/docs/user/packages.html - Annotate - Metacat - Ecoinformatics Redmine

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berkley

<!--

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  * packages.html

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  *      Authors: Chad Berkley

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  *    Copyright: 2000 Regents of the University of California and the

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  *               National Center for Ecological Analysis and Synthesis

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  *  For Details: http://www.nceas.ucsb.edu/

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  *      Created: 2001 January 23

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  *      Version:

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  *    File Info: '$ '

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<TITLE>Metacat</TITLE>

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  <table width="100%">

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      <td class="tablehead" colspan="2"><p class="label">Packages and Relationships</p></td>

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      <td class="tablehead" colspan="2" align="right">

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        <a href="./metacatapi.html">Back</a> | <a href="./metacattour.html">Home</a> |

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        <a href="./replication.html">Next</a>

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      </td>

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  </table>

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  <p>Metacat allows a user to create a virtual link between XML documents within

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  the system.  These links are called <i>Relationships</i> and are defined by triples

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  in <i>eml-dataset-2.0</i> files.  A relationship can be defined between two

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  XML or <a href="./datafiles.html">non-XML</a> files.

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  The following is an example of an eml-dataset-2.0 file holding triples at the end:</p>

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  <pre>

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&lt;?xml version="1.0"?&gt;

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&lt;!DOCTYPE dataset PUBLIC "-//NCEAS//eml-dataset-2.0//EN" "eml-dataset-2.0.dtd"&gt;

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&lt;dataset&gt;

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  &lt;identifier system="null"&gt;berkley.5.3&lt;/identifier&gt;

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  &lt;shortName&gt;allsp&lt;/shortName&gt;

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  &lt;title&gt;MARINE sampling data collected between spring 1992 and fall 1996&lt;/title&gt;

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  &lt;originator&gt;

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    &lt;individualName&gt;

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      &lt;salutation&gt;Dr.&lt;/salutation&gt;

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      &lt;givenName&gt;Peter&lt;/givenName&gt;

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      &lt;surName&gt;Raimondi&lt;/surName&gt;

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    &lt;/individualName&gt;

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    &lt;organizationName&gt;UCSC&lt;/organizationName&gt;

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    &lt;positionName&gt; &lt;/positionName&gt;

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    &lt;address&gt;

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      &lt;deliveryPoint&gt;Biology Dept.&lt;/deliveryPoint&gt;

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      &lt;deliveryPoint&gt;A309 Earth and Marine Science Building&lt;/deliveryPoint&gt;

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      &lt;city&gt;Santa Cruz&lt;/city&gt;

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      &lt;administrativeArea&gt;CA&lt;/administrativeArea&gt;

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      &lt;postalCode&gt;95060&lt;/postalCode&gt;

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      &lt;country&gt;USA&lt;/country&gt;

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    &lt;/address&gt;

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    &lt;phone phonetype="voice"&gt;831-459-1234 x5674&lt;/phone&gt;

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    &lt;electronicMailAddress&gt;raimondi@biology.ucsc.edu&lt;/electronicMailAddress&gt;

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    &lt;onlineLink&gt; &lt;/onlineLink&gt;

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    &lt;role&gt;Originator&lt;/role&gt;

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  &lt;/originator&gt;

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  &lt;pubdate&gt; &lt;/pubdate&gt;

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  &lt;pubplace&gt; &lt;/pubplace&gt;

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  &lt;series&gt; &lt;/series&gt;

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  &lt;abstract&gt;

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    &lt;paragraph&gt; &lt;/paragraph&gt;

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  &lt;/abstract&gt;

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  &lt;keywordSet&gt;

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    &lt;keyword keywordType="null"&gt;intertidal&lt;/keyword&gt;

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    &lt;keyword keywordType="null"&gt;santa barbara&lt;/keyword&gt;

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    &lt;keyword keywordType="null"&gt;photoplot&lt;/keyword&gt;

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    &lt;keyword keywordType="null"&gt;quadrat&lt;/keyword&gt;

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    &lt;keywordThesaurus&gt; &lt;/keywordThesaurus&gt;

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  &lt;/keywordSet&gt;

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  &lt;additionalInfo&gt;

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    &lt;paragraph&gt; &lt;/paragraph&gt;

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  &lt;/additionalInfo&gt; <font color="red">

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  &lt;triple&gt;

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    &lt;subject&gt;berkley.6.1&lt;/subject&gt;

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    &lt;relationship&gt;isRelatedTo&lt;/relationship&gt;

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    &lt;object&gt;berkley.5.3&lt;/object&gt;

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  &lt;/triple&gt;

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  &lt;triple&gt;

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    &lt;subject&gt;berkley.7.1&lt;/subject&gt;

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    &lt;relationship&gt;isRelatedTo&lt;/relationship&gt;

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    &lt;object&gt;berkley.6.1&lt;/object&gt;

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  &lt;/triple&gt;

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  &lt;triple&gt;

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    &lt;subject&gt;berkley.8.1&lt;/subject&gt;

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    &lt;relationship&gt;isRelatedTo&lt;/relationship&gt;

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    &lt;object&gt;berkley.5.3&lt;/object&gt;

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  &lt;/triple&gt;

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  &lt;triple&gt;

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    &lt;subject&gt;berkley.8.1&lt;/subject&gt;

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    &lt;relationship&gt;isRelatedTo&lt;/relationship&gt;

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    &lt;object&gt;berkley.6.1&lt;/object&gt;

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  &lt;/triple&gt;

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  &lt;triple&gt;

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    &lt;subject&gt;berkley.8.1&lt;/subject&gt;

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    &lt;relationship&gt;isRelatedTo&lt;/relationship&gt;

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    &lt;object&gt;berkley.7.1&lt;/object&gt;

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  &lt;/triple&gt;

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  &lt;triple&gt;

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    &lt;subject&gt;berkley.14.1&lt;/subject&gt;

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    &lt;relationship&gt;isRelatedTo&lt;/relationship&gt;

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    &lt;object&gt;berkley.6.1&lt;/object&gt;

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  &lt;/triple&gt; </font>

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  &lt;temporalCoverage&gt; 1992 to 1996&lt;/temporalCoverage&gt;

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  &lt;geographicCoverage&gt; &lt;/geographicCoverage&gt;

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  &lt;taxonomicCoverage&gt; &lt;/taxonomicCoverage&gt;

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&lt;/dataset&gt;

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  </pre>

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  <b>Description of the Package File</b>

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  <p>Note that the doctype of this document is an unregistered NCEAS specific

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  DTD (-//NCEAS//eml-dataset-2.0//EN).  The package doctype is an application

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  property of Metacat.  Setting this property (and others) is described in

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  <a href="./properties.html">Setting Metacat Properties</a>.  The package file

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  is broken up into <i>n</i> triples.  Each triple has a subject, relationship,

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  and an object.  This grouping can be read as follows:  &lt;subject&gt; has

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  &lt;relationship&gt; to &lt;object&gt;.  Each triple is a logical link

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  between the subject and object with the relationship being a description of that

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  link.</p>

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  <b>The Utility of Relations</b>

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  <p>Relations become useful because many XML data schemas are broken up into

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  multiple DTDs.  Thus, there may be many different XML files that are all

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  related to each other yet are stored seperately within the system.  Also,

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  since we, here at NCEAS, are developing Metacat for use as a metadata

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  repository for ecological data, we need some way of linking our metadata

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  to the datafiles that they describe.  Packages are the way we do this.</p>

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  <b>Post Processed Relations</b>

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  <p>The package file is inserted into Metacat as any other file is.  Its doctype

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  is checked against the packagedoctype property in the <a href="properties.html">

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  Metacat.properties file</a>.  If it is of that type, the file is sent

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  to a postprocessor to be analyzed and inserted into the xml_relation table.

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  The table looks like the following:</p>

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  <table border="1">

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    <tr>

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      <td>relationid</td><td>docid</td><td>packagetype</td>

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      <td>subject</td><td>subjectdoctype</td>

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      <td>relationship</td><td>object</td><td>objectdoctype</td>

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    </tr>

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    <tr>

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      <td>1</td>

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      <td>berkley.5</td>

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      <td>-//NCEAS//eml-dataset-2.0//EN</td>

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      <td>berkley.6.1</td>

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      <td>null</td>

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      <td>isRelatedTo</td>

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      <td>berkley.5.3</td>

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      <td>null</td>

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    </tr>

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    <tr>

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      <td>2</td>

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      <td>berkley.5</td>

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      <td>-//NCEAS//eml-dataset-2.0//EN</td>

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      <td>berkley.7.1</td>

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      <td>null</td>

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      <td>isRelatedTo</td>

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      <td>berkley.6.1</td>

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      <td>null</td>

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    </tr>

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    <tr>

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      <td>3</td>

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      <td>berkley.5</td>

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      <td>-//NCEAS//eml-dataset-2.0//EN</td>

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      <td>berkley.8.1</td>

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      <td>null</td>

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      <td>isRelatedTo</td>

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      <td>berkley.5.3</td>

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      <td>null</td>

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    </tr>

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    <tr>

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      <td>4</td>

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      <td>berkley.5</td>

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      <td>-//NCEAS//eml-dataset-2.0//EN</td>

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      <td>berkley.8.1</td>

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      <td>null</td>

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      <td>isRelatedTo</td>

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      <td>berkley.6.1</td>

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      <td>null</td>

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    </tr>

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    <tr>

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      <td>5</td>

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      <td>berkley.5</td>

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      <td>-//NCEAS//eml-dataset-2.0//EN</td>

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      <td>berkley.8.1</td>

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      <td>null</td>

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      <td>isRelatedTo</td>

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      <td>berkley.7.1</td>

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      <td>null</td>

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    </tr>

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    <tr>

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      <td>6</td>

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      <td>berkley.5</td>

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      <td>-//NCEAS//eml-dataset-2.0//EN</td>

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      <td>berkley.14.1</td>

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      <td>null</td>

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      <td>isRelatedTo</td>

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      <td>berkley.6.1</td>

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      <td>null</td>

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    </tr>

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  </table>

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  <p>Once, the system has processed the package file and inserted the relations

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  into the xml_relation table, the files relations are always returned to with it

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  in the <a href="./metacatquery.html">resultset</a> of a query.</p>

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  <b>Package Views (formerly known as 'backtracking')</b>

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  <p>Package View is a feature that was intentionally left out of the

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  <a href="./Metacatquery.html">Queries and Results</a> section.  Package views

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  involves sending a doctype (called a returndoctype) along with a query request.

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  When there is a hit from that query, the system will check the doctype of the

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  hit document against the returndoctype.  If the doctypes do not match,

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  the system checks the xml_relation table to see if that document has been packed

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  by document of that doctype. If such package document exists, it

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  is returned instead of the one which was originally hit.  If no such

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  package document exists, then the document which was originally hit is returned.

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  This allows a display system (such as a web browser) to try to display a

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  certain type of document.</p>

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  <p>For example:  Take our package file from above.  Say we do a query for

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  "intertidal" which returns the document berkley.6 of type -//NCEAS//eml-entity-2.0//EN.

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  However, we have set returndoctype equal to "-//NCEAS//eml-dataset-2.0//EN".

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  When berkley.6 is hit, the system will check its package documents to see if

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  it is of type -//NCEAS//eml-dataset-2.0//EN.  Since it is,

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  (relationid 1, 2 and 4) document berkley.5 is returned instead of berkley.6.

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  <p>From a client the returndoctype is a servlet parameter.

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  A URL with a returndoctype would look something like: </p>

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  <pre>http://server.domain.com/Metacat?action=query&amp;anyfield=%&amp;qformat=html&amp;returndoctype=-//NCEAS//eml-dataset-2.0//EN</pre>

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  <p>The system then inserts the returndoctype parameter value into a pathquery

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  document as illustrated in <a href="./metacatquery.html">Queries and Results</a>.

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  </p>

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