# # '$RCSfile$' # '$Author: jones $' # '$Revision: 2599 $' # '$Date: 2005-09-27 16:48:07 -0700 (Tue, 27 Sep 2005) $' # Metacat: XML Metadata and Data Management System ------------------------------------------------ Version: 1.5.0 Release Send feedback and bugs to: metacat-dev@ecoinformatics.org http://bugzilla.ecoinformatics.org Contributors: Matt Jones (jones@nceas.ucsb.edu) Chad Berkley (berkley@nceas.ucsb.edu) Jing Tao (tao@nceas.ucsb.edu) Jivka Bojilova (bojilova@nceas.ucsb.edu) Dan Higgins (higgins@nceas.ucsb.edu) Saurabh Garg (sgarg@nceas.ucsb.edu) Duane Costa (dcosta@lternet.edu) Veronique Connolly (connolly@nceas.ucsb.edu) Patch contributors: Andrea Chadden (chadden@nceas.ucsb.edu) Chris Jones (cjones@msi.ucsb.edu) Johnoel Ancheta (johnoel@hawaii.edu) Owen Jones (owen.jones@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 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 1.5.0: ------------------------ 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. 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.