</a> </li>
-   <li> <a href="#overview"> Overview of the major components </a>
-      <ul>
-        <li> <a href="#spatial_harvester"> Spatial Harvester </a> </li>
-        <li> <a href="#wms"> Web Mapping Service </a> </li>
-        <li> <a href="#spatial_query"> Spatial Query </a> </li>
-        <li> <a href="#html_client"> HTML Mapping Client</a> </li>
-      </ul>
-   </li>
-   <li> <a href="#install">Installing and Configuring the Spatial Option</a> </li>
-   <li> <a href="#adding_data">Adding Other Spatial Datasets to the Web Map</a> </li>
-   <li> <a href="#dev">Developers Notes</a> </li>
-   <li> <a href="#future">Future Directions</a> </li>
-
- </ul> 
-
-  <h4> <a name="definitions">Definitions</a></h4>
-The following table defines a number of terms that are useful in discussing
-Harvester and its features.
-  <br><br>
-  <table border="1">
-    <tr>
-      <td><b>Term</b></td>
-      <td><b>Definition</b></td>
-    </tr>
-    <tr>
-      <td>Spatial Cache</td>
-      <td>
-          A cached version of the metacat documents representing their geographic coverages in a GIS-compatible data format; the ESRI Shapefile. 
-      </td>
-    </tr>
-    <tr>
-      <td>Web Mapping Service (WMS)</td>
-      <td>
-         A standard interface specification for requesting spatial data as a web-deliverable map image. WMS servers accept a common set of parameters via http, render the spatial dataset into an appropriate image and deliver it back to the client. The <a href="http://www.opengeospatial.org/standards/wms">WMS spec</a> was developed by the <a href="http://www.opengeospatial.org/">Open Geospatial Consortium</a>. 
-    </tr>
-    <tr>
-      <td>Bounding Box (BBOX)</td>
-      <td>
-          A Bounding Box is two sets of geographic coordinates representing the full geographic extent of an entity; the minimum lat/long (the lower-left) and the maximum lat/long (the upper-right).  
-      </td>
-    </tr>
-    <tr>
-      <td>Spatial Dataset</td>
-      <td>
-        A collection of <em>spatial features</em> in a common datastore.
-      </td>
-    </tr>
-    <tr>
-      <td>Spatial Features</td>
-      <td>
-        Analagous to a "row" in a tabular dataset, a feature is an entity comprised of both tabular attributes and a <em>spatial geometry</em>.
-      </td>
-    </tr>
-    <tr>
-      <td>Spatial Geometry</td>
-      <td>
-        The geometry is a vector representation of an entities' geographic location. This can be a point (a single vertex), line (a series of vertices) or polygon (a series of vertices forming a closed area).
-      </td>
-    </tr>
-    <tr>
-      <td>Multi-Geometry</td>
-      <td>
-       A <em> Spatial geometry </em> represented by one or more geometry primitives (points,lines and polygons). For example a single species census (the <em> spatial feature </em>) might have mutltiple sample sites and could be represented as a multi-point geometry.
-      </td>
-    </tr>
-    <tr>
-      <td>Styled Layer Descriptor (SLD)</td>
-      <td>
-       Styled Layer Descriptors are an OGC standard for defining the filtering, classification and styling of datasets. They are essentially the configuration file which describes how to convert your raw spatial dataset into a cartographic product.
-      </td>
-    </tr>
-    <tr>
-      <td>Web Map Context (WMC)</td>
-      <td>
-       Web Map Context documents are an OGC standard for combining various WMS layers into a coherent map. WMC describes which wms servers and layers comprise the map, the layer order, the initial map extent, the requested image formats, etc. This is used by the HTML web map client to construct the interactive map.
-      </td>
-    </tr>
-  </table>
-
-  <h4><a name="overview">Overview Of the Major Components<a/></h4>
-
-
-        <h5> <a name="spatial_harvester"> Spatial Harvester </a> </h5>
-
-
-
-
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	The Spatial Harvester component syncs the metacat database with the spatial cache (an ESRI shapefile which contains the geographic coverages of the documents). </span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	The Spatial Harvester is implemented entirely in Java using the Geotools library which allows manipulation of spatial datasets. In rough terms, a spatial dataset is a collection of Features which are comprised of a geometry (i.e. the geographic coverage) and associated attributes (i.e. the document's title).</span></p>
-   <p dir="ltr" style="text-align:left;margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	There are a number of Java classes which, collectively, make up the spatial harvester functionality. They are found in the </span><span style="font-style:italic" lang="en-US">edu.ucsb.nceas.metacat.spatial</span><span lang="en-US"> package:</span></p>
-   <ul>
-    <li style="margin-bottom:12pt"><span lang="en-US">&nbsp;</span><span style="font-weight:bold" lang="en-US">SpatialDataset</span><span lang="en-US"> : Provides read/write access to the spatial cache.</span></li>
-    <li style="margin-bottom:12pt"><span lang="en-US">&nbsp;</span><span style="font-weight:bold" lang="en-US">SpatialDocument</span><span lang="en-US"> : Represents the geographic coverage of a document as a Geotools Feature. </span></li>
-    <li style="margin-bottom:12pt"><span lang="en-US">&nbsp;</span><span style="font-weight:bold" lang="en-US">SpatialFeatureSchema</span><span lang="en-US"> : A class of static members defining the properties of the spatial cache (location on the file system, attribute and geometry schemas, etc.)</span></li>
-    <li style="margin-bottom:12pt"><span lang="en-US">&nbsp;</span><span style="font-weight:bold" lang="en-US">SpatialHarvester</span><span lang="en-US"> : The high-level interface for manipulating the spatial cache and initiating the harvesting process.</span>    </li>
-   </ul>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	The spatial cache currently represents the geographic coverage of XML documents based on a bounding box. The four bounding coordinates (either latitudes or longitudes) can be specified in the metacat.properties file by their xpaths. For example, the geographic coverage of EML documents is defined as:</span></p>
-
-<pre>
-westBoundingCoordinatePath=geographicCoverage/boundingCoordinates/westBoundingCoordinate
-eastBoundingCoordinatePath=geographicCoverage/boundingCoordinates/eastBoundingCoordinate
-southBoundingCoordinatePath=geographicCoverage/boundingCoordinates/southBoundingCoordinate
-northBoundingCoordinatePath=geographicCoverage/boundingCoordinates/northBoundingCoordinate
-</pre>
-
-   <p dir="ltr" style="text-align:left;margin-bottom:12pt;margin-left:0.1250in;text-indent:0in"></p>
-   <p dir="ltr" style="text-align:left;margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	&nbsp;It is important to note that, at the moment, only one set of xpaths are defined in metacat.properties meaning only documents of the chosen schema can be accessed by the spatial harvester. Also note that, for performance reasons, the xpaths to the bounding coordinates must also appear in your indexPath (defined in build.properties).</span></p>
-   <p dir="ltr" style="text-align:left;margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	The bounding coordinates are spatially cached in two ways: t</span><span lang="en-US">he centroid(s) of the bounding box(s) and the actual bounding box(es). These are stored as two seperate shapefiles with multi-point and multi-polygon geometry types respectively. By default, </span><span style="font-size:8pt;font-family:'Courier New'" lang="en-US">${tomcat_webapps_directory}/${context}/data/metacat_shps/</span><span style="font-size:8pt;font-family:'Courier New'" lang="en-US">data_points.shp</span><span lang="en-US"> is the storage location of the point cache while </span><span style="font-size:8pt;font-family:'Courier New'" lang="en-US">data_bounds.shp</span><span lang="en-US"> represents the polygon cache. </span></p>
-   <p dir="ltr" style="text-align:left;margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	The bounding polygon is not relevant to every document as bounding coordinates are allowed to be of zero-area (ie west = = east and north = = south). In this case they are represented only as a point. In cases where no bounding coordinates are defined, the document is not represented at all in the spatial cache. Note that special care has been taken to account for cases where the bounding box crosses the international dateline or polar regions (at which point Cartesian calculations are invalid).</span></p>
-   <p dir="ltr" style="text-align:left;margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	Because documents may have more than one geographic coverage, it is necessary to define the two spatial caches as </span><span style="font-style:italic" lang="en-US">multi</span><span lang="en-US">-point and </span><span style="font-style:italic" lang="en-US">multi</span><span lang="en-US">-polygon geometry types. This means that each feature's geometry field can contain a collection of one </span><span style="font-style:italic" lang="en-US">or more </span><span lang="en-US">primitive geometries.</span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	&nbsp;With the spatial option properly installed, the default metacat.properties setting is to set </span><span style="font-style:italic" lang="en-US">regenerateCacheOnRestart=true.</span><span lang="en-US"> This is very useful the first time you install metacat since it will generate the spatial cache from scratch when your servlet container is restarted. Depending on how many documents you have in your metacat database, this can take a considerable amount of time; several minutes in the case of a few thousand documents. For this reason, Metacat sets this property to <em>false</em> after the spatial cache has been generated the first time. This prevents the regeneration of the spatial cache every time you restart your servlet container. Note that if you upgrade or reinstall metacat, the spatial cache will be regenerated again.  </span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	Once the spatial cache has been generated, the Metacat servlet will keep the spatial cache in sync with the metacat database by triggering the spatial harvester on every insert, update or delete. This does not regenerate the whole spatial cache, instead simply updating features in the cache as needed. It is fairly quick and should not add more than 1/2 second to any given transaction. As mentioned earlier, all high-level interactions with the spatial cache are handled through the SpatialHarvester class. </span></p>
-   <ul>
-    <li style="margin-bottom:12pt"><span lang="en-US">	W</span><span lang="en-US">hen a document is deleted, the SpatialHarvester.addToDeleteQue() method is called directly from the Metacat Servlet. </span></li>
-    <li style="margin-bottom:12pt"><span lang="en-US">	Inserts and updates are handled during the indexing process; after BuildIndex for a document has completed successfully (see </span><span style="font-style:italic" lang="en-US">DocumentImpl.java </span><span lang="en-US">) the SpatialHarvester.addToUpdateQue() method is invoked. The document is purged from the spatial cache (if updating) and the new document (or document revision) is added.</span>    </li>
-   </ul>
-   <p dir="ltr" style="text-align:left;margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	There is one very important note about document authentication. While metacat provides very fine-grained permissions control at the document level, the Web Mapping Server component does not. For this reason, only documents that are publicly readable (i.e. documents which match the following SQL query : </span><span style="font-size:9pt;font-family:'Courier New'" lang="en-US">select distinct docid from xml_access where principal_name = 'public' and perm_type = 'allow')</span><span lang="en-US">will be added to the spatial cache. </span><span lang="en-US">In the Future Directions section of this document, the potential for adding feature-level permissions to the WMS server are discussed.</span></p>
-
-
-        <h5> <a name="wms"> Web Mapping Server </a> </h5>
-
-
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	The primary function of the Web Mapping Server component is to render the spatial cache as a web-deliverable map image. It is also responsible for rendering other geographic data to provide base maps or other auxillary map layers.</span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	The OpenGIS consortium has defined a standard for requesting maps, the Web Mapping Service or WMS standard. WMS servers accept a common set of parameters via http, render the spatial dataset into an appropriate image and deliver it back to the client. </p>
-   <p> For Metacat, we chose to go with GeoServer, a WMS-capable application written in Java. Geoserver (and the Geotools library upon which it depends) are seamlessly integrated into the metacat servlet context. This allows all of the Geoserver/Geotools functionality to be accessible to all of metacat and allows easier deployment than if it were distributed seperately. The downside to this approach is that upgrading geoserver later becomes slightly more complicated.</span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US"> Geoserver comes with a default configuration that is already aware of the spatial cache and a world countries base layer. In order to configure existing data and add new data sources, geoserver comes with an web-based configuration utility. It is available at http://your.server/context/geoserver.jsp </span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US"> Geoserver has lots of built in functionality and can support a wide variety of vector GIS data sources. These data sources can be styled using SLDs and can be made available via open distribution standards such as WMS and WFS. For our purposes, it mainly outputs Images (via WMS) but can be used to output raw vector data in the form of GML or KML.</span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US"> There are several issues with geoserver tha users should be aware of. The version of Geoserver (1.4) used by Metacat does not support raster input dataset (ie satellite imagery or digital elevation models). For distributing rasters, we recommend UMN Mapserver be set up independently. Geoserver, though it offers a web configuration interface, is lacking in several key areas and you may still have to hand-edit some XML files in order to customize your WMS server. </span></p>
-
-
-
-
-        <h5> <a name="spatial_query"> Spatial Query </a> </h5>
-
-
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	Displaying the spatial cache as a map is important but users also need to query the spatial cache in order to answer the question "What documents lie in this geographic region?". The functionality is invoked through the metacat servlet itself; there is a </span><span style="font-style:italic" lang="en-US">spatial_query </span><span lang="en-US">action for this purpose. An example spatial query would be:</span></p>
-   <p dir="ltr" style="text-align:left;margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span style="font-size:8pt;font-family:'Courier New'" lang="en-US">http://localhost/knb/metacat?action=spatial_query&amp;xmin=-117.5&amp;xmax=-64&amp;ymin=3&amp;ymax=46&amp;skin=default</span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">Where xmin, xmax, ymin and ymax represent the west, east, south and northern bounding coordinates respectively. This will return an html document listing (in the style of the specified skin) all documents whose geographic coverage intersect the given bounding box.</span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	The core functionality of the spatial query mechanism is found in the </span><span style="font-style:italic" lang="en-US">edu.ucsb.nceas.metacat.spatial.SpatialQuery</span><span lang="en-US"> class and, like the spatial harvester, relies heavily on the Geotools library. This class has a single method,</span><span style="font-style:italic" lang="en-US"> filterByBbox()</span><span lang="en-US">, which compares the bounding box to both the point and polygon cache. For each shapefile, the process requires two steps: First, filter the spatial cache for features whose bounding box overlaps the specified bounding coordinates; Second, iterate through the remaining features to find those that are fully contained by the bounding box. The second step, though more costly than comparing the bbox, is necessary because the feature's geometry may be a multi-geometry whose bounding box is large but whose component primitive geometries are scattered over that area. The end result is a vector of docids matching the spatial query.</span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	This docid list is then sent to DBQuery. Using a special constructor that takes a vector of docids, the DBQuery class is able to use the Docid override mechanism to perform an optimized query (for cases where the list of docids is already known).</span></p>
-
-
-
-
-
-
-        <h5> <a name="html_client"> HTML Mapping Client</a> </h5>
-
-
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	In order to provide a web-based user interface to the WMS and the spatial query functionality, Metacat relies on Community Mapbuilder. Mapbuilder is a pure HTML/javascript application which uses AJAX and XSLT on the client side to create a desktop-GIS-like environment for interacting with geographic data through a web browser.</span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	The main function of mabuilder is to act as a front-end to WMS services. The WMS layers are configured through a Web Map Context document (typically found in the skin directory under spatial/context.xml). This context document (or WMC) can define the initial extent of the map, the ordering and visibility of layers and, of course, the source and name of the WMS layer.</span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	Mapbuilder provides several interface components or widgets (map, box zooms, layer list, "select location" dropdown, scalebar, coordinates, info query) that make it easy to deploy highly-functional web mapping applications with minimal coding. There are three main configuration files you need to work with in order to customize the map interface: The context document discussed above, the mapbuilder configuration file (typically under spatial/config.xml) which defined the widgets and their behavior and finally the html file (typically spatial/map.html) which loads the mapbuilder javascript library and places the widgets in your html layout.</span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	For integration with metacat, we built a custom mapbuilder widget, the AOIMetacat Query, which allows you to click query the map, either by box or point, and call the metacat spatial_query action. </span></p>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"><span lang="en-US">	The cleanest way to integrate a mapbuilder interactive map with any page in your application is to simply create an iframe element with the src pointing to a standalone map.html. </span></p>
-
-
-
-
-
-<h4> <a name="install">Installing and Configuring the Spatial Option</a> </h4>
-
- <h5> Initial Installation </h5>
- <p style="margin-bottom:12pt"><span lang="en-US">To install the spatial option, choose a version of metacat &gt;= 1.7.0. You'll want to ensure that </span><span style="font-style:italic" lang="en-US">runSpatialOption</span><span lang="en-US"> is set to </span><em>true</em><span lang="en-US"> in lib/metacat.properties before you build. Running the spatial option is <em> true </em> by default so, unless you explicitly set it to be false, the spatial option will install and run automatically when you install metacat.</span></p>
-
- <p>
-   Regardless of whether you plan on using the spatial functionality you should,
-   for security purposes, configure geoserver initially so that it doesn't use
-   the default password.
-   To configure geoserver with a new admin password:
-   <ol>
-    <li> Point your browser to http://your.server/context/geoserver.jsp. </li>
-     <li> Login using the default username and password ( <em>admin</em> / <em>geoserver</em> ) </li>
-    <li> Point your browser to http://your.server/context/config/loginEdit.do, enter a new user and password then submit. </li>
-     <li> In the upper-left, click <em>Apply</em> then <em>Save</em> to save your new password.
-    </ol>
- </p>
-
- <h5>How do I configure the layout of the html mapping interface?</h5>
-   The layout of the map components is defined in the spatial/map.html file within the skin's directory. It is a simple tabular layout and the map components are abstracted into "widgets", blocks with a specific id, which can be reorganized within the table. For deeper customization you can modify the web map context document (spatial/context.xml) and the mapbuilder config file (spatial/config.xml).
-   <h5> How can I change the lat/long display to degree-minutes-seconds ? </h5>
-      By default, the map display shows the cursors position in decimal degrees since this is the prefered format for many GPS/GIS applications. However, there may be cases where you need to report coordinates as degrees minutes-seconds. To do so, go into you skins spatial configuration file (usually ${skin.dir}/spatial/config.xml) and edit the CursorTrack widget as shown below:
-       <pre> 
-        &lt;CursorTrack id="cursorTrack"&gt;
-          &lt;mouseHandler&gt;mainMap&lt;/mouseHandler&gt;
-          &lt;showDMS&gt;true&lt;/showDMS&gt;
-          &lt;showLatLong&gt;true&lt;/showLatLong&gt;
-        &lt;/CursorTrack&gt;
-       </pre>
-
-   <h5>How can I configure the size and initial extent of the map?</h5>
-  The map's initial extent is defined in the web map context document for each skin. To change the map size and/or initial extent, edit the following lines:
-<pre>
-    &lt;Window width="720" height="360" /&gt;
-    &lt;BoundingBox SRS="EPSG:4326" minx="-180" miny="-90" maxx="180" maxy="90" /&gt;
-</pre>
-  Where the width and height are the image size in pixels and the minx/maxx represent the range of longitudes and miny/maxy reprsent the range of latitudes.
-
-   <h5>How do I configure the "select location" dropdown to contain different predefined locations?</h5>
- The locations data are held in a file called "named_locations.xml" in your skin's spatial directory. This defines each location as a gml:featureMember. Within each featureMember, you can edit the gml:name and gml:coordinates fields to edit or add new locations.
-
-   <h5>Can I use a different web mapping interface?</span></h5>
-<p>Certainly. Since our mapping server conforms to the WMS standard, you can develop a map interface using any WMS client application. There are many of WMS clients ranging from desktop GIS applications (ArcGIS, QGIS, JUMP, UDig) to javascript web mapping frameworks (openlayers, mapbender, mapbuilder) and anyone of them could be used to build a novel spatial application from the metacat wms.</p>
-<p> There is an experimental version of OpenLayers (a tiled, google-maps-esque web interface) included with Metacat spatial. This can be accessed at http://your.server/context/style/common/spatial_templates/openlayers1/map.html. Keep in mind that this is experimental and not supported as an official interface.
-
-   <h5>How do I configure the styling and classification of the data?</h5>
-
-  The datasets are styled through the use of Styled Layer Descriptors (SLD). The default SLDs used for the data points and data bounding boxes are in {context}/data/styles and named <em> data_points_style.sld </em> and <em> data_bounds_style.sld </em> respectively. 
-You can find more a more detailed tutorial on using SLD with geoserver at : <a href="http://docs.codehaus.org/display/GEOSDOC/SLD+Intro+Tutorial"> http://docs.codehaus.org/display/GEOSDOC/SLD+Intro+Tutorial</a>.
-
-   <h5>What versions of tomcat are supported?</h5>
-
-   <p>The spatial functionality has only been tested on tomcat 5. The web.xml.tomcat4 distributed with metacat is no longer supported after Metacat 1.6.0 . If you <em>need</em> to use tomcat 4, you might be able to update this file to reflect the incorporation of geoserver (see web.xml.tomcat5) though we have no intention of supporting its use.</p>
-
-   <h5>How do I add the map to another page or metacat skin?</h5>
-
-The map interface is held in a seperate html document and can be easily included in any html page through the use of an iframe :
-<pre>
-  &lt;iframe scrolling="no" frameborder="0" width="736" height="520" 
-             src="/knb/style/common/spatial_templates/spatial1/map.html"&gt;
-  &lt;/iframe&gt;
-</pre>
-The map URL referenced here is the default, common spatial template for use in any skin. If you plan on doing any customization of the map interface, you should copy that spatial template into your skin's directory:
-<pre>
- cp -r style/common/spatial_templates/spatial1 style/skins/myskin/spatial
-</pre>
-and access it with the url "/knb/style/skins/myskin/spatial/map.html".
-  
-
-<h4> <a name="adding_data">Adding Other Spatial Datasets to the Web Map</a> </h4>
-
- <h5> Adding your own spatial datasets </h5>
-If you have other vector GIS datasets on your server that you'd like to include in the interactive map, there are two main tasks:<ul>
-<li> Registering the dataset with geoserver </li> <li> Adding the layer to the web map context </li> </ul>
-
-<h6> Registering your dataset with geoserver </h6>
-There is a <a href="http://docs.codehaus.org/display/GEOSDOC/User+Tutorial+Shapefile"> geoserver tutorial </a> which covers the precise steps of adding a new layer via the web interface. The actual process will differ slightly depending on your configuration so we'll clarify and summarize the steps below:
-<ol>
- <li>Creating a datastore (ie registering the raw data)</li>
-  <ul>
-    <li> Point your browser to http://your.server/context/geoserver.jsp, login and navigate to the "data stores" config page.</li>
-    <li> Define your new shapefile datastore and point to the shp file on the filesystem (relative to {tomcat.dir}/webapps/{context}/ ). </li> 
-    <li> Use the "metacat" namespace to describe your data </li>
-  </ul>
- <li> Creating the feature type (ie registering the data as a recognizable layer)</li>
-   <ul> 
-     <li> You must define a spatial reference system number for each layer. Most lat/long data is "4326". If your data is in another projection, you'll have to determine its SRS using the help links provided. </li>
-     <li> The dropdown list of styles provides some good default choices but to get more control over the styling, you'll need to create a new Style object and corresponding SLD. </li>
-   </ul>
- <li> Testing </li>
-   <ul>
-    <li> Make sure you "Apply" and "Save" ! </li>
-    <li> Try out the featureType as a WMS layer using a URL like:<br/>
-      <span style="font-family:monospace; font-size:9pt;">http://your.server/context/wms?VERSION=1.1.1&REQUEST=GetMap&SERVICE=WMS&LAYERS=metacat:<strong>newLayer</strong>&SRS=EPSG:4326&BBOX=<strong>-180,-90,180,90</strong>&WIDTH=720&HEIGHT=360&FORMAT=image/gif&STYLES=&TRANSPARENT=TRUE&UNIQUEID= </span></li>
-    <li> If this displays your data properly, it's time to add it to your map context document. </li></ul>
-</ol>
-  
-<h6> Adding your layer to the web map context </h6>
-  
-  <ol>
-   <li> Locate the web map context document (usually {skin}/spatial/context.xml) and open in a text editor </li>
-   <li> Locate the Layer entry for an existing layer next to which you want your layer stacked (the first layers in the context are rendered at the bottom). </li>
-   <li> Create a new Layer entry, copying an existing entry for the metacat data_points layer to use as an example. </li>
-   <li> Edit the layer Name to reflect the name of your new feature type (ie metacat:newLayer ) </li>
-   <li> Edit the Title; this will be displayed in the map legend. </li>
-   <li> Special note about the image format: image/gif is the only option if you want transparency (since IE pre-7 has trouble with PNG transparency). image/jpeg is a good option for base layers.
-   <li> Point your browser to the map interface using this context document and your layer should show up stacked with the others </li>
-  </ol>
-   
-
- <h5> External WMS data sources </h5>
-
-There are hundreds of sources of spatial data made publically available through WMS. Check out <a href="http://wms-sites.com/"> wms-sites.com </a> for good catalog. In order to add these data sources to your map, locate your skin's context document and add a Layer as appropriate. Using an existing Layer as an example, modify the OnlineResourceURL, Name, Title and Style to match the WMS layer you're after. See the mapbuilder <a href="http://communitymapbuilder.org/display/MAP/Add+WMS+Tutorial"> Add WMS Tutorial</a> for further details.
-
- <h5> Raster Images </h5>
-
- The version of geoserver currently shipping with metacat (geoserver 1.4) does not support raster images as input data sources. We suggest setting up UMN Mapserver if you aim to serve raster data as a WMS. Note that once a WMS service is set up, the process of adding it to your map context is the same regardless of what WMS software is serving it. (ahhh the beauty of open standards).
-
-
-<h4> <a name="dev">Developers Notes</a></h4>
-
- <h5>web.xml</h5>
-
-The process of integrating geoserver with metacat involved merging the two web.xml documents. Special care must be taken to preserve the order of loading for various components in the geoserver stack. The web.xml.tomcat5 document is commented in the relevant places to indicate its purpose.
-
- <h5>Upgrading geoserver</h5>
-Great care has been taken not to modify geoserver so heavily as to "fork" it. Any small changes made should be submitted to the geoserver development team or maintained as patches against released versions. 
-
- Still, upgrading geoserver is not as seamless as one might hope. Most notably, any changes in the geoserver web.xml will have to be integrated by hand into out metacat/geoserver hybrid web.xml.tomcat5 document. In addition, geoserver distributes some unneccesary files that have been cut from the metacat version. When upgrading geoserver, make sure any old files get deleted, new files get added to cvs (if they are needed) or removed (if superfluous). 
-
-
-<h4> <a name="future">Future Directions</a> </h4>
-
-   <h5>Automatically handle spatial datasets</h5>
-   <p style="margin-bottom:12pt">When users put spatial data into the Morpho system, it would be nice if we could automatically pull all the avialable metadata from the spatial dataset itself. </p>
-   <p style="margin-bottom:12pt">On the metacat side, it might be worth trying to auto-detect spatial datasets and add them to the WMS service do that they could be displayed along with the metadata coverages. This is tricky since the styling of spatial data is intentionally seperated from the data itself; we'd have to have some sort of easy way to prompt the user for the classification and styling info and construct the appropriate SLDs. </p>
-   <p style="margin-bottom:12pt">It's worth noting that, currently, one could do this manually. There is nothing, aside from editing a few configuration files, to prevent any Geotools-supported dataset from being displayed through the WMS map interface.</p>
-   <p style="margin-bottom:12pt">For vector datasets, it would be possible to store the data directly in the database itself (This is a logical extension of the future work to put tabular data directly in a relational database). Postgresql has the PostGIS extensions to handle this so we would have to require postgresql if we went this route.</p>
-
-   <h5>WMS bypass</h5>
-   <p style="margin-bottom:12pt"> Filter which spatial cache features are displayed by access contraints, skin constraints and the current non-spatial query set. This would involve intercepting incoming WMS requests and appending a styled layer descriptor (SLD) with an OGC filter to prevent/allow certain docids. </p>
-
-   <h5>SLD factory</h5>
-   <p style="margin-bottom:12pt">Closely related to the WMS bypass implemetation, the SLD factory would be in charge of constructing the filter based on on the contraints mentioned above. In other words, it would construct a document specifying which docids were to appear in the map. Because it would have to generate this list of docids on every wms request, performance is a big concern. Likely we'll need to cache docid lists as session variables.</p>
-
-  <p> There is currently a stub implementation of the SLD Factory servlet in <em>src/edu/ucsb/nceas/metacat/spatial/SldFactory.java</em>. It is functional except that it doesn't generate a dynamic list of allowable docids.  Assuming we can modify the SldFactory servlet to quickly generate a list of allowable docids based on stored session variables, applying this SLD to a WMS request is fairly easy and simply requires appending the URL of the sldfactory as an "SLD" parameter to the WMS GetMap request: </p>
-
-   <pre> http://indus/knb/wms?REQUEST=GetMap&SERVICE=WMS....&SLD=http://indus.msi.ucsb.edu/knb/sldfactory?originalSld=data_points_style.sld</pre>
-
-<p> where data_points_style.sld is the original style document existing in <em>{context}/data/styles/</em>. The sldfactory servlet will construct a list of allowable docids, append those to the original sld as an ogc filter, an return a (modified) SLD document. There are two possibilities for implementing this:</p>
-
-   <ol>
-   <li>
-     Mapbuilder (the WMS client in charge of constructing WMS request) can be told to append this SLD parameter through the use of the WMC config document. This would work for the skins but, alone, would not ensure that every WMS request were filtered since other clients could simply ommit the SLD parameter.
-   </li>
-   <li> 
-     An alternative, one that would ensure that EVERY wms request was filtered, would be to handle it all server side with a WMS bypass.
-   </li>
-   </ol>
-   
-   
-
-   <h5>Map configuration interface </h5>
-   <p style="margin-bottom:12pt">Geoserver currently offers a nice web-based configuration but it is lacking a few key features and may be difficult for a novice GIS user. We may want to reinvent a custom geoserver configuration interface to</p>
-   <ul>
-    <li style="margin-bottom:12pt"><span lang="en-US">	D</span>efine the available datasets (ie editing the geoserver xml config files)</li>
-    <li style="margin-bottom:12pt"><span lang="en-US">	Define</span> classification and styling (ie editing the SLDs)</li>
-    <li style="margin-bottom:12pt"><span lang="en-US">	Define which layers get displayed in which map (ie editing the Mapbuilder WMCs)</span></li>
-    <li style="margin-bottom:12pt"><span lang="en-US">	Picking a layout ( from a list of pre-configure mapbuilder templates)</span>    </li>
-   </ul>
-   <p style="margin-bottom:12pt;margin-left:0pt;text-indent:0in"> Ideally we could pull as much information as possible from the metadata and make the UI very intuitive. This does bring up issues of web-based admin access constraints and developing a subsytem to handle who has edit access to the map configuration.</p>
-
-
-
-   <table> <tr>
-      <td align="right">
-        <a href="./lsid_authority.html">Back</a> | 
-        <a href="./metacattour.html">Home</a> | 
-        <a href="./pagedreturn.html">Next</a>
-      </td>
-   </tr> </table>
-
-</BODY>
-</HTML>

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-# People from KNB - The Knowledge Network for Biocomplexity
-dn: uid=bojilova,o=NCEAS,dc=ecoinformatics,dc=org
-objectClass: top
-objectclass: person
-objectClass: organizationalPerson
-objectClass: inetOrgPerson
-objectclass: uidObject
-uid: bojilova
-cn: Jivka Bojilova
-sn: Bojilova
-givenName: Jivka Bojilova
-telephoneNumber: 805-892-2530
-mail: bojilova@nceas.ucsb.edu
-title: Data Integration Developer
-
-dn: uid=berkley,o=NCEAS,dc=ecoinformatics,dc=org
-objectClass: top
-objectclass: person
-objectClass: organizationalPerson
-objectClass: inetOrgPerson
-objectClass: uidObject
-uid: berkley
-cn: Chad Berkley
-sn: Berkley
-givenName: Chad Berkley
-telephoneNumber: 805-892-2531
-mail: berkley@nceas.ucsb.edu
-title: Metadata Systems Developer
-
-dn: uid=jones,o=NCEAS,dc=ecoinformatics,dc=org
-objectClass: top
-objectclass: person
-objectClass: organizationalPerson
-objectClass: inetOrgPerson
-objectClass: uidObject
-uid: jones
-cn: Matt Jones
-sn: Jones
-givenName: Matt Jones
-telephoneNumber: 907-789-0496
-mail: jones@nceas.ucsb.edu
-title: Project Manager
-
-dn: uid=higgins,o=NCEAS,dc=ecoinformatics,dc=org
-objectClass: top
-objectclass: person
-objectClass: organizationalPerson
-objectClass: inetOrgPerson
-objectClass: uidObject
-uid: higgins
-cn: Daniel Higgins
-sn: Higgins
-givenName: Daniel Higgins
-telephoneNumber: 805-892-2531
-mail: higgins@nceas.ucsb.edu
-title: Interface System Developer
-
-dn: uid=harris,o=NCEAS,dc=ecoinformatics,dc=org
-objectClass: top
-objectclass: person
-objectClass: organizationalPerson
-objectClass: inetOrgPerson
-objectClass: uidObject
-uid: harris
-cn: John Harris
-sn: Harris
-givenName: John Harris
-telephoneNumber: 805-892-2531
-mail: harris@nceas.ucsb.edu
-title: Software Developer for National Plots Database

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-    "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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-<head>
-  <meta http-equiv="Content-Type" content=
-  "text/html; charset=us-ascii" />
-  <meta name="generator" content="pandoc" />
-  <style type="text/css">
-/*<![CDATA[*/
-  ol.decimal { list-style-type: decimal; }
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-  <title>Metacat Install - Registry</title>
-  <link rel="stylesheet" type="text/css" href="default.css" />
-</head>
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-<body>
-  <table class="tabledefault" width="100%">
-    <tr>
-      <td rowspan="2"><img src="images/KNBLogo.gif" /></td>
-
-      <td colspan="7">
-        <div class="title">
-          Metacat Installation - Registry
-        </div>
-      </td>
-    </tr>
-
-    <tr>
-      <td><a href="/" class="toollink">KNB Home</a></td>
-
-      <td><a href="/data.html" class="toollink">Data</a></td>
-
-      <td><a href="/people.html" class="toollink">People</a></td>
-
-      <td><a href="/informatics" class=
-      "toollink">Informatics</a></td>
-
-      <td><a href="/biodiversity" class=
-      "toollink">Biocomplexity</a></td>
-
-      <td><a href="/education" class="toollink">Education</a></td>
-
-      <td><a href="/software" class="toollink">Software</a></td>
-    </tr>
-  </table>
-  <hr />
-
-  <table class="tabledefault" width="100%">
-    <tr>
-      <td class="tablehead" colspan="2">
-        <p class="emphasis">Installing the Metacat Registry</p>
-      </td>
-    </tr>
-
-    <tr>
-      <td>Author: Shaun Walbridge<br />
-      Date: 06/06/2008<br /></td>
-    </tr>
-  </table>
-
-  <h1 id="registry-installation">Registry Installation</h1>
-
-  <h2 id="whats-it-for">What's it for?</h2>
-
-  <p>The Metacat Registry provides an easy mechanism to create and
-  edit simple EML metadata documents, and accounts for your Metacat
-  users. It is an optional component of Metacat, but is useful when
-  you need very low barriers to creating simple EML, or have users
-  unable to use Morpho. The LDAP account management interface is
-  useful if you are authenticating users against LDAP, and need to
-  provide a basic mechanism for managing user accounts.</p>
-
-  <h2 id="installation-instructions">Installation Instructions</h2>
-
-  <p>The Registry can be installed on any machine Metacat runs on,
-  but does require additional legwork to get it installed. It
-  requires that Metacat is set deployed behind Apache, as our
-  recommended installation platform, and the instructions assume
-  Apache is already installed and working correctly.</p>
-
-  <h2 id="steps">Steps</h2>
-
-  <ol class="decimal">
-    <li>
-      <p>Download and extract the Metacat release:</p>
-      <blockquote>
-<pre><span class="type">mkdir</span> metacat &amp;&amp; cd metacat 
-<span class="type">wget</span> http://knb.ecoinformatics.org/software/dist/metacat-src-1.8.0.zip
-<span class="type">unzip</span> metacat-src-1.8.0.zip
-<span class="type">cd</span> metacat-1.8.0
-<span class="type">export</span> METACAT=`pwd`
-</pre>
-</blockquote>
-    </li>
-
-    <li>
-      <p>Build the Metacat Perl client library:</p>
-      <blockquote>
-<pre><span class="type">cd</span> $METACAT/src/perl/Metacat
-<span class="type">perl</span> Makefile.PL
-<span class="type">sudo make</span>
-<span class="type">sudo make install</span>
-</pre>
-</blockquote>
-    </li>
-
-    <li>
-      <p>Install the system libraries needed. On Redhat:
-      <blockquote>
-<pre><span class="type">sudo yum install</span> gcc libxml2-devel libxslt-devel ant openssl -y
-</pre>
-</blockquote>
-
-      On Debian:
-      <blockquote>
-			<pre>
-<span class="type">sudo apt-get install</span> ant libappconfig-perl libxml-libxml-perl libxml-libxslt-perl \
-libtemplate-perl libcgi-session-perl libdigest-sha1-perl libnet-ldap-perl \ 
-libterm-readkey-perl libxml-dom-perl libsoap-lite-perl libio-socket-ssl-perl -y
-</pre>
-</blockquote>
-	  You will need to install one package using cpan
-      <blockquote><pre><span class="type">sudo cpan</span> -i Config::Properties</pre></blockquote>
-      <blockquote><pre><span class="type">sudo cpan</span> -i scalar::util</pre></blockquote>
-
-      Debian users should skip ahead to step 6.
-</p>
-    </li>
-
-    <li>
-      <p>Install CPAN, which allows us to install the Perl
-      dependencies for the registry and account management parts of
-      Metacat. If asked to manually configure cpan, type 'no' and
-      CPAN will be setup with its default values.</p>
-      <blockquote>
-<pre><span class="type">sudo yum install</span> perl-CPAN
-<span class="type">sudo cpan</span>
-</pre>
-</blockquote>
-
-      <p>You should now see a prompt which looks like:</p>
-      <blockquote>
-<pre><span class="string">cpan&gt;</span>
-</pre>
-</blockquote>
-
-      <p>The rest of the commands will assume you're inside of
-      CPAN. Let's get the most recent version of the CPAN software.
-      Just press return after any prompts you recieve during this
-      process.</p>
-      <blockquote>
-<pre>install Bundle::CPAN
-reload cpan
-</pre>
-</blockquote>
-    </li>
-
-    <li>
-      <p>Install the required modules. Here we're installing an old
-      LibXSLT, as the current one requires a newer libxslt than is
-      available on Redhat 4 &amp; 5. Again, just answer 'yes' to
-      any questions.</p>
-      <blockquote>
-<pre>install AutoLoader
-install CGI
-install CGI::Session
-install LWP::UserAgent
-install IO::Socket:SSL
-install Net::LDAP
-install Template 
-install URI
-install MSERGEANT/XML-LibXSLT-1.58.tar.gz
-install Digest::SHA1
-install Crypt::SSLeay
-</pre>
-</blockquote>
-    </li>
-
-		<li>
-			<p>Double check that Metacat's temporary folder, <code><span class="string">application.tempDir</span></code>, is writable by the apache user, usually <code><span class="string">www-data</span></code> or <code><span class="string">apache</span></code>.
-    <li>
-      <p>Now visit the resulting URL:</p>
-      <blockquote>
-<pre>http://localhost/knb/cgi-bin/register-dataset.cgi?cfg=nceas
-</pre>
-</blockquote>
-
-      <p>If everything worked correctly, you should see a page like
-      this: <img src="images/registry-login.jpg" alt=
-      "Registry Login Page" /></p>
-    </li>
-  </ol>
-
-  <h2 id="installing-the-nceas-registry">Installing the NCEAS
-  Registry</h2>
-
-  <p>These are special instructions required for the NCEAS skin to
-  get a current projects list from the AdminDB, and can safely be
-  ignored in all other uses.</p>
-
-  <ol class="decimal">
-    <li>
-      <p>Download and install the Oracle Instant Client RPMs. These
-      can be obtained from the <a href=
-      "http://www.oracle.com/technology/software/tech/oci/instantclient/htdocs/linuxsoft.html">
-      oracle website</a>.</p>
-      <blockquote>
-<pre><span class="type">rpm -i</span> oracle-instantclient-basic-10.2.0.3-1.i386.rpm
-<span class="type">rpm -i</span> oracle-instantclient-devel-10.2.0.3-1.i386.rpm
-<span class="type">rpm -i</span> oracle-instantclient-sqlplus-10.2.0.3-1.i386.rpm
-</pre>
-</blockquote>
-    </li>
-
-    <li>
-      <p>Next, we'll need an <pre>tnsnames.ora</pre> file for
-      Oracle to locate the server we're connecting to. In this
-      example, we'll copy it from a remote location:</p>
-      <blockquote>
-<pre><span class="type">mkdir -p</span> /usr/lib/oracle/10.2.0.3/network/admin/ &amp;&amp; <span class="type">cd !$</span>
-<span class="type">scp</span> walbridge@knb.ecoinformatics.org:/usr/lib/oracle/10.1.0.4/network/admin/tnsnames.ora .
-</pre>
-</blockquote>
-    </li>
-
-    <li>
-      <p>The AdminDB is accessed via Perl, so install the needed
-      Oracle driver using CPAN:</p>
-      <blockquote>
-<pre>cpan
-install DBI
-install DBD::Oracle
-</pre>
-</blockquote>
-    </li>
-
-    <li>
-      <p>Now we can install the AdminDB module itself:</p>
-      <blockquote>
-<pre>mkdir -p ~/projects/admindb &amp;&amp; cd !$
-export CVSROOT=:ext:walbridge@cvs.nceas.ucsb.edu:/cvsnceas
-cvs co admindb
-cd admindb/perl/NCEAS/AdminDB
-perl Makefile.PL
-make
-sudo make install
-</pre>
-</blockquote>
-    </li>
-
-    <li>
-      <p>Finally, set the correct properties in the
-      <pre>nceas.cfg</pre> file:</p>
-      <blockquote>
-<pre>nceas_db = //hyperion.nceas.ucsb.edu:1521/nceasp.nceas.ucsb.edu
-nceas_db_user = admowner
-nceas_db_password = NCEAS_DB_READ_PASSWORD_HERE
-</pre>
-</blockquote>
-    </li>
-
-    <li>
-      <p>A quick check of <pre>register-dataset.cgi</pre> should
-      now show a complete list of projects: <img src=
-      "images/registry-nceas-projects.png" alt=
-      "NCEAS Project list" /></p>
-    </li>
-  </ol>
-
-  <h2 id="notes">Notes</h2>
-
-  <p>Redhat based, tested on Centos 5</p>
-
-  <p>Debian based, tested on Ubuntu 8.04</p>
-</body>
-</html>

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Index: docs/user/clientapi.html
===================================================================
--- docs/user/clientapi.html	(revision 5315)
+++ docs/user/clientapi.html	(nonexistent)
@@ -1,103 +0,0 @@
-<!--
-  * metacatread.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Metacat Client
-       Application Programming Interface</p></td>
-       <td class="tablehead" colspan="2" align="right">
-         <a href="./metacatdom.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-         <a href="./metacatload.html">Next</a>
-       </td>
-    </tr>
-  </table>
-  <p>Metacat provides a client programming interface for communicating with
-     the server.  The client API is available in Java and Perl, but the
-     Java interface will be described here. This interface allows a client
-     application to easily authenticate users and perform basic metacat
-     operations such as reading metadata and data files, inserting, updating,
-     and deleting files, and searching for packages based on metadata matches.
-  </p>
-  <p>To use the client, developers must include the 'metacat-client.jar',
-     'utilities.jar',  and 'httpclient.jar' in their classpath.  Then, the API
-     methods can be used.  For example, a typical session to read a document
-     from the database might look like this:<br>
-     <pre>
-        String metacatUrl = "http://foo.com/context/metacat";
-        String username = "uid=jones,o=NCEAS,dc=ecoinformatics,dc=org";
-        String password = "neverHarcodeAPasswordInCode";
-        try {
-            Metacat m = MetacatFactory.createMetacatConnection(metacatUrl);
-            m.login(username, password);
-            Reader r = m.read("testdocument.1.1");
-            // Do whatever you want with Reader r
-        } catch (MetacatAuthException mae) {
-            handleError("Authorization failed:\n" + mae.getMessage());
-        } catch (MetacatInaccessibleException mie) {
-            handleError("Metacat Inaccessible:\n" + mie.getMessage());
-        } catch (Exception e) {
-            handleError("General exception:\n" + e.getMessage());
-        }
-     </pre>
-  </p>
-  <p>The Client API is defined by the interface
-     <code>edu.ucsb.nceas.metacat.client.Metacat</code>, and all operations
-     are fully defined inthe javadoc documentation.  Briefly, the API 
-     provides the following operations:</p>
-    <ul>
-    <li><code>public String <b>login</b>(String username, String password)
-           throws MetacatAuthException, MetacatInaccessibleException;</code></li>
-    <li><code>public String <b>logout</b>() throws MetacatInaccessibleException,
-        MetacatException;</code></li>
-    <li><code>public Reader <b>read</b>(String docid) throws InsufficientKarmaException,
-        MetacatInaccessibleException, MetacatException;</code></li>
-    <li><code>public Reader <b>readInlineData</b>(String inlinedataid)
-        throws InsufficientKarmaException,
-        MetacatInaccessibleException, MetacatException;</code></li>
-    <li><code>public Reader <b>query</b>(Reader xmlQuery) throws MetacatInaccessibleException,
-                                                IOException;</code></li>
-    <li><code>public String <b>insert</b>(String docid, Reader xmlDocument, Reader schema)
-        throws InsufficientKarmaException, MetacatException, IOException,
-        MetacatInaccessibleException;</code></li>
-    <li><code>public String <b>update</b>(String docid, Reader xmlDocument, Reader schema)
-        throws InsufficientKarmaException, MetacatException, IOException,
-        MetacatInaccessibleException;</code></li>
-    <li><code>public String <b>upload</b>(String docid, File file)
-        throws InsufficientKarmaException, MetacatException, IOException,
-        MetacatInaccessibleException;</code></li>
-    <li><code>public String <b>upload</b>(String docid, String fileName,
-                         InputStream fileData, int size)
-        throws InsufficientKarmaException, MetacatException, IOException,
-        MetacatInaccessibleException;</code></li>
-    <li><code>public String <b>delete</b>(String docid)
-        throws InsufficientKarmaException, MetacatException,
-        MetacatInaccessibleException;</code></li>
-    <li><code>public void <b>setMetacatUrl</b>(String metacatUrl);</code></li>
-    <li><code>public String <b>getSessionId</b>();</code></li>
-    <li><code>public void <b>setSessionId</b>(String sessionId);</code></li>
-    <li><code>public int <b>getNewestDocRevision</b>(String docId) throws MetacatException;</code></li>
-    <li><code>public String <b>setAccess</b>(String docid, String principal, String permission, String permType, String permOrder );</code></li>
-  </ul>
-  <br>
-  <a href="./metacatdom.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./metacatload.html">Next</a>
-
-</BODY>
-</HTML>
-

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--- docs/user/metacat-linux-install.html	(revision 5315)
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@@ -1,679 +0,0 @@
-<!-- 
-  *   '$RCSfile$'
-  *     Purpose: web page describing the installation of Metacat
-  *   Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *     Authors: Chad Berkley
-  *
-  *    '$Author$'
-  *    '$Date$'
-  *    '$Revision$'
-  *
-  *
-  -->
-  
-<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>Metacat Linux Installation Instructions</title>
-  <link rel="stylesheet" type="text/css" href="./common.css">
-  <link rel="stylesheet" type="text/css" href="./default.css">
-</head>
-
-<body>
-
-<table class="tabledefault" width="100%">
-<tr><td rowspan="2"><img src="./images/KNBLogo.gif"></td>
-<td colspan="7">
-<div class="title">Metacat Linux Installation Instructions</div>
-</td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
-<div class="header1">Table of Contents</div>
-  <div class="toc">
-    <div class="toc1"><a href="#Intro">Introduction</a></div> 
-      <div class="toc2"><a href="#DifferentOptions">Different Installation Options</a></div> 
-      <div class="toc2"><a href="#ThisDoc">Organization Of This Page</a></div>
-    <div class="toc1"><a href="#QuickInstallation">Quick Installation</a></div> 
-      <div class="toc2"><a href="#DownloadMetacatInstall">Download Metacat Package</a></div> 
-      <div class="toc2"><a href="#CreateDirs">Create Metacat Directories</a></div> 
-      <div class="toc2"><a href="#InstallJava">Install Java</a></div> 
-      <div class="toc2"><a href="#InstallApache">Install Apache</a></div> 
-      <div class="toc2"><a href="#InstallTomcat">Install Tomcat</a></div> 
-      <div class="toc2"><a href="#InstallPostgres">Install PostgreSQL Database</a></div> 
-      <div class="toc2"><a href="#QuickInstallMetacatWar">Install Metacat War</a></div> 
-      <div class="toc2"><a href="#QuickInstallLsidWar">Install LSID War</a></div> 
-      <div class="toc2"><a href="#ConfigureMetacatInstall">Configure Metacat</a></div> 
-    <div class="toc1"><a href="#QuickUpdate">Quick Update</a></div>
-      <div class="toc2"><a href="#DownloadMetacatUpdate">Download Metacat Package</a></div> 
-      <div class="toc2"><a href="#BackupApplication">Backup Existing Metacat Installation</a></div> 
-      <div class="toc2"><a href="#QuickUpdateMetacatWar">Update Metacat War</a></div> 
-      <div class="toc2"><a href="#QuickUpdateLsidWar">Update LSID War</a></div> 
-      <div class="toc2"><a href="#ConfigureMetacatUpdate">Configure Metacat</a></div> 
-    <div class="toc1"><a href="#PreInstallation">Pre-Installation</a></div>
-      <div class="toc2"><a href="#MinRequirements">Minimum Requirements</a></div> 
-      <div class="toc2"><a href="#AdditionalRequiredSoftware">Additional Required Software</a></div>
-    <div class="toc1"><a href="#AdditionalSoftwareSetup">Additional Software Setup</a></div>
-      <div class="toc2"><a href="#AdditionalSoftwareJava">Java</a></div> 
-      <div class="toc2"><a href="#AdditionalSoftwareOracle">Oracle</a></div>
-      <div class="toc2"><a href="#AdditionalSoftwarePostgreSQL">PostgreSQL</a></div>
-      <div class="toc2"><a href="#AdditionalSoftwareAnt">Ant</a></div>
-      <div class="toc2"><a href="#AdditionalSoftwareApache">Apache</a></div>
-      <div class="toc2"><a href="#AdditionalSoftwareTomcat">Tomcat</a></div>
-    <div class="toc1"><a href="#DownloadingMetacat">Download Metacat and Get War File</a></div>
-      <div class="toc2"><a href="#DownloadMetacatBinary">Download Metacat Binary and Get War File</a></div>
-      <div class="toc2"><a href="#DownloadMetacatSourceDist">Download Metacat Source Distribution</a></div>
-      <div class="toc2"><a href="#DownloadMetacatSourceSVN">Download Metacat Source From SVN</a></div>
-      <div class="toc2"><a href="#CreateSourceWar">Create War From Source</a></div>
-    <div class="toc1"><a href="#InstallingMetacat">Installing Metacat</a></div>
-      <div class="toc2"><a href="#CreateMetacatDirs">Create Metacat Directories</a></div>
-      <div class="toc2"><a href="#InstallMetacatWar">Install Metacat Binary (War)</a></div>
-      <div class="toc2"><a href="#InstallMetacatSource">Install Metacat From Source</a></div>
-    <div class="toc1"><a href="#UpgradingMetacat">Upgrading Existing Metacat</a></div>
-      <div class="toc2"><a href="#UpgradeStopMetacat">Stop the Running Metacat</a></div>
-      <div class="toc2"><a href="#UpgradeDownloadMetacat">Download Latest Metacat Application</a></div>
-      <div class="toc2"><a href="#UpgradeMetacatWar">Upgrade Metacat Binary (War)</a></div>
-      <div class="toc2"><a href="#UpgradeMetacatSource">Upgrade Metacat From Source</a></div>
-   <div class="toc1"><a href="#RestartTomcat">Restart Tomcat</a></div>
-      <div class="toc2"><a href="#UpgradeTroubleshooting">Troubleshooting</a></div>
-      <div class="toc2"><a href="#UpgradeConfigureMetacat">Configure Metacat</a></div>       
-    <div class="toc1"><a href="#Registry">Web Based Registry</a></div>
-  </div> 
-
-<a name="Intro"></a><div class="header1">Introduction</div>
-  <a name="DifferentOptions"></a><div class="header2">Different Installation Options</div>
-  <p>There are many different options to consider when installing Metacat.  Some of these
-  are: </p>
-  <ul>
-  <li>Operating System - Metacat is a Java servlet application.  As such, you can run
-  it on many different operating system.  It has been tested against Linux, MacOS and 
-  MicroSoft Windows.  The optimal installation is on Ubuntu Linux.</li>
-  <li>Tomcat standalone or in conjunction with Apache web server - The Tomcat server 
-  can be run alone as a web server.  However, it is not as robust a server,
-  and does't allow for the same level of customization as Apache.  The recommended 
-  configuration is Tomcat running in conjunction with Apache</li>
-  <li>Binary versus source installation - There are three ways to get and install 
-  the Metacat installation.
-    <ul>
-  	<li>Binary Distribution Installation - download the Metacat war distribution and install it 
-  	into the web applications directory</li>
-  	<li>Source Distribution Installation - download the source code distribution, build it and 
-  	install the resultant war file into the web application directory.</li>
-  	<li>Source Checkout Installation - check the source code out from the Subversion 
-  	repository, build it and install the resultant war file into the web application directory.</li>
-  	</ul>
-  The recommended installation procedure is binary distribution installation.</li>
-  </ul>
-  
-  <p>The administrator will need to decide which combinations of these option are best
-  suited to their system</p>
-  
-  <a name="ThisDoc"></a><div class="header2">Organization Of This Page</div>
-  <p> The first couple of sections on this page deal with quick command line 
-  instructions for installing and upgrading Metacat in the optimal environment, which
-  is a binary distribution installation with Apache on Ubuntu Linux.</p>
-  
-  <p>The remainder of the page deals with more detailed instructions including other 
-  installation options.</p>
-
-<a name="QuickInstallation"></a><div class="header1">Quick Installation</div>
-  <p>These are the installation instructions for a system that has Ubuntu 8.04 installed
-  and has never had Metacat installed on it:</p>
- 
-  <a name="DownloadMetacatInstall"></a><div class="header2">Download Metacat Package</div>
-    <ul>
-    <li>Browse to the 
-      <a href="http://knb.ecoinformatics.org/software/download.html">KNB Software Download Page</a>.
-      In the Metacat section, select the link that looks like:
-	  <div class="code">metacat-bin-X.X.X.tar.gz</div>
-    where X.X.X is the latest version of Metacat.  Choose to save the file locally.</li>
-    <li>Extract the Metacat package files by typing:
-      <div class="code">tar -xvzf metacat-bin-X.X.X.tar.gz</div></li>
-    <li>You should see a war file and several supporting files.  The location where these files
-    were extracted will be refered to as the the &lt;metacat_package_dir&gt; for the remainder 
-    of this documentation.</li>
-    </ul>
-  
-  <a name="CreateDirs"></a><div class="header2">Create Metacat Directories</div>
-    <ul>
-    <li>Create the metacat utility base directory by typing:
-      <div class="code">sudo mkdir /var/metacat</div>
-	  <div class="code">sudo chown -R &lt;tomcat_user&gt; /var/metacat</div>
-    where &lt;tomcat_user&gt; is the user that will start Tomcat.  If you are 
-	starting Tomcat as the root user, you do not need to run the chown command.</li>
-    </ul>
-
-  <a name="InstallJava"></a><div class="header2">Install Java</div>
-    <ul>
-    <li>Install Java by typing:
-      <div class="code">sudo apt-get install sun-java5-jdk</div></li>
-	<li>hit "ok" then "yes" for license agreement</li>
-	</ul>
-
-  <a name="InstallApache"></a><div class="header2">Install Apache</div>
-    <ul>
-    <li>Install Apache and and Mod JK packages by typing:	
-      <div class="code">sudo apt-get install apache2 libapache2-mod-jk</div></li>
-    <li>Set up Mod JK apache configuration by typing:
-      <div class="code">sudo cp &lt;metacat_package_dir&gt;/jk.conf /etc/apache2/mods-available</div>
-      <div class="code">sudo cp &lt;metacat_package_dir&gt;/workers.properties /etc/apache2</div></li>
-    <li>Enable Apache Mod JK by typing:
-      <div class="code">sudo a2dismod jk</div>
-      <div class="code">sudo a2enmod jk</div></li>
-    <li>Set up and enable knb (Metacat) site configurations by typing:
-      <div class="code">sudo cp &lt;metacat_package_dir&gt;/knb /etc/apache2/sites-available</div>
-      <div class="code">sudo a2ensite knb</div></li>
-    <li>If you want to run an LSID server along with the Metacat server, set up and enable the authority service site 
-      configurations by typing:
-      <div class="code">sudo cp &lt;metacat_package_dir&gt;/authority /etc/apache2/sites-available</div>
-      <div class="code">sudo a2ensite authority</div></li>
-    <li>Restart apache to bring in changes by typing:
-      <div class="code">sudo /etc/init.d/apache2 force-reload</div></li>
-    </ul>
-     
-  <a name="InstallTomcat"></a><div class="header2">Install Tomcat</div>
-    <ul>
-    <li>Install Tomcat 5.5 by typing:
-      <div class="code">sudo sudo apt-get install tomcat5.5</div> </li>
-    <li>Install Metacat friendly Tomcat startup script by typing:    
-      <div class="code">sudo /etc/init.d/tomcat5.5 stop</div>    
-      <div class="code">sudo mv /etc/init.d/tomcat5.5 /etc/init.d/tomcat5.5.bak</div>
-      <div class="code">sudo cp &lt;metacat_package_dir&gt;/tomcat5.5 /etc/init.d/tomcat5.5</div>
-      <div class="code">sudo chmod +x /etc/init.d/tomcat5.5</div></li>
-    </ul>
-    
-  <a name="InstallPostgres"></a><div class="header2">Install PostgreSQL Database</div> 
-    <ul>
-    <li>Install PostgreSQL by typing:</p>
-      <div class="code">sudo apt-get install postgresql</div></li>
-    <li>Change to postgres user:
-      <div class="code">sudo su - postgres</div></li>
-    <li>Setup empty Metacat database instance editing the postgreSQL configuration file:  
-      <div class="code">gedit /etc/postgresql/8.3/main/pg_hba.conf</div></li>
-    and adding the following line:
-      <div class="code">host metacat metacat 127.0.0.1 255.255.255.255 password</div></li>
-    <li>Save the file, then create the metacat instance:
-      <div class="code">createdb metacat</div></li>
-    <li>Log into postgreSQL by typing:
-	  <div class="code">psql metacat</div>
-	and create the metacat user by typing at the psql prompt:
-	  <div class="code">CREATE USER metacat WITH UNENCRYPTED PASSWORD 'your_password';</div>
-	where your_password is whatever password you would like for the metacat user.</li>
-	<li>Exit PostgreSQL by typing
-	  <div class="code">\q</div></li>
-	<li>Restart the PostgreSQL database to bring in changes:
-	  <div class="code">/etc/init.d/postgresql-8.3 restart</div></li>
-	<li>Log out of the postgres user account by typing:
-	  <div class="code">logout</div></li>
-	<li>Test the installation and metacat account by typing:
-	  <div class="code">psql -U metacat -W -h localhost metacat</div></li>
-	<li>Log back out of postgreSQL:
-	  <div class="code">\q</div></li>
-	</ul>
-	
-  <a name="QuickInstallMetacatWar"></a><div class="header2">Install Metacat War</div> 
-    <ul>
-    <li>Copy the war file to Tomcat:
-	  <div class="code">sudo cp &lt;metacat_package_dir&gt;/knb.war /usr/share/tomcat5.5/webapps</div></li>
-	<li>Restart Tomcat:
-	  <div class="code">sudo /etc/init.d/tomcat5.5 restart</div></li>
-  	</ul>
-  	
-  <a name="QuickInstallLsidWar"></a><div class="header2">Install LSID War</div> 
-    <ul>
-    <li>If you want to run an LSID server along with the Metacat server, copy the 
-    authority.war file to Tomcat:
-	  <div class="code">sudo cp &lt;metacat_package_dir&gt;/authority.war /usr/share/tomcat5.5/webapps</div></li>
-	<li>Restart Tomcat:  
-	  <div class="code">sudo /etc/init.d/tomcat5.5 restart</div></li>
-	</ul>
-		
-  <a name="ConfigureMetacatInstall"></a><div class="header2">Configure Metacat</div> 
-    <p>Refer to the documentation on <a href="./metacat-configure.html">Metacat Confguration</a>
-    to complete your installation of Metacat.</p>
-    
-  <a name="QuickUpdate"></a><div class="header1">Quick Update</div>
-  <p>These are the instructions for a system that already has Metacat installed on it, 
-  but needs a Metacat upgrade:</p>
-  
-  <a name="DownloadMetacatUpdate"></a><div class="header2">Download Metacat Package</div>
-    <ul>
-    <li>Browse to the 
-      <a href="http://knb.ecoinformatics.org/software/download.html">KNB Software Download Page</a>.
-      In the Metacat section, select the link that looks like:
-	  <div class="code">metacat-bin-X.X.X.tar.gz</div>
-    where X.X.X is the latest version of Metacat.  Choose to save the file locally.</li>
-    <li>Extract the Metacat package files by typing:
-      <div class="code">tar -xvzf metacat-bin-X.X.X.tar.gz</div>
-    You should see a war file and several supporting files.  The location where these files
-    were extracted will be refered to as the the &lt;metacat_package_dir&gt; for the remainder 
-    of this documentation.</li>
-    </ul>
-    
-  <a name="BackupApplication"></a><div class="header2">Backup Existing Metacat Installation</div>
-    <ul>
-    <li>To be safe, it is best to backup the existing Metacat installation.  Do so by typing: </p>
-	  <div class="code">cp &lt;web_app_dir&gt;/knb &lt;web_app_dir&gt;/knb.&lt;yyyymmdd&gt;</div>
-	  <div class="code">cp &lt;web_app_dir&gt;/knb.war &lt;web_app_dir&gt;/knb.war.&lt;yyyymmdd&gt;</div>
-	Of course, you can use any backup strategy you like (or none at all).</p>
-	</ul>
-  
-  <a name="QuickUpdateMetacatWar"></a><div class="header2">Update Metacat War</div> 
-    <ul>
-    <li>Copy the war file to Tomcat:
-	  <div class="code">sudo cp knb.war /usr/share/tomcat5.5/webapps</div></li>
-	<li>Restart Tomcat:  
-	  <div class="code">sudo /etc/init.d/tomcat5.5 restart</div></li>
-	</ul>
-  	
-  <a name="QuickUpdateLsidWar"></a><div class="header2">Update LSID War</div> 
-    <ul>
-    <li>If you want to run an LSID server along with the Metacat server, copy the 
-    authority.war file to Tomcat:
-	  <div class="code">sudo cp &lt;metacat_package_dir&gt;/authority.war /usr/share/tomcat5.5/webapps</div></li>
-	<li>Restart Tomcat:  
-	  <div class="code">sudo /etc/init.d/tomcat5.5 restart</div></li>
-	</ul>
-		
-  <a name="ConfigureMetacatUpdate"></a><div class="header2">Configure Metacat</div> 
-    <p>Refer to the documentation on <a href="./metacat-configure.html">Metacat Confguration</a>
-    to complete your installation of Metacat.</p>
-
-<a name="PreInstallation"></a><div class="header1">Pre-Installation</div>
-  <a name="MinRequirements"></a><div class="header2">Minimum Requirements</div> 
-  <p>
-   Installing Metacat requires a server running an SQL92 compliant database
-   (Oracle 8i or Postgresql recommended) with at least 128MB RAM, and a Pentium III class
-   processor or higher.  The amount of disk space required depends on the
-   size of your RDBMS tablespace (which should be at least 10 MB, 
-   however Metacat itself requires only about 1 MB of free space after 
-   installation).  These instructions assume a Linux environment but may
-   work on other UNIX type environments, however this has not been tested.
-  </p>
-  
-  <a name="AdditionalRequiredSoftware"></a><div class="header2">Additional Required Software</div>
-  <p>
-   The server on which you wish to install Metacat must have the following
-   software installed and running correctly before attempting to install
-   Metacat.
-   <ul>
-     <li><a href="http://www.oracle.com">Oracle 8i</a> (or another SQL92
-         compliant RDBMS like Postgres)</li>
-     <li><a href="http://jakarta.apache.org/ant/index.html">Apache Jakarta-Ant</a>
-     </li>
-     <li><a href="http://jakarta.apache.org/tomcat/index.html">Apache Jakarta-Tomcat</a>
-       <p class="emphasis">Note: For a more robust web serving environment, 
-       Apache web server should
-       be installed along with Tomcat and the two should be integrated
-       as described on the Apache web site.</p>
-     </li>
-   </ul>
-  </p>
-
-<a name="AdditionalSoftwareSetup"></a><div class="header1">Additional Software Setup</div>
-  <a name="AdditionalSoftwareJava"></a><div class="header2">Java</div>
-  <p>You'll need a recent Java SDK; J2SE 1.4.2 or later is required.  The latest metacat release
-  has been tested most extensively with <a href="http://java.sun.com/j2se/1.5.0/">J2SE 5.0</a>
-  and this is the recommended version.
-  Make sure that JAVA_HOME environment variable is properly set and that both
-  java and javac are on your PATH. 
-  </p>
-  <a name="AdditionalSoftwareOracle"></a><div class="header2">Oracle 8i</div>
-  <p>The Oracle RDBMS must be installed and running as a daemon on the system.
-   In addition the JDBC listener must be enabled.  You can enable it by
-   logging in as your Oracle user and typing the following:</p>
-   
-     <div class="code">lsnrctl start</div>
-     
-   <p>Your instance should have a table space of at least 5 MB (10 MB or higher 
-   recommended).  You should also have a username specific to Metacat
-   created and enabled.  This user must have most normal permissions 
-   including CREATE SESSION, CREATE TABLE, CREATE INDEX, CREATE TRIGGER, 
-   EXECUTE PROCEDURE, EXECUTE TYPE, etc.  If an action is unexplainably 
-   rejected by Metacat it is probably because the user permissions are not
-   correctly set.</p>
-   
-  <a name="AdditionalSoftwarePostgreSQL"></a><div class="header2">PostgreSQL</div>
-  <p>PostgreSQL can be easily installed on most linux distributions and on
-  Windows (using cygwin) and Mac OS X.  Using Fedora Core or RedHat Linux,
-  you can install the rpms for postgres and then run </p>
-  
-    <div class="code">/etc/init.d/postgresql start</div> 
-    
-  <p>in order to start the database. 
-  On Ubuntu and other Debian-based Linux distributions, you can use the apt-get command
-  to install postgres: 
-    <div class="code">sudo apt-get install postgresql-8.0</div> and 
-  then run 
-    <div class="code">/etc/init.d/postgresql-8.0 start</div> to start.
-  
-  This initializes the data files.  You need to do a bit of configuration
-  to create a database and set up a user account and allow internet access
-  via jdbc.  See the postgres documentation for this, but here is a quick 
-  start:
-  <ul>
-     <li>Switch to the "postgres" user account 
-       <div class="code">sudo su - postgres</div></li>
-     <li>Edit "data/pg_hba.conf", adding the following line to the file:<br>
-       <div class="code">host   metacat  metacat      127.0.0.1         255.255.255.255   password</div>
-     If your host uses IPv6 addresses, you may need this line instead:
-       <div class="code">host   metacat  metacat      ::1               ffff:ffff:ffff:ffff:ffff:ffff:ffff:ffff password</div></li>
-     <li>If you are using Postgresql pre-8.0, you must edit the "data/postgres.conf" file and uncomment and edit the line
-     starting with "tcpip_socket" so that it reads 
-       <div class="code">tcpip_socket = true</div></li>
-     <li>Create metacat database by typing: 
-       <div class="code">createdb metacat</div></li>
-     <li>Log in using the postgres account and create a new "metacat" user account by typing:
-       <div class="code">psql metacat</div> 
-     <ul>
-        <li>In postgres, run <div class="code">CREATE USER metacat WITH UNENCRYPTED PASSWORD 'apasswordyoulike';</div></li>
-        <li>This creates a new account called metacat on the database named metacat</li>
-        <li>Note: there are many ways to do this, so others such as using 
-        ENCRYPTED passwords will work fine.</li>
-     </ul>
-     </li>
-     <li>Exit the postgres account back to root and restart the postgres 
-     database by typing:
-       <div class="code">/etc/init.d/postgresql restart</div></li>
-     <li>Test logging into the postgres db using the metacat account with 
-     the following command: 
-       <div class="code">psql -U metacat -W -h localhost metacat</div></li>
-  </ul>
-  </p>
-  
-  <a name="AdditionalSoftwareAnt"></a><div class="header2">Ant</div>
-  <p>
-   Ant is a Java based build application similar to Make on UNIX systems.  
-   It takes in installation parameters from a file in the root installation
-   directory named "build.xml".  The Metacat CVS module contains a default
-   build.xml file that may require some modification upon installation.  Ant
-   should be installed on the system and the "ant" executable shell script 
-   should be available in the users path. The latest metacat release was tested with 
-   Ant 1.6.5. <!-- We note that the current build is 
-   not working with Ant 1.6.x, so you'll need to use an earler version.  We have 
-   successfully used Ant 1.5.1, 1.5.2, and some earlier versions. -->
-  </p>
-  
-  <a name="AdditionalSoftwareApache"></a><div class="header2">Apache</div>
-  <p>
-    If you are running Ubuntu/Debian, you can install the Apache web server by typing:</p>
-      <div class="code">sudo apt-get install apache2</div>
-    Otherwise, you can get Apache from <a href="http://httpd.apache.org/download.cgi">the Apache Tomcat page</a>.
-  </p>
-  
-  <a name="AdditionalSoftwareTomcat"></a><div class="header2">Tomcat</div>
-  <p>
-    Install Tomcat into the directory of your choice. The directory in which 
-    you install Tomcat itself will be referred to as the &lt;tomcat_home&gt;.
-    We recommend that you install Tomcat version 5.5.  If you are running 
-    Ubuntu/Debian, you can get Tomcat by typing:</p>
-      <div class="code">sudo apt-get install tomcat5.5</div>
-    Otherwise, you can get Tomcat from <a href=" http://jakarta.apache.org/tomcat/index.html">the Apache Tomcat page</a>.
-  </p>
-
-<a name="DownloadingMetacat"></a><div class="header1">Download Metacat and Get War File</div>
- <p>There are several ways to wind up with a Metacat war file, which is needed for 
- installation.  These are: </p>
-    <ul>
-      <li>Download Metacat binary distribution - which will have a pre-built war file.</li>
-      <li>Download Metacat source distribution - which will then need to be built in order to create a war file.</li>
-      <li>Download Metacat source from SVN - which will then need to be built in order to create a war file.</li>
-    </ul>
-  <p>Since downloading the binary distribution is the easiest and most common install, it
-  will be discussed here in detail.  Links to source download/build instructions are also
-  included in case you would like to go that route.</p>
-
-<a name="DownloadMetacatBinary"></a><div class="header2">Download Metacat Binary and Get War File</div>
-    <p>Browse to the 
-      <a href="http://knb.ecoinformatics.org/software/download.html">KNB Software Download Page</a>.
-      In the Metacat section, for Linux based systems, select the link that looks like:</p>
-	  <div class="code">metacat-bin-X.X.X.tar.gz</div>
-	  <p>for Windows systems, select the link that looks like:</p>
-	  <div class="code">metacat-bin-X.X.X.zip</div>
-    <p>where X.X.X is the latest version of Metacat.  Choose to save the file locally.</p>
-    <p>Extract the Metacat package files on Linux systems by typing:
-      <div class="code">tar -xvzf metacat-bin-X.X.X.tar.gz</div>
-    <p>or, on Windows, use your system unzip utility to extract the zip file.</p>
-    <p>You should see a war file and several supporting files.  The location where these files
-    were extracted will be refered to as the the &lt;metacat_package_dir&gt; for the remainder 
-    of this documentation.
-    
-<a name="DownloadMetacatSourceDist"></a><div class="header2">Download Metacat Source Distribution</div>	
-  <p>To get the Metacat source distribution, browse to the 
-      <a href="http://knb.ecoinformatics.org/software/download.html">KNB Software Download Page</a>.
-      In the Metacat section, for Linux based systems, select the link that looks like:</p>
-	  <div class="code">metacat-src-X.X.X.tar.gz</div>
-	  <p>for Windows systems, select the link that looks like:</p>
-	  <div class="code">metacat-src-X.X.X.zip</div>
-    <p>where X.X.X is the latest version of Metacat.  Choose to save the file locally in the directory 
-    where your source should live.</p>
-    <p>Extract the Metacat package files on Linux systems by typing:
-      <div class="code">tar -xvzf metacat-src-X.X.X.tar.gz</div>
-    <p>or, on Windows, use your system unzip utility to extract the zip file.</p>
-    <p>Rename the metacat-X.X.X directory to metacat.</p>
-    <p>Note that you do not need to create the war file directly with a source installation
-    since the Ant build file has an "install" target that will build and deploy the war
-    for you.  See the <a href="#InstallingMetacat">Installing Metacat</a> for instructions.</p>
-
-<a name="DownloadMetacatSourceSVN"></a><div class="header2">Download Metacat Source From SVN</div>
-  <p>If you are checking out Metacat code from the SVN repository, you will need both 
-  Subversion (SVN) and CVS clients installed and configured on your system.  Both are needed
-  because, while Metacat has been migrated to SVN, some of its supporting libraries (eml, 
-  utilities and seek) have not yet been migrated.  Eventually, SVN will be the only versioning 
-  client you will need.  You will need to make sure you have the appropriate accounts on these 
-  systems.  You won't have to worry about SVN or CVS if you are installing from a Metacat
-  source distribution.  These have all the required dependencies built in.</p>
-  
-  <p>If you have not already installed Subversion and you are running Ubuntu/Debian, you can 
-  get it by typing:</p>
-    <div class="code">sudo apt-get install subversion</div>
-    
-  <p>Otherwise, you can get if from <a href="http://subversion.tigris.org">The Subversion homepage</a></p>
-  
-  <p>If you have not already installed CVS and you are running Ubuntu/Debian, you can 
-  get it by typing:</p>
-    <div class="code">sudo apt-get install cvs</div>
-    
-  <p>Otherwise, you can get it from <a href="http://ximbiot.com/cvs/wiki/">The Ximbiot CVS homepage</a></p>
-  
-  <p>To check out the code from SVN, go to the directory where you would like the code 
-    to live and type:</p>
-      <div class="code">svn co https://code.ecoinformatics.org/code/metacat/tags/METACAT_&lt;rev&gt; metacat</div>
-    <p>Where &lt;rev&gt; is the version of the code you want to check out (like 1_9). </p>
-    
-    <p>If you are trying to check out the head, type:</p>
-      <div class="code">svn co https://code.ecoinformatics.org/code/metacat/trunk metacat</div>
-      
-    <p>You should see a list of files as they check out.</p>
-    
-    <p>Note that you do not need to create the war file directly with a source installation
-    since the Ant build file has an "install" target that will build and deploy the war
-    for you.  See the <a href="#InstallingMetacat">Installing Metacat</a> for instructions.</p>
-
-
-<a name="InstallingMetacat"></a><div class="header1">Installing Metacat</div>
-  <p>This section is only for a new installation. If you are upgrading an existing Metacat, please skip
-  this section and go to the next one - <a href="#UpgradingMetacat">Upgrading Existing Metacat</a></p>
-  
-  <p>Tomcat will look for it's application files (war files) in a configured directory.  
-  This is typically the &lt;tomcat_home&gt;/webapps directory, but your instance of Tomcat may 
-  be configured to look in a different directory.  We will refer to your Tomcat application directory 
-  as &lt;tomcat_app_dir&gt;.</p>
-     
-  <a name="CreateMetacatDirs"></a><div class="header2">Create Metacat Directories</div>
-    <p>Metacat uses a base directory to store such things as store data and metadata,
-    temporary files and configuration backups.  This directory should be outside of the 
-    Tomcat application directory since the application directory gets wiped out during an
-    upgrade. Create the metacat utility base directory 
-    by typing:</p>
-      <div class="code">sudo mkdir <metacat_base_dir></div>
-    <p>(Typically <metacat_base_dir> is '/var/metacat'.)  Remember the directory you 
-    choose, since you will be asked to configure Metacat to point to it after startup.</p>
-    
-    <p>Change the ownership of the directory by typing:</p>   
-	  <div class="code">sudo chown -R &lt;tomcat_user&gt; /var/metacat</div>
-    <p>where &lt;tomcat_user&gt; is the user that will start Tomcat.  If you are 
-	starting Tomcat as the root user, you do not need to run the chown command.</p>
-	
-  <a name="InstallMetacatWar"></a><div class="header2">Install Metacat Binary (War)</div> 
-    <p>Copy the war file to Tomcat:</p>
-	  <div class="code">sudo cp knb.war &lt;tomcat_app_dir&gt;</div>
-  
-  <a name="InstallMetacatSource"></a><div class="header2">Install Metacat From Source</div> 
-    <p>You will need Apache Ant to do the build.  If you have not already 
-    installed Ant and you are running Ubuntu/Debian, you can get it by typing:</p>
-      <div class="code">sudo apt-get install ant</div>
-  
-    <p>Otherwise, you can get ant from
-    <a href="http://ant.apache.org/">The Apache Ant homepage</a></p>
-
-    <p>You should now have the Metacat source in a directory named "metacat" in your
-    code directory (We will refer to the metacat source directory as &lt;metacat_src_dir&gt;.
-       
-    <p>To prepare for the build, edit the file at:</p>
-      <div class="code">&lt;metacat_src_dir&gt;/build.properties</div> 
-    <p>Make sure that the "build.tomcat.dir" property is set to your tomcat installation
-    directory.  For instance:</p>
-      <div class="code">build.tomcat.dir=/usr/local/tomcat</div>
-    <p>Metacat will use some of the native Tomcat libraries during the build.</p>
-    
-    <p>Make sure that the "app.deploy.dir" property is set to your application deployment
-    directory.  For instance:</p>
-      <div class="code">app.deploy.dir=/usr/local/tomcat/webapps</div>
-    
-    <p>If your cvs user is something other than the user your are logged in as, you
-    will need to change the ${env.USER} part of the cvsroot property to be your cvs 
-    user.  For instance:</p>
-      <div class="code">cvsroot=:ext:cvs-user@cvs.ecoinformatics.org:/cvs</div>
-    <p> where your cvs user name is "cvs-user"</p> 
-    
-    <p>In the &lt;metacat_src_dir&gt;, run: </p>
-      <div class="code">ant clean install</div>
-      
-    <p>You will see the individual modules get built.  You will be prompted
-    for your cvs password several times.  You should see a "BUILD SUCCESSFUL"
-    message at the end.</p>
-    
-    <p>You should see a new file named knb.war in your application deployment directory.</div>
-	  
-  <a name="ApacheConfig"></a><div class="header2">Configure Apache</div> 
-    <p>You have the option of running Tomcat stand-alone or with with the Apache web
-    server.  Running with Apache is the more traditional setup since Apache is a 
-    more robust web server.  There are some initial setup steps to get Apache talking
-    to the Metacat application at the </p>
-	  <a href="./metacat-apache-config.html"> the Metacat Apache Configuration page</a></p>
-
-<a name="UpgradingMetacat"></a><div class="header1">Upgrading Existing Metacat</div>
-  <a name="protocol"></a>
-  <p>The following instructions are for upgrading an existing Metacat.
-  
-  <a name="UpgradeStopMetacat"></a><div class="header2">Stop the Running Metacat</div>
-   <p>To do this, login as the user that runs your tomcat server (often "tomcat"),
-   go to &lt;tomcat_home&gt;/bin and type:</p>
-   
-   <div class="code">./shutdown.sh</div>  
-  
-  <a name="UpgradeDownloadMetacat"></a><div class="header2">Download Latest Metacat Application</div>
-    <p>Browse to the 
-      <a href="http://knb.ecoinformatics.org/software/download.html">KNB Software Download Page</a>.
-      In the Metacat section, select the link that looks like:</p>
-	  <div class="code">metacat-bin-X.X.X.tar.gz</div>
-    <p>where X.X.X is the latest version of Metacat.  Choose to save the file locally.</p>
-    <p>Extract the Metacat package files by typing:</p>
-      <div class="code">tar -xvzf metacat-bin-X.X.X.tar.gz</div>
-    <p>You should see several files:</p>
-    
-    <ul>
-    <li>knb.war - the Metacat application web archive file.</li>
-    <li>knb - the web definition file used by Apache on ubuntu/debian Linux systems.</li>
-    <li>jk.conf - the JkMount configuration file used by Apache on ubuntu/debian Linux systems.</li>
-    <li>workers.properties - the workers definition file used by Apache on ubuntu/debian Linux systems.</li>
-    <li>tomcat5.5 - the Tomcat startup script for Tomcat 5.5 installed with apt-get on ubuntu/debian Linux systems.</li>
-    <li>authority - the optional LSID Server application web archive file.</li>
-    </ul>
-    
-    <p>The location where these files
-    were extracted will be refered to as the the &lt;metacat_package_dir&gt; for the remainder 
-    of this documentation.</p>
- 
-   <a name="UpgradeMetacatWar"></a><div class="header2">Upgrade Metacat Binary (War)</div> 
-    <p>Tomcat will look for it's application files (war files) in a configured directory.  
-    This is typically the &lt;tomcat_home&gt;/webapps directory, but your instance of Tomcat may 
-    be configured to look in a different directory.  We will refer to your Tomcat application directory 
-    as &lt;tomcat_app_dir&gt;.</p>
-    
-    <p>If desired, back up your existing war file with a date:</p>
-      <div class="code">sudo mv &lt;tomcat_app_dir&gt;/knb.war &lt;tomcat_app_dir&gt;/knb.war.&lt;yyyymmdd&gt;</div>
-    
-    <p>Copy the war file to the Tomcat applications directory:</p>
-	  <div class="code">sudo cp knb.war &lt;tomcat_app_dir&gt;</div>
-	<p>Remove (or rename) the existing application directory:</p>
-	  <div class="code">sudo rm -rf &lt;tomcat_home&gt;/webapps/knb</div>
-	  <p> or </p>
-	  <div class="code">sudo mv &lt;tomcat_home&gt;/webapps/knb &lt;tomcat_home&gt;/webapps/knb.&lt;yyyymmdd&gt;</div>
-	<p>Restart Tomcat:</p>  
-	  <div class="code">sudo /etc/init.d/tomcat5.5 restart</div>
-	<p>Tomcat will expand your war file into a new application directory at startup time.</p>
- 
-  <a name="UpgradeMetacatSource"></a><div class="header2">Upgrade Metacat From Source</div>
-    <p>The steps to upgrade Metacat from source are the same as installing from source.  See
-    the <a href="#InstallMetacatSource">Install Metacat From Source</a> section above.</p>
- 
-  <a name="RestartTomcat"></a><div class="header1">Restart Tomcat</div>
-    <p>Once you have successfully installed Metacat, there is one more step.  Tomcat
-    (and Apache if you have Tomcat integrated with it) must be restarted.  To do
-    this, login as the user that runs your tomcat server (often "tomcat"),
-    go to &lt;tomcat_home&gt;/bin and type: </p>
-   
-      <div class="code">./startup.sh</div>
-   
-    <p>In the Tomcat startup messages you should see something in the log file like:</p>
-   
-      <div class="code">Metacat: [WARN]: Metacat (1.8.0) initialized. [edu.ucsb.nceas.metacat.MetaCatServlet]</div>
-     
-    If you see that message Tomcat has successfully loaded the Metacat servlet.
-    Next, try to run your new servlet.  Go to a web browser and type:</p>
-   
-      <div class="code">http://yourserver.yourdomain.com/yourcontext/</div>
-     
-    <p>You should substitute your context name for "yourcontext" in the url above.
-    If everything is working correctly, you should see a query page followed
-    by an empty result set.  Note that if you do not have Tomcat integrated with
-    Apache you will probably have to type</p>
-   
-    <div class="code">http://yourserver.yourdomain.com:8080/yourcontext/</div>
-
-  <a name="UpgradeTroubleshooting"></a><div class="header2">Troubleshooting</div>
-  <p>If you see something like: 
-  
-    <div class="code">java.lang.InternalError: Can't connect to X11 window server using 'yourservanme:0.0' as the value of the DISPLAY variable.</div>
-  
-  <p>You should add this line: </p>
-  
-    <div class="code">JAVA_OPTS="-Djava.awt.headless=true $JAVA_OPTS"</div> 
-    
-  <p>at the first line of the catalina.sh file in the tomcat bin directory. The reason is that 
-  GeoServer uses X11 windows to draw graphics.</p>
-  
-  <a name="UpgradeConfigureMetacat"></a><div class="header2">Configure Metacat</div>
-  <p>Once you see the Metacat configuration screen, you can follow the instructions in the 
-  <a href="./metacat-configure.html"> Configuring Metacat Section</a> 
-  to complete the internal configuration of Metacat.</p>
-
-<a name="Registry"></a><div class="header1">Web Based Registry</div>
-  <p>The registry allows users to upload simple metadata documents directly from the web.  See the separate 
-  <a href="registry_installation.html">Registry Installation Guide</a>.</p><br/><br/>
-</body>
-</html>

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===================================================================
--- docs/user/metacatdb.html	(revision 5315)
+++ docs/user/metacatdb.html	(nonexistent)
@@ -1,68 +0,0 @@
-<!--
-  * Metacatdb.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Metacat Database</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./metacat.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./metacatdom.html">Next</a>
-      </td>
-    </tr>
-  </table>
-
-  <P>Metacat's backend database stores the structure and data of any arbitrary 
-  XML document. The Metacat database uses the DOM 
-  approach to store XML documents as a hierarchy of nodes. All nodes are stored 
-  as records in database tables. The hierarchical relationship between the nodes 
-  is saved to preserve the structure of the documents.</p>
-  
-  <p>The database Entity Relationship Diagram (ERD) currently looks like this:</p>
-  <img alt="Entity Relationship Diagram of the Metacat Database" src="metacatdb.gif">
-  <br><br>
-  <b>Table Descriptions</b>
-  <ul>
-    <li><b>xml_documents</b> contains document level information.  It
-    stands as a tie in to xml_nodes with the rootnodeid field.</li>
-    <li><b>xml_nodes</b> contains all of the data needed to recreate an
-    XML document that has been inserted into the system.  Each document's xml tree
-    is represented by the node pointers in the table.  </li>
-    <li><b>xml_index</b> contains indexing information for the paths in 
-    xml_nodes.  This is data that has been denormalized for performance reasons.  
-    xml_index allows the fast searching of paths within an xml document.</li>
-    <li><b>xml_revisions</b> contains the document information (including the 
-    rootnode pointer) to any document that has been deleted (either by an explicit
-    delete or by an update).  This ensures that a complete lineage of any document
-    is traced.</li>
-    <li><b>xml_replication</b> contains the list of Metacat servers that this
-    server replicates to or from.</li>
-    <li><b>xml_relation</b> contains any relation information inserted by a 
-    <a href="./packages.html">Package</a> document.</li>
-    <li><b>xml_access</b> contains all <a href="acontrol.html">Access Control List</a> (ACL) information 
-    relevent to a document.</li>
-    <li><b>xml_catalog</b>  contains catalog information that represents DTDs 
-    and XSL stylesheets that are registered with the system.</li>
-  </ul>
-  
-  <br>
-  <a href="./metacat.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./metacatdom.html">Next</a>
-  </BODY>
-</HTML>
-

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--- docs/user/metacatapi.html	(revision 5315)
+++ docs/user/metacatapi.html	(nonexistent)
@@ -1,431 +0,0 @@
-<!--
-  * Metacatapi.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Metacat High Level API</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./metacatout.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./packages.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <p>
-      <b>Multiple client interface</b> <br>
-      Since Metacat Servlet is a subclass of HttpServlet, this allows any client
-      to communicate with Metacat by essentially passing a URL with embedded
-      servlet parameters.
-      Metacat Servlet provides an HTTP Interface and can handle GET and POST 
-      requests. HTTP requests are sent from the the Client application and contain 
-      a number of parameters. These parameters, in form of name/value pairs, provide 
-      input data for the Servlet and also provide the Servlet any extra information it 
-      needs to handle the request. </p>
-  <P> <b>Extensions of HttpServlet</b> <br>
-      Metacat Server adds the functionality for writing, quering, and reading of 
-      XML stored in the Metacat Database as well functions for validating and 
-      transforming XML documents. </p>
-  <b>MetacatServlet Parameters</b>
-  <table border="1">
-    <tr>
-      <td><b>Action</b></td>
-      <td><b>Supplemental Parameters</b></td>
-      <td><b>Description</b></td>
-    </tr>
-    <tr>
-      <td>login</td>
-      <td>
-        <ul>
-          <li>username - the user's login name</li>
-          <li>password - the user's password</li>
-        </ul>
-      </td>
-      <td>Log the user in.</td>
-    </tr>
-    <tr>
-      <td>logout</td>
-      <td>none</td>
-      <td>Log the current user out and destroy the associated session.</td>
-    </tr>
-    <tr>
-      <td>query</td>
-      <td>
-        <ul>
-          <li>returndoctype - the doctype that you wish to use for your 
-          <a href="./packages.html">Package View</a></li>
-          <li>qformat - the format that you wish to return the resultset in.  
-          Possible values are 'html' or 'xml'.</li>
-          <li>querytitle - OPTIONAL - the title of the query</li>
-          <li>doctype - OPTIONAL - if doctype is specified, the search is limited
-          only to the doctype(s) specified.</li>
-          <li>returnfield - a custom field to be returned by any hit document.  
-          This is explained in more detail in <a href="./metacatquery.html">
-          Queries and Results</a>.</li>
-          <li>operator - the boolean operator to apply to the query - Possible
-          values are: UNION or INTERSECT</li>
-          <li>searchmode - the type of search to be performed.  Possible values
-          are: contains, starts-with, ends-with, equals, isnot-equal, greater-than,
-          less-than, greater-than-equals, less-than-equals.</li>
-          <li>anyfield - a freetext search variable.  A value placed in this 
-          parameter will be searched for in any document in any node.</li>
-        </ul>
-      </td>
-      <td>Perform a free text query.</td>
-    </tr>
-    <tr>
-      <td>squery</td>
-      <td>
-      <ul>
-        <li>query - the text of the pathquery document that is being sent to the
-        server</li>
-      </ul>
-      </td>
-      <td>Perform a structured query.</td>
-    </tr>
-    <tr>
-      <td>spatial_query</td>
-      <td>
-      <ul>
-        <li>xmax - max x spacial coordinate</li>
-        <li>ymax - max y spacial coordinate</li>
-        <li>xmin - min x spacial coordinate</li>
-        <li>ymin - min y spacial coordinate</li>
-      </ul>
-      </td>
-      <td>Perform a spatial query.  These queries may include any of the 
-          queries supported by the WFS / WMS standards.</td>
-    </tr>
-    <tr>
-      <td>read</td>
-      <td>
-      <ul>
-        <li>docid - the docid of the document to read</li>
-        <li>qformat - the format to return the document in.  Possible values 
-        are: html, xml</li>
-      </ul>
-      </td>
-      <td>Get docid from the database and return it in qformat form.</td>
-    </tr>
-    <tr>
-      <td>readinlinedata</td>
-      <td>
-      <ul>
-        <li>inlinedataid - the id of the inline data to read</li>
-      </ul>
-      </td>
-      <td>Read inline data only.</td>
-    </tr>
-    <tr>
-      <td>insert</td>
-      <td>
-        <ul>
-          <li>docid - the user defined docid to assign to the new XML document.</li>
-          <li>doctext - the text of the XML document to insert</li>
-        </ul>
-      </td>
-      <td>Insert an XML document into the database.</td>
-    </tr>
-    <tr>
-      <td>insertmultipart</td>
-      <td>
-        <ul>
-          <li>docid - the user defined docid to assign to the new XML document.</li>
-          <li>doctext - the text of the XML document to insert</li>
-        </ul>
-      </td>
-      <td>insert an xml document into the database using multipart encoding.</td>
-    </tr>
-    <tr>
-      <td>update</td>
-      <td>
-      <ul>
-        <li>docid - the docid of the document to update</li>
-        <li>doctext - the text with which to update the XML document</li>
-      </ul>
-      </td>
-      <td>Overwrite an XML document with a new one and give the new one 
-          the same docid but with next revision number.</td>
-    </tr>
-    <tr>
-      <td>upload</td>
-      <td>
-      <ul>
-        <li>docid - the docid of the data document to upload</li>
-        <li>datafile - the data document to upload</li>
-      </ul>
-      </td>
-      <td>Upload (insert or update) a data document into metacat. Data files are stored on 
-               metacat and may be in any format (binary or text), but they are all
-               treated as if they were binary.</td>
-    </tr>
-    <tr>
-      <td>delete</td>
-      <td>
-        <ul>
-          <li>docid - the docid of the document to delete</li>
-        </ul>
-      </td>
-      <td>Delete the specified docid from the database.</td>
-    </tr>
-    <tr>
-      <td>setaccess</td>
-      <td>
-        <ul>
-          <li>docid - the docid of the document whose access we want to change</li>
-          <li>principal - the user or group whose permissions want to change</li>
-          <li>permission - the permission we want to set (read, write, all)</li>
-          <li>permType - the type of permission to set (allow, deny)</li>
-          <li>permOrder - the order to apply the permission (allowFirst, denyFirst)</li>
-        </ul>
-      </td>
-      <td>Change access permissions for a user on a document.</td>
-    </tr>
-    <tr>
-      <td>validate</td>
-      <td>
-      <ul>
-        <li>docid - the docid of the document to validate</li>
-        <li>valtext - the DTD by which to validate this document</li>
-      </ul>
-      </td>
-      <td>Validate docid against its DTD.</td>
-    </tr>
-    <tr>
-      <td>getaccesscontrol</td>
-      <td>
-      <ul>
-        <li>docid - the docid of the document to get the ACL for</li>
-      </ul>
-      </td>
-      <td>Get ACL for document with that docid</td>
-    </tr>
-    <tr>
-      <td>getprincipals</td>
-      <td>none</td>
-      <td>Get all users and groups in the current authentication schema</td>
-    </tr>
-    <tr>
-      <td>getdoctypes</td>
-      <td>none</td>
-      <td>Get all doctypes currently available in Metacat Catalog System.</td>
-    </tr>
-    <tr>
-      <td>getdtdschema</td>
-      <td>
-        <ul>
-          <li>doctype - the doctype which DTD or XMLSchema file to read.</td>
-        </ul>
-      </td>
-      <td>Read DTD or XMLSchema file for the specified doctype.</td>
-    </tr>
-    <tr>
-      <td>getdataguide</td>
-      <td>
-        <ul>
-          <li>doctype - the doctype for which to get the data guide</li> <br>
-          <i><b> Deprecated. </b></i> Use getdtdschema action instead.
-        </ul>
-      </td>
-      <td>Read a dataguide for doctype.</td>
-    </tr>
-    <tr>
-      <td>getlastdocid</td>
-      <td>
-        <ul>
-          <li>username - the user's login name which last docid to get.</td>
-        </ul>
-      </td>
-      <td>Get the latest docid with rev number used by user.</td>
-    </tr>
-    <tr>
-      <td>getalldocids</td>
-      <td>
-        <ul>
-          <li>scope - a string used to match a range of docids in a SQL LIKE statement.</td>
-        </ul>
-      </td>
-      <td>retrieves a list of all docids registered with the system.</td>
-    </tr>
-    <tr>
-      <td>isregistered</td>
-      <td>
-        <ul>
-          <li>docid - the docid of the document to check for.</td>
-        </ul>
-      </td>
-      <td>checks if an individual document exists in either the xml_documents
-          or xml_revisions tables.</td>
-    </tr>
-    <tr>
-      <td>getrevisionanddoctype</td>
-      <td>
-        <ul>
-          <li>docid - the docid of the document to check for.</td>
-        </ul>
-      </td>
-      <td>Return the revision and doctype of a document. The output is String 
-      that looks like "rev;doctype"</td>
-    </tr>
-    <tr>
-      <td>getversion - get Metacat version.</td>
-      <td>none</td>
-      <td>Returns the current version of Metacat as XML.</td>
-    </tr>
-    <tr>
-      <td>protocoltest</td>
-      <td>
-        <ul>
-          <li>url - the url to test against the protocol handler</li>
-        </ul>
-      </td>
-      <td>Test the protocol handlers installed for metacat:// URLs.</td>
-    </tr>
-    <tr>
-      <td>export</td>
-      <td>
-        <ul>
-          <li>docid - the docid of the package you wish to export</li>
-        </ul>
-      </td>
-      <td>
-        Exports a data package in a zip file.
-      </td>
-    </tr>
-    <tr>
-      <td>getlog</td>
-      <td>
-        <ul>
-            <li>ipaddress - the internet protocol address for the event</li>
-            <li>principal - the principal for the event (a username, etc)</li>
-            <li>docid - the identifier of the document to which the event applies</li>
-            <li>event - the string code for the event</li>
-            <li>start - beginning of date range for query</li>
-            <li>end - end of date range for query</li>
-        </ul>
-      </td>
-      <td>Print a report from the Metacat event log.</td>
-    </tr>
-    <tr>
-      <td>getloggedinuserinfo</td>
-      <td>none</td>
-      <td>Get user info for the currently logged in user.</td>
-    </tr>
-  </table>
-  
-  <br>
-  <b><a href="./replication.html">MetacatReplication</a> Parameters</b>
-    <table border="1">
-    <tr>
-      <td><b>Action</b></td>
-      <td><b>Supplemental Parameters</b></td>
-      <td><b>Description</b></td>
-    </tr>
-    <tr>
-      <td>forcereplicate</td>
-      <td>
-        <ul>
-          <li>server - The server to which this document is being sent</li>
-          <li>docid - The docid of the document to send</li>
-          <li>dbaction - DEFAULTS TO UPDATE - The action to perform on the 
-          document.  INSERT or UPDATE.</li>
-        </ul>
-      </td>
-      <td>Force this server to get docid from the remote host.</td>
-    </tr>
-    <tr>
-      <td>getall</td>
-      <td>none</td>
-      <td>Forces the local server to check all known servers for updated
-      documents.</td>
-    </tr>
-    <tr>
-      <td>getcatalog</td>
-      <td>none</td>
-      <td>Sends the contents of the xml_catalog table encoded in XML.</td>
-    </tr>
-    <tr>
-      <td>getlock</td>
-      <td>
-        <ul>
-          <li>docid - the docid to get the lock for</li>
-          <li>updaterev - the revision number of docid</li>
-        </ul>
-      </td>
-      <td>Request a lock on docid.</td>
-    </tr>
-    <tr>
-      <td>gettime</td>
-      <td>none</td>
-      <td>Return the local time on this server.</td>
-    </tr>
-    <tr>
-      <td>servercontrol</td>
-      <td>
-        <ul>
-          <li>subaction - The replication control to be performed.  Possible
-          values: 
-            <ul>
-              <li>add - add a new server to the replication list</li>
-              <li>delete - remove a server from the replication list</li>
-              <li>list - list all of the servers currently in the server list</li>
-            </ul>
-          <li>replicate - a boolean flag (1 or 0) which determines if this
-          server is to copy files from the newly added server.</li>
-          <li>server - the server to add/delete</li>
-        </ul>
-      </td>
-      <td>Perform subaction on the Replication daemon.</td>
-    </tr>
-    <tr>
-      <td>read</td>
-      <td>
-        <ul>
-          <li>docid - the docid to read</li>
-        </ul>
-      </td>
-      <td>Sends docid to the remote host.</td>
-    </tr>
-    <tr>
-      <td>start</td>
-      <td>
-        <ul>
-          <li>rate - DEFAULTS TO 1000 - The rate (in seconds) at which you want
-          the replication daemon to check for updated documents.  The value
-          cannot be less than 30.</li>
-        </ul>
-      </td>
-      <td>Start the Replication daemon with a time interval of deltaT.</td>
-    </tr>
-    <tr>
-      <td>stop</td>
-      <td>none</td>
-      <td>Stop the Replication daemon.</td>
-    </tr>
-    <tr>
-      <td>update</td>
-      <td>none</td>
-      <td>Send a list of all documents on the local server along with their
-      revision numbers.</td>
-    </tr>
-  </table>
-  <br>
-  <a href="./metacatout.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./packages.html">Next</a>
-</BODY>
-</HTML>
-

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--- docs/user/harvester.html	(revision 5315)
+++ docs/user/harvester.html	(nonexistent)
@@ -1,680 +0,0 @@
-<!--
-  * harvester.html
-  *
-  *      Authors: Duane Costa
-  *    Copyright: 2004 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis,
-  *               and the University of New Mexico.
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2004 April 9
-  *      Version: 
-  *    File Info: '$ '
-  * 
-  * 
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat Harvester</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2">
-        <p class="label">Metacat Harvester</p>
-      </td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./properties.html">Back</a> | 
-        <a href="./metacattour.html">Home</a> | 
-        <a href="./lsid_authority.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <h4>Introduction</h4>
-The Metacat Harvester (henceforth referred to as "Harvester") is a
-program that automates the retrieval of EML documents from one or more sites
-and their subsequent upload (insert or update) to Metacat. Harvester uses pull
-technology to retrieve and upload documents to Metacat on a regularly
-scheduled basis.
-<P>
-Although Harvester is included with a Metacat installation (beginning with
-Metacat version 1.4.0), it is an extention to Metacat's functionality
-that may be used optionally.
-</P>
-  <h4>Definitions</h4>
-The following table defines a number of terms that are useful in discussing
-Harvester and its features.
-  <br><br>
-  <table border="1">
-    <tr>
-      <td><b>Term</b></td>
-      <td><b>Definition</b></td>
-    </tr>
-    <tr>
-      <td>Harvester</td>
-      <td>The Harvester program, a Java application that is bundled with the
-          Metacat distribution. When a user installs Metacat on a system, 
-          the Harvester program is automatically included in the 
-          installation.
-      </td>
-    </tr>
-    <tr>
-      <td>Harvester Administrator</td>
-      <td>The individual who installs and manages Harvester. Typically, this
-          would be the same individual who installs and manages Metacat at a
-          given installation.
-      </td>
-    </tr>
-    <tr>
-      <td>Harvest Site</td>
-      <td>A location from which Harvester can retrieve EML documents. A given 
-          Harvester can retrieve documents from any number of different 
-          Harvest Sites.
-      </td>
-    </tr>
-    <tr>
-      <td>Harvest</td>
-      <td>The act (by Harvester) of visiting a Harvest Site, retrieving a
-          number of EML documents, and inserting or updating the documents to 
-          Metacat.
-      </td>
-    </tr>
-    <tr>
-      <td><a name="HarvestList" >Harvest List</a></td>
-      <td>An XML document that lists a set of EML documents to be harvested. The
-          Harvest List must conform to an XML Schema, 
-          <a href="../../lib/harvester/harvestList.xsd">harvestList.xsd</a>.
-      </td>
-    </tr>
-    <tr>
-      <td>Site Contact</td>
-      <td>The individual at a particular Harvest Site who registers with 
-          Harvester, composes a Harvest List, and periodically prepares
-          the site's EML documents for retrieval and upload to Metacat.
-      </td>
-    </tr>
-    <tr>
-      <td>Harvest List URL</td>
-      <td>A URL to the Harvest List, as specified by the Site Contact. 
-          Each Harvest Site corresponds to a Harvest List URL. Harvester 
-          uses the URL to locate and read a site's Harvest List.
-      </td>
-    </tr>
-    <tr>
-      <td>Document URL</td>
-      <td>A URL to an EML document, as specified in the Harvest List.
-          The Harvest List may contain any number of Document URLs. Each
-          Document URL provides a locator to a document to be harvested.
-      </td>
-    </tr>
-    <tr>
-      <td>Harvester Registration Page</td>
-      <td>A web page that provides a means for a Site Contact
-          to register with Harvester to schedule regular harvests from the
-          site. Registration involves logging in and then specifying various
-          settings for the Harvest Site, such as the Harvest List URL, the 
-          harvest frequency, and the email address of the Site Contact.
-      </td>
-    </tr>
-  </table>
-  <h4>Managing Harvester</h4>
-  Harvester is managed by the Harvester Administrator. Typically, the same
-  individual who manages a Metacat server would also act as the Harvester
-  Administrator. The responsibilities of the Harvester Administrator include:
-    <ul>
-      <li><a href="#Configuring Harvester">Configuring Harvester</a></li>
-      <li><a href="#Running Harvester">Running Harvester</a></li>
-      <li><a href="#Reviewing Harvester">Reviewing Harvester reports to 
-      the Harvester Administrator</a></li>
-    </ul>
-  <h5><a name="Configuring Harvester">Configuring Harvester</a></h5>
-  <p>Harvester must be configured to interact with a working Metacat
-     installation. Thus, a Metacat installation that has been properly
-     configured and installed is a pre-requisite to running Harvester.
-     Additionally, Harvester has a number of settable properties that
-     control its behavior. All Harvester configuration information is managed 
-     in a single file, 
-     <a href=../../lib/metacat.properties>metacat.properties</a>, 
-     located at:
-  <pre>      METACAT_HOME/lib/metacat.properties</pre>
-     where METACAT_HOME is the top-level directory that Metacat is 
-     installed in. 
-  </p>
-  <p>Harvester properties are grouped together in 
-     <a href=../../lib/metacat.properties>metacat.properties</a>, beginning
-     after the comment line:
-  <pre><code>      # Harvester properties</code></pre>
-  </p>
-  <p>The Harvester Administrator should edit 
-     <a href=../../lib/metacat.properties>metacat.properties</a>, 
-     setting appropriate values for the <code><b>harvesterAdministrator</b></code>
-     property, the <code><b>smtpServer</b></code> property, and possibly other 
-     properties. The following table is a summary of each property and its function.
-  </p>
-  <table border="1">
-    <tr>
-      <td><b>Property</b></td>
-      <td><b>Description</b></td>
-      <td><b>Possible or default value</b></td>
-    </tr>
-    <tr>
-      <td>connectToMetacat</td>
-      <td>This property determines whether Harvester should connect to
-          Metacat to upload documents. It should be set to <code>true</code>
-          under most circumstances. Setting this property to <code>false</code>
-          can be useful for testing whether Harvester is able to retrieve 
-          documents from a site without actually connecting to Metacat to 
-          upload the documents.</td>
-      <td><code>true</code> | <code>false</code><br>
-          Default: <code>true</code>
-    </tr>
-    <tr>
-      <td>delay</td>
-      <td>The number of hours that Harvester will wait before beginning its
-          first harvest. For example, if Harvester is run at  1:00 p.m., and
-          the delay is set to 12, Harvester will begin its first harvest at 
-          1:00 a.m.</td>
-      <td>Default: 0</td>
-    </tr>
-    <tr>
-      <td>harvesterAdministrator</td>
-      <td>The email address of the Harvester Administrator. Harvester will
-          send email reports to this address after every harvest. You may
-          enter multiple email addresses by separating each address with
-          a comma or semicolon, for example, "name1@abc.edu,name2@abc.edu".
-      </td>
-      <td>An email address, or multiple email addresses separated by commas
-          or semi-colons</td>
-    </tr>
-    <tr>
-      <td>logPeriod</td>
-      <td>The number of days that Harvester should retain log entries of harvest
-          operations in the database. Harvester log entries record information
-          such as which documents were harvested, from which sites, and
-          whether any errors were encountered during the harvest. Log entries
-          older than <code>logPeriod</code> number of days are purged from the 
-          database at the end of each harvest.</td>
-      <td>Default: 90</td>
-    </tr>
-    <tr>
-      <td>maxHarvests</td>
-      <td>The maximum number of harvests that Harvester should execute before
-          shutting down. When the Harvester program is executed, it will
-          continue running until it has executed <code>maxHarvests</code>
-          number of harvests and then the program will terminate. If
-          the value of <code>maxHarvests</code> is set to 0 or a negative
-          number, it will be ignored and Harvester will execute indefinitely.
-          </td>
-      <td>Default: 0</td>
-    </tr>
-    <tr>
-      <td>period</td>
-      <td>The number of hours between harvests. Harvester will run a new
-          harvest every <code>period</code> number of hours, until the 
-          <code>maxHarvests</code> number of harvests have been run, or
-          indefinitely if <code>maxHarvests</code> is set to a value of
-          0 or a negative number.
-      <td>Default: 24</td>
-    </tr>
-    <tr>
-      <td>smtpServer</td>
-      <td>The SMTP server that Harvester uses for sending email messages
-          to the Harvester Administrator and to Site Contacts.</td>
-      <td>A host name, for example: <code>somehost.institution.edu</code>
-          <br><br>
-          Default: <code>localhost</code>
-          <br><br>
-          Note that the default value will only work if the Harvester 
-          host machine has been configured as a SMTP server.
-      </td>
-    </tr>
-    <tr>
-      <td>Harvester Operation Properties (GetDocError, GetDocSuccess, etc.)</td>
-      <td>This group of properties is used by Harvester to report information
-          about the operations it performs for inclusion in log
-          entries and email messages. Under most circumstances the values 
-          of these properties should not be modified.</td>
-      <td>&nbsp;</td>
-    </tr>
-  </table>
-  <br>
-  <h5><a name="Running Harvester">Running Harvester</a></h5>
-  After Harvester has been appropriately 
-  <a href="#Configuring Harvester">configured</a>, 
-  it can be run in either of two ways: (A) in a command window, or, (B)
-  as a servlet. If you wish only to test that Harvester is functioning, 
-  or if you expect to use Harvester infrequently, it may desirable to run it from a 
-  command window. However, under most circumstances you will want Harvester to 
-  run continuously as a background servlet process. This eliminates the
-  need to keep a command window continuously open while Harvester is running.
-  Both of these procedures are described below.
-  <ul>
-  <li> (A) Running Harvester in a Command Window
-  <ol>
-  <li>Open a system command window or terminal window.</li>
-  <li>Set the METACAT_HOME environment variable to the value of the Metacat
-      installation directory. Some examples follow:
-      <ul>
-        <li>On Windows:
-        <pre>set METACAT_HOME=C:\somePath\metacat</pre></li>
-        <li>On Linux/Unix (bash shell):
-        <pre>export METACAT_HOME=/home/somePath/metacat</pre></li>
-      </ul>
-  <li>cd to the following directory:
-      <ul>
-        <li>On Windows:
-        <pre>cd %METACAT_HOME%\lib\harvester</pre></li>
-        <li>On Linux/Unix:
-        <pre>cd $METACAT_HOME/lib/harvester</pre></li>
-      </ul>
-  <li>Run the appropriate Harvester shell script, as determined by the
-      operating system:
-      <ul>
-        <li>On Windows:
-        <pre>runHarvester.bat</pre></li>
-        <li>On Linux/Unix:
-        <pre>sh runHarvester.sh</pre></li>
-      </ul>
-  </li>
- </ol>
-  <p>The Harvester application will start executing. It will begin its first
-  harvest after <code><b>delay</b></code> number of hours (as specified in the
-  <a href=../../lib/metacat.properties>metacat.properties</a>
-  file). The application will continue running a new harvest every
-  <code><b>period</b></code> number of hours until a <code><b>maxHarvests</b></code>
-  number of harvests have been completed (if <code><b>maxHarvests</b></code> is set 
-  to a value greater than 0), or until you interrupt the process by hitting CTRL/C 
-  in the command window.
-  </p>
-  </li>
-  <li> (B) Running Harvester as a Servlet
-  <ol>
-  <li>Edit the file in your Metcat installation, <code>lib/web.xml.<em>tomcatN</em></code>, where <em>tomcatN</em> corresponds to the
-  version of Tomcat you are running. For example, if you are running Tomcat 5,
-  edit file <code>lib/web.xml.tomcat5</code>.</li>
-  <li>Remove the comment symbols around the HarvesterServlet entry, so that:
-  <pre><code>
-  &lt;!--
-  &lt;servlet>
-  &lt;servlet-name>HarvesterServlet&lt;/servlet-name>
-  &lt;servlet-class>edu.ucsb.nceas.metacat.harvesterClient.HarvesterServlet&lt;/servlet-class>
-  &lt;init-param>
-    &lt;param-name>debug&lt;/param-name>
-    &lt;param-value>1&lt;/param-value>
-  &lt;/init-param>
-  &lt;init-param>
-    &lt;param-name>listings&lt;/param-name>
-    &lt;param-value>true&lt;/param-value>
-  &lt;/init-param>
-  &lt;load-on-startup>1&lt;/load-on-startup>
-  &lt;/servlet>
-  --&gt;
-  </code></pre>
-  is changed to:
-  <pre><code>
-  &lt;servlet>
-  &lt;servlet-name>HarvesterServlet&lt;/servlet-name>
-  &lt;servlet-class>edu.ucsb.nceas.metacat.harvesterClient.HarvesterServlet&lt;/servlet-class>
-  &lt;init-param>
-    &lt;param-name>debug&lt;/param-name>
-    &lt;param-value>1&lt;/param-value>
-  &lt;/init-param>
-  &lt;init-param>
-    &lt;param-name>listings&lt;/param-name>
-    &lt;param-value>true&lt;/param-value>
-  &lt;/init-param>
-  &lt;load-on-startup>1&lt;/load-on-startup>
-  &lt;/servlet>
-  </code></pre>
-  Save the edited file.
-  </li>
-  <li>Shutdown Tomcat.</li>
-  <li>Redeploy Metacat by running the following two ant commands from the top-level
-  directory of your Metacat installation:
-  <code><pre>
-  ant cleanweb
-  ant install</code></pre>
-  </li>
-  <li>Restart Tomcat.</li>
- </ol>
-  <p>About thirty seconds after you restart Tomcat, the Harvester servlet will 
-  start executing. It will begin its first
-  harvest after <code><b>delay</b></code> number of hours (as specified in the
-  <a href=../../lib/metacat.properties>metacat.properties</a>
-  file). The servlet will continue running a new harvest every
-  <code><b>period</b></code> number of hours until a <code><b>maxHarvests</b></code>
-  number of harvests have been completed (if <code><b>maxHarvests</b></code> is set
-  to a value greater than 0), or until Tomcat shuts down.
-  </p>
-  </li>
-   <h5><a name="Reviewing Harvester">
-  Reviewing Harvester Reports to the Harvester Administrator</a></h5>
-  <P>
-  After every harvest, Harvester will send an email report to the Harvester
-  Administrator detailing the operations that were performed during the
-  harvest. The report will contain information about each of the Harvest Sites
-  that were harvested from, such as which EML documents were
-  harvested and whether any errors were encountered.
-  </P>
-  <p>
-  The harvest report will contain a list of log entries, where each log entry
-  describes an operation that was performed by Harvester. Log entries that
-  show a status value of 1 indicate that an error occurred during the
-  operation, while those that show a status value of 0 indicate that the
-  operation was completed successfully.
-  </p>
-  <P>The Harvester Administrator should review the report, paying particularly 
-  close attention to any errors that are reported and to the accompanying error
-  messages that are displayed. When errors are reported at
-  a particular site, the Harvester Administrator should contact the Site
-  Contact to determine the source of the error and its resolution. See 
-  <a href=#Reviewing>Reviewing Harvester Reports to the Site Contact</a> for a
-  description of common sources of errors at a Harvest Site.
-  </P>
-  <p>Errors that are independent of a particular site may indicate a problem 
-  with Harvester itself, Metacat, or the database connection. Refer to the
-  error message to determine the source of the error and its resolution.
-  </p>
-  <h4>Managing a Harvest Site</h4>
-  A Harvest Site is managed by a Site Contact.
-  The responsibilities of a Site Contact fall into the following categories:
-    <ul>
-      <li><a href=#Registering>Registering with Harvester</a></li>
-      <li><a href=#Composing>Composing a Harvest List</a></li>
-      <li><a href=#Preparing>Preparing EML Documents for harvest</a></li>
-      <li><a href=#Reviewing>Reviewing Harvester reports to the Site Contact</a></li>
-    </ul>
-    <h5><a name="Registering">Registering with Harvester</a></h5>
-  <p>
-  A Site Contact registers a site with Harvester by logging in to the
-  Harvester Registration page and entering several items of information
-  that Harvester needs to know about the site.
-  </p>
-  <ol>
-    <li>Logging in to the Harvester Registration Page
-  <p>
-  The Harvester Registration page is accessed from Metacat. For example, if
-  the Metacat server that you wish to register with resides at the following 
-  URL:
-  <pre>  http://somehost.somelocation.edu:8080/knb/index.jsp</pre>
-  then the Harvester Registration page would be accessed at:
-  <pre>  http://somehost.somelocation.edu:8080/knb/style/skins/knb/harvesterRegistrationLogin.html</pre>
-  </p>
-  <p>
-  After bringing up this page in your browser, login to your Metacat account 
-  by entering your username, organization, and password. For example:
-      <table bgcolor="#ffffff" border="0" cellpadding="2" width='100%' >
-        <tr > 
-          <td colspan=3 align=center >&nbsp;</td> 
-        </tr>
-        <tr > 
-          <td colspan=3 align=center >
-            <font face=verdana size=1%>
-              <b>Please  Enter Username, Organization, and Password </b>
-            </font>
-          </td> 
-        </tr>
-        <tr>
-          <td width='10%'> &nbsp;</td>
-          <td width="25%" bgcolor="#4682b4">
-            <p align="center">
-            <font color="white" face=verdana size=2%>
-            <b>Username</b>
-            </font>
-          </td>
-          <td><p><input type="text" name="uid" value="jdoe" maxlength="100" size="28"></td>
-        </tr>
-        <tr>
-          <td width='10%'> &nbsp;</td>
-          <td width="25%" bgcolor="#4682b4">
-            <p align="center">
-            <font color="white" face=verdana size=2%>
-            <b>Organization</b>
-            </font>
-          </td>
-          <td>
-            <input type="radio" name="o" value="NCEAS" checked>NCEAS
-            <input type="radio" name="o" value="LTER">LTER
-            <input type="radio" name="o" value="NRS">NRS
-            <br>
-            <input type="radio" name="o" value="PISCO">PISCO
-            <input type="radio" name="o" value="OBFS">OBFS
-            <input type="radio" name="o" value="Unaffiliated">Unaffiliated
-        </tr>
-        <tr>
-          <td width='10%'> &nbsp;</td>
-          <td bgcolor="#4682b4">
-            <p align="center">
-            <font color="white" face=verdana size=2%>
-            <b>Password</b>
-            </font>
-          </td>
-          <td><p><input type="password" name="passwd" value="*******" maxlength="60" size="28">
-          </td>
-        </tr>
-        <tr> 
-          <td colspan=3 align=center >&nbsp;</td>
-        </tr>
-      </table>
-  In some cases, a Site Contact may need to login to an anonymous account
-  rather than his or her personal account. For example, a LTER Information 
-  Manager may need to login to a dedicated account, named with a three-letter 
-  acronym, that has been set up for the LTER site. The username
-  "GCE" would be used by the LTER Information Mangager at the GCE (Georgia 
-  Coastal Ecosystems) site.
-  </p>
-    </li>
-    <li>Registering with Harvester
-  <p>
-  After logging in, you will be presented with a web form that prompts you
-  to enter information about your site and how often you want to schedule
-  harvests at your site. For example:
-      <table bgcolor="#ffffff" border="0" cellpadding="2" width='100%' >
-        <tr > 
-          <td colspan=3 align=center >&nbsp;</td> 
-        </tr>
-        <tr > 
-          <td colspan=3 align=center >
-            <font face=verdana size=1%>
-              <b>Metacat Harvester Registration </b>
-            </font>
-          </td> 
-        </tr>
-        <tr>
-          <td width='10%'> &nbsp;</td>
-          <td width="25%" bgcolor="#4682b4">
-            <p align="center">
-            <font color="white" face=verdana size=2%>
-            <b>Email address:</b>
-            </font>
-          </td>
-          <td><p><input type="text" size="55" name="uid" value="myname@institution.edu" maxlength="100" size="28"></td>
-        </tr>
-        <tr>
-          <td width='10%'> &nbsp;</td>
-          <td bgcolor="#4682b4">
-            <p align="center">
-            <font color="white" face=verdana size=2%>
-            <b>Harvest List URL:</b>
-            </font>
-          </td>
-          <td><p><input type="text" size="55" name="passwd" value="http://somehost.institution.edu/~myname/harvestList.xml" maxlength="60" size="28">
-          </td>
-        </tr>
-        <tr> 
-          <td colspan=3 align=center >&nbsp;</td>
-        </tr>
-        <tr>
-          <td width='10%'> &nbsp;</td>
-          <td bgcolor="#4682b4">
-            <p align="center">
-            <font color="white" face=verdana size=2%>
-            <b>Harvest Frequency (1-99):</b>
-            </font>
-          </td>
-          <td><p><input type="text" size="3" name="passwd" value="2" maxlength="60" size="28">
-          </td>
-        </tr>
-        <tr> 
-          <td colspan=3 align=center >&nbsp;</td>
-        </tr>
-        <tr>
-          <td width='10%'> &nbsp;</td>
-          <td width="25%" bgcolor="#4682b4">
-            <p align="center">
-            <font color="white" face=verdana size=2%>
-            <b>Unit:</b>
-            </font>
-          </td>
-          <td>
-            <input type="radio" name="o" value="days" >day(s)
-            <input type="radio" name="o" value="weeks" checked>week(s)
-            <input type="radio" name="o" value="months">month(s)
-        </tr>
-      </table>
-  <p>
-  After values have been entered for each of these fields, click the Register 
-  button to register your site with Harvester.
-  </p>
-  <P>
-  In the example shown above, Harvester will attempt to harvest documents from 
-  the site once every 2 weeks, it will access the site's Harvest List at URL
-  "http://somehost.institution.edu/~myname/harvestList.xml", and it will send
-  email reports to the Site Contact at email address "myname@institution.edu".
-  </P>
-  <P>
-  Note that you may enter multiple email addresses by separating each
-  address with a comma or a semi-colon. For example, 
-  "myname@institution.edu,anothername@institution.edu".
-  </P>
-    </li>
-    <li>Unregistering with Harvester
-  <p>
-  At any time after you have registered with Harvester, you may discontinue 
-  harvests at your site by unregistering. Simply login as described above and 
-  then click the Unregister button. After doing so, Harvester will discontinue 
-  harvests at the site.
-  </p>
-    </li>
-  </ol>
-  <h5><a name="Composing">Composing a Harvest List</a></h5>
-  <p>
-  A Harvest List is an XML file that holds a list of EML documents to be
-  harvested. For each EML document in the list, the following information
-  must be specified:
-  <ul>
-    <li><code>docid</code>, which consists of the:
-      <ul>
-        <li><code>scope</code>, e.g. "demoDocument". The scope is an identifier 
-            that indicates which group of documents this document belongs to.
-        </li>
-        <li><code>identifier</code>, e.g. "1". The identifier is a number that 
-            uniquely identifies this document within the scope.
-        </li>
-        <li><code>revision</code>, e.g. "5". The revision is a number that 
-            indicates the current revision of this document.
-        </li>
-      </ul>
-    </li>
-    <li><code>documentType</code>, e.g. "eml://ecoinformatics.org/eml-2.0.0".
-        The documentType identifies the document as an EML document.</li>
-    <li><code>documentURL</code>, e.g. "http://www.lternet.edu/~dcosta/document1.xml".
-        The documentURL specifies a place where Harvester can locate 
-        and retrieve the document via HTTP.</li>
-  </ul>
-  </p>
-  <p>
-  The contents of a Harvest List XML file must conform to a particular
-  XML Schema, as defined in file <a href="../../lib/harvester/harvestList.xsd">
-  harvestList.xsd</a>. The contents of a valid Harvest List 
-  can best be illustrated by example. The sample Harvest List
-  below contains two &lt;<code>document</code>&gt; elements that specify the 
-  information that Harvester needs to retrieve a pair of EML documents and 
-  upload them to Metacat:
-  <pre>
-&lt;?xml version="1.0" encoding="UTF-8" ?&gt;
-&lt;hrv:harvestList xmlns:hrv="eml://ecoinformatics.org/harvestList" &gt;
-    &lt;document&gt;
-        &lt;docid&gt;
-            &lt;scope&gt;demoDocument&lt;/scope&gt;
-            &lt;identifier&gt;1&lt;/identifier&gt;
-            &lt;revision&gt;5&lt;/revision&gt;
-        &lt;/docid&gt;
-        &lt;documentType&gt;eml://ecoinformatics.org/eml-2.0.0&lt;/documentType&gt;
-        &lt;documentURL&gt;http://www.lternet.edu/~dcosta/document1.xml&lt;/documentURL&gt;
-    &lt;/document&gt;
-    &lt;document&gt;
-        &lt;docid&gt;
-            &lt;scope&gt;demoDocument&lt;/scope&gt;
-            &lt;identifier&gt;2&lt;/identifier&gt;
-            &lt;revision&gt;1&lt;/revision&gt;
-        &lt;/docid&gt;
-        &lt;documentType&gt;eml://ecoinformatics.org/eml-2.0.0&lt;/documentType&gt;
-        &lt;documentURL&gt;http://www.lternet.edu/~dcosta/document2.xml&lt;/documentURL&gt;
-    &lt;/document&gt;
-&lt;/hrv:harvestList&gt;
-  </pre>
-  <p>
-  After editing the Harvest List, ensure that the Harvest List XML file resides
-  at the appropriate location on disk as specified by the URL that was entered
-  during the <a href=#Registering>registration</a> process.
-  </p>
-  <p>
-  The <a href=./harvestListEditor.html>Harvest List Editor</a> is a tool that 
-  assists in composing and editing a Harvest List. (Click 
-  <a href=./harvestListEditor.html>here</a> for additional details.)
-  </p>
-    <h5><a name="Preparing">Preparing EML Documents for harvest</a></h5>
-  <p>
-  To prepare a set of EML documents for harvest, ensure that the following is 
-  true for each document:
-  <ul>
-    <li>The document contains valid EML</li>
-    <li>The document is specified in a &lt;document&gt; element in the 
-        site's Harvest List, as described above</li>
-    <li>The file resides at the appropriate location on disk as specified
-        by its URL in the Harvest List</li>
-  </ul>
-  </p>
-    <h5><a name="Reviewing" >Reviewing Harvester Reports to the Site Contact</a></h5>
-  <P>
-  After every scheduled harvest that takes place at a particular Harvest
-  Site, Harvester will send an email report to the Site Contact detailing the 
-  operations that were performed during the harvest.
-  The report will contain information about the operations that were
-  performed by Harvester at that site, such as 
-  which EML documents were harvested and whether any errors were encountered.
-  </P>
-  <P>
-  The Site Contact should review the report, paying particularly 
-  close attention to any errors that are reported. Errors are indicated
-  by operations that display a status value of 1, while operations that
-  display a status value of 0 indicate that the operation completed
-  successfully.
-  </P>
-  <p>
-  When errors are reported,
-  the Site Contact should try to determine whether the source of the error
-  is something that can be corrected at the site. Common causes of errors 
-  might be:
-  <ul>
-    <li>A document URL specified in the Harvest List does not match
-        the location of the actual EML file on the disk</li>
-    <li>The Harvest List does not contain valid XML as specified in
-        the <a href=../../lib/harvester/harvestList.xsd>harvestList.xsd</a> schema</li>
-    <li>The URL to the Harvest List that was specified during
-        registration with Harvester does not match the actual location of
-        the Harvest List on the disk</li>
-    <li>An EML document that Harvester attempted to upload to Metacat does
-        not contain valid EML</li>
-  </ul>
-  </P> 
-  <p>
-  If the Site Contact is unable to determine the cause of the error and its
-  resolution, he or she should contact the Harvester Administrator for assistance.
-  </p>
-  <a href="./properties.html">Back</a> | 
-  <a href="./metacattour.html">Home</a> | 
-  <a href="./lsid_authority.html">Next</a>
-</BODY>
-</HTML>

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___________________________________________________________________
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Index: docs/user/harvestListEditor.html
===================================================================
--- docs/user/harvestListEditor.html	(revision 5315)
+++ docs/user/harvestListEditor.html	(nonexistent)
@@ -1,287 +0,0 @@
-<!--
-  * harvestListEditor.html
-  *
-  *      Authors: Duane Costa
-  *    Copyright: 2004 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis,
-  *               and the University of New Mexico.
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2004 June 11
-  *      Version: 
-  *    File Info: '$ '
-  * 
-  * 
--->
-<HTML>
-<HEAD>
-<TITLE>Harvest List Editor</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2">
-        <p class="label">Harvest List Editor</p>
-      </td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./harvester.html">Back</a>
-      </td>
-    </tr>
-  </table>
-
-<h4>Introduction</h4>
-<p>
-The Harvest List Editor is a tool that assists in composing and editing a 
-<a href="./harvester.html#HarvestList">Harvest List</a>. The Harvest List
-editor displays a Harvest List as a table of rows and fields. Each row in
-the table corresponds to a single &lt;document&gt; element in the 
-corresponding Harvest List XML file, where a &lt;document&gt; represents
-a single document to be harvested. Each row contains the following fields:
-<ul>
-<li>Row #<br>Displays the table row number. This field is used for visual reference only;
-it is non-editable and its value is not included in the
-XML file that is generated when the Harvest List is saved to disk.</li>
-<li>Scope<br>the value of the &lt;scope&gt; element for this document</li>
-<li>Identifier<br>the value of the &lt;identifier&gt; element for this document</li>
-<li>Revision<br>the value of the &lt;revision&gt; element for this document</li>
-<li>Document Type<br>the value of the &lt;documentType&gt; element for this document</li>
-<li>Document URL<br>the value of the &lt;documentURL&gt; element for this document</li>
-</ul>
-</p>
-<p>For each &lt;document&gt; element to be included in the Harvest List, edit a row in the
-table, filling
-in values for each of the five editable fields: Scope, Identifier, Revision,
-Document Type, and Document URL. When you have finished adding &lt;document&gt;
-elements to the Harvest List, save the Harvest List to disk. Each of these steps are 
-explained in more detail <a href=#Using>below</a>.</p>
-
-<h4><a name="Configuring">Configuring the Harvest List Editor</a></h4>
-<p></p>
-The Harvest List Editor has a number of settable properties that control its
-behavior. All configuration information is managed in a single file,
-<b>.</b>harvestListEditor (note the leading dot character), which should be 
-created using a plain text editor and placed in the user's home directory. 
-To determine the user's home directory, open a system command window or terminal 
-window and typing the following:
-<ul>
-<li></li>
-On Windows:
-<code><pre>
-  echo %USERPROFILE%
-</pre></code>
-</li>
-<li>
-On Linux/Unix:
-<code><pre>
-  echo $HOME
-</pre></code>
-</li>
-</ul>
-</p>
-<p>
-The following table summarizes the properties that can be configured in the
-.harvestListEditor file. Note that all properties are optional;
-setting them improves the convenience of using the Harvest List Editor
-but it is not a requirement.
-<p>
-  <table border="1">
-    <tr>
-      <td><b>Property</b></td>
-      <td><b>Description</b></td>
-      <td><b>Possible or default value</b></td>
-    </tr>
-    <tr>
-      <td>defaultHarvestList</td>
-      <td>This property determines the location of a Harvest List
-          file that the Harvest List Editor will automatically open for
-          editing on startup. Set this
-          property to the path to the Harvest List file that
-          you expect to edit most frequently.</td>
-      <td>Examples:
-        <br><code>/home/jdoe/public_html/harvestList.xml</code><br>
-            <code>C:/temp/harvestList.xml</code>
-      </td>
-    </tr>
-    <tr>
-      <td>defaultScope</td>
-      <td>Determines the value that is pasted into the <em>Scope</em> field
-          of the currently selected row when the 
-          <code>Paste Defaults</code> button is clicked. The <em>Scope</em> 
-          field should contain a symbolic identifer that indicates which 
-          family of documents this EML document belongs to.</td>
-      <td>
-          Example:&nbsp;&nbsp;&nbsp;xyz_dataset<br>
-          Default:&nbsp;&nbsp;&nbsp;&nbsp;dataset
-      </td>
-    </tr>
-    <tr>
-      <td>defaulIdentifer</td>
-      <td>Determines the value that is pasted into the <em>Identifier</em> field
-          of the currently selected row when the <code>Paste Defaults</code> button 
-          is clicked. The <em>Identifier</em> field should contain
-          a numeric value indicating the identifier for this particular
-          EML document within the Scope.</td>
-      <td>
-          Example:&nbsp;&nbsp;&nbsp;2<br>
-          Default:&nbsp;&nbsp;&nbsp;&nbsp;1
-      </td>
-    </tr>
-    <tr>
-      <td>defaultRevision</td>
-      <td>Determines the value that is pasted into the <em>Revision</em> field
-          of the currently selected row when the <code>Paste Defaults</code> button 
-          is clicked. The <em>Revision</em> field should contain a numeric
-          value indicating the revision number of this EML document within
-          the Scope and Identifier.</td>
-      <td>
-          Example:&nbsp;&nbsp;&nbsp;2<br>
-          Default:&nbsp;&nbsp;&nbsp;&nbsp;1
-      </td>
-    </tr>
-    <tr>
-      <td>defaultDocumentType</td>
-      <td>Determines the value that is pasted into the <em>Document Type</em> field
-          of the currently selected row when the <code>Paste Defaults</code> button 
-          is clicked.</td>
-      <td>A document type specification
-          <br><br>
-          Default:<br> <code>eml://ecoinformatics.org/eml-2.0.0<code>
-      </td>
-    </tr>
-    <tr>
-      <td>defaultDocumentURL</td>
-      <td>Determines the value that is pasted into the <em>Document URL</em> field
-          of the currently selected row when the <code>Paste Defaults</code> button 
-          is clicked. Typically, this value would be set to the portion
-          of the URL that all harvested EML documents at your site share in common.</td>
-      <td>A URL, or partial URL
-          <br><br>
-          Example:<br> <code>http://somehost.institution.edu/somepath/<code>
-          <br><br>
-          Default:<br> <code>http://<code>
-      </td>
-    </tr>
-  </table>
-</p>
-The contents of a sample .harvestListEditor configuration file appear below:
-<pre><code>
-defaultHarvestList=C:/temp/harvestList.xml
-defaultScope=demo_document
-defaultIdentifier=1
-defaultRevision=1
-defaultDocumentURL=http://www.lternet.edu/~dcosta/
-defaultDocumentType=eml://ecoinformatics.org/eml-2.0.0
-</code></pre>
-
-<h4><a name=#Running>Running the Harvest List Editor</a></h4>
-  After the Harvest List Editor has been appropriately 
-  <a href=#Configuring>configured</a>, it can be run as follows:
-  <ol>
-  <li>Open a system command window or terminal window.</li>
-  <li>Set the METACAT_HOME environment variable to the value of the Metacat
-      installation directory. Some examples follow:
-      <ul>
-        <li>On Windows:
-        <pre>set METACAT_HOME=C:\somePath\metacat</pre></li>
-        <li>On Linux/Unix (bash shell):
-        <pre>export METACAT_HOME=/home/somePath/metacat</pre></li>
-      </ul>
-  <li>cd to the following directory:
-      <ul>
-        <li>On Windows:
-        <pre>cd %METACAT_HOME%\lib\harvester</pre></li>
-        <li>On Linux/Unix:
-        <pre>cd $METACAT_HOME/lib/harvester</pre></li>
-      </ul>
-  <li>Run the appropriate Harvester shell script, as determined by the
-      operating system:
-      <ul>
-        <li>On Windows:
-        <pre>runHarvestListEditor.bat</pre></li>
-        <li>On Linux/Unix:
-        <pre>sh runHarvestListEditor.sh</pre></li>
-      </ul>
-  </li>
-  </ol>
-  <p>The Harvest List Editor application will start executing, automatically
-     opening the default Harvest List for editing if the 
-     <code>defaultHarvestList</code>
-     property has been appropriately configured in the 
-     <code>.harvestListEditor</code>
-     file in the user's home directory.
-  </p>
-
-<h4><a name=#Using>Using the Harvest List Editor</a></h4>
-
-<h5>The File Menu</h5>
-The File Menu contains the following menu items:
-<ul>
-<li><code>New</code>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-Opens a new (empty) Harvest List file for editing.
-</li>
-<li><code>Open...</code>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-Opens an existing Harvest List file for editing.
-</li>
-<li><code>Save</code>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-Saves the Harvest List file to disk using its current file name.
-</li>
-<li><code>Save As...</code>
-Saves the Harvest List file to disk, prompting for a different file name.
-</li>
-<li><code>Validate</code>&nbsp;&nbsp;&nbsp;&nbsp;
-Validates the currently open Harvest List and issues messages about any errors that are detected.
-</li>
-<li><code>Exit</code>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-Exits the Harvest List Editor.
-</li>
-</ul>
-
-<h5>The Button Pallette</h6>
-The Harvest List Editor contains the following buttons in the button pallette
-at the bottom of the editor window:
-<ul>
-<li><code>Cut</code>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-Cut the currently selected row from the table and save the values to the clipboard.
-</li>
-<li><code>Copy</code>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-Copy the values from the currently selected row into the clipboard.
-</li>
-<li><code>Paste</code>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-Paste the values from the clipboard into the currently selected row.
-</li>
-<li><code>Paste Defaults</code>
-Paste the default values into the currently selected row. The default values
-are specified in the <a href=#Configuring>.harvestListEditor</a> configuration file.
-</li>
-</ul>
-
-<h5>Editing the Harvest List</h5>
-<p>
-To edit the Harvest List, enter values for each of the five editable fields
-(all fields except the "Row #" field) for a given row in the table. Each
-row in the table corresponds to a single document that you wish to add to
-the Harvest List.
-</p>
-<p>
-Empty rows in the table are ignored when generating the Harvest List;
-therefore, "holes" in the table are allowed.
-For example, rows #1 and #3 may contain values while row #2 may be empty.
-However, if any one of the editable fields in a row contains a value, then
-all five of the editable fields should contain values. Partially filled-in
-rows will cause errors that will result in an invalid Harvest List.
-</p>
-<p>
-You can <code>Cut</code>, <code>Copy</code>, and <code>Paste</code> rows 
-from one location to another by selecting a row
-and clicking the corresponding button. You can paste the default
-values into the currently selected row by clicking the 
-<code>Paste Defaults</code> button.
-Only one row may be selected at any given time: all cut, copy, and paste
-operations work on only a single row rather than on a range of rows.
-</p>
-
-<a href="./harvester.html">Back</a>
-
-</BODY>
-</HTML>

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-native
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-*
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Index: docs/user/xmlindex.html
===================================================================
--- docs/user/xmlindex.html	(revision 5315)
+++ docs/user/xmlindex.html	(nonexistent)
@@ -1,265 +0,0 @@
-<!--
-  * xmlindex.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Indexing for Performance</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./saxparser.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./acontrol.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <P>Metacat DB stores indeces for the current version of all documents in <i>xml_index</i> 
-  table. All relative and absolute paths to any node in a document are stored in 
-  this table. These paths are used for structured query searches to a specified 
-  location in an XML tree. Path expressions specified in the 
-  <a href="./metacatquery.html">pathquery</a> document are queried from this 
-  table.</p>
-  <p>Indeces become necessary because relational databases are not efficient
-  at querying tree structures.  By slightly denormalizing the database and listing
-  the tree structure in a flat table, the relational database engine can more
-  effectively handle large path queries.</p>
-  <p>Example: </p>
-  <pre>
-    &lt;?xml version="1.0"?&gt;
-    &lt;!DOCTYPE employee&gt;
-    &lt;employee&gt;
-      &lt;name&gt;
-        &lt;first&gt;Chad&lt;/first&gt;
-        &lt;last&gt;Berkley&lt;/last&gt;
-      &lt;/name&gt;
-      &lt;address&gt;
-        &lt;street&gt;735 State St. Ste. 303&lt;/street&gt;
-        &lt;city&gt;Santa Barbara&lt;/city&gt;
-        &lt;state&gt;California&lt;/state&gt; 
-        &lt;zip&gt;93101&lt;/zip&gt;
-      &lt;/address&gt;
-      &lt;occupation&gt;
-        &lt;title&gt;Metadata Systems Developer&lt;/title&gt;
-        &lt;location&gt;
-          &lt;type&gt;
-            &lt;grant&gt;
-              &lt;name&gt;DBA&lt;/name&gt;
-              &lt;grantor&gt;NSF&lt;/grantor&gt;
-              &lt;PI&gt;Jim Reichman&lt;/PI&gt;
-              &lt;PI&gt;Matt Jones&lt;/PI&gt;
-              &lt;PI&gt;Mark Schildhauer&lt;/PI&gt;
-            &lt;/grant&gt;
-          &lt;/type&gt;
-          &lt;system&gt;UC&lt;/system&gt;
-          &lt;location&gt;Santa Barbara&lt;/location&gt;
-        &lt;/location&gt;
-      &lt;/occupation&gt;
-    &lt;/employee&gt;
-  </pre>
-  <p>The XML document above is logically deconstructed into all possible paths
-  through the document.  Each path (relative and absolute) is entered as a record
-  in xml_index along with the nodeid of the deepest node.  In this way, any path
-  can be quickly queried.  It's contents can be assertained from cross linking
-  the nodeid back to the <a href="#xml_nodes">xml_nodes</a> table.  
-  <table border="1">
-    <tr>
-      <td><b>PATH</b></td><td><b>NODEID</b></td><td><b>PARENTNODEID</b></td>
-    </tr>
-    <tr><td>occupation/location/type/grant/grantor</td><td>200150</td><td>200145<td></tr>
-    <tr><td>location/type/grant/grantor</td><td>200150</td><td>200145<td></tr>
-    <tr><td>grantor</td><td>200150</td><td>200145<td></tr>
-    <tr><td>location/type/grant/PI</td><td>200153</td><td>200145<td></tr>
-    <tr><td>grant/PI</td><td>200153</td><td>	  200145<td></tr>
-    <tr><td>/employee/occupation/location/type/grant/PI</td><td>200153</td><td>	  200145<td></tr>
-    <tr><td>employee/occupation/location/type/grant/PI</td><td>200153</td><td>	  200145<td></tr>
-    <tr><td>occupation/location/type/grant/PI</td><td>200153</td><td>	  200145<td></tr>
-    <tr><td>type/grant/PI</td><td>200153</td><td>	  200145<td></tr>
-    <tr><td>PI</td><td>200153</td><td>	  200145<td></tr>
-    <tr><td>location/type/grant/PI</td><td>200156</td><td>	  200145<td></tr>
-    <tr><td>grant/PI</td><td>200156</td><td>	  200145<td></tr>
-    <tr><td>/employee/occupation/location/type/grant/PI</td><td>200156</td><td>	  200145<td></tr>
-    <tr><td>employee/occupation/location/type/grant/PI</td><td>200156</td><td>	  200145<td></tr>
-    <tr><td>occupation/location/type/grant/PI</td><td>200156</td><td>	  200145<td></tr>
-    <tr><td>type/grant/PI</td><td>200156</td><td>	  200145<td></tr>
-    <tr><td>PI</td><td>	200156</td><td>	  200145<td></tr>
-    <tr><td>location/type/grant/PI</td><td>200159</td><td>	  200145<td></tr>
-    <tr><td>grant/PI</td><td>200159</td><td>	  200145
-    <tr><td>/employee/occupation/location/type/grant/PI</td><td>200159</td><td>	  200145<td></tr>
-    <tr><td>employee/occupation/location/type/grant/PI</td><td>200159</td><td>	  200145<td></tr>
-    <tr><td>occupation/location/type/grant/PI</td><td>200159</td><td>	  200145<td></tr>
-    <tr><td>type/grant/PI</td><td>200159</td><td>	  200145<td></tr>
-    <tr><td>PI</td><td>200159</td><td>	  200145<td></tr>
-    <tr><td>occupation/location/system</td><td>200164</td><td>	  200141<td></tr>
-    <tr><td>system</td><td>200164</td><td>	  200141<td></tr>
-    <tr><td>employee/occupation/location/system</td><td>200164</td><td>	  200141<td></tr>
-    <tr><td>location/system</td><td>200164</td><td>	  200141<td></tr>
-    <tr><td>/employee/occupation/location/system</td><td>200164</td><td>	  200141<td></tr>
-    <tr><td>/employee/occupation/location/location</td><td>200167</td><td>	  200141<td></tr>
-    <tr><td>employee/occupation/location/location</td><td>200167</td><td>	  200141<td></tr>
-    <tr><td>occupation/location/location</td><td>200167</td><td>	  200141<td></tr>
-    <tr><td>location</td><td>200167</td><td>	  200141<td></tr>
-    <tr><td>location/location</td><td>200167</td><td>	  200141<td></tr>
-    <tr><td>/employee/name</td><td>200112</td><td>	  200110<td></tr>
-    <tr><td>name</td><td>200112</td><td>	  200110<td></tr>
-    <tr><td>employee/name</td><td>200112</td><td>	  200110<td></tr>
-    <tr><td>/employee/name/first</td><td>200114</td><td>	  200112<td></tr>
-    <tr><td>name/first</td><td>200114</td><td>	  200112<td></tr>
-    <tr><td>/employee</td><td>200110</td><td>	  200109<td></tr>
-    <tr><td>employee</td><td>200110</td><td>	  200109<td></tr>
-    <tr><td>employee/name/first</td><td>200114</td><td>	  200112<td></tr>
-    <tr><td>first</td><td>200114</td><td>	  200112<td></tr>
-    <tr><td>name/last</td><td>200117</td><td>	  200112<td></tr>
-    <tr><td>/employee/name/last</td><td>200117</td><td>	  200112<td></tr>
-    <tr><td>employee/name/last</td><td>200117</td><td>	  200112<td></tr>
-    <tr><td>last</td><td>200117</td><td>	  200112<td></tr>
-    <tr><td>employee/address</td><td>200121</td><td>	  200110<td></tr>
-    <tr><td>address</td><td>200121</td><td>	  200110<td></tr>
-    <tr><td>/employee/address</td><td>200121</td><td>	  200110<td></tr>
-    <tr><td>/employee/address/street</td><td>200123</td><td>	  200121<td></tr>
-    <tr><td>employee/address/street</td><td>200123</td><td>	  200121<td></tr>
-    <tr><td>address/street</td><td>200123</td><td>	  200121<td></tr>
-    <tr><td>street</td><td>200123</td><td>	  200121<td></tr>
-    <tr><td>employee/address/city</td><td>200126</td><td>	  200121<td></tr>
-    <tr><td>address/city</td><td>200126</td><td>	  200121<td></tr>
-    <tr><td>/employee/address/city</td><td>200126</td><td>	  200121<td></tr>
-    <tr><td>city</td><td>200126</td><td>	  200121<td></tr>
-    <tr><td>address/state</td><td>200129</td><td>	  200121<td></tr>
-    <tr><td>/employee/address/state</td><td>200129</td><td>	  200121<td></tr>
-    <tr><td>employee/address/state</td><td>200129</td><td>	  200121<td></tr>
-    <tr><td>state</td><td>200129</td><td>	  200121<td></tr>
-    <tr><td>employee/address/zip</td><td>200132</td><td>	  200121<td></tr>
-    <tr><td>zip</td><td>200132</td><td>	  200121<td></tr>
-    <tr><td>/employee/address/zip</td><td>200132</td><td>	  200121<td></tr>
-    <tr><td>address/zip</td><td>200132</td><td>	  200121<td></tr>
-    <tr><td>employee/occupation</td><td>200136</td><td>	  200110<td></tr>
-    <tr><td>/employee/occupation</td><td>200136</td><td>	  200110<td></tr>
-    <tr><td>occupation</td><td>200136</td><td>	  200110<td></tr>
-    <tr><td>/employee/occupation/title</td><td>200138</td><td>	  200136<td></tr>
-    <tr><td>employee/occupation/title</td><td>200138</td><td>	  200136<td></tr>
-    <tr><td>occupation/title</td><td>200138</td><td>  200136<td></tr>
-    <tr><td>title</td><td>200138</td><td>	  200136<td></tr>
-    <tr><td>location</td><td>200141</td><td>	  200136<td></tr>
-    <tr><td>employee/occupation/location</td><td>200141</td><td>	  200136<td></tr>
-    <tr><td>/employee/occupation/location</td><td>200141</td><td>	  200136<td></tr>
-    <tr><td>occupation/location</td><td>200141</td><td>	  200136<td></tr>
-    <tr><td>occupation/location/type</td><td>200143</td><td>	  200141<td></tr>
-    <tr><td>type</td><td>200143</td><td>	  200141<td></tr>
-    <tr><td>/employee/occupation/location/type</td><td>200143</td><td>	  200141<td></tr>
-    <tr><td>location/type</td><td>200143</td><td>	  200141<td></tr>
-    <tr><td>employee/occupation/location/type</td><td>200143</td><td>	  200141<td></tr>
-    <tr><td>type/grant</td><td>200145</td><td>	  200143<td></tr>
-    <tr><td>occupation/location/type/grant</td><td>200145</td><td>	  200143<td></tr>
-    <tr><td>grant</td><td>200145</td><td>	  200143<td></tr>
-    <tr><td>location/type/grant</td><td>200145</td><td>	  200143<td></tr>
-    <tr><td>/employee/occupation/location/type/grant</td><td>200145</td><td>	  200143<td></tr>
-    <tr><td>employee/occupation/location/type/grant</td><td>200145</td><td>	  200143<td></tr>
-    <tr><td>grant/name</td><td>200147</td><td>	  200145<td></tr>
-    <tr><td>/employee/occupation/location/type/grant/name</td><td>200147</td><td>	  200145<td></tr>
-    <tr><td>occupation/location/type/grant/name</td><td>200147</td><td>	  200145<td></tr>
-    <tr><td>name</td><td>200147</td><td>	  200145<td></tr>
-    <tr><td>type/grant/name</td><td>200147</td><td>	  200145<td></tr>
-    <tr><td>location/type/grant/name</td><td>200147</td><td>	  200145<td></tr>
-    <tr><td>employee/occupation/location/type/grant/name</td><td>200147</td><td>	  200145<td></tr>
-    <tr><td>/employee/occupation/location/type/grant/grantor</td><td>200150</td><td>	  200145<td></tr>
-    <tr><td>type/grant/grantor</td><td>200150</td><td>	  200145<td></tr>
-    <tr><td>grant/grantor</td><td>200150</td><td>	  200145<td></tr>
-    <tr><td>employee/occupation/location/type/grant/grantor</td><td>200150</td><td>	  200145<td></tr>
-  </table>
-  <br>
-  <a name="xml_nodes"></a>
-  <p>The following is the document in xml_nodes.</p>
-  <br>
-  <table border="1">
-    <tr>
-      <td><b>nodeid</b></td><td><b>nodetype</b></td><td><b>nodename</b></td>
-      <td><b>nodedata</b></td><td><b>rootnodeid</b></td><td><b>parentnodeid</b></td>
-    </tr>
-    
-    <tr><td>200164</td> <td>ELEMENT </td> <td>system</td><td>&nbsp;</td><td>200109</td><td>200141</td> </tr>
-    <tr><td>200165</td> <td>TEXT </td> <td>&nbsp;</td><td>UC</td><td>200109</td><td>200164</td> </tr>
-    <tr><td>200166</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200141</td> </tr>
-    <tr><td>200167</td> <td>ELEMENT </td> <td> location</td><td>&nbsp;</td><td>200109</td><td>200141</td> </tr>
-    <tr><td>200168</td> <td>TEXT </td> <td>&nbsp;</td><td>Santa Barbara</td><td>200109</td><td>200167</td> </tr>
-    <tr><td>200169</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200141</td> </tr>
-    <tr><td>200170</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200136</td> </tr>
-    <tr><td>200171</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200110</td> </tr>
-    <tr><td>200109</td> <td>DOCUMENT </td> <td> employee</td><td>&nbsp;</td><td>200109</td><td>&nbsp;</td> </tr>
-    <tr><td>200110</td> <td>ELEMENT </td> <td> employee</td><td>&nbsp;</td><td>200109</td><td>200109</td> </tr>
-    <tr><td>200111</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200110</td> </tr>
-    <tr><td>200112</td> <td>ELEMENT </td> <td> name</td><td>&nbsp;</td><td>200109</td><td>200110</td> </tr>
-    <tr><td>200113</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200112</td> </tr>
-    <tr><td>200114</td> <td>ELEMENT </td> <td> first</td><td>&nbsp;</td><td>200109</td><td>200112</td> </tr>
-    <tr><td>200115</td> <td>TEXT </td> <td>&nbsp;</td><td>Chad</td><td>200109</td><td>200114</td> </tr>
-    <tr><td>200116</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200112</td> </tr>
-    <tr><td>200117</td> <td>ELEMENT </td> <td> last</td><td>&nbsp;</td><td>200109</td><td>200112</td> </tr>
-    <tr><td>200118</td> <td>TEXT </td> <td>&nbsp;</td><td>Berkley</td><td>200109</td><td>200117</td> </tr>
-    <tr><td>200119</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200112</td> </tr>
-    <tr><td>200120</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200110</td> </tr>
-    <tr><td>200121</td> <td>ELEMENT </td> <td> address</td><td>&nbsp;</td><td>200109</td><td>200110</td> </tr>
-    <tr><td>200122</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200121</td> </tr>
-    <tr><td>200123</td> <td>ELEMENT </td> <td> street</td><td>&nbsp;</td><td>200109</td><td>200121</td> </tr>
-    <tr><td>200124</td> <td>TEXT </td> <td>&nbsp;</td><td>735 State St. Ste. 303</td><td>200109</td><td>200123</td> </tr>
-    <tr><td>200125</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200121</td> </tr>
-    <tr><td>200126</td> <td>ELEMENT </td> <td> city</td><td>&nbsp;</td><td>200109</td><td>200121</td> </tr>
-    <tr><td>200127</td> <td>TEXT </td> <td>&nbsp;</td><td>Santa Barbara</td><td>200109</td><td>200126</td> </tr>
-    <tr><td>200128</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200121</td> </tr>
-    <tr><td>200129</td> <td>ELEMENT </td> <td> state</td><td>&nbsp;</td><td>200109</td><td>200121</td> </tr>
-    <tr><td>200130</td> <td>TEXT </td> <td>&nbsp;</td><td>California</td><td>200109</td><td>200129</td> </tr>
-    <tr><td>200131</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200121</td> </tr>
-    <tr><td>200132</td> <td>ELEMENT </td> <td> zip</td><td>&nbsp;</td><td>200109</td><td>200121</td> </tr>
-    <tr><td>200133</td> <td>TEXT </td> <td>&nbsp;</td><td>93101</td><td>200109</td><td>200132</td> </tr>
-    <tr><td>200134</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200121</td> </tr>
-    <tr><td>200135</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200110</td> </tr>
-    <tr><td>200136</td> <td>ELEMENT </td> <td> occupation</td><td>&nbsp;</td><td>200109</td><td>200110</td> </tr>
-    <tr><td>200137</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200136</td> </tr>
-    <tr><td>200138</td> <td>ELEMENT </td> <td> title</td><td>&nbsp;</td><td>200109</td><td>200136</td> </tr>
-    <tr><td>200139</td> <td>TEXT </td> <td>&nbsp;</td><td>Metadata Systems Developer</td><td>200109</td><td>200138</td> </tr>
-    <tr><td>200140</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200136</td> </tr>
-    <tr><td>200141</td> <td>ELEMENT </td> <td> location</td><td>&nbsp;</td><td>200109</td><td>200136</td> </tr>
-    <tr><td>200142</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200141</td> </tr>
-    <tr><td>200143</td> <td>ELEMENT </td> <td> type</td><td>&nbsp;</td><td>200109</td><td>200141</td> </tr>
-    <tr><td>200144</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200143</td> </tr>
-    <tr><td>200145</td> <td>ELEMENT </td> <td> grant</td><td>&nbsp;</td><td>200109</td><td>200143</td> </tr>
-    <tr><td>200146</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200145</td> </tr>
-    <tr><td>200147</td> <td>ELEMENT </td> <td> name</td><td>&nbsp;</td><td>200109</td><td>200145</td> </tr>
-    <tr><td>200148</td> <td>TEXT </td> <td>&nbsp;</td><td>DBA</td><td>200109</td><td>200147</td> </tr>
-    <tr><td>200149</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200145</td> </tr>
-    <tr><td>200150</td> <td>ELEMENT </td> <td> grantor</td><td>&nbsp;</td><td>200109</td><td>200145</td> </tr>
-    <tr><td>200151</td> <td>TEXT </td> <td>&nbsp;</td><td>NSF</td><td>200109</td><td>200150</td> </tr>
-    <tr><td>200152</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200145</td> </tr>
-    <tr><td>200153</td> <td>ELEMENT </td> <td> PI</td><td>&nbsp;</td><td>200109</td><td>200145</td> </tr>
-    <tr><td>200154</td> <td>TEXT </td> <td>&nbsp;</td><td>Jim Reichman</td><td>200109</td><td>200153</td> </tr>
-    <tr><td>200155</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200145</td> </tr>
-    <tr><td>200156</td> <td>ELEMENT </td> <td> PI</td><td>&nbsp;</td><td>200109</td><td>200145</td> </tr>
-    <tr><td>200157</td> <td>TEXT </td> <td>&nbsp;</td><td>Matt Jones</td><td>200109</td><td>200156</td> </tr>
-    <tr><td>200158</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200145</td> </tr
-    <tr><td>200159</td> <td>ELEMENT </td> <td> PI</td><td>&nbsp;</td><td>200109</td><td>200145</td> </tr>
-    <tr><td>200160</td> <td>TEXT </td> <td>&nbsp;</td><td>Mark Schilhauer</td><td>200109</td><td>200159</td> </tr>
-    <tr><td>200161</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200145</td> </tr>
-    <tr><td>200162</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200143</td> </tr>
-    <tr><td>200163</td> <td>TEXT </td> <td>&nbsp;</td><td>&nbsp;</td><td>200109</td><td>200141</td> </tr>
-  </table>
-  
-  
-  
-  
-  <br>
-  <a href="./saxparser.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./acontrol.html">Next</a>
-  
-</BODY>
-</HTML>
-

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Index: docs/user/metacat.html
===================================================================
--- docs/user/metacat.html	(revision 5315)
+++ docs/user/metacat.html	(nonexistent)
@@ -1,211 +0,0 @@
-<!--
-  * metacat.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Metacat Server</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./domapi.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./metacatdb.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <P>The Metacat Server stores arbitrary XML 
-  documents in a relational 
-  database without foreknowledge of the document schema.  It does this by implementing
-  the DOM within the table structure of the relational database.
-  Metacat also performs optimized free-text 
-  and structured 
-  searches across the entire document collection. Metacat provides 
-  standardized interfaces to client software for document processing, storing 
-  and searching. 
-
-  <P> <img alt="Structural diagram of Metacat architecture" src="metacat.gif">
-  </p>
-  <p>
-	Metacat provides several means of access for communicating with the
-	server to access and submit metadata and data.  First, users can
-	access the flexible web user interface.  Second, the servlet can be
-	queried using basic HTML forms.  Third, a 
-	<a href="./clientapi.html">client API</a> exists for 
-	writing software for accessing the server's contents.
-  </p>
-  <p>	
-	When accessing the servlet interface either through 'GET' or 'POST'
-	HTTP requests, the request is directed to the appropriate handler based
-	on an 'action' parameter in the request.  For example, using the 
-	parameter 'action=getversion' one could construct an HTTP GET
-	request to retrive the Metacat version string:<br>
-  	<code>http://some.metacat.host/context/metacat?action=getversion</code>
-  </p>
-  <p>
-	The complete list of "actions" which can be used in request to Metacat 
-	along with the additional parameters associated with each action are
-	as follows.
-  </p>
-  <p>	Primary actions for the most important features:<br>
-  <ul>
-      <li><code>action=login</code>
-          <ul>
-          <li><code>username</code></li>
-          <li><code>password</code></li>
-          </ul>
-      </li>
-      <li><code>action=logout</code>
-      </li>
-      <li><code>action=query</code>
-          <ul>
-          <li><code>meta_file_id</code></li>
-          <li><code>returndoctype</code></li>
-          <li><code>filterdoctype</code></li>
-          <li><code>returnfield</code></li>
-          <li><code>owner</code></li>
-          <li><code>site</code></li>
-          <li><code>operator</code></li>
-          <li><code>casesensitive</code></li>
-          <li><code>searchmode</code></li>
-          <li><code>anyfield</code></li>
-          <li><code>sessionid</code></li>
-          <li>Any other parameter passed in will be interpreted as a query
-              term unless it is listed in the 'query.ignored.params'
-              property in metacat.properties</li>
-          </ul>
-      </li>
-      <li><code>action=squery</code>
-          <ul>
-          <li><code>query</code></li>
-          <li><code>qformat</code></li>
-          </ul>
-      </li>
-      <li><code>action=read</code>
-          <ul>
-          <li><code>docid</code></li>
-          <li><code>qformat</code></li>
-          </ul>
-      </li>
-      <li><code>action=insert</code>
-          <ul>
-          <li><code>docid</code></li>
-          <li><code>doctext</code></li>
-          <li><code>dtdtext</code></li>
-          </ul>
-      </li>
-      <li><code>action=update</code>
-          <ul>
-          <li><code>docid</code></li>
-          <li><code>doctext</code></li>
-          <li><code>dtdtext</code></li>
-          </ul>
-      </li>
-      <li><code>action=delete</code>
-          <ul>
-          <li><code>docid</code></li>
-          </ul>
-      </li>
-  </ul>
-	Actions for less important features:<br>
-  <ul>
-      <li><code>action=spatial_query</code>
-          <ul>
-          <li><code>xmin</code></li>
-          <li><code>xmax</code></li>
-          <li><code>ymin</code></li>
-          <li><code>ymax</code></li>
-          <li><code>skin</code></li>
-          </ul>
-      </li>
-      <li><code>action=export</code>
-          <ul>
-          <li><code>docid</code></li>
-          </ul>
-      </li>
-      <li><code>action=readinlinedata</code>
-          <ul>
-          <li><code>inlinedataid</code></li>
-          </ul>
-      </li>
-      <li><code>action=validate</code>
-          <ul>
-          <li><code>valtext</code></li>
-          <li><code>docid</code></li>
-          </ul>
-      </li>
-      <li><code>action=setaccess</code>
-          <ul>
-          <li><code>docid</code></li>
-          <li><code>principal</code></li>
-          <li><code>permission</code></li>
-          <li><code>permType</code></li>
-          <li><code>permOrder</code></li>
-          <li><code>principal</code></li>
-          </ul>
-      </li>
-      <li><code>action=getaccesscontrol</code>
-          <ul>
-          <li><code>docid</code></li>
-          </ul>
-      </li>
-      <li><code>action=getprincipals</code>
-      </li>
-      <li><code>action=getdoctypes</code>
-      </li>
-      <li><code>action=getdtdschema</code>
-          <ul>
-          <li><code>doctype</code></li>
-          </ul>
-      </li>
-      <li><code>action=getlastdocid</code>
-          <ul>
-          <li><code>scope</code></li>
-          <li><code>username</code></li>
-          </ul>
-      </li>
-      <li><code>action=getrevisionanddoctype</code>
-          <ul>
-          <li><code>docid</code></li>
-          </ul>
-      </li>
-      <li><code>action=getversion</code>
-      </li>
-      <li><code>action=getlog</code>
-          <ul>
-          <li><code>ipaddress</code></li>
-          <li><code>principal</code></li>
-          <li><code>docid</code></li>
-          <li><code>event</code></li>
-          <li><code>start</code></li>
-          <li><code>end</code></li>
-          </ul>
-      </li>
-      <li><code>action=buildindex</code>
-          <ul>
-          <li><code>docid</code></li>
-          </ul>
-      </li>
-      <li><code>action=shrink</code>
-      </li>
-  </ul>
-  </p>
-
-  <br>
-  <a href="./domapi.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./metacatdb.html">Next</a>
-</BODY>
-</HTML>
-

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===================================================================
--- docs/user/entries-init.ldif	(revision 5315)
+++ docs/user/entries-init.ldif	(nonexistent)
@@ -1,20 +0,0 @@
-#The root context for KNB ecoinformatics.org
-dn: dc=ecoinformatics,dc=org
-objectClass: top
-objectclass: dcObject
-dc: ecoinformatics
-
-#The admin entry
-dn: cn=Directory Manager,dc=ecoinformatics,dc=org
-objectclass: top
-objectclass: organizationalRole
-cn: Directory Manager
-description: Directory Manager
-
-#The naming context for NCEAS's subtree
-dn: o=NCEAS,dc=ecoinformatics,dc=org
-objectclass: top
-objectclass: organization
-o: NCEAS
-description: NCEAS's KNB subtree
-

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Index: docs/user/sitemaps.html
===================================================================
--- docs/user/sitemaps.html	(revision 5315)
+++ docs/user/sitemaps.html	(nonexistent)
@@ -1,103 +0,0 @@
-<!--
-  * sitemaps.html
-  *
-  *      Authors: Michael Daigle
-  *    Copyright: 2008 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2008 November 4
-  *      Version: 
-  *    File Info: '$ '
-  * 
-  * 
--->
-<HTML>
-<HEAD>
-<TITLE>Search Engine Sitemaps</TITLE>
-<link rel="stylesheet" type="text/css" href="./common.css">
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Search Engine Sitemaps</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./pagedreturn.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./unimplem.html">Next</a>
-      </td>
-    </tr>
-  </table>
-      
-  <div class="header1">Table of Contents</div>
-  <div class="toc">
-    <div class="toc1"><a href="#Intro">About Sitemaps</a></div>
-      <div class="toc2"><a href="#Overview">Overview</a></div>
-      <div class="toc2"><a href="#Implementation">Metacat Implementation</a></div>
-    <div class="toc1"><a href="#SubmitSitemap">Submit Your Sitemap</a></div>
-       <div class="toc2"><a href="#GoogleRegister">Register With Google</a></div>
-       <div class="toc2"><a href="#GoogleReRegister">Re-Register With Google</a></div>
-  </div>  
-  
-  <a name="Intro"></a><div class="header1">About Sitemaps</div>
-  <a name="Overview"></a><div class="header2">Overview</div>
-  <p>Sitemaps are xml files that tell search engines which sites you would like to
-  be available in a web search.  This is especially useful in Metacat for making 
-  individual metadata entries available via web searches.  This does not happen now
-  because of lack of a web accessible browse heirarchy of metadata.</p>
-     
-  <p>The site map file contains metadata about the available sites on your server.  For 
-  information on the sitemap protocol, please refer to 
-  <a href="https://www.google.com/webmasters/tools/docs/en/protocol.html"> the Google 
-  page on using the sitemap protocol</a>.  The sitemap file must be available via the
-  web on your server.</p>
-     
-  <p>Metacat generates the sitemap file automatically on a daily basis (more on this in
-  the next section).  You will need to manually register the sitemap file with Google in
-  order for it to take effect.  We discuss that in the 
-  <a href="#SubmitSitemap">Submit Your Sitemap</a> section.</p>
-  
-  <p>The scope of this discussion encompasses Google
-  web searches only.</p>
-  
-  <a name="Implementation"></a><div class="header2">Metacat Implementation</div>
-  <p>Metacat automatically generates sitemap files for all public documents in 
-  your catalog.  You can view the sitemap files at:
-  <div class="code">&lt;webapps_dir&gt;/sitemaps</div>
-  You should see one or more files in this directory that look like
-  <div class="code">metacat&lt;X&gt;.xml</div>
-  Metacat limits the number of entries to 25,000 (Google's limit is 50,000).  So for
-  every group of 25,000 public documents in Metacat, you will see additional sitemap
-  files where &lt;X&gt; increments for each file.</p>
-  
-  <p>You should verify that your sitemap files are available to the web by browsing
-  to
-  <div class="code">&lt;your_web_context&gt;/sitemaps/metacat&lt;X&gt;.xml</div>
-  for instance 
-  <div class="code">your.server.org/knb/sitemaps/metacat1.xml</div></p>
-  
-  <a name="SubmitSitemap"></a><div class="header1">Submit Your Sitemap</div>
-  <a name="GoogleRegister"></a><div class="header2">Register With Google</div>
-  <p>You will need to register for a Google Webmaster Tools account in order to
-  register your sitemaps.  A good description of how to do this is on 
-  <a href="http://www.google.com/support/webmasters/bin/answer.py?answer=34575&topic=8496">
-  the Google help site</a>.  Follow the instructions there to get your sitemaps registered.</p>
-  
-  <p>One note: you should register the full url path to your sitemap files, including 
-  the http:// (or https://) headers.</p>
-
-  <a name="GoogleReRegister"></a><div class="header2">Re-Register With Google</div>  
-  <p>You will need to periodically revisit the Google Webmaster Tools utility to 
-  refresh your sitemap registration as you add more publicly accessible data to
-  Metacat.</p>
-  <p>A future enhancement to Metacat will automatically refresh the sitemap 
-  registration when necessary, although you will still need to do the initial
-  registration manually.</p>
-  
-  <br>
-  <a href="./pagedreturn.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./unimplem.html">Next</a>
-  </ul>
-  
-
-</BODY>
-</HTML>

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===================================================================
--- docs/user/entries-refs.ldif	(revision 5315)
+++ docs/user/entries-refs.ldif	(nonexistent)
@@ -1,10 +0,0 @@
-#The referral to LTER's subtree
-dn: o=LTER,dc=ecoinformatics,dc=org
-objectclass: top
-objectclass: organization
-objectClass: referral
-objectclass: extensibleObject
-o: LTER
-description: referral to LTER's KNB subtree
-ref: ldap://alpha.nceas.ucsb.edu/o=LTER,dc=ecoinformatics,dc=org
-

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===================================================================
--- docs/user/domapi.html	(revision 5315)
+++ docs/user/domapi.html	(nonexistent)
@@ -1,75 +0,0 @@
-<!--
-  * domapi.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Document Object
-      Model (DOM)</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./xmltree.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./metacat.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  
-  <P> The Document Object Model (DOM) is an 
-  application programming interface (API) that defines the logical structure 
-  of HTML and XML documents. It provides interfaces for accessing and 
-  manipulating of documents. With DOM, programmers can build documents, 
-  navigate their structure, and add, modify, or delete elements and content. 
-  Anything found in an HTML or XML document can be accessed, changed, deleted, 
-  or added using DOM. The DOM presents documents as a hierarchy of 
-  Node objects.
-  <P> <img alt="tree representation of the DOM API" src="domapi.gif">
-  <P> The name "Document Object Model" was chosen because it is an 
-  "object model" in the traditional object oriented design sense: documents 
-  are modeled using objects, and the model encompasses not only the structure 
-  of a document, but also the behavior of a document and the objects of which 
-  it is composed. In other words, the nodes in the above diagram do not 
-  represent a data structure, they represent objects, which have functions 
-  and identity. As an object model, the DOM identifies:<br>
-  <ul>
-    <li>the interfaces and objects used to represent and manipulate a document</li>
-    <li>the semantics of these interfaces and objects - including both behavior 
-    and attributes </li>
-    <li>the relationships and collaborations among these interfaces and 
-    objects</li> 
-  </ul>
-  <P> The DOM specifies interfaces which may be used to manage XML or HTML 
-  documents. It is important to realize that these interfaces are an abstraction 
-  - much like "abstract base classes" in C++, they are a means of specifying a 
-  way to access and manipulate an application's internal representation of a 
-  document. Interfaces do not imply a particular concrete implementation. 
-  <b>Each DOM application is free to maintain documents in any convenient 
-  representation, as long as the interfaces shown in this specification are 
-  supported. </b>
-  <P> The DOM is designed to be used with any programming language. In order 
-  to provide a precise, language-independent specification of the DOM 
-  interfaces, W3C have chosen to define the specifications in Object Management 
-  Group (OMG) IDL [OMGIDL]. They provide language bindings for Java [Java] and 
-  ECMAScript [ECMAScript] (an industry-standard scripting language based on 
-  JavaScript [JavaScript] and JScript [JScript]).
-
-  <br>
-  <a href="./xmltree.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./metacat.html">Next</a>
-  
-</BODY>
-</HTML>
-

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Index: docs/user/properties.html
===================================================================
--- docs/user/properties.html	(revision 5315)
+++ docs/user/properties.html	(nonexistent)
@@ -1,1711 +0,0 @@
-<!--
-  * properties.html
-  *
-  *      Authors: Chad Berkley
-  *    Copyright: 2008 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2001 January 23
-  *      Version: 
-  *    File Info: '$ '
-  * 
-  * 
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat Properties Files</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Metacat Properties File</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./datafiles.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./harvester.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <p> Metacat Server has properties that are stored in two general locations. 
-     Global properties are held in:
-     <p class="indent"><em>&lt;CONTEXT_DIR&gt;*/WEB_INF/metacat.properties</em>.</p>
-     Skin specific properties are set on a per-skin basis in:  
-     <p class="indent"><em>&lt;CONTEXT_DIR&gt;*/WEB_INF/style/skins/&lt;SKIN_NAME&gt;/&lt;SKIN_NAME&gt;.properties</em></p>
-  </p>  
-   
-  <p> 
-     The most dynamic properties are modified using the internal <a href="./metacat-configure.html">Metacat configuration utility </a>.
-     However, it may be necessary to manually edit a configuration file to update more static values.
-  </p>   
-   
-  <p>   
-     The list of properties shown on this page gives the following information about each property:
-     <ul>
-       <li> <b>Property Name</b> - the header for each section is the name of the 
-         property as it appears in the property file.</li>
-       <li> <b>Default Value</b> - the default value set for that property if any. </li>
-       <li> <b>Description</b> - what does the property control and how can it be set. </li>
-       <li> <b>Set Method</b> - how does the value get set in the properties file.  There are
-         two options:
-         <ul>
-           <li> Configuration Utility - the value is set via the internal <a href="./metacat-configure.html">Metacat configuration utility </a></li>
-           <li> Manually - the value is set to a default that can only be changed by manually editing the configuration file. </li>
-         </ul>  
-       <li> <b>Example</b> - an example setting for the property.</li>
-     </ul>
-  </p>
-  
-  <p class="footnote">    
-     (* CONTEXT_DIR refers to the directory where the Metacat application code
-     lives.  This is a combination of the web application directory and the 
-     metacat context directory.  This usually looks something like 
-     /usr/local/tomcat/webapps/knb.  However, your webapps directory could
-     be somewhere besides the tomcat directory and your context could be 
-     something other than knb.)
-  </p>
-  
-  <h1>Index</h1>
-  <div class="index-header"><a href="#GlobalMetacatProperties">Global Metacat Properties</a></div>
-    <div class="index-entry"><a href="#server.name">Server Values</a></div>
-    <div class="index-entry"><a href="#application.metacatVersion">Application Values</a></div>
-    <div class="index-entry"><a href="#database.connectionURI">Database Values</a></div>
-    <div class="index-entry"><a href="#auth.class">Authorization Values</a></div>
-    <div class="index-entry"><a href="#auth.administrators">Authentication Values</a></div>
-    <div class="index-entry"><a href="#xml.saxparser">XML/EML Values</a></div>    
-  
-  <a name="GlobalMetacatProperties"></a><h1>Global Metacat Properties - (metacat.properties) </h1>
-  <hr>
-  
-  <a name="server.name"></a><h1 class="property-main"> server.name </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">localhost</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">The network host name that will be 
-      used to access Metacat.  Note that this is not necessarily the physical
-      name of the server running Metacat.  The host name should not include
-      the protocol prefix (http://).</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">knb.ecoinformatics.org</p>
-  </div>
-
-  <a name="server.httpPort"></a><h1 class="property-main"> server.httpPort </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">80</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">The network port that will be 
-      used to access Metacat for non-secure (standard) connections.
-      This is usually 80 if Apache web server is running (typical install), and 
-      8080 if Tomcat is running alone, but both Apache and Tomcat could
-      have been configured to listen on alternate ports. </p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">80</p>
-  </div>  
-    
-  <a name="server.httpSSLPort"></a><h1 class="property-main"> server.httpSSLPort </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">443</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">The network port that will be 
-      used to access Metacat for secure connections.
-      This is usually 443 if Apache web server is running (typical install), and 
-      8443 if Tomcat is running alone, but both Apache and Tomcat could
-      have been configured to listen on alternate ports. </p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">443</p>
-  </div>  
-  
-  <br>
-  
-  <a name="application.metacatVersion"></a><h1 class="property-main"> application.metacatVersion </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">1.9.0</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">The Metacat version number.  usually, this should
-    never be changed.  It is set by the build engineer at build time.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">1.9.0</p>
-  </div>   
-  
-  <a name="application.metacatReleaseInfo"></a><h1 class="property-main"> application.metacatReleaseInfo </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">none</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">This allows for some more detailed information about the 
-    release for display purposes.  Typically it is used during the release candidate cycle
-    to let users know which candidate they are downloading.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">Release Candidate 1</p>
-  </div>         
- 
-  <a name="application.deployDir"></a><h1 class="property-main"> application.deployDir </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">(none)</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">The directory where web applications are deployed.
-      Many times this is in a directory named "webapps" in the Tomcat installation 
-      directory.  However, Tomcat may be configured to look in a different directory.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">/usr/local/tomcat/webapps</p>
-  </div>    
-  
-  <a name="application.context"></a><h1 class="property-main"> application.context </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">(none)</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">Applications run in individual directories in the applicaton 
-      deployment directory.  The name of the application directory is the application 
-      context. This corresponds to the first part of the war file name (the part before .war).  
-      Most commonly, this is "knb", but it can be changed to other things.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">knb</p>
-  </div>    
-  
-  <a name="application.default-style"></a><h1 class="property-main"> application.default-style </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">default</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">There are some custom web skins available in Metacat.  
-    Typically these are associated with an organizational theme.  If there is not
-    a custom skin for your organization, you should leave it as "default".</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">default</p>
-  </div>    
-  
-  <a name="application.knbSiteURL"></a><h1 class="property-main"> application.knbSiteURL </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">http://knb.ecoinformatics.org</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">The KNB site to redirect to.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">http://knb.ecoinformatics.org</p>
-  </div>   
-  
-  <a name="application.datafilepath"></a><h1 class="property-main"> application.datafilepath </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">/var/metacat/data</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">This is the directory whera data files will be stored.
-      This should be some directory outside the Metacat installation directories so
-      data files will not get lost when Metacat is upgraded.  The data file directory
-      must be writable by the user that starts Tomcat (and thus Metacat).</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">/var/metacat/data</p>
-  </div>     
-  
-  <a name="application.inlinedatafilepath"></a><h1 class="property-main"> application.inlinedatafilepath </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">/var/metacat/inline-data</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">This is the directory where inline data files will 
-      be stored.  Inline data files are created from data that is embedded in EML 
-      metadata.  This should be some directory outside the Metacat installation 
-      directories so data files will not get lost when Metacat is upgraded.  For 
-      clarity of data, this should probably not be the same as application.datafilepath.
-      The data file directory must be writable by the user that starts Tomcat (and thus Metacat).</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">/var/metacat/inline-data</p>
-  </div>  
-  
-  <a name="application.documentfilepath"></a><h1 class="property-main"> application.documentfilepath </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">/var/metacat/documents</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">This is the directory where metadata document files will 
-      be stored.  This should be some directory outside the Metacat installation 
-      directories so document files will not get lost when Metacat is upgraded.  For 
-      clarity of organization, this should probably not be the same as application.datafilepath
-      or application.inlinedatafilepath. The data file directory must be writable by the 
-      user that starts Tomcat (and thus Metacat).</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">/var/metacat/documents</p>
-  </div>   
-  
-  <a name="application.tempDir"></a><h1 class="property-main"> application.tempDir </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">/var/metacat/temporary</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">This is the directory that Metacat data registry uses 
-      to store temporary files. This should not be the same as application.datafilepath
-      or application.inlinedatafilepath (or any other persistant file path) since all files
-      in this may be purged programatically. The temporary file directory must be writable 
-      by the user that starts Apache. </p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">/var/metacat/temporary</p>
-  </div>         
-   
-  <a name="application.cgiDir"></a><h1 class="property-main"> application.cgiDir </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">/cgi</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">This is the directory that is configured in 
-      Apache web server to point to Metacat cgi executables.  The directory is given 
-      relative to the Metacat context directory since the Metacat cgi scripts
-      are installed with the application code.  For example, if Metacat is installed
-      in /usr/local/tomcat/knb, then an application.cgiDir of /cgi would point to <br>
-      &nbsp;&nbsp;&nbsp;&nbsp/usr/local/tomcat/knb/cgi-dir</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">/cgi-bin</p>
-  </div>   
-  
-  <a name="replication.logdir"></a><h1 class="property-main"> replication.logdir </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">none</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">If you are using replication, you will need to specify where
-    you would like the replication log to be written.  You must choose a directoy
-    that is writable by the user that starts Tomcat.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">/usr/locat/tomcat/logs</p>
-  </div>     
-  
-  <br> 
-
-  <a name="database.connectionURI"></a><h1 class="property-main"> database.connectionURI </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">jdbc:postgresql://localhost/metacat</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">The jdbc connection URI for the main 
-    database instance of Metacat.  The uri is formatted like: <br>
-    &nbsp;&nbsp;&nbsp;&nbsp;jdbc:&lt;database_type&gt;:thin@&lt;your_server_name&gt;:1521:&lt;metacat_database_name&gt;<br>
-    An empty database must have been created prior to Metacat 
-    configuration.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">jdbc:postgresql://yourserver.yourdomain.edu/metacat</p>
-  </div>   
-  
-  <a name="database.user"></a><h1 class="property-main"> database.user </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">(none)</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">The user for the main database instance 
-    of Metacat.  The user must have already been created on the database.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">metacat-user</p>
-  </div>     
-  
-  <a name="database.password"></a><h1 class="property-main"> database.password </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">(none)</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">The password of the user for the main 
-    database instance of Metacat.  The password must have already been created
-    for the user.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">securepassword4843</p>
-  </div>   
-
-  <a name="database.type"></a><h1 class="property-main"> database.type </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">(none)</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">The type of database you are running.  Currently, 
-    there are two supported types, Oracle and Postgres.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">postgres</p>
-  </div>   
-  
-  <a name="database.driver"></a><h1 class="property-main"> database.driver </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">(none)</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">The JDBC driver to be used to access the main 
-    database instance of Metacat.  There is one of these associated with each
-    type of database.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">org.postgresql.Driver</p>
-  </div> 
-  
-  <a name="database.adapter"></a><h1 class="property-main"> database.adapter </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">(none)</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">The adapter class that allows Metacat to access your 
-    database type.  There is one of these associated with each type of database.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">edu.ucsb.nceas.dbadapter.PostgresqlAdapter</p>
-  </div>   
-  
-  <a name="database.scriptsuffix"></a><h1 class="property-main"> database.scriptsuffix.&lt;database_type&gt; </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">
-      <br>&nbsp;&nbsp;&nbsp;&nbsp;database.scriptsuffix.postgres=postgres.sql<br>
-      &nbsp;&nbsp;&nbsp;&nbsp;database.scriptsuffix.oracle=oracle.sql
-    </p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">There is a database.scriptsuffix entry for every
-      supported type of database.  These tell the system which database scripts
-      to run when installing or updating database schema.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">postgres.sql</p>
-  </div>   
-  
-  <a name="database.upgradeVersion"></a><h1 class="property-main"> database.upgradeVersion.&lt;database_version&gt; </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">
-      <br>&nbsp;&nbsp;&nbsp;&nbsp;database.upgradeVersion.0.0.0=xmltables,loaddtdschema<br>
-          &nbsp;&nbsp;&nbsp;&nbsp;database.upgradeVersion.1.2.0=upgrade-db-to-1.2<br>
-          &nbsp;&nbsp;&nbsp;&nbsp;database.upgradeVersion.1.3.0=upgrade-db-to-1.3<br>
-          &nbsp;&nbsp;&nbsp;&nbsp;database.upgradeVersion.1.4.0=upgrade-db-to-1.4<br>
-          &nbsp;&nbsp;&nbsp;&nbsp;database.upgradeVersion.1.5.0=upgrade-db-to-1.5<br>
-          &nbsp;&nbsp;&nbsp;&nbsp;database.upgradeVersion.1.6.0=upgrade-db-to-1.6<br>
-          &nbsp;&nbsp;&nbsp;&nbsp;database.upgradeVersion.1.7.0=upgrade-db-to-1.7<br>
-          &nbsp;&nbsp;&nbsp;&nbsp;database.upgradeVersion.1.8.0=upgrade-db-to-1.8<br>
-          &nbsp;&nbsp;&nbsp;&nbsp;database.upgradeVersion.1.9.0=upgrade-db-to-1.9
-    </p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text">There is a database.scriptsuffix entry for every
-      metacat database schema version. (Note that a schema version corresponds
-      to an application version.) These tell the system which database scripts
-      to run when installing or updating database schema.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">upgrade-db-to-1.2</p>
-  </div>   
-  
-  <a name="database.initialConnections"></a><h1 class="property-main"> database.initialConnections </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">5</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The number of initial connection that 
-      Metacat creates to the database.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">5</p>
-  </div>   
-  
-  <a name="database.incrementConnections"></a><h1 class="property-main"> database.incrementConnections </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">5</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The number of connections that are created 
-      when Metacat needs more connections.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">5</p>
-  </div>   
-  
-  <a name="database.maximumConnections"></a><h1 class="property-main"> database.maximumConnections </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">25</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The maximum number of database connections 
-      Metacat can make.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">25</p>
-  </div>   
-
-  <a name="database.maximumConnectionAge"></a><h1 class="property-main"> database.maximumConnectionAge </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">120000</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The maximum time in milliseconds that a database
-      connection can live.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">120000</p>
-  </div>   
-  
-  <a name="database.maximumConnectionTime"></a><h1 class="property-main"> database.maximumConnectionTime </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">60000</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The maximum time in milliseconds that a database
-      connection can accumulate in actual connection time.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">60000</p>
-  </div>   
-
-  <a name="database.maximumUsageNumber"></a><h1 class="property-main"> database.maximumUsageNumber </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">100</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The maximum number of times a single connection
-      can be used.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">100</p>
-  </div>   
-
-  <a name="database.numberOfIndexingThreads"></a><h1 class="property-main"> database.numberOfIndexingThreads </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">5</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The number of threads available for indexing.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">5</p>
-  </div>   
-  
-  <a name="database.indexingTimerTaskTime"></a><h1 class="property-main"> database.indexingTimerTaskTime </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">604800000</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The time in milliseconds between indexing.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">604800000</p>
-  </div>    
-  
-  <a name="database.indexingInitialDelay"></a><h1 class="property-main"> database.indexingInitialDelay </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">3600000</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The delay in milliseconds before first indexing is executed.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">3600000</p>
-  </div>  
- 
-  <a name="database.maximumIndexDelay"></a><h1 class="property-main"> database.maximumIndexDelay </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">5000</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The time in milliseconds that an indexing thread
-      will wait when it can't get a doc id before retrying the indexing.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">5000</p>
-  </div>   
- 
-  <a name="database.runDBConnectionRecycleThread"></a><h1 class="property-main"> database.runDBConnectionRecycleThread </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">off</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> Determines whether the database connection
-      pool should run a thread to recycle connections.  Possible values are
-      "on" and "off"</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">off</p>
-  </div>  
-  
-  <a name="database.cycleTimeOfDBConnection"></a><h1 class="property-main"> database.cycleTimeOfDBConnection </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">30000</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The time in milliseconds between connection
-      recycling runs.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">30000</p>
-  </div>   
-  
-  <a name="database.queryignoredparams"></a><h1 class="property-main"> database.queryignoredparams </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">enableediting,foo</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> Parameters to ignore in a structured
-      xml query.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">enableediting</p>
-  </div> 
-  
-  <a name="database.usexmlindex"></a><h1 class="property-main"> database.usexmlindex </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">true</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> Determines whether to use xml 
-      indexes when finding documents.  Possible values are true
-      and false.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">true</p>
-  </div>
-  
-  <a name="database.appResultsetSize"></a><h1 class="property-main"> database.appResultsetSize </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">7000</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> Determines the number of results that get sent
-    back to an application from a query.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">7000</p>
-  </div>  
-     
-  <a name="database.webResultsetSize"></a><h1 class="property-main"> database.webResultsetSize </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">7000</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> Determines the number of results that get sent
-    back to a web browser from a query.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">7000</p>
-  </div>  
-
-  <a name="database.xmlReturnfieldCount"></a><h1 class="property-main"> database.xmlReturnfieldCount </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">0</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> If the results of a query have been returned
-    more times than database.xmlReturnfieldCount, then those results will be
-    inserted into the xml_queryresult table in the database.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">0</p>
-  </div>  
-
-  <a name="database.queryresultStringLength"></a><h1 class="property-main"> database.queryresultStringLength </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">500000</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> This is used to set the max size of 
-    the query result string in the queryresult table. This should be
-    set to some number less than 4000 if an Oracle database is being 
-    used.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">500000</p>
-  </div>  
-
-  <a name="database.queryresultCacheSize"></a><h1 class="property-main"> database.queryresultCacheSize </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">500</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The number of query results that will be cached.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">500</p>
-  </div>  
-
-  <a name="database.queryCacheOn"></a><h1 class="property-main"> database.queryCacheOn </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">on</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> Determines whether query caching is turned on.  Acceptible
-    values are &quot;on&quot; and &quot;off&quot;</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">on</p>
-  </div>  
-  
-  <br>
-  
-  <a name="auth.class"></a><h1 class="property-main"> auth.class </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">edu.ucsb.nceas.metacat.AuthLdap</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The class that is used for user authentication.  Currently,
-    only the AuthLdap class is included in the Metacat distribution, but it is possible
-    for an admin to implement other authentication strategies by implementing a Java
-    class that extends the AuthInterface interface and rebuilding Metacat.  Change this to 
-    be the fully qualified class name of your custom authentication mechanism.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">edu.ucsb.nceas.metacat.AuthLdap</p>
-  </div>  
-
-  <a name="auth.timeoutMinutes"></a><h1 class="property-main"> auth.timeoutMinutes </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">180</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The number of minutes that a user will stay logged
-    in to Metacat without any activity.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">180</p>
-  </div>  
-  
-  <br>
-
-  <a name="auth.administrators"></a><h1 class="property-main"> auth.administrators </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">(none)</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> A colon separated list of The ldap users
-    or groups that have administrative privileges to Metacat.  Note that 
-    during the intial installation of Metacat, the installer will be 
-    asked to enter this value.  <font color="red">At least one 
-    user or group must be entered and all accounts must exist in LDAP, 
-    or the installer will not be allowed to continue with the 
-    configuration.</font></p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> <br>
-    <p class="property-text">uid=youruser,o=NCEAS,dc=ecoinformatics,dc=org</p><br>
-    <p class="property-text">cn=yourgroup,o=NCEAS,dc=ecoinformatics,dc=org</p>
-  </div>  
-  
-  <a name="auth.url"></a><h1 class="property-main"> auth.url </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">ldap://ldap.ecoinformatics.org:389/</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The url of the server that Metacat
-    should use for authentication.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">ldap://ldap.ecoinformatics.org:389/</p>
-  </div> 
-  
-  <a name="auth.surl"></a><h1 class="property-main"> auth.surl </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">ldap://ldap.ecoinformatics.org:389/</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The url of the server that Metacat
-    should use for  secure authentication.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">ldap://ldap.ecoinformatics.org:389/</p>
-  </div>   
-
-  <a name="auth.base"></a><h1 class="property-main"> auth.base </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">dc=ecoinformatics,dc=org</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The base part of the distinguished name that 
-    metacat uses for authentication.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">dc=ecoinformatics,dc=org</p>
-  </div> 
- 
-  <a name="auth.allowedSubmitters"></a><h1 class="property-main"> auth.allowedSubmitters </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">(none)</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> A colon delimited list of users who should 
-    be allowed to submit documents. If no value is specified, all users will 
-    be allowed to submit documents.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">uid=youruser,o=NCEAS,dc=ecoinformatics,dc=org</p>
-  </div>   
-  
-  <a name="auth.deniedSubmitters"></a><h1 class="property-main"> auth.deniedSubmitters </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">(none)</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Configuration Utility</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> A colon delimited list of users who should not
-    be allowed to submit documents. If no value is specified, all users will 
-    be allowed to submit documents.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">uid=youruser,o=NCEAS,dc=ecoinformatics,dc=org</p>
-  </div> 
-
-  <a name="ldap.connectTimeLimit"></a><h1 class="property-main"> ldap.connectTimeLimit </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">5000</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The time in milliseconds allowed for ldap 
-    server connections.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">5000</p>
-  </div> 
-  
-  <a name="ldap.searchTimeLimit"></a><h1 class="property-main"> ldap.searchTimeLimit </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">30000</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The time in milliseconds allowed for ldap server searches.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">30000</p>
-  </div>   
-  
-  <a name="ldap.searchCountLimit"></a><h1 class="property-main"> ldap.searchCountLimit </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">30000</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> the count of return entries allowed for ldap server searches.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">30000</p>
-  </div>     
- 
-  <a name="ldap.referral"></a><h1 class="property-main"> ldap.referral </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">follow</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The type of ldap referrals to use. Acceptible values are
-    &quot;follow&quot;, &quot;throw&quot; or &quot;none&quot;. Refer to ldap documentation 
-    for further information.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">follow</p>
-  </div>         
-
-  <a name="ldap.onlySecureConnection"></a><h1 class="property-main"> ldap.onlySecureConnection </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">false</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> Determines whether to only use secure ldap server.
-    Acceptible values are &quot;true&quot; and &quot;false&quot;.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">false</p>
-  </div>   
-
-  <a name="ldap.onlySecureReferalsConnection"></a><h1 class="property-main"> ldap.onlySecureReferalsConnection </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">false</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> Determines whether to only use secure referral server.
-    Acceptible values are &quot;true&quot; and &quot;false&quot;.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">false</p>
-  </div>   
-
-  <br>
-
-  <a name="xml.saxparser"></a><h1 class="property-main"> xml.saxparser </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">org.apache.xerces.parsers.SAXParser</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The SAX parser used to parse XML documents. 
-    See: <a href="./saxparser.html">SAX parser documentation</a>. </p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">org.apache.xerces.parsers.SAXParser</p>
-  </div>   
-
-  <a name="xml.eml2_0_0namespace"></a><h1 class="property-main"> xml.eml2_0_0namespace </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">eml://ecoinformatics.org/eml-2.0.0</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The namespace of EML 2.0.0 documents. </p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">eml://ecoinformatics.org/eml-2.0.0</p>
-  </div>
-  
-  <a name="xml.eml2_0_1namespace"></a><h1 class="property-main"> xml.eml2_0_1namespace </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">eml://ecoinformatics.org/eml-2.0.1</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The namespace of EML 2.0.1 documents. </p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">eml://ecoinformatics.org/eml-2.0.1</p>
-  </div>
-
-  <a name="xml.eml2_1_0namespace"></a><h1 class="property-main"> xml.eml2_1_0namespace </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">eml://ecoinformatics.org/eml-2.1.0</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The namespace of EML 2.1.0 documents. </p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">eml://ecoinformatics.org/eml-2.1.0</p>
-  </div>
-
-  <a name="xml.packagedoctype"></a><h1 class="property-main"> xml.packagedoctype </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">-//ecoinformatics.org//eml-dataset-2.0.0beta6//EN, -//ecoinformatics.org//eml-dataset-2.0.0beta4//EN</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The doctype of a package file. The system will only 
-    recognize documents of this type as package files. See: 
-    <a href="./packages.html">package documentation</a>.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">-//ecoinformatics.org//eml-dataset-2.0.0beta6//EN, -//ecoinformatics.org//eml-dataset-2.0.0beta4//EN</p>
-  </div>
-
-  <a name="xml.accessdoctype"></a><h1 class="property-main"> xml.accessdoctype </h1>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Default Value: </h2> 
-    <p class="property-text">-//ecoinformatics.org//eml-access-2.0.0beta6//EN, -//ecoinformatics.org//eml-access-2.0.0beta4//EN</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Set Method: </h2> 
-    <p class="property-text">Manual</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Description: </h2> 
-    <p class="property-text"> The doctype of an access control list (ACL) file. The 
-    system will only recognize documents of this type as access files. See: 
-    <a href="./acontrol.html">access control documentation</a>.</p>
-  </div>
-  <div class="property-description-line">
-    <h2 class="property-inline"> Example: </h2> 
-    <p class="property-text">-//ecoinformatics.org//eml-access-2.0.0beta6//EN, -//ecoinformatics.org//eml-access-2.0.0beta4//EN</p>
-  </div>
-
-
-
-
-
-  <!-- table border="1">
-    <tr>
-      <td><b>Property</b></td>
-      <td><b>Description</b></td>
-      <td><b>Possible or default value</b></td>
-    </tr>
-    <tr>
-      <td>config-dir</td>
-      <td>directory where the style-sets exist</td>
-      <td>/opt/tomcat/webapps/metacat/lib</td>
-    </tr>
-    <tr>
-      <td>default-style</td>
-      <td>the style-set to use if qformat is set to 'html'</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td>xmlcatalogfile</td>
-      <td>The default file type catalog file location.<br>
-      DEPRECATED</td>
-      <td>/opt/tomcat/webapps/xmltodb/catalog.txt</td>
-    </tr>
-    <tr>
-      <td>siteCode</td>
-      <td>The code for the current site.</td>
-      <td>nceas</td>
-    </tr>
-    <tr>
-      <td>accNumSeparator</td>
-      <td>The separator that is used to separate the three parts 
-          of the accession number: codename, sequence and revision number.
-           changing this parameter will likely break the application, so make
-           sure you know what you are doing.  It should be synchronized with 
-           the Client application.</td>
-      <td>. (period)</td>
-    </tr>
-    <tr>
-      <td>saxparser</td>
-      <td>The SAX parser to be used to <a href="./saxparser.html">parse</a> 
-      XML documents.</td>
-      <td>org.apache.xerces.parsers.SAXParser</td>
-    </tr>
-    <tr>
-      <td>servletpath</td>
-      <td>The path on the local machine to the Metacat Servlet.</td>
-      <td>/knb/servlet/metacat</td>
-    </tr>
-    <tr>
-      <td>htmlpath</td>
-      <td>The path to the HTML server for this Metacat context.  This is where
-      the Metacat web interface would be served from.</td>
-      <td>/knb</td>
-    </tr>
-    <tr>
-      <td>packagedoctype</td>
-      <td>The doctype of a package file.  The system will only recognize documents
-      of this type as a <a href="./packages.html">Package</a> files.</td>
-      <td>-//NCEAS//eml-dataset-2.0//EN</td>
-    </tr>
-    <tr>
-      <td>accessdoctype</td>
-      <td>The doctype of an access control list (ACL) file.  The system will 
-          only recognize documents of this type as an <a href="./acontrol.html">Access</a> 
-          files.</td>
-      <td>-//NCEAS//eml-access-2.0//EN</td>
-    </tr>
-    <tr>
-      <td>server</td>
-      <td>The server on which this Metacat server runs.</td>
-      <td>dev.nceas.ucsb.edu:8090</td>
-    </tr>
-    <tr>
-      <td>authclass</td>
-      <td>The authorization plugin to use.  In this example, LDAP.</td>
-      <td>edu.ucsb.nceas.metacat.AuthLdap</td>
-    </tr>
-    <tr>
-      <td>ldapurl</td>
-      <td>The path to your LDAP server (if LDAP authentication is being used.</td>
-      <td>ldap://ldap.nceas.ucsb.edu:389/</td>
-    </tr>
-    <tr>
-      <td>ldapsurl</td>
-      <td>The path to your LDAP server with SSL support.
-          (if LDAP authentication is being used and if your LDAT server is set
-          with SSL support.) 2 ports are used to listen: 389 for plain sockets 
-          and 636 for SSL Sockect. If your LDAP server is not set to support SSL
-          this property should be the same as ldapurl, else Metacat will
-          retieve an error.</td>
-      <td>ldap://ldap.nceas.ucsb.edu:636/</td>
-    </tr>
-    <tr>
-      <td>ldapbase</td>
-      <td>LDAP base parameters for the LDAP server.</td>
-      <td>o=NCEAS,c=US</td>
-    </tr>
-    <tr>
-      <td>referral</td>
-      <td>The type of ldap referrals you want to use.  Eithe 'follow', 'throw' or 
-      'none'.  See the ldap documentation for further information</td>
-      <td>follow</td>
-    </tr>
-    <tr>
-      <td>deltaT</td>
-      <td>The default delta T used for <a href="./replication.html">replication</a>.</td>
-      <td>60</td>
-    </tr>
-    <tr>
-      <td>replicationpath</td>
-      <td>The relative path to the replication servlet.</td>
-      <td>/knb/servlet/replication</td>
-    </tr>
-    <tr>
-      <td>replicationlog</td>
-      <td>Location of the replication log file.</td>
-      <td>/logs/Metacatreplication.log</td>
-    </tr>
-    <tr>
-      <td>dtdPath</td>
-      <td>Path to which DTDs are uploaded.</td>
-      <td>/opt/tomcat/webapps/knb/dtd/</td>
-    </tr>
-    <tr>
-      <td>dtdURL</td>
-      <td>The HTTP accessable URL to the DTD files specified in dtdPath.</td>
-      <td>http://server.domain.com/knb/dtd/</td>
-    </tr>
-    <tr>
-      <td>datafilepath</td>
-      <td>The path to which you want data files uploaded.</td>
-      <td>/opt/tomcat/webapps/knb/data</td>
-    </tr>
-    <tr>
-      <td>certPath</td>
-      <td>path to the SSL keys for secure transmissions.</td>
-      <td>/opt/tomcat/webapps/metacat/lib</td>
-    </tr>
-    <tr>
-      <td>administrators</td>
-      <td>The administrators parameter lists the accounts that are allowed to
-          perform administrative actions such as rebuilding indices for 
-          documents. The list can can contain more than one account separated
-          by colons.</td>
-      <td>Default:&nbsp;&nbsp;
-          <code>uid=jones,o=NCEAS,dc=ecoinformatics,dc=org</code>
-      <br><br>Examples:&nbsp;&nbsp;
-          <code>uid=localadmin,o=ucnrs.org</code>
-      </td>
-    </tr>
-    <tr><td> </td></tr>
-
-
-    <tr><td colspan="3"><b>Additional properties that probably do not need to be changed</b></td></tr>
-    <tr><td>configured</td><td>Configuration flag</td><td>true</td></tr>
-    <tr><td>configurationPage</td><td>The page to do metacat configuration<td>/configure.jsp</td></tr>
-    <tr><td>configurationSuccessPage</td><td>The page to show successful message after configuration</td><td>/configure-restart.jsp</td></tr>
-    <tr><td>version</td><td>Release version.</td><td>1.7.1</td></tr>
-    <tr><td>maximumConnectionAge</td><td> </td><td>120000</td></tr>
-    <tr><td>maximumConnectionTime</td><td> </td><td>60000</td></tr>
-    <tr><td>maximumUsageNumber</td><td> </td><td>100</td></tr>
-    <tr><td>numberOfIndexingThreads</td><td> </td><td>5</td></tr>
-    <tr><td>indexingTimerTaskTime</td><td> </td><td>604800000</td></tr>
-    <tr><td>indexingInitialDelay</td><td> </td><td>3600000</td></tr>
-    <tr><td>maximumIndexDelay</td><td> </td><td>5000</td></tr>
-    <tr><td>runDBConnectionRecycleThread</td><td> </td><td>off</td></tr>
-    <tr><td>cycleTimeOfDBConnection</td><td> </td><td>30000</td></tr>
-    <tr>
-      <td>timedreplication</td>
-      <td>Determines whether timed replication to other metacat servers is being used.</td>
-      <td>Default:&nbsp;&nbsp;
-          <code>false</code>
-      <br><br>Other possible values:&nbsp;&nbsp;
-          <code>true</code>
-      </td>
-    </tr>
-    <tr>
-      <td>firsttimedreplication</td>
-      <td>The time for starting first timed replication if timedreplication is true.
-          (See comments in build.properties file for additional details.)</td>
-      <td>Default:&nbsp;&nbsp;
-          <code>10:00 PM</code>
-          <code>&nbsp;</code>
-      </td>
-    </tr>
-    <tr>
-      <td>timedreplicationinterval</td>
-      <td>The interval to next timed replication if timedreplication is true.
-          The value is in milliseconds and default value is 48 hours.</td>
-      <td>Default:&nbsp;&nbsp;
-          <code>172800000</code>
-          <code>&nbsp;</code>
-      </td>
-    </tr>
-    <tr><td>forcereplicationwaitingtime</td><td> </td><td></td></tr>
-    <tr><td>eml2_0_0namespace</td><td>Namespace of EML 2.0.0 documents.</td><td>eml://ecoinformatics.org/eml-2.0.0</td></tr>
-    <tr><td>eml2_0_1namespace</td><td>Namespace of EML 2.0.1 documents.</td><td>eml://ecoinformatics.org/eml-2.0.1</td></tr>
-    <tr><td>eml2_1_0namespace</td><td>Namespace of EML 2.1.0 documents. Currently unused, reserved.</td><td>eml://ecoinformatics.org/eml-2.1.0</td></tr>
-    <tr><td>physicaldoctype</td><td> </td><td>-//ecoinformatics.org//eml-physical-2.0.0beta6//EN, -//ecoinformatics.org//eml-physical-2.0.0beta4//EN</td></tr>
-    <tr><td>entitydoctype</td><td> </td><td>-//ecoinformatics.org//eml-entity-2.0.0beta6//EN, -//ecoinformatics.org//eml-entity-2.0.0beta4//EN</td></tr>
-    <tr><td>packagedoctypeset</td><td> </td><td> </td></tr>
-    <tr>
-      <td>httpserver</td>
-      <td>httpserver is the plain HTTP address and port number that Metacat uses for purposes
-          other than replication. Since this property is usually composed of the <code>config.hosthame</code> and <code>config.port</code>
-          properties (described above), the default setting can be used in most cases.</td>
-      <td>Default:&nbsp;&nbsp;<code>${config.hostname}:${config.port}</code>
-      </td>
-    </tr>
-    <tr><td>junittesturl</td><td>The url of the test server.</td><td></td></tr>
-    <tr><td>replicationerrorlog</td><td> </td><td></td></tr>
-    <tr><td>schemaPath</td><td>Path to installed XSD schemas.</td><td></td></tr>
-    <tr><td>schemaURL</td><td>URL to installed XSD schemas.</td><td></td></tr>
-    <tr><td>inlinedatafilepath</td><td>Path for storing data that was extracted from <code>inline</code> element of EML documents.</td><td></td></tr>
-    <tr><td>context</td><td>The name of the servlet context</td><td></td></tr>
-    <tr><td>debuglevel</td><td>Verbosity of debugging messages.  Higher numbers means more debugging detail.</td><td></td></tr>
-    <tr><td>datafileflag</td><td> </td><td>datafile</td></tr>
-    <tr><td>datafilesizelimit</td><td>Limit on file size for uploaded data files.</td><td>1000</td></tr>
-    <tr><td>defaultcontenttype</td><td> </td><td></td></tr>
-    <tr><td>query.ignored.params</td><td>Parameters that are passed through to XSLT style sheets without modification.</td><td>enableediting,foo</td></tr>
-    <tr><td>usexmlindex</td><td>Flag indicating whether to use the traditional xml_index table or not.  This needs to be set on startup, and once set to false can not be changed back to true without significant database modifications.  Setting this option to 'false' also slows down queries significantly, but it does allow arbitrarily deep dcoument paths.  Not recommended to change this setting -- data loss may result.</td><td>true</td></tr>
-    <tr><td>app_resultsetsize</td><td>Used for the setting the size of resultset that is processed at a time for applications like morpho</td><td>400</td></tr>
-    <tr><td>web_resultsetsize</td><td>Used for the setting the size of resultset for search done using browser</td><td>900</td></tr>
-    <tr><td>queryresult_string_length</td><td>Used for the setting the size of queryresult_string in queryresult table</td><td>4000</td></tr>
-    <tr>
-      <td>queryresult_cache_size</td>
-      <td>The size of query result cache.</td>
-      <td>Default:&nbsp;&nbsp;500</td>
-    </tr>
-    <tr>
-      <td>query_cache_on</td>
-      <td>Turn the query result cache on or off</td>
-      <td>Default:&nbsp;&nbsp;true</td>
-    </tr>
-    <tr><td>xml_returnfield_count</td><td>Value of xml_returnfield.usage_count should be more than this value for records to be entered into xml_queryresult</td><td>0</td></tr>
-    <tr>
-      <td><a name="moderators">moderators</a></td>
-      <td>Moderator accounts, in a colon-separated list. Special users who will review general user's submission. 
-             Moderators can approve, revise and reject the submission after reviewing. This property is only used in ESA skin.</td>
-      <td>Default:&nbsp;&nbsp;<code>cn=knb-prod,o=NCEAS,dc=ecoinformatics,dc=org</code></td>
-    </tr>
-    <tr>
-      <td>allowedSubmitters</td>
-      <td>Specifies the list of users who should be allowed to submit documents. 
-          If no value is specified (the default setting), all users will be allowed to submit documents.
-      </td>
-      <td>Default:&nbsp;&nbsp;(no value)</td>
-    </tr>
-    <tr>
-      <td>deniedSubmitters</td>
-      <td>Specify the list of users who should not be allowed to submit documents. 
-          If no value is specified (the default setting), all users will be allowed to submit documents.</td>
-      <td>Default:&nbsp;&nbsp;(no value)</td>
-    </tr>
-    <tr>
-      <td>indexNamespaces</td>
-      <td>A comma-separated list of doctypes which will be indexed</td>
-      <td>Default:&nbsp;&nbsp;eml://ecoinformatics.org/eml-2.0.0,eml://ecoinformatics.org/eml-2.0.1</td>
-    </tr>
-    <tr>
-      <td>indexPaths</td>
-      <td>See <a href="./metacat-install.html#buildProperties">description of build properties</a></td>
-      <td>Default:&nbsp;&nbsp;<code>organizationName,originator/individualName/surName,...</code></td>
-    </tr>
-    <tr>
-      <td>ldapconnecttimelimit</td>
-      <td>The time in milliseconds allowed for ldap server connections.</td>
-      <td>Default:&nbsp;&nbsp;5000</td>
-    </tr>
-    <tr>
-      <td>ldapsearchtimelimit</td>
-      <td>The time in milliseconds allowed for ldap server searches.</td>
-      <td>Default:&nbsp;&nbsp;30000</td>
-    </tr>
-    <tr>
-      <td>ldapsearchcountlimit</td>
-      <td>The count of return entries allowed for ldap server searches.</td>
-      <td>Default:&nbsp;&nbsp;30000</td>
-    </tr>
-    <tr>
-      <td>onlySecureLDAPConnection</td>
-      <td>When set to true, connects main LDAP server only by SSL</td>
-      <td>Default:&nbsp;&nbsp;false</td>
-    </tr>
-    <tr>
-      <td>onlySecureLDAPReferalsConnection</td>
-      <td>When set to true, connects referal LDAP server only by SSL</td>
-      <td>Default:&nbsp;&nbsp;false</td>
-    </tr>
-    <tr>
-      <td>skinconfigfiles</td>
-      <td>List of skins which have configure files</td>
-      <td>Default:&nbsp;&nbsp;esa,nceas,knb,obfs,nrs,sanparks</td>
-    </tr>
-    <tr>
-      <td>writeDebugToFile</td>
-      <td>Used for writing debug info into a another output file.</td>
-      <td>Default:&nbsp;&nbsp;true</td>
-    </tr>
-    <tr>
-      <td>debugOutputFile</td>
-      <td>Output file name where debug info will be written.</td>
-      <td>Default:&nbsp;&nbsp;/tmp/metacat.debug</td>
-    </tr>
-    <tr>
-      <td>delimiteredOutputFile</td>
-      <td>Delimited text output file name where debug info will be written.</td>
-      <td>Default:&nbsp;&nbsp;/tmp/metacat.debug.delimitered</td>
-    </tr>
-    <tr>
-      <td><em>Metacat Harvester properties</em>:<br/><br/>
-          connectToMetacat, delay, harvesterAdministrator, 
-          logPeriod, maxHarvests, period, smtpServer, GetDocError, GetDocSuccess, GetHarvestListError,
-          GetHarvestListSuccess, HarvesterStartup, HarvesterShutdown, InsertDocError, InsertDocSuccess,
-          MetacatHasDoc, UpdateDocError, UpdateDocSuccess, ValidateDocError, ValidateDocSuccess,
-          ValidateHarvestListError, ValidateHarvestListSuccess</td>
-      <td>See <a href="./harvester.html">Metacat Harvester</a> documentation</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td><em>Spatial properties</em>:<br/><br/>
-              runSpatialOption,
-              regenerateCacheOnRestart,
-              spatialDocnameList,
-              eml_westBoundingCoordinatePath,
-              eml_eastBoundingCoordinatePath,
-              eml_southBoundingCoordinatePath,
-              eml_northBoundingCoordinatePath,
-              fgdc_westBoundingCoordinatePath,
-              fgdc_eastBoundingCoordinatePath,
-              fgdc_southBoundingCoordinatePath,
-              fgdc_northBoundingCoordinatePath,
-              metadata_westBoundingCoordinatePath,
-              metadata_eastBoundingCoordinatePath,
-              metadata_southBoundingCoordinatePath,
-              metadata_northBoundingCoordinatePath,
-              docTitle,
-              metacatUrl,
-              baseUrl
-      </td>
-      <td>See <a href="./spatial_option.html">Metacat Spatial Option</a> documentation</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td>sitemapDirectory</td>
-      <td>The relative directory path in which sitemap files should be written.</td>
-      <td>Default:&nbsp;&nbsp;{tomcat_dir}/webapps/{context_name}/sitemaps</td>
-    </tr>
-    <tr>
-      <td>sitemapInterval</td>
-      <td>The time interval (in milliseconds) between rebuilding the sitemap.</td>
-      <td>Default:&nbsp;&nbsp;86400000</td>
-    </tr>
-  </table -->
-  
-  <br>
-  <a href="./datafiles.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./harvester.html">Next</a>
-  
-
-</BODY>
-</HTML>

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Index: docs/user/default.css
===================================================================
--- docs/user/default.css	(revision 5315)
+++ docs/user/default.css	(nonexistent)
@@ -1,197 +0,0 @@
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-  *     Purpose: Default style sheet for KNB project web pages 
-  *              Using this stylesheet rather than placing styles directly in 
-  *              the KNB web documents allows us to globally change the 
-  *              formatting styles of the entire site in one easy place.
-  *   Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *     Authors: Matt Jones
-  *
-  *    '$Author$'
-  *      '$Date$'
-  *  '$Revision$'
-  *
-  * This program is free software; you can redistribute it and/or modify
-  * it under the terms of the GNU General Public License as published by
-  * the Free Software Foundation; either version 2 of the License, or
-  * (at your option) any later version.
-  *
-  * This program is distributed in the hope that it will be useful,
-  * but WITHOUT ANY WARRANTY; without even the implied warranty of
-  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  * GNU General Public License for more details.
-  *
-  * You should have received a copy of the GNU General Public License
-  * along with this program; if not, write to the Free Software
-  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-  */
-
-body { 
-    color: black; 
-    background: white;
-    font-size: 1em; 
-    font-family: Arial,Helvetica,sans-serif; }
-a {
-    color: green;
-    text-decoration: none; }
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-    color: green;
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-    color: green;
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-    font-weight: bold; }
-.logo {
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-    color: green;
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-.tabledefault {
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-.pagesub {
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-p { 
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Index: docs/user/ldap.html
===================================================================
--- docs/user/ldap.html	(revision 5315)
+++ docs/user/ldap.html	(nonexistent)
@@ -1,108 +0,0 @@
-<!--
-  * ldap.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">LDAP for User
-      Authentication in Metacat</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./acontrol.html">Back</a> | 
-        <a href="./metacattour.html">Home</a> | 
-        <a href="./metacatout.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <p><b>Network of LDAP servers</b></p>
-    <p>In the distributed network of Metacat servers, network of LDAP servers
-      is implemented as a distributed storage of Metacat's users.
-      Any Metacat instance running on particular site is configured to use 
-      certain LDAP instance both usually running on the same host.
-      Several Metacat instances can use one LDAP instance. </p>
-
-    <P> <img src="KNB-LDAP-system-small.gif"> </p>
-
-    <p>
-      The distributed scheme of LDAP servers represents a hierarchy of nodes
-      where in the leaves are the particular users used by the Metacat servers 
-      for authentication.
-      <br>
-      The LDAP tree starts from the root context for the Knowledge 
-      Network of Biocomplexity.:
-      <pre>      dc=ecoinformatics,dc=org </pre>
-      The nodes on the second level represent the subtrees of the major Metacat
-      sites such as NCEAS, LTER, etc.:  </p>
-<pre>
-      o=NCEAS,dc=ecoinformatics,dc=org <br>
-      or <br>
-      o=LTER,dc=ecoinformatics,dc=org </pre>
-
-      Look at the example for the
-<a target="_top" href="entries-init.ldif">initial entries of KNB main tree</a>
-      . <br><br>
-
-      The third level contains the nodes of the particular users and groups.
-      Users can be organized in groups. This allow Metacat to control access 
-      to a group of users.
-
-<pre>Definition of KNB development group at NCEAS:
-      dn: cn=knb-dev,o=NCEAS,dc=ecoinformatics,dc=org
-      objectClass: top
-      objectclass: groupOfUniqueNames
-      cn: knb-dev
-      uniqueMember: uid=jones,o=NCEAS,dc=ecoinformatics,dc=org
-      uniqueMember: uid=bojilova,o=NCEAS,dc=ecoinformatics,dc=org
-      uniqueMember: uid=berkley,o=NCEAS,dc=ecoinformatics,dc=org
-      uniqueMember: uid=higgins,o=NCEAS,dc=ecoinformatics,dc=org
-      uniqueMember: uid=harris,o=NCEAS,dc=ecoinformatics,dc=org
-      description: KNB development group at NCEAS </pre>
-
-      Look at the example for a 
-      <a target="_top" href="entries-groups.ldif">group entry in KNB</a>.
-      <br><br>
-
-<pre>Definition of a user from NCEAS subtree:
-      dn: uid=bojilova,o=NCEAS,dc=ecoinformatics,dc=org
-      objectClass: top
-      objectclass: person
-      objectClass: organizationalPerson
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-      uid: bojilova
-      cn: Jivka Bojilova
-      sn: Bojilova
-      givenName: Jivka Bojilova
-      title: Data Integration Developer </pre>
-
-      Look at the example for <a target="_top" href="entries-users.ldif">
-      user entries in KNB</a>.<br><br>
-
-      Any LDAP subtree can reside on remote site. In that case the main tree holds
-      referrals to all remotely running LDAP servers.
-      <br><br>
-
-      Look at the example for <a target="_top" href="entries-refs.ldif">
-      referral entries in KNB</a>.<br><br>
-    </p>
-    
-  <br>
-  <a href="./acontrol.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./metacatout.html">Next</a>
-</BODY>
-</HTML>
-

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Index: docs/user/xmltree.html
===================================================================
--- docs/user/xmltree.html	(revision 5315)
+++ docs/user/xmltree.html	(nonexistent)
@@ -1,36 +0,0 @@
-<!--
-  * xmltree.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
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-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">XML Tree</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./xmldoc.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./domapi.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <p>The structure of an XML document can be represented visually as a tree.</p>
-  <P> <img alt="tree representation of an xml document" src="xmltree.gif">
-  <br>
-  <a href="./xmldoc.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./domapi.html">Next</a>
-</BODY>
-</HTML>
-

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Index: docs/user/metacat-windows-install.html
===================================================================
--- docs/user/metacat-windows-install.html	(revision 5315)
+++ docs/user/metacat-windows-install.html	(nonexistent)
@@ -1,203 +0,0 @@
-<!-- 
-  *   '$RCSfile$'
-  *     Purpose: web page describing the installation of Metacat
-  *   Copyright: 2008 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *     Authors: Michael Daigle
-  *
-  *    '$Author: daigle $'
-  *    '$Date: 2008-12-03 08:56:36 -0800 (Wed, 03 Dec 2008) $'
-  *    '$Revision: 4646 $'
-  *
-  *
-  -->
-  
-<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>Metacat Windows Installation Instructions</title>
-  <link rel="stylesheet" type="text/css" href="./common.css">
-  <link rel="stylesheet" type="text/css" href="./default.css">
-</head>
-
-<body>
-
-<table class="tabledefault" width="100%">
-<tr><td rowspan="2"><img src="./images/KNBLogo.gif"></td>
-<td colspan="7">
-<div class="title">Metacat Windows Installation Instructions</div>
-</td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
-<div class="header1">Table of Contents</div>
-  <div class="toc">
-    <div class="toc1"><a href="#QuickInstallation">Quick Installation</a></div> 
-      <div class="toc2"><a href="#DownloadMetacatInstall">Download Metacat Package</a></div> 
-      <div class="toc2"><a href="#CreateDirs">Create Metacat Directories</a></div> 
-      <div class="toc2"><a href="#InstallJava">Install Java</a></div> 
-      <div class="toc2"><a href="#InstallTomcat">Install Tomcat</a></div> 
-      <div class="toc2"><a href="#InstallPostgres">Install PostgreSQL Database</a></div> 
-      <div class="toc2"><a href="#QuickInstallMetacatWar">Install Metacat War</a></div> 
-      <div class="toc2"><a href="#ConfigureMetacatInstall">Configure Metacat</a></div> 
-    <div class="toc1"><a href="#QuickUpdate">Quick Update</a></div>
-      <div class="toc2"><a href="#DownloadMetacatUpdate">Download Metacat Package</a></div> 
-      <div class="toc2"><a href="#BackupApplication">Backup Existing Metacat Installation</a></div> 
-      <div class="toc2"><a href="#QuickUpdateMetacatWar">Update Metacat War</a></div> 
-      <div class="toc2"><a href="#ConfigureMetacatUpdate">Configure Metacat</a></div> 
-   </div> 
-
-<a name="QuickInstallation"></a><div class="header1">Quick Installation</div> 
-  <p>These are the installation instructions for a system that has Windows installed
-  and has never had Metacat installed on it:</p>
- 
-  <a name="DownloadMetacatInstall"></a><div class="header2">Download Metacat Package</div>
-  <ul>
-  <li>Browse to the 
-    <a href="http://knb.ecoinformatics.org/software/download.html">KNB Software Download Page</a>.
-    In the Metacat section, select the link that looks like:
-      <div class="code">metacat-bin-X.X.X.zip</div></li>
-  <li>where X.X.X is the latest version of Metacat.  Choose to save the file locally.</li>
-  <li>Extract the Metacat package files using your windows zip utility.</li>
-  <li>You should see a war file and several supporting files (we will only use the war).  
-  The location where these files were extracted will be refered to as the the 
-  &lt;metacat_package_dir&gt; for the remainder of this documentation.</li>
- </ul>
-  
-  <a name="CreateDirs"></a><div class="header2">Create Metacat Directories</div>
-  <ul>
-  <li>Create the metacat utility base directory at:
-    <div class="code">C:/Program Files/metacat</div></li>
-  </ul>
-
-  <a name="InstallJava"></a><div class="header2">Install Java</div>
-  <ul>
-  <li> Browse to:
-    <div class="code">http://java.sun.com/javase/downloads/index_jdk5.jsp</div></li>
-  <li>Follow instructions to download JDK 5.0 Update 17</li>
-  <li>Run the installer executable that you downloaded</li>
-  <li>Set the JAVA_HOME environment variable:</li>
-	<ul>
-	<li>In "My Computer" properties, go to: advanced settings -> environment variables</li>
-	<li>Add System Variable: JAVA_HOME C:\Program Files\Java\jdk1.5.0_17</li>
-	</ul>
-  </ul>
-  
-  <!--div class=indent>
-   <a name="InstallApache"></a><div class="header2">Install Apache</div>
-	<p>Install Apache and and Mod JK packages by typing:</p>	
-      <div class="code">sudo apt-get install apache2 libapache2-mod-jk</div>
-    <p>Set up Mod JK apache configuration by typing:</p>
-      <div class="code">sudo cp &lt;metacat_package_dir&gt;/jk.conf /etc/apache2/mods-available</div>
-      <div class="code">sudo cp &lt;metacat_package_dir&gt;/workers.properties /etc/apache2</div>
-    <p>Enable Apache Mod JK by typing:</p>
-      <div class="code">sudo a2dismod jk</div>
-      <div class="code">sudo a2enmod jk</div>
-    <p>Set up and enable knb (Metacat) site configurations by typing:</p>
-      <div class="code">sudo cp &lt;metacat_package_dir&gt;/knb /etc/apache2/sites-available</div>
-      <div class="code">sudo a2ensite knb</div>
-    <p>If you want to run an LSID server along with the Metacat server, set up and enable the authority service site 
-      configurations by typing:</p>
-      <div class="code">sudo cp &lt;metacat_package_dir&gt;/authority /etc/apache2/sites-available</div>
-      <div class="code">sudo a2ensite authority</div>
-    <p>Restart apache to bring in changes by typing:</p>
-      <div class="code">sudo /etc/init.d/apache2 force-reload</div>
-  </div -->
-     
-  <a name="InstallTomcat"></a><div class="header2">Install Tomcat</div>
-  <ul>
-  <li>Browse to: http://tomcat.apache.org/download-55.cgi</li>
-  <li>Download tomcat core zip file</li>
-  <li>Extract tomcat files to 
-	<div class="code">C:\Program Files\tomcat</div>
-  using the windows zip utility.</li>
-  </ul>
-
-  <a name="InstallPostgres"></a><div class="header2">Install PostgreSQL Database</div> 
-  <ul>
-  <li>Browse to http://www.postgresql.org/download/windows</li>
-  <li>Download the one-click installer</li>
-  <li>run the installer executable</li>
-  <li>Edit C:\Program Files\PostgreSQL\8.3\data and add:
-	<div class="code">host metacat metacat 127.0.0.1 255.255.255.255 password</div></li>
-  <li>Create user. At command line, go to 
-	<div class="code">C:\Program Files\PostgreSQL\8.3\bin</div>
-  and run:
-	<div class="code">createdb -U postgres metacat (enter super user password)</div></li>
-  <li>Create metacat user.  First log into postgres:
-	<div class="code">psql -U postgres metacat (enter super user password)</div>
-    and create user by running:
-    <div class="code">CREATE USER metacat WITH UNENCRYPTED PASSWORD 'your_password'</div>
-	<div class="code">type: \q to exit</div></li>
-  <li>Restart postgres from the start menu by selecting:
-	<div class="code">run start/All Programs/PostgreSQL 8.3/Stop Server</div>
-	<div class="code">run start/All Programs/PostgreSQL 8.3/Start Server</div></li>
-  <li>Test the installation by logging in as metacat user: 
-	<div class="code">psql -U metacat -W -h localhost metacat</div>
-    <div class="code">type: \q to exit</div></li>
-  </ul>    
-
-  <a name="QuickInstallMetacatWar"></a><div class="header2">Install Metacat War</div> 
-  <ul>
-  <li>Copy the war file to Tomcat:
-	<div class="code">copy &lt;metacat_package_dir&gt;\knb.war C:\Program Files\tomcat\webapps</div></li>
-  <li>Restart Tomcat: 
-	<div class="code">sudo /etc/init.d/tomcat5.5 restart</div></li>
-	</ul>
-	
-  <a name="ConfigureMetacatInstall"></a><div class="header2">Configure Metacat</div> 
-  <p>Refer to the documentation on <a href="./metacat-configure.html">Metacat Confguration</a>
-  to complete your installation of Metacat.</p>
-    
-  <a name="QuickUpdate"></a><div class="header1">Quick Update</div>
-  <p>These are the instructions for a Windows system that already has Metacat installed on it, 
-  but needs a Metacat upgrade:</p>
-  
-  <a name="DownloadMetacatUpdate"></a><div class="header2">Download Metacat Package</div>
-  <ul>
-  <li>Browse to the 
-    <a href="http://knb.ecoinformatics.org/software/download.html">KNB Software Download Page</a>.
-    In the Metacat section, select the link that looks like:
-	  <div class="code">metacat-bin-X.X.X.zip</div></li>
-  <li>where X.X.X is the latest version of Metacat.  Choose to save the file locally.</li>
-  <li>Extract the Metacat package files using your windows zip utility.</li>
-  <li>You should see a war file and several supporting files (we will only use the war).  
-  The location where these files were extracted will be refered to as the the 
-  &lt;metacat_package_dir&gt; for the remainder of this documentation.</li>
-  </ul>
-  
-  <a name="BackupApplication"></a><div class="header2">Backup Existing Metacat Installation</div>
-  <ul>
-  <li>To be safe, it is best to backup the existing Metacat installation.  Do so by copying: 
-	<div class="code">&lt;web_app_dir&gt;/knb to &lt;web_app_dir&gt;/knb.&lt;yyyymmdd&gt;</div>
-	<div class="code">&lt;web_app_dir&gt;/knb.war to &lt;web_app_dir&gt;/knb.war.&lt;yyyymmdd&gt;</div></li>
-  <li>Of course, you can use any backup strategy you like (or none at all).</li>
-  </ul>
-  	
-  <a name="QuickUpdateMetacatWar"></a><div class="header2">Update Metacat War</div> 
-    <ul>
-    <li>Copy the war file to Tomcat:
-	  <div class="code">sudo cp knb.war to C:\Program Files\tomcat\webapps</div></li>
-	<li>Restart Tomcat: 
-	  <div class="code">C:\Program Files\tomcat\shutdown.bat</div>
-	  <div class="code">C:\Program Files\tomcat\startup.bat</div></li>
-    </ul>
-	
-  <a name="ConfigureMetacatUpdate"></a><div class="header2">Configure Metacat</div> 
-    <p>Refer to the documentation on <a href="./metacat-configure.html">Metacat Confguration</a>
-    to complete your installation of Metacat.</p>
-
-  <br>
-</body>
-</html>

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Index: docs/user/metacatgetlog.html
===================================================================
--- docs/user/metacatgetlog.html	(revision 5315)
+++ docs/user/metacatgetlog.html	(nonexistent)
@@ -1,116 +0,0 @@
-<!--
-  * metacatread.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Metacat
-       getlog action</p></td>
-       <td class="tablehead" colspan="2" align="right">
-         <a href="./metacatread.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-         <a href="./saxparser.html">Next</a>
-       </td>
-    </tr>
-  </table>
-  <p>
-	The Metacat servlet provides an 'action' for retrieving a log of the
-        events that have occurred, including document insertions, updates,
-        deletes, and reads.  This allows a simple reporting facility where
-        event reports can be output in XML format.  The report can be subset to
-        only include events from a particular IP address, user, event type,
-        after a start date, or before an end date.
-  </p>
-  <p>
-	The basic log can be viewed using the <code>getlog</code> servlet 
-	action, as in the following URL:<br>
-     	<code>http://some.metacat.host/context/metacat?action=getlog</code>
-  </p>
-  <p>
-  	This will return an XML formatted log of all events since the log was
-	initiated, which can be quite extensive.  To subset the report, provide
-        parameters to restrict the set of matching events:
-        <ul>
-        <li>ipAddress -- restrict the report to this ipAddress (repeatable)</li>
-        <li>principal -- restrict the report to this principal (repeatable)</li>
-        <li>docid -- restrict the report to this docid (repeatable)</li>
-        <li>event -- restrict the report to this event type (repeatable)
-            <ul>
-            <li><code>insert</code></li>
-            <li><code>update</code></li>
-            <li><code>delete</code></li>
-            <li><code>read</code></li>
-            </ul>
-        </li>
-        <li>start -- restrict the report to events after this date
-            <ul>
-            <li><code>YYYY-MM-DD+hh:mm:ss</code></li>
-            </ul>
-        </li>
-        <li>end -- restrict the report to events before this date
-            <ul>
-            <li><code>YYYY-MM-DD+hh:mm:ss</code></li>
-            </ul>
-        </li>
-        </ul>
-  </p>
-  <p>
-	Some example queries follow.  To view only the 'read' events, use a url like:<br>
-     	<code>http://some.metacat.host/context/metacat?action=getlog&event=read</code>
-  </p>
-  <p>
-	To view only the events for a particular IP address, use a url like:<br>
-     	<code>http://some.metacat.host/context/metacat?action=getlog&ipaddress=107.9.1.31</code>
-  </p>
-  <p>
-	To view only the events for a given user, use a url like:<br>
-     	<code>http://some.metacat.host/context/metacat?action=getlog&principal=uid=johndoe,o=NCEAS,dc=ecoinformatics,dc=org</code>
-  </p>
-  <p>
-	To view only the events for a particular document, use a url like:<br>
-     	<code>http://some.metacat.host/context/metacat?action=getlog&docid=knb.5.1</code>
-  </p>
-  <p>
-	To view only the events after a given date, use a url like:<br>
-     	<code>http://some.metacat.host/context/metacat?action=getlog&start=2004-09-15+12:00:00</code>
-  </p>
-  <p>
-	To view only the events before a given date, use a url like:<br>
-     	<code>http://some.metacat.host/context/metacat?action=getlog&end=2004-09-15+12:00:00</code>
-  </p>
-  <p>
-	Query parameters can be combined, so to view the 'insert' events for September 2004 use a url like:<br>
-     	<code>http://some.metacat.host/context/metacat?action=getlog&event=insert&start=2004-09-01+12:00:00&end=2004-09-30+23:59:59</code>
-  </p>
-  <p>
-	The log is returned in XML format.  Here is an example log format:<br>
-        <pre>
-&lt;?xml version="1.0"?&gt;
-&lt;log&gt;
-&lt;logEntry&gt;&lt;entryid&gt;44&lt;/entryid&gt;&lt;ipAddress&gt;34.237.20.142&lt;/ipAddress&gt;&lt;principal&gt;uid=jones,o=NCEAS,dc=ecoinformatics,dc=org&lt;/principal&gt;&lt;docid&gt;esa.2.1&lt;/docid&gt;&lt;event&gt;insert&lt;/event&gt;&lt;dateLogged&gt;2004-09-08 19:08:18.16&lt;/dateLogged&gt;&lt;/logEntry&gt;
-&lt;logEntry&gt;&lt;entryid&gt;47&lt;/entryid&gt;&lt;ipAddress&gt;34.237.20.142&lt;/ipAddress&gt;&lt;principal&gt;uid=jones,o=NCEAS,dc=ecoinformatics,dc=org&lt;/principal&gt;&lt;docid&gt;esa.3.1&lt;/docid&gt;&lt;event&gt;insert&lt;/event&gt;&lt;dateLogged&gt;2004-09-14 19:50:40.61&lt;/dateLogged&gt;&lt;/logEntry&gt;
-&lt;/log&gt;
-
-        </pre>
-  </p>
-  <br>
-  <a href="./metacatread.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./saxparser.html">Next</a>
-
-</BODY>
-</HTML>
-

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Index: docs/user/metacatdom.html
===================================================================
--- docs/user/metacatdom.html	(revision 5315)
+++ docs/user/metacatdom.html	(nonexistent)
@@ -1,63 +0,0 @@
-<!--
-  * Metacatdom.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">The Metacat DOM</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./metacatdb.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./clientapi.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <P>In the Metacat DOM implementation XML documents 
-  are disassembled into their composite nodes. All nodes are stored as records 
-  in the database tables. The structure of each XML document is preserved 
-  by saving the parent-child relationship between the nodes.
-    <ul>
-    <li> Each XML document in the Metacat database starts with one root node of 
-    type DOCUMENT. All other nodes in the document are its children. 
-    The document node can 
-    have multiple COMMENT or PI (processing instruction) nodes and only 
-    one ELEMENT node. The element node is the root node of the document and will
-    be pointed to by all of its children.
-    <li> Each node is described as a single record in the <i>xml_nodes</i> table. 
-    All nodes have a unique System ID (<i>nodeid</i>). Each node stores 
-    the ID of 
-    its direct parent (in <i>parentnodeid</i>), the ID of its documents root node 
-    (in <i>rootnodeid</i>) and its Document ID (<i>docid</i>).
-    <li> Document attributes (such as docid, doctype, etc.) are stored in 
-    the xml_documents table.
-    <li> Unimplemented DOM features:
-         <ul>
-         <li> Node types: Doctype, Entity, EntityReference, Notation.
-         <li> Persistant DOM interface. This would allow a DOM compliant 
-         editor to work with an xml document in the database as if it were
-         in memory.
-         <li>Object Oriented representation of each node.
-         </ul>
-    </ul>
-  <P> <img alt="Entity Relationship Diagram of the Metacat DOM"  src="metacatdom.jpg">
-  
-  <br>
-  <a href="./metacatdb.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./clientapi.html">Next</a>
-</BODY>
-</HTML>
-

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Index: docs/user/acontrol.html
===================================================================
--- docs/user/acontrol.html	(revision 5315)
+++ docs/user/acontrol.html	(nonexistent)
@@ -1,126 +0,0 @@
-<!--
-  * acontrol.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Metacat User 
-      Authentication and Access Control</p></td>
-      <td class="tablehead" colspan="2" align="right">
-        <a href="./xmlindex.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-        <a href="./ldap.html">Next</a>
-      </td>
-    </tr>
-  </table>
-  <p><b>Authentication</b></p>
-    <p>Metacat has a public interface for porting authentication 
-      schemes to Metacat.  Currently an LDAP scheme is implemented. 
-      LDAP stands for Lightweight Directory Access Protocol. 
-      It is an optimized database for fast retrival of stored data:
-      It is used by Metacat to store its users and their information. 
-      The users can be organized in one or more groups.
-    </p>
-    <P> <img src="auth.gif"> 
-    <P> <b>Access control in Metacat. </b></p>
-    <ul>
-      <li> Metacat users stored in the LDAP directory database are authenticated
-      to use Metacat services and resources.</li>
-      <li> A persistant session is assigned to an authenticated user.</li>
-      <li> Metacat also allows document level access control via Access Control 
-      Lists (ACLs).</li>
-    </ul>
-  <p style="color: red; font-face: bold">WARNING: The rest of this page is 
-   out-of-date and no longer accurate. It is left only for reference purposes.
-   ACL information is now set through EML 2.0.0 access control elements.
-  </p>
-  <!--<img src="acontrol.gif">-->
-  <b>ACLs</b>
-  <p>Metacat allows a user to set permissions for users or groups on individual 
-  documents by using
-  a special XML file called an Access file.  
-  The <a href="./packages.html">Package</a> file
-  specifies which documents the Access file refers to. 
-  A sample Access file looks like the following:</p>
-  <pre>
-    &lt;?xml version="1.0"?&gt;
-    &lt;!DOCTYPE acl PUBLIC "-//NCEAS//eml-access-2.0//EN" "eml-access-2.0.dtd"&gt;
-    &lt;acl authSystem="knb" order="allowFirst"&gt;
-      &lt;identifier&gt;nceas.36.1&lt;/identifier&gt;
-      &lt;allow&gt;
-        &lt;principal&gt;jones&lt;/principal&gt;
-        &lt;principal&gt;higgins&lt;/principal&gt;
-        &lt;principal&gt;berkley&lt;/principal&gt;
-        &lt;principal&gt;bojilova&lt;/principal&gt;
-        &lt;permission&gt;read&lt;/permission&gt;
-        &lt;duration&gt;
-          &lt;startDate&gt;10/9/2000&lt;/startDate&gt;
-          &lt;stopDate&gt;10/9/2001&lt;/stopDate&gt;
-        &lt;/duration&gt;
-        &lt;ticketCount&gt;100&lt;/ticketCount&gt;
-      &lt;/allow&gt;
-      &lt;allow&gt;
-        &lt;principal&gt;bojilova&lt;/principal&gt;
-        &lt;permission&gt;write&lt;/permission&gt;
-        &lt;ticketCount&gt;10&lt;/ticketCount&gt;
-      &lt;/allow&gt;
-      &lt;allow&gt;
-        &lt;principal&gt;reviewers&lt;/principal&gt;
-        &lt;permission&gt;read&lt;/permission&gt;
-        &lt;ticketCount&gt;5&lt;/ticketCount&gt;
-      &lt;/allow&gt;
-      &lt;allow&gt;
-        &lt;principal&gt;blankman&lt;/principal&gt;
-        &lt;permission&gt;all&lt;/permission&gt;
-      &lt;/allow&gt;
-      &lt;deny&gt;
-        &lt;principal&gt;eddins&lt;/principal&gt;
-        &lt;permission&gt;all&lt;/permission&gt;
-      &lt;/deny&gt;
-    &lt;/acl&gt;
-  </pre>
-  
-  <p>This file is read into Metacat like any other XML file.  Like 
-     <a href="./packages.html">Packages</a> the doctype is checked against
-     the accessdoctype parameter in the <a href="./properties.html">Metacat
-     Properties</a> file.  If the doctype matches, special postprocessing
-     is performed on the document and the persmissions described in the file
-     are applied to the specified document.
-  </p>
-  <p>The main tag &lt;acl&gt; has attributes 'order' and 'authSystem'.  
-     Order refers to which permission type to process first, allow or deny.
-     The allowed values are "allowFirst" and  "denyFirst".  The default is "allowFirst".
-  </p>
-  <p>The &lt;identifier&gt; tag specifies the document identifier for the Access file
-     itself as stored in Metacat.
-  </p>
-  <p>Next are the permissions themselves.  An allow tag gives permissions to 
-  the specified user(s) (&lt;principal&gt;) and a deny tag takes the permissions
-  away from the user(s).  A principal should be a registered user or group.
-  A timed duration can be set on the permission after
-  which the user(s) will no longer have the specified permission.  A ticket count
-  can also be set.  This gives the user the number of accesses specified.  After
-  the user has accessed the document that number of times, the permissions are 
-  revoked. 
-  </p>
-    
-  <br>
-  <a href="./xmlindex.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./ldap.html">Next</a>
-</BODY>
-</HTML>
-

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Index: docs/user/metacatread.html
===================================================================
--- docs/user/metacatread.html	(revision 5315)
+++ docs/user/metacatread.html	(nonexistent)
@@ -1,86 +0,0 @@
-<!--
-  * metacatread.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Reading a Document
-       from the Database</p></td>
-       <td class="tablehead" colspan="2" align="right">
-         <a href="./metacatquery.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-         <a href="./metacatgetlog.html">Next</a>
-       </td>
-    </tr>
-  </table>
-  <p>Metacat allows clients to read a document in several different ways,
-  depending on how the client wants the document returned and how the client
-  wants to specify the requested document.  </p>
-  <P> <img alt="architecture diagram of the Metacat read process" 
-           src="metadataread.gif">  </p>
-  <p>The documents are requested by the <b>docid</b> servlet parameter by specifying
-  the document id that you wish to read.<br>
-  </p>
-  <p>
-    Metacat allows the dynamic transformation of read documents through the use
-    of style-sets.  A style-set is an xsl stylesheet or a group of stylesheets
-    that are specified in a config file.  The following is an example of a style-set
-    config file:
-  </p>
-  <pre>
-    &lt;?xml version="1.0"?&gt;
-    &lt;style-set name="knb"&gt;
-      &lt;default-style&gt;http://http://server.domain.com/metacat/style/ascii-treeview.xsl&lt;/default-style&gt;
-      &lt;doctype publicid="-//NCEAS//resultset//EN"&gt;
-        &lt;target publicid="-//W3C//HTML//EN"&gt;http://http://server.domain.com/metacat/style/resultset.xsl&lt;/target&gt;
-      &lt;/doctype&gt;
-      &lt;doctype publicid="-//NCEAS//login//EN"&gt;
-        &lt;target publicid="-//W3C//HTML//EN"&gt;http://http://server.domain.com/metacat/style/login.xsl&lt;/target&gt;
-      &lt;/doctype&gt;
-      &lt;doctype publicid="-//NCEAS//eml-dataset-2.0//EN"&gt;
-        &lt;target publicid="-//W3C//HTML//EN"&gt;http://http://server.domain.com/metacat/style/eml-dataset-display.xsl&lt;/target&gt;  
-      &lt;/doctype&gt;
-      &lt;doctype publicid="-//NCEAS//eml-dataset//EN"&gt;
-        &lt;target publicid="-//W3C//HTML//EN"&gt;http://http://server.domain.com/metacat/style/eml-dataset-display.xsl&lt;/target&gt;  
-      &lt;/doctype&gt;
-      &lt;doctype publicid="-//NCEAS//eml-resource//EN"&gt;
-        &lt;target publicid="-//W3C//HTML//EN"&gt;http://http://server.domain.com/metacat/style/eml-dataset-display.xsl&lt;/target&gt;  
-      &lt;/doctype&gt;      
-      &lt;doctype publicid="-//ecoinformatics.org//eml-dataset-2.0.0beta4//EN"&gt;
-        &lt;target publicid="-//W3C//HTML//EN"&gt;http://http://server.domain.com/metacat/style/eml-dataset-display.xsl&lt;/target&gt;  
-      &lt;/doctype&gt;
-    &lt;/style-set&gt;
-  </pre>
-
-  <p>
-    Whenever a read action is requested from Metacat, you can also provide a qformat parameter.
-    This qformat parameter should be the name of the style-set that you wish to use
-    to transform the document you are requesting.  Note that the value that you set
-    qformat to must equal the &lt;style-set&gt; name parameter.
-  </p>
-  <p>
-    A default style-set can be set in the metacat.properties file.  If qformat
-    is set to 'html', Metacat will use the default.  If qformat is set to 'xml',
-    Metacat will return the XML document untransformed.
-  </p>
-  <br>
-  <a href="./metacatquery.html">Back</a> | <a href="./metacattour.html">Home</a> | 
-  <a href="./metacatgetlog.html">Next</a>
-
-</BODY>
-</HTML>
-

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===================================================================
--- docs/user/entries-groups.ldif	(revision 5315)
+++ docs/user/entries-groups.ldif	(nonexistent)
@@ -1,11 +0,0 @@
-# KNB development group at NCEAS
-dn: cn=knb-dev,o=NCEAS,dc=ecoinformatics,dc=org
-objectClass: top
-objectclass: groupOfUniqueNames
-cn: knb-dev
-uniqueMember: uid=bojilova,o=NCEAS,dc=ecoinformatics,dc=org
-uniqueMember: uid=berkley,o=NCEAS,dc=ecoinformatics,dc=org
-uniqueMember: uid=jones,o=NCEAS,dc=ecoinformatics,dc=org
-uniqueMember: uid=higgins,o=NCEAS,dc=ecoinformatics,dc=org
-uniqueMember: uid=harris,o=NCEAS,dc=ecoinformatics,dc=org
-description: KNB development group at NCEAS

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===================================================================
--- docs/user/unimplem.html	(revision 5315)
+++ docs/user/unimplem.html	(nonexistent)
@@ -1,41 +0,0 @@
-<!--
-  * unimplem.html
-  *
-  *      Authors: Jivka Bojilova
-  *    Copyright: 2000 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *  For Details: http://www.nceas.ucsb.edu/
-  *      Created: 2000 April 5
-  *      Version: 0.01
-  *    File Info: '$Id$'
-  * 
-  * October Meeting SDSC, 2000
--->
-<HTML>
-<HEAD>
-<TITLE>Metacat</TITLE>
-<link rel="stylesheet" type="text/css" href="./default.css">
-</HEAD> 
-<BODY>
-  <table width="100%">
-    <tr>
-      <td class="tablehead" colspan="2"><p class="label">Wishlist</p></td>
-      <td class="tablehead" colspan="2" align="right">
-       <a href="./sitemaps.html">Back</a> | <a href="./metacattour.html">Home</a>
-      </td>
-    </tr>
-  </table>
-  <UL>
-  <LI> DOM API for Metacat Server.
-  <LI> Split xml_nodes table in many tables for every doctype.
-  <LI> Optimization of different operations.
-  <LI> Mapping and convertion between metadata standarts.
-  </UL>
-  
-  <br>
-  <a href="./sitemaps.html">Back</a> | <a href="./metacattour.html">Home</a> 
-  
-
-</BODY>
-</HTML>
-

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Index: docs/dev/troubleshooting.html
===================================================================
--- docs/dev/troubleshooting.html	(nonexistent)
+++ docs/dev/troubleshooting.html	(revision 5316)
@@ -0,0 +1,131 @@
+<!-- 
+  *   '$RCSfile$'
+  *     Purpose: web page describing the installation of Metacat
+  *   Copyright: 2008 Regents of the University of California and the
+  *               National Center for Ecological Analysis and Synthesis
+  *     Authors: Chad Berkley
+  *
+  *    '$Author: daigle $'
+  *    '$Date: 2008-11-19 16:48:24 -0800 (Wed, 19 Nov 2008) $'
+  *    '$Revision: 4597 $'
+  *
+  *
+  -->
+  
+<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
+<html>
+
+<head>
+  <title>Troubleshooting Metacat</title>
+  <link rel="stylesheet" type="text/css" href="../user/common.css">
+  <link rel="stylesheet" type="text/css" href="./default.css">
+</head>
+
+<body>
+
+  <table width="100%">
+    <tr>
+      <td class="tablehead" colspan="2"><p class="label">Troubleshooting Metacat</p></td>
+      <td class="tablehead" colspan="2" align="right">
+        <a href="./testing-metacat.html">Back</a> | <a href="./index.html">Home</a> | 
+        <!-- a href="put next page here" -->Next<!-- /a -->
+      </td>
+    </tr>
+  </table>
+
+<div class="header1">Table of Contents</div>
+<div class="toc">
+  <div class="toc1"><a href="#BuildIssues">Build Issues</a></div>
+    <div class="toc2"><a href="#HttpServletExceptions">Ant BUILD FAILED : Multiple HttpServlet Exceptions</a></div> 
+  <div class="toc1"><a href="#InstallationIssues">Installation Issues</a></div>
+  <div class="toc1"><a href="#StartupIssues">Startup Issues</a></div>
+    <div class="toc2"><a href="#Jdk14Logger">Metacat doesn't start and Jdk14Logger exception</a></div> 
+  <div class="toc1"><a href="#ConfigurationIssues">Configuration Issues</a></div>
+   <div class="toc2"><a href="#DbUpdateIssue">Database Update Fails (not a connectivity issue)</a></div>
+  <div class="toc1"><a href="#GeneralApplicationIssues">General Application Issues</a></div>
+    <div class="toc2"><a href="#MapDisplayIssue">Maps will not display</a></div>
+  <div class="toc1"><a href="#UnitTestingIssues">Unit Testing Issues</a></div>
+    <div class="toc2"><a href="#503ServiceTemporarilyUnavailable">Mutliple Tests Fail : 503 Service Temporarily Unavailable</a></div>
+</div> 
+
+<a name="BuildIssues"></a><div class="header1">Build Issues</div>
+  <a name="HttpServletExceptions"></a><div class="header2">Ant BUILD FAILED : Multiple HttpSevlet Exceptions</div>
+    <p>During an Ant build of Metacat, you will see many HttpServletRequest, HttpServletResponse and
+    other errors.  The compiler will complain that it cannot find a symbol, for example:</p>
+      <div class="code">
+      [javac] /home/daigle/workspace/metacat/build/src/edu/ucsb/nceas/metacat/MetaCatServlet.java:506: cannot find symbol<br>
+      [javac] symbol  : class HttpServletResponse<br>
+      [javac] location: class edu.ucsb.nceas.metacat.MetaCatServlet<br>
+      [javac] &nbsp;&nbsp;&nbsp;&nbsp;HttpServletResponse response) throws ServletException, IOException {<br>
+      [javac] &nbsp;&nbsp;&nbsp;&nbsp;^<br>
+      </div>
+      
+    <p>This is usually caused by the build not being able to find native Tomcat libraries. edit your
+    build.properties file in  
+      
+<a name="InstallationIssues"></a><div class="header1">Installation Issues</div>
+ 
+<a name="StartupIssues"></a><div class="header1">Startup Issues</div> 
+	<a name="Jdk14Logger"></a><div class="header2">Metacat doesn't start and Jdk14Logger exception</div>
+	<p>The symptoms are that the metacat service will not show up at all, even though Tomcat 
+      is serving, and the following error shows up in the tomcat log (catalina.log):</p>
+      
+      <div class="code">org.apache.commons.logging.LogConfigurationException: User-specified log
+      class 'org.apache.commons.logging.impl.Jdk14Logger' cannot be found or is
+      not useable </div>
+      
+      <p>This message typically occurs in the tomcat log (catalina.log) 
+      when Tomcat has been installed on an Ubuntu/Debian system using apt-get install.  
+      And the application is started using:
+        
+        <div class="code">/etc/init.d/tomcat5.5 start</div>  
+        
+      <p>The problem is that the standard startup scripts reference the 
+      common java service, jsvc.  Metacat will not run under jsvc.  The solutions are:
+      <ul>
+      <li>Download the <a href="http://knb.ecoinformatics.org/software/download.html">Metacat binary install package</a>
+       and replace your /etc/init.d/tomcat5.5 startup script with the one provided in the
+       package.</li>
+      <li>Run Tomcat from the Tomcat binary directory: <tomcat_home>/bin/startup.sh and 
+      <tomcat_home>/bin/shutdown.sh</li>
+      </ul>
+      </p>
+<a name="ConfigurationIssues"></a><div class="header1">Configuration Issues</div>
+  <a name="DbUpdateIssue"></a><div class="header2">Database Update Fails (not a connectivity issue)</div>
+    <p>There are a number of reasons why the database update utility might fail during 
+    configuration.  You will need to determine if the error returned indicates a connectivity issue
+    or some issue with the database schema/data.  If it is the latter, the first step in 
+    troubleshooting the issue is to run the db scripts manually and analyze the output.</p> 
+    
+    <p>The configuration utility will report which scripts it tried to run.  To 
+    run these scripts, refer to 
+    <a href="../user/run-db-scripts.html">how to run database scripts</a></p>
+    
+    <p>If the answer is not obvious, further troubleshooting may require a database 
+    administrator.</p>
+    
+<a name="GeneralApplicationIssues"></a><div class="header1">General Application Issues</div> 
+  <a name="MapDisplayIssue"></a><div class="header2">Maps will not display</div>
+    <p>There are two known reasons why maps might not display in a web browser.</p> 
+    <ul>
+    <li>Sarfari Browser - the safari browser is not supported by the map libraries.  You will
+        need to switch to a different browser.</li>
+    <li>Firefox Browser with the Firebug plugin - Firebug is a plugin that allows a developer
+        to easily view and troubleshoot web page layouts.  Unfortunately, this plugin can
+        keep the maps from displaying.  There is no plan by the third party map display
+        developers to address this issue.  You will need to disable Firebug in your 
+        browser.</li>
+    </ul>
+    
+<a name="UnitTestingIssues"></a><div class="header1">Unit Testing Issues</div>
+  <a name="503ServiceTemporarilyUnavailable"></a><div class="header2">Mutliple Tests Fail : 503 Service Temporarily Unavailable</div>
+    <p>When running "ant test", multiple tests fail.  The output files have the error: </p>
+      <div class="code">503 Service Temporarily Unavailable</div>
+    <p>This typically means your Metacat server is not running.</p>
+    
+    <br>
+    
+    <a href="./testing-metacat.html">Back</a> | <a href="./index.html">Home</a> | 
+    <!--a href="add next file here when one exists" -->Next<!-- /a -->
+  </body>
+</html>
\ No newline at end of file

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===================================================================
--- docs/dev/testing-metacat.html	(revision 5315)
+++ docs/dev/testing-metacat.html	(revision 5316)
@@ -25,8 +25,8 @@
     <tr>
       <td class="tablehead" colspan="2"><p class="label">Testing Metacat</p></td>
       <td class="tablehead" colspan="2" align="right">
-        <a href="./metacat-eclipse-project.html">Back</a> | <a href="./index.html">Home</a> | 
-        <!--a href="add next file here when one exists" -->Next<!-- /a -->
+        <a href="./building-metacat.html">Back</a> | <a href="./index.html">Home</a> | 
+        <a href="./troubleshooting.html">Next</a>
       </td>
     </tr>
   </table>
@@ -650,7 +650,7 @@
   <p>Uncomment the tests you want to run. </p>
   
   <br>
-  <a href="./metacat-eclipse-project.html">Back</a> | <a href="./index.html">Home</a> | 
+  <a href="./building-metacat.html">Back</a> | <a href="./index.html">Home</a> | 
   <!--a href="add next file here when one exists" -->Next<!-- /a -->
 
 </BODY>
Index: docs/dev/building-metacat.html
===================================================================
--- docs/dev/building-metacat.html	(revision 5315)
+++ docs/dev/building-metacat.html	(revision 5316)
@@ -26,7 +26,7 @@
       <td class="tablehead" colspan="2"><p class="label">Building Metacat</p></td>
       <td class="tablehead" colspan="2" align="right">
         <a href="./metacat-eclipse-project.html">Back</a> | <a href="./index.html">Home</a> | 
-        <!--a href="add next file here when one exists" -->Next<!-- /a -->
+        <a href="./testing-metacat.html">Next</a>
       </td>
     </tr>
   </table>
@@ -131,5 +131,9 @@
   <p>The war file will appear in your &gt;metacat_workspace&lt;/dist directory.  Copy the war
   file into your tomcat webapps directory.  Delete the existing code that was expanded
   from the old jar.</p>
+  
+  <br>
+  <a href="./metacat-eclipse-project.html">Back</a> | <a href="./index.html">Home</a> | 
+  <a href="./testing-metacat.html">Next</a>
 </BODY>
 </HTML>
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+*
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+*
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===================================================================
--- docs/dev/images/entries-refs.ldif	(nonexistent)
+++ docs/dev/images/entries-refs.ldif	(revision 5316)
@@ -0,0 +1,10 @@
+#The referral to LTER's subtree
+dn: o=LTER,dc=ecoinformatics,dc=org
+objectclass: top
+objectclass: organization
+objectClass: referral
+objectclass: extensibleObject
+o: LTER
+description: referral to LTER's KNB subtree
+ref: ldap://alpha.nceas.ucsb.edu/o=LTER,dc=ecoinformatics,dc=org
+

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+*
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Property changes on: docs/dev/images/acontrol.gif
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
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Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
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Index: docs/dev/images/global-config.png
===================================================================
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svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/global-config.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
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Index: docs/dev/images/auth-config.png
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/auth-config.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Index: docs/dev/images/geoserver-config.png
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/geoserver-config.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Index: docs/dev/images/metacatdb.gif
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/metacatdb.gif
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Index: docs/dev/images/database-config-2.png
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/database-config-2.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Index: docs/dev/images/xmldoc.gif
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/xmldoc.gif
___________________________________________________________________
Added: svn:executable
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+*
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Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Index: docs/dev/images/database-config.png
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/database-config.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
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Index: docs/dev/images/backup-config.png
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/backup-config.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Index: docs/dev/images/metacatdom.jpg
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/metacatdom.jpg
___________________________________________________________________
Added: svn:executable
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+*
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Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
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Index: docs/dev/images/resultset.gif
===================================================================
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svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/resultset.gif
___________________________________________________________________
Added: svn:executable
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+*
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Added: svn:mime-type
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+application/octet-stream
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Index: docs/dev/images/metacat-logo.png
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/metacat-logo.png
___________________________________________________________________
Added: svn:mime-type
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+application/octet-stream
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Index: docs/dev/images/xmltransform.gif
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/xmltransform.gif
___________________________________________________________________
Added: svn:executable
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+*
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Added: svn:mime-type
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+application/octet-stream
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Index: docs/dev/images/auth.gif
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/auth.gif
___________________________________________________________________
Added: svn:executable
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+*
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Added: svn:mime-type
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+application/octet-stream
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Index: docs/dev/images/main-config-2.png
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/main-config-2.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Index: docs/dev/images/main-config.png
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/main-config.png
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
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Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
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Index: docs/dev/images/skins-config-2.png
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/skins-config-2.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
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Index: docs/dev/images/dataload.gif
===================================================================
Cannot display: file marked as a binary type.
svn:mime-type = application/octet-stream

Property changes on: docs/dev/images/dataload.gif
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
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+application/octet-stream
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Index: docs/dev/metacat-eclipse-project.html
===================================================================
--- docs/dev/metacat-eclipse-project.html	(revision 5315)
+++ docs/dev/metacat-eclipse-project.html	(revision 5316)
@@ -26,7 +26,7 @@
       <td class="tablehead" colspan="2"><p class="label">Setting Up a Metacat Eclipse Project</p></td>
       <td class="tablehead" colspan="2" align="right">
         <a href="./metacat-dev-hardware.html">Back</a> | <a href="./index.html">Home</a> | 
-        <a href="./testing-metacat.html">Next</a>
+        <a href="./building-metacat.html">Next</a>
       </td>
     </tr>
   </table>
@@ -211,7 +211,7 @@
     
   <br>
   <a href="./metacat-dev-hardware.html">Back</a> | <a href="./index.html">Home</a> | 
-  <a href="./testing-metacat.html">Next</a>
+  <a href="./building-metacat.html">Next</a>
   </ul>
 
 </BODY>
Index: docs/dev/index.html
===================================================================
--- docs/dev/index.html	(revision 5315)
+++ docs/dev/index.html	(revision 5316)
@@ -8,23 +8,6 @@
 
 <body>
 
-<table class="tabledefault" width="100%">
-<tr>
-  <td rowspan="2"><img src="./images/KNBLogo.gif"></td>
-  <td colspan="7"><div class="title">KNB Software Development Guide: Metacat</div></td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
 <p>&nbsp;</p>
 <table class="tabledefault" width="100%">
 <tr>
@@ -59,9 +42,10 @@
     <ul>
       <li> <a href="./metacat-architecture.html">Metacat Architecture </a></li>
       <li> <!-- a href="./metacat-dev-hardware.html" -->Metacat developement hardware requirements <!-- /a --></li>
-      <li> <!-- a href="./metacat-eclipse-project.html" -->Setting up a Metacat Eclipse project <!-- /a --></li>
+      <li> <a href="./metacat-eclipse-project.html">Setting up a Metacat Eclipse project </a></li>
       <li> <a href="./building-metacat.html">Building Metacat</a></li>
       <li> <a href="./testing-metacat.html">Testing Metacat</a></li>
+      <li> <a href="./troubleshooting.html">Troubleshooting Metacat</a></li>
     </ul>
   </td>
 </tr>
