Project

General

Profile

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Accessing and Submitting Metadata and Data
2
==========================================
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.. contents::
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The Metacat repository can be accessed and updated using a number of tools, 
7
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
33
------------------
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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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55
Installing the Registry
56
~~~~~~~~~~~~~~~~~~~~~~~
57
In order to install and run the Registry, you must have Metacat installed and 
58
Tomcat must be running behind an Apache Web server (see previous sections for 
59
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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65
  ::
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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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76
    ::
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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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84
    ::
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86
      sudo yum install perl-CPAN
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      sudo cpan
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89
  * You should now see a prompt which looks like:
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91
    ::
92
    
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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 
97
    you receive during this process.
98
    
99
    ::
100
    
101
      install Bundle::CPAN
102
      reload cpan
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104
  * Install the required modules. Here we're installing an old LibXSLT, as the 
105
    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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124
    ::
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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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      libdigest-sha1-perl libnet-ldap-perl libterm-readkey-perl \
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      libxml-dom-perl libsoap-lite-perl -y
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131
  * 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
170
~~~~~~~~~~~~~~~~~~~~~~~~
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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, type: ``sudo /etc/init.d/tomcat6 restart`` or an 
183
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, 
190
   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)
194
-------------------------------------
195
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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204
Supported Actions
205
~~~~~~~~~~~~~~~~~
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Metacat supports get and post requests as well as actions for writing, querying, 
207
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                                                                                                                                                                                                                                         |
216
+==========================+====================================================================================================================================================================================================================================================================+
217
| 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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+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
227
| getaccesscontrol         | Get the access control list (ACL) for the                                                                                                                                                                                                                          |
228
|                          | specified document.                                                                                                                                                                                                                                                |
229
|                          |                                                                                                                                                                                                                                                                    |
230
|                          | ``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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|                          |                                                                                                                                                                                                                                                                    |
234
|                          | ``scope`` - a string used to match a range of docids in a SQL LIKE statement                                                                                                                                                                                       |
235
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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| getdataguide             | Read a data guide for the specified document type                                                                                                                                                                                                                  |
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| DEPRECATED               |                                                                                                                                                                                                                                                                    |
238
| Use getdtdschema instead | ``doctype`` - the doctype for which to get the data guide                                                                                                                                                                                                          |
239
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
240
| getdoctypes              | Get all doctypes currently available in the Metacat Catalog System. No parameters.                                                                                                                                                                                 |
241
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
242
| getdtdschema             | Read the DTD or XMLSchema file for the specified doctype.                                                                                                                                                                                                          |
243
|                          |                                                                                                                                                                                                                                                                    |
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|                          | ``doctype`` - the doctype for which DTD or XMLSchema files to read                                                                                                                                                                                                 |
245
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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| getlastdocid             | Get the latest docid with revision number used by user.                                                                                                                                                                                                            |
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|                          |                                                                                                                                                                                                                                                                    |
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|                          | ``username`` - the user's log-in name                                                                                                                                                                                                                              |
249
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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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.                                                                                                                                                                                                     |
260
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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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                                                                                                                                                                                               |
271
|                          | 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                                                                                                                                                                                                               |
275
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
276
| insertmultipart          | Insert an XML document using multipart encoding into the database.                                                                                                                                                                                                 |
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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                                                                                                                                                                                                               |
280
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
281
| isregistered             | Check if an individual document exists in either the xml_documents or xml_revisions tables.                                                                                                                                                                        |
282
|                          | For more information about Metacat's database schema, please see the developer documentation.                                                                                                                                                                      |
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|                          |                                                                                                                                                                                                                                                                    |
284
|                          | ``docid`` - the docid of the document                                                                                                                                                                                                                              |
285
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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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                                                                                                                                                                                                                                 |
291
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
292
| logout                   | Log the current user out and destroy the associated session. No parameters.                                                                                                                                                                                        |
293
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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| query                    | Perform a free text query. For an example, please see Searching Metacat.                                                                                                                                                                                           |
295
|                          |                                                                                                                                                                                                                                                                    |
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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                                                                                                |
297
|                          | ``qformat`` - the format of the returned result set. Possible values are html or xml or the name of your servlet's Metacat skin.                                                                                                                                   |
298
|                          | ``querytitle`` - OPTIONAL - the title of the query                                                                                                                                                                                                                 |
299
|                          | ``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 |
300
|                          | ``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.                                                                                                                                                  |
306
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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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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|                          |                                                                                                                                                                                                                                                                    |
309
|                          | ``docid`` - the docid of the document to return                                                                                                                                                                                                                    |
310
|                          | ``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.                                                                                                                  |
311
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
312
| readinlinedata           | Read inline data only.                                                                                                                                                                                                                                             |
313
|                          |                                                                                                                                                                                                                                                                    |
314
|                          | ``inlinedataid`` - the id of the inline data to read                                                                                                                                                                                                               |
315
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
316
| setaccess                | Change access permissions for a user on a specified document.                                                                                                                                                                                                      |
317
|                          |                                                                                                                                                                                                                                                                    |
318
|                          | ``docid`` - the docid of the document to be modified.                                                                                                                                                                                                              |
319
|                          | ``principal`` - the user or group whose permissions will be modified                                                                                                                                                                                               |
320
|                          | ``permission`` - the permission  to set (read, write, all)                                                                                                                                                                                                         |
321
|                          | ``permType`` - the type of permission to set (allow, deny)                                                                                                                                                                                                         |
322
|                          | ``permOrder`` - the order in which to apply the permission (allowFirst, denyFirst)                                                                                                                                                                                 |
323
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
324
| spatial_query            | Perform a spatial query. These queries may include any of the queries supported by the                                                                                                                                                                             |
325
|                          | WFS / WMS standards. For more information, see Spatial Queries.                                                                                                                                                                                                    |
326
|                          |                                                                                                                                                                                                                                                                    |
327
|                          | ``xmax`` - max x spatial coordinate                                                                                                                                                                                                                                |
328
|                          | ``ymax`` - max y spatial coordinate                                                                                                                                                                                                                                |
329
|                          | ``xmin`` - min x spatial coordinate                                                                                                                                                                                                                                |
330
|                          | ``ymin`` - min y spatial coordinate                                                                                                                                                                                                                                |
331
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
332
| squery                   | Perform a structured query. For an example, please see Searching Metacat.                                                                                                                                                                                          |
333
|                          |                                                                                                                                                                                                                                                                    |
334
|                          | ``query`` - the text of the pathquery document sent to the server                                                                                                                                                                                                  |
335
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
336
| update                   | Overwrite an XML document with a new one and give the new one the same docid but with                                                                                                                                                                              |
337
|                          | the next revision number. For an example, please see Inserting, Updating, and                                                                                                                                                                                      |
338
|                          | Deleting XML and Data Documents.                                                                                                                                                                                                                                   |
339
|                          |                                                                                                                                                                                                                                                                    |
340
|                          | ``docid`` - the docid of the document to update                                                                                                                                                                                                                    |
341
|                          | ``doctext`` - the text with which to update the XML document                                                                                                                                                                                                       |
342
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
343
| upload                   | Upload (insert or update) a data file into Metacat. Data files are stored on Metacat and may be in any                                                                                                                                                             |
344
|                          | format (binary or text), but they are all treated as if they were binary.                                                                                                                                                                                          |
345
|                          |                                                                                                                                                                                                                                                                    |
346
|                          | ``docid`` - the docid of the data file to upload                                                                                                                                                                                                                   |
347
|                          | ``datafile`` - the data file to upload                                                                                                                                                                                                                             |
348
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
349
| validate                 | Validate a specified document against its DTD.                                                                                                                                                                                                                     |
350
|                          |                                                                                                                                                                                                                                                                    |
351
|                          | ``docid`` - the docid of the document to validate                                                                                                                                                                                                                  |
352
|                          | ``valtext`` - the DTD by which to validate this document                                                                                                                                                                                                           |
353
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
354

    
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356
Metacat Replication Parameters
357

    
358
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
359
| Action         | Description and Parameters                                                                                                                                      |
360
+================+=================================================================================================================================================================+
361
| forcereplicate | Force the local server to get the specified document from the remote host.                                                                                      |
362
|                |                                                                                                                                                                 |
363
|                | ``server`` - The server to which this document is being sent                                                                                                    |
364
|                | ``docid`` - The docid of the document to send                                                                                                                   |
365
|                | ``dbaction`` - The action to perform on the document: insert or update (the default)                                                                            |
366
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
367
| getall         | Force the local server to check all known servers for updated documents. No parameters.                                                                         |
368
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
369
| getcatalog     | Send the contents of the xml_catalog table encoded in XML. No parameters.                                                                                       |
370
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
371
| getlock        | Request a lock on the specified document.                                                                                                                       |
372
|                |                                                                                                                                                                 |
373
|                | ``docid`` - the docid of the document                                                                                                                           |
374
|                | ``updaterev`` - the revision number of docid                                                                                                                    |
375
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
376
| gettime        | Return the local time on this server. No parameters.                                                                                                            |
377
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
378
| servercontrol  | Perform the specified replication control on the Replication daemon.                                                                                            |
379
|                |                                                                                                                                                                 |
380
|                | ``add`` - add a new server to the replication list                                                                                                              |
381
|                | ``delete`` - remove a server from the replication list                                                                                                          |
382
|                | ``list`` - list all of the servers currently in the server list                                                                                                 |
383
|                | ``replicate`` - a Boolean flag (1 or 0) which determines if this server should copy files from the newly added server.                                          |
384
|                | ``server`` - the server to add/delete                                                                                                                           |
385
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
386
| read           | Sends docid to the remote host.                                                                                                                                 |
387
|                |                                                                                                                                                                 |
388
|                | ``docid`` - the docid of the document to read                                                                                                                   |
389
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
390
| start          | Start the Replication daemon with a time interval of deltaT.                                                                                                    |
391
|                |                                                                                                                                                                 |
392
|                | ``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 |
393
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
394
| stop           | Stop the Replication daemon. No parameters.                                                                                                                     |
395
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
396
| update         | Send a list of all documents on the local server along with their revision numbers. No parameters.                                                              |
397
+----------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
398

    
399
Logging In
400
~~~~~~~~~~
401
To log in to Metacat, use the ``login`` action.
402

    
403
The following is an example of a Web form (see figure) that logs a user into 
404
Metact. Example HTML code is included below the screenshot.
405

    
406
.. figure:: images/screenshots/image039.jpg
407
   :align: center
408
   
409
   Logging into Metacat using an HTML form.
410

    
411
::
412

    
413
  <html>
414
  <body>
415
  <form name="loginform" method="post"action="http://yourserver.com/yourcontext/servlet/metacat" 
416
  target="_top" onsubmit="return submitform(this);" id="loginform">
417
    <input type="hidden" name="action" value="login"> <input type=
418
    "hidden" name="username" value=""> <input type="hidden" name=
419
    "qformat" value="xml"> <input type="hidden" name=
420
    "enableediting" value="false">
421

    
422
    <table>
423
      <tr valign="middle">
424
        <td align="left" valign="middle" class="text_plain">
425
        username:</td>
426

    
427
        <td width="173" align="left" class="text_plain" style=
428
        "padding-top: 2px; padding-bottom: 2px;"><input name="uid"
429
        type="text" style="width: 140px;" value=""></td>
430
      </tr>
431

    
432
      <tr valign="middle">
433
        <td height="28" align="left" valign="middle" class=
434
        "text_plain">organization:</td>
435

    
436
        <td align="left" class="text_plain" style=
437
        "padding-top: 2px; padding-bottom: 2px;"><select name=
438
        "organization" style="width:140px;">
439
          <option value=""    selected>&#8212; choose one &#8212;</option>
440
          <option value="NCEAS">NCEAS</option>
441
          <option value="LTER">LTER</option>
442
          <option value="UCNRS">UCNRS</option>
443
          <option value="PISCO">PISCO</option>
444
          <option value="OBFS">OBFS</option>
445
          <option value="OSUBS">OSUBS</option>
446
          <option value="SAEON">SAEON</option>
447
          <option value="SANParks">SANParks</option>
448
          <option value="SDSC">SDSC</option>
449
          <option value="KU">KU</option>
450
          <option value="unaffiliated">unaffiliated</option>
451
        </select></td>
452
      </tr>
453

    
454
      <tr valign="middle">
455
        <td width="85" align="left" valign="middle" class=
456
        "text_plain">password:</td>
457

    
458
        <td colspan="2" align="left" class="text_plain" style=
459
        "padding-top: 2px; padding-bottom: 2px;">
460
          <table width="100%" border="0" cellpadding="0"
461
          cellspacing="0">
462
            <tr>
463
              <td width="150" align="left"><input name="password"
464
              type="password" maxlength="50" style="width:140px;"
465
              value=""></td>
466

    
467
              <td align="center" class="buttonBG_login">
468
              <input type="submit" name="loginAction" value="Login"
469
              class="button_login"></td>
470

    
471
              <td align="left">&nbsp;</td>
472
            </tr>
473
          </table>
474
        </td>
475
      </tr>
476
    </table>
477
  </form>
478
  </body>
479
  </html>
480

    
481
Inserting, Updating, and Deleting XML and Data Documents
482
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
483
Adding, editing, and deleting XML documents in Metacat can be accomplished 
484
using the insert, update, and delete actions, respectively. Before you can 
485
insert, delete, or update documents, you must log in to Metacat using the 
486
login action. See Logging in for an example.
487

    
488
``insert``
489
   Insert a new XML or data document into Metacat. You must specify a document ID.
490
   
491
``update``
492
   Update an existing Metacat document. The original document is archived, 
493
   then overwritten.
494

    
495
``delete``
496
   Archive a document and move the pointer in xml_documents to xml_revisions, 
497
   effectively "deleting" the document from public view, but preserving the 
498
   revision for the revision history.
499

    
500
The following is an example of a Web form (see figure) that can perform all 
501
three tasks. Example HTML code is included in the sidebar.
502

    
503
.. figure:: images/screenshots/image041.jpg
504
   :align: center
505
   
506
   An example of a Web form used to insert, delete, or update XML documents in Metacat.
507

    
508
::
509

    
510
  <html>
511
    <head>
512
    <title>MetaCat</title>
513
    </head>
514
    <body class="emlbody">
515
    <b>MetaCat XML Loader</b>
516
    <p>
517
    Upload, Change, or Delete an XML document using this form.
518
    </p>
519
    <form action="http://yourserver.com/yourcontext/servlet/metacat" method="POST">
520
      <strong>1. Choose an action: </strong>
521
      <input type="radio" name="action" value="insert" checked> Insert
522
      <input type="radio" name="action" value="update"> Update
523
      <input type="radio" name="action" value="delete"> Delete
524
      <input type="submit" value="Process Action">
525
      <br />
526
      <strong>2. Provide a Document ID </strong>
527
      <input type="text" name="docid"> (optional for Insert)
528
         <input type="checkbox" name="public" value="yes" checked><strong>Public Document</strong>
529
      <br />
530
      <strong>3. Provide XML text </strong> (not needed for Delete)<br/>
531
      <textarea name="doctext" cols="65" rows="15"></textarea><br/>
532
      <strong>4. Provide DTD text for upload </strong> (optional; not needed for Delete)
533
      <textarea name="dtdtext" cols="65" rows="15"></textarea>
534
    </form>
535
    </body>
536
  </html>
537

    
538
Searching Metacat
539
~~~~~~~~~~~~~~~~~
540
To search Metacat use the ``query`` or ``squery`` actions. 
541

    
542
``query``:   
543
   Perform a free text query. Specify the returndoctype, qformat, returnfield, 
544
   operator, searchmode, anyfield, and (optionally) a querytitle and doctype. 
545

    
546
``squery``:
547
   Perform a structured query by submitting an XML pathquery document to the 
548
   Metacat server.
549
 
550

    
551
When Metacat receives a query via HTTP (Figure 4.8), the server creates a 
552
"pathquery" document, which is an XML document populated with the specified 
553
search criteria (Figure 4.10). The pathquery document is then translated into 
554
SQL statements that are executed against the data base. Results are translated 
555
into an XML "resultset" document, which can be returned as XML or transformed 
556
into HTML and returned (specify which you would prefer with the returnfield 
557
parameter). You can also opt to submit a pathquery document directly, 
558
using an squery action.
559

    
560
.. figure:: images/screenshots/image043.jpg
561
   :align: center
562
   
563
   Example of a basic search form using a query action. 
564

    
565
::
566

    
567
  <html>
568
  <head>
569
  <title>Search</title>
570
  </head>
571
  <body>
572
  <form method="POST" action="http://panucci.nceas.ucsb.edu/knb/servlet/metacat">
573

    
574
  Search for:
575

    
576
  <input name="action" value="query" type="hidden">
577
  <input name="operator" value="INTERSECT" type="hidden">
578
  <input name="anyfield" type="text" value=" " size="40">
579
  <input name="qformat" value="html" type="hidden">
580
  
581
  <input name="returnfield" value="creator/individualName/surName" type="hidden">
582
  <input name="returnfield" value="creator/individualName/givenName" type="hidden">
583
  <input name="returnfield" value="creator/organizationName" type="hidden">
584
  <input name="returnfield" value="dataset/title" type="hidden">
585
  <input name="returnfield" value="keyword" type="hidden">
586

    
587
  <input name="returndoctype" value="eml://ecoinformatics.org/eml-2.0.1" type="hidden">
588

    
589
  <input value="Start Search" type="submit">
590

    
591
  </form>
592
  </body>
593
  </html>
594
  
595
Metacat's pathquery document can query specific fields of any XML document. 
596
The pathquery can also be used to specify which fields from each hit are 
597
returned and displayed in the search result set.
598

    
599
::
600

    
601
  <pathquery version="1.0">
602
      <meta_file_id>unspecified</meta_file_id>
603
      <querytitle>unspecified</querytitle>
604
      <returnfield>dataset/title</returnfield>
605
      <returnfield>keyword</returnfield>
606
      <returnfield>originator/individualName/surName</returnfield>
607
      <returndoctype>eml://ecoinformatics.org/eml-2.0.1</returndoctype>
608
      <returndoctype>eml://ecoinformatics.org/eml-2.0.0</returndoctype>
609
      <querygroup operator="UNION">
610
        <queryterm casesensitive="false" searchmode="contains">
611
          <value>Plant</value>
612
          <pathexpr>dataset/title</pathexpr>
613
        </queryterm>
614
        <queryterm casesensitive="false" searchmode="contains">
615
          <value>plant</value>
616
          <pathexpr>keyword</pathexpr>
617
        </queryterm>
618
      </querygroup>
619
  </pathquery>
620
  
621
Each ``<returnfield>`` parameter specifies a field that the data base will 
622
return (in addition to the fields Metacat returns by default) for each search 
623
result. 
624

    
625
The ``<returndoctype>`` field limits the type of returned documents 
626
(eg, eml://ecoinformatics.org/eml-2.0.1 and/or eml://ecoinformatics.org/eml-2.0.0). 
627
If no returndoctype element is specified, all document types are returned. 
628

    
629
A ``<querygroup>`` creates an AND or an OR statement that applies to the 
630
nested ``<queryterm>`` tags. The querygroup operator can be UNION or INTERSECT. 
631
A ``<queryterm>`` defines the actual field (contained in ``<pathexpr>`` tags) 
632
against which the query (contained in the ``<value>`` tags) is being performed. 
633

    
634
The ``<pathexpr>`` can also contain a document type keyword contained in 
635
``<returndoc>`` tags. The specified document type applies only to documents 
636
that are packaged together (e.g., a data set and its corresponding metadata file). 
637
If Metacat identifies the search term in a packaged document, the servlet will 
638
check to see if that document's type matches the specified one. If not, 
639
Metacat will check if one of the other documents in the package matches. If so, 
640
Metacat will return the matching document. For more information about packages, 
641
please see the developer documentation.
642

    
643
After Metacat has processed a Pathquery document, it returns a resultset document.
644

    
645
::
646

    
647
  <resultset>
648
        <query>
649
          <pathquery version="1.0">
650
            <meta_file_id>unspecified</meta_file_id>
651
            <querytitle>unspecified</querytitle>
652
            <returnfield>dataset/title</returnfield>
653
            <returnfield>keyword</returnfield>
654
            <returnfield>originator/individualName/surName</returnfield>
655
            <returndoctype>eml://ecoinformatics.org/eml-2.0.1</returndoctype>
656
            <returndoctype>eml://ecoinformatics.org/eml-2.0.0</returndoctype>
657
            <querygroup operator="UNION">
658
                  <queryterm casesensitive="false" searchmode="contains">
659
                      <value>Datos</value>
660
                      <pathexpr>dataset/title</pathexpr>
661
                  </queryterm>
662
                  <queryterm casesensitive="false" searchmode="contains">
663
                     <value>plant</value>
664
                     <pathexpr>keyword</pathexpr>
665
                  </queryterm>
666
           </querygroup>
667
         </pathquery>
668
        </query>  
669
      
670
        <document>
671
          <docid>nceas.44.1</docid>
672
          <docname>resource</docname>
673
          <doctype>eml://ecoinformatics.org/eml-2.0.1</doctype>
674
          <createdate>2001-01-12 16:12:06.0</createdate>
675
          <updatedate>2001-01-12 16:12:06.0</updatedate>
676
          <param name="dataset/title">Datos Meteorologicos</param>
677
          <param name="keyword">intertidal</param>
678
          <param name="originator/individualName/surName">Smith</param>
679
        </document>  
680
        
681
        <document>
682
          <docid>nceas.42.1</docid>
683
          <docname>resource</docname>
684
          <doctype>eml://ecoinformatics.org/eml-2.0.1</doctype>
685
          <createdate>2001-01-12 16:11:31.0</createdate>
686
          <updatedate>2001-01-12 16:11:31.0</updatedate>
687
          <param name="dataset/title">Ocean Surface Temperature</param>
688
          <param name="keyword">Plant</param>
689
          <param name="originator/individualName/surName">Henry</param>   
690
       </document>
691
      .....  
692
  </resultset>
693

    
694
When Metacat returns a resultset document, the servlet always includes the 
695
pathquery used to create it. The pathquery XML is contained in the <query> tag, 
696
the first element in the resultset.
697

    
698
Each XML document returned by the query is represented by a ``<document>`` tag. By 
699
default, Metacat will return the docid, docname, doctype, doctitle, createdate 
700
and updatedate for each search result. If the user specified additional return 
701
fields in the pathquery using ``<returnfield>`` tags (e.g., dataset/title to return 
702
the document title), the additional fields are returned in ``<param>`` tags. 
703

    
704
Metacat can return the XML resultset to your client as either XML or HTML.
705

    
706
Paged Query Returns
707
~~~~~~~~~~~~~~~~~~~
708
Dividing large search result sets over a number of pages speeds load-time and 
709
makes the result sets more readable to users (Figure 4.12). To break your search 
710
results into pages, use the query action's optional pagestart and pagesize 
711
parameters. The pagesize parameter indicates how many results should be 
712
returned for a given page. The pagestart parameter indicates which page you 
713
are currently viewing.
714

    
715
.. figure:: images/screenshots/image045.jpg
716
   :align: center
717
   
718
   An example of paged search results. 
719

    
720
When a paged query is performed, the query's resultset contains four extra 
721
fields: pagestart, pagesize, nextpage, and previouspage (Figure 4.13).  The 
722
nextpage and previouspage fields help Metacat generate navigational links in 
723
the rendered resultset using XSLT to transform the XML to HTML. 
724

    
725
:: 
726

    
727
  <!-- An example of an XML resultset that include support for page breaks. 
728
       The pagestart parameter will always indicate the page you are currently viewing.
729
  -->
730
  <resultset>
731
      <pagestart>1</pagestart>
732
      <pagesize>10</pagesize>
733
      <nextpage>2</nextpage>
734
      <previouspage>0</previouspage>
735
      <query> ...</query>
736
      <document>...</document>
737
      <document>...</document>
738
    </resultset>
739

    
740
The HTML search results displayed in the figure were rendered using Kepler's XSLT, 
741
which can be found in lib/style/skins/kepler. Kepler's XSLT uses the four extra 
742
resultset fields to render the "Next" and "Previous" links.
743

    
744
::
745
  
746
  <a href="metacat?action=query&operator=INTERSECT&enableediting=false&anyfield=actor&qformat=kepler&pagestart=0&pagesize=10">Previous Page</a>
747
  <a href="metacat?action=query&operator=INTERSECT&enableediting=false&anyfield=actor&qformat=kepler&pagestart=2&pagesize=10">Next Page</a>
748
  
749
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.
750

    
751
Reading Data and Metadata
752
~~~~~~~~~~~~~~~~~~~~~~~~~
753
To read data or metadata from Metacat, use the ``read`` action. The ``read`` action 
754
takes two parameters: ``docid``, which specifies the document ID of the document 
755
to return, and ``qformat``, which specifies the return format for the document 
756
(``html`` or ``xml`` or the name of a configured style-set, e.g., ``default``). If ``qformat`` 
757
is set to ``xml``, Metacat will return the XML document untransformed. If the 
758
return format is set to ``html``, Metacat will transform the XML document into 
759
HTML using the default XSLT style sheet (specified in the Metacat 
760
configuration). If the name of a style-set is specified, Metacat will use the 
761
XSLT styles specified in the set to transform the XML.
762

    
763
.. figure:: images/screenshots/image047.jpg
764
   :align: center
765
   
766
   The same document displayed using different qformat parameters (from left 
767
   to right: the default style-set, XML, and HTML). 
768

    
769
Note that the ``read`` action can be used to read both data files and metadata files. 
770
To read a data file, you could use the following request::
771

    
772
  http://yourserver.com/yourcontext/metacat?action=read&docid=nceas.55&qformat=default
773

    
774
Where ``nceas.55`` is the docid of the data file stored in the Metacat and 
775
``default`` is the name of the style (you could also use "html" or "xml" or the 
776
name of a customized skin).
777

    
778
::
779
  
780
  <html>
781
  <head>
782
    <title>Read Document</title>
783
  </head>
784
  <body>
785
    <form method="POST" action="http://your.server/your.context/servlet/metacat">
786
      <input name="action" value="read" type="hidden">
787
      <input name="docid" type="text" value="" size="40">
788
      <input name="qformat" value="default" type="hidden">
789
      <input value="Read" type="submit">
790
    </form>
791
  </body>
792
  </html>
793
  
794
Using the EarthGrid API (aka EcoGrid)
795
-------------------------------------
796

    
797
.. Note::
798

    
799
  The EarthGrid/EcoGrid web service API is *deprecated* as of Metacat 2.0.0 and 
800
  will be removed from a future version of Metacat.  Its functionality is being 
801
  replaced by the standardized DataONE REST service interface. The EarthGrid API
802
  will be completely removed by the end of 2013.
803
   
804
The EarthGrid (aka EcoGrid) provides access to disparate data on different 
805
networks (e.g., KNB, GBIF, GEON) and storage systems (e.g., Metacat and SRB), 
806
allowing scientists access to a wide variety of data and analytic resources 
807
(e.g., data, metadata, analytic workflows and processors) networked at different 
808
sites and at different organizations via the internet. 
809

    
810
Because Metacat supports the EarthGrid API (see table), it can query the 
811
distributed EarthGrid, retrieve metadata and data results, and write new and 
812
updated metadata and data back to the grid nodes.
813

    
814
For more information about each EarthGrid service and its WSDL file, navigate 
815
to the "services" page on your Metacat server 
816
(e.g., http://knb.ecoinformatics.org/knb/services). 
817
Note that the AdminService and Version service that appear on this page are 
818
not part of EarthGrid.
819

    
820
EarthGrid/EcoGrid API Summary
821

    
822
+----------------------------+-----------------------------------------------------------------------------------------------------+
823
| Service                    | Description                                                                                         |
824
+============================+=====================================================================================================+
825
| AuthenticationQueryService | Search for and retrieve protected metadata and data from the EarthGrid as an authenticated user.    |
826
|                            |                                                                                                     |
827
|                            | Methods: ``query``, ``get``                                                                         |
828
+----------------------------+-----------------------------------------------------------------------------------------------------+
829
| AuthenticationService      | Log in and out of the EarthGrid                                                                     |
830
|                            |                                                                                                     |
831
|                            | Methods: ``login``, ``logout``                                                                      |
832
+----------------------------+-----------------------------------------------------------------------------------------------------+
833
| IdentifierService          | List, lookup, validate, and add Life Science Identifiers (LSIDs) to the EarthGrid                   |
834
|                            |                                                                                                     |
835
|                            | Methods: ``isRegistered``, ``addLSID``, ``getNextRevision``, ``getNextObject``, ``getAllIds``       |
836
+----------------------------+-----------------------------------------------------------------------------------------------------+
837
| PutService                 | Write metadata to the EarthGrid                                                                     |
838
|                            |                                                                                                     |
839
|                            | Methods: ``put``                                                                                    |
840
+----------------------------+-----------------------------------------------------------------------------------------------------+
841
| QueryService               | Search for and retrieve metadata from the EarthGrid                                                 |
842
|                            |                                                                                                     |
843
|                            | Methods: ``query``, ``get``                                                                         |
844
+----------------------------+-----------------------------------------------------------------------------------------------------+
845
| RegistryService            | Add, update, remove, and search for registered EarthGrid services.                                  |
846
|                            | Note: The WSDL for this  service is found under http://ecogrid.ecoinformatics.org/registry/services |
847
|                            |                                                                                                     |
848
|                            | Methods: ``add``, ``update``, ``remove``, ``list``, ``query``                                       |
849
+----------------------------+-----------------------------------------------------------------------------------------------------+
850

    
851
Using Morpho
852
------------
853
Morpho is a desktop tool created to facilitate the creation, storage, and 
854
retrieval of metadata. Morpho interfaces with any Metacat server, allowing 
855
users to upload, download, store, query and view relevant metadata and data 
856
using the network. Users can authorize the public or only selected colleagues 
857
to view their data files. 
858

    
859
Morpho is part of the Knowledge Network for Biocomplexity (KNB), a national 
860
network intended to facilitate ecological and environmental research on 
861
biocomplexity. To use Morpho with your Metacat, set the Metacat URL in the 
862
Morpho Preferences to point to your Metacat server.
863

    
864
.. figure:: images/screenshots/image049.png
865
   :align: center
866
   
867
   Set the Metacat URL in the Morpho preferences to point to your Metacat.
868

    
869
For more information about Morpho, please see: http://knb.ecoinformatics.org/morphoportal.jsp
870

    
871
Creating Your Own Client
872
------------------------
873

    
874
.. Note::
875

    
876
  NOTE: The Client API (and underlying servlet implementation) has been 
877
  deprecated as of Metacat 2.0.0. Future development should utilize the DataONE 
878
  REST service methods. The Client API will be completely removed by the end of 2013.
879
  
880
Metacat's client API is available in Java and Perl (the Java interface is 
881
described in this section and further detailed in the appendix). Some of the 
882
API is also available in Python and Ruby. The API allows client applications 
883
to easily authenticate users and perform basic Metacat operations such as 
884
reading metadata and data files; inserting, updating, and deleting files; and 
885
searching for packages based on metadata matches. 
886

    
887
The Client API is defined by the interface edu.ucsb.nceas.metacat.client.Metacat, 
888
and all operations are fully defined in the javadoc_ documentation. To use the 
889
client API, include the ``metacat-client.jar``, ``utilities.jar``, ``commons-io-2.0.jar``, and 
890
``httpclient.jar`` in your classpath. After including these classes, you can 
891
begin using the API methods (see the next table). 
892

    
893
.. _javadoc: http://knb.ecoinformatics.org/software/metacat/dev/api/index.html
894

    
895
The following code block displays a typical session for reading a document 
896
from Metacat using the Java client API.
897

    
898
::
899
  
900
  String metacatUrl = "http://foo.com/context/metacat";
901
  String username = "uid=jones,o=NCEAS,dc=ecoinformatics,dc=org";
902
  String password = "neverHarcodeAPasswordInCode";
903
  try {
904
      Metacat m = MetacatFactory.createMetacatConnection(metacatUrl);
905
      m.login(username, password);
906
      Reader r = m.read("testdocument.1.1");
907
      // Do whatever you want with Reader r
908
  } catch (MetacatAuthException mae) {
909
      handleError("Authorization failed:\n" + mae.getMessage());
910
  } catch (MetacatInaccessibleException mie) {
911
      handleError("Metacat Inaccessible:\n" + mie.getMessage());
912
  } catch (Exception e) {
913
      handleError("General exception:\n" + e.getMessage());
914
  }
915
  
916
  Operations provided by Client API  (Metacat.java class)
917
  
918
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
919
| Method               | Parameters and Throws                                                                                                                                                                                       | Description                                                                                                                               |
920
+======================+=============================================================================================================================================================================================================+===========================================================================================================================================+
921
| delete               | ``public String delete(String docid) throws InsufficientKarmaException, MetacatException, MetacatInaccessibleException;``                                                                                   | Delete an XML document in the repository.                                                                                                 |
922
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
923
| 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.                       |
924
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
925
| 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. |
926
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
927
| getloggedinuserinfo  | ``public String getloggedinuserinfo() throws MetacatInaccessibleException;``                                                                                                                                | Return the logged in user for this session.                                                                                               |
928
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
929
| getNewestDocRevision | ``public int getNewestDocRevision(String docId) throws MetacatException;``                                                                                                                                  | Return the latest revision of specified the document from Metacat                                                                         |
930
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
931
| getSessonId          | ``public String getSessionId();``                                                                                                                                                                           | Return the session identifier for this session.                                                                                           |
932
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
933
| insert               | ``public String insert(String docid, Reader xmlDocument, Reader schema) throws InsufficientKarmaException, MetacatException, IOException, MetacatInaccessibleException;``                                   | Insert an XML document into the repository.                                                                                               |
934
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
935
| isRegistered         | ``public boolean isRegistered(String docid) throws MetacatException;``                                                                                                                                      | Return true if given docid is registered; false if not.                                                                                   |
936
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
937
| login                | ``public String login(String username, String password) throws MetacatAuthException, MetacatInaccessibleException;``                                                                                        | Log in to a Metacat server.                                                                                                               |
938
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
939
| logout               | ``public String logout() throws MetacatInaccessibleException, MetacatException;``                                                                                                                           | Log out of a Metacat server.                                                                                                              |
940
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
941
| query                | ``public Reader query(Reader xmlQuery) throws MetacatInaccessibleException, IOException;``                                                                                                                  | Query the Metacat repository and return the result set as a Reader.                                                                       |
942
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
943
| 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.                        |
944
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
945
| read                 | ``public Reader read(String docid) throws InsufficientKarmaException, MetacatInaccessibleException, DocumentNotFoundException, MetacatException;``                                                          | Read an XML document from the Metacat server.                                                                                             |
946
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
947
| readInlineData       | ``public Reader readInlineData(String inlinedataid) throws InsufficientKarmaException, MetacatInaccessibleException, MetacatException;``                                                                    | Read inline data from the Metacat server session.                                                                                         |
948
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
949
| 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.                                                                            |
950
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
951
| setMetacatUrl        | ``public void setMetacatUrl(String metacatUrl);``                                                                                                                                                           | Set the MetacatUrl to which connections should be made.                                                                                   |
952
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
953
| setSessionId         | ``public void setSessionId(String sessionId);``                                                                                                                                                             | Set the session identifier for this session.                                                                                              |
954
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
955
| 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.                                                  |
956
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
957
| upload               | ``public String upload(String docid, File file) throws InsufficientKarmaException, MetacatException, IOException, MetacatInaccessibleException;``                                                           | Upload a data document into the repository.                                                                                               |
958
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
959
| upload               | ``public String publicupload(String docid, String fileName, InputStream fileData, int size) throws InsufficientKarmaException, MetacatException, IOException, MetacatInaccessibleException;``               | Upload a data document into the repository.                                                                                               |
960
+----------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+
961
  
(20-20/20)