Revision 6843
Added by Matt Jones over 12 years ago
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Accessing and Submitting Metadata and Data |
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========================================== |
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Under construction!
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.. contents::
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Heading 1
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------------
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The Metacat repository can be accessed and updated using a number of tools,
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including:
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Heading 2 |
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* the Registry, Metacat's optional Web interface |
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* user-created HTML forms |
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* Metacat's EarthGrid API |
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* existing clients, such as KNB's Morpho application, designed to help |
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scientists create, edit, and manage metadata |
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* user-created desktop clients that take advantage of Metacat's Java API. |
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In this section, we will look at how to take advantage of these tools to |
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customize Metacat for your user-base. |
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A Brief Note about How Information is Stored |
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-------------------------------------------- |
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Metacat stores XML files as a hierarchy of nodes, where each node is stored as |
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records in database tables. Because many XML data schemas are broken up into |
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multiple DTDs requiring multiple XML files that are related but stored |
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separately in the system, the system uses "packages" to link related but |
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separate documents. Packaged documents contain information that shows how they |
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are related to eachother, essentially stating that file A has a relationship |
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to file B, etc. A package file also allows users to link metadata files to the |
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data files they describe. For more information about the structure of data |
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packages and how XML documents and data are stored in Metacat, please see the |
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developer's documentation. |
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Using the Registry |
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------------------ |
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Metacat's optional Registry provides a simple Web-based interface for creating, |
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editing, and submitting metadata to the Metacat repository (Figure 4.1). The |
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interface includes help documentation, and can be customized using Metacat's |
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configuration settings. The Registry also includes an administrative interface |
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for managing LDAP user accounts, which is useful if you are using LDAP as your |
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Metacat authentication system. Note that you must be running your own LDAP |
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server if you wish to use the LDAP Web interface. If you do not have your own |
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LDAP server, you can create and manage new accounts on the KNB website |
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(http://knb.ecoinformatics.org/). Please note that at this time, the Registry |
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interface has only been tested on Linux systems. |
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.. figure:: images/screenshots/image033.jpg |
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:align: center |
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An example installation of the Register's web interface. Customize the |
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displayed and required modules with the Skins Configuration settings. |
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You can customize which modules (e.g., "Name of Submitter" or "Temporal |
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Coverage of Data") are displayed and which are required using the Skins |
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Configuration settings |
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Installing the Registry |
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~~~~~~~~~~~~~~~~~~~~~~~ |
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In order to install and run the Registry, you must have Metacat installed and |
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Tomcat must be running behind an Apache Web server (see previous sections for |
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information about installing and configuring Apache to run with Tomcat). |
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To install and run the Registry: |
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1. Build the Metacat Perl client library: |
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:: |
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cd $METACAT/src/perl/Metacat |
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perl Makefile.PL |
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sudo make |
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sudo make install |
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.. sidebar:: Instructions for Red Hat (Alternate Step 2) |
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* Install the libraries |
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:: |
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sudo yum install gcc libxml2-devel libxslt-devel ant –y |
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* Install CPAN, which allows us to install the Perl dependencies for the |
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registry and account management parts of Metacat. If asked to manually |
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configure cpan, type 'no' and CPAN will be setup with its default values. |
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:: |
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sudo yum install perl-CPAN |
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sudo cpan |
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* You should now see a prompt which looks like: |
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:: |
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cpan> |
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* The rest of the commands assume you're inside of CPAN. Let's get the most |
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recent version of the CPAN software. Just press return after any prompts |
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you receive during this process. |
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:: |
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install Bundle::CPAN |
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reload cpan |
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* Install the required modules. Here we're installing an old LibXSLT, as the |
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current one requires a newer libxslt than is available on Redhat 4 & 5. |
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Again, just answer 'yes' to any questions. |
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:: |
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install AutoLoader |
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install CGI |
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install CGI::SEssion |
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install LWP::UserAgent |
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install Net::LDAP |
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install Template |
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install URI |
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install MSERGEANT/XML-LibXSLT-1.58.tar.gz |
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2. Install the required system libraries using Ubuntu/Debian (instructions |
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Red Hat in sidebar) |
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* Install the libraries |
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:: |
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sudo apt-get install 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 -y |
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* Install two more package using cpan |
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:: |
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sudo cpan -i Config::Properties |
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sudo cpan -i Scalar::Util |
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3. Double-check that Metacat's temporary folder, application.tempDir, is |
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writable by the apache user, usually www-data or apache. |
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4. Make sure that the following scripts (found in ``<tomcat-home>/webapps/knb/cgi-bin``) |
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are executable: register-dataset.cgi and ldapweb.cgi. |
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:: |
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sudo chmod +x <tomcat-home>/webapps/knb/cgi-bin/*.cgi |
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5. Restart Apache. |
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:: |
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sudo /etc/init.d/apache2 restart |
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6. Visit the resulting URL: |
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http://<your_context_url>/cgi-bin/register-dataset.cgi?cfg=default |
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Where ``<your_context_url>`` is the URL of the server hosting the Metacat |
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followed by the name of the WAR file (i.e., the application context) that |
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you installed. For instance, the context URL for the KNB Metacat is: |
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http://knb.ecoinformatics.org/knb. |
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If everything worked correctly, the registry home page will open (see figure). |
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.. figure:: images/screenshots/image035.jpg |
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:align: center |
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An example of the Registry home page (with the default skin). |
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Customizing the Registry |
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~~~~~~~~~~~~~~~~~~~~~~~~ |
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Before using the registry, you may wish to customize the interface using the |
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Skins Configuration settings. If you are using the default skin, you must |
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disable the 'show site list' setting before you can submit the form without |
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errors. You may also wish to remove (or modify) the list of NCEAS-specific |
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projects that appear in the default registry. To remove these form fields, |
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open Metacat's administrative interface (http://<your.context.url>/knb/admin) |
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and select the Skins Specific Properties Configuration option. On the skins |
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configuration page, uncheck the boxes beside any form elements that you do not |
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wish to appear in the registry. |
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Once you have saved your changes, you must restart Tomcat for them to come |
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into effect. To restart Tomcat, log in as the user that runs your Tomcat |
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server (often "tomcat") and type: /etc/init.d/tomcat5.5 restart or an |
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equivalent command appropriate to your operating system. |
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.. figure:: images/screenshots/image037.jpg |
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:align: center |
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Uncheck the box beside any setting to remove it from the Registry form. In |
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the example, the "Show Site List" and "Show Work Group" form fields, |
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corresponding to the "Station Name" and "NCEAS Project" drop-down lists in |
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the registry form, have been removed. |
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Using HTML Forms (the HTTP Interface) |
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------------------------------------- |
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Metacat's HTTP interface supports Get and Post requests and a variety of actions (Table 4.1) that facilitate information retrieval and storage. HTTP requests can be sent from any client application that communicates using the Web's HTTP protocol. |
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* Supported Actions (API) |
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* Logging in |
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* Inserting, Updating, and Deleting XML and Data Documents |
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* Searching Metacat |
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* Paged Query Return |
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* Reading Data and Metadata |
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Supported Actions |
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~~~~~~~~~~~~~~~~~ |
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Metacat supports get and post requests as well as actions for writing, querying, |
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and reading stored XML. In addition, the HTTP interface includes functions for |
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validating and transforming XML documents (see table). |
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Note that if Replication is enabled, Metacat recognizes several additional |
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actions, included in Table 4.2. For more information about replication, |
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please see :doc:`replication`. |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| Action | Description and Parameters | |
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+==========================+====================================================================================================================================================================================================================================================================+ |
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| delete | Delete the specified document from the database. For an | |
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| | example, please see Inserting, Updating, and | |
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| | Deleting XML and Data Documents. | |
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| | | |
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| | ``docid`` - the docid of the document to delete | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| export | Export a data package in a zip file. | |
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| | | |
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| | ``docid`` - the docid of the document to delete | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getaccesscontrol | Get the access control list (ACL) for the | |
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| | specified document. | |
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| | ``docid`` - the docid of the document to delete | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getalldocids | Retrieve a list of all docids registered with the system. | |
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| | ``scope`` - a string used to match a range of docids in a SQL LIKE statement | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getdataguide | Read a data guide for the specified document type | |
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| DEPRECATED | | |
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| Use getdtdschema instead | ``doctype`` - the doctype for which to get the data guide | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getdoctypes | Get all doctypes currently available in the Metacat Catalog System. No parameters. | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getdtdschema | Read the DTD or XMLSchema file for the specified doctype. | |
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| | ``doctype`` - the doctype for which DTD or XMLSchema files to read | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getlastdocid | Get the latest docid with revision number used by user. | |
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| | ``username`` - the user's log-in name | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getlog | Get the latest docid with revision number used by user. | |
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| | | |
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| | ``ipaddress`` - the internet protocol address for the event | |
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| | ``principal`` - the principal for the event (a username, etc) | |
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| | ``docid`` - the identifier of the document to which the event applies | |
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| | ``event`` - the string code for the event | |
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| | ``start`` - beginning of date-range for query | |
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| | ``end`` - end of date-range for query | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getloggedinuserinfo | Get user info for the currently logged in user. No parameters. | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getpricipals | Get all users and groups in the current authentication schema. No parameters. | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getrevisionanddoctype | Return the revision and doctype of a document. | |
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| | The output is String that looks like "rev;doctype" | |
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| | | |
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| | ``docid`` - the docid of the document | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getversion | Get Metacat version. Return the current version of Metacat as XML. No parameters. | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| insert | Insert an XML document into the database. For an example, please see | |
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| | Inserting, Updating, and Deleting XML and Data Documents | |
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| | | |
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| | ``docid`` - the user-defined docid to assign to the new XML document | |
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| | ``doctext`` - the text of the XML document to insert | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| insertmultipart | Insert an XML document using multipart encoding into the database. | |
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| | ``docid`` - the user-defined docid to assign to the new XML document | |
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| | ``doctext`` - the text of the XML document to insert | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| isregistered | Check if an individual document exists in either the xml_documents or xml_revisions tables. | |
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| | For more information about Metacat's database schema, please see the developer documentation. | |
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| | | |
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| | ``docid`` - the docid of the document | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| login | Log the user in. You must log in using this action before you can perform | |
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| | many of the actions. For an example of the login action, see Logging In. | |
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| | | |
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| | ``username`` - the user's login name | |
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| | ``password`` - the user's password | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| logout | Log the current user out and destroy the associated session. No parameters. | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| query | Perform a free text query. For an example, please see Searching Metacat. | |
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| | | |
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| | ``returndoctype`` - the doctype to use for your Package View. For more information about packages, see http://knb.ecoinformatics.org/software/metacat/packages.html | |
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| | ``qformat`` - the format of the returned result set. Possible values are html or xml or the name of your servlet's Metacat skin. | |
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| | ``querytitle`` - OPTIONAL - the title of the query | |
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| | ``doctype`` - OPTIONAL - if doctype is specified, the search is limited only to the specified doctype(s). (e.g., eml://ecoinformatics.org/eml-2.0.1 and/or eml://ecoinformatics.org/eml-2.0.0) If no doctype element is specified, all document types are returned | |
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| | ``returnfield`` - a custom field to be returned by any hit document. | |
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| | ``operator`` - the Boolean operator to apply to the query. Possible values are: union or intersect | |
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| | ``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. | |
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| | ``anyfield`` - a free-text search variable. The value placed in this parameter will be searched for in any document in any node. | |
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| | ``pagesize`` – the number of search results to display on each search results page (e.g., 10). Used with pagestart. See section 4.3.4 for an example. | |
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| | ``pagestart`` – the displayed search results page (e.g, 1). Used with pagesize. See section 4.3.4 for an example. | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| read | Get a document from the database and return it in the specified format. See Searching Metacat for an example. | |
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| | | |
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| | ``docid`` - the docid of the document to return | |
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| | ``qformat`` - the format to return the document in. Possible values are: ``html``, ``xml``,or, if your Metacat uses a skin, the name of the skin. | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| readinlinedata | Read inline data only. | |
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| | | |
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| | ``inlinedataid`` - the id of the inline data to read | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| setaccess | Change access permissions for a user on a specified document. | |
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| | | |
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| | ``docid`` - the docid of the document to be modified. | |
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| | ``principal`` - the user or group whose permissions will be modified | |
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| | ``permission`` - the permission to set (read, write, all) | |
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| | ``permType`` - the type of permission to set (allow, deny) | |
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| | ``permOrder`` - the order in which to apply the permission (allowFirst, denyFirst) | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| spatial_query | Perform a spatial query. These queries may include any of the queries supported by the | |
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| | WFS / WMS standards. For more information, see Spatial Queries. | |
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| | | |
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| | ``xmax`` - max x spatial coordinate | |
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| | ``ymax`` - max y spatial coordinate | |
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| | ``xmin`` - min x spatial coordinate | |
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| | ``ymin`` - min y spatial coordinate | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| squery | Perform a structured query. For an example, please see Searching Metacat. | |
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| | | |
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| | ``query`` - the text of the pathquery document sent to the server | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| update | Overwrite an XML document with a new one and give the new one the same docid but with | |
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| | the next revision number. For an example, please see Inserting, Updating, and | |
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| | Deleting XML and Data Documents. | |
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| | | |
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| | ``docid`` - the docid of the document to update | |
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| | ``doctext`` - the text with which to update the XML document | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| upload | Upload (insert or update) a data file into Metacat. Data files are stored on Metacat and may be in any | |
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| | format (binary or text), but they are all treated as if they were binary. | |
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| | | |
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| | ``docid`` - the docid of the data file to upload | |
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| | ``datafile`` - the data file to upload | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| validate | Validate a specified document against its DTD. | |
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| | | |
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| | ``docid`` - the docid of the document to validate | |
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| | ``valtext`` - the DTD by which to validate this document | |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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Metacat Replication Parameters |
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|
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+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| Action | Description and Parameters | |
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+================+=================================================================================================================================================================+ |
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| forcereplicate | Force the local server to get the specified document from the remote host. | |
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| | | |
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| | ``server`` - The server to which this document is being sent | |
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| | ``docid`` - The docid of the document to send | |
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| | ``dbaction`` - The action to perform on the document: insert or update (the default) | |
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+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getall | Force the local server to check all known servers for updated documents. No parameters. | |
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+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getcatalog | Send the contents of the xml_catalog table encoded in XML. No parameters. | |
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+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
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| getlock | Request a lock on the specified document. | |
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| | | |
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| | ``docid`` - the docid of the document | |
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| | ``updaterev`` - the revision number of docid | |
|
| 373 |
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
|
| 374 |
| gettime | Return the local time on this server. No parameters. | |
|
| 375 |
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
|
| 376 |
| servercontrol | Perform the specified replication control on the Replication daemon. | |
|
| 377 |
| | | |
|
| 378 |
| | ``add`` - add a new server to the replication list | |
|
| 379 |
| | ``delete`` - remove a server from the replication list | |
|
| 380 |
| | ``list`` - list all of the servers currently in the server list | |
|
| 381 |
| | ``replicate`` - a Boolean flag (1 or 0) which determines if this server should copy files from the newly added server. | |
|
| 382 |
| | ``server`` - the server to add/delete | |
|
| 383 |
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
|
| 384 |
| read | Sends docid to the remote host. | |
|
| 385 |
| | | |
|
| 386 |
| | ``docid`` - the docid of the document to read | |
|
| 387 |
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
|
| 388 |
| start | Start the Replication daemon with a time interval of deltaT. | |
|
| 389 |
| | | |
|
| 390 |
| | ``rate`` - The rate (in seconds) at which you want the replication daemon to check for updated documents. The value cannot be less than 30. The default is 1000 | |
|
| 391 |
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
|
| 392 |
| stop | Stop the Replication daemon. No parameters. | |
|
| 393 |
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
|
| 394 |
| update | Send a list of all documents on the local server along with their revision numbers. No parameters. | |
|
| 395 |
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
|
| 396 |
|
|
| 397 |
Logging In |
|
| 398 |
~~~~~~~~~~ |
|
| 399 |
To log in to Metacat, use the ``login`` action. |
|
| 400 |
|
|
| 401 |
The following is an example of a Web form (see figure) that logs a user into |
|
| 402 |
Metact. Example HTML code is included below the screenshot. |
|
| 403 |
|
|
| 404 |
.. figure:: images/screenshots/image039.jpg |
|
| 405 |
:align: center |
|
| 406 |
|
|
| 407 |
Logging into Metacat using an HTML form. |
|
| 408 |
|
|
| 409 |
:: |
|
| 410 |
|
|
| 411 |
<html> |
|
| 412 |
<body> |
|
| 413 |
<form name="loginform" method="post"action="http://yourserver.com/yourcontext/servlet/metacat" |
|
| 414 |
target="_top" onsubmit="return submitform(this);" id="loginform"> |
|
| 415 |
<input type="hidden" name="action" value="login"> <input type= |
|
| 416 |
"hidden" name="username" value=""> <input type="hidden" name= |
|
| 417 |
"qformat" value="xml"> <input type="hidden" name= |
|
| 418 |
"enableediting" value="false"> |
|
| 419 |
|
|
| 420 |
<table> |
|
| 421 |
<tr valign="middle"> |
|
| 422 |
<td align="left" valign="middle" class="text_plain"> |
|
| 423 |
username:</td> |
|
| 424 |
|
|
| 425 |
<td width="173" align="left" class="text_plain" style= |
|
| 426 |
"padding-top: 2px; padding-bottom: 2px;"><input name="uid" |
|
| 427 |
type="text" style="width: 140px;" value=""></td> |
|
| 428 |
</tr> |
|
| 429 |
|
|
| 430 |
<tr valign="middle"> |
|
| 431 |
<td height="28" align="left" valign="middle" class= |
|
| 432 |
"text_plain">organization:</td> |
|
| 433 |
|
|
| 434 |
<td align="left" class="text_plain" style= |
|
| 435 |
"padding-top: 2px; padding-bottom: 2px;"><select name= |
|
| 436 |
"organization" style="width:140px;"> |
|
| 437 |
<option value="" selected>— choose one —</option> |
|
| 438 |
<option value="NCEAS">NCEAS</option> |
|
| 439 |
<option value="LTER">LTER</option> |
|
| 440 |
<option value="UCNRS">UCNRS</option> |
|
| 441 |
<option value="PISCO">PISCO</option> |
|
| 442 |
<option value="OBFS">OBFS</option> |
|
| 443 |
<option value="OSUBS">OSUBS</option> |
|
| 444 |
<option value="SAEON">SAEON</option> |
|
| 445 |
<option value="SANParks">SANParks</option> |
|
| 446 |
<option value="SDSC">SDSC</option> |
|
| 447 |
<option value="KU">KU</option> |
|
| 448 |
<option value="unaffiliated">unaffiliated</option> |
|
| 449 |
</select></td> |
|
| 450 |
</tr> |
|
| 451 |
|
|
| 452 |
<tr valign="middle"> |
|
| 453 |
<td width="85" align="left" valign="middle" class= |
|
| 454 |
"text_plain">password:</td> |
|
| 455 |
|
|
| 456 |
<td colspan="2" align="left" class="text_plain" style= |
|
| 457 |
"padding-top: 2px; padding-bottom: 2px;"> |
|
| 458 |
<table width="100%" border="0" cellpadding="0" |
|
| 459 |
cellspacing="0"> |
|
| 460 |
<tr> |
|
| 461 |
<td width="150" align="left"><input name="password" |
|
| 462 |
type="password" maxlength="50" style="width:140px;" |
|
| 463 |
value=""></td> |
|
| 464 |
|
|
| 465 |
<td align="center" class="buttonBG_login"> |
|
| 466 |
<input type="submit" name="loginAction" value="Login" |
|
| 467 |
class="button_login"></td> |
|
| 468 |
|
|
| 469 |
<td align="left"> </td> |
|
| 470 |
</tr> |
|
| 471 |
</table> |
|
| 472 |
</td> |
|
| 473 |
</tr> |
|
| 474 |
</table> |
|
| 475 |
</form> |
|
| 476 |
</body> |
|
| 477 |
</html> |
|
| 478 |
|
|
| 479 |
Inserting, Updating, and Deleting XML and Data Documents |
|
| 480 |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
|
| 481 |
Adding, editing, and deleting XML documents in Metacat can be accomplished |
|
| 482 |
using the insert, update, and delete actions, respectively. Before you can |
|
| 483 |
insert, delete, or update documents, you must log in to Metacat using the |
|
| 484 |
login action. See Logging in for an example. |
|
| 485 |
|
|
| 486 |
``insert`` |
|
| 487 |
Insert a new XML or data document into Metacat. You must specify a document ID. |
|
| 488 |
|
|
| 489 |
``update`` |
|
| 490 |
Update an existing Metacat document. The original document is archived, |
|
| 491 |
then overwritten. |
|
| 492 |
|
|
| 493 |
``delete`` |
|
| 494 |
Archive a document and move the pointer in xml_documents to xml_revisions, |
|
| 495 |
effectively "deleting" the document from public view, but preserving the |
|
| 496 |
revision for the revision history. |
|
| 497 |
|
|
| 498 |
The following is an example of a Web form (see figure) that can perform all |
|
| 499 |
three tasks. Example HTML code is included in the sidebar. |
|
| 500 |
|
|
| 501 |
.. figure:: images/screenshots/image041.jpg |
|
| 502 |
:align: center |
|
| 503 |
|
|
| 504 |
An example of a Web form used to insert, delete, or update XML documents in Metacat. |
|
| 505 |
|
|
| 506 |
:: |
|
| 507 |
|
|
| 508 |
<html> |
|
| 509 |
<head> |
|
| 510 |
<title>MetaCat</title> |
|
| 511 |
</head> |
|
| 512 |
<body class="emlbody"> |
|
| 513 |
<b>MetaCat XML Loader</b> |
|
| 514 |
<p> |
|
| 515 |
Upload, Change, or Delete an XML document using this form. |
|
| 516 |
</p> |
|
| 517 |
<form action="http://yourserver.com/yourcontext/servlet/metacat" method="POST"> |
|
| 518 |
<strong>1. Choose an action: </strong> |
|
| 519 |
<input type="radio" name="action" value="insert" checked> Insert |
|
| 520 |
<input type="radio" name="action" value="update"> Update |
|
| 521 |
<input type="radio" name="action" value="delete"> Delete |
|
| 522 |
<input type="submit" value="Process Action"> |
|
| 523 |
<br /> |
|
| 524 |
<strong>2. Provide a Document ID </strong> |
|
| 525 |
<input type="text" name="docid"> (optional for Insert) |
|
| 526 |
<input type="checkbox" name="public" value="yes" checked><strong>Public Document</strong> |
|
| 527 |
<br /> |
|
| 528 |
<strong>3. Provide XML text </strong> (not needed for Delete)<br/> |
|
| 529 |
<textarea name="doctext" cols="65" rows="15"></textarea><br/> |
|
| 530 |
<strong>4. Provide DTD text for upload </strong> (optional; not needed for Delete) |
|
| 531 |
<textarea name="dtdtext" cols="65" rows="15"></textarea> |
|
| 532 |
</form> |
|
| 533 |
</body> |
|
| 534 |
</html> |
|
| 535 |
|
|
| 536 |
Searching Metacat |
|
| 537 |
~~~~~~~~~~~~~~~~~ |
|
| 538 |
To search Metacat use the ``query`` or ``squery`` actions. |
|
| 539 |
|
|
| 540 |
``query``: |
|
| 541 |
Perform a free text query. Specify the returndoctype, qformat, returnfield, |
|
| 542 |
operator, searchmode, anyfield, and (optionally) a querytitle and doctype. |
|
| 543 |
|
|
| 544 |
``squery``: |
|
| 545 |
Perform a structured query by submitting an XML pathquery document to the |
|
| 546 |
Metacat server. |
|
| 547 |
|
|
| 548 |
|
|
| 549 |
When Metacat receives a query via HTTP (Figure 4.8), the server creates a |
|
| 550 |
"pathquery" document, which is an XML document populated with the specified |
|
| 551 |
search criteria (Figure 4.10). The pathquery document is then translated into |
|
| 552 |
SQL statements that are executed against the data base. Results are translated |
|
| 553 |
into an XML "resultset" document, which can be returned as XML or transformed |
|
| 554 |
into HTML and returned (specify which you would prefer with the returnfield |
|
| 555 |
parameter). You can also opt to submit a pathquery document directly, |
|
| 556 |
using an squery action. |
|
| 557 |
|
|
| 558 |
.. figure:: images/screenshots/image043.jpg |
|
| 559 |
:align: center |
|
| 560 |
|
|
| 561 |
Example of a basic search form using a query action. |
|
| 562 |
|
|
| 563 |
:: |
|
| 564 |
|
|
| 565 |
<html> |
|
| 566 |
<head> |
|
| 567 |
<title>Search</title> |
|
| 568 |
</head> |
|
| 569 |
<body> |
|
| 570 |
<form method="POST" action="http://panucci.nceas.ucsb.edu/knb/servlet/metacat"> |
|
| 571 |
|
|
| 572 |
Search for: |
|
| 573 |
|
|
| 574 |
<input name="action" value="query" type="hidden"> |
|
| 575 |
<input name="operator" value="INTERSECT" type="hidden"> |
|
| 576 |
<input name="anyfield" type="text" value=" " size="40"> |
|
| 577 |
<input name="qformat" value="html" type="hidden"> |
|
| 578 |
|
|
| 579 |
<input name="returnfield" value="creator/individualName/surName" type="hidden"> |
|
| 580 |
<input name="returnfield" value="creator/individualName/givenName" type="hidden"> |
|
| 581 |
<input name="returnfield" value="creator/organizationName" type="hidden"> |
|
| 582 |
<input name="returnfield" value="dataset/title" type="hidden"> |
|
| 583 |
<input name="returnfield" value="keyword" type="hidden"> |
|
| 584 |
|
|
| 585 |
<input name="returndoctype" value="eml://ecoinformatics.org/eml-2.0.1" type="hidden"> |
|
| 586 |
|
|
| 587 |
<input value="Start Search" type="submit"> |
|
| 588 |
|
|
| 589 |
</form> |
|
| 590 |
</body> |
|
| 591 |
</html> |
|
| 592 |
|
|
| 593 |
Metacat's pathquery document can query specific fields of any XML document. |
|
| 594 |
The pathquery can also be used to specify which fields from each hit are |
|
| 595 |
returned and displayed in the search result set. |
|
| 596 |
|
|
| 597 |
:: |
|
| 598 |
|
|
| 599 |
<pathquery version="1.0"> |
|
| 600 |
<meta_file_id>unspecified</meta_file_id> |
|
| 601 |
<querytitle>unspecified</querytitle> |
|
| 602 |
<returnfield>dataset/title</returnfield> |
|
| 603 |
<returnfield>keyword</returnfield> |
|
| 604 |
<returnfield>originator/individualName/surName</returnfield> |
|
| 605 |
<returndoctype>eml://ecoinformatics.org/eml-2.0.1</returndoctype> |
|
| 606 |
<returndoctype>eml://ecoinformatics.org/eml-2.0.0</returndoctype> |
|
| 607 |
<querygroup operator="UNION"> |
|
| 608 |
<queryterm casesensitive="false" searchmode="contains"> |
|
| 609 |
<value>Plant</value> |
|
| 610 |
<pathexpr>dataset/title</pathexpr> |
|
| 611 |
</queryterm> |
|
| 612 |
<queryterm casesensitive="false" searchmode="contains"> |
|
| 613 |
<value>plant</value> |
|
| 614 |
<pathexpr>keyword</pathexpr> |
|
| 615 |
</queryterm> |
|
| 616 |
</querygroup> |
|
| 617 |
</pathquery> |
|
| 618 |
|
|
| 619 |
Each ``<returnfield>`` parameter specifies a field that the data base will |
|
| 620 |
return (in addition to the fields Metacat returns by default) for each search |
|
| 621 |
result. |
|
| 622 |
|
|
| 623 |
The ``<returndoctype>`` field limits the type of returned documents |
|
| 624 |
(eg, eml://ecoinformatics.org/eml-2.0.1 and/or eml://ecoinformatics.org/eml-2.0.0). |
|
| 625 |
If no returndoctype element is specified, all document types are returned. |
|
| 626 |
|
|
| 627 |
A ``<querygroup>`` creates an AND or an OR statement that applies to the |
|
| 628 |
nested ``<queryterm>`` tags. The querygroup operator can be UNION or INTERSECT. |
|
| 629 |
A ``<queryterm>`` defines the actual field (contained in ``<pathexpr>`` tags) |
|
| 630 |
against which the query (contained in the ``<value>`` tags) is being performed. |
|
| 631 |
|
|
| 632 |
The ``<pathexpr>`` can also contain a document type keyword contained in |
|
| 633 |
``<returndoc>`` tags. The specified document type applies only to documents |
|
| 634 |
that are packaged together (e.g., a data set and its corresponding metadata file). |
|
| 635 |
If Metacat identifies the search term in a packaged document, the servlet will |
|
| 636 |
check to see if that document's type matches the specified one. If not, |
|
| 637 |
Metacat will check if one of the other documents in the package matches. If so, |
|
| 638 |
Metacat will return the matching document. For more information about packages, |
|
| 639 |
please see the developer documentation. |
|
| 640 |
|
|
| 641 |
After Metacat has processed a Pathquery document, it returns a resultset document. |
|
| 642 |
|
|
| 643 |
:: |
|
| 644 |
|
|
| 645 |
<resultset> |
|
| 646 |
<query> |
|
| 647 |
<pathquery version="1.0"> |
|
| 648 |
<meta_file_id>unspecified</meta_file_id> |
|
| 649 |
<querytitle>unspecified</querytitle> |
|
| 650 |
<returnfield>dataset/title</returnfield> |
|
| 651 |
<returnfield>keyword</returnfield> |
|
| 652 |
<returnfield>originator/individualName/surName</returnfield> |
|
| 653 |
<returndoctype>eml://ecoinformatics.org/eml-2.0.1</returndoctype> |
|
| 654 |
<returndoctype>eml://ecoinformatics.org/eml-2.0.0</returndoctype> |
|
| 655 |
<querygroup operator="UNION"> |
|
| 656 |
<queryterm casesensitive="false" searchmode="contains"> |
|
| 657 |
<value>Datos</value> |
|
| 658 |
<pathexpr>dataset/title</pathexpr> |
|
| 659 |
</queryterm> |
|
| 660 |
<queryterm casesensitive="false" searchmode="contains"> |
|
| 661 |
<value>plant</value> |
|
| 662 |
<pathexpr>keyword</pathexpr> |
|
| 663 |
</queryterm> |
|
| 664 |
</querygroup> |
|
| 665 |
</pathquery> |
|
| 666 |
</query> |
|
| 667 |
|
|
| 668 |
<document> |
|
| 669 |
<docid>nceas.44.1</docid> |
|
| 670 |
<docname>resource</docname> |
|
| 671 |
<doctype>eml://ecoinformatics.org/eml-2.0.1</doctype> |
|
| 672 |
<createdate>2001-01-12 16:12:06.0</createdate> |
|
| 673 |
<updatedate>2001-01-12 16:12:06.0</updatedate> |
|
| 674 |
<param name="dataset/title">Datos Meteorologicos</param> |
|
| 675 |
<param name="keyword">intertidal</param> |
|
| 676 |
<param name="originator/individualName/surName">Smith</param> |
|
| 677 |
</document> |
|
| 678 |
|
|
| 679 |
<document> |
|
| 680 |
<docid>nceas.42.1</docid> |
|
| 681 |
<docname>resource</docname> |
|
| 682 |
<doctype>eml://ecoinformatics.org/eml-2.0.1</doctype> |
|
| 683 |
<createdate>2001-01-12 16:11:31.0</createdate> |
|
| 684 |
<updatedate>2001-01-12 16:11:31.0</updatedate> |
|
| 685 |
<param name="dataset/title">Ocean Surface Temperature</param> |
|
| 686 |
<param name="keyword">Plant</param> |
|
| 687 |
<param name="originator/individualName/surName">Henry</param> |
|
| 688 |
</document> |
|
| 689 |
..... |
|
| 690 |
</resultset> |
|
| 691 |
|
|
| 692 |
When Metacat returns a resultset document, the servlet always includes the |
|
| 693 |
pathquery used to create it. The pathquery XML is contained in the <query> tag, |
|
| 694 |
the first element in the resultset. |
|
| 695 |
|
|
| 696 |
Each XML document returned by the query is represented by a ``<document>`` tag. By |
|
| 697 |
default, Metacat will return the docid, docname, doctype, doctitle, createdate |
|
| 698 |
and updatedate for each search result. If the user specified additional return |
|
| 699 |
fields in the pathquery using ``<returnfield>`` tags (e.g., dataset/title to return |
|
| 700 |
the document title), the additional fields are returned in ``<param>`` tags. |
|
| 701 |
|
|
| 702 |
Metacat can return the XML resultset to your client as either XML or HTML. |
|
| 703 |
|
|
| 704 |
Paged Query Returns |
|
| 705 |
~~~~~~~~~~~~~~~~~~~ |
|
| 706 |
Dividing large search result sets over a number of pages speeds load-time and |
|
| 707 |
makes the result sets more readable to users (Figure 4.12). To break your search |
|
| 708 |
results into pages, use the query action's optional pagestart and pagesize |
|
| 709 |
parameters. The pagesize parameter indicates how many results should be |
|
| 710 |
returned for a given page. The pagestart parameter indicates which page you |
|
| 711 |
are currently viewing. |
|
| 712 |
|
|
| 713 |
.. figure:: images/screenshots/image045.jpg |
|
| 714 |
:align: center |
|
| 715 |
|
|
| 716 |
An example of paged search results. |
|
| 717 |
|
|
| 718 |
When a paged query is performed, the query's resultset contains four extra |
|
| 719 |
fields: pagestart, pagesize, nextpage, and previouspage (Figure 4.13). The |
|
| 720 |
nextpage and previouspage fields help Metacat generate navigational links in |
|
| 721 |
the rendered resultset using XSLT to transform the XML to HTML. |
|
| 722 |
|
|
| 723 |
:: |
|
| 724 |
|
|
| 725 |
<!-- An example of an XML resultset that include support for page breaks. |
|
| 726 |
The pagestart parameter will always indicate the page you are currently viewing. |
|
| 727 |
--> |
|
| 728 |
<resultset> |
|
| 729 |
<pagestart>1</pagestart> |
|
| 730 |
<pagesize>10</pagesize> |
|
| 731 |
<nextpage>2</nextpage> |
|
| 732 |
<previouspage>0</previouspage> |
|
| 733 |
<query> ...</query> |
|
| 734 |
<document>...</document> |
|
| 735 |
<document>...</document> |
|
| 736 |
</resultset> |
|
| 737 |
|
|
| 738 |
The HTML search results displayed in the figure were rendered using Kepler's XSLT, |
|
| 739 |
which can be found in lib/style/skins/kepler. Kepler's XSLT uses the four extra |
|
| 740 |
resultset fields to render the "Next" and "Previous" links. |
|
| 741 |
|
|
| 742 |
:: |
|
| 743 |
|
|
| 744 |
<a href="metacat?action=query&operator=INTERSECT&enableediting=false&anyfield=actor&qformat=kepler&pagestart=0&pagesize=10">Previous Page</a> |
|
| 745 |
<a href="metacat?action=query&operator=INTERSECT&enableediting=false&anyfield=actor&qformat=kepler&pagestart=2&pagesize=10">Next Page</a> |
|
| 746 |
|
|
| 747 |
In the example above, the current page is 1, and the previous page (page 0) and next page (page 2) pages are indicated by the values of the pagestart parameters. |
|
| 748 |
|
|
| 749 |
Reading Data and Metadata |
|
| 750 |
~~~~~~~~~~~~~~~~~~~~~~~~~ |
|
| 751 |
To read data or metadata from Metacat, use the ``read`` action. The ``read`` action |
|
| 752 |
takes two parameters: ``docid``, which specifies the document ID of the document |
|
| 753 |
to return, and ``qformat``, which specifies the return format for the document |
|
| 754 |
(``html`` or ``xml`` or the name of a configured style-set, e.g., ``default``). If ``qformat`` |
|
| 755 |
is set to ``xml``, Metacat will return the XML document untransformed. If the |
|
| 756 |
return format is set to ``html``, Metacat will transform the XML document into |
|
| 757 |
HTML using the default XSLT style sheet (specified in the Metacat |
|
| 758 |
configuration). If the name of a style-set is specified, Metacat will use the |
|
| 759 |
XSLT styles specified in the set to transform the XML. |
|
| 760 |
|
|
| 761 |
.. figure:: images/screenshots/image047.jpg |
|
| 762 |
:align: center |
|
| 763 |
|
|
| 764 |
The same document displayed using different qformat parameters (from left |
|
| 765 |
to right: the default style-set, XML, and HTML). |
|
| 766 |
|
|
| 767 |
Note that the ``read`` action can be used to read both data files and metadata files. |
|
| 768 |
To read a data file, you could use the following request:: |
|
| 769 |
|
|
| 770 |
http://yourserver.com/yourcontext/metacat?action=read&docid=nceas.55&qformat=default |
|
| 771 |
|
|
| 772 |
Where ``nceas.55`` is the docid of the data file stored in the Metacat and |
|
| 773 |
``default`` is the name of the style (you could also use "html" or "xml" or the |
|
| 774 |
name of a customized skin). |
|
| 775 |
|
|
| 776 |
:: |
|
| 777 |
|
|
| 778 |
<html> |
|
| 779 |
<head> |
|
| 780 |
<title>Read Document</title> |
|
| 781 |
</head> |
|
| 782 |
<body> |
|
| 783 |
<form method="POST" action="http://your.server/your.context/servlet/metacat"> |
|
| 784 |
<input name="action" value="read" type="hidden"> |
|
| 785 |
<input name="docid" type="text" value="" size="40"> |
|
| 786 |
<input name="qformat" value="default" type="hidden"> |
|
| 787 |
<input value="Read" type="submit"> |
|
| 788 |
</form> |
|
| 789 |
</body> |
|
| 790 |
</html> |
|
| 791 |
|
|
| 792 |
Using the EarthGrid API (aka EcoGrid) |
|
| 793 |
------------------------------------- |
|
| 794 |
|
|
| 795 |
Using Morpho |
|
| 10 | 796 |
------------ |
| 11 | 797 |
|
| 798 |
Creating Your Own Client |
|
| 799 |
------------------------ |
|
| 800 |
|
|
Also available in: Unified diff
Partial conversion of the accessing and submitting metadata section to RST.
More coming later.