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Accessing and Submitting Metadata and Data
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==========================================
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.. contents::
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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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* 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 (screenshot below). 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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install Captcha:reCAPTCHA
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install DateTime
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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 \
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libxml-libxslt-perl libtemplate-perl libcgi-session-perl \
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build-essential libnet-ldap-perl libterm-readkey-perl \
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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 Digest::SHA1
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sudo cpan -i Config::Properties
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sudo cpan -i Scalar::Util
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sudo cpan -i Captcha:reCAPTCHA
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sudo cpan -i DateTime
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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/metacat/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/metacat/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>/metacat/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, type: ``sudo /etc/init.d/tomcat6 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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LDAP account management
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~~~~~~~~~~~~~~~~~~~~~~~~
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If you intend to use Metacat's built-in LDAP account management feature,
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you will need public and private keys for the reCaptcha widget.
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1. Get private and public recaptcha keys from Google using your Google account:
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https://www.google.com/recaptcha/admin/create
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2. Configure Metacat to use those keys in the metacat.properties file:
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::
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ldap.recaptcha.publickey=<your public key>
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ldap.recaptcha.privatekey=<your private key>
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3. Restart Tomcat
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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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| | ``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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| | ``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 scope. |
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| | ``scope`` - the scope to be queried |
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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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| getlog | Get the latest docid with revision number used by user. |
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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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| | ``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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|
|
| | ``returndoctype`` - the doctype to use for your Package View. For more information about packages, see http://knb.ecoinformatics.org/software/metacat/packages.html |
|
| 321 |
|
|
| | ``qformat`` - the format of the returned result set. Possible values are html or xml or the name of your servlet's Metacat skin. |
|
| 322 |
|
|
| | ``querytitle`` - OPTIONAL - the title of the query |
|
| 323 |
|
|
| | ``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 |
|
| 324 |
|
|
| | ``returnfield`` - a custom field to be returned by any hit document. |
|
| 325 |
|
|
| | ``operator`` - the Boolean operator to apply to the query. Possible values are: union or intersect |
|
| 326 |
|
|
| | ``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. |
|
| 327 |
|
|
| | ``anyfield`` - a free-text search variable. The value placed in this parameter will be searched for in any document in any node. |
|
| 328 |
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|
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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. |
|
| 329 |
|
|
| | ``pagestart`` - the displayed search results page (e.g, 1). Used with pagesize. See section 4.3.4 for an example. |
|
| 330 |
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|
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 331 |
|
|
| read | Get a document from the database and return it in the specified format. See Searching Metacat for an example. |
|
| 332 |
|
|
| | |
|
| 333 |
|
|
| | ``docid`` - the docid of the document to return |
|
| 334 |
|
|
| | ``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. |
|
| 335 |
|
|
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 336 |
|
|
| readinlinedata | Read inline data only. |
|
| 337 |
|
|
| | |
|
| 338 |
|
|
| | ``inlinedataid`` - the id of the inline data to read |
|
| 339 |
|
|
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 340 |
|
|
| setaccess | Change access permissions for a user on a specified document. |
|
| 341 |
|
|
| | |
|
| 342 |
|
|
| | ``docid`` - the docid of the document to be modified. |
|
| 343 |
|
|
| | ``principal`` - the user or group whose permissions will be modified |
|
| 344 |
|
|
| | ``permission`` - the permission to set (read, write, all) |
|
| 345 |
|
|
| | ``permType`` - the type of permission to set (allow, deny) |
|
| 346 |
|
|
| | ``permOrder`` - the order in which to apply the permission (allowFirst, denyFirst) |
|
| 347 |
|
|
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 348 |
|
|
| spatial_query | Perform a spatial query. These queries may include any of the queries supported by the |
|
| 349 |
|
|
| | WFS / WMS standards. For more information, see Spatial Queries. |
|
| 350 |
|
|
| | |
|
| 351 |
|
|
| | ``xmax`` - max x spatial coordinate |
|
| 352 |
|
|
| | ``ymax`` - max y spatial coordinate |
|
| 353 |
|
|
| | ``xmin`` - min x spatial coordinate |
|
| 354 |
|
|
| | ``ymin`` - min y spatial coordinate |
|
| 355 |
|
|
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 356 |
|
|
| squery | Perform a structured query. For an example, please see Searching Metacat. |
|
| 357 |
|
|
| | |
|
| 358 |
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|
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|
| | ``query`` - the text of the pathquery document sent to the server |
|
| 359 |
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|
| | ``qformat`` - the format to return the results in. Possible values are: ``xml``, or the name of the a skin. |
|
| 360 |
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|
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 361 |
|
|
| update | Overwrite an XML document with a new one and give the new one the same docid but with |
|
| 362 |
|
|
| | the next revision number. For an example, please see Inserting, Updating, and |
|
| 363 |
|
|
| | Deleting XML and Data Documents. |
|
| 364 |
|
|
| | |
|
| 365 |
|
|
| | ``docid`` - the docid of the document to update |
|
| 366 |
|
|
| | ``doctext`` - the text with which to update the XML document |
|
| 367 |
|
|
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 368 |
|
|
| upload | Upload (insert or update) a data file into Metacat. Data files are stored on Metacat and may be in any |
|
| 369 |
|
|
| | format (binary or text), but they are all treated as if they were binary. |
|
| 370 |
|
|
| | |
|
| 371 |
|
|
| | ``docid`` - the docid of the data file to upload |
|
| 372 |
|
|
| | ``datafile`` - the data file to upload |
|
| 373 |
|
|
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 374 |
|
|
| validate | Validate a specified document against its DTD. |
|
| 375 |
|
|
| | |
|
| 376 |
|
|
| | ``docid`` - the docid of the document to validate |
|
| 377 |
|
|
| | ``valtext`` - the DTD by which to validate this document |
|
| 378 |
|
|
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 379 |
|
|
|
| 380 |
|
|
|
| 381 |
|
|
Metacat Replication Parameters
|
| 382 |
|
|
|
| 383 |
|
|
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 384 |
|
|
| Action | Description and Parameters |
|
| 385 |
|
|
+================+=================================================================================================================================================================+
|
| 386 |
|
|
| forcereplicate | Force the local server to get the specified document from the remote host. |
|
| 387 |
|
|
| | |
|
| 388 |
|
|
| | ``server`` - The server to which this document is being sent |
|
| 389 |
|
|
| | ``docid`` - The docid of the document to send |
|
| 390 |
|
|
| | ``dbaction`` - The action to perform on the document: insert or update (the default) |
|
| 391 |
|
|
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 392 |
|
|
| getall | Force the local server to check all known servers for updated documents. No parameters. |
|
| 393 |
|
|
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 394 |
|
|
| getcatalog | Send the contents of the xml_catalog table encoded in XML. No parameters. |
|
| 395 |
|
|
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 396 |
|
|
| getlock | Request a lock on the specified document. |
|
| 397 |
|
|
| | |
|
| 398 |
|
|
| | ``docid`` - the docid of the document |
|
| 399 |
|
|
| | ``updaterev`` - the revision number of docid |
|
| 400 |
|
|
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 401 |
|
|
| gettime | Return the local time on this server. No parameters. |
|
| 402 |
|
|
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 403 |
|
|
| servercontrol | Perform the specified replication control on the Replication daemon. |
|
| 404 |
|
|
| | |
|
| 405 |
|
|
| | ``add`` - add a new server to the replication list |
|
| 406 |
|
|
| | ``delete`` - remove a server from the replication list |
|
| 407 |
|
|
| | ``list`` - list all of the servers currently in the server list |
|
| 408 |
|
|
| | ``replicate`` - a Boolean flag (1 or 0) which determines if this server should copy files from the newly added server. |
|
| 409 |
|
|
| | ``server`` - the server to add/delete |
|
| 410 |
|
|
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 411 |
|
|
| read | Sends docid to the remote host. |
|
| 412 |
|
|
| | |
|
| 413 |
|
|
| | ``docid`` - the docid of the document to read |
|
| 414 |
|
|
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 415 |
|
|
| start | Start the Replication daemon with a time interval of deltaT. |
|
| 416 |
|
|
| | |
|
| 417 |
|
|
| | ``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 |
|
| 418 |
|
|
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 419 |
|
|
| stop | Stop the Replication daemon. No parameters. |
|
| 420 |
|
|
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 421 |
|
|
| update | Send a list of all documents on the local server along with their revision numbers. No parameters. |
|
| 422 |
|
|
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
| 423 |
|
|
|
| 424 |
|
|
Logging In
|
| 425 |
|
|
~~~~~~~~~~
|
| 426 |
|
|
To log in to Metacat, use the ``login`` action.
|
| 427 |
|
|
|
| 428 |
|
|
The following is an example of a Web form (see figure) that logs a user into
|
| 429 |
|
|
Metact. Example HTML code is included below the screenshot.
|
| 430 |
|
|
|
| 431 |
|
|
.. figure:: images/screenshots/image039.jpg
|
| 432 |
|
|
:align: center
|
| 433 |
|
|
|
| 434 |
|
|
Logging into Metacat using an HTML form.
|
| 435 |
|
|
|
| 436 |
|
|
::
|
| 437 |
|
|
|
| 438 |
|
|
<html>
|
| 439 |
|
|
<body>
|
| 440 |
|
|
<form name="loginform" method="post"action="http://yourserver.com/yourcontext/servlet/metacat"
|
| 441 |
|
|
target="_top" onsubmit="return submitform(this);" id="loginform">
|
| 442 |
|
|
<input type="hidden" name="action" value="login"> <input type=
|
| 443 |
|
|
"hidden" name="username" value=""> <input type="hidden" name=
|
| 444 |
|
|
"qformat" value="xml"> <input type="hidden" name=
|
| 445 |
|
|
"enableediting" value="false">
|
| 446 |
|
|
|
| 447 |
|
|
<table>
|
| 448 |
|
|
<tr valign="middle">
|
| 449 |
|
|
<td align="left" valign="middle" class="text_plain">
|
| 450 |
|
|
username:</td>
|
| 451 |
|
|
|
| 452 |
|
|
<td width="173" align="left" class="text_plain" style=
|
| 453 |
|
|
"padding-top: 2px; padding-bottom: 2px;"><input name="uid"
|
| 454 |
|
|
type="text" style="width: 140px;" value=""></td>
|
| 455 |
|
|
</tr>
|
| 456 |
|
|
|
| 457 |
|
|
<tr valign="middle">
|
| 458 |
|
|
<td height="28" align="left" valign="middle" class=
|
| 459 |
|
|
"text_plain">organization:</td>
|
| 460 |
|
|
|
| 461 |
|
|
<td align="left" class="text_plain" style=
|
| 462 |
|
|
"padding-top: 2px; padding-bottom: 2px;"><select name=
|
| 463 |
|
|
"organization" style="width:140px;">
|
| 464 |
|
|
<option value="" selected>— choose one —</option>
|
| 465 |
|
|
<option value="NCEAS">NCEAS</option>
|
| 466 |
|
|
<option value="LTER">LTER</option>
|
| 467 |
|
|
<option value="UCNRS">UCNRS</option>
|
| 468 |
|
|
<option value="PISCO">PISCO</option>
|
| 469 |
|
|
<option value="OBFS">OBFS</option>
|
| 470 |
|
|
<option value="OSUBS">OSUBS</option>
|
| 471 |
|
|
<option value="SAEON">SAEON</option>
|
| 472 |
|
|
<option value="SANParks">SANParks</option>
|
| 473 |
|
|
<option value="SDSC">SDSC</option>
|
| 474 |
|
|
<option value="KU">KU</option>
|
| 475 |
|
|
<option value="unaffiliated">unaffiliated</option>
|
| 476 |
|
|
</select></td>
|
| 477 |
|
|
</tr>
|
| 478 |
|
|
|
| 479 |
|
|
<tr valign="middle">
|
| 480 |
|
|
<td width="85" align="left" valign="middle" class=
|
| 481 |
|
|
"text_plain">password:</td>
|
| 482 |
|
|
|
| 483 |
|
|
<td colspan="2" align="left" class="text_plain" style=
|
| 484 |
|
|
"padding-top: 2px; padding-bottom: 2px;">
|
| 485 |
|
|
<table width="100%" border="0" cellpadding="0"
|
| 486 |
|
|
cellspacing="0">
|
| 487 |
|
|
<tr>
|
| 488 |
|
|
<td width="150" align="left"><input name="password"
|
| 489 |
|
|
type="password" maxlength="50" style="width:140px;"
|
| 490 |
|
|
value=""></td>
|
| 491 |
|
|
|
| 492 |
|
|
<td align="center" class="buttonBG_login">
|
| 493 |
|
|
<input type="submit" name="loginAction" value="Login"
|
| 494 |
|
|
class="button_login"></td>
|
| 495 |
|
|
|
| 496 |
|
|
<td align="left"> </td>
|
| 497 |
|
|
</tr>
|
| 498 |
|
|
</table>
|
| 499 |
|
|
</td>
|
| 500 |
|
|
</tr>
|
| 501 |
|
|
</table>
|
| 502 |
|
|
</form>
|
| 503 |
|
|
</body>
|
| 504 |
|
|
</html>
|
| 505 |
|
|
|
| 506 |
|
|
Inserting, Updating, and Deleting XML and Data Documents
|
| 507 |
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
| 508 |
|
|
Adding, editing, and deleting XML documents in Metacat can be accomplished
|
| 509 |
|
|
using the insert, update, and delete actions, respectively. Before you can
|
| 510 |
|
|
insert, delete, or update documents, you must log in to Metacat using the
|
| 511 |
|
|
login action. See Logging in for an example.
|
| 512 |
|
|
|
| 513 |
|
|
``insert``
|
| 514 |
|
|
Insert a new XML or data document into Metacat. You must specify a document ID.
|
| 515 |
|
|
|
| 516 |
|
|
``update``
|
| 517 |
|
|
Update an existing Metacat document. The original document is archived,
|
| 518 |
|
|
then overwritten.
|
| 519 |
|
|
|
| 520 |
|
|
``delete``
|
| 521 |
|
|
Archive a document and move the pointer in xml_documents to xml_revisions,
|
| 522 |
|
|
effectively "deleting" the document from public view, but preserving the
|
| 523 |
7256
|
leinfelder
|
revision for the revision history. No further updates will be allowed for
|
| 524 |
|
|
the Metacat document that was "deleted". All revisions of this identifier are no longer
|
| 525 |
|
|
public.
|
| 526 |
6843
|
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|
|
| 527 |
7256
|
leinfelder
|
.. warning::
|
| 528 |
|
|
It is not possible to "delete" one revision without "deleting" all
|
| 529 |
|
|
revisions of a given identifier.
|
| 530 |
|
|
|
| 531 |
6843
|
jones
|
The following is an example of a Web form (see figure) that can perform all
|
| 532 |
|
|
three tasks. Example HTML code is included in the sidebar.
|
| 533 |
|
|
|
| 534 |
|
|
.. figure:: images/screenshots/image041.jpg
|
| 535 |
|
|
:align: center
|
| 536 |
|
|
|
| 537 |
|
|
An example of a Web form used to insert, delete, or update XML documents in Metacat.
|
| 538 |
|
|
|
| 539 |
|
|
::
|
| 540 |
|
|
|
| 541 |
|
|
<html>
|
| 542 |
|
|
<head>
|
| 543 |
|
|
<title>MetaCat</title>
|
| 544 |
|
|
</head>
|
| 545 |
|
|
<body class="emlbody">
|
| 546 |
|
|
<b>MetaCat XML Loader</b>
|
| 547 |
|
|
<p>
|
| 548 |
|
|
Upload, Change, or Delete an XML document using this form.
|
| 549 |
|
|
</p>
|
| 550 |
|
|
<form action="http://yourserver.com/yourcontext/servlet/metacat" method="POST">
|
| 551 |
|
|
<strong>1. Choose an action: </strong>
|
| 552 |
|
|
<input type="radio" name="action" value="insert" checked> Insert
|
| 553 |
|
|
<input type="radio" name="action" value="update"> Update
|
| 554 |
|
|
<input type="radio" name="action" value="delete"> Delete
|
| 555 |
|
|
<input type="submit" value="Process Action">
|
| 556 |
|
|
<br />
|
| 557 |
|
|
<strong>2. Provide a Document ID </strong>
|
| 558 |
|
|
<input type="text" name="docid"> (optional for Insert)
|
| 559 |
|
|
<input type="checkbox" name="public" value="yes" checked><strong>Public Document</strong>
|
| 560 |
|
|
<br />
|
| 561 |
|
|
<strong>3. Provide XML text </strong> (not needed for Delete)<br/>
|
| 562 |
|
|
<textarea name="doctext" cols="65" rows="15"></textarea><br/>
|
| 563 |
|
|
<strong>4. Provide DTD text for upload </strong> (optional; not needed for Delete)
|
| 564 |
|
|
<textarea name="dtdtext" cols="65" rows="15"></textarea>
|
| 565 |
|
|
</form>
|
| 566 |
|
|
</body>
|
| 567 |
|
|
</html>
|
| 568 |
|
|
|
| 569 |
|
|
Searching Metacat
|
| 570 |
|
|
~~~~~~~~~~~~~~~~~
|
| 571 |
|
|
To search Metacat use the ``query`` or ``squery`` actions.
|
| 572 |
|
|
|
| 573 |
|
|
``query``:
|
| 574 |
|
|
Perform a free text query. Specify the returndoctype, qformat, returnfield,
|
| 575 |
|
|
operator, searchmode, anyfield, and (optionally) a querytitle and doctype.
|
| 576 |
|
|
|
| 577 |
|
|
``squery``:
|
| 578 |
|
|
Perform a structured query by submitting an XML pathquery document to the
|
| 579 |
|
|
Metacat server.
|
| 580 |
|
|
|
| 581 |
|
|
|
| 582 |
7256
|
leinfelder
|
When Metacat receives a query via HTTP (screenshot below), the server creates a
|
| 583 |
6843
|
jones
|
"pathquery" document, which is an XML document populated with the specified
|
| 584 |
7256
|
leinfelder
|
search criteria. The pathquery document is then translated into
|
| 585 |
|
|
SQL statements that are executed against the database. Results are translated
|
| 586 |
6843
|
jones
|
into an XML "resultset" document, which can be returned as XML or transformed
|
| 587 |
|
|
into HTML and returned (specify which you would prefer with the returnfield
|
| 588 |
|
|
parameter). You can also opt to submit a pathquery document directly,
|
| 589 |
|
|
using an squery action.
|
| 590 |
|
|
|
| 591 |
|
|
.. figure:: images/screenshots/image043.jpg
|
| 592 |
|
|
:align: center
|
| 593 |
|
|
|
| 594 |
7256
|
leinfelder
|
Example of a basic search form using a query action. The HTML code used to create the form is displayed below.
|
| 595 |
6843
|
jones
|
|
| 596 |
|
|
::
|
| 597 |
|
|
|
| 598 |
|
|
<html>
|
| 599 |
|
|
<head>
|
| 600 |
|
|
<title>Search</title>
|
| 601 |
|
|
</head>
|
| 602 |
|
|
<body>
|
| 603 |
8265
|
leinfelder
|
<form method="POST" action="http://panucci.nceas.ucsb.edu/metacat/metacat">
|
| 604 |
6843
|
jones
|
|
| 605 |
|
|
Search for:
|
| 606 |
|
|
|
| 607 |
|
|
<input name="action" value="query" type="hidden">
|
| 608 |
|
|
<input name="operator" value="INTERSECT" type="hidden">
|
| 609 |
|
|
<input name="anyfield" type="text" value=" " size="40">
|
| 610 |
|
|
<input name="qformat" value="html" type="hidden">
|
| 611 |
|
|
|
| 612 |
|
|
<input name="returnfield" value="creator/individualName/surName" type="hidden">
|
| 613 |
|
|
<input name="returnfield" value="creator/individualName/givenName" type="hidden">
|
| 614 |
|
|
<input name="returnfield" value="creator/organizationName" type="hidden">
|
| 615 |
|
|
<input name="returnfield" value="dataset/title" type="hidden">
|
| 616 |
|
|
<input name="returnfield" value="keyword" type="hidden">
|
| 617 |
|
|
|
| 618 |
|
|
<input name="returndoctype" value="eml://ecoinformatics.org/eml-2.0.1" type="hidden">
|
| 619 |
|
|
|
| 620 |
|
|
<input value="Start Search" type="submit">
|
| 621 |
|
|
|
| 622 |
|
|
</form>
|
| 623 |
|
|
</body>
|
| 624 |
|
|
</html>
|
| 625 |
|
|
|
| 626 |
|
|
Metacat's pathquery document can query specific fields of any XML document.
|
| 627 |
|
|
The pathquery can also be used to specify which fields from each hit are
|
| 628 |
|
|
returned and displayed in the search result set.
|
| 629 |
|
|
|
| 630 |
|
|
::
|
| 631 |
|
|
|
| 632 |
|
|
<pathquery version="1.0">
|
| 633 |
|
|
<meta_file_id>unspecified</meta_file_id>
|
| 634 |
|
|
<querytitle>unspecified</querytitle>
|
| 635 |
|
|
<returnfield>dataset/title</returnfield>
|
| 636 |
|
|
<returnfield>keyword</returnfield>
|
| 637 |
7256
|
leinfelder
|
<returnfield>dataset/creator/individualName/surName</returnfield>
|
| 638 |
|
|
<returndoctype>eml://ecoinformatics.org/eml-2.1.0</returndoctype>
|
| 639 |
6843
|
jones
|
<returndoctype>eml://ecoinformatics.org/eml-2.0.1</returndoctype>
|
| 640 |
|
|
<returndoctype>eml://ecoinformatics.org/eml-2.0.0</returndoctype>
|
| 641 |
|
|
<querygroup operator="UNION">
|
| 642 |
7256
|
leinfelder
|
<queryterm casesensitive="true" searchmode="contains">
|
| 643 |
|
|
<value>Charismatic megafauna</value>
|
| 644 |
|
|
<pathexpr>dataset/title</pathexpr>
|
| 645 |
|
|
</queryterm>
|
| 646 |
|
|
<queryterm casesensitive="false" searchmode="starts-with">
|
| 647 |
|
|
<value>sea otter</value>
|
| 648 |
|
|
<pathexpr>keyword</pathexpr>
|
| 649 |
6843
|
jones
|
</queryterm>
|
| 650 |
|
|
<queryterm casesensitive="false" searchmode="contains">
|
| 651 |
7256
|
leinfelder
|
<value>Enhydra</value>
|
| 652 |
|
|
<pathexpr>abstract/para</pathexpr>
|
| 653 |
6843
|
jones
|
</queryterm>
|
| 654 |
7256
|
leinfelder
|
</querygroup>
|
| 655 |
|
|
</pathquery>
|
| 656 |
6843
|
jones
|
</pathquery>
|
| 657 |
|
|
|
| 658 |
7256
|
leinfelder
|
Each ``<returnfield>`` parameter specifies a field that the database will
|
| 659 |
6843
|
jones
|
return (in addition to the fields Metacat returns by default) for each search
|
| 660 |
|
|
result.
|
| 661 |
|
|
|
| 662 |
|
|
The ``<returndoctype>`` field limits the type of returned documents
|
| 663 |
|
|
(eg, eml://ecoinformatics.org/eml-2.0.1 and/or eml://ecoinformatics.org/eml-2.0.0).
|
| 664 |
|
|
If no returndoctype element is specified, all document types are returned.
|
| 665 |
|
|
|
| 666 |
|
|
A ``<querygroup>`` creates an AND or an OR statement that applies to the
|
| 667 |
|
|
nested ``<queryterm>`` tags. The querygroup operator can be UNION or INTERSECT.
|
| 668 |
|
|
A ``<queryterm>`` defines the actual field (contained in ``<pathexpr>`` tags)
|
| 669 |
|
|
against which the query (contained in the ``<value>`` tags) is being performed.
|
| 670 |
|
|
|
| 671 |
|
|
The ``<pathexpr>`` can also contain a document type keyword contained in
|
| 672 |
|
|
``<returndoc>`` tags. The specified document type applies only to documents
|
| 673 |
|
|
that are packaged together (e.g., a data set and its corresponding metadata file).
|
| 674 |
|
|
If Metacat identifies the search term in a packaged document, the servlet will
|
| 675 |
|
|
check to see if that document's type matches the specified one. If not,
|
| 676 |
|
|
Metacat will check if one of the other documents in the package matches. If so,
|
| 677 |
|
|
Metacat will return the matching document. For more information about packages,
|
| 678 |
|
|
please see the developer documentation.
|
| 679 |
|
|
|
| 680 |
|
|
After Metacat has processed a Pathquery document, it returns a resultset document.
|
| 681 |
|
|
|
| 682 |
|
|
::
|
| 683 |
|
|
|
| 684 |
|
|
<resultset>
|
| 685 |
|
|
<query>
|
| 686 |
|
|
<pathquery version="1.0">
|
| 687 |
7256
|
leinfelder
|
<meta_file_id>unspecified</meta_file_id>
|
| 688 |
|
|
<querytitle>unspecified</querytitle>
|
| 689 |
|
|
<returnfield>dataset/title</returnfield>
|
| 690 |
|
|
<returnfield>keyword</returnfield>
|
| 691 |
|
|
<returnfield>dataset/creator/individualName/surName</returnfield>
|
| 692 |
|
|
<returndoctype>eml://ecoinformatics.org/eml-2.1.0</returndoctype>
|
| 693 |
|
|
<returndoctype>eml://ecoinformatics.org/eml-2.0.1</returndoctype>
|
| 694 |
|
|
<returndoctype>eml://ecoinformatics.org/eml-2.0.0</returndoctype>
|
| 695 |
|
|
<querygroup operator="UNION">
|
| 696 |
|
|
<queryterm casesensitive="true" searchmode="contains">
|
| 697 |
|
|
<value>Charismatic megafauna</value>
|
| 698 |
|
|
<pathexpr>dataset/title</pathexpr>
|
| 699 |
|
|
</queryterm>
|
| 700 |
|
|
<queryterm casesensitive="false" searchmode="starts-with">
|
| 701 |
|
|
<value>sea otter</value>
|
| 702 |
|
|
<pathexpr>keyword</pathexpr>
|
| 703 |
|
|
</queryterm>
|
| 704 |
|
|
<queryterm casesensitive="false" searchmode="contains">
|
| 705 |
|
|
<value>Enhydra</value>
|
| 706 |
|
|
<pathexpr>abstract/para</pathexpr>
|
| 707 |
|
|
</queryterm>
|
| 708 |
|
|
</querygroup>
|
| 709 |
|
|
</pathquery>
|
| 710 |
|
|
</query>
|
| 711 |
|
|
|
| 712 |
|
|
<document>
|
| 713 |
|
|
<docid>nrs.569.3</docid>
|
| 714 |
|
|
<docname>eml</docname>
|
| 715 |
|
|
<doctype>eml://ecoinformatics.org/eml-2.0.0</doctype>
|
| 716 |
|
|
<createdate>2012-06-06</createdate>
|
| 717 |
|
|
<updatedate>2012-06-06</updatedate>
|
| 718 |
|
|
<param name="dataset/title">Marine Mammal slides</param>
|
| 719 |
|
|
<param name="creator/individualName/surName">Bancroft</param>
|
| 720 |
|
|
</document>
|
| 721 |
|
|
|
| 722 |
|
|
<document>
|
| 723 |
|
|
<docid>knb-lter-sbc.61.1</docid>
|
| 724 |
|
|
<docname>eml</docname>
|
| 725 |
|
|
<doctype>eml://ecoinformatics.org/eml-2.1.0</doctype>
|
| 726 |
|
|
<createdate>2012-06-06</createdate>
|
| 727 |
|
|
<updatedate>2012-06-06</updatedate>
|
| 728 |
|
|
<param name="dataset/creator/individualName/surName">Nelson</param>
|
| 729 |
|
|
<param name="dataset/creator/individualName/surName">Harrer</param>
|
| 730 |
|
|
<param name="dataset/creator/individualName/surName">Reed</param>
|
| 731 |
|
|
<param name="dataset/title">SBC LTER: Reef: Sightings of Sea Otters (Enhydra lutris) near Santa Barbara and Channel Islands, ongoing since 2007</param>
|
| 732 |
|
|
</document>
|
| 733 |
6843
|
jones
|
.....
|
| 734 |
|
|
</resultset>
|
| 735 |
|
|
|
| 736 |
|
|
When Metacat returns a resultset document, the servlet always includes the
|
| 737 |
|
|
pathquery used to create it. The pathquery XML is contained in the <query> tag,
|
| 738 |
|
|
the first element in the resultset.
|
| 739 |
|
|
|
| 740 |
|
|
Each XML document returned by the query is represented by a ``<document>`` tag. By
|
| 741 |
|
|
default, Metacat will return the docid, docname, doctype, doctitle, createdate
|
| 742 |
|
|
and updatedate for each search result. If the user specified additional return
|
| 743 |
|
|
fields in the pathquery using ``<returnfield>`` tags (e.g., dataset/title to return
|
| 744 |
|
|
the document title), the additional fields are returned in ``<param>`` tags.
|
| 745 |
|
|
|
| 746 |
|
|
Metacat can return the XML resultset to your client as either XML or HTML.
|
| 747 |
|
|
|
| 748 |
|
|
Paged Query Returns
|
| 749 |
|
|
~~~~~~~~~~~~~~~~~~~
|
| 750 |
|
|
Dividing large search result sets over a number of pages speeds load-time and
|
| 751 |
|
|
makes the result sets more readable to users (Figure 4.12). To break your search
|
| 752 |
|
|
results into pages, use the query action's optional pagestart and pagesize
|
| 753 |
|
|
parameters. The pagesize parameter indicates how many results should be
|
| 754 |
|
|
returned for a given page. The pagestart parameter indicates which page you
|
| 755 |
|
|
are currently viewing.
|
| 756 |
|
|
|
| 757 |
|
|
.. figure:: images/screenshots/image045.jpg
|
| 758 |
|
|
:align: center
|
| 759 |
|
|
|
| 760 |
|
|
An example of paged search results.
|
| 761 |
|
|
|
| 762 |
|
|
When a paged query is performed, the query's resultset contains four extra
|
| 763 |
|
|
fields: pagestart, pagesize, nextpage, and previouspage (Figure 4.13). The
|
| 764 |
|
|
nextpage and previouspage fields help Metacat generate navigational links in
|
| 765 |
|
|
the rendered resultset using XSLT to transform the XML to HTML.
|
| 766 |
|
|
|
| 767 |
|
|
::
|
| 768 |
|
|
|
| 769 |
|
|
<!-- An example of an XML resultset that include support for page breaks.
|
| 770 |
|
|
The pagestart parameter will always indicate the page you are currently viewing.
|
| 771 |
|
|
-->
|
| 772 |
|
|
<resultset>
|
| 773 |
|
|
<pagestart>1</pagestart>
|
| 774 |
|
|
<pagesize>10</pagesize>
|
| 775 |
|
|
<nextpage>2</nextpage>
|
| 776 |
|
|
<previouspage>0</previouspage>
|
| 777 |
|
|
<query> ...</query>
|
| 778 |
|
|
<document>...</document>
|
| 779 |
|
|
<document>...</document>
|
| 780 |
|
|
</resultset>
|
| 781 |
|
|
|
| 782 |
|
|
The HTML search results displayed in the figure were rendered using Kepler's XSLT,
|
| 783 |
|
|
which can be found in lib/style/skins/kepler. Kepler's XSLT uses the four extra
|
| 784 |
|
|
resultset fields to render the "Next" and "Previous" links.
|
| 785 |
|
|
|
| 786 |
|
|
::
|
| 787 |
|
|
|
| 788 |
|
|
<a href="metacat?action=query&operator=INTERSECT&enableediting=false&anyfield=actor&qformat=kepler&pagestart=0&pagesize=10">Previous Page</a>
|
| 789 |
|
|
<a href="metacat?action=query&operator=INTERSECT&enableediting=false&anyfield=actor&qformat=kepler&pagestart=2&pagesize=10">Next Page</a>
|
| 790 |
|
|
|
| 791 |
|
|
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.
|
| 792 |
|
|
|
| 793 |
|
|
Reading Data and Metadata
|
| 794 |
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~
|
| 795 |
|
|
To read data or metadata from Metacat, use the ``read`` action. The ``read`` action
|
| 796 |
|
|
takes two parameters: ``docid``, which specifies the document ID of the document
|
| 797 |
|
|
to return, and ``qformat``, which specifies the return format for the document
|
| 798 |
|
|
(``html`` or ``xml`` or the name of a configured style-set, e.g., ``default``). If ``qformat``
|
| 799 |
|
|
is set to ``xml``, Metacat will return the XML document untransformed. If the
|
| 800 |
|
|
return format is set to ``html``, Metacat will transform the XML document into
|
| 801 |
|
|
HTML using the default XSLT style sheet (specified in the Metacat
|
| 802 |
|
|
configuration). If the name of a style-set is specified, Metacat will use the
|
| 803 |
|
|
XSLT styles specified in the set to transform the XML.
|
| 804 |
|
|
|
| 805 |
|
|
.. figure:: images/screenshots/image047.jpg
|
| 806 |
|
|
:align: center
|
| 807 |
|
|
|
| 808 |
|
|
The same document displayed using different qformat parameters (from left
|
| 809 |
|
|
to right: the default style-set, XML, and HTML).
|
| 810 |
|
|
|
| 811 |
|
|
Note that the ``read`` action can be used to read both data files and metadata files.
|
| 812 |
|
|
To read a data file, you could use the following request::
|
| 813 |
|
|
|
| 814 |
|
|
http://yourserver.com/yourcontext/metacat?action=read&docid=nceas.55&qformat=default
|
| 815 |
|
|
|
| 816 |
|
|
Where ``nceas.55`` is the docid of the data file stored in the Metacat and
|
| 817 |
|
|
``default`` is the name of the style (you could also use "html" or "xml" or the
|
| 818 |
|
|
name of a customized skin).
|
| 819 |
|
|
|
| 820 |
|
|
::
|
| 821 |
|
|
|
| 822 |
|
|
<html>
|
| 823 |
|
|
<head>
|
| 824 |
|
|
<title>Read Document</title>
|
| 825 |
|
|
</head>
|
| 826 |
|
|
<body>
|
| 827 |
|
|
<form method="POST" action="http://your.server/your.context/servlet/metacat">
|
| 828 |
|
|
<input name="action" value="read" type="hidden">
|
| 829 |
|
|
<input name="docid" type="text" value="" size="40">
|
| 830 |
|
|
<input name="qformat" value="default" type="hidden">
|
| 831 |
|
|
<input value="Read" type="submit">
|
| 832 |
|
|
</form>
|
| 833 |
|
|
</body>
|
| 834 |
|
|
</html>
|
| 835 |
|
|
|
| 836 |
|
|
Using the EarthGrid API (aka EcoGrid)
|
| 837 |
|
|
-------------------------------------
|
| 838 |
|
|
|
| 839 |
6844
|
jones
|
.. Note::
|
| 840 |
|
|
|
| 841 |
6870
|
jones
|
The EarthGrid/EcoGrid web service API is *deprecated* as of Metacat 2.0.0 and
|
| 842 |
|
|
will be removed from a future version of Metacat. Its functionality is being
|
| 843 |
|
|
replaced by the standardized DataONE REST service interface. The EarthGrid API
|
| 844 |
|
|
will be completely removed by the end of 2013.
|
| 845 |
6844
|
jones
|
|
| 846 |
|
|
The EarthGrid (aka EcoGrid) provides access to disparate data on different
|
| 847 |
|
|
networks (e.g., KNB, GBIF, GEON) and storage systems (e.g., Metacat and SRB),
|
| 848 |
|
|
allowing scientists access to a wide variety of data and analytic resources
|
| 849 |
|
|
(e.g., data, metadata, analytic workflows and processors) networked at different
|
| 850 |
|
|
sites and at different organizations via the internet.
|
| 851 |
|
|
|
| 852 |
|
|
Because Metacat supports the EarthGrid API (see table), it can query the
|
| 853 |
|
|
distributed EarthGrid, retrieve metadata and data results, and write new and
|
| 854 |
|
|
updated metadata and data back to the grid nodes.
|
| 855 |
|
|
|
| 856 |
|
|
For more information about each EarthGrid service and its WSDL file, navigate
|
| 857 |
|
|
to the "services" page on your Metacat server
|
| 858 |
8265
|
leinfelder
|
(e.g., http://knb.ecoinformatics.org/metacat/services).
|
| 859 |
6844
|
jones
|
Note that the AdminService and Version service that appear on this page are
|
| 860 |
|
|
not part of EarthGrid.
|
| 861 |
|
|
|
| 862 |
|
|
EarthGrid/EcoGrid API Summary
|
| 863 |
|
|
|
| 864 |
|
|
+----------------------------+-----------------------------------------------------------------------------------------------------+
|
| 865 |
|
|
| Service | Description |
|
| 866 |
6845
|
jones
|
+============================+=====================================================================================================+
|
| 867 |
6844
|
jones
|
| AuthenticationQueryService | Search for and retrieve protected metadata and data from the EarthGrid as an authenticated user. |
|
| 868 |
|
|
| | |
|
| 869 |
|
|
| | Methods: ``query``, ``get`` |
|
| 870 |
|
|
+----------------------------+-----------------------------------------------------------------------------------------------------+
|
| 871 |
|
|
| AuthenticationService | Log in and out of the EarthGrid |
|
| 872 |
|
|
| | |
|
| 873 |
|
|
| | Methods: ``login``, ``logout`` |
|
| 874 |
|
|
+----------------------------+-----------------------------------------------------------------------------------------------------+
|
| 875 |
|
|
| IdentifierService | List, lookup, validate, and add Life Science Identifiers (LSIDs) to the EarthGrid |
|
| 876 |
|
|
| | |
|
| 877 |
|
|
| | Methods: ``isRegistered``, ``addLSID``, ``getNextRevision``, ``getNextObject``, ``getAllIds`` |
|
| 878 |
|
|
+----------------------------+-----------------------------------------------------------------------------------------------------+
|
| 879 |
|
|
| PutService | Write metadata to the EarthGrid |
|
| 880 |
|
|
| | |
|
| 881 |
|
|
| | Methods: ``put`` |
|
| 882 |
|
|
+----------------------------+-----------------------------------------------------------------------------------------------------+
|
| 883 |
|
|
| QueryService | Search for and retrieve metadata from the EarthGrid |
|
| 884 |
|
|
| | |
|
| 885 |
|
|
| | Methods: ``query``, ``get`` |
|
| 886 |
|
|
+----------------------------+-----------------------------------------------------------------------------------------------------+
|
| 887 |
|
|
| RegistryService | Add, update, remove, and search for registered EarthGrid services. |
|
| 888 |
|
|
| | Note: The WSDL for this service is found under http://ecogrid.ecoinformatics.org/registry/services |
|
| 889 |
|
|
| | |
|
| 890 |
|
|
| | Methods: ``add``, ``update``, ``remove``, ``list``, ``query`` |
|
| 891 |
|
|
+----------------------------+-----------------------------------------------------------------------------------------------------+
|
| 892 |
|
|
|
| 893 |
6843
|
jones
|
Using Morpho
|
| 894 |
6147
|
jones
|
------------
|
| 895 |
6844
|
jones
|
Morpho is a desktop tool created to facilitate the creation, storage, and
|
| 896 |
|
|
retrieval of metadata. Morpho interfaces with any Metacat server, allowing
|
| 897 |
|
|
users to upload, download, store, query and view relevant metadata and data
|
| 898 |
|
|
using the network. Users can authorize the public or only selected colleagues
|
| 899 |
|
|
to view their data files.
|
| 900 |
6147
|
jones
|
|
| 901 |
6844
|
jones
|
Morpho is part of the Knowledge Network for Biocomplexity (KNB), a national
|
| 902 |
|
|
network intended to facilitate ecological and environmental research on
|
| 903 |
|
|
biocomplexity. To use Morpho with your Metacat, set the Metacat URL in the
|
| 904 |
|
|
Morpho Preferences to point to your Metacat server.
|
| 905 |
|
|
|
| 906 |
|
|
.. figure:: images/screenshots/image049.png
|
| 907 |
|
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:align: center
|
| 908 |
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|
| 909 |
|
|
Set the Metacat URL in the Morpho preferences to point to your Metacat.
|
| 910 |
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|
| 911 |
8265
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leinfelder
|
For more information about Morpho, please see: http://knb.ecoinformatics.org/
|
| 912 |
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jones
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| 913 |
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jones
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Creating Your Own Client
|
| 914 |
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|
------------------------
|
| 915 |
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jones
|
|
| 916 |
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.. Note::
|
| 917 |
|
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|
| 918 |
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NOTE: The Client API (and underlying servlet implementation) has been
|
| 919 |
|
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deprecated as of Metacat 2.0.0. Future development should utilize the DataONE
|
| 920 |
|
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REST service methods. The Client API will be completely removed by the end of 2013.
|
| 921 |
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|
| 922 |
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jones
|
Metacat's client API is available in Java and Perl (the Java interface is
|
| 923 |
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described in this section and further detailed in the appendix). Some of the
|
| 924 |
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API is also available in Python and Ruby. The API allows client applications
|
| 925 |
|
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to easily authenticate users and perform basic Metacat operations such as
|
| 926 |
|
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reading metadata and data files; inserting, updating, and deleting files; and
|
| 927 |
|
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searching for packages based on metadata matches.
|
| 928 |
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jones
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|
| 929 |
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jones
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The Client API is defined by the interface edu.ucsb.nceas.metacat.client.Metacat,
|
| 930 |
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and all operations are fully defined in the javadoc_ documentation. To use the
|
| 931 |
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|
jones
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client API, include the ``metacat-client.jar``, ``utilities.jar``, ``commons-io-2.0.jar``, and
|
| 932 |
6844
|
jones
|
``httpclient.jar`` in your classpath. After including these classes, you can
|
| 933 |
|
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begin using the API methods (see the next table).
|
| 934 |
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|
| 935 |
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.. _javadoc: http://knb.ecoinformatics.org/software/metacat/dev/api/index.html
|
| 936 |
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|
| 937 |
|
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The following code block displays a typical session for reading a document
|
| 938 |
|
|
from Metacat using the Java client API.
|
| 939 |
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|
| 940 |
|
|
::
|
| 941 |
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|
| 942 |
|
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String metacatUrl = "http://foo.com/context/metacat";
|
| 943 |
|
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String username = "uid=jones,o=NCEAS,dc=ecoinformatics,dc=org";
|
| 944 |
|
|
String password = "neverHarcodeAPasswordInCode";
|
| 945 |
|
|
try {
|
| 946 |
|
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Metacat m = MetacatFactory.createMetacatConnection(metacatUrl);
|
| 947 |
|
|
m.login(username, password);
|
| 948 |
|
|
Reader r = m.read("testdocument.1.1");
|
| 949 |
|
|
// Do whatever you want with Reader r
|
| 950 |
|
|
} catch (MetacatAuthException mae) {
|
| 951 |
|
|
handleError("Authorization failed:\n" + mae.getMessage());
|
| 952 |
|
|
} catch (MetacatInaccessibleException mie) {
|
| 953 |
|
|
handleError("Metacat Inaccessible:\n" + mie.getMessage());
|
| 954 |
|
|
} catch (Exception e) {
|
| 955 |
|
|
handleError("General exception:\n" + e.getMessage());
|
| 956 |
|
|
}
|
| 957 |
|
|
|
| 958 |
|
|
Operations provided by Client API (Metacat.java class)
|
| 959 |
|
|
|
| 960 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 961 |
|
|
| Method | Parameters and Throws | Description |
|
| 962 |
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|
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+======================+=============================================================================================================================================================================================================+===========================================================================================================================================+
|
| 963 |
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|
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|
| delete | ``public String delete(String docid) throws InsufficientKarmaException, MetacatException, MetacatInaccessibleException;`` | Delete an XML document in the repository. |
|
| 964 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 965 |
|
|
| getAllDocids | ``public Vector getAllDocids(String scope) throws MetacatException;`` | Return a list of all docids that match a given scope. If scope is null, return all docids registered in the system. |
|
| 966 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 967 |
|
|
| getLastDocid | ``public String getLastDocid(String scope) throws MetacatException;`` | Return the highest document ID for a given scope. Used by clients to determine the next free identifier in a sequence for a given scope. |
|
| 968 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 969 |
|
|
| getloggedinuserinfo | ``public String getloggedinuserinfo() throws MetacatInaccessibleException;`` | Return the logged in user for this session. |
|
| 970 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 971 |
|
|
| getNewestDocRevision | ``public int getNewestDocRevision(String docId) throws MetacatException;`` | Return the latest revision of specified the document from Metacat |
|
| 972 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 973 |
|
|
| getSessonId | ``public String getSessionId();`` | Return the session identifier for this session. |
|
| 974 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 975 |
|
|
| insert | ``public String insert(String docid, Reader xmlDocument, Reader schema) throws InsufficientKarmaException, MetacatException, IOException, MetacatInaccessibleException;`` | Insert an XML document into the repository. |
|
| 976 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 977 |
|
|
| isRegistered | ``public boolean isRegistered(String docid) throws MetacatException;`` | Return true if given docid is registered; false if not. |
|
| 978 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 979 |
|
|
| login | ``public String login(String username, String password) throws MetacatAuthException, MetacatInaccessibleException;`` | Log in to a Metacat server. |
|
| 980 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 981 |
|
|
| logout | ``public String logout() throws MetacatInaccessibleException, MetacatException;`` | Log out of a Metacat server. |
|
| 982 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 983 |
|
|
| query | ``public Reader query(Reader xmlQuery) throws MetacatInaccessibleException, IOException;`` | Query the Metacat repository and return the result set as a Reader. |
|
| 984 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 985 |
|
|
| query | ``public Reader query(Reader xmlQuery, String qformat) throws MetacatInaccessibleException, IOException;`` | Query the Metacat repository with the given metacat-compatible query format and return the result set as a Reader. |
|
| 986 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 987 |
|
|
| read | ``public Reader read(String docid) throws InsufficientKarmaException, MetacatInaccessibleException, DocumentNotFoundException, MetacatException;`` | Read an XML document from the Metacat server. |
|
| 988 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 989 |
|
|
| readInlineData | ``public Reader readInlineData(String inlinedataid) throws InsufficientKarmaException, MetacatInaccessibleException, MetacatException;`` | Read inline data from the Metacat server session. |
|
| 990 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 991 |
|
|
| setAccess | ``public String setAccess(String _docid, String _principal, String _permission, String _permType, String _permOrder ); throws InsufficientKarmaException, MetacatException, MetacatInaccessibleException;`` | Set permissions for an XML document in the Metacat repository. |
|
| 992 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 993 |
|
|
| setMetacatUrl | ``public void setMetacatUrl(String metacatUrl);`` | Set the MetacatUrl to which connections should be made. |
|
| 994 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 995 |
|
|
| setSessionId | ``public void setSessionId(String sessionId);`` | Set the session identifier for this session. |
|
| 996 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 997 |
|
|
| update | ``public String update(String docid, Reader xmlDocument, Reader schema) throws InsufficientKarmaException, MetacatException, IOException, MetacatInaccessibleException;`` | Update an XML document in the repository by providing a new version of the XML document. |
|
| 998 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 999 |
|
|
| upload | ``public String upload(String docid, File file) throws InsufficientKarmaException, MetacatException, IOException, MetacatInaccessibleException;`` | Upload a data document into the repository. |
|
| 1000 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|
| 1001 |
|
|
| upload | ``public String publicupload(String docid, String fileName, InputStream fileData, int size) throws InsufficientKarmaException, MetacatException, IOException, MetacatInaccessibleException;`` | Upload a data document into the repository. |
|
| 1002 |
|
|
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
|