[ecoinfo] Metacat 1.5.0 Release Announcement

Saurabh Garg sgarg at nceas.ucsb.edu
Wed May 25 12:15:19 PDT 2005

The Knowledge Network for Biocomplexity project 
(http://knb.ecoinformatics.org) is pleased to announce its new release 
of Metacat (1.5.0). Metacat is a flexible database storage system for 
XML formatted documents. This release comes with performace improvement, 
user interface enhancements and bug fixes. Please see the attached 
README file for more new features and details.

Source code is available for Linux and Windows 2000/XP - see the 
software download page 
(http://knb.ecoinformatics.org/software/download.html#metacat). The 
README file can be found online here - 
http://knb.ecoinformatics.org/software/metacat/README.txt. Documentation 
for Metacat can be found here - 

We would welcome any input or suggestions (email metacat-dev at 

Saurabh Garg
National Center for Ecological Analysis and Synthesis (NCEAS)
University of California, Santa Barbara
Santa Barbara, CA 93106


Metacat: XML Metadata and Data Management System

Version: 1.5.0 Release

Send feedback and bugs to: metacat-dev at ecoinformatics.org

Contributors: Matt Jones (jones at nceas.ucsb.edu)
             Chad Berkley (berkley at nceas.ucsb.edu)
             Jing Tao (tao at nceas.ucsb.edu)
             Jivka Bojilova (bojilova at nceas.ucsb.edu)
             Dan Higgins (higgins at nceas.ucsb.edu)
             Saurabh Garg (sgarg at nceas.ucsb.edu)
             Duane Costa (dcosta at lternet.edu)
             Veronique Connolly (connolly at nceas.ucsb.edu)

Patch contributors:
             Andrea Chadden (chadden at nceas.ucsb.edu)
             Chris Jones (cjones at msi.ucsb.edu)
             Johnoel Ancheta (johnoel at hawaii.edu)
             Owen Jones (owen.jones at imperial.ac.uk)

Metacat is a flexible database storage system for XML formatted
documents and associated binary files. Metacat models the structure of the
XML document, therefore allowing storage of XML documents with arbitrary
schemas. Metacat supports several databases on the back-end, including 
PostgreSQL and SQL Server (limited).  The server supports XML document
storage, retrieval, query, validation, and transformation (using the XSLT
stylesheet language).  In addition, there is a mechanism for replicating 
database to other metacat instances for backup and load balancing purposes.
Metacat currently uses an LDAP database for authenticating users, but was
written to accomodate other authentication services as well.

See the file "docs/user/metacatinstall.html" for detailed instructions.

Release Notes for 1.5.0:

This release comes with performace improvement, user interface 
and bug fixes. Below is the list of bug fixes and performance improvements.
Bug Fixes:
* Modify property values of harvester registration servlets to match the
 servlet-mapping URL values in web.xml. The old values used the servlet
 class names. This worked in Tomcat 4 but seems to break in Tomcat 5 on
 Windows. The new values use the servlet-mapping URL values. This should
 work in both Tomcat 4 and Tomcat 5. (Bug 162)
* Re-implement logic to prune old log entries from the HARVEST_LOG and
 HARVEST_DETAIL_LOG tables. The old logic caused integrity constraint
 violations in the database because it tried to delete parent records from
 HARVEST_LOG prior to deleting child records from
* In data registry, minor bugs fixed like the error page shows the link 
 to the form when error page was generated because of a document read
 request from search results page,  the successful delete button leading
 to a blank screen and the old ACL overwritten by the registry.
 (Bugs 1307, 1310, 1322, 1344, 1551)
* Changed the code to support insertion of following characters: ', `,
 charcters in the Numeric Character Reference format (&#xyz;) and
 characters like µ. Characters like µ will be converted to and stored in
 Numeric Character Reference format(&#xyz;). They will also be returned
 in Numeric Character Reference and it is upto the client to convert them
 and display them accordingly in the application. Partial fix provided by
 Johnoel Ancheta. (Bug 1538,1711)
* Spatial search failed on Oracle because of invalid entries made by
 some documents in the nodedata column of xml_nodes for paths involving
 'eastBoundingCoordinate', 'westBoundingCoordinate',
 'northBoundingCoordinate', 'southBoundingCoordinate'. A new column
 nodedatanumerical was added to xml_nodes table such that all the numerical
 nodedata is stored in this column and this column is now used for spatial
 search. (Bug 1703, 1718)
* In the default skin, clicking on the keywords on the home page did not
 result is a search being done. Fix provided by Owen Jones. (Bug 1768)
* Metacat generated a success message even when a document which didnt
 exsist was requested for deletion. This has been fixed. (Bug 1850)
* "packagetype" in xml-relation table was entered as eml200 namespace when
 an eml201 document was inserted. This is fixed now so that "packagetype"
 in xml-relation table points to eml201 namespace. (Bug 1979)
* System_id in xml_catalog pointed to http://knb.ecoinformatics.org/knb/
 earlier. Fixed such that it points to the locally installed metacat 
url.  (Bug 1986)
* Changes to the Query subsystem fix bugs that prevented attributes from 
 being expressed solely in the xpath query statement and the returnfield 
 values. For instance, a query URL may now include search strings like 
 '@packageId=sbclter%25' and return strings like 'returnfield=@packageId'.
 Previously, the attribute had to be appended to an element: 
 '/eml/@packageId=sbclter%25'. These fixes change DBQuery.java, 
 QuerySpecification.java, and QueryTerm.java (Bug 2052)
* Search query failed in case of Oracle if number of documents in the 
 were more than 1000. This has been fixed. (Bug 2000)
* Removed any occurence of enum which is now a keyword in Java 1.5

* Major improvements done in user interface for the data registeries and
 various other skins. Improvements done based on suggestions from Mark
 Stromberg, Laura Downey and others. Improvements also done in 
 the default skin and ldap templates. (Bug 1948)
* Coded added such that administrator can delete documents irrespective of
 who the document belongs to.
* Performance impovement done in searching of datasets. A part of the 
 time was taken up because of generation of resultset after the search 
had be
 done. So this was the sequence of events in earlier metacat
 1) Search for the given text
 2) A list of docids generated
 3) For each of the docids
    3a) Use xml_index and xml_nodes table to generate the string descibing
        the document including the returnfields requested in the search
 4) Add all the strings from step 3a to send back the resultant
    document. Here a decent amount of time was being taken by step 3a. 
 The algorithm is now modified by addition of two tables xml_queryresult 
 xml_returnfields and a user defined parameter xml_returnfield_count. The
 new algorithm works as follows:
 1) Search for the given text
 2) A list of docids is generated
 3) For the given set of return fields generate a unique string and check
    if that string exists in xml_returnfields
    3a) If string does not exist in xml_returnfield, then enter a new
        record usage_count as 1 and returnfield_string as the unique string
        generated above.
    3b) Else if the string exists, increment usage_count
 4) Given the docids from step 2 and the id of the returnfield record from
    step 3, query for any docids that already exist in xml_queryresult.
    For the docids that do exist, get the queryresult_string.
 5) For rest of the docids from step2 which were not found in step 4, do
    the following for each of the documents:
    5a) Use xml_index and xml_nodes table to generate the string descibing
        the document including the returnfields requested in the search
    5b) If usage_count of the record from step is more than
        xml_returnfield_count set in metacat.properties, then store the
        string in xml_queryresult as a record which has the returnfield_id
        representing the set of returnfields, docid representing the
        document and the string as queryresult_string.
 6) Add all the strings from step 4 and step 5a to send back the resultant
 So the results from step 3a in previous algorithm are effectively cached
 and hence same computation is not done again and again for each search.
 When a document is deleted, all the entries for that document in
 xml_queryresult table are also deleted. When a document is updated, all
 the entries for that document in xml_queryresult table are deleted. This
 works fine because those entries will be generated and cached again the
 next time the document is part of a search is requested.
* Performance impovement done for % search.
* Following new functions added to metacat client API: a method to set 
 on an xml document and a method to get newest version for a given 
* Implement a new HarvesterServlet for running Harvester as a servlet. This
 eliminates the need to run Harvester in a terminal window. By default, the
 HarvesterServlet is commented out in lib/web.xml.tomcat(3,4,5). The user
 documentation will be modified to instruct Harvester administrators to
 uncomment the HarvesterServlet entry.
* Minor enhancement to support multiple email addresses for harvester
 administrator and site contact. Each address is separated by a comma or
* Increase number of rows in Harvest List Editor from 300 to 1200.
* Changed default maxHarvests value to 0. Added logic to ignore maxHarvests
 value when it is set to 0 or a negative number. This allows Harvester to
 run indefinitely without shutting down after reaching a maximum number of
 harvests. The previous default value of 30 would cause Harvester to
 terminate after 30 harvests.

Details of all changes can be found in the bug database here:

Release Notes for 1.4.0:

This is a major release, and is the first to introduce many new features to
Metacat.  Some of the major new features in this version of Metacat 

* Added a new 'Harvester' that allows documents to be periodically pulled
 from distributed sources into metacat, useful for interfacing with other
 system types. See the Metacat Tour for details.
* Added new 'skins' capability to allow the GUI for the metacat web 
 to be more easily customized to fit into site needs.  The skin is based on
 a flexible mix of XSLT, CSS, and Javascript.
* Added a web-based metadata entry form for submitting limited EML 
 as part of a data registry.  The GUI for the registry is customizable 
and  is integrated with the 'skins' system for the main metacat 
interface.  The
 registry subsystem is written in Perl, and can simultaneously be used 
to  present multiple 'registry' interfaces.
* A new 'client API' has been developed and implemented in Java and in 
Perl  so that metacat functions can be accessed from any program in those
 languages.  The client API supports the major metacat servlet actions,
 including login(), logout(), query(), insert(), update(), delete(), and 
 upload(). See the Metacat Tour for details.
* Added a new 'getlog' action that produces a usage history for all major
 events.  So now an XML report can be generated for document reads, 
 deletes, etc.  See the new section in the Metacat Tour.
* Added a new 'buildindex' action that can rebuild the index entries for 
 document in the database.
* The configuration file for metacat (metacat.properties) has been moved 
 of the jar file and into the WEB-INF directory, allowing far easier 
 to the configuration parameters.
* Results in default web interface are sorted by title in the XSLT 
* Many bugs were fixed.

Details of all changes can be found in the bug database here:

Release Notes for 1.3.1:

This is a simple interim bug fix. No major functionality changes. Bugs 
fixed include:
1) Metacat 1.3.0 doesn't work in Java 1.3 because a subtle API differnce 
in    Java 1.3 and Java 1.4. Currently, Metacat 1.3.1 will work in both 
Java 1.3    and Java 1.4.
2) Distribution package size was reduced.

Release Notes for 1.3.0

In 1.3.0 release, the structure of the xml_access table was changed and 
a new
table, xml_accesssubtree was added. If you try to update a previously 
installed Metacat, you should run a script file to updated the table 
structure before installation.
For Oracle user: At the SQLPLUS prompt type the following -
For Postgresql user: At install directory prompt type the following -
psql exp < src/reviseformetacat13_postgres.sql
(where 'exp' is the database name).

After installation, user should run "ant schemasql" command to register 
schema in xml_catalog table.

If you are a new Metacat user, this step is unneeded.

Note: 1) We recommend to use Tomcat 4 and JAVA 1.4 to run Metacat. 
Otherwise,         it will cause potential replication issues.
     2) Delete the xercesImpl.jar and xmlParserAPIs.jar files         
which are in $CATALINA_HOME/common/endorsed. They are old version and
        don't support XML schema validation.

New Features in 1.3.0
 1) Partialy support EML2 document. User can store, query, read and write
    EML2 documents. However, Metacat only support access control in 
    level. The subtree level access control will be ignored.
 2) Support other xml document base on namespace/schema.
 3) Support query for attribute value
 4) Assign MIME type to data file base on metadata when user try to read 
 5) Owner can assign access rules to a document which does not have 
access     document to apply it.
 6) Support exporting single file, not only whole package
 7) Resupport Microsoft SQL Server.

Fixes in 1.3.0:
 1) Couldn't finish delta T replication for large set of documents.
 2) Couldn't create access control during delta T replication.
 3) Eorr will be written to a seperated log file if some documents
    were failed in replication.
 4) Decrease the time to create access rules during insert or update     
a package.
See the docs directory for detailed documentation and installation

Details of the Metacat architecture can be found on the website for
the Knowledge Network for Biocomplexity (KNB):


Contributions to this work are welcome.  Please see the above web site
for details on how to contribute.

Major Known Bugs or Feature Requests (see 

If you discover a bug please report it, either by email (above) or by using
our bug tracking system (http://bugzilla.ecoinformatics.org). There is a
list of currently unimplemented features in Bugzilla that we are working on
for the next release.

This software is copyrighted by The Regents of the University of California
and the National Center for Ecological Analysis and Synthesis
and licensed under the GNU GPL; see the 'LICENSE' file for

This material is based upon work supported by the
National Science Foundation under Grant No. DEB99-80154, DBI99-04777, and
0225676.  Any opinions, findings and conclusions or recomendations 
in this material are those of the author(s) and do not necessarily reflect
the views of the National Science Foundation (NSF).

This software is partially supported by a grant from the Andrew W. 
Mellon Foundation.

This product includes software developed by the Apache Software
Foundation (http://www.apache.org/). See the LICENSE file in lib/apache
for details.

The source code, object code, and documentation in the com.oreilly.servlet
package is copyright and owned by Jason Hunter. See the cos-license.html 
for details of the license.  Licensor retains title to and ownership of the
Software and all enhancements, modifications, and updates to the Software.

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