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Revision 878

Added by berkley about 23 years ago

moving metacat docs to xmltodb

     <!--
       * 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
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     <HTML>
     <HEAD>
     <TITLE>Metacat</TITLE>
     <link rel="stylesheet" type="text/css" href="@docrooturl@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="./acontrol.html">Back</a> | <a href="./metacattour.html">Home</a> |
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       <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 'html'
       or 'xml'.  When qformat is set to html, Metacat will transform the resultset based
       on the stylesheet specified in the resultStyleURL of the
       <a href="./properties.html">Metacat Properties</a> file.  This XSL stylesheet
       defines the rules for how to translate the XML tags into HTML tags.
       </p>
       <p>A user can specify that a certain doctype is always transformed using a
       specific stylesheet by registering that stylesheet in the Metacat Catalog.
       The Catalog is stored in the database table xml_catalog and contains a
       list of doctypes and the stylesheets used to transform them.  If a doctype
       has an assigned stylesheet, whenever a document of that type is "read" from
       Metacat and qformat is set to HTML, the document will be transformed using
       the assigned stylesheet.
       </p>
       <br>
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     <!--
       * 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: '$ '
+      *
+      *
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     <HTML>
     <HEAD>
     <TITLE>Metacat</TITLE>
     <link rel="stylesheet" type="text/css" href="@docrooturl@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>
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       </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-2.0</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
       is broken up into <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>
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     <!--
       * 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="@docrooturl@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="./metacatread.html">Back</a> | <a href="./metacattour.html">Home</a> |
             <a href="./xmlindex.html">Next</a>
           </td>
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       </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
           MetacatUtil util = new MetacatUtil();
           // Get the class name of SAX driver from some XML parser like:
           // org.apache.xerces.parsers.SAXParser
           <span class="emphasis">String parserName = util.getOption("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>
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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</TITLE>
     <link rel="stylesheet" type="text/css" href="@docrooturl@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>
       <p>Metacat has built in replication to allow different Metacat servers to
       share data between themselves.  The replication scheme that Metacat uses is
       both push and pull.  There are several triggers that can start a replication
       mechanism. </p>
       <ul>
         <li>Delta-T monitoring. At a set time interval a server checks each of the
         other servers in its list for updated documents</li>
         <li>INSERT trigger. Whenever a document is inserted, the server notifies
         the remote hosts in its list that it has a new file available.</li>
         <li>UPDATE trigger. Whenever a document is updated, the server notifies
         each server in its list of the update.</li>
         <li>File locking. 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>
       <p>Each server contains a list of servers to which it can replicate.  One-way
       replication is enabled by the 'replicate' flag 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>
         </tr>
         <tr>
           <td>1</td>
           <td>localhost</td>
           <td>null</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>1</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>
         </tr>
       </table>
       <p>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 server field must always point to the other 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.  The replicate flag is set to 1 if you want this server to
       copy data TO the remote host.  (Note that both servers (the local host and
       the remote host) must have each other in their respective tables or replication
       will not take place.)</p>
       <b>Example:</b>
       <table border="1">
         <tr>
           <td>host</td>
           <td>replication table</td>
         </tr>
         <tr>
          <td>snoopy.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>
             </tr>
             <tr>
               <td>localhost</td>
               <td>null</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>1</td>
             </tr>
             <tr>
               <td>dev.nceas.ucsb.edu/Metacat/servlet/replication</td>
               <td>2001-01-23 9:10:02.5</td>
               <td>1</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>
               </tr>
               <tr>
                 <td>localhost</td>
                 <td>null</td>
                 <td>0</td>
               </tr>
               <tr>
                 <td>snoopy.nceas.ucsb.edu:8080/berkley/servlet/replication</td>
                 <td>2001-01-21 11:33:12.7</td>
                 <td>0</td>
               </tr>
               <tr>
                 <td>dev.nceas.ucsb.edu/Metacat/servlet/replication</td>
                 <td>2001-01-23 10:22:02.5</td>
                 <td>1</td>
               </tr>
             </table>
           </td>
         </tr>
         <tr>
           <td>dev.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>
               </tr>
               <tr>
                 <td>localhost</td>
                 <td>null</td>
                 <td>0</td>
               </tr>
               <tr>
                 <td>snoopy.nceas.ucsb.edu:8080/berkley/servlet/replication</td>
                 <td>2001-01-21 11:33:12.7</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>
               </tr>
             </table>
           </td>
         </tr>
       </table>
       <p>Our three servers, snoopy, alpha and dev are all set up to replicate
       between themselves.  Snoopy is a one way replicator.  Meaning that it only
       pushes data to alpha and dev but does not pull back from them.  This
       is achieved by dev and alpha setting snoopy's 'replicate' value to 0 indicating
       that they do not want to send their files to snoopy.  Alpha and dev have a
       two-way replication agreement since each of them have a 1 in their 'replicate'
       value for the other.</p>
       <p>There is an html control panel for controling replication.  After
       <a href="./Metacatinstall.html">installing</a> Metacat, you can access
       it by going through the Metacat servlet context you have setup and calling up
       replControl.html.  For instance, if you setup a Metacat servlet instance
       called 'Metacat' you would probably type
       http://server.domain.com:8080/Metacat/replControl.html.  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>
       <br>
       <a href="./packages.html">Back</a> | <a href="./metacattour.html">Home</a> |
       <a href="./datafiles.html">Next</a>
     </BODY>
     </HTML>

     <!--
       * 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="@docrooturl@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="./metacatload.html">Next</a>
           </td>
         </tr>
       </table>
       <P>In the Metacat DOM implementation XML documents
       are disassembled in their composing nodes. All nodes are stored as records
       in relational database tables. The structure of each XML document is preserved
       by saving 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="./metacatload.html">Next</a>
     </BODY>
     </HTML>

     <!--
       * 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
       *      Version: 0.01
       *    File Info: '$Id$'
+      *
       * October Meeting SDSC, 2000
     -->
     <HTML>
     <HEAD>
     <TITLE>Metacat</TITLE>
     <link rel="stylesheet" type="text/css" href="@docrooturl@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>

     <!--
       * 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="@docrooturl@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="./properties.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="./properties.html">Back</a> | <a href="./metacattour.html">Home</a>
     </BODY>
     </HTML>

     #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

     # 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

     <!--
       * 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="@docrooturl@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>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>insert</td>
           <td>
             <ul>
               <li>docid - the user defined docid to assign to the new document.</li>
               <li>doctext - the text of the document to insert</li>
             </ul>
           </td>
           <td>Insert doctext into the database.</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 document</li>
           </ul>
           </td>
           <td>Overwrite a document with a new one and give the new one
               the same docid but with next revision number.</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>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>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>
       </table>
       <!--
       <TABLE border=1 width=700>
       <TR>
         <TH WIDTH="50%">Metacat Server Interface functions</TH>
         <TH WIDTH="50%">Parameter list</TH>
       <TR>
         <TD><small>Structured query search through Metacat DB </TD>
         <TD><small>action=squery <br>
           query <br>
           returndoc <br>
           username <br>
           groupname </TD>
       <TR>
         <TD><small>Structured query search. Query parts provided in the parameter
         list </TD>
         <TD><small>action=query <br>
           meta_file_id <br>
           querytitle <br>
           doctype <br>
           returnfield <br>
           operator <br>
           casesensitive <br>
           searchmode <br>
           anyfield </TD>
       <TR>
         <TD><small> Read XML document from Metacat DB, transform into qformat
         and return it </TD>
         <TD><small> action=read <br>
           docid <br>
           qformat </TD>
       <TR>
         <TD><small> Read XML document <br>
           - from Metacat DB if url=Metacat://... <br>
           - from Internet if url=http:// <br>
           Transform into qformat and return it </TD>
         <TD><small>  action=read <br>
           docid <br>
           qformat </TD>
       <TR>
         <TD><small> Read abstract data of a document and return it </TD>
         <TD><small> action=getabstract <br>
           abstractpath <br>
           docid </TD>
       <TR>
         <TD><small> Write XML document into Metacat DB </TD>
         <TD><small> action=insert <br>
           docid <br>
           doctext <br>
           username <br>
           groupname </TD>
       <TR>
         <TD><small> Modify existing in Metacat Db XML document with new content
         provided </TD>
         <TD><small> action=update <br>
           docid <br>
           doctext <br>
           username <br>
           groupname </TD>
       <TR>
         <TD><small> Delete existing in Metacat Db XML document </TD>
         <TD><small> action=delete <br>
           docid <br>
           username <br>
           groupname </TD>
       <TR>
         <TD><small> Validate XML document </TD>
         <TD><small>  action=validate <br>
           docid <br>
           valtext <br>
           username <br>
           groupname </TD>
       <TR>
         <TD><small> Read XML document from Metacat Db and related documents if
         they exist and return them in zip file </TD>
         <TD><small> action=getdatadoc <br>
           docid <br>
           relation </TD>
       <TR>
         <TD><small> Read all different document types currently available in
         Metacat Db </TD>
         <TD><small> action=getdoctypes </TD>
       <TR>
         <TD><small> Read Data Guide for specified doctype </TD>
         <TD><small> action=getdataguide <br>
           doctype </TD>
       <TR>
         <TD><small> Login to Metacat Server </TD>
         <TD><small>  action=login <br>
           username <br>
           password </TD>
       <TR>
         <TD><small> Logout from Metacat Server </TD>
         <TD><small> action=logout </TD>
       </TABLE>
       <P><b>HTTP parameters for Metacat Server </b>
       <TABLE border=1>
       <TR>
         <TH>Name</TH>
         <TH>Value</TH>
       <TR>
         <TD VALIGN=TOP>&nbsp;action</TD>
         <TD>&nbsp;squery <br>
             &nbsp;query <br>
             &nbsp;getdocument <br>
             &nbsp;getrelateddocument <br>
             &nbsp;getabstract <br>
             &nbsp;insert <br>
             &nbsp;update <br>
             &nbsp;delete <br>
             &nbsp;validate <br>
             &nbsp;getdatadoc <br>
             &nbsp;getdoctypes <br>
             &nbsp;getdataguide <br>
             &nbsp;login <br>
             &nbsp;logout </TD>
       <TR>
         <TD>&nbsp;query</TD>
         <TD>&nbsp;<i>XML text of query that conforms to pathquery.dtd</i> </TD>
       <TR>
         <TD>&nbsp;returndoc</TD>
         <TD>&nbsp;<i>array of doctypes to backtrack against</i> </TD>
       <TR>
         <TD>&nbsp;doctype</TD>
         <TD>&nbsp;<i>document type list</i> </TD>
       <TR>
         <TD>&nbsp;docid</TD>
         <TD>&nbsp;<i>docid of document</i></TD>
       <TR>
         <TD>&nbsp;doctext</TD>
         <TD>&nbsp;<i>XML text of document to be load into db</i> </TD>
       <TR>
         <TD>&nbsp;valtext</TD>
         <TD>&nbsp;<i>XML text of document to be validated</i> </TD>
       <TR>
         <TD>&nbsp;abstractpath</TD>
         <TD>&nbsp;<i>XML path to the abstract node to be read</i> </TD>
       <TR>
         <TD>&nbsp;url</TD>
         <TD>&nbsp;<i>URL to document. It can be of type Metacat or http</i> </TD>
       <TR>
         <TD>&nbsp;relation</TD>
         <TD>&nbsp;<i>List of URLs to documents. They can be of type Metacat or
         http</i> </TD>
       <TR>
         <TD>&nbsp;qformat</TD>
         <TD>&nbsp;xml <br>&nbsp;html </TD>
       <TR>
         <TD>&nbsp;username</TD>
         <TD>&nbsp;<i>username for authentication and connection to the server</i></TD>
       <TR>
         <TD>&nbsp;password</TD>
         <TD>&nbsp;<i>user's password for authentication</i> </TD>
       </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>

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Revision 878

Added by berkley about 23 years ago