[ecoinfo] Metacat 1.6.0 Release Announcement

Saurabh Garg sgarg at nceas.ucsb.edu
Fri Aug 18 17:45:40 PDT 2006


The Knowledge Network for Biocomplexity project  
(http://knb.ecoinformatics.org) is pleased to announce its new release 
of Metacat (1.6.0). 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 - 
http://knb.ecoinformatics.org/software/metacat/

We would welcome any input or suggestions (email metacat-dev at 
ecoinformatics.org).

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

=======
README
=======

Metacat: XML Metadata and Data Management System
------------------------------------------------

Version: 1.6.0 Release

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

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 
Oracle,
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 the
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.

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


Release Notes for 1.6.0:
------------------------

This release comes with more performance improvements, initial support for
LSIDs (Life Sciences Identifiers) and FGDC standard, more controls for
Metacat administrators and bug fixes. Below is the list of bug fixes and
performance improvements.

Bug Fixes:
* Improved the indexing algorithm. Earlier indexing failed for some 
documents
  randomly and used to take a lot of time to complete for others. The
  code for indexing was changed to take care of both these problems.
* Earlier, xmlns prefix was used to determine the namespace of the 
document.
  Now schemaLocation is used instead xmlns prefix to determine the 
namespace
  of the document as that is a better indicator of document type.
* INSTR was used in some SQL statements and it is not supported by 
Postgres.
  So SQL statements were modified so that INSTR is not used.
* Replication was changed to include replication of deleted documents also.
* Fixed bug in squery which didnt allow use of not-contains

New Features:
* Added FGDC schema and XSLT so that Metacat can handle FGDC standard
* Added support for LSID. This includes modifying the stylesheets to
  display the LSIDs, modifying the build to include a new target
  'install-ldap'.
* Added following access control levels to Metacat:
    1. Administrators - users who can do the following:
       a. Run replication
       b. Delete any document
       c. Modify any document
       d. run indexing for any document
       e. check the logs
    2. allowedUsers - User who are allowed to submit
    3. deniedUsers - Users not allowed to submit
* Added a new skin for Ecological Society of America.
* Created an Advanced search servlet which can be used from the web.
* Various connections have been modified to be secure. e.g. connection 
between
ldaps is made secure now, replication is done over secure channels. 

Performance:
* Reduced size of xml_nodes by creating a new table for holding nodes from
  deleted documents and old revisions of the documents.
* Provided a new variable in metacat.properties where more frequently 
searched
  for paths can be specified. Seperate indexes are created for these paths
  - so that search is faster.
* Included log4j for logging and debuging to prevent wasting of time in 
printing log statements.

Release Notes for 1.5.0:
------------------------

This release comes with performace improvement, user interface enhancements,
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
  HARVEST_DETAIL_LOG. (Bug 162)
* In data registry, minor bugs fixed like the error page shows the link back
  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 result
  were more than 1000. This has been fixed. (Bug 2000)
* Removed any occurence of enum which is now a keyword in Java 1.5


Enhancements:
* 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 
resultset.xsl,
  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 search
  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 and
  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
     document
  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 
access
  on an xml document and a method to get newest version for a given 
document.
* 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
  semicolon.
* 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:
http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.5


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 include:

* 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 
interface
  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 documents
  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, 
inserts,
  deletes, etc.  See the new section in the Metacat Tour.
* Added a new 'buildindex' action that can rebuild the index entries for any
  document in the database.
* The configuration file for metacat (metacat.properties) has been moved out
  of the jar file and into the WEB-INF directory, allowing far easier 
changes
  to the configuration parameters.
* Results in default web interface are sorted by title in the XSLT
  (configurable)
* Many bugs were fixed.

Details of all changes can be found in the bug database here:
http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.4

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 -
@src/reviseformetacat13.sql
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 EML2
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 
resource
     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 it.
  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.
    
Documentation
-------------
See the docs directory for detailed documentation and installation
instructions.

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

  http://knb.ecoinformatics.org/software/metacat/

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 
http://bugzilla.ecoinformatics.org)
-----------------------------------------------------------------------------
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.

Legalese
--------
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
details.

This material is based upon work supported by the
National Science Foundation under Grant No. DEB99-80154, DBI99-04777, and
0225676 for SEEK.  Any opinions, findings and conclusions or recomendations
expressed 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 
file
for details of the license.  Licensor retains title to and ownership of the
Software and all enhancements, modifications, and updates to the Software.

This software includes the JDBC driver for PostgreSQL.  See the
postgresql-license.txt file for details.



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